Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 50 of 163
Found at i:12434949 original size:58 final size:58
Alignment explanation
Indices: 12434885--12435014 Score: 215
Period size: 58 Copynumber: 2.2 Consensus size: 58
12434875 GAAACTTTCA
*
12434885 AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACT
1 AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
* * *
12434943 AAAATTACCATTTCACCCTCAAATTTCCCTAAATCCCATTTTTAACCCCGATTTCACC
1 AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
12435001 AAAATCTACCATTT
1 AAAAT-TACCATTT
12435015 TGTCCCCGGG
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 59 0.88
59 8 0.12
ACGTcount: A:0.33, C:0.34, G:0.02, T:0.32
Consensus pattern (58 bp):
AAAATTACCATTTCACCCCCAAACTTCCCTAAATCCCATTTTAAACCCCGATTTCACC
Found at i:12434954 original size:30 final size:29
Alignment explanation
Indices: 12434920--12435015 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
12434910 TCCCTAAATC
12434920 CCATTTTAAACCCCGATTTCACTAAAATTA
1 CCATTTT-AACCCCGATTTCACTAAAATTA
* * * *
12434950 CCA-TTTCACCCTCAAATTTCCCT-AAA-TC
1 CCATTTTAACCC-C-GATTTCACTAAAATTA
*
12434978 CCATTTTTAACCCCGATTTCACCAAAATCTA
1 CCA-TTTTAACCCCGATTTCACTAAAAT-TA
12435009 CCATTTT
1 CCATTTT
12435016 GTCCCCGGGT
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
28 14 0.28
29 11 0.22
30 21 0.42
31 4 0.08
ACGTcount: A:0.31, C:0.32, G:0.02, T:0.34
Consensus pattern (29 bp):
CCATTTTAACCCCGATTTCACTAAAATTA
Found at i:12445556 original size:3 final size:3
Alignment explanation
Indices: 12445548--12445609 Score: 81
Period size: 3 Copynumber: 20.7 Consensus size: 3
12445538 CAAAATCAAA
* * *
12445548 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AGT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
12445596 AAAT AAT AA- AAT AA
1 -AAT AAT AAT AAT AA
12445610 AGTATTCTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:12446686 original size:13 final size:13
Alignment explanation
Indices: 12446668--12446700 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12446658 GTTTTTCGAA
12446668 AAAGTCAACGGTC
1 AAAGTCAACGGTC
12446681 AAAGTCAACGGTC
1 AAAGTCAACGGTC
12446694 AACAGTC
1 AA-AGTC
12446701 GATCAACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.39, C:0.24, G:0.21, T:0.15
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:12452753 original size:3 final size:3
Alignment explanation
Indices: 12452745--12452788 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
12452735 TAAAATCCAA
* * * *
12452745 AAT AAT AAT AAT AAT AAT TAT AAT AAT TAT AGT AAT TAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
12452789 ATAGTAAAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
AAT
Found at i:12452759 original size:9 final size:9
Alignment explanation
Indices: 12452746--12452788 Score: 68
Period size: 9 Copynumber: 4.8 Consensus size: 9
12452736 AAAATCCAAA
*
12452746 ATAATAATA
1 ATAATAATT
12452755 ATAATAATT
1 ATAATAATT
12452764 ATAATAATT
1 ATAATAATT
*
12452773 ATAGTAATT
1 ATAATAATT
12452782 ATAATAA
1 ATAATAA
12452789 ATAGTAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (9 bp):
ATAATAATT
Found at i:12453915 original size:22 final size:22
Alignment explanation
Indices: 12453890--12453948 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
12453880 CAACAACTGG
* *
12453890 TCAACGGCCGGTCAACGATCGA
1 TCAACAGCCAGTCAACGATCGA
*
12453912 TCAACAGCCAGTCAACGGTCGA
1 TCAACAGCCAGTCAACGATCGA
*
12453934 TCAACAGTCAGTCAA
1 TCAACAGCCAGTCAA
12453949 TGACTGGTCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.32, C:0.31, G:0.22, T:0.15
Consensus pattern (22 bp):
TCAACAGCCAGTCAACGATCGA
Found at i:12460506 original size:15 final size:15
Alignment explanation
Indices: 12460486--12460517 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12460476 CGTAAACAAA
*
12460486 TAAAATAAAATATTG
1 TAAAATAAAAAATTG
12460501 TAAAATAAAAAATTG
1 TAAAATAAAAAATTG
12460516 TA
1 TA
12460518 CATTTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (15 bp):
TAAAATAAAAAATTG
Found at i:12473018 original size:10 final size:10
Alignment explanation
Indices: 12473005--12473038 Score: 59
Period size: 10 Copynumber: 3.3 Consensus size: 10
12472995 TTGTTCTTAT
12473005 TTTCTGTTGC
1 TTTCTGTTGC
12473015 TTTCTGTTGC
1 TTTCTGTTGC
12473025 TTTCTGTTGTC
1 TTTCTGTTG-C
12473036 TTT
1 TTT
12473039 TGAGCTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 19 0.83
11 4 0.17
ACGTcount: A:0.00, C:0.18, G:0.18, T:0.65
Consensus pattern (10 bp):
TTTCTGTTGC
Found at i:12475841 original size:10 final size:10
Alignment explanation
Indices: 12475815--12475848 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
12475805 TTGTTCTTAT
*
12475815 TTTCTGGTGC
1 TTTCTGTTGC
12475825 TTTCTGTTGC
1 TTTCTGTTGC
12475835 TTTCTGTTGTC
1 TTTCTGTTG-C
12475846 TTT
1 TTT
12475849 TGAGCCTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.00, C:0.18, G:0.21, T:0.62
Consensus pattern (10 bp):
TTTCTGTTGC
Found at i:12477910 original size:71 final size:69
Alignment explanation
Indices: 12477824--12478027 Score: 220
Period size: 71 Copynumber: 2.9 Consensus size: 69
12477814 TCTTTTGTGT
* *
12477824 ATATATGTCTGTTTCCTTAACTTATAGATATATGGCTAGATTTTTTATATATAGTATGTATATAC
1 ATATATTTC-GTTTCCTTAACTTATATATATATGGCTAGATTTTTTATATATAGTATGTATATAC
12477889 TCACCTC
65 TCA-C-C
12477896 ATATATTTCGTTTCCTTAACTTATATATATAT--CTAGAAATTTTTTAT-TCATAGTATGTATAT
1 ATATATTTCGTTTCCTTAACTTATATATATATGGCTAG--ATTTTTTATAT-ATAGTATGTATAT
*
12477958 ATTCACC
63 ACTCACC
* * ** **
12477965 ACATATTCCACTTCCTTAACTTTTATATATATATGG-TTTA-TTTTTATATATAGTATGTATATA
1 ATATATTTCGTTTCCTTAAC--TTATATATATATGGCTAGATTTTTTATATATAGTATGTATATA
12478028 TGTATATTTT
Statistics
Matches: 115, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
69 42 0.37
70 4 0.03
71 60 0.52
72 9 0.08
ACGTcount: A:0.31, C:0.13, G:0.08, T:0.49
Consensus pattern (69 bp):
ATATATTTCGTTTCCTTAACTTATATATATATGGCTAGATTTTTTATATATAGTATGTATATACT
CACC
Found at i:12478028 original size:69 final size:70
Alignment explanation
Indices: 12477836--12478028 Score: 196
Period size: 69 Copynumber: 2.7 Consensus size: 70
12477826 ATATGTCTGT
* * * * *
12477836 TTCCTTAACTTATAGATATATGGCTAG-ATTTTTTATATATAGTATGTATATACTCACCTCATAT
1 TTCCTTAACTTATATATATAT--ATAGAAATTTTTATATATAGTATGTATATATTCACCTCACAT
* **
12477900 ATTTCGT
64 ATTCCAC
*
12477907 TTCCTTAACTTATATATATATCTAGAAATTTTT-TATTCATAGTATGTATATATTCA-C-CACAT
1 TTCCTTAACTTATATATATATATAGAAATTTTTATA-T-ATAGTATGTATATATTCACCTCACAT
12477969 ATTCCAC
64 ATTCCAC
* * **
12477976 TTCCTTAACTTTTATATATATATGGTTTATTTTTATATATAGTATGTATATAT
1 TTCCTTAACTTATATATATATATAG-AAATTTTTATATATAGTATGTATATAT
12478029 GTATATTTTA
Statistics
Matches: 105, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
69 51 0.49
70 15 0.14
71 39 0.37
ACGTcount: A:0.31, C:0.13, G:0.07, T:0.49
Consensus pattern (70 bp):
TTCCTTAACTTATATATATATATAGAAATTTTTATATATAGTATGTATATATTCACCTCACATAT
TCCAC
Found at i:12481667 original size:69 final size:69
Alignment explanation
Indices: 12481580--12481727 Score: 260
Period size: 69 Copynumber: 2.1 Consensus size: 69
12481570 ACAGGTGCTG
* *
12481580 GTAAAAGTCTGCACAGTTCTAAATTGTTCATTGAATTTATTACTATCGATACTTGACCATCAGGT
1 GTAAAAGTCCGCACAGTTCTAAATTGTTCATTGAATTGATTACTATCGATACTTGACCATCAGGT
*
12481645 ACCT
66 ACCA
*
12481649 GTAGAAGTCCGCACAGTTCTAAATTGTTCATTGAATTGATTACTATCGATACTTGACCATCAGGT
1 GTAAAAGTCCGCACAGTTCTAAATTGTTCATTGAATTGATTACTATCGATACTTGACCATCAGGT
12481714 ACCA
66 ACCA
12481718 GTAAAAGTCC
1 GTAAAAGTCC
12481728 CCTAAAAAGT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (69 bp):
GTAAAAGTCCGCACAGTTCTAAATTGTTCATTGAATTGATTACTATCGATACTTGACCATCAGGT
ACCA
Found at i:12488706 original size:13 final size:13
Alignment explanation
Indices: 12488685--12488715 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12488675 AACTCTATTT
*
12488685 TTTAGGATTAATA
1 TTTAAGATTAATA
12488698 TTTAAGATTAATA
1 TTTAAGATTAATA
12488711 TTTAA
1 TTTAA
12488716 ATTCTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (13 bp):
TTTAAGATTAATA
Found at i:12488819 original size:25 final size:25
Alignment explanation
Indices: 12488769--12488823 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
12488759 AATTTGGATC
12488769 TAATTAGTAAATTATTGTTTAGATT
1 TAATTAGTAAATTATTGTTTAGATT
*
12488794 TAATTA-T-AATTATTTTTTTAGAATT
1 TAATTAGTAAATTA-TTGTTTAG-ATT
12488819 TAATT
1 TAATT
12488824 TGGATCTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 5 0.19
24 8 0.30
25 14 0.52
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (25 bp):
TAATTAGTAAATTATTGTTTAGATT
Found at i:12493993 original size:16 final size:16
Alignment explanation
Indices: 12493972--12494005 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12493962 CTTTATCACC
12493972 AACTTGTT-CAGGTTCT
1 AACTTGTTCCA-GTTCT
12493988 AACTTGTTCCAGTTCT
1 AACTTGTTCCAGTTCT
12494004 AA
1 AA
12494006 GCTGATGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.41
Consensus pattern (16 bp):
AACTTGTTCCAGTTCT
Found at i:12501162 original size:23 final size:23
Alignment explanation
Indices: 12501125--12501168 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
12501115 CCATACTTTC
*
12501125 ATTTTTAACAATTTAATATTTTT
1 ATTTTTAACAATTTAAAATTTTT
12501148 ATTTTTAA-AATTTTAAAATTT
1 ATTTTTAACAA-TTTAAAATTT
12501169 AGATCTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATTTTTAACAATTTAAAATTTTT
Found at i:12501697 original size:18 final size:18
Alignment explanation
Indices: 12501674--12501716 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
12501664 GTTCAAGGTG
12501674 TAATTAATTTAAATTT-TT
1 TAATTAA-TTAAATTTATT
12501692 TAATTAATTAAATTTATT
1 TAATTAATTAAATTTATT
12501710 TAATTAA
1 TAATTAA
12501717 AAACCTATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAATTTATT
Found at i:12502322 original size:180 final size:183
Alignment explanation
Indices: 12501999--12502333 Score: 437
Period size: 180 Copynumber: 1.8 Consensus size: 183
12501989 CCAAATTATT
* * *
12501999 TCAAGATTAATGTATAAAAATTAAATCTCAAATTTGAGCAAAATATAAGAATCAAAACTAAAATT
1 TCAAAATTAAAGTATAAAAATTAAATATCAAATTTGAGCAAAATATAAGAATCAAAACTAAAATT
* * **
12502064 TAATCATTCTTATATAATCATAAAATAATAGATGGATTAGTACTTAAATTTAGCCATTATTTTCT
66 TAACCATTCTTATATAATCATAAAATAATAGAGGGATTACAACTTAAATTTAGCCATTATTTTCT
*
12502129 CATATCCAAAGAAAAGAATAAAAAAAAAAAGAAGGGACGTGTATTTAAATGATA
131 CATATCAAAAGAAAAGAA-AAAAAAAAAAAGAAGGGACGTGTATTTAAATGATA
* * * * * *
12502183 TCAAAATTAAAGTAT-AAAATTAAATATTAAGTTTGAGCGAAATAT-AGGATCAAAATTGAAATT
1 TCAAAATTAAAGTATAAAAATTAAATATCAAATTTGAGCAAAATATAAGAATCAAAACTAAAATT
* * *
12502246 TAACCATT-TTAATATAATC-TTATATAGTAGAGGGATTACAAC-TAAATTTAGCCATTATTTTC
66 TAACCATTCTT-ATATAATCATAAAATAATAGAGGGATTACAACTTAAATTTAGCCATTATTTTC
* * *
12502308 TCATGTTAAAAGAAAAGGAAAAAAAA
130 TCATATCAAAAGAAAAGAAAAAAAAA
12502334 CATGTTAAAA
Statistics
Matches: 130, Mismatches: 20, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
179 7 0.05
180 35 0.27
181 19 0.15
182 30 0.23
183 26 0.20
184 13 0.10
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (183 bp):
TCAAAATTAAAGTATAAAAATTAAATATCAAATTTGAGCAAAATATAAGAATCAAAACTAAAATT
TAACCATTCTTATATAATCATAAAATAATAGAGGGATTACAACTTAAATTTAGCCATTATTTTCT
CATATCAAAAGAAAAGAAAAAAAAAAAAAGAAGGGACGTGTATTTAAATGATA
Found at i:12508401 original size:13 final size:13
Alignment explanation
Indices: 12508383--12508415 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
12508373 TCTTTGATTA
*
12508383 TTTCTTTTTCTTT
1 TTTCTTTTTCTGT
12508396 TTTCTTTTTCTGT
1 TTTCTTTTTCTGT
12508409 TTTCTTT
1 TTTCTTT
12508416 ATGGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTCTTTTTCTGT
Found at i:12508776 original size:25 final size:24
Alignment explanation
Indices: 12508748--12508795 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
12508738 AAAAATTATA
* *
12508748 TTGTTGAT-TTTTGG-TGCTGTTT
1 TTGTTGTTGTTTTGGTTGCTATTT
12508770 TTGTTGTTGTTTTGGTTGCTATTT
1 TTGTTGTTGTTTTGGTTGCTATTT
12508794 TT
1 TT
12508796 TACAATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.04, C:0.04, G:0.25, T:0.67
Consensus pattern (24 bp):
TTGTTGTTGTTTTGGTTGCTATTT
Found at i:12508789 original size:24 final size:22
Alignment explanation
Indices: 12508748--12508941 Score: 80
Period size: 23 Copynumber: 8.7 Consensus size: 22
12508738 AAAAATTATA
*
12508748 TTGTTGATTTTTGGTGCTGTTT
1 TTGTTGATTTTTGGTGCTATTT
*
12508770 TTGTTGTTGTTTTGGTTGCTATTT
1 TTGTTGAT-TTTTGG-TGCTATTT
** * * * *
12508794 TT-TACAATTTTGGTGTTGTGT
1 TTGTTGATTTTTGGTGCTATTT
12508815 TT-TT-ACTGTTTTGGTG-T-TTT
1 TTGTTGA-T-TTTTGGTGCTATTT
*
12508835 TT-TTTACTGTTTTGGTGCTATTT
1 TTGTTGA-T-TTTTGGTGCTATTT
* *
12508858 TT-TTTACTATTTTGGTGCTGTTT
1 TTGTTGA-T-TTTTGGTGCTATTT
* *
12508881 TTATTGTTATTTTTGTTGCTATTT
1 TTGTTG--ATTTTTGGTGCTATTT
* *
12508905 TT-TTTATTTTTGCTGCTATTT
1 TTGTTGATTTTTGGTGCTATTT
* *
12508926 TGGTTGTTATTTTGGT
1 TTGTTGAT-TTTTGGT
12508942 TGTTTGGATG
Statistics
Matches: 137, Mismatches: 23, Indels: 23
0.75 0.13 0.13
Matches are distributed among these distances:
20 7 0.05
21 37 0.27
22 25 0.18
23 41 0.30
24 25 0.18
25 1 0.01
26 1 0.01
ACGTcount: A:0.08, C:0.06, G:0.20, T:0.66
Consensus pattern (22 bp):
TTGTTGATTTTTGGTGCTATTT
Found at i:12508828 original size:44 final size:44
Alignment explanation
Indices: 12508777--12508882 Score: 117
Period size: 44 Copynumber: 2.4 Consensus size: 44
12508767 TTTTTGTTGT
12508777 TGTTTTGGTTGCTATTTTTTACAATTTTGGTG-T-TGTGTTTTTAC
1 TGTTTTGG-TGCTATTTTTTACAATTTTGGTGCTAT-TGTTTTTAC
* * ** *
12508821 TGTTTTGGTGTTTTTTTTTACTGTTTTGGTGCTATTTTTTTTAC
1 TGTTTTGGTGCTATTTTTTACAATTTTGGTGCTATTGTTTTTAC
* *
12508865 TATTTTGGTGCTGTTTTT
1 TGTTTTGGTGCTATTTTT
12508883 ATTGTTATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
43 19 0.37
44 32 0.62
45 1 0.02
ACGTcount: A:0.08, C:0.07, G:0.20, T:0.65
Consensus pattern (44 bp):
TGTTTTGGTGCTATTTTTTACAATTTTGGTGCTATTGTTTTTAC
Found at i:12508840 original size:21 final size:21
Alignment explanation
Indices: 12508777--12508874 Score: 106
Period size: 22 Copynumber: 4.5 Consensus size: 21
12508767 TTTTTGTTGT
* *
12508777 TGTTTTGGTTGCTATTTTTTAC
1 TGTTTTGG-TGTTTTTTTTTAC
** *
12508799 AATTTTGGTGTTGTGTTTTTAC
1 TGTTTTGGTGTT-TTTTTTTAC
12508821 TGTTTTGGTGTTTTTTTTTAC
1 TGTTTTGGTGTTTTTTTTTAC
12508842 TGTTTTGGTGCTATTTTTTTTAC
1 TGTTTTGGTG-T-TTTTTTTTAC
*
12508865 TATTTTGGTG
1 TGTTTTGGTG
12508875 CTGTTTTTAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
21 21 0.33
22 24 0.38
23 19 0.30
ACGTcount: A:0.09, C:0.06, G:0.20, T:0.64
Consensus pattern (21 bp):
TGTTTTGGTGTTTTTTTTTAC
Found at i:12508859 original size:12 final size:12
Alignment explanation
Indices: 12508844--12508943 Score: 73
Period size: 12 Copynumber: 8.7 Consensus size: 12
12508834 TTTTTTACTG
*
12508844 TTTTGGTGCTAT
1 TTTTGTTGCTAT
* *
12508856 TTTTTTTACTA-
1 TTTTGTTGCTAT
* *
12508867 TTTTGGTGCTGT
1 TTTTGTTGCTAT
* *
12508879 TTTTATTGTTAT
1 TTTTGTTGCTAT
12508891 TTTTGTTGCTAT
1 TTTTGTTGCTAT
12508903 TTTT-TT--TAT
1 TTTTGTTGCTAT
*
12508912 TTTTGCTGCTAT
1 TTTTGTTGCTAT
* *
12508924 TTTGGTTGTTAT
1 TTTTGTTGCTAT
*
12508936 TTTGGTTG
1 TTTTGTTG
12508944 TTTGGATGTT
Statistics
Matches: 67, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
9 7 0.10
10 1 0.01
11 9 0.13
12 50 0.75
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (12 bp):
TTTTGTTGCTAT
Found at i:12508913 original size:21 final size:23
Alignment explanation
Indices: 12508756--12508926 Score: 124
Period size: 23 Copynumber: 7.7 Consensus size: 23
12508746 TATTGTTGAT
* * ** *
12508756 TTTTGGTGCTGTTTTTGTTGTTG
1 TTTTGGTGCTATTTTTTTTACTA
*
12508779 TTTTGGTTGCTA--TTTTTTACAA
1 TTTTGG-TGCTATTTTTTTTACTA
* *
12508801 TTTTGGTG-T-TGTGTTTTTACTG
1 TTTTGGTGCTAT-TTTTTTTACTA
*
12508823 TTTTGGTG-T-TTTTTTTTACTG
1 TTTTGGTGCTATTTTTTTTACTA
12508844 TTTTGGTGCTATTTTTTTTACTA
1 TTTTGGTGCTATTTTTTTTACTA
* * **
12508867 TTTTGGTGCTGTTTTTATTGTTA
1 TTTTGGTGCTATTTTTTTTACTA
*
12508890 TTTTTGTTGCTATTTTTTTTA-T-
1 -TTTTGGTGCTATTTTTTTTACTA
*
12508912 TTTTGCTGCTATTTT
1 TTTTGGTGCTATTTT
12508927 GGTTGTTATT
Statistics
Matches: 121, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.01
21 34 0.28
22 29 0.24
23 37 0.31
24 20 0.17
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (23 bp):
TTTTGGTGCTATTTTTTTTACTA
Found at i:12508916 original size:45 final size:47
Alignment explanation
Indices: 12508844--12508943 Score: 132
Period size: 45 Copynumber: 2.2 Consensus size: 47
12508834 TTTTTTACTG
* * * *
12508844 TTTTGGTGCTATTTTTTTTACTATTTTGGTGCTGTTTTTATTGTTAT
1 TTTTGTTGCTATTTTTTTTACTATTTTGCTGCTATTTTGATTGTTAT
*
12508891 TTTTGTTGCTATTTTTTTTA-T-TTTTGCTGCTATTTTGGTTGTTAT
1 TTTTGTTGCTATTTTTTTTACTATTTTGCTGCTATTTTGATTGTTAT
*
12508936 TTTGGTTG
1 TTTTGTTG
12508944 TTTGGATGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
45 27 0.57
46 1 0.02
47 19 0.40
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.67
Consensus pattern (47 bp):
TTTTGTTGCTATTTTTTTTACTATTTTGCTGCTATTTTGATTGTTAT
Found at i:12508989 original size:20 final size:19
Alignment explanation
Indices: 12508952--12508989 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
12508942 TGTTTGGATG
12508952 TTATTTTTACGCGTCTTTA
1 TTATTTTTACGCGTCTTTA
12508971 TTATTATTT-CGCTGTCTTT
1 TTATT-TTTACGC-GTCTTT
12508990 TTTAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.13, C:0.16, G:0.11, T:0.61
Consensus pattern (19 bp):
TTATTTTTACGCGTCTTTA
Found at i:12511469 original size:11 final size:11
Alignment explanation
Indices: 12511453--12511500 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
12511443 CAGTATTCAA
*
12511453 AAAATAACAAC
1 AAAATAATAAC
*
12511464 AAAATAATAGC
1 AAAATAATAAC
*
12511475 AATATAATAAC
1 AAAATAATAAC
12511486 AAAATGAA-AAC
1 AAAAT-AATAAC
12511497 AAAA
1 AAAA
12511501 CAAAGACAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 29 0.94
12 2 0.06
ACGTcount: A:0.71, C:0.10, G:0.04, T:0.15
Consensus pattern (11 bp):
AAAATAATAAC
Found at i:12512559 original size:25 final size:25
Alignment explanation
Indices: 12512525--12512584 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
12512515 ATACACTAAT
*
12512525 AAAAA-TTTAAGTGTGAAACTAAAA
1 AAAAAGTTTAAGTGGGAAACTAAAA
*
12512549 AAAAAGTTTAAGTGGGCAACTAAAA
1 AAAAAGTTTAAGTGGGAAACTAAAA
* *
12512574 ACAACGTTTAA
1 AAAAAGTTTAA
12512585 CTAAGAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.23
Consensus pattern (25 bp):
AAAAAGTTTAAGTGGGAAACTAAAA
Found at i:12520770 original size:4 final size:4
Alignment explanation
Indices: 12520761--12520795 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
12520751 AGAAATACGC
12520761 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
12520796 GACGGATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (4 bp):
ACAT
Found at i:12522058 original size:14 final size:14
Alignment explanation
Indices: 12522039--12522071 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12522029 TTATAAAATT
12522039 TTAAATTAATAATG
1 TTAAATTAATAATG
12522053 TTAAATTAATAATG
1 TTAAATTAATAATG
*
12522067 ATAAA
1 TTAAA
12522072 ATTATACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (14 bp):
TTAAATTAATAATG
Found at i:12522075 original size:15 final size:14
Alignment explanation
Indices: 12522041--12522075 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
12522031 ATAAAATTTT
*
12522041 AAATTAATAATGTT
1 AAATTAATAATGTA
12522055 AAATTAATAATGATA
1 AAATTAATAATG-TA
12522070 AAATTA
1 AAATTA
12522076 TACTTTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (14 bp):
AAATTAATAATGTA
Found at i:12522135 original size:15 final size:17
Alignment explanation
Indices: 12522114--12522154 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
12522104 TAACTTTTTA
12522114 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
12522130 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
12522146 AAAATTATA
1 AAAATTATA
12522155 TTTTTACAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:12523664 original size:29 final size:31
Alignment explanation
Indices: 12523622--12523703 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 31
12523612 GAATTGGATC
*
12523622 AAATCAAAATTTCATGTATAAAATTACAC-A-
1 AAATC-AAAGTTCATGTATAAAATTACACAAT
* *
12523652 AAATCAAAGTTCATGTATACAATTGCACAAT
1 AAATCAAAGTTCATGTATAAAATTACACAAT
* *
12523683 AAATCATAGTTAATGTATAAA
1 AAATCAAAGTTCATGTATAAA
12523704 TTTAAAAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 20 0.45
30 6 0.14
31 18 0.41
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.30
Consensus pattern (31 bp):
AAATCAAAGTTCATGTATAAAATTACACAAT
Found at i:12523699 original size:31 final size:28
Alignment explanation
Indices: 12523635--12523705 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 28
12523625 TCAAAATTTC
*
12523635 ATGTATAAAATTACACAAAATCAAAGTTC
1 ATGTAT-AAATTACACAAAATCAAAGTTA
* *
12523664 ATGTATACAATTGCACAATAAATCATAGTTA
1 ATGTATA-AATTACAC-A-AAATCAAAGTTA
12523695 ATGTATAAATT
1 ATGTATAAATT
12523706 TAAAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 1 0.03
29 13 0.36
30 5 0.14
31 17 0.47
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.32
Consensus pattern (28 bp):
ATGTATAAATTACACAAAATCAAAGTTA
Found at i:12524143 original size:6 final size:6
Alignment explanation
Indices: 12524128--12524181 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
12524118 AAACCCAATC
* *
12524128 TTTAAT TTTAAA TTT-AA TTTAAA TTTAAA TTT--A TTCTAAA TTTAAT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
12524174 TTTAAA TT
1 TTTAAA TT
12524182 GAGTTTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 3 0.07
5 6 0.15
6 29 0.71
7 3 0.07
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:12524145 original size:12 final size:12
Alignment explanation
Indices: 12524128--12524181 Score: 60
Period size: 11 Copynumber: 4.7 Consensus size: 12
12524118 AAACCCAATC
*
12524128 TTTAATTTTAAA
1 TTTAAATTTAAA
12524140 TTT-AATTTAAA
1 TTTAAATTTAAA
12524151 TTTAAATTT--A
1 TTTAAATTTAAA
*
12524161 TTCTAAATTTAAT
1 TT-TAAATTTAAA
12524174 TTTAAATT
1 TTTAAATT
12524182 GAGTTTAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 3 0.08
11 17 0.47
12 14 0.39
13 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:12524154 original size:17 final size:17
Alignment explanation
Indices: 12524128--12524178 Score: 68
Period size: 17 Copynumber: 3.0 Consensus size: 17
12524118 AAACCCAATC
*
12524128 TTTAATTTTAAATTTAA
1 TTTAAATTTAAATTTAA
12524145 TTTAAATTTAAATTT-A
1 TTTAAATTTAAATTTAA
*
12524161 TTCTAAATTTAATTTTAA
1 TT-TAAATTTAAATTTAA
12524179 ATTGAGTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 3 0.10
17 26 0.87
18 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:12525931 original size:30 final size:29
Alignment explanation
Indices: 12525886--12526057 Score: 132
Period size: 30 Copynumber: 5.8 Consensus size: 29
12525876 AAAGGTCCCT
* * *
12525886 GAACTATCCAGAAATTATATTTTGACCCTC
1 GAACTTTCCAAAAATTACATTTTGACCC-C
* *
12525916 AAACTTTCCAAAAATTATATTTTGACCCC
1 GAACTTTCCAAAAATTACATTTTGACCCC
* * * *
12525945 TAAACTTTCCAAAAAATAAATTTTAACTCCC
1 -GAACTTTCCAAAAATTACATTTTGAC-CCC
* * *
12525976 GAACTTTCTAAAAAATACATTTTTACCCCC
1 GAACTTTCCAAAAATTACATTTTGA-CCCC
*
12526006 GAACTTTCCAATAATTACCATTTT-ACCCTC
1 GAACTTTCCAAAAATTA-CATTTTGACCC-C
* *
12526036 GAA-TATCCAAAAAATACCATTT
1 GAACTTTCCAAAAATTA-CATTT
12526058 CACCCTCGAA
Statistics
Matches: 121, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.17
30 91 0.75
31 10 0.08
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.33
Consensus pattern (29 bp):
GAACTTTCCAAAAATTACATTTTGACCCC
Found at i:12526053 original size:29 final size:29
Alignment explanation
Indices: 12525950--12526079 Score: 122
Period size: 30 Copynumber: 4.4 Consensus size: 29
12525940 ACCCCTAAAC
*
12525950 TTTCCAAAAAATA-AATTTTAACTCC-CGAA
1 TTTCCAAAAAATACCATTTT-AC-CCTCGAA
* *
12525979 CTTTCTAAAAAATA-CATTTTTACCCCCGAA
1 -TTTCCAAAAAATACCA-TTTTACCCTCGAA
* *
12526009 CTTTCCAATAATTACCATTTTACCCTCGAA
1 -TTTCCAAAAAATACCATTTTACCCTCGAA
* *
12526039 TATCCAAAAAATACCATTTCACCCTCGAA
1 TTTCCAAAAAATACCATTTTACCCTCGAA
*
12526068 TTTCAAAAAAAT
1 TTTCCAAAAAAT
12526080 CACACTTTCA
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
29 37 0.44
30 42 0.49
31 6 0.07
ACGTcount: A:0.40, C:0.25, G:0.03, T:0.32
Consensus pattern (29 bp):
TTTCCAAAAAATACCATTTTACCCTCGAA
Found at i:12526089 original size:30 final size:29
Alignment explanation
Indices: 12526021--12526079 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
12526011 TTCCAATAAT
* *
12526021 TACCATTTTACCCTCGAATATCCAAAAAA
1 TACCATTTCACCCTCGAATATCAAAAAAA
*
12526050 TACCATTTCACCCTCGAATTTCAAAAAAA
1 TACCATTTCACCCTCGAATATCAAAAAAA
12526079 T
1 T
12526080 CACACTTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.27, G:0.03, T:0.29
Consensus pattern (29 bp):
TACCATTTCACCCTCGAATATCAAAAAAA
Found at i:12533386 original size:21 final size:21
Alignment explanation
Indices: 12533362--12533405 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
12533352 TTTTAGGTTT
12533362 AACATATAATATAA-TAATTAA
1 AACAT-TAATATAATTAATTAA
**
12533383 AACATTTTTATAATTAATTAA
1 AACATTAATATAATTAATTAA
12533404 AA
1 AA
12533406 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (21 bp):
AACATTAATATAATTAATTAA
Found at i:12539413 original size:50 final size:52
Alignment explanation
Indices: 12539283--12539476 Score: 259
Period size: 52 Copynumber: 3.8 Consensus size: 52
12539273 ATTTCACTCT
* * * * * *
12539283 ATTCATATACTCACGATGATACATAGCCACCGGACCT-TATAATCCACAAGGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCT-TAATCCATAAAGG
* *
12539335 ATTCATATACTCAAGATGACACTTAGTCATCAGACCTCTTAATCCATAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
* **
12539387 ATTCA-A-ACTCACGATGACATTTAGTCATCGGACCTCTTAATCTGTAAAGG
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
12539437 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
1 ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTT
12539477 CGTTTATGGC
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
50 44 0.35
51 2 0.02
52 78 0.62
53 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (52 bp):
ATTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
Found at i:12546129 original size:52 final size:52
Alignment explanation
Indices: 12546043--12546183 Score: 160
Period size: 52 Copynumber: 2.7 Consensus size: 52
12546033 ATTTCACTTT
* * * * * ** *
12546043 ATTCATATACTCATGATGACACATAGCCACCGGACGT-TATAATCTGTAAGGG
1 ATTCATATACTCAAGATGACACTTAGTCATCGGACCTCT-TAATCCATAAAGG
*
12546095 ATTCATATATTCAAGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
1 ATTCATATACTCAAGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
*
12546147 ATTCATATACTCACA-ATGACACTTAGTCATTGGACCT
1 ATTCATATACTCA-AGATGACACTTAGTCATCGGACCT
12546184 TTCATATACT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 74 0.97
53 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (52 bp):
ATTCATATACTCAAGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGG
Found at i:12546195 original size:36 final size:36
Alignment explanation
Indices: 12546148--12546219 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
12546138 CCATAAAGGA
*
12546148 TTCATATACTCACAATGACACTTAGTCATTGGACCT
1 TTCATATACTCACAATGACACTTAGTCATCGGACCT
*
12546184 TTCATATACTCACGATGACACTTAGTCATCGGACCT
1 TTCATATACTCACAATGACACTTAGTCATCGGACCT
12546220 CTTAATCCGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (36 bp):
TTCATATACTCACAATGACACTTAGTCATCGGACCT
Found at i:12546245 original size:88 final size:88
Alignment explanation
Indices: 12546096--12546271 Score: 307
Period size: 88 Copynumber: 2.0 Consensus size: 88
12546086 CTGTAAGGGA
*
12546096 TTCATATATTCAAGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGATTCATATACTCAC
1 TTCATATACTCAAGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGATTCATATACTCAC
*
12546161 AATGACACTTAGTCATTGGACCT
66 AATGACACTTAGTCATCGGACCT
* *
12546184 TTCATATACTCACGATGACACTTAGTCATCGGACCTCTTAATCCGTAAAGGATTCATATACTCAC
1 TTCATATACTCAAGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGATTCATATACTCAC
*
12546249 GATGACACTTAGTCATCGGACCT
66 AATGACACTTAGTCATCGGACCT
12546272 CTTCGTTTAT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 83 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (88 bp):
TTCATATACTCAAGATGACACTTAGTCATCGGACCTCTTAATCCATAAAGGATTCATATACTCAC
AATGACACTTAGTCATCGGACCT
Found at i:12546643 original size:15 final size:16
Alignment explanation
Indices: 12546614--12546643 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12546604 CTTTTGTTTT
12546614 AACTTACCTAATTTGA
1 AACTTACCTAATTTGA
12546630 AACTTACC-AATTTG
1 AACTTACCTAATTTG
12546644 CCCTTAATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (16 bp):
AACTTACCTAATTTGA
Found at i:12551561 original size:19 final size:15
Alignment explanation
Indices: 12551521--12551550 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12551511 AGGGTAAAGT
12551521 TTGCTTTGAATGAAC
1 TTGCTTTGAATGAAC
12551536 TTGCTTTGAATGAAC
1 TTGCTTTGAATGAAC
12551551 CTCTTCGCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (15 bp):
TTGCTTTGAATGAAC
Found at i:12554033 original size:18 final size:20
Alignment explanation
Indices: 12553992--12554033 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
12553982 AACAAGGAAA
12553992 AAAAATATAATACAACATAT
1 AAAAATATAATACAACATAT
*
12554012 AAAAATATAGTA-AACA-AT
1 AAAAATATAATACAACATAT
12554030 AAAA
1 AAAA
12554034 TGAATAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 11 0.52
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (20 bp):
AAAAATATAATACAACATAT
Found at i:12555856 original size:6 final size:6
Alignment explanation
Indices: 12555845--12555870 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
12555835 CAAACAATCA
12555845 TTGTGT TTGTGT TTGTGT TTGTGT TT
1 TTGTGT TTGTGT TTGTGT TTGTGT TT
12555871 ATAATATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (6 bp):
TTGTGT
Found at i:12563958 original size:18 final size:18
Alignment explanation
Indices: 12563935--12563981 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
12563925 TAGGACTACC
*
12563935 CCTTAGCTTCTTCTTCAT
1 CCTTAGCATCTTCTTCAT
12563953 CCTTAGCATCTTCTTCAT
1 CCTTAGCATCTTCTTCAT
12563971 CCTTAGCATCT
1 CCTTAGCATCT
12563982 AGCATCTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.34, G:0.06, T:0.45
Consensus pattern (18 bp):
CCTTAGCATCTTCTTCAT
Found at i:12564590 original size:16 final size:17
Alignment explanation
Indices: 12564565--12564597 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
12564555 ATAAAATACA
*
12564565 CTCTCTTTCT-TTTGTT
1 CTCTCATTCTCTTTGTT
12564581 CTCTCATTCTCTTTGTT
1 CTCTCATTCTCTTTGTT
12564598 ATTTACTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.03, C:0.27, G:0.06, T:0.64
Consensus pattern (17 bp):
CTCTCATTCTCTTTGTT
Found at i:12566122 original size:29 final size:29
Alignment explanation
Indices: 12566080--12566138 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
12566070 ATTGAAAATC
12566080 TACTACTAGAAATAAGCACGTTTACTTTG
1 TACTACTAGAAATAAGCACGTTTACTTTG
12566109 TACTACTAGAAATAAGCACGTTTACTTTG
1 TACTACTAGAAATAAGCACGTTTACTTTG
12566138 T
1 T
12566139 GTTGGAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (29 bp):
TACTACTAGAAATAAGCACGTTTACTTTG
Found at i:12566836 original size:18 final size:18
Alignment explanation
Indices: 12566802--12566836 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12566792 ATAACAATTA
* *
12566802 TGAAGATTTTTGGATATG
1 TGAAGATTTTAGCATATG
12566820 TGAAGATTTTAGCATAT
1 TGAAGATTTTAGCATAT
12566837 TCCCTGAAGC
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:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (18 bp):
TGAAGATTTTAGCATATG
Found at i:12578823 original size:41 final size:41
Alignment explanation
Indices: 12578745--12578930 Score: 194
Period size: 41 Copynumber: 4.5 Consensus size: 41
12578735 TATGCTCTAT
* * * * *
12578745 CGAGTCATAAGTCTTCCTTTAACCATATTCTCATTCTCATCC
1 CGAGACATGAGTCTTCC-TTAATCATAATCTCATGCTCATCC
* *
12578787 CGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATCT
1 CGAGACATGAGTCTTCCTTAATCATAATCTCATGCTCATCC
* * *
12578828 CGAGATATGAGTCTTCCTTATTCATAATCTCATGCTCATTC
1 CGAGACATGAGTCTTCCTTAATCATAATCTCATGCTCATCC
* * * *
12578869 CGAGTCACGAGTCTTCCATTTATACA-AATTCTCATGCTCAACC
1 CGAGACATGAGTCTTCC-TTAAT-CATAA-TCTCATGCTCATCC
*
12578912 CGAGACATGGGTCTTCCTT
1 CGAGACATGAGTCTTCCTT
12578931 TTTATAAACC
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
41 71 0.59
42 22 0.18
43 28 0.23
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (41 bp):
CGAGACATGAGTCTTCCTTAATCATAATCTCATGCTCATCC
Found at i:12580483 original size:21 final size:20
Alignment explanation
Indices: 12580445--12580484 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
12580435 TACTGAAGCT
12580445 ACCATCTTTCTTTCCTGAGA
1 ACCATCTTTCTTTCCTGAGA
12580465 ACCAT-TTCTCTTCTCCTGAG
1 ACCATCTT-TCTT-TCCTGAG
12580485 CGTACTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.11
20 9 0.50
21 7 0.39
ACGTcount: A:0.17, C:0.33, G:0.10, T:0.40
Consensus pattern (20 bp):
ACCATCTTTCTTTCCTGAGA
Found at i:12583612 original size:20 final size:19
Alignment explanation
Indices: 12583583--12583620 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
12583573 GATTCTGGGT
*
12583583 AAGGTTAATTAGGGTTAAA
1 AAGGTTAATTAGGCTTAAA
12583602 AAGGATTAATTAGGCTTAA
1 AAGG-TTAATTAGGCTTAA
12583621 TGATGAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.32
Consensus pattern (19 bp):
AAGGTTAATTAGGCTTAAA
Found at i:12585504 original size:21 final size:21
Alignment explanation
Indices: 12585480--12585530 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
12585470 GTAAGACATA
*
12585480 TATCGGTAGAA-GAGTCACTTG
1 TATCAGTAGAACGA-TCACTTG
* *
12585501 TATCAATAGAACTATCACTTG
1 TATCAGTAGAACGATCACTTG
12585522 TATCAGTAG
1 TATCAGTAG
12585531 GAATCTGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (21 bp):
TATCAGTAGAACGATCACTTG
Found at i:12597665 original size:22 final size:20
Alignment explanation
Indices: 12597619--12597697 Score: 74
Period size: 20 Copynumber: 3.9 Consensus size: 20
12597609 TATTCCAAAA
*
12597619 ATAATA-TTATTTTAATAGAT
1 ATAATATTTAATTTAATA-AT
*
12597639 TTAATATTTAATTTAGTATAAT
1 ATAATATTTAATTTA--ATAAT
12597661 ATAATATTT-ATCTTAATAAT
1 ATAATATTTAAT-TTAATAAT
*
12597681 ATTATA-TTAATTTAATA
1 ATAATATTTAATTTAATA
12597698 TTAAAGTGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
19 8 0.16
20 17 0.34
21 9 0.18
22 13 0.26
23 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (20 bp):
ATAATATTTAATTTAATAAT
Found at i:12597701 original size:25 final size:25
Alignment explanation
Indices: 12597673--12597727 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
12597663 AATATTTATC
12597673 TTAATAAT-ATTATATTAAT-TTAATA
1 TTAA-AATGATTATATTAATATTAA-A
* *
12597698 TTAAAGTGATTATCTTAATATTAAA
1 TTAAAATGATTATATTAATATTAAA
12597723 TTAAA
1 TTAAA
12597728 TTAAATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 2 0.08
25 20 0.77
26 4 0.15
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (25 bp):
TTAAAATGATTATATTAATATTAAA
Found at i:12601125 original size:18 final size:15
Alignment explanation
Indices: 12601102--12601141 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
12601092 CCATGCTATT
12601102 TTTTTAATTTTTATGAA
1 TTTTTAA-TTTTAT-AA
12601119 CTTTTTAATTTTATAA
1 -TTTTTAATTTTATAA
12601135 TTTTTAA
1 TTTTTAA
12601142 ATTAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 2 0.09
17 6 0.27
18 7 0.32
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTTTAATTTTATAA
Found at i:12601427 original size:23 final size:23
Alignment explanation
Indices: 12601378--12601434 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
12601368 TCATTATACC
*
12601378 AAAATAAAAGATAAAAACAAATT
1 AAAATAAAAGATAAAAACAAATA
* *
12601401 AAAATAAATGATAAATACTAAA-A
1 AAAATAAAAGATAAAAAC-AAATA
*
12601424 AAAAAAAAAGA
1 AAAATAAAAGA
12601435 GAGAACAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 25 0.89
24 3 0.11
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (23 bp):
AAAATAAAAGATAAAAACAAATA
Found at i:12601732 original size:31 final size:31
Alignment explanation
Indices: 12601687--12601793 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 31
12601677 TAATAAAAAT
* *
12601687 AAAATTATACTTTAATTTCTTTAAAAATAATA
1 AAAATTATAATTTAAATT-TTTAAAAATAATA
* * *
12601719 AAAATT-TAATTTAAATTTTTAATAATTATT
1 AAAATTATAATTTAAATTTTTAAAAATAATA
* * ** **
12601749 AAAATTATAAAATTACATTTTT-ATTATCGTA
1 AAAATTAT-AATTTAAATTTTTAAAAATAATA
12601780 AAAATTATAATTTA
1 AAAATTATAATTTA
12601794 TGATTTCGGT
Statistics
Matches: 61, Mismatches: 12, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
30 21 0.34
31 23 0.38
32 17 0.28
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.47
Consensus pattern (31 bp):
AAAATTATAATTTAAATTTTTAAAAATAATA
Found at i:12601753 original size:30 final size:32
Alignment explanation
Indices: 12601686--12601758 Score: 87
Period size: 30 Copynumber: 2.3 Consensus size: 32
12601676 TTAATAAAAA
* *
12601686 TAAAATTATACTTTAATTTCTTTAAAAATAAT
1 TAAAATTATAATTTAAATTCTTTAAAAATAAT
* * *
12601718 AAAAATT-TAATTTAAATT-TTTAATAATTAT
1 TAAAATTATAATTTAAATTCTTTAAAAATAAT
12601748 TAAAATTATAA
1 TAAAATTATAA
12601759 AATTACATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
30 16 0.47
31 12 0.35
32 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (32 bp):
TAAAATTATAATTTAAATTCTTTAAAAATAAT
Found at i:12610279 original size:22 final size:21
Alignment explanation
Indices: 12610246--12610289 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 21
12610236 AAATTATGAC
12610246 AAATTAATTAAGTTTACATTAAT
1 AAATTAATTAAG-TTA-ATTAAT
12610269 AAATT-ATTAAGTTAATTAAT
1 AAATTAATTAAGTTAATTAAT
12610289 A
1 A
12610290 TTAGTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 6 0.29
23 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (21 bp):
AAATTAATTAAGTTAATTAAT
Found at i:12612172 original size:41 final size:41
Alignment explanation
Indices: 12612059--12612451 Score: 227
Period size: 41 Copynumber: 9.6 Consensus size: 41
12612049 CAAAAAATAA
* * *
12612059 AGCAATAGCGGCGCTTT-TGCAAAAA-CGCCGCAAAAGGT-AA
1 AGCATTAGCGGCG-TTTATG-AAAAAGCGCCGCTAAAGGTCAG
* * * * * *
12612099 AGCAATAGCGACGTCTATAGGAAAAGCACCGCTAACGGTCAG
1 AGCATTAGCGGCGTTTAT-GAAAAAGCGCCGCTAAAGGTCAG
* *** *
12612141 AGCAGTAGCGGCGTTTATGGGGAAGCGCCGCTAAAGGTTAG
1 AGCATTAGCGGCGTTTATGAAAAAGCGCCGCTAAAGGTCAG
*
12612182 AGCATTAGCGGCGTTTATGAAAAAACGCCGCTAAAGGTCAG
1 AGCATTAGCGGCGTTTATGAAAAAGCGCCGCTAAAGGTCAG
* * * * * *
12612223 ACCATTAGCGGCGCTTT-TTAGTAAA-CGCCGCCATAGGTTAG
1 AGCATTAGCGGCG-TTTATGA-AAAAGCGCCGCTAAAGGTCAG
*
12612264 AGCATTAGCGGCGCTTTCT-AATAAA-CGCCGCTAAAGGTC-G
1 AGCATTAGCGGCG-TTTATGAA-AAAGCGCCGCTAAAGGTCAG
* ** * *
12612304 AGCATTAGCGGCAATTCCTCATAAA-CGCCGCT-AAGAGTCAG
1 AGCATTAGCGGC-GTTTATGAAAAAGCGCCGCTAAAG-GTCAG
* ** * * *
12612345 AGCATTAGCGGTGCTTCCTCATAAA-CGCCGCTAAAGGTTAG
1 AGCATTAGCGGCG-TTTATGAAAAAGCGCCGCTAAAGGTCAG
* * *
12612386 AGCATTAGCGGCGCTTGT-TG-AAAAGCCCCACTAAAGGTCAC
1 AGCATTAGCGGCG-TT-TATGAAAAAGCGCCGCTAAAGGTCAG
* * *
12612427 AGTAATAGCGGCATTTATGAGAAAA
1 AGCATTAGCGGCGTTTATGA-AAAA
12612452 CGCATCTAAT
Statistics
Matches: 285, Mismatches: 49, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
39 6 0.02
40 54 0.19
41 195 0.68
42 30 0.11
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.20
Consensus pattern (41 bp):
AGCATTAGCGGCGTTTATGAAAAAGCGCCGCTAAAGGTCAG
Found at i:12612213 original size:82 final size:82
Alignment explanation
Indices: 12612059--12612406 Score: 271
Period size: 82 Copynumber: 4.2 Consensus size: 82
12612049 CAAAAAATAA
* * * * * * *
12612059 AGCAATAGCGGCGCTTTTGCA-AAAACGCCGCAAAAGG-TAAAGCAATAGCGACG-TCTATAGGA
1 AGCATTAGCGGCGCTTTTG-AGGAAACGCCGCCAAAGGTTAGAGCATTAGCGGCGCTTTATA--A
* * *
12612121 AAAGCACCGCTAACGGTCAG
63 AAAACGCCGCTAAAGGTCAG
* * * *
12612141 AGCAGTAGCGGCG-TTTATGGGGAAGCGCCGCTAAAGGTTAGAGCATTAGCGGCG-TTTATGAAA
1 AGCATTAGCGGCGCTTT-TGAGGAAACGCCGCCAAAGGTTAGAGCATTAGCGGCGCTTTAT-AAA
12612204 AAACGCCGCTAAAGGTCAG
64 AAACGCCGCTAAAGGTCAG
* * * * * *
12612223 ACCATTAGCGGCGCTTTTTAGTAAACGCCGCCATAGGTTAGAGCATTAGCGGCGCTTTCTAATAA
1 AGCATTAGCGGCGCTTTTGAGGAAACGCCGCCAAAGGTTAGAGCATTAGCGGCGCTTTATAAAAA
12612288 ACGCCGCTAAAGGTC-G
66 ACGCCGCTAAAGGTCAG
** * * * * * * ** * *
12612304 AGCATTAGCGGCAATTCCTCA-TAAACGCCG-CTAAGAGTCAGAGCATTAGCGGTGCTTCCTCAT
1 AGCATTAGCGGCGCTT-TTGAGGAAACGCCGCCAAAG-GTTAGAGCATTAGCGGCGCTTTATAAA
*
12612367 AAACGCCGCTAAAGGTTAG
64 AAACGCCGCTAAAGGTCAG
12612386 AGCATTAGCGGCGCTTGTTGA
1 AGCATTAGCGGCGCTT-TTGA
12612407 AAAGCCCCAC
Statistics
Matches: 218, Mismatches: 39, Indels: 18
0.79 0.14 0.07
Matches are distributed among these distances:
80 3 0.01
81 65 0.30
82 125 0.57
83 24 0.11
84 1 0.00
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.21
Consensus pattern (82 bp):
AGCATTAGCGGCGCTTTTGAGGAAACGCCGCCAAAGGTTAGAGCATTAGCGGCGCTTTATAAAAA
ACGCCGCTAAAGGTCAG
Found at i:12612369 original size:81 final size:81
Alignment explanation
Indices: 12612166--12612397 Score: 245
Period size: 81 Copynumber: 2.8 Consensus size: 81
12612156 TATGGGGAAG
* * * ** * *
12612166 CGCCGCTAAAGGTTAGAGCATTAGCGGCG-TTTATGAAAAAACGCCGCTAAAGGTCAGACCATTA
1 CGCCGCCATAGGTCAGAGCATTAGCGGCGCTTCCT-AATAAACGCCGCTAAAGGTC-GAGCATTA
** * *
12612230 GCGGCGCTTTTTAGTAAA
64 GCGGCAATTCTCAGTAAA
* *
12612248 CGCCGCCATAGGTTAGAGCATTAGCGGCGCTTTCTAATAAACGCCGCTAAAGGTCGAGCATTAGC
1 CGCCGCCATAGGTCAGAGCATTAGCGGCGCTTCCTAATAAACGCCGCTAAAGGTCGAGCATTAGC
12612313 GGCAATTCCTCA-TAAA
66 GGCAATT-CTCAGTAAA
* * * *
12612329 CGCCGCTA-AGAGTCAGAGCATTAGCGGTGCTTCCTCATAAACGCCGCTAAAGGTTAGAGCATTA
1 CGCCGCCATAG-GTCAGAGCATTAGCGGCGCTTCCTAATAAACGCCGCTAAAGG-TCGAGCATTA
12612393 GCGGC
64 GCGGC
12612398 GCTTGTTGAA
Statistics
Matches: 131, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
80 2 0.02
81 63 0.48
82 62 0.47
83 4 0.03
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.22
Consensus pattern (81 bp):
CGCCGCCATAGGTCAGAGCATTAGCGGCGCTTCCTAATAAACGCCGCTAAAGGTCGAGCATTAGC
GGCAATTCTCAGTAAA
Found at i:12612420 original size:122 final size:122
Alignment explanation
Indices: 12612204--12612424 Score: 297
Period size: 122 Copynumber: 1.8 Consensus size: 122
12612194 GTTTATGAAA
* * *
12612204 AAACGCCGCTAAAGGTCAGACCATTAGCGGCGCTTTTTAGTAAACGCCGCCATAGGTTAGAGCAT
1 AAACGCCGCTAAAGGTCAGACCATTAGCGGCGCTTCTCAGTAAACGCCGCCAAAGGTTAGAGCAT
* *
12612269 TAGCGGCGCTTTCTAATAAACGCCGCTAAAGGTCGAGCATTAGCGGCAATTCCTCAT
66 TAGCGGCGCTTTCTAATAAACCCCACTAAAGGTCGAGCATTAGCGGCAATTCCTCAT
* * *
12612326 AAACGCCGCT-AAGAGTCAGAGCATTAGCGGTGCTTCCTCA-TAAACGCCGCTAAAGGTTAGAGC
1 AAACGCCGCTAAAG-GTCAGACCATTAGCGGCGCTT-CTCAGTAAACGCCGCCAAAGGTTAGAGC
*
12612389 ATTAGCGGCGCTTGT-TGAA-AAGCCCCACTAAAGGTC
64 ATTAGCGGCGCTT-TCT-AATAAACCCCACTAAAGGTC
12612425 ACAGTAATAG
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
121 3 0.03
122 78 0.91
123 5 0.06
ACGTcount: A:0.29, C:0.25, G:0.24, T:0.22
Consensus pattern (122 bp):
AAACGCCGCTAAAGGTCAGACCATTAGCGGCGCTTCTCAGTAAACGCCGCCAAAGGTTAGAGCAT
TAGCGGCGCTTTCTAATAAACCCCACTAAAGGTCGAGCATTAGCGGCAATTCCTCAT
Found at i:12613121 original size:18 final size:19
Alignment explanation
Indices: 12613098--12613141 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
12613088 AAAAAATAAA
12613098 AAAATTATT-A-ACATTTCT
1 AAAATTATTGATA-ATTTCT
*
12613116 AAAATTTTTGATAATTTCT
1 AAAATTATTGATAATTTCT
12613135 AAAATTA
1 AAAATTA
12613142 ACATTACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 8 0.36
19 13 0.59
20 1 0.05
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (19 bp):
AAAATTATTGATAATTTCT
Found at i:12614611 original size:41 final size:41
Alignment explanation
Indices: 12614554--12614665 Score: 143
Period size: 41 Copynumber: 2.7 Consensus size: 41
12614544 AGCATTAGCG
* *
12614554 GCGTTTATGAGAAAGCGCTGCTAAAGGTTAGAGAATAAACA
1 GCGTTTATGAGAAAGCGCCGCTAAAGGTCAGAGAATAAACA
* * * *
12614595 GCGTTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAGCT
1 GCGTTTATGAGAAAGCGCCGCTAAAGGTCAGAGAATAAACA
* * *
12614636 GCGTTTATGAAAAAGCGTCGTTAAAGGTCA
1 GCGTTTATGAGAAAGCGCCGCTAAAGGTCA
12614666 CAGCACTAGC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (41 bp):
GCGTTTATGAGAAAGCGCCGCTAAAGGTCAGAGAATAAACA
Found at i:12617909 original size:43 final size:43
Alignment explanation
Indices: 12617844--12617977 Score: 142
Period size: 43 Copynumber: 3.1 Consensus size: 43
12617834 ATCTATTAAT
* *
12617844 TTTAGCAGCGTTTGTGAAAAAAGTGCCACTAAAGATCATGTTA
1 TTTAGCAGCGTTTGTGAAAAAAGAGCCACTAAAGACCATGTTA
* * * *
12617887 TTTAGCAGCGTTTGTTAGAAAAGAGCCGCTAAAGACCATGTTC
1 TTTAGCAGCGTTTGTGAAAAAAGAGCCACTAAAGACCATGTTA
* *** * * * *
12617930 TTTAGCGGCGTTTGTGGGGAAAGCGCCGCTAAAGACCTTGTTC
1 TTTAGCAGCGTTTGTGAAAAAAGAGCCACTAAAGACCATGTTA
12617973 TTTAG
1 TTTAG
12617978 TGACGTTTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 79 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (43 bp):
TTTAGCAGCGTTTGTGAAAAAAGAGCCACTAAAGACCATGTTA
Found at i:12622575 original size:21 final size:21
Alignment explanation
Indices: 12622549--12622588 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12622539 GCAACAATGC
* *
12622549 AGCAGCATGGCACAAGTCAGT
1 AGCAGCAAGGAACAAGTCAGT
12622570 AGCAGCAAGGAACAAGTCA
1 AGCAGCAAGGAACAAGTCA
12622589 TCATCAGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.23, G:0.28, T:0.10
Consensus pattern (21 bp):
AGCAGCAAGGAACAAGTCAGT
Found at i:12625494 original size:21 final size:21
Alignment explanation
Indices: 12625458--12625504 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
12625448 TTTCTTTTTT
* *
12625458 TTAAAAAATTTGATATACATA
1 TTAAAAAATATGATATAAATA
12625479 TATAAAAAATAT-ATATAAATA
1 T-TAAAAAATATGATATAAATA
12625500 TTAAA
1 TTAAA
12625505 TATGAAATGC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 4 0.17
21 10 0.43
22 9 0.39
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
TTAAAAAATATGATATAAATA
Found at i:12637714 original size:21 final size:21
Alignment explanation
Indices: 12637663--12637714 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
12637653 TAGAGGTAAG
** *
12637663 ACTTGTATTAGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
12637684 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
12637705 ACTTGTATCG
1 ACTTGTATCG
12637715 ATACAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:12641551 original size:37 final size:37
Alignment explanation
Indices: 12641499--12641569 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
12641489 CCACTTGACG
* * *
12641499 AAACCTAATTCTAATTGTTTTATTCTGAAGCAAAAAT
1 AAACCTAATTATAATTATTTTATTCGGAAGCAAAAAT
*
12641536 AAACCTAATTATAATTATTTTGTTCGGAAGCAAA
1 AAACCTAATTATAATTATTTTATTCGGAAGCAAA
12641570 GATATCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (37 bp):
AAACCTAATTATAATTATTTTATTCGGAAGCAAAAAT
Found at i:12644834 original size:24 final size:24
Alignment explanation
Indices: 12644806--12644854 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
12644796 ATCATGTATA
12644806 TCAAGTTTGGTATAAATTAAAAAT
1 TCAAGTTTGGTATAAATTAAAAAT
12644830 TCAAGTTTGGTATAAATTAAAAAT
1 TCAAGTTTGGTATAAATTAAAAAT
12644854 T
1 T
12644855 TCGAACTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.04, G:0.12, T:0.39
Consensus pattern (24 bp):
TCAAGTTTGGTATAAATTAAAAAT
Found at i:12645693 original size:67 final size:67
Alignment explanation
Indices: 12645583--12645737 Score: 204
Period size: 67 Copynumber: 2.3 Consensus size: 67
12645573 CGAGTTTGCT
* * **
12645583 GAGTTAAGCTCGCAACTCCGAAACAGCTCGCTGACCTACGTTCTCAGTTGATGATTAAAGGTTAG
1 GAGTTAAGCTCGCAACTCCAAAACAGCTCGATGACCTACGTTCTCAACTGATGATTAAAGGTTAG
12645648 CC
66 CC
* *
12645650 GAGTTAAGCTCGCAACTCCAAAACAGCTC-ATGAACTTATGTTCTCAACTGATGATTAAAGGTTA
1 GAGTTAAGCTCGCAACTCCAAAACAGCTCGATG-ACCTACGTTCTCAACTGATGATTAAAGGTTA
**
12645714 GTT
65 GCC
*
12645717 GAGTTAAGCTTGCAACCTCCA
1 GAGTTAAGCTCGCAA-CTCCA
12645738 GATTATTCAA
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
66 2 0.03
67 70 0.91
68 5 0.06
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (67 bp):
GAGTTAAGCTCGCAACTCCAAAACAGCTCGATGACCTACGTTCTCAACTGATGATTAAAGGTTAG
CC
Found at i:12645836 original size:102 final size:103
Alignment explanation
Indices: 12645643--12645884 Score: 308
Period size: 102 Copynumber: 2.3 Consensus size: 103
12645633 ATGATTAAAG
* * *
12645643 GTTAGCCGAGTTAAGCTCGCAACTCCAAAACAGCTCATGAACTTATGTTCTCAACTGATGATTAA
1 GTTAGCTGAGTTAAGCTCGCAACTCCAAAACAGCT-ATGAAC-TATGTCCCCAACTGATGATTAA
* *
12645708 AGGTTAGTTGAGTTAAGCTTGCAACCTCCAGATTATTCAA
64 AGGTTAGTTGAGTTAAGCTCGAAACCTCCAGATTATTCAA
* * * *
12645748 GTTAGCTGAGTTAAGCTCGTAACTCCGAAACAGCT-TGTAA-TATGTCCCCAATTGATTATTAAA
1 GTTAGCTGAGTTAAGCTCGCAACTCCAAAACAGCTATG-AACTATGTCCCCAACTGATGATTAAA
* *
12645811 GGTTAGTTGAGTTAAGCTCGAAACCTTCAGATTATTCGA
65 GGTTAGTTGAGTTAAGCTCGAAACCTCCAGATTATTCAA
** * *
12645850 GCCAGTTGAGTTAAGCTCGCAACTTCAAAACAGCT
1 GTTAGCTGAGTTAAGCTCGCAACTCCAAAACAGCT
12645885 CCTAGACTTA
Statistics
Matches: 119, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
102 83 0.70
103 2 0.02
104 2 0.02
105 32 0.27
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (103 bp):
GTTAGCTGAGTTAAGCTCGCAACTCCAAAACAGCTATGAACTATGTCCCCAACTGATGATTAAAG
GTTAGTTGAGTTAAGCTCGAAACCTCCAGATTATTCAA
Found at i:12651091 original size:26 final size:28
Alignment explanation
Indices: 12651055--12651127 Score: 96
Period size: 26 Copynumber: 2.6 Consensus size: 28
12651045 TTGGTTCAGG
* *
12651055 ATACATTTTAGTCACTTATGATTG-CA-
1 ATACGTTTTAGTCACTTATGATTGAAAT
*
12651081 ATACGTTTTAGTCACTTATGTTTGAAAT
1 ATACGTTTTAGTCACTTATGATTGAAAT
12651109 ATTACGTTTTAGTCACTTA
1 A-TACGTTTTAGTCACTTA
12651128 CATTATTGCA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
26 22 0.54
27 1 0.02
28 1 0.02
29 17 0.41
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (28 bp):
ATACGTTTTAGTCACTTATGATTGAAAT
Found at i:12652611 original size:29 final size:29
Alignment explanation
Indices: 12652579--12652796 Score: 144
Period size: 29 Copynumber: 7.4 Consensus size: 29
12652569 CGGAAGTGTG
* *
12652579 ATTTTTGGAAATTCGAGTGCAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGCAAAATGGTA
* * *
12652608 ATTTTTTGATGTTCGGGGGCAAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGC-AAAATGGTA
* * * *
12652638 ATATTTAGATGTTCG-GGGGAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGCAAAATGGTA
* *
12652666 ATTTTGTGAAAGTTC-AGGGTCAAAAT-GTG
1 ATTTT-TGGAAGTTCGAGGG-CAAAATGGTA
* *
12652695 ATTTTTGGAAGTTTGGGGGCAAAATGGTA
1 ATTTTTGGAAGTTCGAGGGCAAAATGGTA
* * * *
12652724 ATTTTT-GAATGTTCAAGAGTAAAACGGTA
1 ATTTTTGGAA-GTTCGAGGGCAAAATGGTA
*
12652753 A-TTTTGGAAAAGTTTG-GGGTCAAAAAT-GTA
1 ATTTTTGG--AAGTTCGAGGG-C-AAAATGGTA
12652783 ATTTTTGAGAAGTT
1 ATTTTTG-GAAGTT
12652797 TCGGTAAAAT
Statistics
Matches: 146, Mismatches: 29, Indels: 27
0.72 0.14 0.13
Matches are distributed among these distances:
28 33 0.23
29 62 0.42
30 39 0.27
31 11 0.08
32 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAGTTCGAGGGCAAAATGGTA
Found at i:12652633 original size:30 final size:29
Alignment explanation
Indices: 12652597--12652737 Score: 144
Period size: 28 Copynumber: 4.9 Consensus size: 29
12652587 AAATTCGAGT
12652597 GCAAAATGGTAATTTTTTGATGTTCGGGG
1 GCAAAATGGTAATTTTTTGATGTTCGGGG
* *
12652626 GCAAAAATGGTAATATTTAGATGTTCGGGG
1 GC-AAAATGGTAATTTTTTGATGTTCGGGG
* * *
12652656 G-AAAATGGTAATTTTGTGAAAGTTCAGGG
1 GCAAAATGGTAATTTTTTG-ATGTTCGGGG
* * * * *
12652685 TCAAAAT-GTGATTTTTGGAAGTTTGGGG
1 GCAAAATGGTAATTTTTTGATGTTCGGGG
12652713 GCAAAATGGTAA-TTTTTGAATGTTC
1 GCAAAATGGTAATTTTTTG-ATGTTC
12652738 AAGAGTAAAA
Statistics
Matches: 89, Mismatches: 18, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
28 33 0.37
29 25 0.28
30 31 0.35
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (29 bp):
GCAAAATGGTAATTTTTTGATGTTCGGGG
Found at i:12652691 original size:58 final size:58
Alignment explanation
Indices: 12652597--12652738 Score: 164
Period size: 58 Copynumber: 2.4 Consensus size: 58
12652587 AAATTCGAGT
* *
12652597 GCAAAATGGTAATTTTTTG-ATGTTCGGGGGCAAAAATGGTAATATTTAGATGTTCGGGG
1 GCAAAATGGTAA-TTTTTGAATGTTCAGGGGCAAAAAT-GTAATATTTAGAAGTTCGGGG
* * * * * *
12652656 G-AAAATGGTAATTTTGTGAAAGTTCAGGGTC-AAAATGTGATTTTTGGAAGTTTGGGG
1 GCAAAATGGTAATTTT-TGAATGTTCAGGGGCAAAAATGTAATATTTAGAAGTTCGGGG
12652713 GCAAAATGGTAATTTTTGAATGTTCA
1 GCAAAATGGTAATTTTTGAATGTTCA
12652739 AGAGTAAAAC
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
57 30 0.42
58 31 0.44
59 10 0.14
ACGTcount: A:0.30, C:0.06, G:0.29, T:0.35
Consensus pattern (58 bp):
GCAAAATGGTAATTTTTGAATGTTCAGGGGCAAAAATGTAATATTTAGAAGTTCGGGG
Found at i:12652777 original size:59 final size:58
Alignment explanation
Indices: 12652657--12652947 Score: 165
Period size: 58 Copynumber: 4.9 Consensus size: 58
12652647 TGTTCGGGGG
* * *
12652657 AAAATGGTAATTTTGTGAAAGTTCAGGGTCAAAATGTGATTTTTGGAAGTTTGGGGGC-
1 AAAATGGTAATTTT-TGAAAGTTCAGAGTCAAAAGGTGAATTTTGGAAGTTTGGGGGCA
* *
12652715 AAAATGGTAATTTTTGAATGTTCAAGAGT-AAAACGGT-AATTTTGGAAAAGTTTGGGGTCA
1 AAAATGGTAATTTTTGAAAGTTC-AGAGTCAAAA-GGTGAATTTTGG--AAGTTTGGGGGCA
* * * *
12652775 AAAAT-GTAATTTTTGAGAAGTTTC-G-GT-AAAATGTGAATTTT-GAATGTTCGAGGGTA
1 AAAATGGTAATTTTTGA-AAG-TTCAGAGTCAAAAGGTGAATTTTGGAA-GTTTGGGGGCA
* * * * * **
12652831 AAAATGTGT--TTTTTGAAAAGTTTAAGGGT-AAAATGTGATTTTTTGAAAGTTTAGGGGTAA
1 AAAATG-GTAATTTTTG-AAAG-TTCAGAGTCAAAAGGTGA-ATTTTGGAAGTTT-GGGGGCA
* * * * *
12652891 AAAAT-GTAATTTTTGGAAAGTTCAAGGGTAAAAACGTGATTTTTGGAAAGTTCGGGG
1 AAAATGGTAATTTTT-GAAAGTTC-AGAGTCAAAAGGTGAATTTTGG-AAGTTTGGGG
12652948 ACCTTCTGGG
Statistics
Matches: 188, Mismatches: 22, Indels: 44
0.74 0.09 0.17
Matches are distributed among these distances:
55 2 0.01
56 24 0.13
57 24 0.13
58 47 0.25
59 32 0.17
60 42 0.22
61 17 0.09
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAATGGTAATTTTTGAAAGTTCAGAGTCAAAAGGTGAATTTTGGAAGTTTGGGGGCA
Found at i:12652786 original size:30 final size:29
Alignment explanation
Indices: 12652657--12652947 Score: 150
Period size: 30 Copynumber: 9.9 Consensus size: 29
12652647 TGTTCGGGGG
** *
12652657 AAAATGGTAATTTTGTG-AAAGTTCAGGGTC
1 AAAAT-GTAATTTT-TGAAAAGTTTGGGGTA
* * **
12652687 AAAATGTGATTTTTG-GAAGTTTGGGGGC
1 AAAATGTAATTTTTGAAAAGTTTGGGGTA
* ** *
12652715 AAAATGGTAATTTTTG-AATGTTCAAGAGTA
1 AAAAT-GTAATTTTTGAAAAGTT-TGGGGTA
** *
12652745 AAACGGTAATTTTGGAAAAGTTTGGGGTCA
1 AAAATGTAATTTTTGAAAAGTTTGGGGT-A
* *
12652775 AAAATGTAATTTTTGAGAAGTTT-CGGT-
1 AAAATGTAATTTTTGAAAAGTTTGGGGTA
* *
12652802 AAAATGTGAA-TTTTG-AATGTTCGAGGGTA
1 AAAATGT-AATTTTTGAAAAGTTTG-GGGTA
** *
12652831 AAAATGTGTTTTTTGAAAAGTTTAAGGGT-
1 AAAATGTAATTTTTGAAAAGTTT-GGGGTA
*
12652860 AAAATGTGATTTTTTG-AAAGTTTAGGGGTAA
1 AAAATGT-AATTTTTGAAAAGTTT-GGGGT-A
* **
12652891 AAAATGTAATTTTTGGAAAGTTCAAGGGTA
1 AAAATGTAATTTTTGAAAAGTT-TGGGGTA
* * * *
12652921 AAAACGTGATTTTTGGAAAGTTCGGGG
1 AAAATGTAATTTTTGAAAAGTTTGGGG
12652948 ACCTTCTGGG
Statistics
Matches: 202, Mismatches: 43, Indels: 33
0.73 0.15 0.12
Matches are distributed among these distances:
26 4 0.02
27 12 0.06
28 21 0.10
29 69 0.34
30 79 0.39
31 17 0.08
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAAGTTTGGGGTA
Found at i:12652806 original size:87 final size:85
Alignment explanation
Indices: 12652657--12652833 Score: 207
Period size: 87 Copynumber: 2.0 Consensus size: 85
12652647 TGTTCGGGGG
* * *
12652657 AAAATGGTAATTTTGTGAAAGTTCAGGGTCAAAATGTGATTTTTGGAAGTTTGGGGGCAAAATG-
1 AAAACGGTAATTTTGTGAAAGTTCAGGGTCAAAATGTAATTTTTGGAAGTTT-GCGGCAAAATGT
12652721 GTAATTTTTGAATGTTCAAGAGT
65 G-AA-TTTTGAATGTTCAAGAGT
** *
12652744 AAAACGGTAATTTTG-GAAAAGTTTGGGGTCAAAAATGTAATTTTTGAGAAGTTT-CGGTAAAAT
1 AAAACGGTAATTTTGTG-AAAGTTCAGGGTC-AAAATGTAATTTTTG-GAAGTTTGCGGCAAAAT
* *
12652807 GTGAATTTTGAATGTTCGAGGGT
63 GTGAATTTTGAATGTTCAAGAGT
12652830 AAAA
1 AAAA
12652834 ATGTGTTTTT
Statistics
Matches: 78, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
86 21 0.27
87 35 0.45
88 15 0.19
89 7 0.09
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (85 bp):
AAAACGGTAATTTTGTGAAAGTTCAGGGTCAAAATGTAATTTTTGGAAGTTTGCGGCAAAATGTG
AATTTTGAATGTTCAAGAGT
Found at i:12653699 original size:91 final size:91
Alignment explanation
Indices: 12653600--12653830 Score: 421
Period size: 91 Copynumber: 2.6 Consensus size: 91
12653590 TAGATCTGAC
*
12653600 AGATCTAACCTAGATCTCTTACAAAACCTTTAAAAAAAATCAAAATCTGCCTTTCTGCTCGCCTT
1 AGATCTAACCTAGATCTCCTACAAAACCTTTAAAAAAAATCAAAATCTGCCTTTCTGCTCGCCTT
12653665 TTCTATTTTAAAACCGATCTAGGTAT
66 TTCTATTTTAAAACCGATCTAGGTAT
12653691 AGATCTAACCTAGATCTCCTACAAAACCTTTAAAAAAAATCAAAATCTGCCTTTCTGCTCGCCTT
1 AGATCTAACCTAGATCTCCTACAAAACCTTTAAAAAAAATCAAAATCTGCCTTTCTGCTCGCCTT
*
12653756 TTCTATTTTAAAATCGATCTAGGTAT
66 TTCTATTTTAAAACCGATCTAGGTAT
*
12653782 AGATCTAACCTAGATCTCCTA-AAAACCTTTCAAAAAAATC-AAATCTGCC
1 AGATCTAACCTAGATCTCCTACAAAACCTTTAAAAAAAATCAAAATCTGCC
12653831 CCCTTTTTAT
Statistics
Matches: 137, Mismatches: 3, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
89 9 0.07
90 18 0.13
91 110 0.80
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (91 bp):
AGATCTAACCTAGATCTCCTACAAAACCTTTAAAAAAAATCAAAATCTGCCTTTCTGCTCGCCTT
TTCTATTTTAAAACCGATCTAGGTAT
Found at i:12654701 original size:17 final size:17
Alignment explanation
Indices: 12654675--12654755 Score: 110
Period size: 17 Copynumber: 4.8 Consensus size: 17
12654665 GACTTTTAAT
12654675 TAAATCTTAAATTTAAAA
1 TAAAT-TTAAATTTAAAA
* *
12654693 TAAATTTAAACTCAAAA
1 TAAATTTAAATTTAAAA
*
12654710 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
12654727 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
12654744 T-AATTTAAATTT
1 TAAATTTAAATTT
12654756 GGGTTTATTT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
16 10 0.18
17 40 0.73
18 5 0.09
ACGTcount: A:0.54, C:0.05, G:0.01, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:12654720 original size:34 final size:33
Alignment explanation
Indices: 12654681--12654755 Score: 132
Period size: 34 Copynumber: 2.2 Consensus size: 33
12654671 TAATTAAATC
12654681 TTAAATTTAAAATAAATTTAAACTCAAAATAAGT
1 TTAAATTTAAAATAAATTTAAACTCAAAATAA-T
*
12654715 TTAAATTTAAAATAAATTTAAACTTAAAATAAT
1 TTAAATTTAAAATAAATTTAAACTCAAAATAAT
12654748 TTAAATTT
1 TTAAATTT
12654756 GGGTTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 9 0.22
34 31 0.77
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.40
Consensus pattern (33 bp):
TTAAATTTAAAATAAATTTAAACTCAAAATAAT
Found at i:12655193 original size:39 final size:39
Alignment explanation
Indices: 12655150--12655760 Score: 257
Period size: 39 Copynumber: 15.7 Consensus size: 39
12655140 ACTGATAGTG
* * *
12655150 ATCTGCCCTAGGCTCGAGGTAAGAGATCTATTGGCTGTA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCTGTA
* * ** * *
12655189 ATCTGCCCCAGGCTCG-GTGTAAGAGATTTGCT-GATGATG
1 ATCTGCCCCAAGCTCGAG-GTAAGAGATCTAATGGCTG-TA
* * * * *
12655228 ATCTACCCCAGGCTCG-GGATAAAAGATCGAATGGCTGCA
1 ATCTGCCCCAAGCTCGAGG-TAAGAGATCTAATGGCTGTA
* * * * * * * *
12655267 ATTTACCCCAGGCTCGGGGTAAAAGATCGAATGGTTGCA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCTGTA
* * * * * *
12655306 ATCTACCCCAAGCTTG-GGTAAAATATCGAATGGCTGCA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCTGTA
* *
12655344 ATCTGACCCAAGCTCGAGGTAAGAGATTTGCTAAT-GATG--
1 ATCTGCCCCAAGCTCGAGGTAAGAGA--T-CTAATGGCTGTA
* * * * * * * *
12655383 ATATGCTCTAGGCTCGGGGTAAAAGATCGAATGGTTGTA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCTGTA
* ** *
12655422 ATCTGCCCCAAGCTCGGGGTAAGAGAT-TGGCTGG-TGATG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCT-AATGGCTG-TA
* * * * * *
12655461 ATCTACCCCAAGCTTGGGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCTGTA
* * * * * *
12655500 ATTTGCCCCAAGCTCGAGGTAAGAGAT-TTATTGATAATG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCT-GTA
** * * * *
12655539 ATCTGCCTTAAGCTCGGGGTAAGAGATTTAATAGCTGCA
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCTGTA
* ** *
12655578 ATCTGCCCCAAGCTCGGGGTAAGAGAT-TGGTTGG-TGATG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCT-AATGGCTG-TA
* * *
12655617 ATCTG-CCCAGGCTC-AGGGTAAAAGATCGAATGGCTGTA
1 ATCTGCCCCAAGCTCGA-GGTAAGAGATCTAATGGCTGTA
* ** *
12655655 ATCTGCCCCAAGCTC-AGGGTAAGAGATCAAATAACTGCA
1 ATCTGCCCCAAGCTCGA-GGTAAGAGATCTAATGGCTGTA
* * * ** *
12655694 ATTTGCCCCAGGCTCGAGGTGAGAGAT-TGGCTGG-TGTTG
1 ATCTGCCCCAAGCTCGAGGTAAGAGATCT-AATGGCTG-TA
* *
12655733 ATCTGCCTCAGGCTCGAGGTAAGAGATC
1 ATCTGCCCCAAGCTCGAGGTAAGAGATC
12655761 GAAATCTTCA
Statistics
Matches: 434, Mismatches: 110, Indels: 55
0.72 0.18 0.09
Matches are distributed among these distances:
36 4 0.01
37 4 0.01
38 75 0.17
39 330 0.76
40 13 0.03
41 4 0.01
42 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGAGGTAAGAGATCTAATGGCTGTA
Found at i:12655205 original size:78 final size:78
Alignment explanation
Indices: 12655122--12655678 Score: 482
Period size: 78 Copynumber: 7.2 Consensus size: 78
12655112 TCTGCCCTGG
* * * * * * *
12655122 GCTCGGGGTAACAAATCGACTGAT-AGTGATCTGCCCTAGGCTCGAGGTAAGAGATCTATTGGCT
1 GCTCGGGGTAAGAAATTGACTGATGA-TGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCT
* *
12655186 GTAATCTGCCCCAG
65 GCAATCTGCCCCAA
* * * *
12655200 GCTCGGTGTAAGAGATTTG-CTGATGATGATCTACCCCAGGCTCGGGATAAAAGATCGAATGGCT
1 GCTCGGGGTAAGA-AATTGACTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCT
* * *
12655264 GCAATTTACCCCAG
65 GCAATCTGCCCCAA
* * * * * * *
12655278 GCTCGGGGTAA-AAGATCGAATG--GTTGCAATCTACCCCAAGCT-TGGGTAAAATATCGAATGG
1 GCTCGGGGTAAGAA-ATTGACTGATGATG--ATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGG
*
12655339 CTGCAATCTGACCCAA
63 CTGCAATCTGCCCCAA
* * * * * * *
12655355 GCTCGAGGTAAGAGATTTG-CTAATGATGATATGCTCTAGGCTCGGGGTAAAAGATCGAATGGTT
1 GCTCGGGGTAAGA-AATTGACTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCT
*
12655419 GTAATCTGCCCCAA
65 GCAATCTGCCCCAA
* * * * * *
12655433 GCTCGGGGTAAGAGATTGGCTGGTGATGATCTACCCCAAGCTTGGGGTAAAAGATCGAATGGCTG
1 GCTCGGGGTAAGAAATTGACTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTG
*
12655498 CAATTTGCCCCAA
66 CAATCTGCCCCAA
* * * * * ** * * ** *
12655511 GCTCGAGGTAAGAGATTTATTGATAATGATCTGCCTTAAGCTCGGGGTAAGAGATTTAATAGCTG
1 GCTCGGGGTAAGAAATTGACTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTG
12655576 CAATCTGCCCCAA
66 CAATCTGCCCCAA
* ** * *
12655589 GCTCGGGGTAAGAGATTGGTTGGTGATGATCTG-CCCAGGCTCAGGGTAAAAGATCGAATGGCTG
1 GCTCGGGGTAAGAAATTGACTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTG
*
12655653 TAATCTGCCCCAA
66 CAATCTGCCCCAA
*
12655666 GCTCAGGGTAAGA
1 GCTCGGGGTAAGA
12655679 GATCAAATAA
Statistics
Matches: 380, Mismatches: 87, Indels: 25
0.77 0.18 0.05
Matches are distributed among these distances:
76 4 0.01
77 101 0.27
78 267 0.70
79 8 0.02
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (78 bp):
GCTCGGGGTAAGAAATTGACTGATGATGATCTGCCCCAGGCTCGGGGTAAAAGATCGAATGGCTG
CAATCTGCCCCAA
Found at i:12655638 original size:233 final size:230
Alignment explanation
Indices: 12655148--12655681 Score: 647
Period size: 233 Copynumber: 2.3 Consensus size: 230
12655138 CGACTGATAG
* * * * *
12655148 TGATCTGCCCTAGGCTCGAGGTAAGAGATCTATTGGCTGTAATCTGCCCCAGGCTCGGTGTAAGA
1 TGATCTGCCC-AGGCTCG-GGTAAAAGATCGAATGGCTGTAATCTGCCCCAAGCTCGGGGTAAGA
* * *
12655213 GATTTGCTGATGATGATCTACCCCAGGCTCGGGATAAAAGATCGAATGGCTGCAATTTACCCCAG
64 GATTGGCTGATGATGATCTACCCCAAGCTCGGGATAAAAGATCGAATGGCTGCAATTTACCCCAA
* * * * *
12655278 GCTCGGGGTAAAAGATCGAATGGTTGCAATCTACCCCAAGCTTGGGTAAAATATCGAATGGCTGC
129 GCTCGAGGTAAAAGATCGAATGATTG-AATCTACCCCAAGCTGGGGTAAAAGATCGAATAGCTGC
*
12655343 AATCTGACCCAAGCTCGAGGTAAGAGATTTGCTAATGA
193 AATCTGACCCAAGCTCGAGGTAAGAGATTGGCTAATGA
* * *
12655381 TGATATGCTCTAGGCTCGGGGTAAAAGATCGAATGGTTGTAATCTGCCCCAAGCTCGGGGTAAGA
1 TGATCTGC-CCAGGCTC-GGGTAAAAGATCGAATGGCTGTAATCTGCCCCAAGCTCGGGGTAAGA
* * * *
12655446 GATTGGCTGGTGATGATCTACCCCAAGCTTGGGGTAAAAGATCGAATGGCTGCAATTTGCCCCAA
64 GATTGGCTGATGATGATCTACCCCAAGCTCGGGATAAAAGATCGAATGGCTGCAATTTACCCCAA
* ** * * ** * **
12655511 GCTCGAGGTAAGAGATTTATTGATAATG-ATCTGCCTTAAGCTCGGGGTAAGAGATTTAATAGCT
129 GCTCGAGGTAAAAGATCGAATGAT--TGAATCTACCCCAAGCT-GGGGTAAAAGATCGAATAGCT
* * * **
12655575 GCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGTTGGTGA
191 GCAATCTGACCCAAGCTCGAGGTAAGAGATTGGCTAATGA
*
12655615 TGATCTGCCCAGGCTCAGGGTAAAAGATCGAATGGCTGTAATCTGCCCCAAGCTCAGGGTAAGAG
1 TGATCTGCCCAGGCTC-GGGTAAAAGATCGAATGGCTGTAATCTGCCCCAAGCTCGGGGTAAGAG
12655680 AT
65 AT
12655682 CAAATAACTG
Statistics
Matches: 255, Mismatches: 41, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
233 195 0.76
234 58 0.23
235 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (230 bp):
TGATCTGCCCAGGCTCGGGTAAAAGATCGAATGGCTGTAATCTGCCCCAAGCTCGGGGTAAGAGA
TTGGCTGATGATGATCTACCCCAAGCTCGGGATAAAAGATCGAATGGCTGCAATTTACCCCAAGC
TCGAGGTAAAAGATCGAATGATTGAATCTACCCCAAGCTGGGGTAAAAGATCGAATAGCTGCAAT
CTGACCCAAGCTCGAGGTAAGAGATTGGCTAATGA
Found at i:12658051 original size:3 final size:3
Alignment explanation
Indices: 12658043--12658069 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12658033 GGTCATCCTT
12658043 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
12658070 GATATCATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:12662096 original size:24 final size:24
Alignment explanation
Indices: 12662069--12662118 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
12662059 CTTAACTGTG
*
12662069 TCCTCTTATGAGGTACATACTTCT
1 TCCTCTTAGGAGGTACATACTTCT
12662093 TCCTCTTAGGAGGTACATACTTCT
1 TCCTCTTAGGAGGTACATACTTCT
12662117 TC
1 TC
12662119 TTTTTCCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (24 bp):
TCCTCTTAGGAGGTACATACTTCT
Found at i:12663635 original size:17 final size:17
Alignment explanation
Indices: 12663610--12663643 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12663600 CAATTCCATT
*
12663610 AGAACAACTTCTTTACA
1 AGAAAAACTTCTTTACA
12663627 AGAAAAACTTCTTTACA
1 AGAAAAACTTCTTTACA
12663644 TAAAGCGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (17 bp):
AGAAAAACTTCTTTACA
Found at i:12667500 original size:28 final size:30
Alignment explanation
Indices: 12667452--12667521 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
12667442 GCAAAACAAA
*
12667452 TGGGATCAAAAATGGAGTTTTAGA-GAATT
1 TGGGATCAAAAATGGAATTTTAGAGGAATT
* *
12667481 TGGGAT-AAAAATGTAATTTTCGAGGAATT
1 TGGGATCAAAAATGGAATTTTAGAGGAATT
12667510 TGGGAATCAAAA
1 TGGG-ATCAAAA
12667522 TTGAAATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 14 0.40
29 15 0.43
30 2 0.06
31 4 0.11
ACGTcount: A:0.40, C:0.04, G:0.26, T:0.30
Consensus pattern (30 bp):
TGGGATCAAAAATGGAATTTTAGAGGAATT
Found at i:12667664 original size:29 final size:29
Alignment explanation
Indices: 12667557--12667791 Score: 176
Period size: 29 Copynumber: 8.2 Consensus size: 29
12667547 TGCAAGTGTG
**
12667557 ATTTTTGGAAATTCGAGGGCAAAAT-GATA
1 ATTTTTGGATGTTCGAGGGCAAAATAG-TA
* * *
12667586 ATTTTTGGATGTT-TAGGG-ACAATGGTA
1 ATTTTTGGATGTTCGAGGGCAAAATAGTA
*** * * *
12667613 A-TTTTGGACACTCAAGAGTAAAATAGTA
1 ATTTTTGGATGTTCGAGGGCAAAATAGTA
* *
12667641 ATTTTTGGATGCTCGAGGGCAAAAATGGTA
1 ATTTTTGGATGTTCGAGGGC-AAAATAGTA
* *
12667671 ATTTTTGGATGTTCGGGGGCAAAATGGTA
1 ATTTTTGGATGTTCGAGGGCAAAATAGTA
* * * *
12667700 ATTTTGGGAAAGTT-TAGGGTCAAAAT-GTG
1 ATTTTTGG-ATGTTCGAGGG-CAAAATAGTA
* * * *
12667729 ATTTTTGAAAGTTTGGGGGCAAAATAGTA
1 ATTTTTGGATGTTCGAGGGCAAAATAGTA
*
12667758 ATTTTTGGATGTTCAAGGGCAAAATAGTA
1 ATTTTTGGATGTTCGAGGGCAAAATAGTA
12667787 ATTTT
1 ATTTT
12667792 AAAAAAGTTT
Statistics
Matches: 163, Mismatches: 34, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
26 8 0.05
27 10 0.06
28 24 0.15
29 85 0.52
30 36 0.22
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.34
Consensus pattern (29 bp):
ATTTTTGGATGTTCGAGGGCAAAATAGTA
Found at i:12667706 original size:58 final size:56
Alignment explanation
Indices: 12667632--12667972 Score: 184
Period size: 59 Copynumber: 5.8 Consensus size: 56
12667622 ACTCAAGAGT
* * *
12667632 AAAATAGTAATTTTTGGATGCTCGAGGGCAAAAATGGTAATTTTTGGATGTTCGGGGGC
1 AAAATAGTAATTTTTGGATG-TCAAGGGC-AAAAT-GTAATTTTTGAAAGTTCGGGGGC
* * * ** * *
12667691 AAAATGGTAATTTTGGGAAAGTTTAGGGTCAAAATGTGATTTTTGAAAGTTTGGGGGC
1 AAAATAGTAATTTTTGG-ATGTCAAGGG-CAAAATGTAATTTTTGAAAGTTCGGGGGC
** * *
12667749 AAAATAGTAATTTTTGGATGTTCAAGGGCAAAATAGTAATTTTAAAAAAGTTTGGGGTC
1 AAAATAGTAATTTTTGGATG-TCAAGGGCAAAAT-GTAATTTT-TGAAAGTTCGGGGGC
* *** * * **
12667808 AAAA-ATGTAATTTTTGAGAAGTTTGGGGTAAAAATGTGATTTTTGAAAGTTCGAGGGAA
1 AAAATA-GTAATTTTTG-GATGTCAAGGG-CAAAATGTAATTTTTGAAAGTTCG-GGGGC
* * * * * * * *
12667867 AAAATA-TAATTTTTTGAAGTTCGAGGACAAAAATATGATTTTTGAGAAGTCCGGGGGT
1 AAAATAGTAATTTTTGGATG-TCAAGGGC-AAAATGTAATTTTTGA-AAGTTCGGGGGC
* * * **
12667925 AAAAT-GTGATTTTTTGAAAGTTTAGAGGCAAAAATGTAATTTTTGAAA
1 AAAATAGT-AATTTTTGGATGTCAAG-GGC-AAAATGTAATTTTTGAAA
12667973 ATTTGAGGGA
Statistics
Matches: 219, Mismatches: 47, Indels: 33
0.73 0.16 0.11
Matches are distributed among these distances:
57 12 0.05
58 94 0.43
59 101 0.46
60 12 0.05
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (56 bp):
AAAATAGTAATTTTTGGATGTCAAGGGCAAAATGTAATTTTTGAAAGTTCGGGGGC
Found at i:12667753 original size:87 final size:86
Alignment explanation
Indices: 12667557--12667830 Score: 268
Period size: 87 Copynumber: 3.2 Consensus size: 86
12667547 TGCAAGTGTG
* * *
12667557 ATTTTTGGAAA-TTCGAGGGCAAAATGATAATTTTTGGATGTT-TAGGG-ACAATGGTAATTTTG
1 ATTTTT-GAAAGTTCGAGGGCAAAATGGTAATTTTTGGATGTTCAAGGGCAAAATGGTAATTTTG
* * ** *
12667619 GACACTCAAGAGT-AAAATAGTA
65 GAAAGTTTAGGGTCAAAAT-GTA
* * * **
12667641 ATTTTTGGATGCTCGAGGGCAAAAATGGTAATTTTTGGATGTTCGGGGGCAAAATGGTAATTTTG
1 ATTTTTGAAAGTTCGAGGGC-AAAATGGTAATTTTTGGATGTTCAAGGGCAAAATGGTAATTTT-
*
12667706 GGAAAGTTTAGGGTCAAAATGTG
64 GGAAAGTTTAGGGTCAAAATGTA
* * * * *
12667729 ATTTTTGAAAGTTTGGGGGCAAAATAGTAATTTTTGGATGTTCAAGGGCAAAATAGTAATTTTAA
1 ATTTTTGAAAGTTCGAGGGCAAAATGGTAATTTTTGGATGTTCAAGGGCAAAATGGTAATTTT-G
* *
12667794 AAAAGTTTGGGGTCAAAAATGTA
65 GAAAGTTTAGGGTC-AAAATGTA
12667817 ATTTTTGAGAAGTT
1 ATTTTTGA-AAGTT
12667831 TGGGGTAAAA
Statistics
Matches: 155, Mismatches: 27, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
83 2 0.01
84 14 0.09
85 21 0.14
86 3 0.02
87 64 0.41
88 41 0.26
89 10 0.06
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (86 bp):
ATTTTTGAAAGTTCGAGGGCAAAATGGTAATTTTTGGATGTTCAAGGGCAAAATGGTAATTTTGG
AAAGTTTAGGGTCAAAATGTA
Found at i:12667777 original size:117 final size:114
Alignment explanation
Indices: 12667632--12668127 Score: 358
Period size: 117 Copynumber: 4.2 Consensus size: 114
12667622 ACTCAAGAGT
* *
12667632 AAAATAGTAATTTTTGGATGCTCGAGGGCAAAAATGGTAATTTTTGGATGTTCGGGGGCAAAATG
1 AAAATAGTAATTTTTGGATGTTCGAGGGCAAAAAT-GTAATTTTTGGAAGTTCGGGGGCAAAAT-
* *
12667697 GTAATTTTGGGAAAGTTTAGGGTCAAAATGTGATTTTTGAAAGTTTGGGGGC
64 GTAATTTT-TGAAAGTTTAGGGTCAAAATGTGATTTTTGAAAGTTTGGGGGA
* *** * *
12667749 AAAATAGTAATTTTTGGATGTTCAAGGGC-AAAATAGTAATTTTAAAAAAGTTTGGGGTCAAAAA
1 AAAATAGTAATTTTTGGATGTTCGAGGGCAAAAAT-GTAATTTT-TGGAAGTTCGGGGGC-AAAA
* * * *
12667813 TGTAATTTTTGAGAAGTTTGGGGTAAAAATGTGATTTTTGAAAGTTCGAGGGAA
63 TGTAATTTTTGA-AAGTTTAGGGTCAAAATGTGATTTTTGAAAGTTTG-GGGGA
* * * * * * *
12667867 AAAATA-TAATTTTTTGAAGTTCGAGGACAAAAATATGATTTTTGAGAAGTCCGGGGGTAAAATG
1 AAAATAGTAATTTTTGGATGTTCGAGGGCAAAAATGTAATTTTTG-GAAGTTCGGGGGCAAAATG
* * * *
12667931 TGATTTTTTGAAAGTTTAGAGG-CAAAAATGTAATTTTTGAAAATTTGAGGGAA
65 T-AATTTTTGAAAGTTTAG-GGTC-AAAATGTGATTTTTGAAAGTTTG-GGGGA
* * * ** * * * * ***
12667984 AAAATA-TGATTTTTGAGAAGTCCG-GGGGTAAAATGTGATTTTTTGAAAGTTTAGAGAAAAAAA
1 AAAATAGTAATTTTTG-GATGTTCGAGGGCAAAAATGT-AATTTTTGGAAG-TTCGGGGGCAAAA
* ** * * *
12668047 TGTAATTTTGGGAAA-TTTGAGGGAAAAAATATAATTTTTAGAAAGTTTGGGGATA
63 TGTAATTTT-TGAAAGTTT-AGGGTCAAAATGTGATTTTT-GAAAGTTTGGGG-GA
* *
12668102 AAAAT-GTGATTTTTGGAAGTTCGAGG
1 AAAATAGTAATTTTTGGATGTTCGAGG
12668128 ACCTTCTAGG
Statistics
Matches: 303, Mismatches: 57, Indels: 37
0.76 0.14 0.09
Matches are distributed among these distances:
116 29 0.10
117 201 0.66
118 73 0.24
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (114 bp):
AAAATAGTAATTTTTGGATGTTCGAGGGCAAAAATGTAATTTTTGGAAGTTCGGGGGCAAAATGT
AATTTTTGAAAGTTTAGGGTCAAAATGTGATTTTTGAAAGTTTGGGGGA
Found at i:12667818 original size:30 final size:29
Alignment explanation
Indices: 12667778--12667850 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 29
12667768 GTTCAAGGGC
12667778 AAAATAGTAATTTTAAAAAAGTTTGGGGTCA
1 AAAAT-GTAATTTTAAAAAAGTTTGGGGT-A
** *
12667809 AAAATGTAATTTTTGAGAAGTTTGGGGTA
1 AAAATGTAATTTTAAAAAAGTTTGGGGTA
*
12667838 AAAATGTGATTTT
1 AAAATGTAATTTT
12667851 TGAAAGTTCG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 13 0.34
30 20 0.53
31 5 0.13
ACGTcount: A:0.40, C:0.01, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTAAAAAAGTTTGGGGTA
Found at i:12667850 original size:29 final size:29
Alignment explanation
Indices: 12667709--12668122 Score: 215
Period size: 29 Copynumber: 14.2 Consensus size: 29
12667699 AATTTTGGGA
* *
12667709 AAGTTTAGGGTCAAAATGTGATTTTTGA-
1 AAGTTTGGGGTAAAAATGTGATTTTTGAG
** *
12667737 AAGTTTGGGGGCAAAATAGTAATTTTTG-G
1 AAGTTTGGGGTAAAAAT-GTGATTTTTGAG
* ** * * ** *
12667766 ATGTTCAAGGG-CAAAATAGTAATTTTAAAA
1 AAGTT-TGGGGTAAAAAT-GTGATTTTTGAG
*
12667796 AAGTTTGGGGTCAAAAATGTAATTTTTGAG
1 AAGTTTGGGGT-AAAAATGTGATTTTTGAG
12667826 AAGTTTGGGGTAAAAATGTGATTTTTGA-
1 AAGTTTGGGGTAAAAATGTGATTTTTGAG
* * * * *
12667854 AAGTTCGAGGGAAAAAATATAATTTTT-TG
1 AAGTTTG-GGGTAAAAATGTGATTTTTGAG
* ** *
12667883 AAGTTCGAGGACAAAAATATGATTTTTGAG
1 AAGTTTG-GGGTAAAAATGTGATTTTTGAG
**
12667913 AAGTCCGGGGGT-AAAATGTGATTTTTTGA-
1 AAGT-TTGGGGTAAAAATGTGA-TTTTTGAG
* * *
12667942 AAGTTTAGAGGCAAAAATGTAATTTTTGA-
1 AAGTTT-GGGGTAAAAATGTGATTTTTGAG
* * *
12667971 AAATTTGAGGGAAAAAATATGATTTTTGAG
1 AAGTTTG-GGGTAAAAATGTGATTTTTGAG
**
12668001 AAGTCCGGGGGT-AAAATGTGATTTTTTGA-
1 AAGT-TTGGGGTAAAAATGTGA-TTTTTGAG
* ** * *
12668030 AAGTTTAGAGAAAAAAATGT-AATTTTGGG
1 AAGTTT-GGGGTAAAAATGTGATTTTTGAG
* * * *
12668059 AAATTTGAGGGAAAAAATATAATTTTT-AG
1 AAGTTTG-GGGTAAAAATGTGATTTTTGAG
12668088 AAAGTTTGGGGATAAAAATGTGATTTTTG-G
1 -AAGTTTGGGG-TAAAAATGTGATTTTTGAG
12668118 AAGTT
1 AAGTT
12668123 CGAGGACCTT
Statistics
Matches: 298, Mismatches: 63, Indels: 49
0.73 0.15 0.12
Matches are distributed among these distances:
28 28 0.09
29 169 0.57
30 94 0.32
31 7 0.02
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
AAGTTTGGGGTAAAAATGTGATTTTTGAG
Found at i:12667877 original size:88 final size:85
Alignment explanation
Indices: 12667698--12668127 Score: 318
Period size: 88 Copynumber: 4.9 Consensus size: 85
12667688 GGCAAAATGG
* * * * *
12667698 TAATTTTGGGAAAGTTTAGGGTC-AAAATGTGATTTTTGA-AAGTTTGGGGGCAAAATAGTAATT
1 TAATTTT-GAAAAGTTT-GGGGCAAAAATATGATTTTTGAGAAGTTT-GGGGTAAAAT-GTGATT
* * * *
12667761 TTTGGATGTTCAAGGG-CAAAATA
62 TTTGAAAGTTCGAGGGAAAAAATA
* * *
12667784 GTAATTTTAAAAAAGTTTGGGGTCAAAAATGTAATTTTTGAGAAGTTTGGGGTAAAAATGTGATT
1 -TAATTTT-GAAAAGTTTGGGG-CAAAAATATGATTTTTGAGAAGTTTGGGGT-AAAATGTGATT
12667849 TTTGAAAGTTCGAGGGAAAAAATA
62 TTTGAAAGTTCGAGGGAAAAAATA
*** * * **
12667873 TAATTTTTTGAAGTTCGAGGACAAAAATATGATTTTTGAGAAGTCCGGGGGTAAAATGTGATTTT
1 TAATTTTGAAAAGTTTG-GGGCAAAAATATGATTTTTGAGAAGT-TTGGGGTAAAATGTGA-TTT
* * *
12667938 TTGAAAGTT-TAGAGGCAAAAATG
63 TTGAAAGTTCGAG-GGAAAAAATA
* **
12667961 TAATTTTTGAAAA-TTTGAGGGAAAAAATATGATTTTTGAGAAGTCCGGGGGTAAAATGTGATTT
1 TAA-TTTTGAAAAGTTTG-GGGCAAAAATATGATTTTTGAGAAGT-TTGGGGTAAAATGTGA-TT
* * *
12668025 TTTGAAAGTT-TAGAGAAAAAAATG
62 TTTGAAAGTTCGAG-GGAAAAAATA
* * *
12668049 TAATTTTGGGAAA-TTTGAGGGAAAAAATATAATTTTT-AGAAAGTTTGGGGATAAAAATGTGAT
1 TAATTTT-GAAAAGTTTG-GGGCAAAAATATGATTTTTGAG-AAGTTTGGGG-T-AAAATGTGAT
*
12668112 TTTTGGAAGTTCGAGG
61 TTTTGAAAGTTCGAGG
12668128 ACCTTCTAGG
Statistics
Matches: 291, Mismatches: 37, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
86 3 0.01
87 63 0.22
88 191 0.66
89 34 0.12
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.34
Consensus pattern (85 bp):
TAATTTTGAAAAGTTTGGGGCAAAAATATGATTTTTGAGAAGTTTGGGGTAAAATGTGATTTTTG
AAAGTTCGAGGGAAAAAATA
Found at i:12669159 original size:18 final size:19
Alignment explanation
Indices: 12669136--12669171 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
12669126 CTTTTTTATT
12669136 AATTATTATTA-TTAATAA
1 AATTATTATTATTTAATAA
12669154 AATTATTATTATTTAATA
1 AATTATTATTATTTAATA
12669172 TTTATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
AATTATTATTATTTAATAA
Found at i:12669861 original size:18 final size:18
Alignment explanation
Indices: 12669838--12669882 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12669828 AATTAAATCT
*
12669838 TAAATTTAAAATTCAAAA
1 TAAATTTAAAACTCAAAA
12669856 TAAATTT-AAACTCAAAA
1 TAAATTTAAAACTCAAAA
*
12669873 TAAGTTTAAA
1 TAAATTTAAA
12669883 TTTAAACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (18 bp):
TAAATTTAAAACTCAAAA
Found at i:12669907 original size:23 final size:23
Alignment explanation
Indices: 12669856--12669904 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
12669846 AAATTCAAAA
12669856 TAAATTTAAACTCAAAATAAGTT
1 TAAATTTAAACTCAAAATAAGTT
*
12669879 TAAATTTAAACTTAAAATAA-TT
1 TAAATTTAAACTCAAAATAAGTT
12669901 TAAA
1 TAAA
12669905 ATTGGGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 6 0.24
23 19 0.76
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.37
Consensus pattern (23 bp):
TAAATTTAAACTCAAAATAAGTT
Found at i:12672572 original size:54 final size:54
Alignment explanation
Indices: 12672506--12672617 Score: 215
Period size: 54 Copynumber: 2.1 Consensus size: 54
12672496 CATTCCACTA
12672506 TAGTATTGTGACTAAGCTCTCCCTAACGGTATACCATTACGAAAGCAACTCGAT
1 TAGTATTGTGACTAAGCTCTCCCTAACGGTATACCATTACGAAAGCAACTCGAT
*
12672560 TAGTATTGTGACTAAGCTCTCCCTAACGGTATACCATTACGAAAGCAATTCGAT
1 TAGTATTGTGACTAAGCTCTCCCTAACGGTATACCATTACGAAAGCAACTCGAT
12672614 TAGT
1 TAGT
12672618 TCTCGTCCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (54 bp):
TAGTATTGTGACTAAGCTCTCCCTAACGGTATACCATTACGAAAGCAACTCGAT
Found at i:12678646 original size:26 final size:24
Alignment explanation
Indices: 12678616--12678674 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
12678606 TTATTTCTTA
12678616 TATTAAATATTAAAAAATATGAAAAT
1 TATTAAA-ATTAAAAAATAT-AAAAT
* *
12678642 TATTATAAATTTATAAATATAAAAT
1 TATTA-AAATTAAAAAATATAAAAT
*
12678667 TAATAAAA
1 TATTAAAA
12678675 CATATTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 3 0.10
25 9 0.31
26 15 0.52
27 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TATTAAAATTAAAAAATATAAAAT
Found at i:12679292 original size:32 final size:30
Alignment explanation
Indices: 12679221--12679295 Score: 82
Period size: 32 Copynumber: 2.5 Consensus size: 30
12679211 TTCTAAAACG
*
12679221 TTTTTTTAA-TTT-TAAATCTTTTAAATAA
1 TTTTTATAATTTTATAAATCTTTTAAATAA
* *
12679249 GTTTTATTAATTTTATAAATTCTTTTATATAA
1 TTTTTA-TAATTTTATAAA-TCTTTTAAATAA
12679281 CTTTTTATAATTTTA
1 -TTTTTATAATTTTA
12679296 AGTTTATATT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 4 0.11
29 3 0.08
30 3 0.08
31 4 0.11
32 19 0.50
33 5 0.13
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTTATAATTTTATAAATCTTTTAAATAA
Found at i:12679326 original size:17 final size:18
Alignment explanation
Indices: 12679282--12679327 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
12679272 TTTATATAAC
12679282 TTTTTATAATTTTAAGTTT
1 TTTTTA-AATTTTAAGTTT
* *
12679301 ATATT-AATTTTAA-TTT
1 TTTTTAAATTTTAAGTTT
12679317 TTTTTAAATTT
1 TTTTTAAATTT
12679328 AATCATTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
16 6 0.27
17 13 0.59
19 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTTAAATTTTAAGTTT
Found at i:12683674 original size:3 final size:3
Alignment explanation
Indices: 12683666--12683774 Score: 209
Period size: 3 Copynumber: 36.3 Consensus size: 3
12683656 AAGAAATAAT
12683666 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
12683714 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12683762 TTA TTA TTA TTA T
1 TTA TTA TTA TTA T
12683775 AAGTTTGTAT
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:12694805 original size:48 final size:48
Alignment explanation
Indices: 12694729--12694825 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
12694719 CTTAGAGATA
* * *
12694729 AGAGCATTGAAAGAAGCTCGTAAGAAGGATAAAAGGGAGTTGTTCTTT
1 AGAGCATTGAAAGAAGCTCATAAAAAGGATAAAAGAGAGTTGTTCTTT
12694777 AGAGCATTGAAAGAAGCTCATAAAAAGGATAAAAGAGAGTTGTTCTTT
1 AGAGCATTGAAAGAAGCTCATAAAAAGGATAAAAGAGAGTTGTTCTTT
12694825 A
1 A
12694826 CTTTTCAAGG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.41, C:0.08, G:0.26, T:0.25
Consensus pattern (48 bp):
AGAGCATTGAAAGAAGCTCATAAAAAGGATAAAAGAGAGTTGTTCTTT
Found at i:12696337 original size:30 final size:29
Alignment explanation
Indices: 12696303--12696595 Score: 161
Period size: 30 Copynumber: 9.9 Consensus size: 29
12696293 TCAAACTTTA
12696303 GGAAAATTTGAGGTCGAAAATGTGATTTTT
1 GGAAAATTTGAGGTC-AAAATGTGATTTTT
* * *
12696333 GG-AAATTTAAGGGCAAAATGGTAATTTTT
1 GGAAAATTTGAGGTCAAAAT-GTGATTTTT
* * * * *
12696362 AG-AAGTTTGGGGGCAAAATG-GTAATTTT
1 GGAAAATTTGAGGTCAAAATGTG-ATTTTT
* * *
12696390 GGAAGAATTTGGGGTGAAAATGAGA-TTTT
1 GGAA-AATTTGAGGTCAAAATGTGATTTTT
* * *
12696419 GGAAAAGGTCGAGTGTCAAAATGT-AATTTT
1 GGAAAA-TTTGAG-GTCAAAATGTGATTTTT
* * * *
12696449 AGAGAAGTTCGAGGGTCAAAATGTAATTTTT
1 GGA-AAATTTGA-GGTCAAAATGTGATTTTT
* *
12696480 GGAAAATTCGAGGTCAAAATTTGATTTTT
1 GGAAAATTTGAGGTCAAAATGTGATTTTT
* * *
12696509 -GAGAAGTTTGAGGGTTAAAATGT-AATTTT
1 GGA-AAATTTGA-GGTCAAAATGTGATTTTT
* * *
12696538 GGAAAAGTTTAAAGGTTAAAATGT-AATTTT
1 GGAAAA-TTT-GAGGTCAAAATGTGATTTTT
*
12696568 GGAAAAGTTTGAGGATCAAAATATGATT
1 GGAAAA-TTTGAGG-TCAAAATGTGATT
12696596 CCTAGAAAAT
Statistics
Matches: 208, Mismatches: 37, Indels: 35
0.74 0.13 0.12
Matches are distributed among these distances:
28 16 0.08
29 78 0.38
30 100 0.48
31 14 0.07
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (29 bp):
GGAAAATTTGAGGTCAAAATGTGATTTTT
Found at i:12696360 original size:28 final size:29
Alignment explanation
Indices: 12696319--12696393 Score: 91
Period size: 29 Copynumber: 2.7 Consensus size: 29
12696309 TTTGAGGTCG
*
12696319 AAAAT-GTGATTTTTGGAAATTTAAGGGC
1 AAAATGGTAATTTTTGGAAATTTAAGGGC
* * **
12696347 AAAATGGTAATTTTTAGAAGTTTGGGGGC
1 AAAATGGTAATTTTTGGAAATTTAAGGGC
12696376 AAAATGGTAA-TTTTGGAA
1 AAAATGGTAATTTTTGGAA
12696394 GAATTTGGGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
28 12 0.30
29 28 0.70
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.35
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAATTTAAGGGC
Found at i:12696445 original size:59 final size:59
Alignment explanation
Indices: 12696303--12696589 Score: 241
Period size: 59 Copynumber: 4.9 Consensus size: 59
12696293 TCAAACTTTA
* * *
12696303 GGAAAA-TTTGAGGTCGAAAATGTGATTTTTGGA-AA-TTTAAGGG-CAAAATGGTAATTTT
1 GGAAAAGTTCGAGGTC-AAAATGT-AATTTTGGAGAAGTTTGAGGGTCAAAAT-GTAATTTT
* * * * * *
12696361 -TAGAAGTTTGGGGGCAAAATGGTAATTTTGGAAGAA-TTTG-GGGTGAAAATG-AGATTTT
1 GGAAAAGTTCGAGGTCAAAAT-GTAATTTTGG-AGAAGTTTGAGGGTCAAAATGTA-ATTTT
* * *
12696419 GGAAAAGGTCGAGTGTCAAAATGTAATTTTAGAGAAGTTCGAGGGTCAAAATGTAATTTTT
1 GGAAAAGTTCGAG-GTCAAAATGTAATTTTGGAGAAGTTTGAGGGTCAAAATGTAA-TTTT
* * * *
12696480 GGAAAA-TTCGAGGTCAAAATTTGATTTTTGAGAAGTTTGAGGGTTAAAATGTAATTTT
1 GGAAAAGTTCGAGGTCAAAATGTAATTTTGGAGAAGTTTGAGGGTCAAAATGTAATTTT
** * * *
12696538 GGAAAAGTTTAAAGGTTAAAATGTAATTTTGGAAAAGTTTGAGGATCAAAAT
1 GGAAAAG-TTCGAGGTCAAAATGTAATTTTGGAGAAGTTTGAGGGTCAAAAT
12696590 ATGATTCCTA
Statistics
Matches: 184, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
57 16 0.09
58 33 0.18
59 66 0.36
60 58 0.32
61 11 0.06
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (59 bp):
GGAAAAGTTCGAGGTCAAAATGTAATTTTGGAGAAGTTTGAGGGTCAAAATGTAATTTT
Found at i:12696476 original size:89 final size:87
Alignment explanation
Indices: 12696303--12696589 Score: 240
Period size: 89 Copynumber: 3.2 Consensus size: 87
12696293 TCAAACTTTA
* * * ** *
12696303 GGAAAATTTGAGGTCGAAAATGTGATTTTTGG-AAA-TTTAAGGG-CAAAATGGTAATTTTTAGA
1 GGAAAATTCGAGGTC-AAAATGAGA-TTTTGGAAAAGGTCGAGGGTCAAAAT-GTAATTTTGAGA
*
12696365 AGTTTG-GGGGCAAAATGGTAATTTT
63 AGTTTGAGGGTCAAAAT-GTAATTTT
* * * *
12696390 GGAAGAATTTGGGGTGAAAATGAGATTTTGGAAAAGGTCGAGTGTCAAAATGTAATTTTAGAGAA
1 GGAA-AATTCGAGGTCAAAATGAGATTTTGGAAAAGGTCGAGGGTCAAAATGTAATTTT-GAGAA
*
12696455 GTTCGAGGGTCAAAATGTAATTTTT
64 GTTTGAGGGTCAAAATGTAA-TTTT
** * * * * * *
12696480 GGAAAATTCGAGGTCAAAATTTGATTTTTGAGAAGTTTGAGGGTTAAAATGTAATTTTGGAAAAG
1 GGAAAATTCGAGGTCAAAATGAGATTTTGGAAAAGGTCGAGGGTCAAAATGTAATTTT-GAGAAG
* * *
12696545 TTTAAAGGTTAAAATGTAATTTT
65 TTTGAGGGTCAAAATGTAATTTT
*
12696568 GGAAAAGTTTGAGGATCAAAAT
1 GGAAAA-TTCGAGG-TCAAAAT
12696590 ATGATTCCTA
Statistics
Matches: 163, Mismatches: 28, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
86 6 0.04
87 15 0.09
88 31 0.19
89 87 0.53
90 24 0.15
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.33
Consensus pattern (87 bp):
GGAAAATTCGAGGTCAAAATGAGATTTTGGAAAAGGTCGAGGGTCAAAATGTAATTTTGAGAAGT
TTGAGGGTCAAAATGTAATTTT
Found at i:12697410 original size:29 final size:28
Alignment explanation
Indices: 12697378--12697432 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
12697368 TTGATTTTTT
* * *
12697378 AAATCTATTTTTCCTTTCTTTTTTATTTA
1 AAATATATTTTT-ATTTATTTTTTATTTA
*
12697407 AAATATGTTTTTATTTATTTTTTATT
1 AAATATATTTTTATTTATTTTTTATT
12697433 CTTTTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 12 0.55
29 10 0.45
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (28 bp):
AAATATATTTTTATTTATTTTTTATTTA
Found at i:12697437 original size:10 final size:11
Alignment explanation
Indices: 12697414--12697452 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
12697404 TTAAAATATG
12697414 TTTTTATTTAT
1 TTTTTATTTAT
*
12697425 TTTTTATTCTTT
1 TTTTTATT-TAT
12697437 TTTTTA-TTAT
1 TTTTTATTTAT
12697447 TTTTTA
1 TTTTTA
12697453 AAGAACTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 8 0.32
11 9 0.36
12 8 0.32
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTTAT
Found at i:12698464 original size:17 final size:17
Alignment explanation
Indices: 12698439--12698499 Score: 77
Period size: 17 Copynumber: 3.6 Consensus size: 17
12698429 TTCAAATTTT
12698439 AAATTTAAAATAAATTC
1 AAATTTAAAATAAATTC
* *
12698456 AAGTTTAAAATAAATTT
1 AAATTTAAAATAAATTC
* *
12698473 AAACTTAAAATAAATTT
1 AAATTTAAAATAAATTC
*
12698490 AAAATTAAAA
1 AAATTTAAAA
12698500 ATTGGGTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (17 bp):
AAATTTAAAATAAATTC
Done.