Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003569.1 Kokia drynarioides strain JFW-HI SEQ_116435, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 172734
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 22 characters in sequence are not A, C, G, or T
Found at i:836 original size:26 final size:26
Alignment explanation
Indices: 735--835 Score: 103
Period size: 26 Copynumber: 3.9 Consensus size: 26
725 ATTCTGGGAG
* *
735 CAATTCTGGACATGCTCATACAGCGA
1 CAATTCTGGACATGCTCATGCAGCAA
* * *
761 CAACTCTGAACATGTTCATGCAGCAA
1 CAATTCTGGACATGCTCATGCAGCAA
* * * * *
787 TAATTCTGGACAAGTTCCTGCAGTAA
1 CAATTCTGGACATGCTCATGCAGCAA
*
813 CAATTCTAGACATGCTCATGCAG
1 CAATTCTGGACATGCTCATGCAG
836 TGACATTAGT
Statistics
Matches: 59, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 59 1.00
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (26 bp):
CAATTCTGGACATGCTCATGCAGCAA
Found at i:19501 original size:10 final size:10
Alignment explanation
Indices: 19473--19513 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
19463 GGCAATATAT
*
19473 TTCTTTCTTT
1 TTCTTTCTTC
19483 TCTCTTTTCTTC
1 T-TC-TTTCTTC
19495 TTCTTTCTTC
1 TTCTTTCTTC
19505 TTCTTTCTT
1 TTCTTTCTT
19514 TCTATGAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 17 0.61
11 4 0.14
12 7 0.25
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTCTTTCTTC
Found at i:20144 original size:18 final size:17
Alignment explanation
Indices: 20112--20145 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20102 ATGTACTAAC
*
20112 AAATGAAATGTAATGAA
1 AAATGAAATGCAATGAA
20129 AAATGAAAATGCAATGA
1 AAATG-AAATGCAATGA
20146 CAACAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.59, C:0.03, G:0.18, T:0.21
Consensus pattern (17 bp):
AAATGAAATGCAATGAA
Found at i:24003 original size:89 final size:89
Alignment explanation
Indices: 23852--24026 Score: 341
Period size: 89 Copynumber: 2.0 Consensus size: 89
23842 CTTCCTATCT
23852 CTGATCTCAACATCAAATTCTTGTAAGAGCAGGATCCATCTGATTAATCTTAGTTTTGGTGTCTT
1 CTGATCTCAACATCAAATTCTTGTAAGAGCAGGATCCATCTGATTAATCTTAGTTTTGGTGTCTT
23917 TCTTTGTAAAAAGATATCTCAATG
66 TCTTTGTAAAAAGATATCTCAATG
23941 CTGATCTCAACATCAAATTCTTGTAAGAGCAGGATCCATCTGATTAATCTTAGTTTTGGTGTCTT
1 CTGATCTCAACATCAAATTCTTGTAAGAGCAGGATCCATCTGATTAATCTTAGTTTTGGTGTCTT
*
24006 TCTTTGTAAAAAGTTATCTCA
66 TCTTTGTAAAAAGATATCTCA
24027 GTGCAGAGTG
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
89 85 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (89 bp):
CTGATCTCAACATCAAATTCTTGTAAGAGCAGGATCCATCTGATTAATCTTAGTTTTGGTGTCTT
TCTTTGTAAAAAGATATCTCAATG
Found at i:30080 original size:17 final size:18
Alignment explanation
Indices: 30048--30090 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
30038 AATATATTTC
30048 TCTTCTTTTCTCTTTCAT
1 TCTTCTTTTCTCTTTCAT
* *
30066 TCTTC-TTTCTTTTTCTT
1 TCTTCTTTTCTCTTTCAT
30083 TCTT-TTTT
1 TCTTCTTTT
30091 TTGTGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (18 bp):
TCTTCTTTTCTCTTTCAT
Found at i:30089 original size:10 final size:10
Alignment explanation
Indices: 30044--30089 Score: 56
Period size: 10 Copynumber: 4.3 Consensus size: 10
30034 TTGCAATATA
30044 TTTCTCTTCTT
1 TTTCT-TTCTT
30055 TTCTCTTTCATT
1 TT-TCTTTC-TT
*
30067 CTTCTTTCTT
1 TTTCTTTCTT
30077 TTTCTTTCTT
1 TTTCTTTCTT
30087 TTT
1 TTT
30090 TTTGTGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 14 0.45
11 11 0.35
12 6 0.19
ACGTcount: A:0.02, C:0.24, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:30863 original size:21 final size:20
Alignment explanation
Indices: 30829--30874 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
30819 CTTAAGCACT
* * *
30829 CTCTTTCTTCCTTATGTTTC
1 CTCTTTTTTCCTTACGCTTC
30849 CTCTTTTTGTCCTTACGCTTC
1 CTCTTTTT-TCCTTACGCTTC
30870 CTCTT
1 CTCTT
30875 CTTATCCTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.04, C:0.33, G:0.07, T:0.57
Consensus pattern (20 bp):
CTCTTTTTTCCTTACGCTTC
Found at i:30882 original size:21 final size:21
Alignment explanation
Indices: 30837--30883 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
30827 CTCTCTTTCT
* * * *
30837 TCCTTATGTTTCCTCTTTTTG
1 TCCTTACGCTTCCTCTTCTTA
30858 TCCTTACGCTTCCTCTTCTTA
1 TCCTTACGCTTCCTCTTCTTA
30879 TCCTT
1 TCCTT
30884 CGAACCAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.06, C:0.32, G:0.06, T:0.55
Consensus pattern (21 bp):
TCCTTACGCTTCCTCTTCTTA
Found at i:41584 original size:17 final size:18
Alignment explanation
Indices: 41572--41612 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
41562 TAACAAAATG
41572 AATGCAGTGACAAAATAA
1 AATGCAGTGACAAAATAA
*
41590 AATGCAGTGACAACA-AA
1 AATGCAGTGACAAAATAA
41607 AATGCA
1 AATGCA
41613 TTAAAACTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.36
18 14 0.64
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (18 bp):
AATGCAGTGACAAAATAA
Found at i:51243 original size:26 final size:26
Alignment explanation
Indices: 51214--51282 Score: 129
Period size: 26 Copynumber: 2.7 Consensus size: 26
51204 CATCCCGACC
*
51214 CACAGCTCATGTGAGCAGGCCAACTT
1 CACAACTCATGTGAGCAGGCCAACTT
51240 CACAACTCATGTGAGCAGGCCAACTT
1 CACAACTCATGTGAGCAGGCCAACTT
51266 CACAACTCATGTGAGCA
1 CACAACTCATGTGAGCA
51283 CTATTAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.19
Consensus pattern (26 bp):
CACAACTCATGTGAGCAGGCCAACTT
Found at i:55567 original size:5 final size:5
Alignment explanation
Indices: 55559--55588 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
55549 TTAAAAAATT
*
55559 GAAAA GAAAA GAAAA AAAAA GAAAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
55589 AAATTTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:55580 original size:15 final size:15
Alignment explanation
Indices: 55560--55591 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55550 TAAAAAATTG
55560 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
55575 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
55590 AA
1 AA
55592 TTTATTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAA
Found at i:64836 original size:55 final size:55
Alignment explanation
Indices: 64743--64846 Score: 163
Period size: 55 Copynumber: 1.9 Consensus size: 55
64733 ATTCAATTAC
* *
64743 TCTGTGGTGTCCAAATATATCTTTAATGGCTATCTGATCGATTTACCTTTAGATT
1 TCTGTGGTGTCCAAATACACCTTTAATGGCTATCTGATCGATTTACCTTTAGATT
* * *
64798 TCTGTGGTGTCCAAATACACCTTTAATGGTTATGTGATCGATTTGCCTT
1 TCTGTGGTGTCCAAATACACCTTTAATGGCTATCTGATCGATTTACCTT
64847 AAAATTTTCA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.42
Consensus pattern (55 bp):
TCTGTGGTGTCCAAATACACCTTTAATGGCTATCTGATCGATTTACCTTTAGATT
Found at i:69636 original size:20 final size:19
Alignment explanation
Indices: 69603--69685 Score: 76
Period size: 20 Copynumber: 4.1 Consensus size: 19
69593 CCACGTTCAA
*
69603 GCTATGGCTAAACATAGGTT
1 GCTAT-GCTCAACATAGGTT
* * *
69623 TCTATAGCTCAACACTTGGGCT
1 GCTAT-GCTCAACA--TAGGTT
69645 GCTATGACTCAACATAGGTT
1 GCTATG-CTCAACATAGGTT
69665 GCTATGGCTCAACATAGGTT
1 GCTAT-GCTCAACATAGGTT
69685 G
1 G
69686 TGTGTCGTGC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 34 0.67
21 2 0.04
22 15 0.29
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (19 bp):
GCTATGCTCAACATAGGTT
Found at i:71292 original size:2 final size:2
Alignment explanation
Indices: 71285--71316 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
71275 AATAAGTTGT
71285 TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
71317 CATGTATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:71971 original size:71 final size:71
Alignment explanation
Indices: 71855--72013 Score: 203
Period size: 71 Copynumber: 2.2 Consensus size: 71
71845 TTTTTAAACC
* * * * * *
71855 GACTTAAGTTGTTTCGTAACAACTCAACAAAGTATCTGTAGAAGTACAAGGGATAAGGGA-CATT
1 GACTTGAGTTGTTTCGGAACAACTCAACAAAGTATCGGTAGAAGTACAAGAGATAAGAGATC-TA
71919 GGCTACT
65 GGCTACT
* * * *
71926 GACTTGAGTTGTTTTGGAACAACTCAACAGAGTATCGGTAGAAGTATAATAGATAAGAGATCTAG
1 GACTTGAGTTGTTTCGGAACAACTCAACAAAGTATCGGTAGAAGTACAAGAGATAAGAGATCTAG
71991 GCTACT
66 GCTACT
*
71997 AACTTGAGTTGTTTCGG
1 GACTTGAGTTGTTTCGG
72014 TAGTACTAAT
Statistics
Matches: 75, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
71 74 0.99
72 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (71 bp):
GACTTGAGTTGTTTCGGAACAACTCAACAAAGTATCGGTAGAAGTACAAGAGATAAGAGATCTAG
GCTACT
Found at i:72162 original size:21 final size:20
Alignment explanation
Indices: 72138--72176 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
72128 GAAATTTTGC
*
72138 TAGTATCGGTAGAAGCTATCT
1 TAGTACCGGTAGAA-CTATCT
72159 TAGTACCGGTAGAACTAT
1 TAGTACCGGTAGAACTAT
72177 AGGTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (20 bp):
TAGTACCGGTAGAACTATCT
Found at i:79182 original size:60 final size:60
Alignment explanation
Indices: 79068--79299 Score: 204
Period size: 60 Copynumber: 3.9 Consensus size: 60
79058 GATCAGAATG
* * **
79068 TTTGCACTACGGTGTCCCTATTTGCACTTCGATGCCCTTGTTTGCACTTTGGTTCCCCTA
1 TTTGCACTACGGTGCCCCTATTTGCACTTTGATGCCCTTGTTTGCACTACGGTTCCCCTA
* * *
79128 TTTGCACTACGGTGCCCCTATTTGCACTTTGGA-GCCCTTGTTTGTACTACGGTTCACCTG
1 TTTGCACTACGGTGCCCCTATTTGCACTTT-GATGCCCTTGTTTGCACTACGGTTCCCCTA
* * * * * *
79188 TTAGCACTTCGGTG-TCCTGGA-TTGCACTTTGATTACCC-TATTTGCACTACGGTGCCCCTA
1 TTTGCACTACGGTGCCCCT--ATTTGCACTTTGA-TGCCCTTGTTTGCACTACGGTTCCCCTA
* * * * ** * *
79248 TTTTCACTTCGATGCCCTTATTTGCACTACGAT-CCCCTGTTTGCATTACGGT
1 TTTGCACTACGGTGCCCCTATTTGCACTTTGATGCCCTTGTTTGCACTACGGT
79300 GCCGCTGAAC
Statistics
Matches: 139, Mismatches: 25, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
58 3 0.02
59 20 0.14
60 108 0.78
61 8 0.06
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (60 bp):
TTTGCACTACGGTGCCCCTATTTGCACTTTGATGCCCTTGTTTGCACTACGGTTCCCCTA
Found at i:79276 original size:40 final size:39
Alignment explanation
Indices: 79068--79292 Score: 141
Period size: 40 Copynumber: 5.7 Consensus size: 39
79058 GATCAGAATG
* *
79068 TTTGCACTACGGTGTCCCTATTTGCACTTCGATGCCCTTG
1 TTTGCACTACGGTGCCCCTATTTGCACTTCGATGCCC-TA
** * * *
79108 TTTGCACTTTGGTTCCCCTATTTGCACTACGGTGCCCCTA
1 TTTGCACTACGGTGCCCCTATTTGCACTTCGATG-CCCTA
** * * * * * * * *
79148 TTTGCACTTTGGAGCCCTTGTTTGTACTACGGTTCACCTG
1 TTTGCACTACGGTGCCCCTATTTGCACTTCGATGC-CCTA
* * * * *
79188 TTAGCACTTCGGTG-TCCTGGA-TTGCACTTTGATTACCCTA
1 TTTGCACTACGGTGCCCCT--ATTTGCACTTCGA-TGCCCTA
*
79228 TTTGCACTACGGTGCCCCTATTTTCACTTCGATGCCCTTA
1 TTTGCACTACGGTGCCCCTATTTGCACTTCGATGCCC-TA
* *
79268 TTTGCACTACGAT-CCCCTGTTTGCA
1 TTTGCACTACGGTGCCCCTATTTGCA
79293 TTACGGTGCC
Statistics
Matches: 142, Mismatches: 35, Indels: 17
0.73 0.18 0.09
Matches are distributed among these distances:
39 18 0.13
40 116 0.82
41 8 0.06
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.38
Consensus pattern (39 bp):
TTTGCACTACGGTGCCCCTATTTGCACTTCGATGCCCTA
Found at i:79292 original size:19 final size:20
Alignment explanation
Indices: 79068--79302 Score: 109
Period size: 20 Copynumber: 11.8 Consensus size: 20
79058 GATCAGAATG
* *
79068 TTTGCACTACGGTGTCCCTA
1 TTTGCACTACGATGCCCCTA
* * *
79088 TTTGCACTTCGATGCCCTTG
1 TTTGCACTACGATGCCCCTA
** * *
79108 TTTGCACTTTGGTTCCCCTA
1 TTTGCACTACGATGCCCCTA
*
79128 TTTGCACTACGGTGCCCCTA
1 TTTGCACTACGATGCCCCTA
** * *
79148 TTTGCACTTTGGA-GCCCTTG
1 TTTGCAC-TACGATGCCCCTA
* * * * *
79168 TTTGTACTACGGTTCACCTG
1 TTTGCACTACGATGCCCCTA
* * * *
79188 TTAGCACTTCGGTG-TCCTGGA
1 TTTGCACTACGATGCCCCT--A
** **
79209 -TTGCACTTTGATTACCCTA
1 TTTGCACTACGATGCCCCTA
*
79228 TTTGCACTACGGTGCCCCTA
1 TTTGCACTACGATGCCCCTA
* * *
79248 TTTTCACTTCGATGCCCTTA
1 TTTGCACTACGATGCCCCTA
*
79268 TTTGCACTACGAT-CCCCTG
1 TTTGCACTACGATGCCCCTA
* *
79287 TTTGCATTACGGTGCC
1 TTTGCACTACGATGCC
79303 GCTGAACGCA
Statistics
Matches: 157, Mismatches: 51, Indels: 14
0.71 0.23 0.06
Matches are distributed among these distances:
19 21 0.13
20 131 0.83
21 5 0.03
ACGTcount: A:0.14, C:0.29, G:0.19, T:0.37
Consensus pattern (20 bp):
TTTGCACTACGATGCCCCTA
Found at i:83593 original size:24 final size:24
Alignment explanation
Indices: 83541--83593 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
83531 TTAATAACGC
*
83541 AATA-AAAATATAATTATAGTATT
1 AATATAAAATATAATTATAGTAAT
*
83564 AA-ATAAAATATTAATTA-ATTAAT
1 AATATAAAATA-TAATTATAGTAAT
83587 AATATAA
1 AATATAA
83594 GCAACAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 1 0.04
23 14 0.56
24 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
AATATAAAATATAATTATAGTAAT
Found at i:84061 original size:25 final size:25
Alignment explanation
Indices: 84021--84068 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
84011 AATAAATAAC
84021 CAAAAAAATCAATAAAT-TAAATGT
1 CAAAAAAATCAATAAATATAAATGT
84045 CAAAATAAA-CAACTAAATATAAAT
1 CAAAA-AAATCAA-TAAATATAAAT
84069 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (25 bp):
CAAAAAAATCAATAAATATAAATGT
Found at i:86078 original size:2 final size:2
Alignment explanation
Indices: 86071--86095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
86061 GTTTAAGATG
86071 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
86096 TGATGTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87064 original size:20 final size:20
Alignment explanation
Indices: 87039--87251 Score: 185
Period size: 20 Copynumber: 10.7 Consensus size: 20
87029 TAGATCAGTA
*
87039 TGTTTGCACTACGATGCCCC
1 TGTTTGCACTACGGTGCCCC
* ** *
87059 TGTTTGAACTTTGGTGCCGC
1 TGTTTGCACTACGGTGCCCC
* ** *
87079 TGTTTGCATTTTGGTGCCCA
1 TGTTTGCACTACGGTGCCCC
* * * *
87099 TGTTTGTACTTCAGTAG-CCT
1 TGTTTGCACTACGGT-GCCCC
* * *
87119 TGATTGCACTTCGGTACCCC
1 TGTTTGCACTACGGTGCCCC
*
87139 TGTTTGCACTACAGTGCCCC
1 TGTTTGCACTACGGTGCCCC
*
87159 TGTTTGCACTACGGTGTCCC
1 TGTTTGCACTACGGTGCCCC
*
87179 TGTTTTCACTACGGTGCCCC
1 TGTTTGCACTACGGTGCCCC
* *
87199 TATTTACACTACGGTGCCCC
1 TGTTTGCACTACGGTGCCCC
* * * *
87219 TGTGTGCATTATGGTGCTCC
1 TGTTTGCACTACGGTGCCCC
87239 TGTTTGCACTACG
1 TGTTTGCACTACG
87252 TTTCCTCTAT
Statistics
Matches: 153, Mismatches: 38, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
20 152 0.99
21 1 0.01
ACGTcount: A:0.13, C:0.28, G:0.23, T:0.36
Consensus pattern (20 bp):
TGTTTGCACTACGGTGCCCC
Found at i:87199 original size:60 final size:60
Alignment explanation
Indices: 87122--87268 Score: 170
Period size: 60 Copynumber: 2.5 Consensus size: 60
87112 GTAGCCTTGA
* * * *
87122 TTGCACTTCGGTACCCCTGTTTGCACTACAGTGCCCCTGTTTGCACTACGGTG-TCCCTGT
1 TTGCACTACGGTACCCCTATTTACACTACAGTGCCCCTGTGTGCACTACGGTGCT-CCTGT
* * * * *
87182 TTTCACTACGGTGCCCCTATTTACACTACGGTGCCCCTGTGTGCATTATGGTGCTCCTGT
1 TTGCACTACGGTACCCCTATTTACACTACAGTGCCCCTGTGTGCACTACGGTGCTCCTGT
* * *
87242 TTGCACTACGTTTCCTCTATTTACACT
1 TTGCACTACGGTACCCCTATTTACACT
87269 TTGGTTCCCT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
60 72 0.99
61 1 0.01
ACGTcount: A:0.14, C:0.31, G:0.19, T:0.36
Consensus pattern (60 bp):
TTGCACTACGGTACCCCTATTTACACTACAGTGCCCCTGTGTGCACTACGGTGCTCCTGT
Found at i:90262 original size:12 final size:10
Alignment explanation
Indices: 90237--90303 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 10
90227 GCCGATTAGC
*
90237 ATATGTACAT
1 ATATATACAT
90247 ATAT-TACAAT
1 ATATATAC-AT
90257 ATATATACAT
1 ATATATACAT
* *
90267 ATATACAAGTAT
1 ATATA-TA-CAT
90279 ATATATACAT
1 ATATATACAT
90289 ATACTTATACAT
1 ATA--TATACAT
90301 ATA
1 ATA
90304 CATATATAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
9 3 0.06
10 22 0.47
11 5 0.11
12 17 0.36
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (10 bp):
ATATATACAT
Found at i:90265 original size:20 final size:19
Alignment explanation
Indices: 90237--90311 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
90227 GCCGATTAGC
*
90237 ATATGTACATATATTACAAT
1 ATATATACATATA-TACAAT
90257 ATATATACATATATACAAGT
1 ATATATACATATATACAA-T
* * *
90277 ATATATATACATATACTTAT
1 ATATATACATATATAC-AAT
*
90297 ACATATACATATATA
1 ATATATACATATATA
90312 ATTTTTTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 5 0.11
20 40 0.87
21 1 0.02
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.39
Consensus pattern (19 bp):
ATATATACATATATACAAT
Found at i:90304 original size:12 final size:12
Alignment explanation
Indices: 90276--90309 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
90266 TATATACAAG
*
90276 TATATATATACA
1 TATACATATACA
*
90288 TATACTTATACA
1 TATACATATACA
90300 TATACATATA
1 TATACATATA
90310 TAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (12 bp):
TATACATATACA
Found at i:90410 original size:68 final size:66
Alignment explanation
Indices: 90300--90450 Score: 223
Period size: 68 Copynumber: 2.2 Consensus size: 66
90290 TACTTATACA
* *
90300 TATACATATATAATTTTTTTTTCATTATTAATTCTTTACTTCTTTTCCTTTTAATAGATAAGCAT
1 TATATATATATAATATTTTTTTCATTATTAATTCTTTACTTCTTTTCCTTTTAATAGATAAGCAT
90365 T
66 T
*
90366 TATATATATATAATATTTTTTT-ATTATTAATTCTTTGCTTCTTCTTTTCCTTTTAATAGATAAG
1 TATATATATATAATATTTTTTTCATTATTAATTC-TT--TACTTCTTTTCCTTTTAATAGATAAG
90430 CATT
63 CATT
*
90434 TATATATACATACATAT
1 TATATATATATA-ATAT
90451 ATATATATAT
Statistics
Matches: 77, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
65 11 0.14
66 22 0.29
68 40 0.52
69 4 0.05
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.55
Consensus pattern (66 bp):
TATATATATATAATATTTTTTTCATTATTAATTCTTTACTTCTTTTCCTTTTAATAGATAAGCAT
T
Found at i:95099 original size:18 final size:16
Alignment explanation
Indices: 95060--95099 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 16
95050 ATGATTAAAT
95060 AAAAATGAGGGTAATA
1 AAAAATGAGGGTAATA
95076 ATAAAATGAAGGGTAATA
1 A-AAAATG-AGGGTAATA
95094 GAAAAA
1 -AAAAA
95100 GGAGAGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 1 0.05
17 6 0.29
18 13 0.62
19 1 0.05
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (16 bp):
AAAAATGAGGGTAATA
Found at i:95913 original size:21 final size:22
Alignment explanation
Indices: 95887--95936 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
95877 CATAATAACA
*
95887 TAAACGTAT-AGCTGACGAGCG
1 TAAACGTATAAGCTAACGAGCG
95908 TAAACGTATAGAAGCTAACGAGCG
1 TAAACGTAT--AAGCTAACGAGCG
95932 TAAAC
1 TAAAC
95937 ATGTGCAAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
24 16 0.64
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (22 bp):
TAAACGTATAAGCTAACGAGCG
Found at i:95958 original size:24 final size:24
Alignment explanation
Indices: 95896--96083 Score: 101
Period size: 24 Copynumber: 7.8 Consensus size: 24
95886 ATAAACGTAT
* * *
95896 AGCTGACGAGCGTAAACGTATAG-A
1 AGCTGATGAGAGTAAACGTGT-GCA
* * * *
95920 AGCTAACGAGCGTAAACATGTGCA
1 AGCTGATGAGAGTAAACGTGTGCA
* * * **
95944 AGCTGATGAGTGTAAGCGTATATA
1 AGCTGATGAGAGTAAACGTGTGCA
* * *
95968 AGCTGA-CAAATGTAAACATGTGCA
1 AGCTGATGAGA-GTAAACGTGTGCA
* * **
95992 ATCTGATGAGAGTAAACGTATATA
1 AGCTGATGAGAGTAAACGTGTGCA
*
96016 AGCTGATGAGCGTAAACGTGTGCA
1 AGCTGATGAGAGTAAACGTGTGCA
* * * **
96040 AGCTGACGAGAGTAAATGTATATA
1 AGCTGATGAGAGTAAACGTGTGCA
* *
96064 ATCTGATGAGTGTAAACGTG
1 AGCTGATGAGAGTAAACGTG
96084 CTGACGAGCG
Statistics
Matches: 119, Mismatches: 42, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
23 2 0.02
24 115 0.97
25 2 0.02
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.23
Consensus pattern (24 bp):
AGCTGATGAGAGTAAACGTGTGCA
Found at i:96055 original size:72 final size:72
Alignment explanation
Indices: 95943--96082 Score: 156
Period size: 72 Copynumber: 1.9 Consensus size: 72
95933 AAACATGTGC
* * * * *
95943 AAGCTGATGAGTGTAAGCGTATATAAGCTGACAAATGTAAACATGTGCAATCTGATGAGAGTAAA
1 AAGCTGATGAGCGTAAACGTATACAAGCTGACAAATGTAAACATATACAATCTGATGAGAGTAAA
96008 CGTATAT
66 CGTATAT
* * * ** * *
96015 AAGCTGATGAGCGTAAACGTGTGCAAGCTGACGAGA-GTAAATGTATATAATCTGATGAGTGTAA
1 AAGCTGATGAGCGTAAACGTATACAAGCTGAC-AAATGTAAACATATACAATCTGATGAGAGTAA
96079 ACGT
65 ACGT
96083 GCTGACGAGC
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
72 53 0.96
73 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (72 bp):
AAGCTGATGAGCGTAAACGTATACAAGCTGACAAATGTAAACATATACAATCTGATGAGAGTAAA
CGTATAT
Found at i:96083 original size:48 final size:48
Alignment explanation
Indices: 95896--96080 Score: 217
Period size: 48 Copynumber: 3.9 Consensus size: 48
95886 ATAAACGTAT
* * *
95896 AGCTGACGAGCGTAAACGTATAGAAGCTAACGAGCGTAAACATGTGCA
1 AGCTGACGAGAGTAAACGTATATAAGCTGACGAGCGTAAACATGTGCA
* * * * **
95944 AGCTGATGAGTGTAAGCGTATATAAGCTGACAAATGTAAACATGTGCA
1 AGCTGACGAGAGTAAACGTATATAAGCTGACGAGCGTAAACATGTGCA
* * * *
95992 ATCTGATGAGAGTAAACGTATATAAGCTGATGAGCGTAAACGTGTGCA
1 AGCTGACGAGAGTAAACGTATATAAGCTGACGAGCGTAAACATGTGCA
* * * *
96040 AGCTGACGAGAGTAAATGTATATAATCTGATGAGTGTAAAC
1 AGCTGACGAGAGTAAACGTATATAAGCTGACGAGCGTAAAC
96081 GTGCTGACGA
Statistics
Matches: 116, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 116 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (48 bp):
AGCTGACGAGAGTAAACGTATATAAGCTGACGAGCGTAAACATGTGCA
Found at i:96662 original size:71 final size:71
Alignment explanation
Indices: 96545--96703 Score: 203
Period size: 71 Copynumber: 2.2 Consensus size: 71
96535 TGATTTTTTA
* *
96545 TACTGACTTGAGTTGTTTCGAAACAACTCAACAAAGTATCGTTAGAAGCACAGGGGATAAGGGAC
1 TACTGACTTGAGTTGTTTCGAAACAACTCAACAAAGTATCGGTAGAAGCACAAGGGATAAGGGAC
*
96610 CTTG-GT
66 C-TGAGC
* * * * * * * *
96616 TACTGACTTGAGTTGTTTTGGAACAACTCAACAAAGTATTGGTAGAAGTATAATGGATGAGGGAT
1 TACTGACTTGAGTTGTTTCGAAACAACTCAACAAAGTATCGGTAGAAGCACAAGGGATAAGGGAC
96681 CTGAGC
66 CTGAGC
96687 TACTGACTTGAGTTGTT
1 TACTGACTTGAGTTGTT
96704 CCGGTAATAC
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
70 2 0.03
71 74 0.97
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (71 bp):
TACTGACTTGAGTTGTTTCGAAACAACTCAACAAAGTATCGGTAGAAGCACAAGGGATAAGGGAC
CTGAGC
Found at i:116360 original size:13 final size:13
Alignment explanation
Indices: 116342--116366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116332 CCCATTTTAT
116342 CATTTTTAGCATG
1 CATTTTTAGCATG
116355 CATTTTTAGCAT
1 CATTTTTAGCAT
116367 TTTTAACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:131570 original size:20 final size:21
Alignment explanation
Indices: 131545--131583 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
131535 GCAAGGAATT
131545 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
131565 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
131584 TAACAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:147019 original size:17 final size:17
Alignment explanation
Indices: 146994--147039 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
146984 ATAAACTACT
* *
146994 CAATCGAAAACCCGAAA
1 CAATAGAAAACACGAAA
147011 CAATAGAAAACACGAAA
1 CAATAGAAAACACGAAA
147028 CAATAGAAAACA
1 CAATAGAAAACA
147040 ACTTGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.61, C:0.22, G:0.11, T:0.07
Consensus pattern (17 bp):
CAATAGAAAACACGAAA
Found at i:148006 original size:21 final size:21
Alignment explanation
Indices: 147977--148018 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
147967 TATAATAAAA
*
147977 ATTACGTCTAAAAAAACAAAC
1 ATTAAGTCTAAAAAAACAAAC
147998 ATTAAGTCTAAAAAAACAAAC
1 ATTAAGTCTAAAAAAACAAAC
148019 TCAATATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.19
Consensus pattern (21 bp):
ATTAAGTCTAAAAAAACAAAC
Found at i:150334 original size:16 final size:14
Alignment explanation
Indices: 150312--150511 Score: 84
Period size: 15 Copynumber: 13.1 Consensus size: 14
150302 ATAACAAAAG
150312 TAAATAACAAATAAA
1 TAAATAA-AAATAAA
150327 TAAAATAAAAAAATAAA
1 T-AAAT--AAAAATAAA
150344 TAAATAAAAATTAAA
1 TAAATAAAAA-TAAA
* **
150359 TGAAAGGCGAGAGTATAAA
1 T-AAA---TA-AAAATAAA
*
150378 TAGCATAAAAAGTAAA
1 TA-AATAAAAA-TAAA
*
150394 TAAAT-AAAATACA
1 TAAATAAAAATAAA
*
150407 TAAA-AACAATAAA
1 TAAATAAAAATAAA
*
150420 TAAATAAAATTAAA
1 TAAATAAAAATAAA
*
150434 TAAAGACAATAATATAAA
1 T-AA-ATAA-AA-ATAAA
*
150452 TAAGATAAAAATGAA
1 TAA-ATAAAAATAAA
*
150467 TAGCAA-ATAAATAAA
1 TA--AATAAAAATAAA
* *
150482 TAAATAAGAA-CAA
1 TAAATAAAAATAAA
150495 TAAATAAAAATTAAA
1 TAAATAAAAA-TAAA
150510 TA
1 TA
150512 CTAAATAAAA
Statistics
Matches: 139, Mismatches: 24, Indels: 44
0.67 0.12 0.21
Matches are distributed among these distances:
13 30 0.22
14 20 0.14
15 31 0.22
16 24 0.17
17 17 0.12
18 8 0.06
19 7 0.05
20 2 0.01
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.21
Consensus pattern (14 bp):
TAAATAAAAATAAA
Found at i:150342 original size:17 final size:16
Alignment explanation
Indices: 150320--150546 Score: 70
Period size: 17 Copynumber: 13.5 Consensus size: 16
150310 AGTAAATAAC
150320 AAATAAATAAAATAAAA
1 AAATAAAT-AAATAAAA
150337 AAATAAATAAAT-AAA
1 AAATAAATAAATAAAA
* ** *
150352 AATTAAATGAAAGGCGAGA
1 AAATAAAT-AAA--TAAAA
** *
150371 GTATAAATAGCAT-AAA
1 AAATAAATA-AATAAAA
*
150387 AAGTAAATAAATAAAA
1 AAATAAATAAATAAAA
* * *
150403 TACATAAAAACAATAAAT
1 -AAATAAATA-AATAAAA
150421 AAATAAAATTAAATAAAGA
1 AAAT-AAA-TAAATAAA-A
* *
150440 CAATAATATAAATAAGA
1 AAATAA-ATAAATAAAA
* *
150457 TAA-AAATGAATAGCAAA
1 AAATAAATAAATA--AAA
150474 TAAATAAATAAATAAGAA
1 -AAATAAATAAATAA-AA
* **
150492 CAATAAATAAA-AATT
1 AAATAAATAAATAAAA
*
150507 AAAT-ACTAAATAAAA
1 AAATAAATAAATAAAA
* *
150522 CAATACAA-ATAATATAA
1 AAATA-AATA-AATAAAA
150539 AAATAAAT
1 AAATAAAT
150547 GGGACCAAAT
Statistics
Matches: 150, Mismatches: 38, Indels: 44
0.65 0.16 0.19
Matches are distributed among these distances:
14 5 0.03
15 26 0.17
16 25 0.17
17 44 0.29
18 29 0.19
19 21 0.14
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (16 bp):
AAATAAATAAATAAAA
Found at i:150450 original size:5 final size:4
Alignment explanation
Indices: 150390--150520 Score: 67
Period size: 4 Copynumber: 32.0 Consensus size: 4
150380 GCATAAAAAG
* *
150390 TAAA TAAA TAAAA TACA TAAA AACAA TAAA TAAA TAAAA TTAAA TAAA
1 TAAA TAAA T-AAA TAAA TAAA TA-AA TAAA TAAA T-AAA -TAAA TAAA
* * * *
150438 GACAA TAATA TAAA TAAGA T-AA -AAA TGAA T-AG CAAA TAAA TAAA TAAA
1 TA-AA TAA-A TAAA TAA-A TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* *
150486 TAAGA -ACAA TAAA TAAA -AAT TAAA T-AC TAAA TAAA
1 TAA-A TA-AA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
150521 ACAATACAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 30
0.68 0.11 0.21
Matches are distributed among these distances:
3 8 0.08
4 63 0.65
5 25 0.26
6 1 0.01
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (4 bp):
TAAA
Found at i:150485 original size:75 final size:74
Alignment explanation
Indices: 150307--150511 Score: 213
Period size: 75 Copynumber: 2.7 Consensus size: 74
150297 TATAGATAAC
* * *
150307 AAAAGTAAATAACAAATAAATAAAATAAAAAAATAAATAAATAAAAATTAAATGAAAGGCGAGAG
1 AAAAGT-AAT-ACAAATAAAT-AAATAAAAAAATAAATAAATAAAAATTAAAT-AAAGACAAGAA
150372 TATAAATAGCATA
62 TATAAATAGCATA
* * *
150385 AAAAGTAA-ATAAATAAAATACATAAAAACAATAAATAAAT-AAAATTAAATAAAGACAATAATA
1 AAAAGTAATACAAAT-AAATAAATAAAAA-AATAAATAAATAAAAATTAAATAAAGACAAGAATA
150448 TAAATAAG-ATA
64 TAAAT-AGCATA
*
150459 AAAA-TGAATAGCAAATAAATAAATAAATAAGAA-CAATAAATAAAAATTAAATA
1 AAAAGT-AATA-CAAATAAATAAATAAA-AA-AATAAATAAATAAAAATTAAATA
150512 CTAAATAAAA
Statistics
Matches: 109, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
73 1 0.01
74 23 0.21
75 43 0.39
76 34 0.31
77 2 0.02
78 6 0.06
ACGTcount: A:0.69, C:0.04, G:0.07, T:0.20
Consensus pattern (74 bp):
AAAAGTAATACAAATAAATAAATAAAAAAATAAATAAATAAAAATTAAATAAAGACAAGAATATA
AATAGCATA
Found at i:150520 original size:11 final size:10
Alignment explanation
Indices: 150391--150511 Score: 58
Period size: 11 Copynumber: 11.9 Consensus size: 10
150381 CATAAAAAGT
150391 AAATAAAT-A
1 AAATAAATAA
*
150400 AAATACATAA
1 AAATAAATAA
*
150410 AAA-CAAT--
1 AAATAAATAA
150417 AAATAAATAA
1 AAATAAATAA
*
150427 AATTAAATAA
1 AAATAAATAA
*
150437 AGACA-ATAATAT
1 A-A-ATA-AATAA
150449 AAATAAGATAA
1 AAATAA-ATAA
* *
150460 AAATGAATAGC
1 AAATAAATA-A
150471 AAATAAAT--
1 AAATAAATAA
150479 AAATAAATAAGA
1 AAATAAAT-A-A
150491 ACAATAAATAA
1 A-AATAAATAA
150502 AAATTAAATA
1 AAA-TAAATA
150512 CTAAATAAAA
Statistics
Matches: 85, Mismatches: 11, Indels: 30
0.67 0.09 0.24
Matches are distributed among these distances:
7 3 0.04
8 11 0.13
9 9 0.11
10 21 0.25
11 27 0.32
12 7 0.08
13 7 0.08
ACGTcount: A:0.70, C:0.04, G:0.04, T:0.21
Consensus pattern (10 bp):
AAATAAATAA
Found at i:150533 original size:79 final size:78
Alignment explanation
Indices: 150391--150542 Score: 184
Period size: 79 Copynumber: 1.9 Consensus size: 78
150381 CATAAAAAGT
* * *
150391 AAATAAATAAAATACATAAAAACAATAAATAAATAAAATTAAATAAAGACAATAATATAAATAAG
1 AAATAAATAAAATAAATAAAAACAATAAATAAATAAAACTAAATAAAGAC-A-AATACAAATAAG
150456 ATAAAAATGAATAGC
64 ATAAAAATGAATAGC
*
150471 AAATAAAT-AAATAAATAAGAACAATAAATAAAAATTAAATACTAAATAAA-AC-AATACAAATA
1 AAATAAATAAAATAAATAAAAACAATAAAT--AAA-TAAA-ACTAAATAAAGACAAATACAAATA
*
150533 ATATAAAAAT
62 AGATAAAAAT
150543 AAATGGGACC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
79 37 0.59
80 8 0.13
81 3 0.05
82 6 0.10
83 9 0.14
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.22
Consensus pattern (78 bp):
AAATAAATAAAATAAATAAAAACAATAAATAAATAAAACTAAATAAAGACAAATACAAATAAGAT
AAAAATGAATAGC
Found at i:150665 original size:30 final size:29
Alignment explanation
Indices: 150613--150686 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 29
150603 CTAAATGGGG
*
150613 CAAAATTAAATAAAGGACTAAATTGAA-AA
1 CAAAAATAAATAAAGGACTAAATT-AATAA
*
150642 CACAAATAAATTAAAGGTA-TAAATTAATAA
1 CAAAAATAAA-TAAAGG-ACTAAATTAATAA
150672 CAAAAATAAAATAAA
1 CAAAAAT-AAATAAA
150687 ATAAAAGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
29 10 0.26
30 24 0.63
31 4 0.11
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.22
Consensus pattern (29 bp):
CAAAAATAAATAAAGGACTAAATTAATAA
Found at i:151974 original size:12 final size:12
Alignment explanation
Indices: 151959--152009 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
151949 TTTTAATTTG
151959 TTTTGTTTTGTT
1 TTTTGTTTTGTT
*
151971 TTTTATTTTG-T
1 TTTTGTTTTGTT
151982 TTTTGTTTTGGTT
1 TTTTGTTTT-GTT
151995 TGTTT-TATTTGTT
1 T-TTTGT-TTTGTT
152008 TT
1 TT
152010 ATTCTGGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
11 9 0.27
12 11 0.33
13 7 0.21
14 6 0.18
ACGTcount: A:0.04, C:0.00, G:0.16, T:0.80
Consensus pattern (12 bp):
TTTTGTTTTGTT
Found at i:151974 original size:22 final size:23
Alignment explanation
Indices: 151942--152009 Score: 93
Period size: 22 Copynumber: 2.9 Consensus size: 23
151932 TTTTTTGGAC
151942 TTTGGTTTTTTAATTTGTTTTGT
1 TTTGGTTTTTTAATTTGTTTTGT
*
151965 TTT-GTTTTTTATTTTGTTTTTGT
1 TTTGGTTTTTTAATTTG-TTTTGT
*
151988 TTTGGTTTGTTTTATTTGTTTT
1 TTTGGTTT-TTTAATTTGTTTT
152010 ATTCTGGGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
22 12 0.31
23 12 0.31
24 8 0.21
25 7 0.18
ACGTcount: A:0.06, C:0.00, G:0.16, T:0.78
Consensus pattern (23 bp):
TTTGGTTTTTTAATTTGTTTTGT
Found at i:152322 original size:50 final size:50
Alignment explanation
Indices: 152254--152380 Score: 146
Period size: 50 Copynumber: 2.5 Consensus size: 50
152244 GTCTTACTCC
* ** * *
152254 ACTGCATCTTCAGGGAGATAAGATTTGGTGTTATATCTTCATCTTGCTCT
1 ACTGCAACTTCAAAGAGATAAGATTTGGTGTTATAGCTTCATATTGCTCT
* * * * * *
152304 GCTGCAACTTTAATGAGATAAGAATTGGTGTTATGGCTTCGTATTGCTCT
1 ACTGCAACTTCAAAGAGATAAGATTTGGTGTTATAGCTTCATATTGCTCT
152354 ACTGCAACTTCAAAGAGATAAAGATTT
1 ACTGCAACTTCAAAGAGAT-AAGATTT
152381 TTCACTGTTA
Statistics
Matches: 62, Mismatches: 14, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
50 56 0.90
51 6 0.10
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (50 bp):
ACTGCAACTTCAAAGAGATAAGATTTGGTGTTATAGCTTCATATTGCTCT
Found at i:152659 original size:101 final size:101
Alignment explanation
Indices: 152396--152696 Score: 361
Period size: 101 Copynumber: 3.0 Consensus size: 101
152386 TGTTAGTTTT
* * * **
152396 AATCTGATCCACTACAACTTCAGGGATATTGGATTTGATGTCATAGCTTTATCTTGTTACACTAC
1 AATCTGATCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGCTTTATCTTGTTCCACTGT
* * * * * *
152461 AACTTCAAGGAGGCAAAGATTCTCTTTTATAGCTTT
66 AACTTTAGGGAGACAAAGATTCACTTTTGTAGCTTC
** * * * *
152497 AATCTGATCCACTGTAACTTTAGGGACATAGGATTTAATGTCGTAGCTTCATCTTGTTCCACTGT
1 AATCTGATCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGCTTTATCTTGTTCCACTGT
*
152562 AACTTTAGGGAGACAAATATTCACTTTTGTAGCTTC
66 AACTTTAGGGAGACAAAGATTCACTTTTGTAGCTTC
* * * * *
152598 AATCCGATCCACTACAACATCAAGGATATAGGATTTGATGTCGTAGCTTTAACTTGCTCCACTGT
1 AATCTGATCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGCTTTATCTTGTTCCACTGT
* * *
152663 AACTTTTGGGAGA-TAAGATTCGCTTTTGTAGCTT
66 AACTTTAGGGAGACAAAGATTCACTTTTGTAGCTT
152697 TATCTTGCTG
Statistics
Matches: 167, Mismatches: 33, Indels: 1
0.83 0.16 0.00
Matches are distributed among these distances:
100 18 0.11
101 149 0.89
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.36
Consensus pattern (101 bp):
AATCTGATCCACTACAACTTCAGGGATATAGGATTTGATGTCGTAGCTTTATCTTGTTCCACTGT
AACTTTAGGGAGACAAAGATTCACTTTTGTAGCTTC
Found at i:152659 original size:151 final size:151
Alignment explanation
Indices: 152490--152785 Score: 357
Period size: 151 Copynumber: 2.0 Consensus size: 151
152480 TTCTCTTTTA
* * *
152490 TAGCTTTAATCTGATCCACTGTAACTTTAGGGACATAGGATTTAATGTCGTAGCTTCATCTTGTT
1 TAGCTTTAATCTGATCCACTGTAACTTTAGGGACATAAGATTCAATGTCGTAGCTTCATCTTGCT
* *
152555 CCACTGTAACTTT-AGGGAGACAA-ATATTCAC-TTTTGTAGCTTCAATCCGATCCACTACAACA
66 CCACTGCAA-TTTCAGGGAGACAAGAT-TT-ACTTTTTGTAGCTTCAATCCAATCCACTACAACA
152617 TCAAGGATATAGGATTTGATGTCG
128 TCAAGGATATAGGATTTGATGTCG
* * * ** * * *
152641 TAGCTTTAA-CTTGCTCCACTGTAACTTTTGGGAGATAAGATTCGCTTTTGTAGCTTTATCTTGC
1 TAGCTTTAATC-TGATCCACTGTAACTTTAGGGACATAAGATTCAATGTCGTAGCTTCATCTTGC
* * * * *
152705 TGCACTGCAATTTCAGGGAGATAAGATTTACTTTTTGTAGCTTTAATCCAATCCACTGCAACTTC
65 TCCACTGCAATTTCAGGGAGACAAGATTTACTTTTTGTAGCTTCAATCCAATCCACTACAACATC
*
152770 AAGTATATAGGATTTG
130 AAGGATATAGGATTTG
152786 CTATTTTCAC
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
150 6 0.05
151 114 0.93
152 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (151 bp):
TAGCTTTAATCTGATCCACTGTAACTTTAGGGACATAAGATTCAATGTCGTAGCTTCATCTTGCT
CCACTGCAATTTCAGGGAGACAAGATTTACTTTTTGTAGCTTCAATCCAATCCACTACAACATCA
AGGATATAGGATTTGATGTCG
Found at i:152694 original size:50 final size:51
Alignment explanation
Indices: 152640--152750 Score: 145
Period size: 50 Copynumber: 2.2 Consensus size: 51
152630 ATTTGATGTC
* * *
152640 GTAGCTTTAACTTGCTCCACTGTAACTTT-TGGGAGATAAGATTCGC-TTTT
1 GTAGCTTTAACTTGCTCCACTGCAA-TTTCAGGGAGATAAGATTCACTTTTT
* * *
152690 GTAGCTTTATCTTGCTGCACTGCAATTTCAGGGAGATAAGATTTACTTTTT
1 GTAGCTTTAACTTGCTCCACTGCAATTTCAGGGAGATAAGATTCACTTTTT
152741 GTAGCTTTAA
1 GTAGCTTTAA
152751 TCCAATCCAC
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
49 3 0.06
50 36 0.69
51 13 0.25
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (51 bp):
GTAGCTTTAACTTGCTCCACTGCAATTTCAGGGAGATAAGATTCACTTTTT
Found at i:154229 original size:52 final size:52
Alignment explanation
Indices: 154151--154449 Score: 397
Period size: 52 Copynumber: 5.8 Consensus size: 52
154141 CATTTAATAG
* * * * *
154151 TCACGATGACAC-TAAGTCATCGGACCTTA-AATCCGTAAGTGGATCCATATGC
1 TCACGATGACACAT-AGTCATCAGACCTCATAATCCGTAA-AGGATTCATATAC
* *
154203 TCACGATGACACATAGTTATTAGACCTCATAATCCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATATAC
* *
154255 TCATGATGACACATAGTCATC-GAGCCTCATAATTCGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCAGA-CCTCATAATCCGTAAAGGATTCATATAC
* * *
154307 TCATGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATATAC
* * *
154359 TCACGATGGCACATTGTCATCAGACCTCATAATCTGTAAAGGATTCATATAC
1 TCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATATAC
* *
154411 TCATGATGACACATAGTCATCGGACCTCATAATCCGTAA
1 TCACGATGACACATAGTCATCAGACCTCATAATCCGTAA
154450 CTCACGATGA
Statistics
Matches: 219, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
51 2 0.01
52 205 0.94
53 12 0.05
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (52 bp):
TCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCATATAC
Found at i:154439 original size:156 final size:156
Alignment explanation
Indices: 154155--154449 Score: 443
Period size: 156 Copynumber: 1.9 Consensus size: 156
154145 TAATAGTCAC
* * * *
154155 GATGACACTAAGTCATCGGACCTTAAATCCGTAAGTGGATCCATATGCTCACGATGACACATAGT
1 GATGACACTAAGTCATCGGACCTCAAATCCATAAGAGGATCCATATACTCACGATGACACATAGT
* *
154220 TATTAGACCTCATAATCCGTAAAGGATTCATATACTCATGATGACACATAGTCATCGAGCCTCAT
66 CATCAGACCTCATAATCCGTAAAGGATTCATATACTCATGATGACACATAGTCATCGAGCCTCAT
*
154285 AATTCGTAAAGGATTCATATACTCAT
131 AATCCGTAAAGGATTCATATACTCAT
* * *
154311 GATGACAC-ATAGTCATCGGACCTCATAATCCATAA-AGGATTCATATACTCACGATGGCACATT
1 GATGACACTA-AGTCATCGGACCTCA-AATCCATAAGAGGATCCATATACTCACGATGACACATA
*
154374 GTCATCAGACCTCATAATCTGTAAAGGATTCATATACTCATGATGACACATAGTCATCG-GACCT
64 GTCATCAGACCTCATAATCCGTAAAGGATTCATATACTCATGATGACACATAGTCATCGAG-CCT
154438 CATAATCCGTAA
128 CATAATCCGTAA
154450 CTCACGATGA
Statistics
Matches: 125, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
155 2 0.02
156 115 0.92
157 8 0.06
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (156 bp):
GATGACACTAAGTCATCGGACCTCAAATCCATAAGAGGATCCATATACTCACGATGACACATAGT
CATCAGACCTCATAATCCGTAAAGGATTCATATACTCATGATGACACATAGTCATCGAGCCTCAT
AATCCGTAAAGGATTCATATACTCAT
Found at i:159374 original size:70 final size:72
Alignment explanation
Indices: 159296--159437 Score: 207
Period size: 70 Copynumber: 2.0 Consensus size: 72
159286 CCAAAGAAGA
* * * *
159296 AATGAATTTAAGAATGATTGATTGTATGGTATGGGTATGAA-TAAA-TTGTTTGTCAAATTGGAC
1 AATGAATTTAAGAATGATTAATTGTATGGTATGAGTATAAACAAAATTTGTTTGTCAAATTGGAC
159359 AAGAACG
66 AAGAACG
* *
159366 AATGAATTTAAGAATGATTAATTGTATGGTATGAGTATAAACAAAATTTTTTTTGTCAAATTGTA
1 AATGAATTTAAGAATGATTAATTGTATGGTATGAGTATAAACAAAA-TTTGTTTGTCAAATTGGA
159431 CAAGAAC
65 CAAGAAC
159438 AAAAGAATGA
Statistics
Matches: 63, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
70 38 0.60
71 3 0.05
73 22 0.35
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (72 bp):
AATGAATTTAAGAATGATTAATTGTATGGTATGAGTATAAACAAAATTTGTTTGTCAAATTGGAC
AAGAACG
Found at i:160997 original size:16 final size:17
Alignment explanation
Indices: 160976--161007 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
160966 GCTCTTAAAG
160976 TCTTCCA-TCCATTTTC
1 TCTTCCATTCCATTTTC
160992 TCTTCCATTCCATTTT
1 TCTTCCATTCCATTTT
161008 TGATTTCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.12, C:0.34, G:0.00, T:0.53
Consensus pattern (17 bp):
TCTTCCATTCCATTTTC
Found at i:161956 original size:13 final size:13
Alignment explanation
Indices: 161924--161962 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
161914 TGTCTTTAAC
*
161924 TTAGATTAATTTAGT
1 TTAGATTAA--TACT
161939 TTAGATTAATACT
1 TTAGATTAATACT
161952 TTAGATTAATA
1 TTAGATTAATA
161963 TCCTTCACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
15 9 0.39
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (13 bp):
TTAGATTAATACT
Found at i:163222 original size:26 final size:27
Alignment explanation
Indices: 163186--163244 Score: 102
Period size: 26 Copynumber: 2.2 Consensus size: 27
163176 AGTTCTAAAT
*
163186 TCGACACATTCTTGGATTTCATGCTG-
1 TCGACACATTCTTGGATTTCATGCCGC
163212 TCGACACATTCTTGGATTTCATGCCGC
1 TCGACACATTCTTGGATTTCATGCCGC
163239 TCGACA
1 TCGACA
163245 GCATGAAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 25 0.81
27 6 0.19
ACGTcount: A:0.20, C:0.27, G:0.19, T:0.34
Consensus pattern (27 bp):
TCGACACATTCTTGGATTTCATGCCGC
Done.