Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012868.1 Kokia drynarioides strain JFW-HI SEQ_127882, 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: 161180
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 553 characters in sequence are not A, C, G, or T
Found at i:377 original size:17 final size:17
Alignment explanation
Indices: 352--391 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
342 ATATTGATAC
*
352 AATTGCTTGAAAGGAGA
1 AATTACTTGAAAGGAGA
369 AATTACTTGAAAGGAGA
1 AATTACTTGAAAGGAGA
386 AATTAC
1 AATTAC
392 GTTTATTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (17 bp):
AATTACTTGAAAGGAGA
Found at i:1048 original size:130 final size:131
Alignment explanation
Indices: 704--1049 Score: 437
Period size: 132 Copynumber: 2.6 Consensus size: 131
694 AATTTTGGGT
* * * *
704 GCTGGTTTTAGATGTCCTACCGATGGCTAAGGACCTT-CATTGGTTGCAGATTCTCCACAGCTCG
1 GCTGGTCTTAGATGTCCTACCGATGGCTAAGG-TCTTGCATTTGTTGCGGATTCTCCACAGCTCG
* * *
768 TGTGAGCAGCATCGTGTAGCCCCACATCTCGACCCACAACTCTTGTGAGCATTACAGGTTATATG
65 TGTGAGCAGCATCGTGTAGCCCCACATCTCGACCCACAACTCGTGTGAGCATTACA-GTGATACG
*
833 GGT
129 GGA
* ** * *
836 GCTAGTCTTAGATGTCCTACCGATGGCTGGGGTC-TGACATTTATTGCGGATTCTCCATAGCTCG
1 GCTGGTCTTAGATGTCCTACCGATGGCTAAGGTCTTG-CATTTGTTGCGGATTCTCCACAGCTCG
* * **
900 TGTGAGTAGTATCGTGTAGCCCCACATCTCGACCCACGGCTCGTGTGAGCATTACA-TGATACGG
65 TGTGAGCAGCATCGTGTAGCCCCACATCTCGACCCACAACTCGTGTGAGCATTACAGTGATACGG
964 GA
130 GA
* * * * *
966 GCTGGTCTTGGATGTCTTATCGATGGCTAAGGTCTTGCATTTGTTGCGGATTCTCCACAACTCAT
1 GCTGGTCTTAGATGTCCTACCGATGGCTAAGGTCTTGCATTTGTTGCGGATTCTCCACAGCTCGT
*
1031 GTGAGCAGCATCATGTAGC
66 GTGAGCAGCATCGTGTAGC
1050 TAACATCCCA
Statistics
Matches: 181, Mismatches: 30, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
130 76 0.42
131 3 0.02
132 102 0.56
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (131 bp):
GCTGGTCTTAGATGTCCTACCGATGGCTAAGGTCTTGCATTTGTTGCGGATTCTCCACAGCTCGT
GTGAGCAGCATCGTGTAGCCCCACATCTCGACCCACAACTCGTGTGAGCATTACAGTGATACGGG
A
Found at i:9029 original size:88 final size:88
Alignment explanation
Indices: 8880--9056 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
8870 TTACAAATCT
8880 AGTGGATTTGGGAATATCCTTAGTGGTGGAAAGCTAAGGTAGTTTAGTAGGCATTTGAGGCTGAA
1 AGTGGATTTGGGAATATCCTTAGTGGTGGAAAGCTAAGGTAGTTTAGTAGGCATTTGAGGCTGAA
8945 CCACTCTAAATTCTTTGTGTCAA
66 CCACTCTAAATTCTTTGTGTCAA
8968 AGTGGATTTGGGAATATCCTTAGTGGTGGAAAGCTAAGGTAGTTTAGTAGGCATTTGAGGCTGAA
1 AGTGGATTTGGGAATATCCTTAGTGGTGGAAAGCTAAGGTAGTTTAGTAGGCATTTGAGGCTGAA
9033 CCACTCTAAATTCTTTGTGTCAA
66 CCACTCTAAATTCTTTGTGTCAA
9056 A
1 A
9057 TTGTTTTGAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.28, C:0.12, G:0.27, T:0.33
Consensus pattern (88 bp):
AGTGGATTTGGGAATATCCTTAGTGGTGGAAAGCTAAGGTAGTTTAGTAGGCATTTGAGGCTGAA
CCACTCTAAATTCTTTGTGTCAA
Found at i:11829 original size:26 final size:24
Alignment explanation
Indices: 11800--11848 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
11790 ATTAAAAATA
*
11800 CTAAAAAACATTAAAATAAATATTTC
1 CTAAAAAA-ATGAAAATAAA-ATTTC
*
11826 CTAACAAAATGAAAATAAAATTT
1 CTAAAAAAATGAAAATAAAATTT
11849 AAAAAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 10 0.48
26 7 0.33
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (24 bp):
CTAAAAAAATGAAAATAAAATTTC
Found at i:11930 original size:30 final size:30
Alignment explanation
Indices: 11894--11958 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
11884 CAACTTAACA
*
11894 AACAAATGCCTT-TAAAATAGTAACAAAATT
1 AACAAATG-CTTCTAAAATAATAACAAAATT
11924 AACAAATGCTTCTAAAATAATAACAAAATT
1 AACAAATGCTTCTAAAATAATAACAAAATT
11954 AACAA
1 AACAA
11959 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 3 0.09
30 30 0.91
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.25
Consensus pattern (30 bp):
AACAAATGCTTCTAAAATAATAACAAAATT
Found at i:13551 original size:20 final size:20
Alignment explanation
Indices: 13523--13563 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
13513 TTTCTGCTTG
*
13523 AATCGATTCATTT-TTGTTTA
1 AATCAATTC-TTTGTTGTTTA
13543 AATCAATTCTTTGTTGTTTA
1 AATCAATTCTTTGTTGTTTA
13563 A
1 A
13564 CTCGATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (20 bp):
AATCAATTCTTTGTTGTTTA
Found at i:15157 original size:17 final size:17
Alignment explanation
Indices: 15124--15212 Score: 63
Period size: 17 Copynumber: 5.0 Consensus size: 17
15114 AAAATTTTAA
15124 ATATGTTTTATTAATTTT
1 ATATGTTTTA-TAATTTT
15142 ATATGTTTTATAATTTATT
1 ATATGTTTTATAA-TT-TT
* * *
15161 AGATTTTTTTATATTTTT
1 ATA-TGTTTTATAATTTT
***
15179 ATAACATTTATAATATTT
1 ATATGTTTTATAAT-TTT
*
15197 -TATATTTTATAATTTT
1 ATATGTTTTATAATTTT
15213 CATAAGTTCA
Statistics
Matches: 56, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
16 3 0.05
17 20 0.36
18 19 0.34
19 6 0.11
20 8 0.14
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (17 bp):
ATATGTTTTATAATTTT
Found at i:15200 original size:10 final size:10
Alignment explanation
Indices: 15088--15200 Score: 51
Period size: 10 Copynumber: 11.7 Consensus size: 10
15078 TTTTTTATGT
*
15088 TTTTATAAAA
1 TTTTATAATA
* * *
15098 TTTAATATTT
1 TTTTATAATA
*
15108 TTTTATAAAA
1 TTTTATAATA
15118 TTTTA-AATA
1 TTTTATAATA
*
15127 TGTTT-TATTAA
1 T-TTTATAAT-A
*
15138 TTTTAT-ATG
1 TTTTATAATA
15147 TTTTATAAT-
1 TTTTATAATA
* * *
15156 TTATTAGATTT
1 TT-TTATAATA
15167 TTTTAT-AT-
1 TTTTATAATA
*
15175 TTTTATAACA
1 TTTTATAATA
15185 -TTTATAATA
1 TTTTATAATA
15194 TTTTATA
1 TTTTATA
15201 TTTTATAATT
Statistics
Matches: 75, Mismatches: 18, Indels: 20
0.66 0.16 0.18
Matches are distributed among these distances:
8 6 0.08
9 22 0.29
10 42 0.56
11 5 0.07
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (10 bp):
TTTTATAATA
Found at i:15217 original size:26 final size:27
Alignment explanation
Indices: 15137--15208 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
15127 TGTTTTATTA
15137 ATTTTATATGTTTTAT-A-ATTTATTAGATT
1 ATTTTATAT-TTTTATAACATTTA-TA-A-T
*
15166 TTTTTATATTTTTATAACATTTATAAT
1 ATTTTATATTTTTATAACATTTATAAT
15193 ATTTTATA-TTTTATAA
1 ATTTTATATTTTTATAA
15209 TTTTCATAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
26 8 0.21
27 8 0.21
28 7 0.18
29 11 0.28
30 5 0.13
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.62
Consensus pattern (27 bp):
ATTTTATATTTTTATAACATTTATAAT
Found at i:15294 original size:9 final size:9
Alignment explanation
Indices: 15071--15316 Score: 80
Period size: 9 Copynumber: 26.8 Consensus size: 9
15061 TTTTAATTCC
*
15071 TTTTATATT
1 TTTTATAAT
*
15080 TTTTAT-GT
1 TTTTATAAT
*
15088 TTTTATAAAA
1 TTTTAT-AAT
* *
15098 TTTAATATTT
1 TTTTATA-AT
*
15108 TTTTATAAAA
1 TTTTAT-AAT
*
15118 TTTTAAATAT
1 TTTTATA-AT
15128 GTTTTATTAA-
1 -TTTTA-TAAT
15138 TTTTAT-AT
1 TTTTATAAT
15146 GTTTTATAAT
1 -TTTTATAAT
*
15156 TTATTA-GAT
1 TT-TTATAAT
*
15165 TTTTTTATAT
1 TTTTATA-AT
*
15175 TTTTATAAC
1 TTTTATAAT
*
15184 ATTTATAAT
1 TTTTATAAT
15193 ATTTTAT-A-
1 -TTTTATAAT
15201 TTTTATAAT
1 TTTTATAAT
*
15210 TTTCATAAGT
1 TTTTATAA-T
**
15220 TCATATCAAT
1 TTTTAT-AAT
*
15230 TTTCAT-AT
1 TTTTATAAT
15238 TTTTA-AAT
1 TTTTATAAT
15246 ATTTT-TAAT
1 -TTTTATAAT
* *
15255 ATATAATAAT
1 -TTTTATAAT
*
15265 TTATAT-AT
1 TTTTATAAT
*
15273 TTTTATATTT
1 TTTTATA-AT
15283 TTTTATAAT
1 TTTTATAAT
* *
15292 TTTTGTGAT
1 TTTTATAAT
* *
15301 TTTAATCAT
1 TTTTATAAT
15310 TTTTATA
1 TTTTATA
15317 GGAAAATATT
Statistics
Matches: 170, Mismatches: 43, Indels: 48
0.65 0.16 0.18
Matches are distributed among these distances:
7 7 0.04
8 26 0.15
9 73 0.43
10 54 0.32
11 9 0.05
12 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTATAAT
Found at i:15742 original size:3 final size:3
Alignment explanation
Indices: 15734--15760 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
15724 AATTAATCAT
15734 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
15761 TTATTATTAT
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:15765 original size:3 final size:3
Alignment explanation
Indices: 15759--15786 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
15749 ATAATAATAA
15759 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
15787 TCAAAAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:16259 original size:25 final size:25
Alignment explanation
Indices: 16202--16256 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
16192 ACCTTCATTG
*
16202 AAAAATTAAAAATCAAATTTAACTA
1 AAAAAATAAAAATCAAATTTAACTA
* *
16227 AAAAAATAAAATTCAAA-TTAAGTA
1 AAAAAATAAAAATCAAATTTAACTA
16251 AAAAAA
1 AAAAAA
16257 ATATAAACAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAAAATAAAAATCAAATTTAACTA
Found at i:18948 original size:41 final size:42
Alignment explanation
Indices: 18858--18968 Score: 188
Period size: 41 Copynumber: 2.7 Consensus size: 42
18848 AAAAAAGAAA
*
18858 GAGAAAAGCATCAGATAAGTTGGCTCCACTAATTCCAATTTT
1 GAGAAAAGCATCAGATAAGTTGGCTCCACTAATTCCAAATTT
18900 GAGAAAAGCATCAGATAAGTTGGCTCCACTAA-TCCAAATTT
1 GAGAAAAGCATCAGATAAGTTGGCTCCACTAATTCCAAATTT
* *
18941 GAGAAAAGCATCAGTTTAGTTGGCTCCA
1 GAGAAAAGCATCAGATAAGTTGGCTCCA
18969 TTAAGATCGA
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
41 34 0.52
42 32 0.48
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (42 bp):
GAGAAAAGCATCAGATAAGTTGGCTCCACTAATTCCAAATTT
Found at i:21832 original size:4 final size:4
Alignment explanation
Indices: 21819--21849 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
21809 GAAAGAGAGA
*
21819 GAGG GGGG GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG
21850 ATGAGACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.77, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:24452 original size:36 final size:39
Alignment explanation
Indices: 24412--24483 Score: 96
Period size: 36 Copynumber: 1.9 Consensus size: 39
24402 AAATAAACAT
24412 TTTTAAAAATTTAAT-TT-AA-TAATTATCTTAATAATA
1 TTTTAAAAATTTAATATTAAAGTAATTATCTTAATAATA
** *
24448 TTTTATCAATTTAATATTAAAGTTATTATCTTAATA
1 TTTTAAAAATTTAATATTAAAGTAATTATCTTAATA
24484 TTAAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 13 0.43
37 2 0.07
38 2 0.07
39 13 0.43
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (39 bp):
TTTTAAAAATTTAATATTAAAGTAATTATCTTAATAATA
Found at i:24544 original size:61 final size:59
Alignment explanation
Indices: 24478--24593 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 59
24468 AGTTATTATC
* * ** *
24478 TTAATATTAAATTAAATTTAATGTTTATTTTGTAGATAATATTCTATTAATTTAATAAGAT
1 TTAATATTAAATTAAATATAATATTTAAATTG-AGA-AATATTATATTAATTTAATAAGAT
* *
24539 TTAATATTAAATTTAATATAATATTTAAATTGATAAATATTATATTAATTTAATA
1 TTAATATTAAATTAAATATAATATTTAAATTGAGAAATATTATATTAATTTAATA
24594 TTAAAGTGAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 19 0.40
60 2 0.04
61 27 0.56
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (59 bp):
TTAATATTAAATTAAATATAATATTTAAATTGAGAAATATTATATTAATTTAATAAGAT
Found at i:24554 original size:12 final size:12
Alignment explanation
Indices: 24537--24598 Score: 51
Period size: 12 Copynumber: 5.1 Consensus size: 12
24527 ATTTAATAAG
24537 ATTTAATATTAA
1 ATTTAATATTAA
24549 ATTTAATA-TAA
1 ATTTAATATTAA
24560 TATTTAA-ATTGATAA
1 -ATTTAATA-T--TAA
24575 ATATT-ATATT-A
1 AT-TTAATATTAA
24586 ATTTAATATTAA
1 ATTTAATATTAA
24598 A
1 A
24599 GTGATTAAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
10 2 0.05
11 12 0.29
12 17 0.41
14 4 0.10
15 6 0.15
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:24593 original size:32 final size:32
Alignment explanation
Indices: 24541--24603 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
24531 AATAAGATTT
*
24541 AATATTAAATTTAATATAATATTTAAATTGATA
1 AATATTAAATTTAATATAATA-TTAAAGTGATA
* *
24574 AATATTATA-TTAATTTAATATTAAAGTGAT
1 AATATTAAATTTAATATAATATTAAAGTGAT
24604 TAAGTTTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 9 0.33
32 10 0.37
33 8 0.30
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (32 bp):
AATATTAAATTTAATATAATATTAAAGTGATA
Found at i:25679 original size:18 final size:19
Alignment explanation
Indices: 25653--25688 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
25643 AAAATAAAAA
25653 TTAATTAAAGAAAAATAAT
1 TTAATTAAAGAAAAATAAT
*
25672 TTAA-TAAATAAAAATAA
1 TTAATTAAAGAAAAATAA
25689 GCTAAAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
TTAATTAAAGAAAAATAAT
Found at i:28739 original size:42 final size:41
Alignment explanation
Indices: 28660--28742 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 41
28650 CAAATATTTT
* *
28660 TAAACCCAATATAATTTCATTATTCAAAAACACTCATAAAC
1 TAAACCCAATATAATTTCATTACTCAAAAACAATCATAAAC
* *
28701 TAAACCCAAATATAATTTTATTCCT-AAATAACAATCATAAAC
1 TAAACCC-AATATAATTTCATTACTCAAA-AACAATCATAAAC
28743 AACTCTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 10 0.28
42 26 0.72
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.30
Consensus pattern (41 bp):
TAAACCCAATATAATTTCATTACTCAAAAACAATCATAAAC
Found at i:41096 original size:12 final size:12
Alignment explanation
Indices: 41075--41122 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
41065 TCGTTACAAA
41075 TTCTTCTTCTTT
1 TTCTTCTTCTTT
* *
41087 TTCTTTTTCTGT
1 TTCTTCTTCTTT
*
41099 TGCTTCTTCTTT
1 TTCTTCTTCTTT
41111 CTTC-TCTTCTTT
1 -TTCTTCTTCTTT
41123 CTCCCCTTCT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 27 0.93
13 2 0.07
ACGTcount: A:0.00, C:0.25, G:0.04, T:0.71
Consensus pattern (12 bp):
TTCTTCTTCTTT
Found at i:43062 original size:13 final size:14
Alignment explanation
Indices: 43044--43076 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
43034 TTATTCCTGC
43044 AAAGAACT-AAAGA
1 AAAGAACTAAAAGA
*
43057 AAAGAATTAAAAGA
1 AAAGAACTAAAAGA
43071 AAAGAA
1 AAAGAA
43077 AATACAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.73, C:0.03, G:0.15, T:0.09
Consensus pattern (14 bp):
AAAGAACTAAAAGA
Found at i:47410 original size:18 final size:18
Alignment explanation
Indices: 47372--47425 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
47362 TATAGTCTGC
* *
47372 TGTGGTTGCATATGAGCA
1 TGTGGTTGCATCTGATCA
*
47390 TGTGGTTGCATCTGATTA
1 TGTGGTTGCATCTGATCA
**
47408 TGTGACTGCATCTGATCA
1 TGTGGTTGCATCTGATCA
47426 GGATGTGAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.37
Consensus pattern (18 bp):
TGTGGTTGCATCTGATCA
Found at i:54506 original size:20 final size:20
Alignment explanation
Indices: 54483--54549 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
54473 AAGCACCGAA
54483 GTGCAAATAGGGGCACAGAT
1 GTGCAAATAGGGGCACAGAT
* *
54503 GTGCAAATAGAGGCACCGAT
1 GTGCAAATAGGGGCACAGAT
* * * * *
54523 GTGTATACAGGGGCACTGAA
1 GTGCAAATAGGGGCACAGAT
54543 GTGCAAA
1 GTGCAAA
54550 CAAGGGTACT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.33, T:0.16
Consensus pattern (20 bp):
GTGCAAATAGGGGCACAGAT
Found at i:58109 original size:13 final size:13
Alignment explanation
Indices: 58074--58109 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
58064 TCTGATTCAT
58074 TCAATGAATAT-A
1 TCAATGAATATCA
58086 TCAA-G-ATATCA
1 TCAATGAATATCA
58097 TCAATGAATATCA
1 TCAATGAATATCA
58110 CAACAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 5 0.24
13 6 0.29
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.31
Consensus pattern (13 bp):
TCAATGAATATCA
Found at i:77196 original size:62 final size:62
Alignment explanation
Indices: 77120--77251 Score: 228
Period size: 62 Copynumber: 2.1 Consensus size: 62
77110 ATCATGCCTT
* *
77120 CGACACATAGCACTATGGCGACATTAGACCGTATGTGTTTATTGCATTCTATCTTGCACTTC
1 CGACACATAGCACTATGGCGACATTAGACCATATGTGTTTATTGCATTCTATCCTGCACTTC
* *
77182 CGACACATAGCACTATGGTGACTTTAGACCATATGTGTTTATTGCATTCTATCCTGCACTTC
1 CGACACATAGCACTATGGCGACATTAGACCATATGTGTTTATTGCATTCTATCCTGCACTTC
77244 CGACACAT
1 CGACACAT
77252 CGACATCGGA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (62 bp):
CGACACATAGCACTATGGCGACATTAGACCATATGTGTTTATTGCATTCTATCCTGCACTTC
Found at i:78533 original size:17 final size:18
Alignment explanation
Indices: 78511--78550 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
78501 AAAGATTTCA
*
78511 TGCATTTT-TATTGTCAT
1 TGCATTTTATATTGTCAC
*
78528 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
78546 TGCAT
1 TGCAT
78551 CTCTTTTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:79569 original size:30 final size:30
Alignment explanation
Indices: 79533--79592 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
79523 TTCATACTTA
79533 GTTTTTTATATTTGCCAACTTATTTCTAGT
1 GTTTTTTATATTTGCCAACTTATTTCTAGT
*
79563 GTTTTTTATATTTTCCAACTTATTTCTAGT
1 GTTTTTTATATTTGCCAACTTATTTCTAGT
79593 TAGTTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.13, G:0.08, T:0.58
Consensus pattern (30 bp):
GTTTTTTATATTTGCCAACTTATTTCTAGT
Found at i:93986 original size:21 final size:21
Alignment explanation
Indices: 93962--94003 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
93952 AAATATAGAA
93962 ATTATTAATTAATTTTTTTTT
1 ATTATTAATTAATTTTTTTTT
93983 ATTATTAATTAATTTTTTTTT
1 ATTATTAATTAATTTTTTTTT
94004 GTAATTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTATTAATTAATTTTTTTTT
Found at i:96808 original size:21 final size:20
Alignment explanation
Indices: 96782--96851 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
96772 GGTTTTAGGA
96782 TTTGGGTATTGGGTCAAAAG-G
1 TTTGGGT-TT-GGTCAAAAGTG
*
96803 TTTGGGTTTGTTCAAAAGTG
1 TTTGGGTTTGGTCAAAAGTG
* * *
96823 TTTGGGTTAGGTTCAAAGGGG
1 TTTGGGTTTGG-TCAAAAGTG
96844 TTTGGGTT
1 TTTGGGTT
96852 AGGTTGGCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 8 0.19
20 12 0.29
21 22 0.52
ACGTcount: A:0.19, C:0.04, G:0.37, T:0.40
Consensus pattern (20 bp):
TTTGGGTTTGGTCAAAAGTG
Found at i:96852 original size:21 final size:21
Alignment explanation
Indices: 96795--96856 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
96785 GGGTATTGGG
*
96795 TCAAAA-GGTTTGGGTT-TGT
1 TCAAAAGGGTTTGGGTTAGGT
*
96814 TCAAAAGTGTTTGGGTTAGGT
1 TCAAAAGGGTTTGGGTTAGGT
*
96835 TCAAAGGGGTTTGGGTTAGGT
1 TCAAAAGGGTTTGGGTTAGGT
96856 T
1 T
96857 GGCTTGTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.16
20 9 0.24
21 22 0.59
ACGTcount: A:0.21, C:0.05, G:0.35, T:0.39
Consensus pattern (21 bp):
TCAAAAGGGTTTGGGTTAGGT
Found at i:97430 original size:20 final size:21
Alignment explanation
Indices: 97405--97443 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
97395 TTCACTTGCA
*
97405 TCACAAA-TAAGTCCCAAACT
1 TCACAAATTAACTCCCAAACT
97425 TCACAAATTAACTCCCAAA
1 TCACAAATTAACTCCCAAA
97444 TTAGATCTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.46, C:0.31, G:0.03, T:0.21
Consensus pattern (21 bp):
TCACAAATTAACTCCCAAACT
Found at i:103897 original size:21 final size:20
Alignment explanation
Indices: 103869--103926 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
103859 GTATTGGGTT
*
103869 AAAAGGTTTGGGTTTGATTC
1 AAAAGGTTTGGGTTAGATTC
*
103889 AAAATGGTTTGGGTTAGGTTC
1 AAAA-GGTTTGGGTTAGATTC
*
103910 AAAGGGGTTTGGGTTAG
1 AAA-AGGTTTGGGTTAG
103927 TTTGGCTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.24, C:0.03, G:0.36, T:0.36
Consensus pattern (20 bp):
AAAAGGTTTGGGTTAGATTC
Found at i:104853 original size:23 final size:22
Alignment explanation
Indices: 104827--104870 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
104817 TATGTAGACC
* *
104827 GTACATGTTTAGTTATGTGAACT
1 GTACATATTTA-TTATGCGAACT
*
104850 GTACTTATTTATTATGCGAAC
1 GTACATATTTATTATGCGAAC
104871 CCTAAACTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.27, C:0.11, G:0.18, T:0.43
Consensus pattern (22 bp):
GTACATATTTATTATGCGAACT
Found at i:106655 original size:12 final size:12
Alignment explanation
Indices: 106638--106687 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
106628 ATTTTAATCG
106638 ATTTAATATTAA
1 ATTTAATATTAA
106650 ATTTAATA-TAA
1 ATTTAATATTAA
*
106661 TATCTATTATATT-A
1 -AT-T-TAATATTAA
106675 ATTTAATATTAA
1 ATTTAATATTAA
106687 A
1 A
106688 GTGATTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
11 9 0.29
12 13 0.42
13 3 0.10
14 5 0.16
15 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:110261 original size:17 final size:17
Alignment explanation
Indices: 110241--110294 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
110231 ACTACAATGC
* *
110241 AAATGTACTAACAACTA
1 AAATGTAATGACAACTA
* *
110258 AAATGTAGTGACAATTAA
1 AAATGTAATGACAACT-A
110276 AAATGTAATGACAACTA
1 AAATGTAATGACAACTA
110293 AA
1 AA
110295 TGATATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (17 bp):
AAATGTAATGACAACTA
Found at i:110280 original size:18 final size:18
Alignment explanation
Indices: 110241--110294 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
110231 ACTACAATGC
* *
110241 AAATGTACTAACAACT-A
1 AAATGTAATGACAACTAA
* *
110258 AAATGTAGTGACAATTAA
1 AAATGTAATGACAACTAA
110276 AAATGTAATGACAACTAA
1 AAATGTAATGACAACTAA
110294 A
1 A
110295 TGATATGCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (18 bp):
AAATGTAATGACAACTAA
Found at i:125902 original size:11 final size:11
Alignment explanation
Indices: 125886--125915 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
125876 TCACTCAGTT
125886 CTCTCAATTTC
1 CTCTCAATTTC
*
125897 CTCTCAATTTT
1 CTCTCAATTTC
125908 CTCTCAAT
1 CTCTCAAT
125916 AAACTCTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.20, C:0.33, G:0.00, T:0.47
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:126098 original size:9 final size:9
Alignment explanation
Indices: 126080--126154 Score: 50
Period size: 9 Copynumber: 8.3 Consensus size: 9
126070 ATTTTAATTT
126080 TTTATATTA
1 TTTATATTA
*
126089 TTTATTTTA
1 TTTATATTA
*
126098 TTTTTATT-
1 TTTATATTA
126106 TTTATA--A
1 TTTATATTA
*
126113 TTTAATTATTT
1 TTT-A-TATTA
*
126124 TTTAATAATA
1 TTT-ATATTA
126134 TTTA-ATTA
1 TTTATATTA
126142 TTTTATATTA
1 -TTTATATTA
126152 TTT
1 TTT
126155 TTAAAACTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
7 3 0.06
8 9 0.18
9 24 0.47
10 10 0.20
11 5 0.10
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:126121 original size:17 final size:20
Alignment explanation
Indices: 126101--126145 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
126091 TATTTTATTT
126101 TTATTTTT-AT-A-ATTTAA
1 TTATTTTTAATAATATTTAA
126118 TTATTTTTTAATAATATTTAA
1 TTA-TTTTTAATAATATTTAA
126139 TTATTTT
1 TTATTTT
126146 ATATTATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 2 0.08
20 5 0.21
21 9 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTTAATAATATTTAA
Found at i:129028 original size:23 final size:23
Alignment explanation
Indices: 128999--129053 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
128989 CAGTATACTA
128999 AAAAATAAATAATAAAT-ATTT-AT
1 AAAAATAAAT--TAAATAATTTAAT
129022 AAAAAT-AATTAAATAATTTGAAT
1 AAAAATAAATTAAATAATTT-AAT
129045 AAAAATAAA
1 AAAAATAAA
129054 ACAAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 5 0.18
21 4 0.14
22 3 0.11
23 14 0.50
24 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (23 bp):
AAAAATAAATTAAATAATTTAAT
Found at i:129029 original size:19 final size:22
Alignment explanation
Indices: 129005--129052 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
128995 ACTAAAAAAT
129005 AAATAA-TAAAT-ATTT-ATAA
1 AAATAATTAAATAATTTAATAA
129024 AAATAATTAAATAATTTGAATAA
1 AAATAATTAAATAATTT-AATAA
129047 AAATAA
1 AAATAA
129053 AACAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.24
20 5 0.20
21 4 0.16
23 10 0.40
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATAATTAAATAATTTAATAA
Found at i:129510 original size:20 final size:19
Alignment explanation
Indices: 129485--129534 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
129475 GGTAATAGCA
*
129485 TTTTTTTCTAAAAAAAGTAG
1 TTTTTTTATAAAAAAA-TAG
*
129505 TTTTTTTATAATAAAATAG
1 TTTTTTTATAAAAAAATAG
129524 TTTTTTTATAA
1 TTTTTTTATAA
129535 GAATATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (19 bp):
TTTTTTTATAAAAAAATAG
Found at i:132182 original size:27 final size:26
Alignment explanation
Indices: 132152--132242 Score: 69
Period size: 27 Copynumber: 3.3 Consensus size: 26
132142 AATTGAATCT
132152 AAAAAATGCTTAGGTACCAAATTAGGA
1 AAAAAAT-CTTAGGTACCAAATTAGGA
* *
132179 AAAATATCAAGTTCAGGTACCAAATTGGGTCA
1 AAAAAATC---TT-AGGTACCAAATTAGG--A
* *
132211 AAAAAAT-TTAGATACCAAATTA-AA
1 AAAAAATCTTAGGTACCAAATTAGGA
132235 AAAAAATC
1 AAAAAATC
132243 AAATTCAAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
24 8 0.16
26 1 0.02
27 17 0.33
28 2 0.04
29 2 0.04
30 14 0.27
32 7 0.14
ACGTcount: A:0.52, C:0.12, G:0.13, T:0.23
Consensus pattern (26 bp):
AAAAAATCTTAGGTACCAAATTAGGA
Found at i:132197 original size:59 final size:56
Alignment explanation
Indices: 132128--132259 Score: 165
Period size: 59 Copynumber: 2.3 Consensus size: 56
132118 AATATCTAAT
* * * *
132128 AAATTCAGGTACCAAATTGAATCTAAAAAATGCTTAGGTACCAAATTAGGAAAAATATC
1 AAATTCAGGTACCAAATTGAATCAAAAAAAT--TTAGATACCAAATTA-AAAAAAAATC
* **
132187 AAGTTCAGGTACCAAATTGGGTCAAAAAAATTTAGATACCAAATTAAAAAAAAATC
1 AAATTCAGGTACCAAATTGAATCAAAAAAATTTAGATACCAAATTAAAAAAAAATC
*
132243 AAATTCAAGTACCAAAT
1 AAATTCAGGTACCAAAT
132260 ATTATATTAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
56 23 0.36
57 14 0.22
59 27 0.42
ACGTcount: A:0.50, C:0.14, G:0.12, T:0.24
Consensus pattern (56 bp):
AAATTCAGGTACCAAATTGAATCAAAAAAATTTAGATACCAAATTAAAAAAAAATC
Found at i:132689 original size:19 final size:19
Alignment explanation
Indices: 132652--132690 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
132642 CAATTATTAA
*
132652 TTAATATATTTGCATTTTT
1 TTAATATATTTGCAATTTT
132671 TTAATAT-TTTGACAATTTT
1 TTAATATATTTG-CAATTTT
132690 T
1 T
132691 ATGTATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (19 bp):
TTAATATATTTGCAATTTT
Found at i:134148 original size:12 final size:13
Alignment explanation
Indices: 134119--134161 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
134109 TGAGACTGTT
134119 TTTTTAAGTTATG
1 TTTTTAAGTTATG
*
134132 TTTTTAATTTATG
1 TTTTTAAGTTATG
* *
134145 TTTTAAAGCTATG
1 TTTTTAAGTTATG
134158 TTTT
1 TTTT
134162 ATGTGTACTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.23, C:0.02, G:0.12, T:0.63
Consensus pattern (13 bp):
TTTTTAAGTTATG
Found at i:135341 original size:29 final size:29
Alignment explanation
Indices: 135265--135343 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
135255 ATTTTGGATT
* *
135265 AAGGATTAAATTGGAATTTTTTAGAAATTT
1 AAGGACTAAATT-GAATTTTTTAGAAATTC
* *
135295 AAGGTCTAATTTGTAATTTTAGTT-G-AATTC
1 AAGGACTAAATTG-AATTTT--TTAGAAATTC
135325 AAGGACTAAATTGAATTTT
1 AAGGACTAAATTGAATTTT
135344 GATTAAAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
29 7 0.17
30 30 0.75
31 1 0.03
32 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (29 bp):
AAGGACTAAATTGAATTTTTTAGAAATTC
Found at i:135412 original size:50 final size:50
Alignment explanation
Indices: 135325--135419 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
135315 AGTTGAATTC
* * *
135325 AAGGACTAAATTGAATTTTGATTAAAGTTTTGTGGCTAATTTGAATGCTT
1 AAGGACTAAATTGAATTTTGATGAAAGTTTTGAGGCTAATGTGAATGCTT
*
135375 AAGGACTAAATTGAGTCTTT-AGTGAAAG-TTTGAGGCTAATGTGAA
1 AAGGACTAAATTGAAT-TTTGA-TGAAAGTTTTGAGGCTAATGTGAA
135420 AACCCTAGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
50 31 0.79
51 8 0.21
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (50 bp):
AAGGACTAAATTGAATTTTGATGAAAGTTTTGAGGCTAATGTGAATGCTT
Found at i:141780 original size:30 final size:30
Alignment explanation
Indices: 141746--141820 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
141736 AAATTTTGGA
141746 TTAAGGATTAAATTAGAAATTTT-TAGAAAT
1 TTAAGGATTAAATTAGAAATTTTATA-AAAT
* * *
141776 TTAAGG-TTTAATTTGTAATTTTAATAAAAT
1 TTAAGGATTAAATTAGAAATTTT-ATAAAAT
* *
141806 TTAGGGACTAAATTA
1 TTAAGGATTAAATTA
141821 AATTTTGATT
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
29 13 0.37
30 15 0.43
31 7 0.20
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (30 bp):
TTAAGGATTAAATTAGAAATTTTATAAAAT
Found at i:144408 original size:36 final size:36
Alignment explanation
Indices: 144368--144504 Score: 156
Period size: 36 Copynumber: 3.9 Consensus size: 36
144358 GTGAAAGTGG
144368 ATATGTGGGTATGTTATTCATGTCATGAGACAATAA
1 ATATGTGGGTATGTTATTCATGTCATGAGACAATAA
*
144404 ATATGTGGGTATGTTATTCATGCCATGAG--AATAA
1 ATATGTGGGTATGTTATTCATGTCATGAGACAATAA
* ** * * *
144438 AAATGTGACTGA-GTT-TTCATGTCGTGAGATAGTAA
1 ATATGTGGGT-ATGTTATTCATGTCATGAGACAATAA
* *
144473 ATATGTTGGTATGTTATTCATGACATGAGACA
1 ATATGTGGGTATGTTATTCATGTCATGAGACA
144505 GTGAATACAT
Statistics
Matches: 82, Mismatches: 14, Indels: 10
0.77 0.13 0.09
Matches are distributed among these distances:
33 11 0.13
34 16 0.20
35 14 0.17
36 41 0.50
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (36 bp):
ATATGTGGGTATGTTATTCATGTCATGAGACAATAA
Found at i:145109 original size:120 final size:120
Alignment explanation
Indices: 144759--145118 Score: 472
Period size: 120 Copynumber: 3.0 Consensus size: 120
144749 GCTTCCACAA
* * * * * *
144759 GCTATAATCCAGAATTTCATCCTCATGTTTGTATCAACTCTGTTACCAGTATACGATGTTGCTCG
1 GCTATAATCTAGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACAATGCTGCTCA
* * * *
144824 CACGAG-TTGTCGAGGACTCGCAACATATACGATACCTCAGCCATCAATACATTAT
66 CACGAGCTT-TCGAGGACTCACAACATATACGGTACCTCAGCCATCGATACAGTAT
* *
144879 GCAATAATCTAGAATTTCATTCTCATGTCTGTATTAACTCTGTTACCAGTATACAATGCTGCTCA
1 GCTATAATCTAGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACAATGCTGCTCA
* * * *
144944 CACGAGCTGTCGAGGACTCACAACATATGCGGTA-CTCCAACCATCGATACCGTAT
66 CACGAGCTTTCGAGGACTCACAACATATACGGTACCT-CAGCCATCGATACAGTAT
*
144999 GCTATAATCTAGAATTTCATTCTCATGTCTGTATCAACTCTGTTACTAGTATACAATGCTGCTCA
1 GCTATAATCTAGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACAATGCTGCTCA
* * * * * * *
145064 TACAAGCTTTTGAGGACTCACAACATATATGGTACCTGAGTCATCGATACGGTAT
66 CACGAGCTTTCGAGGACTCACAACATATACGGTACCTCAGCCATCGATACAGTAT
145119 TTGTGCATAT
Statistics
Matches: 208, Mismatches: 29, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
119 2 0.01
120 203 0.98
121 3 0.01
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (120 bp):
GCTATAATCTAGAATTTCATTCTCATGTCTGTATCAACTCTGTTACCAGTATACAATGCTGCTCA
CACGAGCTTTCGAGGACTCACAACATATACGGTACCTCAGCCATCGATACAGTAT
Found at i:154245 original size:19 final size:18
Alignment explanation
Indices: 154214--154272 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
154204 GATTATTATT
154214 TTTTG-AAAT-TTTTATAA
1 TTTTGAAAATATTTT-TAA
*
154231 TTTT-ATAAATATTTTGAA
1 TTTTGA-AAATATTTTTAA
154249 TTTTGAAAATTATTTTGTAA
1 TTTTGAAAA-TATTTT-TAA
154269 TTTT
1 TTTT
154273 TATTAAGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 4 0.12
18 13 0.38
19 11 0.32
20 6 0.18
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
TTTTGAAAATATTTTTAA
Found at i:154250 original size:18 final size:20
Alignment explanation
Indices: 154223--154272 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
154213 TTTTTGAAAT
*
154223 TTTTATAATTTT-ATAAA-TA
1 TTTTGTAATTTTGA-AAATTA
154242 TTTTG-AATTTTGAAAATTA
1 TTTTGTAATTTTGAAAATTA
154261 TTTTGTAATTTT
1 TTTTGTAATTTT
154273 TATTAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
TTTTGTAATTTTGAAAATTA
Found at i:158178 original size:2 final size:2
Alignment explanation
Indices: 158171--158195 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
158161 ATAAAAATAA
158171 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
158196 AATGACGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.