Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167979.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_237, 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: 44953
ACGTcount: A:0.20, C:0.10, G:0.06, T:0.65
File 2 of 2
Found at i:28513 original size:59 final size:60
Alignment explanation
Indices: 28401--28518 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 60
28391 ACAAAATTAT
*** * *
28401 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTATTTTATTTATTAT-TTTGG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
* *
28460 ATTGTATAATATTTATCTTTTATTTGATACAATTT-G-TTAAGAGATAATAATTATCTTTG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATT-A-AGATAATAATTATCTTTG
28519 TTATTTTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
57 2 0.04
58 2 0.04
59 41 0.84
60 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.55
Consensus pattern (60 bp):
ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
Found at i:29766 original size:24 final size:22
Alignment explanation
Indices: 29710--29766 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
29700 GTGAACTTCC
29710 TTTTGATTTTATTTATATTTTG
1 TTTTGATTTTATTTATATTTTG
*
29732 TATTGACTTTTATTT-TACTTTTTG
1 TTTTGA-TTTTATTTATA--TTTTG
29756 TCTTTGATTTT
1 T-TTTGATTTT
29767 TTATGTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
24 10 0.34
25 4 0.14
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTGATTTTATTTATATTTTG
Found at i:29899 original size:15 final size:16
Alignment explanation
Indices: 29881--29918 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
29871 CGTTTTATAT
29881 TTTTTTATTCTC-TAA
1 TTTTTTATTCTCTTAA
* *
29896 TTTTTTATTTTCTTAC
1 TTTTTTATTCTCTTAA
29912 TTTTTTA
1 TTTTTTA
29919 CTTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTATTCTCTTAA
Found at i:29915 original size:16 final size:15
Alignment explanation
Indices: 29881--29923 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
29871 CGTTTTATAT
*
29881 TTTTTTATTCTCTAA
1 TTTTTTATTTTCTAA
*
29896 TTTTTTATTTTCTTAC
1 TTTTTTATTTTC-TAA
29912 TTTTTTACTTTT
1 TTTTTTA-TTTT
29924 TGTTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTATTTTCTAA
Found at i:29980 original size:8 final size:7
Alignment explanation
Indices: 29881--30125 Score: 67
Period size: 8 Copynumber: 33.4 Consensus size: 7
29871 CGTTTTATAT
29881 TTTTTTA
1 TTTTTTA
* *
29888 TTCTCTAA
1 TT-TTTTA
29896 TTTTTTA
1 TTTTTTA
29903 TTTTCTTA
1 TTTT-TTA
29911 CTTTTTTA
1 -TTTTTTA
*
29919 CTTTTTGTT
1 -TTTTT-TA
29928 TTTGTTTA
1 TTT-TTTA
29936 -TTTTTA
1 TTTTTTA
* *
29942 ATTGTTA
1 TTTTTTA
29949 TTTTTTTA
1 -TTTTTTA
*
29957 GTATTTTA
1 -TTTTTTA
29965 --TTTTA
1 TTTTTTA
29970 TTTTTTCA
1 TTTTTT-A
29978 TTTATATTA
1 TTT-T-TTA
**
29987 AATTTT-
1 TTTTTTA
**
29993 TTTTCAA
1 TTTTTTA
30000 TTTTTGTA
1 TTTTT-TA
*
30008 TTTTTGA
1 TTTTTTA
**
30015 TTCATTA
1 TTTTTTA
30022 TTTTTTA
1 TTTTTTA
*
30029 TTATCTTA
1 TT-TTTTA
**
30037 CCTTTTA
1 TTTTTTA
30044 TATTTTTA
1 T-TTTTTA
*
30052 --TTGTA
1 TTTTTTA
30057 TTTTTGT-
1 TTTTT-TA
30064 TTCTTTTA
1 TT-TTTTA
30072 TTTTTT-
1 TTTTTTA
30078 TTGTTTTA
1 TT-TTTTA
**
30086 CTTTAATA
1 -TTTTTTA
*
30094 TTGTTTTC
1 TT-TTTTA
30102 TTATTTTA
1 TT-TTTTA
30110 -TTTTTA
1 TTTTTTA
30116 TTTTTTA
1 TTTTTTA
30123 TTT
1 TTT
30126 CTTTCTTTAT
Statistics
Matches: 172, Mismatches: 40, Indels: 52
0.65 0.15 0.20
Matches are distributed among these distances:
5 9 0.05
6 13 0.08
7 67 0.39
8 69 0.40
9 12 0.07
10 2 0.01
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (7 bp):
TTTTTTA
Found at i:30371 original size:22 final size:23
Alignment explanation
Indices: 30333--30390 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
30323 CTTTTCTCTC
*
30333 TTTTA-ATTTTTTGTCTT-TGATT
1 TTTTATATTGTTT-TCTTATGATT
*
30355 TTTTATATTGTTTTCTTATTATT
1 TTTTATATTGTTTTCTTATGATT
*
30378 TCTTATA-TGTTTT
1 TTTTATATTGTTTT
30391 TCAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTATATTGTTTTCTTATGATT
Found at i:30494 original size:7 final size:7
Alignment explanation
Indices: 30473--30594 Score: 66
Period size: 7 Copynumber: 15.7 Consensus size: 7
30463 ATTTTTGTCT
30473 TTTTTTA
1 TTTTTTA
**
30480 TTCATTA
1 TTTTTTA
30487 TTTTTTA
1 TTTTTTA
30494 TTTTCTTA
1 TTTT-TTA
30502 CTTTTTATA
1 -TTTTT-TA
30511 TTTTTTA
1 TTTTTTA
30518 TTGTATTT-
1 TT-T-TTTA
*
30526 TTGTTTA
1 TTTTTTA
*
30533 TTTTATA
1 TTTTTTA
*
30540 TTTTTTGT
1 TTTTTT-A
30548 TTTGCTTTAA
1 TTT--TTT-A
30558 TATTTTTA
1 T-TTTTTA
30566 TTTTTTA
1 TTTTTTA
*
30573 TTTCTTTC
1 TTT-TTTA
30581 TTTATTTA
1 TTT-TTTA
30589 TATTTT
1 T-TTTT
30595 CATAAATTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
6 3 0.03
7 37 0.42
8 29 0.33
9 14 0.16
10 4 0.04
11 2 0.02
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (7 bp):
TTTTTTA
Found at i:30741 original size:19 final size:19
Alignment explanation
Indices: 30719--30760 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
30709 CCTTTTCCTT
* *
30719 TTTTACATTTTTTTTTTTG
1 TTTTACACTTTTTTCTTTG
30738 TTTT-CACTTTTTTCTTTG
1 TTTTACACTTTTTTCTTTG
30756 TTTTA
1 TTTTA
30761 AAATTTTCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (19 bp):
TTTTACACTTTTTTCTTTG
Found at i:31649 original size:59 final size:60
Alignment explanation
Indices: 31537--31654 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 60
31527 ACAAAATTAT
*** * *
31537 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTATTTTATTTATTAT-TTTGG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
* *
31596 ATTGTATAATATTTATCTTTTATTTGATACAATTT-G-TTAAGAGATAATAATTATCTTTG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATT-A-AGATAATAATTATCTTTG
31655 TTATTTTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
57 2 0.04
58 2 0.04
59 41 0.84
60 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.55
Consensus pattern (60 bp):
ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
Found at i:32252 original size:30 final size:28
Alignment explanation
Indices: 32211--32266 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
32201 TTTTATCCAC
*
32211 ACTTCTTTCTTTTGTTTTTATTTTTTATTA
1 ACTTCTTTC-TTT-TTTTAATTTTTTATTA
*
32241 ACTTTTTTCTTTTTTTAATTTTTTAT
1 ACTTCTTTCTTTTTTTAATTTTTTAT
32267 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 3 0.12
30 8 0.33
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (28 bp):
ACTTCTTTCTTTTTTTAATTTTTTATTA
Found at i:32319 original size:8 final size:8
Alignment explanation
Indices: 32243--32320 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
32233 TTTTATTAAC
*
32243 TTTTTTCT
1 TTTTTTAT
*
32251 TTTTTTAA
1 TTTTTTAT
32259 TTTTTTA-
1 TTTTTTAT
** *
32266 TCATTGAT
1 TTTTTTAT
32274 TTTTTTAT
1 TTTTTTAT
* *
32282 ATCTTTAT
1 TTTTTTAT
32290 TTCTTATTAT
1 TT-TT-TTAT
*
32300 TTGTTATAT
1 TT-TTTTAT
32309 TTTTTTAT
1 TTTTTTAT
32317 TTTT
1 TTTT
32321 CGTTTGTATT
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
7 4 0.08
8 34 0.65
9 6 0.12
10 8 0.15
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.76
Consensus pattern (8 bp):
TTTTTTAT
Found at i:32409 original size:9 final size:9
Alignment explanation
Indices: 32369--32425 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
32359 TTTTCTTTTC
*
32369 TTTTTTTCA
1 TTTTTTTAA
*
32378 TTTTTATTAG
1 TTTTT-TTAA
* *
32388 TTTTTGTAT
1 TTTTTTTAA
32397 TTTTTTTAA
1 TTTTTTTAA
* *
32406 TTTTCTTAC
1 TTTTTTTAA
32415 TTTTTTTAA
1 TTTTTTTAA
32424 TT
1 TT
32426 GCGTTTTTGT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
9 30 0.81
10 7 0.19
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:32906 original size:24 final size:22
Alignment explanation
Indices: 32850--32906 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
32840 TGAACTTCCC
32850 TTTTGATTTTATTTATATTTTG
1 TTTTGATTTTATTTATATTTTG
*
32872 TATTGACTTTTATTT-TACTTTTTG
1 TTTTGA-TTTTATTTATA--TTTTG
32896 TCTTTGATTTT
1 T-TTTGATTTT
32907 TTATGTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
24 10 0.34
25 4 0.14
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTGATTTTATTTATATTTTG
Found at i:33039 original size:15 final size:16
Alignment explanation
Indices: 33021--33058 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
33011 CGTTTTATAT
33021 TTTTTTATTCTC-TAA
1 TTTTTTATTCTCTTAA
* *
33036 TTTTTTATTTTCTTAC
1 TTTTTTATTCTCTTAA
33052 TTTTTTA
1 TTTTTTA
33059 CTTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTATTCTCTTAA
Found at i:33055 original size:16 final size:15
Alignment explanation
Indices: 33021--33063 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
33011 CGTTTTATAT
*
33021 TTTTTTATTCTCTAA
1 TTTTTTATTTTCTAA
*
33036 TTTTTTATTTTCTTAC
1 TTTTTTATTTTC-TAA
33052 TTTTTTACTTTT
1 TTTTTTA-TTTT
33064 TGTTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTATTTTCTAA
Found at i:33120 original size:8 final size:7
Alignment explanation
Indices: 33021--33265 Score: 67
Period size: 8 Copynumber: 33.4 Consensus size: 7
33011 CGTTTTATAT
33021 TTTTTTA
1 TTTTTTA
* *
33028 TTCTCTAA
1 TT-TTTTA
33036 TTTTTTA
1 TTTTTTA
33043 TTTTCTTA
1 TTTT-TTA
33051 CTTTTTTA
1 -TTTTTTA
*
33059 CTTTTTGTT
1 -TTTTT-TA
33068 TTTGTTTA
1 TTT-TTTA
33076 -TTTTTA
1 TTTTTTA
* *
33082 ATTGTTA
1 TTTTTTA
33089 TTTTTTTA
1 -TTTTTTA
*
33097 GTATTTTA
1 -TTTTTTA
33105 --TTTTA
1 TTTTTTA
33110 TTTTTTCA
1 TTTTTT-A
33118 TTTATATTA
1 TTT-T-TTA
**
33127 AATTTT-
1 TTTTTTA
**
33133 TTTTCAA
1 TTTTTTA
33140 TTTTTGTA
1 TTTTT-TA
*
33148 TTTTTGA
1 TTTTTTA
**
33155 TTCATTA
1 TTTTTTA
33162 TTTTTTA
1 TTTTTTA
*
33169 TTATCTTA
1 TT-TTTTA
**
33177 CCTTTTA
1 TTTTTTA
33184 TATTTTTA
1 T-TTTTTA
*
33192 --TTGTA
1 TTTTTTA
33197 TTTTTGT-
1 TTTTT-TA
33204 TTCTTTTA
1 TT-TTTTA
33212 TTTTTT-
1 TTTTTTA
33218 TTGTTTTA
1 TT-TTTTA
**
33226 CTTTAATA
1 -TTTTTTA
*
33234 TTGTTTTC
1 TT-TTTTA
33242 TTATTTTA
1 TT-TTTTA
33250 -TTTTTA
1 TTTTTTA
33256 TTTTTTA
1 TTTTTTA
33263 TTT
1 TTT
33266 CTTTCTTTAT
Statistics
Matches: 172, Mismatches: 40, Indels: 52
0.65 0.15 0.20
Matches are distributed among these distances:
5 9 0.05
6 13 0.08
7 67 0.39
8 69 0.40
9 12 0.07
10 2 0.01
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (7 bp):
TTTTTTA
Found at i:33511 original size:22 final size:23
Alignment explanation
Indices: 33473--33530 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
33463 CTTTTCTCTC
*
33473 TTTTA-ATTTTTTGTCTT-TGATT
1 TTTTATATTGTTT-TCTTATGATT
*
33495 TTTTATATTGTTTTCTTATTATT
1 TTTTATATTGTTTTCTTATGATT
*
33518 TCTTATA-TGTTTT
1 TTTTATATTGTTTT
33531 TCAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTATATTGTTTTCTTATGATT
Found at i:33634 original size:7 final size:7
Alignment explanation
Indices: 33613--33734 Score: 66
Period size: 7 Copynumber: 15.7 Consensus size: 7
33603 ATTTTTGTCT
33613 TTTTTTA
1 TTTTTTA
**
33620 TTCATTA
1 TTTTTTA
33627 TTTTTTA
1 TTTTTTA
33634 TTTTCTTA
1 TTTT-TTA
33642 CTTTTTATA
1 -TTTTT-TA
33651 TTTTTTA
1 TTTTTTA
33658 TTGTATTT-
1 TT-T-TTTA
*
33666 TTGTTTA
1 TTTTTTA
*
33673 TTTTATA
1 TTTTTTA
*
33680 TTTTTTGT
1 TTTTTT-A
33688 TTTGCTTTAA
1 TTT--TTT-A
33698 TATTTTTA
1 T-TTTTTA
33706 TTTTTTA
1 TTTTTTA
*
33713 TTTCTTTC
1 TTT-TTTA
33721 TTTATTTA
1 TTT-TTTA
33729 TATTTT
1 T-TTTT
33735 CATAAATTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
6 3 0.03
7 37 0.42
8 29 0.33
9 14 0.16
10 4 0.04
11 2 0.02
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (7 bp):
TTTTTTA
Found at i:33882 original size:19 final size:19
Alignment explanation
Indices: 33851--33901 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
33841 CGTTAACTCC
* *
33851 TTTTCCTTT-TTTTACATT
1 TTTTTCTTTGTTTTACACT
*
33869 TTTTTTTTTGTTTT-CACT
1 TTTTTCTTTGTTTTACACT
33887 TTTTTCTTTGTTTTA
1 TTTTTCTTTGTTTTA
33902 AAATTTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTTCTTTGTTTTACACT
Found at i:34073 original size:17 final size:17
Alignment explanation
Indices: 34038--34073 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
34028 TTACACTTCC
* *
34038 TTATTTTGTTTTTATTT
1 TTATTTTGTTTTAACTT
34055 TTATTTTGTTTTAACTT
1 TTATTTTGTTTTAACTT
34072 TT
1 TT
34074 CCCTCTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (17 bp):
TTATTTTGTTTTAACTT
Found at i:34792 original size:59 final size:60
Alignment explanation
Indices: 34680--34797 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 60
34670 ACAAAATTAT
*** * *
34680 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTATTTTATTTATTAT-TTTGG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
* *
34739 ATTGTATAATATTTATCTTTTATTTGATACAATTT-G-TTAAGAGATAATAATTATCTTTG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATT-A-AGATAATAATTATCTTTG
34798 TTATTTTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
57 2 0.04
58 2 0.04
59 41 0.84
60 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.55
Consensus pattern (60 bp):
ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
Found at i:35393 original size:30 final size:28
Alignment explanation
Indices: 35352--35407 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
35342 TTTTATCCAC
*
35352 ACTTCTTTCTTTTGTTTTTATTTTTTATTA
1 ACTTCTTTC-TTT-TTTTAATTTTTTATTA
*
35382 ACTTTTTTCTTTTTTTAATTTTTTAT
1 ACTTCTTTCTTTTTTTAATTTTTTAT
35408 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 3 0.12
30 8 0.33
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (28 bp):
ACTTCTTTCTTTTTTTAATTTTTTATTA
Found at i:35460 original size:8 final size:8
Alignment explanation
Indices: 35384--35461 Score: 50
Period size: 8 Copynumber: 9.5 Consensus size: 8
35374 TTTTATTAAC
*
35384 TTTTTTCT
1 TTTTTTAT
*
35392 TTTTTTAA
1 TTTTTTAT
35400 TTTTTTA-
1 TTTTTTAT
** *
35407 TCATTGAT
1 TTTTTTAT
35415 TTTTTTAT
1 TTTTTTAT
* *
35423 ATCTTTAT
1 TTTTTTAT
35431 TTCTTATTAT
1 TT-TT-TTAT
*
35441 TTGTTATAT
1 TT-TTTTAT
35450 TTTTTTAT
1 TTTTTTAT
35458 TTTT
1 TTTT
35462 CGTTTGTATT
Statistics
Matches: 52, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
7 4 0.08
8 34 0.65
9 6 0.12
10 8 0.15
ACGTcount: A:0.17, C:0.05, G:0.03, T:0.76
Consensus pattern (8 bp):
TTTTTTAT
Found at i:35550 original size:9 final size:9
Alignment explanation
Indices: 35510--35566 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
35500 TTTTCTTTTC
*
35510 TTTTTTTCA
1 TTTTTTTAA
*
35519 TTTTTATTAG
1 TTTTT-TTAA
* *
35529 TTTTTGTAT
1 TTTTTTTAA
35538 TTTTTTTAA
1 TTTTTTTAA
* *
35547 TTTTCTTAC
1 TTTTTTTAA
35556 TTTTTTTAA
1 TTTTTTTAA
35565 TT
1 TT
35567 GCGTTTTTGT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
9 30 0.81
10 7 0.19
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:36046 original size:24 final size:22
Alignment explanation
Indices: 35990--36046 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
35980 TGAACTTCCC
35990 TTTTGATTTTATTTATATTTTG
1 TTTTGATTTTATTTATATTTTG
*
36012 TATTGACTTTTATTT-TACTTTTTG
1 TTTTGA-TTTTATTTATA--TTTTG
36036 TCTTTGATTTT
1 T-TTTGATTTT
36047 TTATGTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
24 10 0.34
25 4 0.14
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTGATTTTATTTATATTTTG
Found at i:36180 original size:15 final size:16
Alignment explanation
Indices: 36162--36199 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
36152 CGTTTTATAT
36162 TTTTTTATTCTC-TAA
1 TTTTTTATTCTCTTAA
* *
36177 TTTTTTATTTTCTTAC
1 TTTTTTATTCTCTTAA
36193 TTTTTTA
1 TTTTTTA
36200 CTTTTTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTATTCTCTTAA
Found at i:36196 original size:16 final size:15
Alignment explanation
Indices: 36162--36204 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
36152 CGTTTTATAT
*
36162 TTTTTTATTCTCTAA
1 TTTTTTATTTTCTAA
*
36177 TTTTTTATTTTCTTAC
1 TTTTTTATTTTC-TAA
36193 TTTTTTACTTTT
1 TTTTTTA-TTTT
36205 TGTTTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 11 0.46
16 9 0.38
17 4 0.17
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTATTTTCTAA
Found at i:36261 original size:8 final size:7
Alignment explanation
Indices: 36162--36406 Score: 67
Period size: 8 Copynumber: 33.4 Consensus size: 7
36152 CGTTTTATAT
36162 TTTTTTA
1 TTTTTTA
* *
36169 TTCTCTAA
1 TT-TTTTA
36177 TTTTTTA
1 TTTTTTA
36184 TTTTCTTA
1 TTTT-TTA
36192 CTTTTTTA
1 -TTTTTTA
*
36200 CTTTTTGTT
1 -TTTTT-TA
36209 TTTGTTTA
1 TTT-TTTA
36217 -TTTTTA
1 TTTTTTA
* *
36223 ATTGTTA
1 TTTTTTA
36230 TTTTTTTA
1 -TTTTTTA
*
36238 GTATTTTA
1 -TTTTTTA
36246 --TTTTA
1 TTTTTTA
36251 TTTTTTCA
1 TTTTTT-A
36259 TTTATATTA
1 TTT-T-TTA
**
36268 AATTTT-
1 TTTTTTA
**
36274 TTTTCAA
1 TTTTTTA
36281 TTTTTGTA
1 TTTTT-TA
*
36289 TTTTTGA
1 TTTTTTA
**
36296 TTCATTA
1 TTTTTTA
36303 TTTTTTA
1 TTTTTTA
*
36310 TTATCTTA
1 TT-TTTTA
**
36318 CCTTTTA
1 TTTTTTA
36325 TATTTTTA
1 T-TTTTTA
*
36333 --TTGTA
1 TTTTTTA
36338 TTTTTGT-
1 TTTTT-TA
36345 TTCTTTTA
1 TT-TTTTA
36353 TTTTTT-
1 TTTTTTA
36359 TTGTTTTA
1 TT-TTTTA
**
36367 CTTTAATA
1 -TTTTTTA
*
36375 TTGTTTTC
1 TT-TTTTA
36383 TTATTTTA
1 TT-TTTTA
36391 -TTTTTA
1 TTTTTTA
36397 TTTTTTA
1 TTTTTTA
36404 TTT
1 TTT
36407 CTTTCTTTAT
Statistics
Matches: 172, Mismatches: 40, Indels: 52
0.65 0.15 0.20
Matches are distributed among these distances:
5 9 0.05
6 13 0.08
7 67 0.39
8 69 0.40
9 12 0.07
10 2 0.01
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.73
Consensus pattern (7 bp):
TTTTTTA
Found at i:36652 original size:22 final size:23
Alignment explanation
Indices: 36614--36671 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
36604 CTTTTCTCTC
*
36614 TTTTA-ATTTTTTGTCTT-TGATT
1 TTTTATATTGTTT-TCTTATGATT
*
36636 TTTTATATTGTTTTCTTATTATT
1 TTTTATATTGTTTTCTTATGATT
*
36659 TCTTATA-TGTTTT
1 TTTTATATTGTTTT
36672 TCAATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
22 15 0.48
23 16 0.52
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (23 bp):
TTTTATATTGTTTTCTTATGATT
Found at i:36775 original size:7 final size:7
Alignment explanation
Indices: 36754--36875 Score: 66
Period size: 7 Copynumber: 15.7 Consensus size: 7
36744 ATTTTTGTCT
36754 TTTTTTA
1 TTTTTTA
**
36761 TTCATTA
1 TTTTTTA
36768 TTTTTTA
1 TTTTTTA
36775 TTTTCTTA
1 TTTT-TTA
36783 CTTTTTATA
1 -TTTTT-TA
36792 TTTTTTA
1 TTTTTTA
36799 TTGTATTT-
1 TT-T-TTTA
*
36807 TTGTTTA
1 TTTTTTA
*
36814 TTTTATA
1 TTTTTTA
*
36821 TTTTTTGT
1 TTTTTT-A
36829 TTTGCTTTAA
1 TTT--TTT-A
36839 TATTTTTA
1 T-TTTTTA
36847 TTTTTTA
1 TTTTTTA
*
36854 TTTCTTTC
1 TTT-TTTA
36862 TTTATTTA
1 TTT-TTTA
36870 TATTTT
1 T-TTTT
36876 CATAAATTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 23
0.71 0.11 0.18
Matches are distributed among these distances:
6 3 0.03
7 37 0.42
8 29 0.33
9 14 0.16
10 4 0.04
11 2 0.02
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.75
Consensus pattern (7 bp):
TTTTTTA
Found at i:37023 original size:19 final size:19
Alignment explanation
Indices: 36992--37042 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
36982 CGTTAACTCC
* *
36992 TTTTCCTTT-TTTTACATT
1 TTTTTCTTTGTTTTACACT
*
37010 TTTTTTTTTGTTTT-CACT
1 TTTTTCTTTGTTTTACACT
37028 TTTTTCTTTGTTTTA
1 TTTTTCTTTGTTTTA
37043 AAATTTTCTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTTCTTTGTTTTACACT
Found at i:37214 original size:17 final size:17
Alignment explanation
Indices: 37179--37214 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
37169 TTACACTTCC
* *
37179 TTATTTTGTTTTTATTT
1 TTATTTTGTTTTAACTT
37196 TTATTTTGTTTTAACTT
1 TTATTTTGTTTTAACTT
37213 TT
1 TT
37215 CCCTCTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (17 bp):
TTATTTTGTTTTAACTT
Found at i:37773 original size:12 final size:12
Alignment explanation
Indices: 37756--37805 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
37746 AATTAAAATC
*
37756 ATCTTGTATTTT
1 ATCTTGTAATTT
*
37768 ATCTTGAAATTT
1 ATCTTGTAATTT
*
37780 AT-TT-TTATTT
1 ATCTTGTAATTT
*
37790 ATCGTGTAATTT
1 ATCTTGTAATTT
37802 ATCT
1 ATCT
37806 AATTAACAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 6 0.21
11 3 0.10
12 20 0.69
ACGTcount: A:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
ATCTTGTAATTT
Found at i:37933 original size:59 final size:60
Alignment explanation
Indices: 37821--37938 Score: 134
Period size: 59 Copynumber: 2.0 Consensus size: 60
37811 ACAAAATTAT
*** * *
37821 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTATTTTATTTATTAT-TTTGG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
* *
37880 ATTGTATAATATTTATCTTTTATTTGATACAATTT-G-TTAAGAGATAATAATTATCTTTG
1 ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATT-A-AGATAATAATTATCTTTG
37939 TTATTTTCTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
57 2 0.04
58 2 0.04
59 41 0.84
60 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.55
Consensus pattern (60 bp):
ATTGTATAATATTTATCTTTTATTTAATAAAATTTGGATTAAGATAATAATTATCTTTGG
Found at i:38534 original size:30 final size:28
Alignment explanation
Indices: 38493--38548 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
38483 TTTTATCCAC
*
38493 ACTTCTTTCTTTTGTTTTTATTTTTTATTA
1 ACTTCTTTC-TTT-TTTTAATTTTTTATTA
*
38523 ACTTTTTTCTTTTTTTAATTTTTTAT
1 ACTTCTTTCTTTTTTTAATTTTTTAT
38549 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 3 0.12
30 8 0.33
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (28 bp):
ACTTCTTTCTTTTTTTAATTTTTTATTA
Found at i:39187 original size:24 final size:22
Alignment explanation
Indices: 39131--39187 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
39121 TGAACTTCCC
39131 TTTTGATTTTATTTATATTTTG
1 TTTTGATTTTATTTATATTTTG
*
39153 TATTGACTTTTATTT-TACTTTTTG
1 TTTTGA-TTTTATTTATA--TTTTG
39177 TCTTTGATTTT
1 T-TTTGATTTT
39188 TTATGTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 7 0.24
23 8 0.28
24 10 0.34
25 4 0.14
ACGTcount: A:0.16, C:0.05, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTGATTTTATTTATATTTTG
Found at i:39318 original size:15 final size:16
Alignment explanation
Indices: 39300--39338 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
39290 ATCGTTTTAT
39300 ATTTTTTATTCTC-TA
1 ATTTTTTATTCTCTTA
*
39315 ATTTTTTATTTTCTTA
1 ATTTTTTATTCTCTTA
*
39331 CTTTTTTA
1 ATTTTTTA
39339 CTTTTTGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTTATTCTCTTA
Found at i:39335 original size:16 final size:15
Alignment explanation
Indices: 39300--39343 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
39290 ATCGTTTTAT
*
39300 ATTTTTTATTCTCTA
1 ATTTTTTATTTTCTA
39315 ATTTTTTATTTTCTTA
1 ATTTTTTATTTTC-TA
*
39331 CTTTTTTACTTTT
1 ATTTTTTA-TTTT
39344 TGTTTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 12 0.48
16 9 0.36
17 4 0.16
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTTTTATTTTCTA
Found at i:39400 original size:8 final size:7
Alignment explanation
Indices: 39294--39542 Score: 57
Period size: 8 Copynumber: 33.4 Consensus size: 7
39284 CATTTTATCG
*
39294 TTTTATA
1 TTTTTTA
39301 TTTTTTA
1 TTTTTTA
* *
39308 TTCTCTAA
1 TT-TTTTA
39316 TTTTTTA
1 TTTTTTA
39323 TTTTCTTA
1 TTTT-TTA
39331 CTTTTTTA
1 -TTTTTTA
*
39339 CTTTTTGTT
1 -TTTTT-TA
39348 TTTGTTTA
1 TTT-TTTA
39356 -TTTTTA
1 TTTTTTA
* *
39362 ATTGTTA
1 TTTTTTA
39369 TTTTTTTA
1 -TTTTTTA
*
39377 GTATTTTA
1 -TTTTTTA
39385 --TTTTA
1 TTTTTTA
39390 TTTTTTCA
1 TTTTTT-A
39398 TTTATATTAAA
1 TTT-T-TT--A
39409 TTTTTTTCAA
1 -TTTTTT--A
39419 TTTTTGTA
1 TTTTT-TA
*
39427 TTTTTGA
1 TTTTTTA
**
39434 TTCATTA
1 TTTTTTA
39441 TTTTTTA
1 TTTTTTA
*
39448 TTATCTTA
1 TT-TTTTA
**
39456 CCTTTTA
1 TTTTTTA
39463 TATTTTTA
1 T-TTTTTA
*
39471 --TTGTA
1 TTTTTTA
39476 TTTTTGT-
1 TTTTT-TA
39483 TTCTTTTA
1 TT-TTTTA
39491 TTTTTT-
1 TTTTTTA
*
39497 TTGTTTA
1 TTTTTTA
**
39504 CTTTAATA
1 -TTTTTTA
*
39512 TTGTTTTC
1 TT-TTTTA
39520 TTATTTTA
1 TT-TTTTA
39528 --TTTTA
1 TTTTTTA
39533 TTTTTTA
1 TTTTTTA
39540 TTT
1 TTT
39543 CTTTCTTTAT
Statistics
Matches: 178, Mismatches: 37, Indels: 54
0.66 0.14 0.20
Matches are distributed among these distances:
5 14 0.08
6 9 0.05
7 61 0.34
8 69 0.39
9 13 0.07
10 7 0.04
11 2 0.01
12 3 0.02
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.73
Consensus pattern (7 bp):
TTTTTTA
Found at i:39497 original size:18 final size:21
Alignment explanation
Indices: 39466--39507 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 21
39456 CCTTTTATAT
39466 TTTTATTGTATTTTTGTTT-C
1 TTTTATTGTATTTTTGTTTAC
39486 TTTTATT-T-TTTTTGTTTAC
1 TTTTATTGTATTTTTGTTTAC
39505 TTT
1 TTT
39508 AATATTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
19 5 0.24
20 7 0.33
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.79
Consensus pattern (21 bp):
TTTTATTGTATTTTTGTTTAC
Found at i:39561 original size:24 final size:24
Alignment explanation
Indices: 39516--39561 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39506 TTAATATTGT
* *
39516 TTTCTTATTTTATTTTATTTTTTA
1 TTTCTTATTTTATTTAAATTTTTA
39540 TTTCTT-TCTTTATTTAAATTTT
1 TTTCTTAT-TTTATTTAAATTTT
39562 CATAAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.05
24 18 0.95
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTCTTATTTTATTTAAATTTTTA
Found at i:39915 original size:7 final size:7
Alignment explanation
Indices: 39890--40012 Score: 59
Period size: 8 Copynumber: 15.7 Consensus size: 7
39880 AATTTTGTCT
39890 TTTTTTA
1 TTTTTTA
**
39897 TTCATTA
1 TTTTTTA
39904 TTTTTTTA
1 -TTTTTTA
39912 TTTTCTTA
1 TTTT-TTA
39920 CTTTTTATA
1 -TTTTT-TA
39929 TTTTTTA
1 TTTTTTA
39936 TTGTATTT-
1 TT-T-TTTA
*
39944 TTGTTTA
1 TTTTTTA
*
39951 TTTTATA
1 TTTTTTA
*
39958 TTTTTTGT
1 TTTTTT-A
39966 TTTGCTTTAA
1 TTT--TTT-A
39976 TATTTTTA
1 T-TTTTTA
39984 TTTTTTA
1 TTTTTTA
*
39991 TTTCTTTC
1 TTT-TTTA
39999 TTTATTTA
1 TTT-TTTA
40007 TATTTT
1 T-TTTT
40013 CATAAATTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 25
0.70 0.11 0.20
Matches are distributed among these distances:
6 3 0.03
7 32 0.36
8 34 0.38
9 14 0.16
10 4 0.04
11 2 0.02
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (7 bp):
TTTTTTA
Found at i:39924 original size:17 final size:18
Alignment explanation
Indices: 39888--39932 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39878 TCAATTTTGT
39888 CTTTTTTTA--TTCATTA
1 CTTTTTTTATTTTCATTA
39904 -TTTTTTTATTTTC-TTA
1 CTTTTTTTATTTTCATTA
*
39920 CTTTTTATATTTT
1 CTTTTTTTATTTT
39933 TTATTGTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 8 0.32
16 3 0.12
17 14 0.56
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (18 bp):
CTTTTTTTATTTTCATTA
Found at i:40153 original size:21 final size:21
Alignment explanation
Indices: 40137--40178 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40127 CCTTTTCCTT
*
40137 TTTTTACTTTTTTTTTTTTTG
1 TTTTCACTTTTTTTTTTTTTG
*
40158 TTTTCACTTTTTCTTTGTTTT
1 TTTTCACTTTTT-TTTTTTTT
40179 AAAATTTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.81
Consensus pattern (21 bp):
TTTTCACTTTTTTTTTTTTTG
Found at i:41824 original size:9 final size:9
Alignment explanation
Indices: 41785--41841 Score: 53
Period size: 9 Copynumber: 6.2 Consensus size: 9
41775 TTTTCTTTTC
*
41785 TTTTTTTCA
1 TTTTTTTAA
*
41794 TTTTTATTAG
1 TTTTT-TTAA
41804 TTTTTTGT-A
1 TTTTTT-TAA
41813 TTTTTTTAA
1 TTTTTTTAA
* *
41822 TTTTCTTAC
1 TTTTTTTAA
41831 TTTTTTTAA
1 TTTTTTTAA
41840 TT
1 TT
41842 GCGTTTTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
8 1 0.03
9 29 0.76
10 8 0.21
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:41825 original size:18 final size:18
Alignment explanation
Indices: 41793--41864 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 18
41783 TCTTTTTTTC
*
41793 ATTTTTATTAGTTTTTTGT
1 ATTTTT-TTAATTTTTTGT
*
41812 ATTTTTTTAATTTTCT-T
1 ATTTTTTTAATTTTTTGT
41829 ACTTTTTTTAATTGCGTTTTGT
1 A-TTTTTTTAATT---TTTTGT
*
41851 -TATTTTTAATTTTT
1 ATTTTTTTAATTTTT
41865 CTCTTTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.11
18 19 0.43
19 6 0.14
20 10 0.23
21 3 0.07
22 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.07, T:0.72
Consensus pattern (18 bp):
ATTTTTTTAATTTTTTGT
Found at i:42322 original size:24 final size:23
Alignment explanation
Indices: 42265--42321 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
42255 TGAACTTCCC
42265 TTTTGATTTTATTTATAATTTTG
1 TTTTGATTTTATTTATAATTTTG
* *
42288 TATTGACTTTTATTT-TACTTTTG
1 TTTTGA-TTTTATTTATAATTTTG
42311 TCTTTGATTTT
1 T-TTTGATTTT
42322 TTATGTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.18, C:0.05, G:0.09, T:0.68
Consensus pattern (23 bp):
TTTTGATTTTATTTATAATTTTG
Found at i:43074 original size:17 final size:17
Alignment explanation
Indices: 43047--43100 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
43037 TTTGGGGTCT
43047 TTTTTTA-TTTCATTTA
1 TTTTTTATTTTCATTTA
43063 TTTTTTATTTTC--TTA
1 TTTTTTATTTTCATTTA
*
43078 CTTTTTATATTTTTATTGTA
1 -TTTTT-TATTTTCATT-TA
43098 TTT
1 TTT
43101 GTTGTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
15 3 0.10
16 12 0.39
17 10 0.32
19 4 0.13
20 2 0.06
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTTTATTTTCATTTA
Found at i:43092 original size:8 final size:7
Alignment explanation
Indices: 43047--43125 Score: 52
Period size: 7 Copynumber: 10.6 Consensus size: 7
43037 TTTGGGGTCT
43047 TTTTTTA
1 TTTTTTA
43054 TTTCATTTA
1 TTT--TTTA
43063 TTTTTTA
1 TTTTTTA
43070 TTTTCTTA
1 TTTT-TTA
*
43078 CTTTTTA
1 TTTTTTA
43085 TATTTTTA
1 T-TTTTTA
*
43093 TTGTATTTG
1 TT-T-TTTA
*
43102 TTGTTT-
1 TTTTTTA
*
43108 TTTTATA
1 TTTTTTA
*
43115 TTTTTTG
1 TTTTTTA
43122 TTTT
1 TTTT
43126 GCCTTTAAAT
Statistics
Matches: 57, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
6 4 0.07
7 27 0.47
8 14 0.25
9 12 0.21
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (7 bp):
TTTTTTA
Found at i:43505 original size:17 final size:17
Alignment explanation
Indices: 43470--43505 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
43460 TTACACTTCC
* *
43470 TTATTTTGTTTTTATTT
1 TTATTTTGTTTTAACTT
43487 TTATTTTGTTTTAACTT
1 TTATTTTGTTTTAACTT
43504 TT
1 TT
43506 CCCTCTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.78
Consensus pattern (17 bp):
TTATTTTGTTTTAACTT
Found at i:44070 original size:12 final size:12
Alignment explanation
Indices: 44055--44106 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
44045 CTAATTAAAA
*
44055 TATCTTGTATTT
1 TATCTTGTAATT
*
44067 TATCTTGAAATT
1 TATCTTGTAATT
* *
44079 TAT-TTTTTATT
1 TATCTTGTAATT
*
44090 TATCGTGTAATT
1 TATCTTGTAATT
44102 TATCT
1 TATCT
44107 AATTAACAAA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
11 8 0.27
12 22 0.73
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (12 bp):
TATCTTGTAATT
Found at i:44823 original size:30 final size:28
Alignment explanation
Indices: 44782--44837 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
44772 TTTTATCCAC
*
44782 ACTTCTTTCTTTTGTTTTTATTTTTTATTA
1 ACTTCTTTC-TTT-TTTTAATTTTTTATTA
*
44812 ACTTTTTTCTTTTTTTAATTTTTTAT
1 ACTTCTTTCTTTTTTTAATTTTTTAT
44838 CATTGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 3 0.12
30 8 0.33
ACGTcount: A:0.14, C:0.09, G:0.02, T:0.75
Consensus pattern (28 bp):
ACTTCTTTCTTTTTTTAATTTTTTATTA
Found at i:44834 original size:34 final size:33
Alignment explanation
Indices: 44710--44834 Score: 78
Period size: 34 Copynumber: 3.7 Consensus size: 33
44700 GTACTCTTTT
* *
44710 ACTTTTTATCTTATTTT-TTTTTATTTTTTTCTTA
1 ACTTTTT-TCTTTTTTTATTTTTA-TTTTTTATTA
** * *
44744 AGGTTTTTCTTCTTTTTAATTTGTTGTTTTTTATCCA
1 ACTTTTTTCTT-TTTTT-ATTT-TTATTTTTTAT-TA
* *
44781 CACTTCTTTC---TTTTGTTTTTATTTTTTATTA
1 -ACTTTTTTCTTTTTTTATTTTTATTTTTTATTA
44812 ACTTTTTTCTTTTTTTAATTTTT
1 ACTTTTTTCTTTTTTT-ATTTTT
44835 TATCATTGAT
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
30 8 0.12
31 1 0.01
32 10 0.15
33 11 0.16
34 18 0.27
36 10 0.15
37 3 0.04
38 6 0.09
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.72
Consensus pattern (33 bp):
ACTTTTTTCTTTTTTTATTTTTATTTTTTATTA
Done.