Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167891.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_158, 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: 63048
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:344 original size:22 final size:21
Alignment explanation
Indices: 316--361 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
306 AATCTTCCTT
*
316 AATTCTAGGGATACAAATACTA
1 AATTCTAGAGATACAAATA-TA
*
338 AATTCTAGAGATGCAAATATA
1 AATTCTAGAGATACAAATATA
359 AAT
1 AAT
362 ATACAGATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (21 bp):
AATTCTAGAGATACAAATATA
Found at i:4238 original size:22 final size:22
Alignment explanation
Indices: 4210--4253 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
4200 CTAAATCTTC
*
4210 CTTAATTCTAGGGATACAAATA
1 CTTAATTCTAGAGATACAAATA
4232 CTTAATTCTAGAGATACAAATA
1 CTTAATTCTAGAGATACAAATA
4254 TAAATATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (22 bp):
CTTAATTCTAGAGATACAAATA
Found at i:7293 original size:28 final size:24
Alignment explanation
Indices: 7244--7291 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
7234 ATATGTTTTT
7244 TTACTTACATTATTTAGGAAAGAA
1 TTACTTACATTATTTAGGAAAGAA
7268 TTACTTACATTATTTAGGAAAGAA
1 TTACTTACATTATTTAGGAAAGAA
7292 AGGAAGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (24 bp):
TTACTTACATTATTTAGGAAAGAA
Found at i:9209 original size:72 final size:72
Alignment explanation
Indices: 9118--9261 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
9108 TTTTGAATTA
*
9118 GGTCCAAACAAATATATTTTTATATTTTTATTCTTGATTTGAGCTTGCTATTTTATGTGTGGGTG
1 GGTCCAAACAAATATATTTTTATATTTTTATTCTTGATTTGAGCTTGCTATTTTACGTGTGGGTG
9183 TTGTGTG
66 TTGTGTG
* * * *
9190 GGTCGAAACAAATATATTTTTATATTTTTATTTTTGATTTGAGCTTGTTATTTTGCGTGTGGGTG
1 GGTCCAAACAAATATATTTTTATATTTTTATTCTTGATTTGAGCTTGCTATTTTACGTGTGGGTG
9255 TTGTGTG
66 TTGTGTG
9262 TGCGTGTTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.20, C:0.07, G:0.22, T:0.51
Consensus pattern (72 bp):
GGTCCAAACAAATATATTTTTATATTTTTATTCTTGATTTGAGCTTGCTATTTTACGTGTGGGTG
TTGTGTG
Found at i:9344 original size:58 final size:58
Alignment explanation
Indices: 9268--9385 Score: 166
Period size: 58 Copynumber: 2.0 Consensus size: 58
9258 TGTGTGCGTG
* * * *
9268 TTGATTTCTCAATTATTTCTTAACAAAATCTCATTTGGATTAAGT-GACCCCTCAATTT
1 TTGATTTCCCAATGATTTCCTAACAAAAGCTCATTTGGATTAAGTAG-CCCCTCAATTT
* *
9326 TTGATTTCCCAATGATTTCCTAACAGAAGCTTATTTGGATTAAGTAGCCCCTCAATTT
1 TTGATTTCCCAATGATTTCCTAACAAAAGCTCATTTGGATTAAGTAGCCCCTCAATTT
9384 TT
1 TT
9386 TCAACAAATT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 52 0.98
59 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (58 bp):
TTGATTTCCCAATGATTTCCTAACAAAAGCTCATTTGGATTAAGTAGCCCCTCAATTT
Found at i:9625 original size:32 final size:31
Alignment explanation
Indices: 9589--9669 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 31
9579 GTATATGAAG
*
9589 AAAGAAAGACAAGATATATATATAGAAAGTAA
1 AAAGAAAGACAAGATATATATAAAGAAAG-AA
* * * *
9621 AAAGAAAAAAAATATAAATATAAAGAAAGAA
1 AAAGAAAGACAAGATATATATAAAGAAAGAA
*
9652 AGA-AAAGACAAGAT-TATA
1 AAAGAAAGACAAGATATATA
9670 AAACTACTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
29 3 0.08
30 8 0.21
31 4 0.10
32 24 0.62
ACGTcount: A:0.68, C:0.02, G:0.14, T:0.16
Consensus pattern (31 bp):
AAAGAAAGACAAGATATATATAAAGAAAGAA
Found at i:10313 original size:33 final size:33
Alignment explanation
Indices: 10254--10318 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
10244 ATGAATTTTT
* *
10254 GAAAACTTCTCTAATGTATTGGAAATTTATTTC
1 GAAAACTTCTCTAATGTATTGAAAATTCATTTC
10287 GAAAACTTCT-TAAT-TATATCGAAAATTCATTT
1 GAAAACTTCTCTAATGTAT-T-GAAAATTCATTT
10319 ATGGAAAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.11
32 5 0.18
33 20 0.71
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (33 bp):
GAAAACTTCTCTAATGTATTGAAAATTCATTTC
Found at i:11670 original size:16 final size:16
Alignment explanation
Indices: 11631--11674 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
11621 ATTTTGTTTT
*
11631 CTTATTTAATT-TTTA
1 CTTATTTATTTATTTA
*
11646 -TTATATATTTATTTA
1 CTTATTTATTTATTTA
11661 CTTATTTATTTATT
1 CTTATTTATTTATT
11675 AGAAAAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 12 0.50
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
CTTATTTATTTATTTA
Found at i:13878 original size:2 final size:2
Alignment explanation
Indices: 13871--13897 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13861 CTCTAGGGTT
13871 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
13898 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:13902 original size:2 final size:2
Alignment explanation
Indices: 13897--13932 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13887 ACACACACAC
13897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13933 GCACACCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16055 original size:22 final size:22
Alignment explanation
Indices: 16030--16166 Score: 61
Period size: 22 Copynumber: 6.3 Consensus size: 22
16020 AATATACTTC
16030 TAAATTATTAATGATTTATTAT
1 TAAATTATTAATGATTTATTAT
* *
16052 TAAATTAGCTT--TAATTTATTAC
1 TAAATTA--TTAATGATTTATTAT
* * *
16074 TAATTTATGAAT-ATTTTACTAT
1 TAAATTATTAATGA-TTTATTAT
* * *
16096 TAAGTTA-TAACTAATTTACTAT
1 TAAATTATTAA-TGATTTATTAT
** *
16118 TAAATTATGGATGATTT-TATAA
1 TAAATTATTAATGATTTAT-TAT
** *
16140 TAAATTGCTAAAGATTTATTA-
1 TAAATTATTAATGATTTATTAT
16161 TAAATT
1 TAAATT
16167 TATAATTAAT
Statistics
Matches: 86, Mismatches: 19, Indels: 21
0.68 0.15 0.17
Matches are distributed among these distances:
20 1 0.01
21 9 0.10
22 71 0.83
23 3 0.03
24 2 0.02
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
TAAATTATTAATGATTTATTAT
Found at i:16080 original size:33 final size:33
Alignment explanation
Indices: 16034--16124 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 33
16024 TACTTCTAAA
* * *
16034 TTATTAATGATTTATTATTAAATTAGCT-TTAAT
1 TTATTACTAATTTATTATTAAATTA-CTATTAAG
* * **
16067 TTATTACTAATTTATGAATATTTTACTATTAAG
1 TTATTACTAATTTATTATTAAATTACTATTAAG
* *
16100 TTATAACTAATTTACTATTAAATTA
1 TTATTACTAATTTATTATTAAATTA
16125 TGGATGATTT
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
32 2 0.05
33 42 0.95
ACGTcount: A:0.38, C:0.05, G:0.04, T:0.52
Consensus pattern (33 bp):
TTATTACTAATTTATTATTAAATTACTATTAAG
Found at i:16169 original size:11 final size:11
Alignment explanation
Indices: 16153--16191 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16143 ATTGCTAAAG
*
16153 ATTTATTATAA
1 ATTTATTATTA
*
16164 ATTTATAATTA
1 ATTTATTATTA
*
16175 ATTTATTGTTA
1 ATTTATTATTA
16186 ATTTAT
1 ATTTAT
16192 CAATAAATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:28775 original size:15 final size:14
Alignment explanation
Indices: 28755--28786 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
28745 TATCATCATT
28755 TTTAT-TTGTGAAA
1 TTTATATTGTGAAA
28768 TTTATATTGTGAAA
1 TTTATATTGTGAAA
28782 TTTAT
1 TTTAT
28787 GTGTCTTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (14 bp):
TTTATATTGTGAAA
Found at i:33952 original size:76 final size:75
Alignment explanation
Indices: 33814--33963 Score: 273
Period size: 76 Copynumber: 2.0 Consensus size: 75
33804 AAGTGGTCCC
*
33814 TCAATTTTTTTCAACAATTCTAAAGTATGAGAAAAAGAATTTTTACTTCTTTCCTCTATTATCAT
1 TCAATTTTTTTCAACAATTCTAAAGTATGAGAAAAAGAATTTCTACTTCTTTCCTCTATTATCAT
33879 ATCCAACCTT
66 ATCCAACCTT
*
33889 TCAATTTCTTTTTAACAATTCTAAAGTATGAGAAAAAGAATTTCTACTTCTTTCCTCTATTATCA
1 TCAATTT-TTTTCAACAATTCTAAAGTATGAGAAAAAGAATTTCTACTTCTTTCCTCTATTATCA
33954 TATCCAACCT
65 TATCCAACCT
33964 GTTCTCCAAA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
75 7 0.10
76 65 0.90
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.42
Consensus pattern (75 bp):
TCAATTTTTTTCAACAATTCTAAAGTATGAGAAAAAGAATTTCTACTTCTTTCCTCTATTATCAT
ATCCAACCTT
Found at i:34133 original size:28 final size:30
Alignment explanation
Indices: 34095--34163 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
34085 ATCGTATATG
*
34095 AAGAAAGAAAGAAAAGACAT-ATATAAAGA
1 AAGAAAGAAAGAAAAAACATAATATAAAGA
34124 AAGAAA-AAAGAAAAAACATAAATATAAAGA
1 AAGAAAGAAAGAAAAAACAT-AATATAAAGA
34154 AAGAAAGAAA
1 AAGAAAGAAA
34164 AGATAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
28 12 0.33
29 6 0.17
30 15 0.42
31 3 0.08
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (30 bp):
AAGAAAGAAAGAAAAAACATAATATAAAGA
Found at i:34424 original size:2 final size:2
Alignment explanation
Indices: 34417--34447 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
34407 CTAACACGTG
*
34417 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34448 AGCCAACAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:34861 original size:34 final size:34
Alignment explanation
Indices: 34779--34853 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
34769 TTAATTATAT
* * * * *
34779 CAAAAATTCATTTATGGAAAGTATTGCAGTTATC
1 CAAAAATACATTTTTAGAAAGCATTGCAATTATC
34813 CAAAAATACATTTTTAGAAAGCATTGCAATTATC
1 CAAAAATACATTTTTAGAAAGCATTGCAATTATC
*
34847 CATAAAT
1 CAAAAAT
34854 GTATTTTTGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.33
Consensus pattern (34 bp):
CAAAAATACATTTTTAGAAAGCATTGCAATTATC
Found at i:39548 original size:21 final size:21
Alignment explanation
Indices: 39527--39652 Score: 89
Period size: 21 Copynumber: 6.2 Consensus size: 21
39517 GTAAAATTTA
39527 ATAACTTTTGATATAA-TTT-
1 ATAACTTTTGATATAATTTTG
* *
39546 -TAA-TTTTAATAAAATTTTG
1 ATAACTTTTGATATAATTTTG
* * * * *
39565 GTGACCTTCGATATAATTTTC
1 ATAACTTTTGATATAATTTTG
*
39586 ATAACTTATGATATAATTTTG
1 ATAACTTTTGATATAATTTTG
* * *
39607 GTAACTATTGATACAATTTTG
1 ATAACTTTTGATATAATTTTG
* * * *
39628 ATAATTTTTTATAAAATTTTA
1 ATAACTTTTGATATAATTTTG
39649 ATAA
1 ATAA
39653 GCTCTTAATG
Statistics
Matches: 79, Mismatches: 24, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
17 9 0.11
18 6 0.08
20 2 0.03
21 62 0.78
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.48
Consensus pattern (21 bp):
ATAACTTTTGATATAATTTTG
Found at i:39646 original size:42 final size:42
Alignment explanation
Indices: 39549--39647 Score: 101
Period size: 42 Copynumber: 2.4 Consensus size: 42
39539 ATAATTTTAA
* *
39549 TTTTAATAAAATTTTGGTGACCTTCGATATAATTTTCATAAC
1 TTTTAATAAAATTTTGGTGAACTTCGATACAATTTTCATAAC
* * * * * *
39591 TTATGATATAATTTTGGT-AACTATTGATACAATTTTGATAAT
1 TTTTAATAAAATTTTGGTGAACT-TCGATACAATTTTCATAAC
*
39633 TTTTTATAAAATTTT
1 TTTTAATAAAATTTT
39648 AATAAGCTCT
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 3 0.07
42 42 0.93
ACGTcount: A:0.34, C:0.07, G:0.09, T:0.49
Consensus pattern (42 bp):
TTTTAATAAAATTTTGGTGAACTTCGATACAATTTTCATAAC
Found at i:40180 original size:11 final size:11
Alignment explanation
Indices: 40164--40202 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
40154 ATTACTAAAT
*
40164 ATTTATTATAA
1 ATTTATTATTA
*
40175 ATTTATAATTA
1 ATTTATTATTA
40186 ATTTATTATTA
1 ATTTATTATTA
40197 ATTTAT
1 ATTTAT
40203 CAATAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTATTATTA
Found at i:40773 original size:21 final size:22
Alignment explanation
Indices: 40749--40790 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
40739 AGTTATCAAT
40749 TTTAAATTTATAAC-ATTTTTA
1 TTTAAATTTATAACAATTTTTA
* *
40770 TTTAATTTTATCACAATTTTT
1 TTTAAATTTATAACAATTTTT
40791 CATTAGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTAAATTTATAACAATTTTTA
Found at i:50473 original size:19 final size:19
Alignment explanation
Indices: 50430--50476 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
50420 CTTTTTTCTC
*
50430 ATTTTTATTACTTATTTTT
1 ATTTTTATTACTTAATTTT
* *
50449 A-ATTTATTAGTTAATTTT
1 ATTTTTATTACTTAATTTT
50467 ATTTTTATTA
1 ATTTTTATTA
50477 AAAGAAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTTTTATTACTTAATTTT
Found at i:51747 original size:3 final size:3
Alignment explanation
Indices: 51741--51783 Score: 59
Period size: 3 Copynumber: 13.7 Consensus size: 3
51731 TAAAGAAAGA
*
51741 AAT AAT AAT AAT AAT AAT AAAT ACAT AAA AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT AAT AAT AAT AA
51784 AATGGTGTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:51773 original size:20 final size:19
Alignment explanation
Indices: 51740--51780 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
51730 ATAAAGAAAG
*
51740 AAATAATAATAATAATAAT
1 AAATAATAAAAATAATAAT
51759 AAATACATAAAAATAATAAT
1 AAATA-ATAAAAATAATAAT
51779 AA
1 AA
51781 TAAAATGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
AAATAATAAAAATAATAAT
Found at i:51977 original size:50 final size:49
Alignment explanation
Indices: 51905--52136 Score: 251
Period size: 47 Copynumber: 4.8 Consensus size: 49
51895 TTTTTAATTT
* * *
51905 AAAAGCTCCTTTAATTAAAGGCTTAACAACTTTAAAATTCATCATCTT-A
1 AAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAATTC-TCATCTTGA
* * * *
51954 GGAAAGCTCCTCTAAGTAGAGGCTCAACACCTTTAAAA-T-TCATTTTGA
1 -AAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAATTCTCATCTTGA
* * *
52002 AAAAGCTCTTATAAGTAGAGGCTTAATAACTTTAAAATT-TCATCTTG-
1 AAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAATTCTCATCTTGA
* *
52049 AAAAGCTCTTCTAAGTAGAAGCTTAACAACTTTAAAATTCTCATCTTAGA
1 AAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAATTCTCATCTT-GA
* * * *
52099 GAAA-CTCCTCTAAGCAGAGGCTCAATAACTTTAAAATT
1 AAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAATT
52137 ACACTATTGA
Statistics
Matches: 154, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
47 73 0.47
48 16 0.10
49 31 0.20
50 34 0.22
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (49 bp):
AAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAATTCTCATCTTGA
Found at i:52369 original size:99 final size:98
Alignment explanation
Indices: 52254--52500 Score: 300
Period size: 100 Copynumber: 2.5 Consensus size: 98
52244 CAAATGATTT
* ** * ** *
52254 TTTAACACTCAAATATCACCATCGAGAAAATATAAATGACTTTGGATA-CCATCATCGAAAGAAA
1 TTTAACACTCAAATATCACCATCGAGAATATGCAAATGACTTCGGATACCCA-CA-AAAAAAAAA
* *
52318 CTTGGATATCATCATTGAGAAAAA-GTAATTCAAGC
64 CTCGCATATCATCATTGA-AAAAATGTAATTCAAGC
* * * *
52353 TTTAACACTTAGATATCACCACCGAGAATATGCAAATGACTTCGAATATCGCCACAAAAAAAAAA
1 TTTAACACTCAAATATCACCATCGAGAATATGCAAATGACTTCGGATA-C-CCACAAAAAAAAAA
52418 CTCGCATATCATCATTGAAAAAATGTAATTCAAGC
64 CTCGCATATCATCATTGAAAAAATGTAATTCAAGC
* *
52453 TTTAACACTCAAATATCACTATCTAGAATATGCAAATGACTTCGGATA
1 TTTAACACTCAAATATCACCATCGAGAATATGCAAATGACTTCGGATA
52501 TCGTCACTGA
Statistics
Matches: 125, Mismatches: 19, Indels: 7
0.83 0.13 0.05
Matches are distributed among these distances:
99 45 0.36
100 75 0.60
101 2 0.02
102 3 0.02
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (98 bp):
TTTAACACTCAAATATCACCATCGAGAATATGCAAATGACTTCGGATACCCACAAAAAAAAAACT
CGCATATCATCATTGAAAAAATGTAATTCAAGC
Found at i:52523 original size:75 final size:75
Alignment explanation
Indices: 52423--52687 Score: 341
Period size: 75 Copynumber: 3.5 Consensus size: 75
52413 AAAAACTCGC
* * * * * * *
52423 ATATCATCATTGAAAAAATGTAATTCAAGCTTTAACACTCAAATATCACTATCTAGAATATGCAA
1 ATATCACCATTGAAAAAATGCAATTCAAACTTTGACACTCAAATATCACCACCGAGAATATGCAA
52488 ATGACTTCGG
66 ATGACTTCGG
** * * * * * *
52498 ATATCGTCACTGAGAAAATGCAATTCAAACCTTGACACCCGAATATCACCACCGAGAATATACAA
1 ATATCACCATTGAAAAAATGCAATTCAAACTTTGACACTCAAATATCACCACCGAGAATATGCAA
52563 ATGACTTCGG
66 ATGACTTCGG
* *
52573 ATATCACCATTGAAAAAATGCAATTCAAACTTTGACACTCAGATATCACCACCGAGAATATGAAA
1 ATATCACCATTGAAAAAATGCAATTCAAACTTTGACACTCAAATATCACCACCGAGAATATGCAA
*
52638 ATGACTTCAG
66 ATGACTTCGG
* * *
52648 ATATCACCATCGAGAAAAGGCAATTCAAACTTTGACACTC
1 ATATCACCATTGAAAAAATGCAATTCAAACTTTGACACTC
52688 GAAAAATGCA
Statistics
Matches: 163, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 163 1.00
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.25
Consensus pattern (75 bp):
ATATCACCATTGAAAAAATGCAATTCAAACTTTGACACTCAAATATCACCACCGAGAATATGCAA
ATGACTTCGG
Found at i:52693 original size:28 final size:29
Alignment explanation
Indices: 52657--52714 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
52647 GATATCACCA
52657 TCGAGAAAAGGCAATTCAAACTTTGACAC
1 TCGAGAAAAGGCAATTCAAACTTTGACAC
*
52686 TCGA-AAAATGCAATTCAAACTTTGACAC
1 TCGAGAAAAGGCAATTCAAACTTTGACAC
52714 T
1 T
52715 TATATATCAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (29 bp):
TCGAGAAAAGGCAATTCAAACTTTGACAC
Found at i:52724 original size:103 final size:103
Alignment explanation
Indices: 52586--52789 Score: 345
Period size: 103 Copynumber: 2.0 Consensus size: 103
52576 TCACCATTGA
52586 AAAAATGCAATTCAAACTTTGACACTCAGATATCACCACCGAGAATATGAAAATGACTTCAGATA
1 AAAAATGCAATTCAAACTTTGACACTCAGATATCACCACCGAGAATATGAAAATGACTTCAGATA
* *
52651 TCACCATCGAGAAAAGGCAATTCAAACTTTGACACTCG
66 TCACCACCGAGAAAAAGCAATTCAAACTTTGACACTCG
* * *
52689 AAAAATGCAATTCAAACTTTGACACTTATATATCACCACCGAGAATATGCAAATGACTTCAGATA
1 AAAAATGCAATTCAAACTTTGACACTCAGATATCACCACCGAGAATATGAAAATGACTTCAGATA
**
52754 TTGCCACCGAGAAAAAGCAATTCAAACTTTGACACT
66 TCACCACCGAGAAAAAGCAATTCAAACTTTGACACT
52790 TGGATATCAC
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 94 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.24
Consensus pattern (103 bp):
AAAAATGCAATTCAAACTTTGACACTCAGATATCACCACCGAGAATATGAAAATGACTTCAGATA
TCACCACCGAGAAAAAGCAATTCAAACTTTGACACTCG
Found at i:53523 original size:61 final size:60
Alignment explanation
Indices: 53399--53701 Score: 226
Period size: 60 Copynumber: 4.9 Consensus size: 60
53389 CATTTGGAAG
* * * *
53399 TTTTTA-TTTTAAGAAAAATTGATACTTT-AACTTTTCCTTCAAAAATATTTTTTTTATAA-
1 TTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCC-CCTAAAATATTTTTTATA-AAT
* * *
53458 TTTTTATTTTTAAGGAAAATTGGTACTTCCAACTTTTCCCCTAAAATATTTTTTAGAAAT
1 TTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAATATTTTTTATAAAT
** * * ***
53518 CTTTTTATTTGGAAGGGAAATTGATATTTTCAAC-TTT-CCCTAAAAATATTATATTT-TTTTT
1 -TTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCT-AAAATATT-T-TTTATAAAT
* *
53579 GTTACTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAATTTTTG
1 -TT--TTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAATATTTTTT-A----T-
53644 AAA-
57 AAAT
* * *
53647 ATTTTATTTTTAAGAAAAATTGATACTTTTAACTTTT-CCCTAAAAATATTATTTT
1 TTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCT-AAAATATT-TTTT
53702 TTTGGAATTT
Statistics
Matches: 192, Mismatches: 32, Indels: 33
0.75 0.12 0.13
Matches are distributed among these distances:
59 12 0.06
60 44 0.23
61 40 0.21
62 6 0.03
63 28 0.15
64 13 0.07
65 43 0.22
66 4 0.02
67 1 0.01
68 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (60 bp):
TTTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCCCTAAAATATTTTTTATAAAT
Found at i:53693 original size:65 final size:63
Alignment explanation
Indices: 53401--53704 Score: 235
Period size: 65 Copynumber: 4.9 Consensus size: 63
53391 TTTGGAAGTT
* * **
53401 TTTA-TTTTAAGAAAAATTGATAC-TTTAACTTTTCCTTCAAAAATA-T-TTTTTTTAT-AATT
1 TTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCT-AAAAATATTATTTTTTTTTGAAAC
* * ** *
53460 TTTATTTTTAAGGAAAATTGGTACTTCCAACTTTTCCCCT--AAA-A-TA--TTTTTTAGAAATC
1 TTTATTTTTAAGAAAAATTGATACTTTTAACTTTT-CCCTAAAAATATTATTTTTTTTTGAAA-C
** *
53519 TTT-TTATTTGGAAGGGAAATTGATA-TTTTCAAC-TTTCCCTAAAAATATTATATTTTTTTTGT
1 TTTATT-TTT--AAGAAAAATTGATACTTTT-AACTTTTCCCTAAAAATATTAT-TTTTTTTTGA
*
53581 TAC
61 AAC
* * *
53584 TTTATTTTTAAGGAAAATTGATACTTTCAACTTTT-CCTCGAAAATATT-TTTTAATTTTTGAAA
1 TTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCT-AAAAATATTATTTT--TTTTTG-AA
*
53647 AT
62 AC
53649 TTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCTAAAAATATTATTTTTTT
1 TTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCTAAAAATATTATTTTTTT
53705 GGAATTTTTA
Statistics
Matches: 194, Mismatches: 25, Indels: 47
0.73 0.09 0.18
Matches are distributed among these distances:
57 5 0.03
58 6 0.03
59 17 0.09
60 22 0.11
61 26 0.13
62 7 0.04
63 22 0.11
64 23 0.12
65 49 0.25
66 17 0.09
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (63 bp):
TTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCTAAAAATATTATTTTTTTTTGAAAC
Found at i:53696 original size:124 final size:121
Alignment explanation
Indices: 53400--53704 Score: 316
Period size: 124 Copynumber: 2.5 Consensus size: 121
53390 ATTTGGAAGT
* * *
53400 TTTTA-TTTTAAGAAAAATTGATAC-TTTAACTTTTCCTTCAAAAATATTTTTTTTATAATTTTT
1 TTTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCTAAAAAATATTTTTTTTATAATCTTT
* * *
53463 ATTTTTAAGGAAAATTGGTACTTCCAACTTTTCCCCTAAAATATTTTTTAGAAATCT
66 ATTTTTAAGGAAAATTGATACTTCCAACTTTTCCCCGAAAATATTTTTTAGAAA-CA
** ** **
53520 TTTTATTTGGAAGGGAAATTGATA-TTTTCAAC-TTTCCCTAAAAATATTATATTTTTTT-TGTT
1 TTTTATTTTTAAGAAAAATTGATACTTTT-AACTTTTCCCTAAAAA-A-TAT-TTTTTTTATAAT
* *
53582 ACTTTATTTTTAAGGAAAATTGATACTTTCAACTTTTCCTCGAAAATATTTTTTAATTTTTGAAA
62 -CTTTATTTTTAAGGAAAATTGATACTTCCAACTTTTCCCCGAAAATATTTTTT-A-----GAAA
53647 -A
120 CA
53648 TTTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCTAAAAATATTATTTTTTT
1 TTTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCTAAAAA-A-TATTTTTTT
53705 GGAATTTTTA
Statistics
Matches: 152, Mismatches: 18, Indels: 22
0.79 0.09 0.11
Matches are distributed among these distances:
120 5 0.03
121 27 0.18
122 4 0.03
123 5 0.03
124 55 0.36
125 1 0.01
128 29 0.19
129 22 0.14
130 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.50
Consensus pattern (121 bp):
TTTTATTTTTAAGAAAAATTGATACTTTTAACTTTTCCCTAAAAAATATTTTTTTTATAATCTTT
ATTTTTAAGGAAAATTGATACTTCCAACTTTTCCCCGAAAATATTTTTTAGAAACA
Found at i:53748 original size:3 final size:3
Alignment explanation
Indices: 53742--53816 Score: 77
Period size: 3 Copynumber: 25.7 Consensus size: 3
53732 AAAAAAGAAA
* * *
53742 AAT AAT AAT AA- AAT AA- AAC AA- AAT AAT AAT AAA AATT AAGG AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT
53785 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
53817 AACTTTAATG
Statistics
Matches: 63, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
2 8 0.13
3 51 0.81
4 4 0.06
ACGTcount: A:0.71, C:0.01, G:0.03, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:53750 original size:21 final size:20
Alignment explanation
Indices: 53724--53818 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 20
53714 ATTTTAGGAA
53724 AATAATTAAAAAAAGAAAAAT
1 AATAA-TAAAAAAAGAAAAAT
53745 AATAATAAAATAAA-ACAAAAT
1 AATAATAAAA-AAAGA-AAAAT
*
53766 AATAATAAAAATTAAGGAAAAT
1 AATAATAAAAA--AAGAAAAAT
* * *
53788 AATAATAATAATAATAATAAT
1 AATAATAA-AAAAAGAAAAAT
53809 AATAATAAAA
1 AATAATAAAA
53819 CTTTAATGCG
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
20 9 0.14
21 37 0.59
22 15 0.24
23 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.03, T:0.23
Consensus pattern (20 bp):
AATAATAAAAAAAGAAAAAT
Found at i:54094 original size:23 final size:22
Alignment explanation
Indices: 54068--54114 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
54058 TTTTTACAGA
54068 TTCCTTCTTTTCCTCTCTCTCTC
1 TTCCTTCTTTTCCTCT-TCTCTC
* * *
54091 TTCCTTTTTTTTCTCTTCTTTC
1 TTCCTTCTTTTCCTCTTCTCTC
54113 TT
1 TT
54115 TCAAAAGAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (22 bp):
TTCCTTCTTTTCCTCTTCTCTC
Found at i:54544 original size:16 final size:16
Alignment explanation
Indices: 54525--54678 Score: 63
Period size: 16 Copynumber: 9.3 Consensus size: 16
54515 GTAAAAAAAA
54525 ATAATAATAATAATAG
1 ATAATAATAATAATAG
* *
54541 ATAAAAAT-ATATATTG
1 ATAATAATAATA-ATAG
54557 ATAGATAAATAA-AA-AG
1 ATA-AT-AATAATAATAG
*
54573 A-AATTAATAAATTAATAA
1 ATAA-TAAT-AA-TAATAG
*
54591 ATAA-ATATATTAATAG
1 ATAATA-ATAATAATAG
* *
54607 ATAAATAAAAAAATTAACAG
1 AT-AAT--AATAA-TAATAG
* *
54627 ATAAATAATAA-AAAAT
1 AT-AATAATAATAATAG
54643 ATAAATAATAATAATA-
1 AT-AATAATAATAATAG
54659 ATAATAATAATAATA-
1 ATAATAATAATAATAG
54674 ATAAT
1 ATAAT
54679 GCAAATGGGC
Statistics
Matches: 107, Mismatches: 14, Indels: 35
0.69 0.09 0.22
Matches are distributed among these distances:
14 4 0.04
15 25 0.23
16 38 0.36
17 11 0.10
18 12 0.11
19 5 0.05
20 12 0.11
ACGTcount: A:0.66, C:0.01, G:0.04, T:0.30
Consensus pattern (16 bp):
ATAATAATAATAATAG
Found at i:54568 original size:4 final size:4
Alignment explanation
Indices: 54561--54650 Score: 51
Period size: 4 Copynumber: 23.0 Consensus size: 4
54551 ATATTGATAG
* * * * * *
54561 ATAA AT-A A-AA AGAA ATTA ATAA ATTA ATAA ATAA ATAT ATTA ATAG
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
* * * * *
54607 ATAA ATAA AAAA ATTA ACAG ATAA AT-A ATAA AAAA TATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA
54651 TAATAATAAT
Statistics
Matches: 61, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
3 7 0.11
4 51 0.84
5 3 0.05
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:54610 original size:20 final size:20
Alignment explanation
Indices: 54587--54640 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
54577 TAATAAATTA
* * *
54587 ATAAATAAATATATTAATAG
1 ATAAATAAAAAAATTAACAG
54607 ATAAATAAAAAAATTAACAG
1 ATAAATAAAAAAATTAACAG
54627 ATAAATAATAAAAA
1 ATAAATAA-AAAAA
54641 ATATAAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 25 0.83
21 5 0.17
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.26
Consensus pattern (20 bp):
ATAAATAAAAAAATTAACAG
Found at i:54636 original size:3 final size:3
Alignment explanation
Indices: 54630--54678 Score: 68
Period size: 3 Copynumber: 17.0 Consensus size: 3
54620 TTAACAGATA
54630 AAT AAT AA- AA- AAT -AT AAAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
54673 AAT AAT
1 AAT AAT
54679 GCAAATGGGC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 35 0.81
4 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:54643 original size:46 final size:44
Alignment explanation
Indices: 54532--54645 Score: 126
Period size: 46 Copynumber: 2.5 Consensus size: 44
54522 AAAATAATAA
*
54532 TAAT-AATAGATAAAAATATATATTGATAGATAAATAAAAAGAAAT
1 TAATAAATA-ATAAAAA-ATATATTAATAGATAAATAAAAAGAAAT
54577 TAATAAATTAATAAATAAATATATTAATAGATAAAT-AAAA-AAAT
1 TAATAAA-TAATAAA-AAATATATTAATAGATAAATAAAAAGAAAT
54621 TAACAGATAAATAATAAAAAATATA
1 T---A-ATAAATAATAAAAAATATA
54646 AATAATAATA
Statistics
Matches: 61, Mismatches: 1, Indels: 13
0.81 0.01 0.17
Matches are distributed among these distances:
44 5 0.08
45 8 0.13
46 31 0.51
47 12 0.20
48 5 0.08
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (44 bp):
TAATAAATAATAAAAAATATATTAATAGATAAATAAAAAGAAAT
Found at i:54844 original size:15 final size:14
Alignment explanation
Indices: 54825--54879 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
54815 AACTTGACAC
*
54825 TTTTTTTTTTTTTG
1 TTTTTTTTGTTTTG
*
54839 CTTTTTTTGTTTTG
1 TTTTTTTTGTTTTG
54853 TTTTGTTTTGTTTTG
1 TTTT-TTTTGTTTTG
*
54868 -TTGTTTTGTTTT
1 TTTTTTTTGTTTT
54880 TGGTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
13 9 0.25
14 17 0.47
15 10 0.28
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.84
Consensus pattern (14 bp):
TTTTTTTTGTTTTG
Found at i:54845 original size:10 final size:10
Alignment explanation
Indices: 54825--54879 Score: 64
Period size: 10 Copynumber: 5.9 Consensus size: 10
54815 AACTTGACAC
*
54825 TTTT-TTTTT
1 TTTTGTTTTG
*
54834 TTTTGCTTT-
1 TTTTGTTTTG
54843 TTTTGTTTTG
1 TTTTGTTTTG
54853 TTTTGTTTTG
1 TTTTGTTTTG
54863 TTTTG--TTG
1 TTTTGTTTTG
54871 TTTTGTTTT
1 TTTTGTTTT
54880 TGGTTAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
8 8 0.20
9 12 0.30
10 20 0.50
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.84
Consensus pattern (10 bp):
TTTTGTTTTG
Found at i:54856 original size:23 final size:22
Alignment explanation
Indices: 54825--54880 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
54815 AACTTGACAC
* *
54825 TTTTTTTTTTTTTGCTTTTTTTG
1 TTTTGTTTTTTTTG-TTTTGTTG
54848 TTTTGTTTTGTTTTGTTTTGTTG
1 TTTTGTTTT-TTTTGTTTTGTTG
54871 TTTTGTTTTT
1 TTTTGTTTTT
54881 GGTTAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 1 0.03
23 24 0.80
24 5 0.17
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.84
Consensus pattern (22 bp):
TTTTGTTTTTTTTGTTTTGTTG
Found at i:54991 original size:44 final size:43
Alignment explanation
Indices: 54896--55062 Score: 173
Period size: 44 Copynumber: 3.9 Consensus size: 43
54886 AAATTTTGAT
* * *
54896 CAAAGCTCCTCTAAGTAGAGGCTAAATGAC-TTG-AAAA-AAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATAACTTTGAAAAATAAA
54936 CAAAG-TCCCTCT-AATCAGAGGCTCAATAACTTTGAAAAAATAAA
1 CAAAGCT-CCTCTAAAT-AGAGGCTCAATAACTTTG-AAAAATAAA
* *
54980 CAAAGCTCCTCTAAATAGAGGCACCATAACTTTTGAAAAATAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATAAC-TTTGAAAAATAAA
* * * **
55024 TAAAGCTCCTCTCAACAGAGGCTCAACGACTTTGAAAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATAACTTTGAAAAA
55063 AATAAATTGC
Statistics
Matches: 106, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
39 3 0.03
40 22 0.21
41 3 0.03
43 13 0.12
44 57 0.54
45 8 0.08
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.22
Consensus pattern (43 bp):
CAAAGCTCCTCTAAATAGAGGCTCAATAACTTTGAAAAATAAA
Found at i:56197 original size:16 final size:16
Alignment explanation
Indices: 56099--56199 Score: 69
Period size: 16 Copynumber: 5.8 Consensus size: 16
56089 TCACCTTGAG
*
56099 TTTTTCTTTTTATTTT
1 TTTTTATTTTTATTTT
56115 TTCTTTA-TTTTATTTT
1 TT-TTTATTTTTATTTT
* *
56131 TTCTTTGTTTTTCTTATT
1 TT-TTTATTTTTATT-TT
*
56149 TTTTCATTTTTCAAATTTTCT
1 TTTTTATTTTT---A-TTT-T
56170 TTTCTTATTTTTTATTTT
1 TTT-TTA-TTTTTATTTT
56188 TTTTTATTTTTA
1 TTTTTATTTTTA
56200 AGCATAGTAC
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
16 23 0.34
17 19 0.28
18 8 0.12
19 3 0.04
20 2 0.03
21 6 0.09
22 2 0.03
23 5 0.07
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.79
Consensus pattern (16 bp):
TTTTTATTTTTATTTT
Found at i:56198 original size:7 final size:7
Alignment explanation
Indices: 56105--56189 Score: 55
Period size: 7 Copynumber: 11.7 Consensus size: 7
56095 TGAGTTTTTC
56105 TTTTTAT
1 TTTTTAT
*
56112 TTTTTCTT
1 TTTTT-AT
56120 TATTTTAT
1 T-TTTTAT
*
56128 TTTTTCT
1 TTTTTAT
*
56135 TTGTT-T
1 TTTTTAT
*
56141 TTCTTAT
1 TTTTTAT
56148 TTTTTCAT
1 TTTTT-AT
* *
56156 TTTTCAA
1 TTTTTAT
* *
56163 ATTTTCT
1 TTTTTAT
56170 TTTCTTAT
1 TTT-TTAT
56178 TTTTTAT
1 TTTTTAT
56185 TTTTT
1 TTTTT
56190 TTTATTTTTA
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
6 5 0.08
7 34 0.58
8 16 0.27
9 4 0.07
ACGTcount: A:0.12, C:0.08, G:0.01, T:0.79
Consensus pattern (7 bp):
TTTTTAT
Found at i:58688 original size:13 final size:13
Alignment explanation
Indices: 58670--58695 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58660 TTAGTTAAAG
58670 AAAAATCAAAATA
1 AAAAATCAAAATA
58683 AAAAATCAAAATA
1 AAAAATCAAAATA
58696 GAAAGGAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:58802 original size:58 final size:60
Alignment explanation
Indices: 58732--59008 Score: 391
Period size: 59 Copynumber: 4.7 Consensus size: 60
58722 TTTTGTGTAG
* *
58732 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT-GAAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTCGAAAATTTGATTTTCAA
* * *
58790 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTTTTCGAAAATTTGATTTTCAA
* * *
58852 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTTCAAAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTCGAAAATTTGATTTTCAA
* * *
58911 GGAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTTGGAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTCGAAAATTTGATTTTCAA
* *
58970 GGAAAATTGATACTTTTAACTTTTTCTCAAAAATATTTT
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTT
59009 CTTTTTGAAA
Statistics
Matches: 196, Mismatches: 17, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
58 52 0.27
59 67 0.34
60 30 0.15
61 7 0.04
62 40 0.20
ACGTcount: A:0.34, C:0.12, G:0.08, T:0.46
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTCGAAAATTTGATTTTCAA
Found at i:60301 original size:20 final size:19
Alignment explanation
Indices: 60274--60318 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 19
60264 AACATTTTCA
60274 TTTTTTGT-TTTTTTTGTTT
1 TTTTTTGTGTTTTTTT-TTT
60293 TTCTTTTGTGTTTTTTTTTT
1 TT-TTTTGTGTTTTTTTTTT
60313 TTTTTT
1 TTTTTT
60319 TACCAAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 11 0.46
21 7 0.29
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (19 bp):
TTTTTTGTGTTTTTTTTTT
Found at i:60317 original size:23 final size:23
Alignment explanation
Indices: 60268--60316 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
60258 CAACTCAACA
*
60268 TTTTCATTTTTTGTTTTTTTTGT
1 TTTTCATTTTGTGTTTTTTTTGT
*
60291 TTTTC-TTTTGTGTTTTTTTTTT
1 TTTTCATTTTGTGTTTTTTTTGT
60313 TTTT
1 TTTT
60317 TTTACCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.86
Consensus pattern (23 bp):
TTTTCATTTTGTGTTTTTTTTGT
Found at i:60426 original size:14 final size:13
Alignment explanation
Indices: 60398--60444 Score: 60
Period size: 14 Copynumber: 3.6 Consensus size: 13
60388 CAACTTTTTC
*
60398 TTTTGTTTT-CTT
1 TTTTTTTTTACTT
60410 TTTTTTTTTACTCT
1 TTTTTTTTTACT-T
*
60424 TTTTTTTTTGCTT
1 TTTTTTTTTACTT
60437 TTTTTTTT
1 TTTTTTTT
60445 AAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
12 8 0.26
13 11 0.35
14 12 0.39
ACGTcount: A:0.02, C:0.09, G:0.04, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTACTT
Found at i:60531 original size:1 final size:1
Alignment explanation
Indices: 60525--60600 Score: 62
Period size: 1 Copynumber: 76.0 Consensus size: 1
60515 TAGAGGCAAC
* * * * * * * * *
60525 TTTTTTTTGTTCTTTTTTTTATTTTTGTCTTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
60590 TTTTGTTTTTT
1 TTTTTTTTTTT
60601 ACTAAAGCTC
Statistics
Matches: 55, Mismatches: 20, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.87
Consensus pattern (1 bp):
T
Found at i:60549 original size:9 final size:9
Alignment explanation
Indices: 60525--60600 Score: 86
Period size: 9 Copynumber: 8.7 Consensus size: 9
60515 TAGAGGCAAC
60525 TTTTTTTTG
1 TTTTTTTTG
60534 TTCTTTTTT-
1 TT-TTTTTTG
*
60543 TTATTTTTG
1 TTTTTTTTG
*
60552 TCTTTTTT-
1 TTTTTTTTG
*
60560 TTTGTTTT-
1 TTTTTTTTG
*
60568 TTTGTTTTG
1 TTTTTTTTG
60577 TTTTTTTTG
1 TTTTTTTTG
60586 TTTTTTTTG
1 TTTTTTTTG
60595 TTTTTT
1 TTTTTT
60601 ACTAAAGCTC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
8 19 0.33
9 33 0.57
10 6 0.10
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.87
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:60551 original size:18 final size:17
Alignment explanation
Indices: 60525--60600 Score: 84
Period size: 17 Copynumber: 4.4 Consensus size: 17
60515 TAGAGGCAAC
60525 TTTTTTTTGTTCTTTTT
1 TTTTTTTTGTTCTTTTT
60542 TTTATTTTTG-TCTTTTT
1 TTT-TTTTTGTTCTTTTT
* * *
60559 TTTTGTTTTTTTGTTTTG
1 TTTT-TTTTGTTCTTTTT
60577 TTTTTTTTGTT-TTTTT
1 TTTTTTTTGTTCTTTTT
60593 TGTTTTTT
1 T-TTTTTT
60601 ACTAAAGCTC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
16 6 0.12
17 29 0.58
18 15 0.30
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.87
Consensus pattern (17 bp):
TTTTTTTTGTTCTTTTT
Found at i:60580 original size:23 final size:23
Alignment explanation
Indices: 60525--60598 Score: 86
Period size: 22 Copynumber: 3.4 Consensus size: 23
60515 TAGAGGCAAC
*
60525 TTTT-TTTTGTTCTTTTTT-TTAT
1 TTTTGTTTTGTT-TTTTTTGTTTT
*
60547 TTTTG-TCT-TTTTTTTTG-TTT
1 TTTTGTTTTGTTTTTTTTGTTTT
60567 TTTTGTTTTGTTTTTTTTGTTTT
1 TTTTGTTTTGTTTTTTTTGTTTT
60590 TTTTGTTTT
1 TTTTGTTTT
60599 TTACTAAAGC
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
20 13 0.30
21 4 0.09
22 15 0.34
23 12 0.27
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.86
Consensus pattern (23 bp):
TTTTGTTTTGTTTTTTTTGTTTT
Found at i:60581 original size:31 final size:30
Alignment explanation
Indices: 60525--60600 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
60515 TAGAGGCAAC
*
60525 TTTTTTTTGTTCTTTTTTTTATTTTTGTCT-
1 TTTTTTTTGTTTTTTTTTTTATTTTT-TCTG
* *
60555 TTTTTTTTGTTTTTTTGTTTTGTTTTTTTTG
1 TTTTTTTTGTTTTTTT-TTTTATTTTTTCTG
60586 TTTTTTTTGTTTTTT
1 TTTTTTTTGTTTTTT
60601 ACTAAAGCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
30 17 0.41
31 24 0.59
ACGTcount: A:0.01, C:0.03, G:0.09, T:0.87
Consensus pattern (30 bp):
TTTTTTTTGTTTTTTTTTTTATTTTTTCTG
Found at i:60895 original size:82 final size:82
Alignment explanation
Indices: 60607--61220 Score: 999
Period size: 81 Copynumber: 7.5 Consensus size: 82
60597 TTTTACTAAA
* *
60607 GCTCCTCTAAGCAGAGGCTCAACG-ACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGG--CAACGAACTTTGA-AAAGTAAATTGCTCCTCTAAACAGAGGTACCA
*
60671 CGACTTTGGAAATGTAAATT
63 CGACTTTGGAAAAGTAAATT
* * *
60691 GCTCCTCTAAACAGAGGCAACGAACTTTG-AAAGTAAATTGCTCCTATAAACAGAGGCACCACAA
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
60755 CTTTTGGAAAGAGTAAATT
66 C-TTTGGAAA-AGTAAATT
60774 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGT-AATTGCTCCTCTAAACAGAGGTACCGACG
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACC-ACG
60838 ACTTTGGAAAAGTAAATT
65 ACTTTGGAAAAGTAAATT
* * *
60856 GCTCCTCTAAATAGAGGCAATGAACTTTG-AAAGTAAATTGCTCCTCTAGACAGAGGTACCACGA
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
60920 CTTTGGAAAAGTAAATT
66 CTTTGGAAAAGTAAATT
60937 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
*
61002 CTTTGGAAAATTAAATT
66 CTTTGGAAAAGTAAATT
* *
61019 GCTCCTCTAAACAGAGGCACCACG-ACTTTGCAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCA--ACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCAC
61083 GACTTTGG-AAAGTAAATT
64 GACTTTGGAAAAGTAAATT
61101 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
61166 CTTTGGAAAA-TAAATT
66 CTTTGGAAAAGTAAATT
61182 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
61221 ACTCCTAGAC
Statistics
Matches: 500, Mismatches: 19, Indels: 25
0.92 0.03 0.05
Matches are distributed among these distances:
80 3 0.01
81 178 0.36
82 172 0.34
83 119 0.24
84 28 0.06
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (82 bp):
GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
CTTTGGAAAAGTAAATT
Found at i:61087 original size:246 final size:246
Alignment explanation
Indices: 60607--61220 Score: 990
Period size: 246 Copynumber: 2.5 Consensus size: 246
60597 TTTTACTAAA
* *
60607 GCTCCTCTAAGCAGAGGCTCAACG-ACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGG--CAACGAACTTT--GAAAGTAAATTGCTCCTCTAAACAGAGGTACCA
*
60671 CGACTTTGGAAATGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTG-AAAGTAAATTGCTCC
62 CGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCC
60735 TATAAACAGAGGCACCACAACTTTTGGAAAGAGTAAATTGCTCCTCTAAACAGAGGCAACGAACT
127 TATAAACAGAGGCACCACAACTTTTGGAAAGAGTAAATTGCTCCTCTAAACAGAGGCAACGAACT
*
60800 TTGAAAAGTAATTGCTCCTCTAAACAGAGGTACCGACGACTTTGGAAAAGTAAATT
192 TTGAAAAGTAATTGCTCCTCTAAACAGAGGCACCGACGACTTTGG-AAAGTAAATT
* * *
60856 GCTCCTCTAAATAGAGGCAATGAACTTTGAAAGTAAATTGCTCCTCTAGACAGAGGTACCACGAC
1 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGAC
*
60921 TTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTA
66 TTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTATA
* * *
60986 AACAGAGGTACCACGAC-TTTGGAAA-ATTAAATTGCTCCTCTAAACAGAGGCACCACG-ACTTT
131 AACAGAGGCACCACAACTTTTGGAAAGAGTAAATTGCTCCTCTAAACAGAGGCA--ACGAACTTT
*
61048 GCAAAGTAAATTGCTCCTCTAAACAGAGGCACC-ACGACTTTGGAAAGTAAATT
194 GAAAAGT-AATTGCTCCTCTAAACAGAGGCACCGACGACTTTGGAAAGTAAATT
61101 GCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
1 GCTCCTCTAAACAGAGGCAACGAACTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGTACCACGA
61166 CTTTGGAAAA-TAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
65 CTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAAT
61221 ACTCCTAGAC
Statistics
Matches: 344, Mismatches: 15, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
245 108 0.31
246 152 0.44
247 64 0.19
248 5 0.01
249 15 0.04
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.23
Consensus pattern (246 bp):
GCTCCTCTAAACAGAGGCAACGAACTTTGAAAGTAAATTGCTCCTCTAAACAGAGGTACCACGAC
TTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGAAAAGTAAATTGCTCCTATA
AACAGAGGCACCACAACTTTTGGAAAGAGTAAATTGCTCCTCTAAACAGAGGCAACGAACTTTGA
AAAGTAATTGCTCCTCTAAACAGAGGCACCGACGACTTTGGAAAGTAAATT
Found at i:62855 original size:14 final size:16
Alignment explanation
Indices: 62836--62868 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
62826 TGGCCTTTTA
62836 TTTTTCT-TTTCC-TT
1 TTTTTCTCTTTCCATT
62850 TTTTTCTCTTTCCATT
1 TTTTTCTCTTTCCATT
62866 TTT
1 TTT
62869 GAGACCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 5 0.29
16 5 0.29
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTCTTTCCATT
Done.