Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 126 of 126
Found at i:25632100 original size:2 final size:2
Alignment explanation
Indices: 25632093--25632124 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25632083 AACAACAATC
25632093 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
25632125 CACCTGTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25651603 original size:11 final size:11
Alignment explanation
Indices: 25651587--25651614 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
25651577 TCTTTTTCTT
25651587 TAAATATAAAA
1 TAAATATAAAA
25651598 TAAATATAAAA
1 TAAATATAAAA
25651609 TAAATA
1 TAAATA
25651615 ATTATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAATATAAAA
Found at i:25655005 original size:2 final size:2
Alignment explanation
Indices: 25654998--25655042 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
25654988 ATATTGTAAC
* *
25654998 AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25655040 AT A
1 AT A
25655043 CACTAGTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:25656535 original size:2 final size:2
Alignment explanation
Indices: 25656528--25656565 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
25656518 TTATATTTAC
*
25656528 AT AT AT AT AT AT GT 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 AT
25656566 CTCGAGAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25669977 original size:24 final size:25
Alignment explanation
Indices: 25669919--25669978 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 25
25669909 TACAGACATG
*
25669919 ACTATTTA-TTTTGAATAGACGAAA
1 ACTATTCATTTTTGAATAGACGAAA
* **
25669943 ACTATTTATTTTTGAATAGTTG-AA
1 ACTATTCATTTTTGAATAGACGAAA
*
25669967 ACTGTTCATTTT
1 ACTATTCATTTT
25669979 AAACAGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (25 bp):
ACTATTCATTTTTGAATAGACGAAA
Found at i:25674826 original size:21 final size:20
Alignment explanation
Indices: 25674783--25674823 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
25674773 AAAACTTTTA
** *
25674783 TAAAAAAAAAATCTGGAGTT
1 TAAAAAAAAAAGATAGAGTT
25674803 TAAAAAAAAAAGATAGAGTT
1 TAAAAAAAAAAGATAGAGTT
25674823 T
1 T
25674824 TAAGAATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.59, C:0.02, G:0.15, T:0.24
Consensus pattern (20 bp):
TAAAAAAAAAAGATAGAGTT
Found at i:25674982 original size:23 final size:23
Alignment explanation
Indices: 25674956--25675007 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
25674946 TAAAATTATT
* *
25674956 TATTTTAAATAGATTTATCTGTC
1 TATTTTAAACAGATTTATCTATC
25674979 TATTTTAAACAGATTTATCTATC
1 TATTTTAAACAGATTTATCTATC
25675002 TATTTT
1 TATTTT
25675008 TATTGTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.54
Consensus pattern (23 bp):
TATTTTAAACAGATTTATCTATC
Found at i:25684367 original size:134 final size:136
Alignment explanation
Indices: 25684141--25684401 Score: 463
Period size: 134 Copynumber: 1.9 Consensus size: 136
25684131 TAGAATTGAT
* *
25684141 GGAATGATCATGAAAAAAGACTTGTGTAGGCATGATTAAAGACAGATTTCTCCTGATTTTGACTG
1 GGAATGATCAAGAAAAAAGACTTGTGTAGGCATGATTAAAGACAGATTTCTCCTAATTTTGACTG
*
25684206 AAGTTTAACATTTGAACCTTTGCAAAAGCTTGATTTTACATTACTACATTGAACTTAGTTTTATG
66 AAGTTGAACATTTGAACCTTTGCAAAAGCTTGATTTTACATTACTACATTGAACTTAGTTTTATG
25684271 TATGAA
131 TATGAA
*
25684277 GGAATGATCAAG-AAAAATACTTGTGTAGGCATGATT-AAGACAGATTTCTCCTAATTTTGACTG
1 GGAATGATCAAGAAAAAAGACTTGTGTAGGCATGATTAAAGACAGATTTCTCCTAATTTTGACTG
*
25684340 AAGTTGAACATTTGAACCTTTGCAAAAGCTTGATTTTACTTTACTACATTGAACTTAGTTTT
66 AAGTTGAACATTTGAACCTTTGCAAAAGCTTGATTTTACATTACTACATTGAACTTAGTTTT
25684402 GTTTCTGAAT
Statistics
Matches: 120, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
134 86 0.72
135 23 0.19
136 11 0.09
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.36
Consensus pattern (136 bp):
GGAATGATCAAGAAAAAAGACTTGTGTAGGCATGATTAAAGACAGATTTCTCCTAATTTTGACTG
AAGTTGAACATTTGAACCTTTGCAAAAGCTTGATTTTACATTACTACATTGAACTTAGTTTTATG
TATGAA
Found at i:25684451 original size:35 final size:37
Alignment explanation
Indices: 25684403--25684480 Score: 115
Period size: 35 Copynumber: 2.2 Consensus size: 37
25684393 CTTAGTTTTG
* * *
25684403 TTTCTGAATCTATCATAATCATACATAATAGA-T-TA
1 TTTCTGAACCTATCATAATCATACACAACAGACTCTA
25684438 TTTCTGAACCTATCATAATCATACACAACAGACTCTA
1 TTTCTGAACCTATCATAATCATACACAACAGACTCTA
25684475 TTTCTG
1 TTTCTG
25684481 GCAACATTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
35 29 0.76
36 1 0.03
37 8 0.21
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (37 bp):
TTTCTGAACCTATCATAATCATACACAACAGACTCTA
Found at i:25688744 original size:17 final size:17
Alignment explanation
Indices: 25688718--25688751 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
25688708 ATCAAAAGAG
*
25688718 GAGTCTTGAATCCCACA
1 GAGTCCTGAATCCCACA
*
25688735 GAGTCCTGAATCTCACA
1 GAGTCCTGAATCCCACA
25688752 TCAAAAGAAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (17 bp):
GAGTCCTGAATCCCACA
Found at i:25688759 original size:43 final size:43
Alignment explanation
Indices: 25688693--25688777 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
25688683 CCTAAAAAAA
* *
25688693 AGTCATGAATTTCACATCAAAAGAGGAGTCTTGAATCCCACAG
1 AGTCATGAATCTCACATCAAAAGAAGAGTCTTGAATCCCACAG
* * *
25688736 AGTCCTGAATCTCACATCAAAAGAAGAGTTTTGAATCTCACA
1 AGTCATGAATCTCACATCAAAAGAAGAGTCTTGAATCCCACA
25688778 TCGAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (43 bp):
AGTCATGAATCTCACATCAAAAGAAGAGTCTTGAATCCCACAG
Found at i:25693430 original size:25 final size:24
Alignment explanation
Indices: 25693389--25693441 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
25693379 AATAATAATT
*
25693389 ATTATTATAATTGTGATTGAAAAAA
1 ATTATTATAATTATGATT-AAAAAA
*
25693414 ATTATTATAGTTATGATTAAAAAA
1 ATTATTATAATTATGATTAAAAAA
25693438 ATTA
1 ATTA
25693442 ATAAAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (24 bp):
ATTATTATAATTATGATTAAAAAA
Found at i:25694271 original size:15 final size:15
Alignment explanation
Indices: 25694251--25694286 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
25694241 TACCAAGTCT
* *
25694251 AATAAAACAAATATC
1 AATAAAACAAACATA
25694266 AATAAAACAAACATA
1 AATAAAACAAACATA
25694281 AATAAA
1 AATAAA
25694287 GAGTTACACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.72, C:0.11, G:0.00, T:0.17
Consensus pattern (15 bp):
AATAAAACAAACATA
Found at i:25698922 original size:9 final size:9
Alignment explanation
Indices: 25698905--25698935 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
25698895 ACTAAAGGTC
25698905 TTCAGCACT
1 TTCAGCACT
*
25698914 TTTAGCACT
1 TTCAGCACT
25698923 TTCAGCACT
1 TTCAGCACT
25698932 TTCA
1 TTCA
25698936 AGGGTGACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.39
Consensus pattern (9 bp):
TTCAGCACT
Found at i:25704403 original size:36 final size:36
Alignment explanation
Indices: 25704356--25704427 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
25704346 AAATGATCTT
*
25704356 ACTTTATAAAAGAAGCAACCTCAATAGAATTAAATA
1 ACTTTATAAAAGAAGCAACCTCAATAGAAGTAAATA
*
25704392 ACTTTATAAAAGGAGCAACCTCAATAGAAGTAAATA
1 ACTTTATAAAAGAAGCAACCTCAATAGAAGTAAATA
25704428 GCACATATCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.24
Consensus pattern (36 bp):
ACTTTATAAAAGAAGCAACCTCAATAGAAGTAAATA
Found at i:25708036 original size:2 final size:2
Alignment explanation
Indices: 25708029--25708058 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25708019 GCCCATACAT
25708029 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
25708059 TCATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:25716857 original size:20 final size:20
Alignment explanation
Indices: 25716832--25716870 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
25716822 TTTATTTTAA
25716832 TAATTTACTTACCAATAAAT
1 TAATTTACTTACCAATAAAT
* *
25716852 TAATTTATTTATCAATAAA
1 TAATTTACTTACCAATAAA
25716871 AATATTTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (20 bp):
TAATTTACTTACCAATAAAT
Found at i:25716961 original size:18 final size:18
Alignment explanation
Indices: 25716922--25716957 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
25716912 TAAATAAAAT
*
25716922 ATTATTCATATTTTATAA
1 ATTATTCATATTTAATAA
25716940 ATTATT-ATATTTAATAA
1 ATTATTCATATTTAATAA
25716957 A
1 A
25716958 ATTAAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATTCATATTTAATAA
Found at i:25726262 original size:2 final size:2
Alignment explanation
Indices: 25726255--25726288 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
25726245 TCAGTAACCA
25726255 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
25726289 CTACCTCAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25729908 original size:2 final size:2
Alignment explanation
Indices: 25729901--25729930 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25729891 AACATAGAAC
25729901 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
25729931 TGAAGATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25736910 original size:2 final size:2
Alignment explanation
Indices: 25736897--25736937 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
25736887 ACAAAAAGGA
*
25736897 AG AG AA AG AG AG AG AG 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 AG AG AG AG AG AG AG AG A
25736938 CTGACTCGGC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25741773 original size:16 final size:16
Alignment explanation
Indices: 25741752--25741784 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
25741742 TTTCTTGCCA
25741752 TTGCTTCCTTCAAATT
1 TTGCTTCCTTCAAATT
25741768 TTGCTTCCTTCAAATT
1 TTGCTTCCTTCAAATT
25741784 T
1 T
25741785 CCTTCAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.06, T:0.52
Consensus pattern (16 bp):
TTGCTTCCTTCAAATT
Found at i:25745815 original size:124 final size:124
Alignment explanation
Indices: 25745664--25745918 Score: 503
Period size: 124 Copynumber: 2.1 Consensus size: 124
25745654 TGGTTCATGC
25745664 ATGCTGCATTTTTTGCATTGCCTTTCTGCTAGTGCTGATAAAGCCTGTTGGAGTCAGTTGGTGGA
1 ATGCTGCATTTTTTGCATTGCCTTTCTGCTAGTGCTGATAAAGCCTGTTGGAGTCAGTTGGTGGA
25745729 TGACTAGTTATTTACTCTTAGTGCATGGCGGTTATAGCTGACTTCAAAAGTTGGTTAGA
66 TGACTAGTTATTTACTCTTAGTGCATGGCGGTTATAGCTGACTTCAAAAGTTGGTTAGA
25745788 ATGCTGCATTTTTTGCATTGCCTTTCTGCTAGTGCTGATAAAGCCTGTTGGAGTCAGTTGGTGGA
1 ATGCTGCATTTTTTGCATTGCCTTTCTGCTAGTGCTGATAAAGCCTGTTGGAGTCAGTTGGTGGA
25745853 TGACTAGTTATTTACTCTTAGTGCATGGCGGTTATAGCTGACTTCAAAAGTTGGTTAGA
66 TGACTAGTTATTTACTCTTAGTGCATGGCGGTTATAGCTGACTTCAAAAGTTGGTTAGA
25745912 ATG-TGCA
1 ATGCTGCA
25745919 AAAGGAGGGA
Statistics
Matches: 131, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
123 4 0.03
124 127 0.97
ACGTcount: A:0.21, C:0.15, G:0.26, T:0.38
Consensus pattern (124 bp):
ATGCTGCATTTTTTGCATTGCCTTTCTGCTAGTGCTGATAAAGCCTGTTGGAGTCAGTTGGTGGA
TGACTAGTTATTTACTCTTAGTGCATGGCGGTTATAGCTGACTTCAAAAGTTGGTTAGA
Found at i:25749337 original size:4 final size:4
Alignment explanation
Indices: 25749328--25749432 Score: 111
Period size: 4 Copynumber: 26.2 Consensus size: 4
25749318 ATTTCTTTAA
* * * * * * *
25749328 ATAT ATAT ATAT GTAT GTAT ATAT ATAC ACAT ACAT ATAT ATAC ATAC
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * *
25749376 ATAT ACAT ACAT ATAT ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
25749424 ATAT ATAT A
1 ATAT ATAT A
25749433 AAAGAGAAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 89 1.00
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:25749365 original size:14 final size:14
Alignment explanation
Indices: 25749346--25749432 Score: 97
Period size: 14 Copynumber: 6.4 Consensus size: 14
25749336 ATATGTATGT
25749346 ATATATATAC--AC
1 ATATATATACATAC
* *
25749358 ATACATATATATAC
1 ATATATATACATAC
*
25749372 ATACATATACATAC
1 ATATATATACATAC
25749386 ATATATATACATAC
1 ATATATATACATAC
* *
25749400 ATATATATATATAT
1 ATATATATACATAC
* *
25749414 ATATATATATATAT
1 ATATATATACATAC
25749428 ATATA
1 ATATA
25749433 AAAGAGAAAC
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
12 8 0.12
14 59 0.88
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATATATACATAC
Found at i:25749373 original size:10 final size:10
Alignment explanation
Indices: 25749348--25749432 Score: 89
Period size: 10 Copynumber: 8.5 Consensus size: 10
25749338 ATGTATGTAT
*
25749348 ATATATACAC
1 ATATATACAT
* *
25749358 ATACATATAT
1 ATATATACAT
*
25749368 ATACATACAT
1 ATATATACAT
*
25749378 ATACATACAT
1 ATATATACAT
25749388 ATATATACAT
1 ATATATACAT
* *
25749398 ACATATATAT
1 ATATATACAT
*
25749408 ATATATATAT
1 ATATATACAT
*
25749418 ATATATATAT
1 ATATATACAT
25749428 ATATA
1 ATATA
25749433 AAAGAGAAAC
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 67 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (10 bp):
ATATATACAT
Found at i:25753372 original size:20 final size:20
Alignment explanation
Indices: 25753347--25753384 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
25753337 TTTGTCCTTA
*
25753347 ATTCTAGGGATACAAATACT
1 ATTCTAGAGATACAAATACT
25753367 ATTCTAGAGATACAAATA
1 ATTCTAGAGATACAAATA
25753385 TAAATATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (20 bp):
ATTCTAGAGATACAAATACT
Found at i:25756317 original size:59 final size:60
Alignment explanation
Indices: 25756254--25756414 Score: 208
Period size: 59 Copynumber: 2.8 Consensus size: 60
25756244 AACCAATTTT
25756254 AACAACTAT-ATAATCAAAATCCAAATAAATTTTAATAAATATAA-AATCAACAAAAACTC
1 AACAACTATGATAATCAAAATCCAAATAAATTTTAATAAATA-AATAATCAACAAAAACTC
* * * * * *
25756313 AACAAAT-TGCTAAACAAAACCCAAATAAATTTTAACAAATAAATAATTAACAAAAACTC
1 AACAACTATGATAATCAAAATCCAAATAAATTTTAATAAATAAATAATCAACAAAAACTC
25756372 AAC-AC-ATTGATAATCAAAATCCAAATAAATTTTAATAAA-AAAT
1 AACAACTA-TGATAATCAAAATCCAAATAAATTTTAATAAATAAAT
25756415 TAAATCATAT
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
58 8 0.09
59 79 0.91
ACGTcount: A:0.59, C:0.15, G:0.01, T:0.25
Consensus pattern (60 bp):
AACAACTATGATAATCAAAATCCAAATAAATTTTAATAAATAAATAATCAACAAAAACTC
Found at i:25756353 original size:14 final size:15
Alignment explanation
Indices: 25756334--25756366 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
25756324 AAACAAAACC
*
25756334 CAAATAAAT-TTTAA
1 CAAATAAATAATTAA
25756348 CAAATAAATAATTAA
1 CAAATAAATAATTAA
25756363 CAAA
1 CAAA
25756367 AACTCAACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (15 bp):
CAAATAAATAATTAA
Found at i:25757580 original size:31 final size:35
Alignment explanation
Indices: 25757509--25757585 Score: 101
Period size: 36 Copynumber: 2.3 Consensus size: 35
25757499 GGTCTCTATC
*
25757509 TTTT-TCTGCTACAGTGACTGCTACAATGATATTT
1 TTTTGTCTGCTACAATGACTGCTACAATGATATTT
25757543 TATTTGTCTGCTACAATGACTGCTAC-A-GA-A-TT
1 T-TTTGTCTGCTACAATGACTGCTACAATGATATTT
25757575 TTTTGTCTGCT
1 TTTTGTCTGCT
25757586 GGTTGTGGGC
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
31 10 0.25
32 3 0.08
33 1 0.03
34 3 0.08
35 4 0.10
36 19 0.47
ACGTcount: A:0.22, C:0.18, G:0.16, T:0.44
Consensus pattern (35 bp):
TTTTGTCTGCTACAATGACTGCTACAATGATATTT
Found at i:25759050 original size:28 final size:29
Alignment explanation
Indices: 25759018--25759087 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
25759008 AAAATGGTTG
*
25759018 TTAGTAAAGATAT-AATCCTTGGTTAGGA
1 TTAGTAAAGATATAAATCCTGGGTTAGGA
*
25759046 TTAGTGTAAAAAT-TAAATCCTGGGTTAGGA
1 TTA--GTAAAGATATAAATCCTGGGTTAGGA
* *
25759076 TTTGTAGAGATA
1 TTAGTAAAGATA
25759088 AGAGGTCTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
28 9 0.27
29 1 0.03
30 23 0.70
ACGTcount: A:0.36, C:0.06, G:0.23, T:0.36
Consensus pattern (29 bp):
TTAGTAAAGATATAAATCCTGGGTTAGGA
Found at i:25767411 original size:14 final size:15
Alignment explanation
Indices: 25767381--25767414 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
25767371 ATAAATTTGC
25767381 AAATGAATAGAAAAA
1 AAATGAATAGAAAAA
*
25767396 AAATGAATGGAAAAA
1 AAATGAATAGAAAAA
25767411 AAAT
1 AAAT
25767415 TGAGCCTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (15 bp):
AAATGAATAGAAAAA
Found at i:25768678 original size:11 final size:12
Alignment explanation
Indices: 25768656--25768684 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
25768646 CAAAAAGAAG
25768656 ATTTTTTAAAAA
1 ATTTTTTAAAAA
25768668 ATTTTTTAAAAA
1 ATTTTTTAAAAA
25768680 ATTTT
1 ATTTT
25768685 CAGATTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTTTTAAAAA
Found at i:25769290 original size:25 final size:26
Alignment explanation
Indices: 25769257--25769316 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
25769247 TTTAGAATAA
* *
25769257 ATAATAATTATCCAATGATGAAATTT-T
1 ATAA-AATTATCAAATAAT-AAATTTCT
*
25769284 -TAAAATTTTCAAATAATAAATTTCT
1 ATAAAATTATCAAATAATAAATTTCT
25769309 ATAAAATT
1 ATAAAATT
25769317 CTTAAGTGAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 6 0.21
25 12 0.43
26 10 0.36
ACGTcount: A:0.48, C:0.07, G:0.03, T:0.42
Consensus pattern (26 bp):
ATAAAATTATCAAATAATAAATTTCT
Found at i:25769716 original size:45 final size:45
Alignment explanation
Indices: 25769626--25769721 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
25769616 TCCAAAGATA
25769626 AAAAAAATTTTCTAAATAGACCAAAATGGTGAAAATTTTAAAAATTT
1 AAAAAAA-TTTCTAAATAGACCAAAATGGTGAAAATTTTAAAAA-TT
* * * * *
25769673 AAAAAAA-TTCTAAATAGGCCCAAATTGTG-GAATATTTAGAAATT
1 AAAAAAATTTCTAAATAGACCAAAATGGTGAAAAT-TTTAAAAATT
25769717 AAAAA
1 AAAAA
25769722 GAGAAGATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
44 10 0.23
45 26 0.60
47 7 0.16
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.29
Consensus pattern (45 bp):
AAAAAAATTTCTAAATAGACCAAAATGGTGAAAATTTTAAAAATT
Found at i:25770393 original size:17 final size:17
Alignment explanation
Indices: 25770373--25770410 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
25770363 TGTCTTTTAT
25770373 TTATGGGGG-CTGACATA
1 TTATGGGGGACTGACA-A
25770390 TTATGGGGGACTGACAA
1 TTATGGGGGACTGACAA
25770407 TTAT
1 TTAT
25770411 ATGTTCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (17 bp):
TTATGGGGGACTGACAA
Found at i:25776462 original size:2 final size:2
Alignment explanation
Indices: 25776455--25776492 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
25776445 GAGTATTTGT
*
25776455 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
25776493 CACACCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:25777806 original size:28 final size:28
Alignment explanation
Indices: 25777775--25777859 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 28
25777765 TTGATAAATG
25777775 TTTCTAATTTCTTTCTTTTTATTATTTT
1 TTTCTAATTTCTTTCTTTTTATTATTTT
* * *
25777803 TTTC-AATTTTTGTTCATATT-TTATTTT
1 TTTCTAATTTCT-TTCTTTTTATTATTTT
**
25777830 TTT-T-CGTTCTTTCTTTTTATTGATTTT
1 TTTCTAATTTCTTTCTTTTTATT-ATTTT
25777857 TTT
1 TTT
25777860 ATCTAAAAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
25 6 0.13
26 5 0.11
27 24 0.53
28 10 0.22
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTCTAATTTCTTTCTTTTTATTATTTT
Found at i:25777810 original size:27 final size:27
Alignment explanation
Indices: 25777775--25777859 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 27
25777765 TTGATAAATG
25777775 TTTCTAATTTCTTTCTTTTTATTATTTT
1 TTTC-AATTTCTTTCTTTTTATTATTTT
*
25777803 TTTCAATTTTTGTTCATATTTTA-T-TTTT
1 TTTCAATTTCT-TTC-T-TTTTATTATTTT
*
25777831 TTTC--GTTCTTTCTTTTTATTGATTTT
1 TTTCAATTTCTTTCTTTTTATT-ATTTT
25777857 TTT
1 TTT
25777860 ATCTAAAAGC
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
23 5 0.10
24 2 0.04
25 3 0.06
26 10 0.21
27 6 0.12
28 15 0.31
29 2 0.04
30 5 0.10
ACGTcount: A:0.13, C:0.09, G:0.04, T:0.74
Consensus pattern (27 bp):
TTTCAATTTCTTTCTTTTTATTATTTT
Found at i:25779332 original size:25 final size:25
Alignment explanation
Indices: 25779298--25779347 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
25779288 AAGTGAAAGC
25779298 GGACCTCACTTCCAATGGTTAACAA
1 GGACCTCACTTCCAATGGTTAACAA
25779323 GGACCTCACTTCCAATGGTTAACAA
1 GGACCTCACTTCCAATGGTTAACAA
25779348 CATAGAGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (25 bp):
GGACCTCACTTCCAATGGTTAACAA
Found at i:25802860 original size:24 final size:24
Alignment explanation
Indices: 25802833--25802896 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
25802823 AAGAATGTAA
*
25802833 AAAGT-AAAAATGAAAATATTAAAT
1 AAAGTAAAAAATGAAAA-ATAAAAT
* *
25802857 AAAGTGAAATATGAAAAATAAAAT
1 AAAGTAAAAAATGAAAAATAAAAT
*
25802881 AAAATAAAAAATGAAA
1 AAAGTAAAAAATGAAA
25802897 TTTGAATCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 24 0.71
25 10 0.29
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (24 bp):
AAAGTAAAAAATGAAAAATAAAAT
Found at i:25808085 original size:26 final size:26
Alignment explanation
Indices: 25808049--25808101 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
25808039 AAGTAAAGAG
25808049 ATAGAAATAGAGAAATCAAACACAAT
1 ATAGAAATAGAGAAATCAAACACAAT
25808075 ATAGAAATAGAGAAATCAAACACAAT
1 ATAGAAATAGAGAAATCAAACACAAT
25808101 A
1 A
25808102 ATTTATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.15
Consensus pattern (26 bp):
ATAGAAATAGAGAAATCAAACACAAT
Found at i:25810905 original size:18 final size:19
Alignment explanation
Indices: 25810859--25810906 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
25810849 TTTAAATTAT
25810859 TTCAATGCATA-GTGAAGTA
1 TTCAAT-CATATGTGAAGTA
* *
25810878 TTTAAACATATGT-AAGTA
1 TTCAATCATATGTGAAGTA
25810896 TTCAATCATAT
1 TTCAATCATAT
25810907 ATTTCAATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (19 bp):
TTCAATCATATGTGAAGTA
Found at i:25814137 original size:23 final size:23
Alignment explanation
Indices: 25814111--25814154 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25814101 TTATTTTTTT
*
25814111 AAAAAATATTTTTTACATTTATC
1 AAAAAATATTTTTAACATTTATC
*
25814134 AAAAATTATTTTTAACATTTA
1 AAAAAATATTTTTAACATTTA
25814155 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAAAATATTTTTAACATTTATC
Done.