Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004275.1 Hibiscus syriacus cultivar Beakdansim tig00009371_pilon, 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: 121830
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:875 original size:16 final size:16
Alignment explanation
Indices: 850--882 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
840 AATTATTGAA
850 ATAAAATGTAA-ATAT
1 ATAAAATGTAACATAT
865 ATAAGAATGTAACATAT
1 ATAA-AATGTAACATAT
882 A
1 A
883 CTGTTCCTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 7 0.44
17 5 0.31
ACGTcount: A:0.58, C:0.03, G:0.09, T:0.30
Consensus pattern (16 bp):
ATAAAATGTAACATAT
Found at i:3117 original size:20 final size:20
Alignment explanation
Indices: 3081--3123 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3071 ATCTAGTTCA
* *
3081 ATTTAAATTAATAATAAATT
1 ATTTAAATAAATAATAAAAT
3101 ATTTAAATAAA-ATATAAAAT
1 ATTTAAATAAATA-ATAAAAT
3121 ATT
1 ATT
3124 AGTATAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATTTAAATAAATAATAAAAT
Found at i:14237 original size:38 final size:36
Alignment explanation
Indices: 14195--14302 Score: 98
Period size: 38 Copynumber: 2.9 Consensus size: 36
14185 AACTTATTGG
14195 AAATTTCATCTTGGTTGGTGGCCAAACTTTGAACATGT
1 AAATTTCAT-TTGGTTGGTGG-CAAACTTTGAACATGT
* *
14233 AAATTTCATAT--TTGGTGGCTAAC-TTGTACACATTGT
1 AAATTTCATTTGGTTGGTGGCAAACTTTG-A-ACA-TGT
* *
14269 AAAATTC-TTTGGTAGGTGGTCAAACTTTGAACAT
1 AAATTTCATTTGGTTGGTGG-CAAACTTTGAACAT
14303 ATTGTTCTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 16
0.72 0.08 0.20
Matches are distributed among these distances:
33 3 0.05
34 5 0.09
35 12 0.21
36 10 0.18
37 10 0.18
38 14 0.25
39 3 0.05
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (36 bp):
AAATTTCATTTGGTTGGTGGCAAACTTTGAACATGT
Found at i:15689 original size:2 final size:2
Alignment explanation
Indices: 15680--15721 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
15670 TAAAAAATAG
*
15680 AT AT -T AT AT AT -T AA 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 AT AT AT
15720 AT
1 AT
15722 TTGTCCACTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15693 original size:21 final size:23
Alignment explanation
Indices: 15667--15713 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
15657 TTTTTTGAGT
15667 TATTAAA-AAATAGATAT-TATA
1 TATTAAATAAATAGATATATATA
* *
15688 TATTAAATATATATATATATATA
1 TATTAAATAAATAGATATATATA
15711 TAT
1 TAT
15714 ATATATATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 8 0.36
23 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTAAATAAATAGATATATATA
Found at i:19027 original size:3 final size:3
Alignment explanation
Indices: 19019--19043 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19009 TGTTGGACCA
19019 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
19044 TGGAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:20937 original size:24 final size:24
Alignment explanation
Indices: 20906--20954 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20896 GATACACAAT
20906 ATCATCAAAAATATTA-ACATTATC
1 ATCATCAAAAATATTAGAC-TTATC
* *
20930 ATCATCAACATTATTAGACTTATC
1 ATCATCAAAAATATTAGACTTATC
20954 A
1 A
20955 ATTGTAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.45, C:0.18, G:0.02, T:0.35
Consensus pattern (24 bp):
ATCATCAAAAATATTAGACTTATC
Found at i:22540 original size:24 final size:24
Alignment explanation
Indices: 22505--22559 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
22495 TTTGAGACAT
*
22505 TTCTACGTGGTCATTCAGGACAAA
1 TTCTACGCGGTCATTCAGGACAAA
* *
22529 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCGGTCATTCAGGACAAA
22553 TTCTACG
1 TTCTACG
22560 TGGCACTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (24 bp):
TTCTACGCGGTCATTCAGGACAAA
Found at i:23767 original size:23 final size:23
Alignment explanation
Indices: 23749--23809 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
23739 CTCGTATAAA
23749 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
23772 TGCACCGAAGTACCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
23795 TGTACCGTAGTGCCA
1 TGCACCGAAGTGCCA
23810 TATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:26548 original size:15 final size:15
Alignment explanation
Indices: 26528--26557 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
26518 GACAAAGGTG
26528 GCCCTGCCTCCCTCA
1 GCCCTGCCTCCCTCA
*
26543 GCCCTGTCTCCCTCA
1 GCCCTGCCTCCCTCA
26558 TGCATGCAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.57, G:0.13, T:0.23
Consensus pattern (15 bp):
GCCCTGCCTCCCTCA
Found at i:27139 original size:140 final size:132
Alignment explanation
Indices: 26881--27131 Score: 315
Period size: 140 Copynumber: 1.8 Consensus size: 132
26871 TATTAATCGC
* *
26881 GTGATATGGAGCATTATTTTGCTCCTCTCATGCATGACCTACATGATTTGCACGTTATAAAAGTA
1 GTGATATAGAGCATTATTTTCCTCCTCTCATGCATGACCTACATGATTTGCACGTTATAAAAGTA
* ** *
26946 GCAAATGGATGAATTATTACAGCAGTTACTTTAGAGTTTATGGGGTCAATTTAGCAATTATAGTA
66 GCAAATAGATGAATTATTACAGCAACTAATTTAGAGTTTATGGGGTCAATTTAGCAATTATAGTA
27011 GT
131 GT
* * *
27013 GTGATATAGAGCATTATTTTCCTCCTCTCATGCATGCATGCCTACATGATTTGCATGTTTTAATA
1 GTGATATAGAGCATTATTTTCCTCCTCTCATGCATG-A--CCTACATGATTTGCACGTTATAAAA
* *
27078 GTAGCATTGAAAATAGATGAATTATTGTC-GCAACTAATTTAGGGTTTATGGGGT
63 GTAGC-----AAATAGATGAATTATT-ACAGCAACTAATTTAGAGTTTATGGGGT
27132 TAGTTTAGGG
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
132 34 0.34
133 1 0.01
135 27 0.27
140 36 0.36
141 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (132 bp):
GTGATATAGAGCATTATTTTCCTCCTCTCATGCATGACCTACATGATTTGCACGTTATAAAAGTA
GCAAATAGATGAATTATTACAGCAACTAATTTAGAGTTTATGGGGTCAATTTAGCAATTATAGTA
GT
Found at i:27292 original size:28 final size:30
Alignment explanation
Indices: 27259--27321 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
27249 TAGTTTAAAT
27259 TATTAGTTGGTTAGTTTAAG-T-TATATTA
1 TATTAGTTGGTTAGTTTAAGTTATATATTA
*
27287 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTGGTTAGTTTAAGTTATATATTA
27317 TATTA
1 TATTA
27322 TATGAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.30, C:0.00, G:0.14, T:0.56
Consensus pattern (30 bp):
TATTAGTTGGTTAGTTTAAGTTATATATTA
Found at i:30457 original size:33 final size:33
Alignment explanation
Indices: 30394--30466 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
30384 GATTTATTAT
* * *
30394 TAAT-ATTTAATGATTTGATAGTAACGATTTAG
1 TAATGATTTAATGATTTGATACTAACAATTTAA
* *
30426 TAATGATTTATTGATTTGATACTAATAATTTAA
1 TAATGATTTAATGATTTGATACTAACAATTTAA
*
30459 TAACGATT
1 TAATGATT
30467 ACTAATAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.45
Consensus pattern (33 bp):
TAATGATTTAATGATTTGATACTAACAATTTAA
Found at i:30480 original size:24 final size:22
Alignment explanation
Indices: 30448--30498 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 22
30438 GATTTGATAC
*
30448 TAATAATTTAATAACGATTACTAA
1 TAATTATTTAATAACGATTA--AA
*
30472 TAATTATTTAATAATGATTAAA
1 TAATTATTTAATAACGATTAAA
30494 TAATT
1 TAATT
30499 TAATATAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
24 18 0.72
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (22 bp):
TAATTATTTAATAACGATTAAA
Found at i:30547 original size:16 final size:16
Alignment explanation
Indices: 30522--30552 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
30512 TCAATTTAAA
30522 TTGAAATTATAAATAG
1 TTGAAATTATAAATAG
*
30538 TTGAATTTATAAATA
1 TTGAAATTATAAATA
30553 CTCGAACTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
TTGAAATTATAAATAG
Found at i:31725 original size:23 final size:22
Alignment explanation
Indices: 31660--31722 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
31650 TAAACTACAA
*
31660 AATTAAAATAAA-AATA-AAGTT
1 AATTTAAATAAATAATATAA-TT
*
31681 GATTTAAATCAAATAATATAATT
1 AATTTAAAT-AAATAATATAATT
31704 AATTTAAAT-AATAAT-TAAT
1 AATTTAAATAAATAATATAAT
31723 AATAACATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
20 4 0.11
21 13 0.36
22 3 0.08
23 14 0.39
24 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.37
Consensus pattern (22 bp):
AATTTAAATAAATAATATAATT
Found at i:33346 original size:11 final size:11
Alignment explanation
Indices: 33330--33389 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
33320 CTCGTTACCT
33330 TTCTTCCTTTC
1 TTCTTCCTTTC
33341 TTCTTCCTTTCC
1 TTCTTCCTTT-C
* *
33353 ATC-ACCTTTC
1 TTCTTCCTTTC
33363 TTCTTCC-TTC
1 TTCTTCCTTTC
** *
33373 ACCTTTCTTTC
1 TTCTTCCTTTC
33384 TTCTTC
1 TTCTTC
33390 TTACAACAGA
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
10 10 0.28
11 23 0.64
12 3 0.08
ACGTcount: A:0.05, C:0.38, G:0.00, T:0.57
Consensus pattern (11 bp):
TTCTTCCTTTC
Found at i:33374 original size:17 final size:18
Alignment explanation
Indices: 33349--33386 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
33339 TCTTCTTCCT
33349 TTCCATCACCTTTC-TTC
1 TTCCATCACCTTTCTTTC
*
33366 TTCCTTCACCTTTCTTTC
1 TTCCATCACCTTTCTTTC
33384 TTC
1 TTC
33387 TTCTTACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.08, C:0.39, G:0.00, T:0.53
Consensus pattern (18 bp):
TTCCATCACCTTTCTTTC
Found at i:33652 original size:29 final size:29
Alignment explanation
Indices: 33606--33669 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
33596 CAAATTCACC
*
33606 TGGCGACCTACAACGTCGCCCCAACTGCA
1 TGGCGAACTACAACGTCGCCCCAACTGCA
* * *
33635 TGGCGAACTATAAGGTCGCCCCTACTGCA
1 TGGCGAACTACAACGTCGCCCCAACTGCA
33664 TGGCGA
1 TGGCGA
33670 CATACCTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.17
Consensus pattern (29 bp):
TGGCGAACTACAACGTCGCCCCAACTGCA
Found at i:35225 original size:13 final size:14
Alignment explanation
Indices: 35186--35244 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
35176 ATGGTAAACG
*
35186 AACACAAATGAACA
1 AACATAAATGAACA
*
35200 AACATAAACGAACA
1 AACATAAATGAACA
*
35214 CA-ATAAATGAACATA
1 AACATAAATGAAC--A
*
35229 AACGTAAATGAACA
1 AACATAAATGAACA
35243 AA
1 AA
35245 ACAAACGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
13 9 0.25
14 16 0.44
15 2 0.06
16 9 0.25
ACGTcount: A:0.63, C:0.17, G:0.08, T:0.12
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:35230 original size:23 final size:24
Alignment explanation
Indices: 35180--35232 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
35170 CATTAAATGG
*
35180 TAAACGAACACAAATGAACAAACA
1 TAAACGAACACAAATAAACAAACA
**
35204 TAAACGAACAC-AATAAATGAACA
1 TAAACGAACACAAATAAACAAACA
35227 TAAACG
1 TAAACG
35233 TAAATGAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.60, C:0.19, G:0.09, T:0.11
Consensus pattern (24 bp):
TAAACGAACACAAATAAACAAACA
Found at i:35238 original size:16 final size:15
Alignment explanation
Indices: 35217--35259 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
35207 ACGAACACAA
35217 TAAATGAACATAAAC
1 TAAATGAACATAAAC
35232 GTAAATGAACA-AAAC
1 -TAAATGAACATAAAC
*
35247 -AAACGAACATAAA
1 TAAATGAACATAAA
35260 TGAACATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 8 0.32
14 3 0.12
15 4 0.16
16 10 0.40
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (15 bp):
TAAATGAACATAAAC
Found at i:35241 original size:29 final size:29
Alignment explanation
Indices: 35189--35259 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
35179 GTAAACGAAC
*
35189 ACAAATGAAC--AAACATAAACGAACACA
1 ACAAATGAACATAAACATAAACGAACAAA
* * *
35216 ATAAATGAACATAAACGTAAATGAACAAA
1 ACAAATGAACATAAACATAAACGAACAAA
*
35245 ACAAACGAACATAAA
1 ACAAATGAACATAAA
35260 TGAACATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 9 0.25
29 27 0.75
ACGTcount: A:0.63, C:0.17, G:0.08, T:0.11
Consensus pattern (29 bp):
ACAAATGAACATAAACATAAACGAACAAA
Found at i:36667 original size:2 final size:2
Alignment explanation
Indices: 36660--36688 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36650 ACATATCCTA
36660 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36689 CTTATACTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47253 original size:11 final size:11
Alignment explanation
Indices: 47239--47272 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
47229 CAAAATTTTG
47239 TAAAAAAAAAA
1 TAAAAAAAAAA
*
47250 TAAAAAAATAA
1 TAAAAAAAAAA
*
47261 TAATAAAAAAA
1 TAAAAAAAAAA
47272 T
1 T
47273 TTGATTCACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
TAAAAAAAAAA
Found at i:47272 original size:14 final size:13
Alignment explanation
Indices: 47240--47272 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
47230 AAAATTTTGT
47240 AAAAAA-AAAATA
1 AAAAAATAAAATA
47252 AAAAAATAATAATA
1 AAAAAATAA-AATA
47266 AAAAAAT
1 AAAAAAT
47273 TTGATTCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 2 0.11
14 11 0.58
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAAATAAAATA
Found at i:50368 original size:9 final size:9
Alignment explanation
Indices: 50356--50399 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
50346 TCCATTGCCT
50356 CCACCTCCA
1 CCACCTCCA
*
50365 CCACCTCCT
1 CCACCTCCA
50374 CCACCGCTTCCA
1 CCA-C-C-TCCA
50386 CCACCTCCA
1 CCACCTCCA
50395 CCACC
1 CCACC
50400 GCTTCCAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
9 20 0.67
10 2 0.07
11 2 0.07
12 6 0.20
ACGTcount: A:0.18, C:0.66, G:0.02, T:0.14
Consensus pattern (9 bp):
CCACCTCCA
Found at i:50387 original size:21 final size:21
Alignment explanation
Indices: 50361--50406 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
50351 TGCCTCCACC
*
50361 TCCACCACCTCCTCCACCGCT
1 TCCACCACCTCCACCACCGCT
50382 TCCACCACCTCCACCACCGCT
1 TCCACCACCTCCACCACCGCT
50403 TCCA
1 TCCA
50407 GACCCGTATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.61, G:0.04, T:0.17
Consensus pattern (21 bp):
TCCACCACCTCCACCACCGCT
Found at i:50422 original size:12 final size:12
Alignment explanation
Indices: 50403--50438 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
50393 CACCACCGCT
*
50403 TCCAGACCCGTA
1 TCCAGACCCATA
*
50415 TCCGGACCCATA
1 TCCAGACCCATA
50427 TCCAGACCCATA
1 TCCAGACCCATA
50439 CCCACTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.28, C:0.42, G:0.14, T:0.17
Consensus pattern (12 bp):
TCCAGACCCATA
Found at i:51061 original size:15 final size:15
Alignment explanation
Indices: 51043--51073 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51033 AAATTCTAAA
51043 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
51058 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
51073 T
1 T
51074 CTATTTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:55103 original size:2 final size:2
Alignment explanation
Indices: 55096--55134 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55086 TTTACATTCT
55096 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55135 TAATGAACTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57989 original size:20 final size:18
Alignment explanation
Indices: 57964--58022 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
57954 CTAGACTACC
57964 AGGAAAAGAGTCAAAAGCAA
1 AGGAAAA-A-TCAAAAGCAA
*
57984 AGGAAAAATTAAAAGCAA
1 AGGAAAAATCAAAAGCAA
*
58002 AGGAAAATAATCAAAATCAA
1 AGG-AAA-AATCAAAAGCAA
58022 A
1 A
58023 AGCAAAGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 12 0.35
19 4 0.12
20 18 0.53
ACGTcount: A:0.64, C:0.08, G:0.17, T:0.10
Consensus pattern (18 bp):
AGGAAAAATCAAAAGCAA
Found at i:60718 original size:109 final size:107
Alignment explanation
Indices: 60568--61030 Score: 437
Period size: 114 Copynumber: 4.3 Consensus size: 107
60558 TTTGCTGAGC
* * * * *
60568 AATATAAATTATTGGACTAATTATTTTTATTTTACAGATTAAATCATATTTGAGTGGTTTGATAA
1 AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATCATATTTGAGTAGTTTGATAA
60633 GTTTAGTTTAAATTTTATTGTTTTGTTTTTTGTTTTTATTGTA
66 GTTTAGTTTAAATTTTATTGTTTTGTTTTTT-TTTTTATTGTA
* ** * *
60676 AATATAAATTAATTAGACTATTTATTTTGATTTTACAAATTAAATTGTATTCGAGTGGTTTGATA
1 AATATAAATT-ATTAGACTATTTATTTTGATTTTACATATTAAATCATATTTGAGTAGTTTGATA
* * * **
60741 A-TTGTAATTTTAATTTTTATATTATTTTTAGTATAGTTTTTTTCAATT-TA
65 AGTT-T-AGTTTAA-ATTT-TATT-GTTTT-GT-T--TTTTTTTTTATTGTA
* * ** *
60791 AAT-TATAATTATTAGACAATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAGTTTGGTA
1 AATATA-AATTATTAGACTATTTATTTTGATTTTACATATTAAATCATATTTGAGTAGTTTGATA
* * * * *
60855 AGTTTAGTTTAAATTATA-TG-TTTATTTGTTTATTGA--GT-
65 AGTTTAGTTTAAATTTTATTGTTTTGTTTTTTTTTTTATTGTA
* *
60893 AATATAATTTATTAGACTA---ATTTT-ATTTTACATATTAAATCATATTTGAGTAGTTTGGTAA
1 AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATCATATTTGAGTAGTTTGATAA
* *
60954 GTTTAATTTAAATTTTATTGTTTTGTTTTTTGTTTTTAATGTA
66 GTTTAGTTTAAATTTTATTGTTTTGTTTTTT-TTTTTATTGTA
*
60997 AATATAAATAAATTAGACTATTTATTTTTGATTT
1 AATATAAAT-TATTAGACTATTTA-TTTTGATTT
61031 AACAGATTTT
Statistics
Matches: 289, Mismatches: 40, Indels: 50
0.76 0.11 0.13
Matches are distributed among these distances:
98 49 0.17
99 7 0.02
100 8 0.03
101 4 0.01
102 14 0.05
103 5 0.02
104 14 0.05
105 9 0.03
106 1 0.00
107 1 0.00
108 16 0.06
109 53 0.18
110 11 0.04
111 5 0.02
112 6 0.02
113 10 0.03
114 54 0.19
115 12 0.04
116 6 0.02
117 4 0.01
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.54
Consensus pattern (107 bp):
AATATAAATTATTAGACTATTTATTTTGATTTTACATATTAAATCATATTTGAGTAGTTTGATAA
GTTTAGTTTAAATTTTATTGTTTTGTTTTTTTTTTTATTGTA
Found at i:60880 original size:114 final size:107
Alignment explanation
Indices: 60303--61030 Score: 432
Period size: 109 Copynumber: 6.8 Consensus size: 107
60293 TGGTAAGCGA
* * * ***
60303 TTTGATAAATTTAGTGTGAATTTTATTGTTTCA-TTTTAAATTTTTATT-TGAAATATAAATTAA
1 TTTGATAAGTTTAGTTTAAATTTTA-TGTTT-ATTTTTTTGTTTTTATTGT-AAATATAAATT-A
* * * * *
60366 ATAGATTAA-TTATTTTGA-TTTACATATTAAACTGTATTCGAGTGG
62 TTAGA-CAATTTATTTTGATTTTACAAATTAAATTGTATTTGAGTGG
* ** * *
60411 TTTGGTAAGTTTAAATTAAATTTTTTGTGTAATTTTATTT-TTAATTTAGTT-TAAAT-TATAAT
1 TTTGATAAGTTTAGTTTAAATTTTATGT-TTATTTT-TTTGTT--TTTA-TTGTAAATATA-AAT
* ** * * * **
60473 TATTATAGTATTTATTTTGATTTTACATATTAAGTTGTATTAGAGTAAAA
60 TATTAGACAATTTATTTTGATTTTACAAATTAAATTGTATTTGAGT--GG
* * * * * * * *
60523 CTTGGTAAGTTTAGTTTAAATTATATTTTTATTTTTTTG--CTGA--G-CAATATAAATTATTGG
1 TTTGATAAGTTTAGTTTAAATTTTATGTTTATTTTTTTGTTTTTATTGTAAATATAAATTATTAG
* * **
60583 ACTAA-TTATTTTTATTTTACAGATTAAATCATATTTGAGTGG
66 AC-AATTTATTTTGATTTTACAAATTAAATTGTATTTGAGTGG
60625 TTTGATAAGTTTAGTTTAAATTTTATTGTTT-TGTTTTTTGTTTTTATTGTAAATATAAATTAAT
1 TTTGATAAGTTTAGTTTAAATTTTA-TGTTTAT-TTTTTTGTTTTTATTGTAAATATAAATT-AT
* *
60689 TAGACTATTTATTTTGATTTTACAAATTAAATTGTATTCGAGTGG
63 TAGACAATTTATTTTGATTTTACAAATTAAATTGTATTTGAGTGG
* * *
60734 TTTGATAA-TTGTAATTTTAATTTTTAT-ATTATTTTTAGTATAGTTTTTTTCAATT-TAAAT-T
1 TTTGATAAGTT-T-AGTTTAAATTTTATGTTTATTTTT--T-T-G--TTTTT--ATTGTAAATAT
* * *
60795 ATAATTATTAGACAATTTATTTTGATTTTACATATTAAGTTGTATTTGAGTAG
56 A-AATTATTAGACAATTTATTTTGATTTTACAAATTAAATTGTATTTGAGTGG
* * * * * *
60848 TTTGGTAAGTTTAGTTTAAATTATATGTTTA-TTTGTT-TATTGA--GT-AATATAATTTATTAG
1 TTTGATAAGTTTAGTTTAAATTTTATGTTTATTTTTTTGTTTTTATTGTAAATATAAATTATTAG
* * ** *
60908 AC---TAATTTT-ATTTTACATATTAAATCATATTTGAGTAG
66 ACAATTTATTTTGATTTTACAAATTAAATTGTATTTGAGTGG
* * * *
60946 TTTGGTAAGTTTAATTTAAATTTTATTGTTT-TGTTTTTTGTTTTTAATGTAAATATAAATAAAT
1 TTTGATAAGTTTAGTTTAAATTTTA-TGTTTAT-TTTTTTGTTTTTATTGTAAATATAAAT-TAT
*
61010 TAGACTATTTATTTTTGATTT
63 TAGACAATTTA-TTTTGATTT
61031 AACAGATTTT
Statistics
Matches: 483, Mismatches: 84, Indels: 104
0.72 0.13 0.15
Matches are distributed among these distances:
98 49 0.10
99 11 0.02
100 5 0.01
101 4 0.01
102 36 0.07
103 16 0.03
104 49 0.10
105 12 0.02
106 3 0.01
107 7 0.01
108 46 0.10
109 69 0.14
110 54 0.11
111 11 0.02
112 23 0.05
113 14 0.03
114 60 0.12
115 11 0.02
116 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.54
Consensus pattern (107 bp):
TTTGATAAGTTTAGTTTAAATTTTATGTTTATTTTTTTGTTTTTATTGTAAATATAAATTATTAG
ACAATTTATTTTGATTTTACAAATTAAATTGTATTTGAGTGG
Found at i:60978 original size:321 final size:321
Alignment explanation
Indices: 60343--61030 Score: 935
Period size: 321 Copynumber: 2.1 Consensus size: 321
60333 TCATTTTAAA
* * * *
60343 TTTTTATT-TGAAATATAAATTAAATAGATTAATTATTTTGA-TTTACATATTAAACTGTATTCG
1 TTTTTATTGT-AAATATAAATTAATTAGACTATTTATTTTGATTTTACAAATTAAACTGTATTCG
* * *
60406 AGTGGTTTGGTAAGTTTAAATTAAATTTTTTGTGTAATTTTATTTTTAATTTAGTTTAAATTATA
65 AGTGGTTTGATAAGTTTAAATTAAATTTTTTATGTAATTTTATTTTTAATTTAATTTAAATTATA
* **
60471 ATTATTATAGTATTTATTTTGATTTTACATATTAAGTTGTATTAGAGTAAAACTTGGTAAGTTTA
130 ATTATTAGACAATTTATTTTGATTTTACATATTAAGTTGTATTAGAGT-AAACTTGGTAAGTTTA
* * * *
60536 GTTTAAATTATATTTTTATTTTTTTGCTGAGCAATATAAATTATTGGACTAATTATTTTTATTTT
194 GTTTAAATTATATGTTTATTTGTTTACTGAGCAATATAAATTATTAGACTAA-TATTTTTATTTT
* *
60601 ACAGATTAAATCATATTTGAGTGGTTTGATAAGTTTAGTTTAAATTTTATTGTTTTGTTTTTTG
258 ACAGATTAAATCATATTTGAGTAGTTTGATAAGTTTAATTTAAATTTTATTGTTTTGTTTTTTG
*
60665 TTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAAATTAAATTGTATTCGA
1 TTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAAATTAAACTGTATTCGA
* * * *
60730 GTGGTTTGATAA-TTGTAATTTTAATTTTTATAT-TATTTTTAGTATAGTTT-TTTTCAATTTAA
66 GTGGTTTGATAAGTT-TAAATTAAATTTTT-TATGTAATTTTA-T-T--TTTAATTT-AATTTAA
* **
60792 ATTATAATTATTAGACAATTTATTTTGATTTTACATATTAAGTTGTATTTGAGT-AGTTTGGTAA
124 ATTATAATTATTAGACAATTTATTTTGATTTTACATATTAAGTTGTATTAGAGTAAACTTGGTAA
* * *
60856 GTTTAGTTTAAATTATATGTTTATTTGTTTATTGAGTAATATAATTTATTAGACT-A-A-TTTTA
189 GTTTAGTTTAAATTATATGTTTATTTGTTTACTGAGCAATATAAATTATTAGACTAATATTTTTA
* *
60918 TTTTACATATTAAATCATATTTGAGTAGTTTGGTAAGTTTAATTTAAATTTTATTGTTTTGTTTT
254 TTTTACAGATTAAATCATATTTGAGTAGTTTGATAAGTTTAATTTAAATTTTATTGTTTTGTTTT
60983 TTG
319 TTG
* *
60986 TTTTTAATGTAAATATAAATAAATTAGACTATTTATTTTTGATTT
1 TTTTTATTGTAAATATAAATTAATTAGACTATTTA-TTTTGATTT
61031 AACAGATTTT
Statistics
Matches: 325, Mismatches: 31, Indels: 20
0.86 0.08 0.05
Matches are distributed among these distances:
321 102 0.31
322 48 0.15
323 52 0.16
324 4 0.01
325 57 0.18
326 3 0.01
327 59 0.18
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.54
Consensus pattern (321 bp):
TTTTTATTGTAAATATAAATTAATTAGACTATTTATTTTGATTTTACAAATTAAACTGTATTCGA
GTGGTTTGATAAGTTTAAATTAAATTTTTTATGTAATTTTATTTTTAATTTAATTTAAATTATAA
TTATTAGACAATTTATTTTGATTTTACATATTAAGTTGTATTAGAGTAAACTTGGTAAGTTTAGT
TTAAATTATATGTTTATTTGTTTACTGAGCAATATAAATTATTAGACTAATATTTTTATTTTACA
GATTAAATCATATTTGAGTAGTTTGATAAGTTTAATTTAAATTTTATTGTTTTGTTTTTTG
Found at i:63264 original size:63 final size:63
Alignment explanation
Indices: 63142--63264 Score: 158
Period size: 63 Copynumber: 2.0 Consensus size: 63
63132 ATTCACATAG
* * * * *
63142 AAATATTTATATTAATCACATTCATTCAAATATAACATCAACAAATATCTATTACATTCATTC
1 AAATATTGATATTAATCACATTCATTCAAATATAACATCAACAAATAACCATGAAATTCATTC
* * *
63205 AAATATTGATATTAATCATATTCATTCAAATTTAACATCAACAAGTAGACCA-GAAATTCA
1 AAATATTGATATTAATCACATTCATTCAAATATAACATCAACAAATA-ACCATGAAATTCA
63265 ATTATTCGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 49 0.96
64 2 0.04
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.35
Consensus pattern (63 bp):
AAATATTGATATTAATCACATTCATTCAAATATAACATCAACAAATAACCATGAAATTCATTC
Found at i:65653 original size:10 final size:10
Alignment explanation
Indices: 65638--65674 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
65628 AAACCAGTTC
65638 GACCGGTTTT
1 GACCGGTTTT
65648 GACCGG-TTT
1 GACCGGTTTT
65657 GACCGGTTTT
1 GACCGGTTTT
65667 GACCGGTT
1 GACCGGTT
65675 CGAACCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.11, C:0.22, G:0.32, T:0.35
Consensus pattern (10 bp):
GACCGGTTTT
Found at i:65659 original size:9 final size:9
Alignment explanation
Indices: 65638--65698 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
65628 AAACCAGTTC
65638 GACCGGTTTT
1 GACCGG-TTT
65648 GACCGGTTT
1 GACCGGTTT
65657 GACCGGTTTT
1 GACCGG-TTT
*
65667 GACCGGTTC
1 GACCGGTTT
**
65676 GAACCATTTT
1 G-ACCGGTTT
*
65686 GACCGGTCT
1 GACCGGTTT
65695 GACC
1 GACC
65699 CGACCCAACC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
9 21 0.50
10 21 0.50
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (9 bp):
GACCGGTTT
Found at i:65662 original size:19 final size:19
Alignment explanation
Indices: 65638--65698 Score: 79
Period size: 19 Copynumber: 3.2 Consensus size: 19
65628 AAACCAGTTC
65638 GACCGGTTTTGACCGGTTT
1 GACCGGTTTTGACCGGTTT
*
65657 GACCGGTTTTGACCGGTTC
1 GACCGGTTTTGACCGGTTT
* *
65676 GAACC-ATTTTGACCGGTCT
1 G-ACCGGTTTTGACCGGTTT
65695 GACC
1 GACC
65699 CGACCCAACC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
18 3 0.08
19 31 0.84
20 3 0.08
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (19 bp):
GACCGGTTTTGACCGGTTT
Found at i:65709 original size:5 final size:5
Alignment explanation
Indices: 65695--65749 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
65685 TGACCGGTCT
* * *
65695 GACCC GACCC AACCC GA-CC AACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC
65746 GACC
1 GACC
65750 GTTGACCGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
4 3 0.07
5 34 0.83
7 4 0.10
ACGTcount: A:0.24, C:0.55, G:0.18, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:65720 original size:19 final size:19
Alignment explanation
Indices: 65696--65732 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
65686 GACCGGTCTG
65696 ACCCGACCCAACCCGACCA
1 ACCCGACCCAACCCGACCA
*
65715 ACCCGACCCGACCCGACC
1 ACCCGACCCAACCCGACC
65733 GTTGACCCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.59, G:0.14, T:0.00
Consensus pattern (19 bp):
ACCCGACCCAACCCGACCA
Found at i:65741 original size:17 final size:17
Alignment explanation
Indices: 65719--65756 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
65709 CGACCAACCC
65719 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
65736 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
65753 GACC
1 GACC
65757 GTTGACTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:72827 original size:20 final size:19
Alignment explanation
Indices: 72802--72874 Score: 92
Period size: 20 Copynumber: 3.7 Consensus size: 19
72792 TGCTGGAAAT
72802 CGGTTTGACCGGTTTACAAC
1 CGGTTTGACCGGTTT-CAAC
*
72822 CGGTTTGGACCGGTTTCGAC
1 CGGTTT-GACCGGTTTCAAC
* *
72842 CGGTTTTGACCGGTCTGAAC
1 CGG-TTTGACCGGTTTCAAC
72862 CGGTTTGACCGGT
1 CGGTTTGACCGGT
72875 CTGACCCGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 10 0.21
20 25 0.53
21 12 0.26
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.30
Consensus pattern (19 bp):
CGGTTTGACCGGTTTCAAC
Found at i:72835 original size:10 final size:9
Alignment explanation
Indices: 72802--72880 Score: 77
Period size: 10 Copynumber: 8.1 Consensus size: 9
72792 TGCTGGAAAT
72802 CGGTTTGAC
1 CGGTTTGAC
*
72811 CGGTTTACAAC
1 CGGTTT--GAC
72822 CGGTTTGGAC
1 CGGTTT-GAC
72832 CGGTTTCGAC
1 CGGTTT-GAC
72842 CGGTTTTGAC
1 CGG-TTTGAC
*
72852 CGGTCTGAAC
1 CGGTTTG-AC
72862 CGGTTTGAC
1 CGGTTTGAC
*
72871 CGGTCTGAC
1 CGGTTTGAC
72880 C
1 C
72881 CGACCCGACC
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
9 20 0.34
10 28 0.47
11 11 0.19
ACGTcount: A:0.14, C:0.27, G:0.30, T:0.29
Consensus pattern (9 bp):
CGGTTTGAC
Found at i:72854 original size:30 final size:30
Alignment explanation
Indices: 72802--72874 Score: 94
Period size: 30 Copynumber: 2.4 Consensus size: 30
72792 TGCTGGAAAT
* *
72802 CGGTTTGACCGGTTTACAACCGGTTTGGAC
1 CGGTTTGACCGGTTTACAACCGGTCTGAAC
**
72832 CGGTTTCGACCGGTTT-TGACCGGTCTGAAC
1 CGGTTT-GACCGGTTTACAACCGGTCTGAAC
72862 CGGTTTGACCGGT
1 CGGTTTGACCGGT
72875 CTGACCCGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 7 0.18
30 22 0.58
31 9 0.24
ACGTcount: A:0.14, C:0.25, G:0.32, T:0.30
Consensus pattern (30 bp):
CGGTTTGACCGGTTTACAACCGGTCTGAAC
Found at i:72887 original size:5 final size:5
Alignment explanation
Indices: 72877--72926 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
72867 TGACCGGTCT
* *
72877 GACCC GACCC GA-CC AACCC GACCC GACCC GACCATT GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACC
72927 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
4 3 0.08
5 31 0.82
7 4 0.11
ACGTcount: A:0.24, C:0.54, G:0.18, T:0.04
Consensus pattern (5 bp):
GACCC
Found at i:72890 original size:19 final size:19
Alignment explanation
Indices: 72868--72927 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
72858 GAACCGGTTT
*
72868 GACCGGTCTGACCCGACCC
1 GACCGATCTGACCCGACCC
* * *
72887 GACCAACCCGACCCGACCC
1 GACCGATCTGACCCGACCC
72906 GACC-AT-TGACCCGACCC
1 GACCGATCTGACCCGACCC
72923 GACCG
1 GACCG
72928 TTGACCGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 14 0.41
18 1 0.03
19 19 0.56
ACGTcount: A:0.22, C:0.50, G:0.22, T:0.07
Consensus pattern (19 bp):
GACCGATCTGACCCGACCC
Found at i:72895 original size:14 final size:14
Alignment explanation
Indices: 72878--72904 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72868 GACCGGTCTG
72878 ACCCGACCCGACCA
1 ACCCGACCCGACCA
72892 ACCCGACCCGACC
1 ACCCGACCCGACC
72905 CGACCATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.59, G:0.15, T:0.00
Consensus pattern (14 bp):
ACCCGACCCGACCA
Found at i:72918 original size:17 final size:17
Alignment explanation
Indices: 72876--72933 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
72866 TTGACCGGTC
*
72876 TGACCCGACCCGACCAACC
1 TGACCCGACCCGACC-A-T
*
72895 CGACCCGACCCGACCAT
1 TGACCCGACCCGACCAT
*
72912 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCAT
72929 TGACC
1 TGACC
72934 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 20 0.57
18 1 0.03
19 14 0.40
ACGTcount: A:0.22, C:0.50, G:0.19, T:0.09
Consensus pattern (17 bp):
TGACCCGACCCGACCAT
Found at i:75465 original size:17 final size:17
Alignment explanation
Indices: 75440--75475 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
75430 AGATATTCAG
75440 AATAAATAAAAAAATAA
1 AATAAATAAAAAAATAA
* *
75457 AATACATAAATAAATAA
1 AATAAATAAAAAAATAA
75474 AA
1 AA
75476 CAATTTTTGA
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:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (17 bp):
AATAAATAAAAAAATAA
Found at i:75508 original size:16 final size:16
Alignment explanation
Indices: 75487--75525 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
75477 AATTTTTGAC
75487 ATATTAGATTAAAATT
1 ATATTAGATTAAAATT
*
75503 ATATTAGATTAAAGTT
1 ATATTAGATTAAAATT
75519 ACTATTA
1 A-TATTA
75526 CTATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (16 bp):
ATATTAGATTAAAATT
Found at i:75535 original size:3 final size:3
Alignment explanation
Indices: 75521--75554 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
75511 TTAAAGTTAC
*
75521 TAT TAC TAT TAT TAT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
75555 AAATTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:75541 original size:17 final size:17
Alignment explanation
Indices: 75521--75554 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
75511 TTAAAGTTAC
75521 TATTACTATTATTATTA
1 TATTACTATTATTATTA
*
75538 TATTATTATTATTATTA
1 TATTACTATTATTATTA
75555 AAATTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTACTATTATTATTA
Found at i:75636 original size:46 final size:46
Alignment explanation
Indices: 75580--75694 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
75570 TTTTTAACGT
* *
75580 TTTTTCTAGAAATACTAAATCAATATTATTTTAACATTTTTAAAAA
1 TTTTACTAGAAATACTAAATCAATATTATTTTAACAATTTTAAAAA
* * * *
75626 TTTTACTAGAAAAACTAAATCAATATTATTTTAATAATTTTAACAT
1 TTTTACTAGAAATACTAAATCAATATTATTTTAACAATTTTAAAAA
75672 TTTTACTAGAAATACTAAATCAA
1 TTTTACTAGAAATACTAAATCAA
75695 ATTTTGATCA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.43
Consensus pattern (46 bp):
TTTTACTAGAAATACTAAATCAATATTATTTTAACAATTTTAAAAA
Found at i:75870 original size:16 final size:17
Alignment explanation
Indices: 75839--75870 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
75829 ATAACTACTT
75839 ATGATTAAATTATAATA
1 ATGATTAAATTATAATA
75856 ATGATTAAA-TATAAT
1 ATGATTAAATTATAAT
75871 TAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (17 bp):
ATGATTAAATTATAATA
Found at i:79417 original size:17 final size:17
Alignment explanation
Indices: 79389--79421 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
79379 TTGAGTATTT
79389 ATATTGTAGTTTAGAATC
1 ATATTGTAGTTT-GAATC
79407 ATATT-TAGTTTGAAT
1 ATATTGTAGTTTGAAT
79422 TTGAATATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.48
Consensus pattern (17 bp):
ATATTGTAGTTTGAATC
Found at i:80311 original size:15 final size:15
Alignment explanation
Indices: 80291--80319 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
80281 AATAATTTTG
80291 ATAGCCGCCCATGTC
1 ATAGCCGCCCATGTC
80306 ATAGCCGCCCATGT
1 ATAGCCGCCCATGT
80320 TTTGTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (15 bp):
ATAGCCGCCCATGTC
Found at i:84923 original size:15 final size:15
Alignment explanation
Indices: 84903--84931 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
84893 AATAATTTTG
84903 ATAGCCGCCCATGTC
1 ATAGCCGCCCATGTC
84918 ATAGCCGCCCATGT
1 ATAGCCGCCCATGT
84932 TTTGTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (15 bp):
ATAGCCGCCCATGTC
Found at i:94708 original size:9 final size:9
Alignment explanation
Indices: 94694--94720 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
94684 TAATAACTCG
94694 GATATTTCT
1 GATATTTCT
94703 GATATTTCT
1 GATATTTCT
94712 GATATTTCT
1 GATATTTCT
94721 ACCCATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (9 bp):
GATATTTCT
Found at i:96174 original size:49 final size:49
Alignment explanation
Indices: 96080--96174 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
96070 CACACTCCAA
* * * *
96080 TTTGCCTTTTCATCGCGACTAGGAGGGTTGGATAGAGCCATTTATCGAG
1 TTTGCCTTTCCATCGCGACTAGGAGGGTTCGATAGAGACACTTATCGAG
* *
96129 TTTGCCTTTCCATTGTGACTAGGAGGGGTTCGATAG-GACACTTATC
1 TTTGCCTTTCCATCGCGACTAGGA-GGGTTCGATAGAGACACTTATC
96175 CATCTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 29 0.74
50 10 0.26
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (49 bp):
TTTGCCTTTCCATCGCGACTAGGAGGGTTCGATAGAGACACTTATCGAG
Found at i:97897 original size:15 final size:16
Alignment explanation
Indices: 97867--97909 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
97857 ATAAATCACT
97867 TACCCGGATGTTTCGGA
1 TACCCGGAT-TTTCGGA
*
97884 TACCC-GATTTTCGGG
1 TACCCGGATTTTCGGA
97899 TACCCGGATTT
1 TACCCGGATTT
97910 GCACACCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 11 0.46
16 8 0.33
17 5 0.21
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (16 bp):
TACCCGGATTTTCGGA
Found at i:102599 original size:20 final size:20
Alignment explanation
Indices: 102564--102624 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
102554 CCGAGTGATG
102564 ATTAT-TATATATATATGT-T
1 ATTATATATATATATAT-TAT
102583 ATTATATATA-ATAATATTAT
1 ATTATATATATAT-ATATTAT
102603 ATTATA-A-ATAT-TATTAT
1 ATTATATATATATATATTAT
102620 -TTATA
1 ATTATA
102625 AATCCTGAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 5 0.13
17 6 0.16
18 1 0.03
19 11 0.29
20 15 0.39
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
ATTATATATATATATATTAT
Found at i:102626 original size:16 final size:16
Alignment explanation
Indices: 102564--102627 Score: 76
Period size: 16 Copynumber: 4.0 Consensus size: 16
102554 CCGAGTGATG
*
102564 ATTATTATATATATAT
1 ATTATTATATATAAAT
*
102580 GTTATTATATAT-AAT
1 ATTATTATATATAAAT
*
102595 AATATTATATTATAAAT
1 ATTATTATA-TATAAAT
*
102612 ATTATTATTTATAAAT
1 ATTATTATATATAAAT
102628 CCTGAAGGCC
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
15 9 0.22
16 21 0.52
17 10 0.25
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTATTATATATAAAT
Found at i:109286 original size:22 final size:22
Alignment explanation
Indices: 109258--109339 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
109248 AATTCGGTAT
*
109258 TGTTCACGGTACTGTTAATTAC
1 TGTTCACGGTACTGTTCATTAC
*
109280 TGTTCACGGTAATGTTCATTAC
1 TGTTCACGGTACTGTTCATTAC
* * * *
109302 TATTCACAGCACTGTTCATTAT
1 TGTTCACGGTACTGTTCATTAC
*
109324 TGTTCACGGTTCTGTT
1 TGTTCACGGTACTGTT
109340 TATATCATAG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.21, C:0.20, G:0.17, T:0.43
Consensus pattern (22 bp):
TGTTCACGGTACTGTTCATTAC
Found at i:110272 original size:21 final size:21
Alignment explanation
Indices: 110246--110307 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
110236 GAGTCGAGAT
* * *
110246 TACAGTGTTTTTTCGGGATAA
1 TACAGTGGTCTTTCGGGACAA
*
110267 TACAGTGGTCTTTCAGGACAA
1 TACAGTGGTCTTTCGGGACAA
110288 TACAGTGGTCTTTCGGGACA
1 TACAGTGGTCTTTCGGGACA
110308 TAGTGGTCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (21 bp):
TACAGTGGTCTTTCGGGACAA
Found at i:110314 original size:18 final size:20
Alignment explanation
Indices: 110265--110326 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
110255 TTTTCGGGAT
110265 AATACAGTGGTCTTTCAGGAC
1 AATA-AGTGGTCTTTCAGGAC
*
110286 AATACAGTGGTCTTTCGGGAC
1 AATA-AGTGGTCTTTCAGGAC
110307 -AT-AGTGGTCATTT-AGGAC
1 AATAAGTGGTC-TTTCAGGAC
110325 AA
1 AA
110327 ATTTCAGTGC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 11 0.30
19 4 0.11
20 2 0.05
21 20 0.54
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (20 bp):
AATAAGTGGTCTTTCAGGAC
Found at i:110593 original size:18 final size:18
Alignment explanation
Indices: 110570--110613 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
110560 AATGTTAATA
*
110570 CATGATAGTGATAGAGAT
1 CATGATAATGATAGAGAT
110588 CATGATAATGATAGAGAT
1 CATGATAATGATAGAGAT
110606 CATGATAA
1 CATGATAA
110614 AGATGTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (18 bp):
CATGATAATGATAGAGAT
Found at i:113300 original size:22 final size:22
Alignment explanation
Indices: 113272--113313 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
113262 ATGTTGTAAA
113272 GATGATAGATTCTCTTTTCAAG
1 GATGATAGATTCTCTTTTCAAG
*
113294 GATGATAGATTTTCTTTTCA
1 GATGATAGATTCTCTTTTCA
113314 TAGACAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (22 bp):
GATGATAGATTCTCTTTTCAAG
Found at i:114107 original size:20 final size:20
Alignment explanation
Indices: 114082--114132 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
114072 AACCAACAAA
*
114082 AACCCTAGGGTGCTCATTGC
1 AACCCTAGGGCGCTCATTGC
114102 AACCCTAGGGCGCTCATTGC
1 AACCCTAGGGCGCTCATTGC
114122 AACCCTAGGGC
1 AACCCTAGGGC
114133 CTATTCTGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.22, C:0.33, G:0.25, T:0.20
Consensus pattern (20 bp):
AACCCTAGGGCGCTCATTGC
Found at i:117980 original size:16 final size:17
Alignment explanation
Indices: 117954--117986 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
117944 TTAACTGTAC
117954 AAATAATTAAAATAAAT
1 AAATAATTAAAATAAAT
117971 AAATAA-TAAAATAAAT
1 AAATAATTAAAATAAAT
117987 TTTACATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAATAATTAAAATAAAT
Done.