Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009125.1 Hibiscus syriacus cultivar Beakdansim tig00112616_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: 108628
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Found at i:575 original size:13 final size:13
Alignment explanation
Indices: 553--602 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
543 TCCTTCTTCA
*
553 TTTTTCTTTCTTT
1 TTTTTTTTTCTTT
566 TTTTTTTTTCTTT
1 TTTTTTTTTCTTT
*
579 TTTTCTTTTCTTT
1 TTTTTTTTTCTTT
592 TCATTTTTTTT
1 T--TTTTTTTT
603 TCTTCAAGCA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
13 25 0.78
15 7 0.22
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTTTTTCTTT
Found at i:584 original size:21 final size:21
Alignment explanation
Indices: 549--606 Score: 50
Period size: 23 Copynumber: 2.8 Consensus size: 21
539 ACCCTCCTTC
*
549 TTCATTTTTCTTTCTTTT-TT
1 TTCATTTTTTTTTCTTTTCTT
*
569 TT--TTTTCTTTTTTTCTTTTCTT
1 TTCATTTT-TTTTTCT-TTT-CTT
591 TTCATTTTTTTTTCTT
1 TTCATTTTTTTTTCTT
607 CAAGCATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
18 4 0.14
19 5 0.17
20 5 0.17
22 5 0.17
23 6 0.21
24 4 0.14
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (21 bp):
TTCATTTTTTTTTCTTTTCTT
Found at i:17700 original size:23 final size:22
Alignment explanation
Indices: 17673--17718 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
17663 ATATGTCACA
* *
17673 TTTTAATAATTTTAAAATTTTAT
1 TTTTAA-AAATTTAAAATATTAT
17696 TTTTAAAAATTTAAAATATTAT
1 TTTTAAAAATTTAAAATATTAT
17718 T
1 T
17719 ATATTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAAAATTTAAAATATTAT
Found at i:26211 original size:13 final size:13
Alignment explanation
Indices: 26159--26219 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
26149 AGTATTAAGA
26159 TAAAA-TAAAATT
1 TAAAATTAAAATT
*
26171 CTAACATTAAATATT
1 -TAAAATTAAA-ATT
*
26186 T-AAA-TATAATT
1 TAAAATTAAAATT
26197 TAAAATTAAAATT
1 TAAAATTAAAATT
*
26210 TAACATTAAA
1 TAAAATTAAA
26220 TATTAAACTC
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
11 4 0.10
12 6 0.15
13 21 0.54
14 5 0.13
15 3 0.08
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATTAAAATT
Found at i:26214 original size:38 final size:38
Alignment explanation
Indices: 26159--26236 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
26149 AGTATTAAGA
26159 TAAAATAAAATTCTAACATTAAATATTTAAA-TATAATT
1 TAAAATAAAATTCTAACATTAAATA-TTAAACTATAATT
*
26197 TAAAATTAAAATT-TAACATTAAATATTAAACTCTAATT
1 TAAAA-TAAAATTCTAACATTAAATATTAAACTATAATT
26235 TA
1 TA
26237 CCCGCACTAC
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 5 0.14
38 25 0.68
39 7 0.19
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (38 bp):
TAAAATAAAATTCTAACATTAAATATTAAACTATAATT
Found at i:26220 original size:18 final size:19
Alignment explanation
Indices: 26159--26226 Score: 68
Period size: 19 Copynumber: 3.5 Consensus size: 19
26149 AGTATTAAGA
26159 TAAAA-TAAAATTCTAACAT
1 TAAAATTAAAATT-TAACAT
* * *
26178 TAAATATTTAAATATAA-TT
1 TAAA-ATTAAAATTTAACAT
26197 TAAAATTAAAATTTAACAT
1 TAAAATTAAAATTTAACAT
26216 TAAATATTAAA
1 TAAA-ATTAAA
26227 CTCTAATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
18 10 0.26
19 14 0.36
20 10 0.26
21 5 0.13
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATTAAAATTTAACAT
Found at i:26225 original size:13 final size:14
Alignment explanation
Indices: 26172--26223 Score: 58
Period size: 13 Copynumber: 4.0 Consensus size: 14
26162 AATAAAATTC
26172 TAACATTAAATATT
1 TAACATTAAATATT
*
26186 TAA-A-TATA-ATT
1 TAACATTAAATATT
*
26197 TAAAATTAAA-ATT
1 TAACATTAAATATT
26210 TAACATTAAATATT
1 TAACATTAAATATT
26224 AAACTCTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 6 0.19
12 4 0.12
13 16 0.50
14 6 0.19
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (14 bp):
TAACATTAAATATT
Found at i:28324 original size:48 final size:48
Alignment explanation
Indices: 28253--28349 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
28243 TCACGGTATA
28253 TCAAATACGATACGTTAACTGATAGAGGTTGGTTCAAATGGTTAGTAG
1 TCAAATACGATACGTTAACTGATAGAGGTTGGTTCAAATGGTTAGTAG
28301 TCAAATACGATACGTTAACTGATAGAGGTTGGTTCAAATGGTTAGTAG
1 TCAAATACGATACGTTAACTGATAGAGGTTGGTTCAAATGGTTAGTAG
28349 T
1 T
28350 TTGATATCGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (48 bp):
TCAAATACGATACGTTAACTGATAGAGGTTGGTTCAAATGGTTAGTAG
Found at i:30034 original size:35 final size:35
Alignment explanation
Indices: 29988--30056 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
29978 CAATCCTCAA
* *
29988 TTTCATTCTAAACCCCAATTTCCAAAGTAATTCAT
1 TTTCATTCTAAACCCCAAATTCCAAAATAATTCAT
*
30023 TTTCATTCTAAACCCTAAATTCCAAAATAATTCA
1 TTTCATTCTAAACCCCAAATTCCAAAATAATTCA
30057 ATTAAATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.01, T:0.36
Consensus pattern (35 bp):
TTTCATTCTAAACCCCAAATTCCAAAATAATTCAT
Found at i:30596 original size:130 final size:130
Alignment explanation
Indices: 30455--30702 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
30445 TATTTATATA
**
30455 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
*
30520 TTAGCACATGATCATGACACGTGTCATTGGTAACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACGTGTCATTGGTAACACATGTCACCACCTAATTATTTATATATGCT
30585 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
30650 TTAACACATGATCATGATATGTGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACGTGTCATTGGTAACACATGTCACCACCTAATTA
30703 GAAGAAAATT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACGTGTCATTGGTAACACATGTCACCACCTAATTATTTATATATGCT
Found at i:30672 original size:23 final size:21
Alignment explanation
Indices: 30629--30675 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
30619 AATTAATCAT
30629 TTAACCAGGATCTGACATGTG
1 TTAACCAGGATCTGACATGTG
* *
30650 TTAACACATGATCATGATATGTG
1 TTAAC-CAGGATC-TGACATGTG
30673 TTA
1 TTA
30676 TTGGTGACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (21 bp):
TTAACCAGGATCTGACATGTG
Found at i:30733 original size:130 final size:129
Alignment explanation
Indices: 30469--30733 Score: 318
Period size: 130 Copynumber: 2.0 Consensus size: 129
30459 ATTTGGTCCT
** *
30469 AAATTAAATAAAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
*** * * **** *
30534 TGACACGTGTCATTGGTAACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACGTGTCATTGGTAACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
30599 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
30664 TGATATGTGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACGTGTCATTGGTAACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
30728 -A
128 CA
30729 AAATT
1 AAATT
30734 TGGGTCTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
130 101 0.89
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACGTGTCATTGGTAACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:31195 original size:16 final size:18
Alignment explanation
Indices: 31174--31206 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
31164 ATTTCTTATT
31174 AAAAATA-AAAT-ATTCC
1 AAAAATATAAATGATTCC
31190 AAAAATATAAATGATTC
1 AAAAATATAAATGATTC
31207 ATACATTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.61, C:0.09, G:0.03, T:0.27
Consensus pattern (18 bp):
AAAAATATAAATGATTCC
Found at i:32297 original size:154 final size:152
Alignment explanation
Indices: 32032--32325 Score: 403
Period size: 154 Copynumber: 1.9 Consensus size: 152
32022 AAAATTACCA
* *
32032 ATACTTTTGAATTAAAAAAAATGAAAAATGATATTTTAACTTTCGAAGTTAAAAGTATCGATACT
1 ATACTTTCGAATTAAAAAAAATGAAAAATGATATTTTAACTTTCGAAGTTAAAAGTATCAATACT
* **
32097 TTTGGAAAAATATTGATACTTTGCAGCCTTCTCATTTTCCGTGTTTTTCTTTAAATTCGAAAGTA
66 TTTGGAAAAATATCGATACTTTGCAGCCTTCTCATTTTCCACGTTTTT-TTTAAATTCGAAAGTA
*
32162 TCGATACTTTTGGAATTGTATCG
130 TCAATACTTTTGGAATTGTATCG
*
32185 ATACTTTCGAATTAAAAAATATAT-ATAAAATGATATTTTAACTTTC-AATTTAAAAGTATCAAT
1 ATACTTTCGAATTAAAAAA-A-ATGA-AAAATGATATTTTAACTTTCGAAGTTAAAAGTATCAAT
* * * * * * * *
32248 CCTTTTGTAAAATTATCGATACTTTGCAGTCTTTTCATTTTTCACGTTTTTTTTTAATTTGAAAG
63 ACTTTTGGAAAAATATCGATACTTTGCAGCCTTCTCATTTTCCACGTTTTTTTTAAATTCGAAAG
32313 TATCAATACTTTT
128 TATCAATACTTTT
32326 AGAAAAGTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
153 42 0.34
154 59 0.48
155 22 0.18
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.44
Consensus pattern (152 bp):
ATACTTTCGAATTAAAAAAAATGAAAAATGATATTTTAACTTTCGAAGTTAAAAGTATCAATACT
TTTGGAAAAATATCGATACTTTGCAGCCTTCTCATTTTCCACGTTTTTTTTAAATTCGAAAGTAT
CAATACTTTTGGAATTGTATCG
Found at i:32406 original size:51 final size:51
Alignment explanation
Indices: 32308--32406 Score: 162
Period size: 51 Copynumber: 1.9 Consensus size: 51
32298 TTTTTAATTT
**
32308 GAAAGTATCAATACTTTTAGAAAAGTATTCATACTTTCAAATTTTTTAGTC
1 GAAAGTATCAATACTTTTAGAAAAGTATTCATACTTTCAAAAATTTTAGTC
* *
32359 GAAAGTATCAATACTTTTGGAAAATTATTCATACTTTCAAAAATTTTA
1 GAAAGTATCAATACTTTTAGAAAAGTATTCATACTTTCAAAAATTTTA
32407 TAATAGAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (51 bp):
GAAAGTATCAATACTTTTAGAAAAGTATTCATACTTTCAAAAATTTTAGTC
Found at i:32551 original size:77 final size:76
Alignment explanation
Indices: 32468--32692 Score: 267
Period size: 77 Copynumber: 2.9 Consensus size: 76
32458 ACATTATTAT
* *
32468 GTGCAACTCATTTTATTAATAAAAATATTAATATTTCAGATTGCAACCTATTTATTAGTGAATCA
1 GTGCAACCCATTTTATTAATAAAAATATTAACATTTCAGATTGCAACCTATTTATTAGTGAATCA
32533 TGACATCCTTAG
66 TGACATCCTT-G
* * * * *
32545 GTGCAACCCATTTTATTTATAAAAGTATTAACATTCCAGATCGCAACATATTTATTAGTGAAAT-
1 GTGCAACCCATTTTATTAATAAAAATATTAACATTTCAGATTGCAACCTATTTATTAGTG-AATC
* *
32609 ATGATATTCTTG
65 ATGACATCCTTG
* * * *
32621 GACGCAACCCATTTTATTAATAAAGATATTAACA-TTCA-ATATCGCAACCTGTTTTTTAGTGAA
1 G-TGCAACCCATTTTATTAATAAAAATATTAACATTTCAGAT-T-GCAACCTATTTATTAGTGAA
32684 TCATGACAT
63 TCATGACAT
32693 TTTTTAGGCG
Statistics
Matches: 124, Mismatches: 19, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
75 2 0.02
76 8 0.06
77 111 0.90
78 3 0.02
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (76 bp):
GTGCAACCCATTTTATTAATAAAAATATTAACATTTCAGATTGCAACCTATTTATTAGTGAATCA
TGACATCCTTG
Found at i:42494 original size:33 final size:33
Alignment explanation
Indices: 42451--42517 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
42441 TTTGTTTCAA
* *
42451 TTATCGAACTTGGAAGTTTTTAAGTATTTAAAT
1 TTATCAAACTTGGAAGTATTTAAGTATTTAAAT
*
42484 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCAAACTTGGAAGTATTTAAGTATTTAAAT
42517 T
1 T
42518 ATCGTAAACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.45
Consensus pattern (33 bp):
TTATCAAACTTGGAAGTATTTAAGTATTTAAAT
Found at i:63635 original size:19 final size:20
Alignment explanation
Indices: 63592--63635 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
63582 CCTTCCCGAA
63592 AAAATAAAAGATCTTATATC
1 AAAATAAAAGATCTTATATC
*
63612 GAAATAAAA-ATCTTA-ATAC
1 AAAATAAAAGATCTTATAT-C
63631 AAAAT
1 AAAAT
63636 CTGTATGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 2 0.10
19 11 0.52
20 8 0.38
ACGTcount: A:0.59, C:0.09, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAATAAAAGATCTTATATC
Found at i:72672 original size:15 final size:16
Alignment explanation
Indices: 72652--72698 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
72642 CGTCGGTGCT
*
72652 GGGAAGAGAGTGG-CG
1 GGGAAGAGAGTGGAAG
*
72667 GGGAAGGGA-TGGAAG
1 GGGAAGAGAGTGGAAG
*
72682 GGGAAGAGAGGGGAAG
1 GGGAAGAGAGTGGAAG
72698 G
1 G
72699 AATTAGGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 3 0.12
15 17 0.65
16 6 0.23
ACGTcount: A:0.32, C:0.02, G:0.62, T:0.04
Consensus pattern (16 bp):
GGGAAGAGAGTGGAAG
Found at i:72843 original size:29 final size:29
Alignment explanation
Indices: 72811--72879 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
72801 TATTTAACGG
* *
72811 TTAAAATTAATGGTTCGTCTTGATCAGAT
1 TTAAAATTAACGGTCCGTCTTGATCAGAT
72840 TTAAAATTAACGGTCCGTCTTGATCAGAT
1 TTAAAATTAACGGTCCGTCTTGATCAGAT
*
72869 TCAAAACTTAA
1 TTAAAA-TTAA
72880 GTTACGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 32 0.89
30 4 0.11
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (29 bp):
TTAAAATTAACGGTCCGTCTTGATCAGAT
Found at i:73124 original size:19 final size:20
Alignment explanation
Indices: 73100--73140 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
73090 AAACATCTGC
73100 ATGTATTT-GTGGATAAATT
1 ATGTATTTAGTGGATAAATT
**
73119 ATGTATTTAGTGTCTAAATT
1 ATGTATTTAGTGGATAAATT
73139 AT
1 AT
73141 TAGTTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (20 bp):
ATGTATTTAGTGGATAAATT
Found at i:78939 original size:30 final size:30
Alignment explanation
Indices: 78903--78966 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
78893 TGGACTAATT
78903 ATTTAATAATAAAGGAAATAATTTGAGCAG
1 ATTTAATAATAAAGGAAATAATTTGAGCAG
78933 ATTTAATAATAAAGGAAATAATTTGAGCAG
1 ATTTAATAATAAAGGAAATAATTTGAGCAG
78963 ATTT
1 ATTT
78967 TCTACGTATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (30 bp):
ATTTAATAATAAAGGAAATAATTTGAGCAG
Found at i:79408 original size:20 final size:20
Alignment explanation
Indices: 79314--79682 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
79304 GATTTTCCAT
* ** *
79314 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
79334 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
79354 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
79374 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
79394 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
79414 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
79434 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
79454 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
79474 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
79494 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
79514 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
79534 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
79554 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
79574 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
79594 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
79614 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
79634 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
79654 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
79674 AATCACAAC
1 AATCGCAAC
79683 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:80395 original size:24 final size:24
Alignment explanation
Indices: 80356--80402 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
80346 AAATTTGGTC
80356 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
80380 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
80403 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:82927 original size:19 final size:19
Alignment explanation
Indices: 82905--83211 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
82895 CGGAAAATAC
*
82905 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
82924 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
82938 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
82958 AATCGCAA--CGAGA-G-A
1 AATCGCAATGCGAAATGAA
*
82973 TA-CGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
82991 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
83010 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
83024 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
83043 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
83062 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
83076 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
83095 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
83114 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
83133 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
83152 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
83166 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
83185 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
83204 AATCGCAA
1 AATCGCAA
83212 CGAGATAATC
Statistics
Matches: 247, Mismatches: 15, Indels: 52
0.79 0.05 0.17
Matches are distributed among these distances:
14 40 0.16
15 5 0.02
16 19 0.08
17 18 0.07
18 6 0.02
19 146 0.59
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:82992 original size:33 final size:33
Alignment explanation
Indices: 82905--83233 Score: 225
Period size: 33 Copynumber: 9.5 Consensus size: 33
82895 CGGAAAATAC
* *
82905 AATCGCAACGCGAAATGAAAATCCCAACATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAA
82938 AATCGCAATGCGGAAATGAAAATCGCAAC--GAGA
1 AATCGCAATGC-GAAATGAAAATCGCAACATGA-A
*
82971 GATACGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AAT-CGCAATGCGAAATGAAAATCGCAA--C---ATGAA
* * *
83010 AATCGCAACGAGAGAATCG-CAAT-GCGAA-ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCGC-AACATGAA
*
83043 AATCGCAATGCGAAATGAAAATCG-AAC-CGACA
1 AATCGCAATGCGAAATGAAAATCGCAACATGA-A
*
83075 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGC-A-AC---ATGAA
83114 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAA
83152 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C---ATGAA
*
83185 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAA
83218 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
83234 TATAAACGCA
Statistics
Matches: 248, Mismatches: 16, Indels: 64
0.76 0.05 0.20
Matches are distributed among these distances:
31 5 0.02
32 9 0.04
33 114 0.46
34 25 0.10
35 8 0.03
36 10 0.04
37 1 0.00
38 59 0.24
39 12 0.05
40 5 0.02
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAA
Found at i:83020 original size:52 final size:53
Alignment explanation
Indices: 82933--83211 Score: 342
Period size: 52 Copynumber: 5.2 Consensus size: 53
82923 AAATCCCAAC
*
82933 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGATA-CGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAAATCGCAATGCGAA
82986 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG-AATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAAATCGCAATGCGAA
* *
83038 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACA-TAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAAATCGCAATGCGAA
* * *
83090 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-AAATCGCAATGCGAA
*
83147 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA-G-AAATCGCAATGCGAA
83199 ATGAAAATCGCAA
1 ATGAAAATCGCAA
83212 CGAGATAATC
Statistics
Matches: 210, Mismatches: 8, Indels: 17
0.89 0.03 0.07
Matches are distributed among these distances:
51 3 0.01
52 153 0.73
53 18 0.09
54 5 0.02
55 5 0.02
57 26 0.12
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAAATCGCAATGCGAA
Found at i:83059 original size:71 final size:71
Alignment explanation
Indices: 82975--83211 Score: 349
Period size: 71 Copynumber: 3.3 Consensus size: 71
82965 ACGAGAGATA
*
82975 CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
83040 GAAAAT
66 GAAAAT
* * * *
83046 CGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAATAC
1 CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAATGC
83106 GAAATGAAAAT
61 GAAATGAAAAT
83117 CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
1 CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
83182 GAAAAT
66 GAAAAT
83188 CGCAATGCGAAATGAAAATCGCAA
1 CGCAATGCGAAATGAAAATCGCAA
83212 CGAGATAATC
Statistics
Matches: 147, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 110 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAAAT
GAAAAT
Found at i:83157 original size:142 final size:137
Alignment explanation
Indices: 82905--83243 Score: 488
Period size: 142 Copynumber: 2.4 Consensus size: 137
82895 CGGAAAATAC
* * * *
82905 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* * *
82968 AGAGATACGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 AAAGAAACGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
83033 GCGAAATGAA
128 GCGAAATGAA
83043 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACGA
83108 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
64 AA-G-AAA-CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
83173 ATGCGAAATGAA
126 ATGCGAAATGAA
83185 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
83244 TTGCGATTTT
Statistics
Matches: 184, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 33 0.18
139 5 0.03
140 1 0.01
141 2 0.01
142 118 0.64
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAAA
GAAACGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:83249 original size:71 final size:71
Alignment explanation
Indices: 82905--83249 Score: 292
Period size: 71 Copynumber: 4.9 Consensus size: 71
82895 CGGAAAATAC
* * * *
82905 AATCGCAACGCGAAATGAAAATCCCAA-C-ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--
1 AATCGCAATGCGAAATGAAAATCGCAACCGA-GATAATCGCAATGC-GAAATTAAAA-CGCAATG
*
82966 CGAGA-G-A
63 CGAAATGAA
* * * * * *
82973 TA-CGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GATAATCGCAATGCGAAATTAAAACGCAAT
83033 GCGAAATGAA
62 GCGAAATGAA
* *
83043 AATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAAAATCGCAATACG
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTAAAA-CGCAATGCG
83107 AAATGAA
65 AAATGAA
* * * *
83114 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA--GAATCGCAAT
1 AATCGCAATGCGAAATGAAAATCGCAA-CCG--A-GATAATCGCAATGCGAAATTAAAACGCAAT
83175 GCGAAATGAA
62 GCGAAATGAA
*
83185 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAACGCATTGCG
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTA-AAACGCAATGCG
83249 A
65 A
83250 TTTTCATTTC
Statistics
Matches: 227, Mismatches: 25, Indels: 47
0.76 0.08 0.16
Matches are distributed among these distances:
66 24 0.11
67 26 0.11
68 14 0.06
69 9 0.04
70 7 0.03
71 113 0.50
72 17 0.07
73 2 0.01
74 5 0.02
75 1 0.00
76 9 0.04
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAACCGAGATAATCGCAATGCGAAATTAAAACGCAATGCGA
AATGAA
Found at i:83349 original size:19 final size:19
Alignment explanation
Indices: 83240--83341 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
83230 AAATTATAAA
83240 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
83259 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
83279 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
83295 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
83312 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
83331 CGCATTGCGAT
1 CGCATTGCGAT
83342 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:83467 original size:14 final size:14
Alignment explanation
Indices: 83448--83484 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
83438 CATCAATTAC
83448 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
83462 ACAAATCATCTTTT
1 ACAAATCAACTTTT
83476 ACAAATCAA
1 ACAAATCAA
83485 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:83496 original size:12 final size:12
Alignment explanation
Indices: 83479--83551 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
83469 ATCTTTTACA
83479 AATCAATTAAAC
1 AATCAATTAAAC
*
83491 AATCAA--AAATTG
1 AATCAATTAAA--C
**
83503 AATCAACTTTTAC
1 AATCAA-TTAAAC
83516 AAATCAATTAAAC
1 A-ATCAATTAAAC
*
83529 AATCAA-AAAAC
1 AATCAATTAAAC
83540 AATCAATTAAAC
1 AATCAATTAAAC
83552 TATTGAATCA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
10 3 0.07
11 10 0.22
12 21 0.46
13 6 0.13
14 5 0.11
15 1 0.02
ACGTcount: A:0.58, C:0.16, G:0.01, T:0.25
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:83513 original size:38 final size:38
Alignment explanation
Indices: 83465--83537 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
83455 AACTTTTACA
*
83465 AATCATCTTTTACAAATCAATTAAACAATCAAAAATTG
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
83503 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
1 AATCAACTTTTACAAATCAATTAAACAATCAAAAA
83538 ACAATCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.53, C:0.16, G:0.01, T:0.29
Consensus pattern (38 bp):
AATCAACTTTTACAAATCAATTAAACAATCAAAAATTG
Found at i:85430 original size:14 final size:14
Alignment explanation
Indices: 85411--85467 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
85401 GCGAAATGAA
*
85411 AATCGCAACGACAG
1 AATCGCAACGAAAG
85425 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
85442 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
85458 AATCGCAACG
1 AATCGCAACG
85468 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:85438 original size:33 final size:33
Alignment explanation
Indices: 85392--85484 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
85382 GCGAAACCAA
*
85392 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
85425 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
85458 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
85485 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:85449 original size:19 final size:19
Alignment explanation
Indices: 85355--85489 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
85345 TAGTTTACTT
* *
85355 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
85375 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
85394 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
85413 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
85427 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
85446 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
85460 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
85479 TCGCAATGCGA
1 TCGCAACGCGA
85490 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:85507 original size:19 final size:19
Alignment explanation
Indices: 85485--85613 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
85475 AAAATCGCAA
85485 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
85504 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
85518 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
85537 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
85551 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
85570 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
85589 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
85609 TGCGA
1 TGCGA
85614 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:85527 original size:33 final size:33
Alignment explanation
Indices: 85485--85576 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
85475 AAAATCGCAA
85485 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
85518 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
85551 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
85577 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:85816 original size:93 final size:93
Alignment explanation
Indices: 85657--86036 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
85647 TTGAATGGAT
85657 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
85722 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
85750 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
85815 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
85843 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
85907 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
85935 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
86000 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
86028 AAATTTACT
1 AAATTTACT
86037 AAGCAATCTA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:85970 original size:185 final size:186
Alignment explanation
Indices: 85657--86036 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
85647 TTGAATGGAT
85657 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
85722 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
85787 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
85843 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
85907 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
85972 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
86028 AAATTTACT
1 AAATTTACT
86037 AAGCAATCTA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:87761 original size:14 final size:14
Alignment explanation
Indices: 87742--87831 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
87732 TTGAAATGAA
87742 AATCGCAACGAGAG
1 AATCGCAACGAGAG
87756 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
87773 ACAATCGCAACGATAG
1 --AATCGCAACGAGAG
*
87789 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
87808 AATCGCAACGAGAG
1 AATCGCAACGAGAG
87822 AATCGCAACG
1 AATCGCAACG
87832 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 28 0.45
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 17 0.27
ACGTcount: A:0.42, C:0.23, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:87779 original size:33 final size:33
Alignment explanation
Indices: 87734--87848 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
87724 TCTTTTGGTT
87734 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
87767 GAGATGACAATCGCAACGATAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
87800 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
87833 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
87849 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:87780 original size:19 final size:19
Alignment explanation
Indices: 87737--87853 Score: 84
Period size: 19 Copynumber: 6.9 Consensus size: 19
87727 TTTGGTTGAA
87737 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
87754 A-G--AATCGCAACGCGAG
1 ATGAAAATCGCAACGCGAG
*
87770 ATGACAATCGCAA--C--G
1 ATGAAAATCGCAACGCGAG
* *
87785 AT-AGAATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
87803 ATGAAAATCGCAA--CGAG
1 ATGAAAATCGCAACGCGAG
*
87820 A-G--AATCGCAACGCGAA
1 ATGAAAATCGCAACGCGAG
*
87836 ATGAAAATCGCAATGCGA
1 ATGAAAATCGCAACGCGA
87854 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
14 25 0.32
15 3 0.04
16 12 0.15
17 8 0.10
18 2 0.03
19 29 0.37
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (19 bp):
ATGAAAATCGCAACGCGAG
Found at i:87884 original size:14 final size:14
Alignment explanation
Indices: 87865--87919 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
87855 TTTGGTTTCG
87865 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
87879 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
87898 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
87912 CGTTGCGA
1 CGTTGCGA
87920 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:88082 original size:33 final size:33
Alignment explanation
Indices: 88040--88110 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
88030 AATACTAACT
*
88040 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
88073 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
88106 TGAAA
1 TGAAA
88111 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:88344 original size:22 final size:22
Alignment explanation
Indices: 88292--88346 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
88282 TGGTTGTGAG
**
88292 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
88314 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
88336 GGATTTCTTCG
1 GGATTTCTTCG
88347 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:88516 original size:20 final size:20
Alignment explanation
Indices: 88491--88684 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
88481 CTTTAAATAT
88491 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
88511 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
88533 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
88552 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
88572 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
88592 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
88612 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
88632 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
88652 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
88672 CGCGTTGCGATTT
1 CGCGTTGCGATTT
88685 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:88678 original size:60 final size:60
Alignment explanation
Indices: 88491--88684 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
88481 CTTTAAATAT
**
88491 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
88552 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
88612 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
88672 CGCGTTGCGATTT
1 CGCGTTGCGATTT
88685 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:88701 original size:21 final size:20
Alignment explanation
Indices: 88677--88753 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
88667 ATATTCGCGT
88677 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
88698 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
88718 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
88740 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
88754 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:88764 original size:20 final size:20
Alignment explanation
Indices: 88739--88790 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
88729 AAGAATCGCG
*
88739 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
88759 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
88779 TTGCGATTCTGG
1 TTGCGATTCTGG
88791 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:89755 original size:30 final size:30
Alignment explanation
Indices: 89719--89783 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
89709 GGGGCAGCCG
*
89719 GTGTCAACGAACCTACTTTCGGAGCTGCCA
1 GTGTCAACGAACCTACGTTCGGAGCTGCCA
* * *
89749 GTGTCAACGAACGTGCGTTCGGAGCTGCCT
1 GTGTCAACGAACCTACGTTCGGAGCTGCCA
89779 GTGTC
1 GTGTC
89784 GATGGACCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.18, C:0.28, G:0.29, T:0.25
Consensus pattern (30 bp):
GTGTCAACGAACCTACGTTCGGAGCTGCCA
Found at i:92814 original size:29 final size:30
Alignment explanation
Indices: 92765--92827 Score: 110
Period size: 29 Copynumber: 2.1 Consensus size: 30
92755 TGGACTAATT
92765 ATTTAATAATAAAGGAAATAATTTGAGCAG
1 ATTTAATAATAAAGGAAATAATTTGAGCAG
*
92795 ATTTAATAA-ATAGGAAATAATTTGAGCAG
1 ATTTAATAATAAAGGAAATAATTTGAGCAG
92824 ATTT
1 ATTT
92828 TCTATGTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 23 0.72
30 9 0.28
ACGTcount: A:0.48, C:0.03, G:0.16, T:0.33
Consensus pattern (30 bp):
ATTTAATAATAAAGGAAATAATTTGAGCAG
Found at i:93791 original size:30 final size:30
Alignment explanation
Indices: 93738--93832 Score: 100
Period size: 30 Copynumber: 3.2 Consensus size: 30
93728 GGCGTAGCGG
* * * * * *
93738 GTGTCGACGAGCCTGCGTCCGGAGCAGCCG
1 GTGTCAACGAACCTACGTTCGGAGCTGCCA
*
93768 GTGTCAACGAACCTACTTTCGGAGCTGCCA
1 GTGTCAACGAACCTACGTTCGGAGCTGCCA
* * *
93798 GTGTCAACGAACGTGCGTTCGGAGCTGCCT
1 GTGTCAACGAACCTACGTTCGGAGCTGCCA
93828 GTGTC
1 GTGTC
93833 GATGGACCAG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.17, C:0.29, G:0.33, T:0.21
Consensus pattern (30 bp):
GTGTCAACGAACCTACGTTCGGAGCTGCCA
Found at i:101144 original size:26 final size:26
Alignment explanation
Indices: 101115--101202 Score: 176
Period size: 26 Copynumber: 3.4 Consensus size: 26
101105 CCTAAGAATG
101115 AAGAATTGTAAATCTTTCTTAATTTA
1 AAGAATTGTAAATCTTTCTTAATTTA
101141 AAGAATTGTAAATCTTTCTTAATTTA
1 AAGAATTGTAAATCTTTCTTAATTTA
101167 AAGAATTGTAAATCTTTCTTAATTTA
1 AAGAATTGTAAATCTTTCTTAATTTA
101193 AAGAATTGTA
1 AAGAATTGTA
101203 TAGCTCAAAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (26 bp):
AAGAATTGTAAATCTTTCTTAATTTA
Done.