Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006786.1 Hibiscus syriacus cultivar Beakdansim tig00017200_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: 73385
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2917 original size:58 final size:54
Alignment explanation
Indices: 2612--2922 Score: 194
Period size: 54 Copynumber: 5.7 Consensus size: 54
2602 CAAACTTATA
* * * **
2612 AAGAAACTAAGCTTGATTTTC-AGGGTTTCTTGATG-T-TTTCAAATGCGTTTTTTT
1 AAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATAATTCAAA---ATAATTTT
* * * * *
2666 TAGAAACTAAGCTTGATTTT-TAGGGTTTCTTGATGATTATTTC-CAATAATTTTT
1 AAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGA-TAATTCAAAATAA-TTTT
* * * * ** *
2720 AAAAGAAGCTAACCCTAATTTT-TAGGGATTTCTTGATG-T--TTTTAAATGAGCTTTT
1 --AAGAAACTAAGCCTGATTTTCAAGGG-TTTCTTGATGATAATTCAAAAT-A-ATTTT
* *
2775 -AGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTATTCCAAATAATTTT
1 AAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATAATTCAAAATAATTTT
* * * *
2828 AAAGAAGCTAAGCCTAATTTT-AGGGGTTTCTTGATGATAATTGAAAATGAAAGATTTT
1 -AAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATAATTCAAAAT---A-ATTTT
*
2886 AAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 AAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGA
2923 GTAAGTCATT
Statistics
Matches: 205, Mismatches: 30, Indels: 40
0.75 0.11 0.15
Matches are distributed among these distances:
52 26 0.13
53 12 0.06
54 64 0.31
55 29 0.14
56 22 0.11
57 32 0.16
58 20 0.10
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (54 bp):
AAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATAATTCAAAATAATTTT
Found at i:2922 original size:112 final size:109
Alignment explanation
Indices: 2663--2922 Score: 359
Period size: 112 Copynumber: 2.4 Consensus size: 109
2653 AATGCGTTTT
*
2663 TTTTAGAAACTAAGCTTGATTTT-TAGGGTTTCTTGATGATTATTTCCAATAATTTTTAAAAGAA
1 TTTTAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGATTATTTCCAATAATTTTTAAAAGAA
** *
2727 GCTAACCCTAATTTTTAGGGATTTCTTGATGTTTTTAAATGAGC
66 GCTAACCCTAATTTTTAGGGATTTCTTGATGTTTGAAAATGAGA
*
2771 TTTTAGAAACTAAGCCTGATTTTCAAGGGTTTCTTGATGATTA-TTCCAAATAA-TTTT-AAAGA
1 TTTTAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGATTATTTCC-AATAATTTTTAAAAGA
* *
2833 AGCTAAGCCTAA-TTTTAGGGGTTTCTTGATGATAATTGAAAATGAAAGA
65 AGCTAACCCTAATTTTTAGGGATTTCTTGATG-T--TTGAAAATG--AGA
2882 TTTTAAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
1 TTTT-AGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGA
2923 GTAAGTCATT
Statistics
Matches: 136, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
106 18 0.13
107 17 0.12
108 30 0.22
109 30 0.22
111 6 0.04
112 35 0.26
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (109 bp):
TTTTAGAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGATTATTTCCAATAATTTTTAAAAGAA
GCTAACCCTAATTTTTAGGGATTTCTTGATGTTTGAAAATGAGA
Found at i:3168 original size:39 final size:39
Alignment explanation
Indices: 3114--3280 Score: 241
Period size: 39 Copynumber: 4.3 Consensus size: 39
3104 AGGGGTCAAC
* *
3114 ATCTCGCTTGAGATAGTTTCACAAGAAACATAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
*
3153 ATCTCGCTTGAGATAGTTTCACTCA-AAACAGAATATTTT
1 ATCTCGCTTGAGATAGTTTCACT-AGAAACAGAAGATTTT
* * *
3192 ATCTCGCTTGAGATAGTTTTACTCGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
*
3231 ATCTCGCTTGAGATAGTTTCACTTGAAA-AGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
3268 ATCTCGCTTGAGA
1 ATCTCGCTTGAGA
3281 ATGAAAGATG
Statistics
Matches: 116, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
37 16 0.14
38 5 0.04
39 94 0.81
40 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTAGAAACAGAAGATTTT
Found at i:14718 original size:9 final size:8
Alignment explanation
Indices: 14700--14737 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
14690 AAGAGAAAAG
14700 AAAAAGAA
1 AAAAAGAA
14708 AAAATAGAA
1 AAAA-AGAA
14717 AAAAA-AA
1 AAAAAGAA
*
14724 GAAAAGAA
1 AAAAAGAA
14732 AAAAAG
1 AAAAAG
14738 GTTAAAGGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 12 0.46
9 8 0.31
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:14718 original size:15 final size:15
Alignment explanation
Indices: 14681--14736 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
14671 TATTACGCCT
*
14681 AAGAAAGAAAAGAGAA
1 AAGAAA-AAAAAAGAA
14697 AAGAAAAAGAAAA-AA
1 AAGAAAAA-AAAAGAA
*
14712 TAGAAAAAAAAAGAA
1 AAGAAAAAAAAAGAA
14727 AAGAAAAAAA
1 AAGAAAAAAA
14737 GGTTAAAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 4 0.11
15 22 0.63
16 9 0.26
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (15 bp):
AAGAAAAAAAAAGAA
Found at i:14722 original size:19 final size:20
Alignment explanation
Indices: 14688--14728 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
14678 CCTAAGAAAG
14688 AAAAGAGAAAAGAAAAAGAA
1 AAAAGAGAAAAGAAAAAGAA
*
14708 AAAATAGAAAA-AAAAAGAA
1 AAAAGAGAAAAGAAAAAGAA
14727 AA
1 AA
14729 GAAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (20 bp):
AAAAGAGAAAAGAAAAAGAA
Found at i:14734 original size:12 final size:12
Alignment explanation
Indices: 14684--14735 Score: 61
Period size: 12 Copynumber: 4.2 Consensus size: 12
14674 TACGCCTAAG
*
14684 AAAGAAAAGAGA
1 AAAGAAAAGAAA
14696 AAAGAAAAAGAAA
1 AAAG-AAAAGAAA
*
14709 AAATAGAAA-AAA
1 AAAGA-AAAGAAA
14721 AAAGAAAAGAAA
1 AAAGAAAAGAAA
14733 AAA
1 AAA
14736 AGGTTAAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 13 0.38
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:15921 original size:136 final size:136
Alignment explanation
Indices: 15673--16493 Score: 903
Period size: 136 Copynumber: 6.1 Consensus size: 136
15663 AACATAAATC
* * * ** *
15673 AATGACAAGAACTCATATGACA-ACAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAAGCTA
1 AATGAGAAGAACTCATCTGACAGA-GGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTA
** * * *
15737 TTGCTCGATTCTTGACATTTCAAATCAGCAATGCCTTGCTTGAGGGATCAACATTTCTAATAGAG
65 TTGCTCGATTCACGACATTTCAAATCAGCAAAGCCTCGCTTGAGGGATCAACATTTCTAATGGAG
15802 AGTTCAT
130 AGTTCAT
* *
15809 AATGAGAAGAACTCATCTGACAGAGGGAGAAGAAATTCATAATAAGAAGAACTTGTTTGACCTAT
1 AATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTAT
* * * * * *
15874 TGCTCGATTCACGACATTTCGAATTAGCAAAGCCTGGCCTGATGGATCAACATTTCCAATGGAGA
66 TGCTCGATTCACGACATTTCAAATCAGCAAAGCCTCGCTTGAGGGATCAACATTTCTAATGGAGA
15939 GTTCAT
131 GTTCAT
* * * *
15945 AATGAGAATAACTCATATGACAGAGGGAGAAGAAATTCGTAATGA-AA-AACTTGTTTGACCTAT
1 AATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTAT
* * * * *
16008 TGCTCGATTCACGACA-TT-AAATCAGCAAAGCCTGGCCTCATGGATCAACATTTCCAATGGAGA
66 TGCTCGATTCACGACATTTCAAATCAGCAAAGCCTCGCTTGAGGGATCAACATTTCTAATGGAGA
16071 GTTCAT
131 GTTCAT
* *
16077 AATAAGAAGAACTCAT-TCGACAGAGGGAAAAGAAGTTCATAATGAGAAGAACTTG-TT--CCTA
1 AATGAGAAGAACTCATCT-GACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTA
** * * * * *
16138 TTGCTCGATTCACGACATTTTGAATCAGTAACGCCTCACTTGAGGGATTAACATTTCCT-GTGGA
65 TTGCTCGATTCACGACATTTCAAATCAGCAAAGCCTCGCTTGAGGGATCAACATTT-CTAATGGA
*
16202 TAGATT-AT
129 GAG-TTCAT
* * * *
16210 AATGAGAAGAATTCATCCGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTATTCGACCTAT
1 AATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTAT
* * * * *
16275 TGCTCGATTCACGACATTTCAAATTAGTAACA-CATCGCTTGAGAGATTAACATTTCTAATGGAG
66 TGCTCGATTCACGACATTTCAAATCAGCAA-AGCCTCGCTTGAGGGATCAACATTTCTAATGGAG
16339 AGTTCAT
130 AGTTCAT
* * * * * *
16346 AATGAGAAGAACTAATCCGATAGAGGGAGAAGAAGTTAATAATGACAAGAACTTATTTGACCTAT
1 AATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTAT
* * ** * * * * * * *
16411 TCCTCGATTCATGGGATTTCAAATTAGTAATGCCTCACTTAAGGGATAAACATTTCCAATAGGA-
66 TGCTCGATTCACGACATTTCAAATCAGCAAAGCCTCGCTTGAGGGATCAACATTTCTAAT-GGAG
*
16475 AGATCAT
130 AGTTCAT
*
16482 GATGAGAAGAAC
1 AATGAGAAGAAC
16494 CCGTAACTTG
Statistics
Matches: 592, Mismatches: 76, Indels: 34
0.84 0.11 0.05
Matches are distributed among these distances:
131 22 0.04
132 88 0.15
133 89 0.15
134 42 0.07
135 6 0.01
136 341 0.58
137 4 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.27
Consensus pattern (136 bp):
AATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTGACCTAT
TGCTCGATTCACGACATTTCAAATCAGCAAAGCCTCGCTTGAGGGATCAACATTTCTAATGGAGA
GTTCAT
Found at i:16714 original size:18 final size:18
Alignment explanation
Indices: 16690--16737 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
16680 GCCCCAGACC
16690 CAAAACCCAACCAAAACA
1 CAAAACCCAACCAAAACA
* * *
16708 TAAAACCCAACCATAACC
1 CAAAACCCAACCAAAACA
16726 CAAAACCCAACC
1 CAAAACCCAACC
16738 CAAGGCCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.54, C:0.42, G:0.00, T:0.04
Consensus pattern (18 bp):
CAAAACCCAACCAAAACA
Found at i:21196 original size:16 final size:16
Alignment explanation
Indices: 21175--21207 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21165 CCCATTTATC
21175 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
21191 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
21207 A
1 A
21208 AAACCACTTC
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:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:23302 original size:20 final size:20
Alignment explanation
Indices: 23265--23303 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23255 AGATTGAGTG
* * *
23265 GATTTTGATGTTGTTTGCAC
1 GATTTTAATGATGATTGCAC
23285 GATTTTAATGATGATTGCA
1 GATTTTAATGATGATTGCA
23304 AGTTTAGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (20 bp):
GATTTTAATGATGATTGCAC
Found at i:23510 original size:23 final size:23
Alignment explanation
Indices: 23484--23548 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
23474 CCCCTGTGGG
23484 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCCTTCAAA
23507 GGGGGAATCGGTT-CCC-TC-AA
1 GGGGGAATCGGTTCCCCTTCAAA
* *
23527 GGGGGGATCGATTCCCTCTTCA
1 GGGGGAATCGGTTCCC-CTTCA
23549 CCAAAATGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
20 13 0.36
21 4 0.11
22 4 0.11
23 15 0.42
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.23
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTTCAAA
Found at i:23530 original size:20 final size:21
Alignment explanation
Indices: 23484--23544 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
23474 CCCCTGTGGG
23484 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
23507 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
23527 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
23545 TTCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:35864 original size:2 final size:2
Alignment explanation
Indices: 35857--35889 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35847 AACATGTCTC
35857 AT AT 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 AT AT A
35890 ACACCTTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36039 original size:36 final size:37
Alignment explanation
Indices: 35977--36068 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 37
35967 ATATCGATGA
* * * * **
35977 GATGAACCAGTCGGTAGTTGGAATTATCTTCGTAATG
1 GATGAACCAGTCAGTAATTAGAATTATCATCCCAATG
*
36014 GATGAA-CAGTTAGTAATTAGAATTATCATCCCAATG
1 GATGAACCAGTCAGTAATTAGAATTATCATCCCAATG
36050 GATGAACCAGTCAGTAATT
1 GATGAACCAGTCAGTAATT
36069 CAGTCACTTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 29 0.63
37 17 0.37
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (37 bp):
GATGAACCAGTCAGTAATTAGAATTATCATCCCAATG
Found at i:38198 original size:152 final size:152
Alignment explanation
Indices: 37917--38199 Score: 478
Period size: 152 Copynumber: 1.9 Consensus size: 152
37907 GTGATCGCTA
*
37917 GTAAATGTATATGCTAAGGCAAGCAAATCTGTGCAAGTATACACAGTCGAATCAAGTAATAAAGG
1 GTAAATGTATATGCTAAGGCAAGCAAATCTATGCAAGTATACACAGTCGAATCAAGTAATAAAGG
** *
37982 GTAAGTGAGTTATAGTCTCGTCAGGGATTGGTAGGGATTTTGAAGTTTCACCACAACTAGAACTA
66 GTAAGTGAGTTATAGTCTCGAAAGGGATTGGTAGGGATTTTGAAGTTTCACCACAACTAAAACTA
38047 GCTCACAAAAACTTGATATCTT
131 GCTCACAAAAACTTGATATCTT
* * *
38069 GTAAATGTATATGCTAAGGCAAGTAAATGTATGCAAGTATACATAGTCGAATCAAGTAATAAAGG
1 GTAAATGTATATGCTAAGGCAAGCAAATCTATGCAAGTATACACAGTCGAATCAAGTAATAAAGG
*
38134 GTAAGTGAGTTATCGTCTAC-AAAGGGATTGGTAGGGATTTTGAAGTTTCACCACAACTAAAACT
66 GTAAGTGAGTTATAGTCT-CGAAAGGGATTGGTAGGGATTTTGAAGTTTCACCACAACTAAAACT
38198 AG
130 AG
38200 GTGTCACGAG
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
152 121 0.99
153 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (152 bp):
GTAAATGTATATGCTAAGGCAAGCAAATCTATGCAAGTATACACAGTCGAATCAAGTAATAAAGG
GTAAGTGAGTTATAGTCTCGAAAGGGATTGGTAGGGATTTTGAAGTTTCACCACAACTAAAACTA
GCTCACAAAAACTTGATATCTT
Found at i:42602 original size:5 final size:5
Alignment explanation
Indices: 42602--42630 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
42592 AAACAAAACA
42602 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
42631 CAAATAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:45357 original size:46 final size:45
Alignment explanation
Indices: 45279--45391 Score: 149
Period size: 46 Copynumber: 2.5 Consensus size: 45
45269 ATTTATTAAT
* *
45279 CATAAGCTCGTAAGCTTA-TTTTACCAAAATACTTACCATT-TATC
1 CATAAGATCATAAGCTTATTTTTACCAAAATACTTACCATTAT-TC
* *
45323 CATAAGATCCATAAGCTTATTTTTACCAATATACTTGCCATTATTC
1 CATAAGAT-CATAAGCTTATTTTTACCAAAATACTTACCATTATTC
*
45369 CATAAGCTCATAAGCTTATTTTT
1 CATAAGATCATAAGCTTATTTTT
45392 CCAGTTTATC
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
44 7 0.11
45 24 0.39
46 29 0.48
47 1 0.02
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (45 bp):
CATAAGATCATAAGCTTATTTTTACCAAAATACTTACCATTATTC
Found at i:47496 original size:13 final size:11
Alignment explanation
Indices: 47455--47539 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
47445 ACAATCTGTC
47455 CATCACCATTAT
1 CATCACCA-TAT
*
47467 CA-CGCCTATAT
1 CATCACC-ATAT
47478 CATCACCATAGT
1 CATCACCATA-T
47490 CCATCACCATTAT
1 -CATCACCA-TAT
*
47503 CA-CGCCTATAT
1 CATCACC-ATAT
47514 CATCACCATATT
1 CATCACCATA-T
47526 CCATCACCATAT
1 -CATCACCATAT
47538 CA
1 CA
47540 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:47499 original size:36 final size:36
Alignment explanation
Indices: 47452--47553 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
47442 GATACAATCT
47452 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
47488 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
47524 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
47554 TCCTTCCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 17 0.27
36 46 0.73
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:47568 original size:33 final size:34
Alignment explanation
Indices: 47453--47569 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
47443 ATACAATCTG
* *
47453 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
47487 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
47525 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
47558 TCCATTACCATT
1 TCCATCACCATT
47570 TCATCACCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:47587 original size:33 final size:33
Alignment explanation
Indices: 47453--47592 Score: 88
Period size: 36 Copynumber: 4.1 Consensus size: 33
47443 ATACAATCTG
* * *
47453 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACACCAATAACATCATCC-T
* * *
47487 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACACCAATAACATCATCC---T
*
47525 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACACCAATAACATCATCCT
* * *
47558 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CACCAATAACATCATCCT
47591 TC
1 TC
47593 ATTCATCAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACACCAATAACATCATCCT
Found at i:51999 original size:13 final size:11
Alignment explanation
Indices: 51958--52042 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
51948 ACAATCTGTC
51958 CATCACCATTAT
1 CATCACCA-TAT
*
51970 CA-CGCCTATAT
1 CATCACC-ATAT
51981 CATCACCATAGT
1 CATCACCATA-T
51993 CCATCACCATTAT
1 -CATCACCA-TAT
*
52006 CA-CGCCTATAT
1 CATCACC-ATAT
52017 CATCACCATATT
1 CATCACCATA-T
52029 CCATCACCATAT
1 -CATCACCATAT
52041 CA
1 CA
52043 CGCCAATAAC
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:52002 original size:36 final size:36
Alignment explanation
Indices: 51955--52056 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
51945 GATACAATCT
51955 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
51991 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* * *
52027 TTCCATCACCA-TATCACGCCAATAACATCA
1 GTCCATCACCATTATCACGCCTATATCATCA
52057 TCCTTCCATT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 17 0.27
36 46 0.73
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.26
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:52071 original size:33 final size:34
Alignment explanation
Indices: 51956--52072 Score: 130
Period size: 36 Copynumber: 3.4 Consensus size: 34
51946 ATACAATCTG
* *
51956 TCCATCACCATTATCACGCCTATATCATCACCAT
1 TCCATCACCATTATCACGCCAATAACATCACCAT
* *
51990 AGTCCATCACCATTATCACGCCTATATCATCACCATAT
1 --TCCATCACCATTATCACGCCAATAACATCACC--AT
52028 TCCATCACCA-TATCACGCCAATAACATCATCC-T
1 TCCATCACCATTATCACGCCAATAACATCA-CCAT
*
52061 TCCATTACCATT
1 TCCATCACCATT
52073 TCATCACCAT
Statistics
Matches: 74, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 10 0.14
34 1 0.01
35 17 0.23
36 44 0.59
38 2 0.03
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (34 bp):
TCCATCACCATTATCACGCCAATAACATCACCAT
Found at i:52090 original size:33 final size:33
Alignment explanation
Indices: 51956--52095 Score: 88
Period size: 36 Copynumber: 4.1 Consensus size: 33
51946 ATACAATCTG
* * *
51956 TCCATCACCATTATCACGCCTATATCATCA-CCAT
1 TCCATCACCA-TATCACACCAATAACATCATCC-T
* * *
51990 AGTCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 --TCCATCACCA-TATCACACCAATAACATCATCC---T
*
52028 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACACCAATAACATCATCCT
* * *
52061 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CACCAATAACATCATCCT
52094 TC
1 TC
52096 ATTCATCAAC
Statistics
Matches: 94, Mismatches: 6, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
33 24 0.26
34 7 0.07
35 17 0.18
36 44 0.47
38 2 0.02
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.30
Consensus pattern (33 bp):
TCCATCACCATATCACACCAATAACATCATCCT
Found at i:54142 original size:17 final size:17
Alignment explanation
Indices: 54120--54172 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
54110 TGAATAAAGT
54120 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
54137 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
54154 TAGTTCATTTATTAGAC
1 TAGTTCATTAATTAAAC
54171 TA
1 TA
54173 ACTCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:59947 original size:11 final size:11
Alignment explanation
Indices: 59919--59964 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
59909 TAGGTGTTGG
*
59919 AAACAAGGTAA
1 AAACAAGATAA
*
59930 GAAACAAGATTA
1 -AAACAAGATAA
59942 AAACAAGATAA
1 AAACAAGATAA
*
59953 AAAAAAGATAA
1 AAACAAGATAA
59964 A
1 A
59965 GAAATTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
11 21 0.70
12 9 0.30
ACGTcount: A:0.70, C:0.07, G:0.13, T:0.11
Consensus pattern (11 bp):
AAACAAGATAA
Done.