Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001038.1 Hibiscus syriacus cultivar Beakdansim tig00002064_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: 91529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:5550 original size:16 final size:16
Alignment explanation
Indices: 5525--5559 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5515 CGTATCGCCG
*
5525 ACGAATTTCACTATTC
1 ACGAAATTCACTATTC
5541 ACGAAATTCACTATTC
1 ACGAAATTCACTATTC
5557 ACG
1 ACG
5560 TGAATAGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (16 bp):
ACGAAATTCACTATTC
Found at i:6205 original size:7 final size:7
Alignment explanation
Indices: 6193--6218 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
6183 ACCGTAAATT
6193 TGTTTCA
1 TGTTTCA
6200 TGTTTCA
1 TGTTTCA
6207 TGTTTCA
1 TGTTTCA
6214 TGTTT
1 TGTTT
6219 ATGCACGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.12, G:0.15, T:0.62
Consensus pattern (7 bp):
TGTTTCA
Found at i:11827 original size:2 final size:2
Alignment explanation
Indices: 11820--11857 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
11810 CGGTAAGGGA
11820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11858 CTTTGCAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21714 original size:2 final size:2
Alignment explanation
Indices: 21707--21733 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
21697 GTAGAAAAGA
21707 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 A
21734 AAAGATTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22012 original size:18 final size:18
Alignment explanation
Indices: 21977--22010 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
21967 ATAAAATTTA
21977 AAAAATATATTTTTAAAT
1 AAAAATATATTTTTAAAT
21995 AAAAATA-ATTTTTAAA
1 AAAAATATATTTTTAAA
22011 ATTTATCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATATATTTTTAAAT
Found at i:30412 original size:75 final size:75
Alignment explanation
Indices: 30333--30482 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
30323 TTAATAAGTT
* *
30333 AAACCATCTTAATATAATGTTACTTTTTAAACATGTGATGATCATCAAATAAATGTCAAATTATA
1 AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
30398 TAAATAATCC
66 TAAATAATCC
30408 AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
1 AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
30473 TAAATAATCC
66 TAAATAATCC
30483 CTATACTTGC
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (75 bp):
AAACCAGCTTAATATAATGTTACTTTTTAAACATGTGATGATCAACAAATAAATGTCAAATTATA
TAAATAATCC
Found at i:34693 original size:3 final size:3
Alignment explanation
Indices: 34685--34852 Score: 282
Period size: 3 Copynumber: 55.7 Consensus size: 3
34675 TTTTTATCCA
*
34685 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
34733 ATAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
34779 TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
34827 TAT TAT TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
34853 ATTTATATTA
Statistics
Matches: 154, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
3 152 0.99
4 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:36990 original size:18 final size:17
Alignment explanation
Indices: 36967--37010 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
36957 TTTCAAATTT
36967 TTTTTATTATATTTATTA
1 TTTTTATTATATTTA-TA
*
36985 TTTTTATAATATTTATA
1 TTTTTATTATATTTATA
37002 TGTTTTATT
1 T-TTTTATT
37011 TGCAAGTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TTTTTATTATATTTATA
Found at i:47594 original size:1 final size:1
Alignment explanation
Indices: 47588--47656 Score: 75
Period size: 1 Copynumber: 69.0 Consensus size: 1
47578 ATGCTTGAAG
* * * * ** *
47588 AAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAGAAAAGAAAAAAAAAAGAAAAGGAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
47653 AAAA
1 AAAA
47657 GAGGGGTCAA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (1 bp):
A
Found at i:47624 original size:26 final size:25
Alignment explanation
Indices: 47588--47656 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 25
47578 ATGCTTGAAG
47588 AAAAAAAAAAAAAAAAAAAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAGAA
*
47613 AAAAAAAGAAAAGAAAAAAAAAAGAA
1 AAAAAAA-AAAAAAAAAAAAAAAGAA
** *
47639 AAGGAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAA
47657 GAGGGGTCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.45
26 22 0.55
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAAAAAAAAGAA
Found at i:47657 original size:16 final size:15
Alignment explanation
Indices: 47588--47658 Score: 99
Period size: 15 Copynumber: 4.7 Consensus size: 15
47578 ATGCTTGAAG
47588 AAAAAAAA-AAAAAA
1 AAAAAAAAGAAAAAA
47602 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
*
47617 AAAGAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
47632 AAAAGAAAAGGAAAAAA
1 AAAA-AAAA-GAAAAAA
*
47649 AGAAAAAAGA
1 AAAAAAAAGA
47659 GGGGTCAAGG
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
14 8 0.16
15 25 0.49
16 8 0.16
17 10 0.20
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAAAAAA
Found at i:49173 original size:52 final size:52
Alignment explanation
Indices: 48594--49172 Score: 1043
Period size: 52 Copynumber: 11.1 Consensus size: 52
48584 TATGTGCTCA
48594 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
48646 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
48698 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
48750 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
*
48802 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
48854 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
48906 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
48958 ATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
49010 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
49062 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
* *
49114 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAA-C
49167 A-AGCAT
1 ATAGCAT
49173 TGAGTTTAGA
Statistics
Matches: 514, Mismatches: 12, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
52 512 1.00
53 2 0.00
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTAGACAGAAC
Found at i:49253 original size:83 final size:83
Alignment explanation
Indices: 49114--49320 Score: 387
Period size: 83 Copynumber: 2.5 Consensus size: 83
49104 TGGACAGAAC
*
49114 ATAGCATTTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
49179 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
49197 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
49262 TAGAAGATGAATTTGCCA
66 TAGAAGATGAATTTGCCA
* *
49280 ATAGCATCTTCTGGAAGTGTTCTTTGAGTCATTTGATCTGA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
49321 AGAAGTGCAT
Statistics
Matches: 121, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 121 1.00
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTAGACAGAATCAAGCATTGAGTT
TAGAAGATGAATTTGCCA
Found at i:50083 original size:119 final size:119
Alignment explanation
Indices: 49872--50398 Score: 901
Period size: 119 Copynumber: 4.5 Consensus size: 119
49862 CAAAGATTCA
49872 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
49937 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
49991 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
50056 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
50110 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
50175 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * *
50229 AATTCATC-ACTTGATGGATCAACATTACCAGA-GAAG-GTTCATAATGAGAAGAA--C-TCATC
1 AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
* *
50288 TGAAGAAGGAAGGAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTG
66 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* ** *
50342 AATTCATC-ATTTGATGGAACATCATCCCCAGCA-GAA-AGTTCGTAATGAGAAGAACTC
1 AATTCATCAATTTGATGGATCATCATTTCCAG-AGGAAGAGTTCATAATGAGAAGAACTC
50399 ATCTGGAGAA
Statistics
Matches: 393, Mismatches: 11, Indels: 11
0.95 0.03 0.03
Matches are distributed among these distances:
113 83 0.21
114 21 0.05
116 18 0.05
117 4 0.01
118 21 0.05
119 246 0.63
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (119 bp):
AATTCATCAATTTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:50562 original size:3 final size:3
Alignment explanation
Indices: 50554--50746 Score: 316
Period size: 3 Copynumber: 64.7 Consensus size: 3
50544 TTTTTATCCA
50554 TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
50601 TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
50649 CAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
50697 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
50745 TA
1 TA
50747 ATTTATATTA
Statistics
Matches: 175, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
2 2 0.01
3 173 0.99
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:60272 original size:22 final size:22
Alignment explanation
Indices: 60242--60283 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
60232 CTTAATTTTA
*
60242 GAAATTTTCAAATAAA-AAATCT
1 GAAAATTTCAAA-AAATAAATCT
60264 GAAAATTTCAAAAAATAAAT
1 GAAAATTTCAAAAAATAAAT
60284 TGAGCTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.29
Consensus pattern (22 bp):
GAAAATTTCAAAAAATAAATCT
Found at i:61854 original size:32 final size:33
Alignment explanation
Indices: 61794--61859 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 33
61784 ATCGCCTTAA
*
61794 CATGAACAAATAATTTATAATGCCACCAGCCCT
1 CATGAAAAAATAATTTATAATGCCACCAGCCCT
*
61827 CATGAAAAAATAA-TTACT-ATGCCACCAGTCCT
1 CATGAAAAAATAATTTA-TAATGCCACCAGCCCT
61859 C
1 C
61860 GTAACATACA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 17 0.57
33 13 0.43
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (33 bp):
CATGAAAAAATAATTTATAATGCCACCAGCCCT
Found at i:76925 original size:60 final size:60
Alignment explanation
Indices: 76845--76972 Score: 161
Period size: 60 Copynumber: 2.1 Consensus size: 60
76835 GTCATTTAAA
* * * *
76845 AGTTTAGGGATGAATTTGAAAAT-TTTAAAAGTTTAAAAATTAATTTATAATGAA-AATTAT
1 AGTTTAAGGATCAAATTG-AAATGTTTAAAAGTTTAAAAATTAATTTAAAAT-AAGAATTAT
* * *
76905 AGTTTAAGGATCAAATTGAAATGTTTTAAAGTTTAAAATTTAATTTAAAATAAGAGTTAT
1 AGTTTAAGGATCAAATTGAAATGTTTAAAAGTTTAAAAATTAATTTAAAATAAGAATTAT
76965 AGTTTAAG
1 AGTTTAAG
76973 AATGTATGAT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 6 0.10
60 53 0.90
ACGTcount: A:0.45, C:0.01, G:0.14, T:0.40
Consensus pattern (60 bp):
AGTTTAAGGATCAAATTGAAATGTTTAAAAGTTTAAAAATTAATTTAAAATAAGAATTAT
Found at i:77829 original size:20 final size:20
Alignment explanation
Indices: 77744--77974 Score: 196
Period size: 20 Copynumber: 11.5 Consensus size: 20
77734 GATTTTCCAT
**
77744 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
77764 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* * *
77783 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATCCGT-A
*
77805 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
77825 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* **
77845 AATCGCAACGCGTATATGTA
1 AATCGCAACGCGAATCCGTA
* *
77865 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
77885 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* * *
77905 AATCGCAATGCGAATACATA
1 AATCGCAACGCGAATCCGTA
** *
77925 AATCGCAATACGAATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
77945 AATCGCAATGCGAATCTGTA
1 AATCGCAACGCGAATCCGTA
77965 AATCGCAACG
1 AATCGCAACG
77975 AGATTCTGAC
Statistics
Matches: 176, Mismatches: 31, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
19 1 0.01
20 156 0.89
21 18 0.10
22 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:77859 original size:40 final size:40
Alignment explanation
Indices: 77785--77974 Score: 229
Period size: 40 Copynumber: 4.7 Consensus size: 40
77775 GATTCTGACT
* *
77785 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
**
77826 ATCGCAACGAGAATACGTAAATCGCAACGCGTATATGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
*
77866 ATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* * * ** * *
77906 ATCGCAATGCGAATACATAAATCGCAATACGAATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
77946 ATCGCAATGCGAAT-CTGTAAATCGCAACG
1 ATCGCAACGAGAATAC-GTAAATCGCAACG
77975 AGATTCTGAC
Statistics
Matches: 132, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 115 0.87
41 16 0.12
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
Found at i:78859 original size:19 final size:19
Alignment explanation
Indices: 78844--78904 Score: 104
Period size: 19 Copynumber: 3.2 Consensus size: 19
78834 GAATCGCATG
78844 GCGAAATGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
*
78863 GCGAAATTAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
*
78882 GCGAAATGAAAATCGCAAT
1 GCGAAATGAAAATCGCAAC
78901 GCGA
1 GCGA
78905 TTTTGGTTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:78935 original size:14 final size:14
Alignment explanation
Indices: 78916--78953 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
78906 TTTGGTTTCG
78916 CGTTGCGATTATCT
1 CGTTGCGATTATCT
* *
78930 CGTTGCAATTCTCT
1 CGTTGCGATTATCT
78944 CGTTGCGATT
1 CGTTGCGATT
78954 TTCATTTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:78964 original size:21 final size:20
Alignment explanation
Indices: 78945--79016 Score: 101
Period size: 20 Copynumber: 3.5 Consensus size: 20
78935 CAATTCTCTC
78945 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
* *
78965 CGTTGCGATTGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
78986 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
79006 GTTGCGATTTT
1 GTTGCGATTTT
79017 AAGTTTAGAA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
20 31 0.66
21 16 0.34
ACGTcount: A:0.11, C:0.17, G:0.19, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:79578 original size:20 final size:20
Alignment explanation
Indices: 79553--79766 Score: 216
Period size: 20 Copynumber: 10.6 Consensus size: 20
79543 TTTTAAAAAT
79553 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
79573 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
79593 TGTCGTTGAGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
79614 CACATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
79634 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
79654 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
79674 CTCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
79694 AGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
79714 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
79735 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
79756 CTCGTTGCGAT
1 CGCGTTGCGAT
79767 AGTCAGAATC
Statistics
Matches: 156, Mismatches: 31, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
20 105 0.67
21 51 0.33
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:79587 original size:40 final size:40
Alignment explanation
Indices: 79550--79847 Score: 241
Period size: 40 Copynumber: 7.4 Consensus size: 40
79540 GCGTTTTAAA
79550 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * * * *
79590 TATTGTCGTTGAGATTTACGGATACACATTGCGA-TTTACG
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * *
79630 TATTCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACG
1 -AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * * *
79670 TATTCTCGTTACGATTTACGGATAAGCGTTGCGATTTTACG
1 -AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* *
79711 TATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
1 AATCG-CGTTGCGATTTACGGATACGCGTTGCGATTTTACG
* * * * *
79752 GATACTCGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATG
1 AAT-CGCGTTGCGAT-TTACGGATA-CGCGTTGCGATTT-TACG
* * ** *
79794 -TTCGCGTTGCGATTTTCATATTCGCGTTGCGATTTT-C-
1 AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
79831 ATATTCGCGTTGCGATT
1 A-A-TCGCGTTGCGATT
79848 ATGGAAAATC
Statistics
Matches: 210, Mismatches: 35, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
39 2 0.01
40 111 0.53
41 93 0.44
42 4 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
AATCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACG
Found at i:79798 original size:20 final size:20
Alignment explanation
Indices: 79775--79847 Score: 121
Period size: 20 Copynumber: 3.6 Consensus size: 20
79765 ATAGTCAGAA
*
79775 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
79795 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
79815 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
79835 TCGCGTTGCGATT
1 TCGCGTTGCGATT
79848 ATGGAAAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 1 0.02
20 50 0.98
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:79802 original size:81 final size:81
Alignment explanation
Indices: 79552--79847 Score: 314
Period size: 81 Copynumber: 3.7 Consensus size: 81
79542 GTTTTAAAAA
* * * *
79552 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGAGATTTACGGATACAC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
* ** *
79617 ATTGCGATTTACGTAT
66 GTTGCGATTTATATGT
* * *
79633 TCTCGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCTCGTTACGATTTACGGATAAGC
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
*
79697 GTTGCGATTT-TACGT
66 GTTGCGATTTATATGT
* * * * * *
79712 ATTGTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGT-CAGA-A
1 -TCG-CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGAT-TTACGGATA
79775 TCGCGTTGCGATTTATATGT
63 -CGCGTTGCGATTTATATGT
* * * * *
79795 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTTT-CATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATT
79848 ATGGAAAATC
Statistics
Matches: 177, Mismatches: 32, Indels: 14
0.79 0.14 0.06
Matches are distributed among these distances:
79 1 0.01
80 51 0.29
81 85 0.48
82 35 0.20
83 5 0.03
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (81 bp):
TCGCGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACGC
GTTGCGATTTATATGT
Found at i:79822 original size:162 final size:162
Alignment explanation
Indices: 79555--79847 Score: 383
Period size: 162 Copynumber: 1.8 Consensus size: 162
79545 TTAAAAATCG
* ** * *
79555 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGAGATTTACGGATACACATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGAGATTCACGAATACACATT
* * * *
79620 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTACGAT
66 GCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCGCGTTACGAT
79685 TTACGGATAAGCGTTGCGATTTTACGTATTGT
131 TTACGGATAAGCGTTGCGATTTTACGTATTGT
* * *
79717 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT-CGCG
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGAGAT--TCACGAATACACA
* * * * * * *
79780 TTGCGATTTATATGTTCGCGTTGCGATTTTCATATTCGCGTTGCGATTTTCATATTCGCGTTGCG
64 TTGCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCGCGTTACG
79845 ATT
129 ATT
79848 ATGGAAAATC
Statistics
Matches: 110, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
162 105 0.95
163 3 0.03
164 2 0.02
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (162 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGAGATTCACGAATACACATT
GCGATTTACATATTCGCGTTGCGATTTACAGATACGCGTTGCGATTTACATATTCGCGTTACGAT
TTACGGATAAGCGTTGCGATTTTACGTATTGT
Found at i:79879 original size:21 final size:20
Alignment explanation
Indices: 79855--79912 Score: 64
Period size: 19 Copynumber: 2.9 Consensus size: 20
79845 ATTATGGAAA
*
79855 ATCGCAATGCGAATTTGTACT
1 ATCGCATTGCGAATTTGTA-T
*
79876 ATCGCATTGCG-ATTTTTAT
1 ATCGCATTGCGAATTTGTAT
* *
79895 TTCGCATTGCGATTTTGT
1 ATCGCATTGCGAATTTGT
79913 TGGTATTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 11 0.35
20 10 0.32
21 10 0.32
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (20 bp):
ATCGCATTGCGAATTTGTAT
Found at i:82951 original size:12 final size:12
Alignment explanation
Indices: 82934--82964 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
82924 GTGAGCAATA
82934 GGCTGGGCGATG
1 GGCTGGGCGATG
82946 GGCTGGGCGATG
1 GGCTGGGCGATG
82958 GGCTGGG
1 GGCTGGG
82965 GGAGAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.16, G:0.61, T:0.16
Consensus pattern (12 bp):
GGCTGGGCGATG
Found at i:84892 original size:2 final size:2
Alignment explanation
Indices: 84885--84909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84875 CGTTTTATTA
84885 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
84910 ACACACACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:90130 original size:5 final size:5
Alignment explanation
Indices: 90109--90144 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
90099 TCTCAAAAGT
* *
90109 ATAAA ATGAA GTAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
90145 ACTATTAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (5 bp):
ATAAA
Done.