Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006701.1 Hibiscus syriacus cultivar Beakdansim tig00016683_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: 71628
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:180 original size:68 final size:68
Alignment explanation
Indices: 49--183 Score: 191
Period size: 68 Copynumber: 2.0 Consensus size: 68
39 TGAAAGAAAT
* ** *
49 CGAGGTCATCCTTTAAGGGAAATGATCTATCATTTTCATCGAGGAATTGATCCTTTTGGTGAAGG
1 CGAGGTCATCCTTTAAGGGAAATGATCGATCATTTTCATCGAGGAATCAATCCTTTTGATGAAGG
114 GAA
66 GAA
* * *
117 CGAGGTCATCCTTTAAGGGAAATGATCGATCCTTTTCATCGA-GAGATCAATCTTTTTTATGAAG
1 CGAGGTCATCCTTTAAGGGAAATGATCGATCATTTTCATCGAGGA-ATCAATCCTTTTGATGAAG
181 GGA
65 GGA
184 TCGATCTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
67 2 0.03
68 57 0.97
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (68 bp):
CGAGGTCATCCTTTAAGGGAAATGATCGATCATTTTCATCGAGGAATCAATCCTTTTGATGAAGG
GAA
Found at i:693 original size:18 final size:20
Alignment explanation
Indices: 672--720 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
662 TATTTTGTTG
672 AATATTTAAATTT-AAA-TT
1 AATATTTAAATTTAAAATTT
*
690 AATATTT-TATTTAAAATTT
1 AATATTTAAATTTAAAATTT
*
709 AAGATTTAAATT
1 AATATTTAAATT
721 AAGTCTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 8 0.32
20 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATATTTAAATTTAAAATTT
Found at i:719 original size:31 final size:30
Alignment explanation
Indices: 661--722 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
651 GAGTTAAATG
* *
661 ATATTTTGTTGAATATTTAAATTTAAATTA
1 ATATTTTATTGAAAATTTAAATTTAAATTA
*
691 ATATTTTATTTAAAATTTAAGATTTAAATTA
1 ATATTTTATTGAAAATTTAA-ATTTAAATTA
722 A
1 A
723 GTCTAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 17 0.61
31 11 0.39
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (30 bp):
ATATTTTATTGAAAATTTAAATTTAAATTA
Found at i:5809 original size:19 final size:18
Alignment explanation
Indices: 5787--5822 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5777 AAATTTTGGA
5787 TTTTTTGGCTCTTTTTTTG
1 TTTTTTGGC-CTTTTTTTG
*
5806 TTTTTTTGCCTTTTTTT
1 TTTTTTGGCCTTTTTTT
5823 TTTGCCTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTTTTGGCCTTTTTTTG
Found at i:5810 original size:20 final size:20
Alignment explanation
Indices: 5787--5867 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 20
5777 AAATTTTGGA
*
5787 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGGCTTTTTTTTTGT
* *
5807 TTTTTTGCCTTTTTTTTTTGCC
1 TTTTTTGGC-TTTTTTTTTG-T
*
5829 TTTTTT-GTTTTTTTTTTGTT
1 TTTTTTGGCTTTTTTTTTG-T
* *
5849 TTTTTTTGTTTTTTTTTTG
1 TTTTTTGGCTTTTTTTTTG
5868 AAAAAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
20 24 0.47
21 21 0.41
22 6 0.12
ACGTcount: A:0.00, C:0.07, G:0.11, T:0.81
Consensus pattern (20 bp):
TTTTTTGGCTTTTTTTTTGT
Found at i:5822 original size:13 final size:13
Alignment explanation
Indices: 5806--5839 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
5796 TCTTTTTTTG
5806 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
5819 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
5832 TTTGTTTT
1 TTT-TTTT
5840 TTTTTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:5855 original size:21 final size:21
Alignment explanation
Indices: 5798--5867 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
5788 TTTTTGGCTC
***
5798 TTTTTTTGTTTTTTTGCCTTT
1 TTTTTTTGTTTTTTTTTGTTT
**
5819 TTTTTTTG-CCTTTTTTGTTT
1 TTTTTTTGTTTTTTTTTGTTT
5839 TTTTTTTGTTTTTTTTTGTTT
1 TTTTTTTGTTTTTTTTTGTTT
5860 TTTTTTTG
1 TTTTTTTG
5868 AAAAAAAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (21 bp):
TTTTTTTGTTTTTTTTTGTTT
Found at i:7310 original size:2 final size:2
Alignment explanation
Indices: 7303--7343 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
7293 TCTATAATTA
7303 AT AT AT AT 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 AT AT AT AT A
7344 CTTGACAATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:7558 original size:20 final size:20
Alignment explanation
Indices: 7513--7558 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
7503 TGACGTAAAA
*
7513 TAAAAAAAATATTTATTTTC
1 TAAAAAAAATAATTATTTTC
*
7533 TCAAAAAAATAATTATTTT-
1 TAAAAAAAATAATTATTTTC
7552 TAAAAAA
1 TAAAAAA
7559 CCATTTTCCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
TAAAAAAAATAATTATTTTC
Found at i:11597 original size:23 final size:23
Alignment explanation
Indices: 11566--11645 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
11556 AAAACTACCA
*
11566 AAAGACAGAGAAAAACGTGTCAC
1 AAAGACAGAAAAAAACGTGTCAC
*
11589 AAGGACAGAAAAAAAACGTGTCAC
1 AAAGACAG-AAAAAAACGTGTCAC
* * * *
11613 AAAGATAGATATAAACATGTCAC
1 AAAGACAGAAAAAAACGTGTCAC
*
11636 AAAGATAGAA
1 AAAGACAGAA
11646 TTATTCTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
23 28 0.58
24 20 0.42
ACGTcount: A:0.55, C:0.14, G:0.19, T:0.12
Consensus pattern (23 bp):
AAAGACAGAAAAAAACGTGTCAC
Found at i:13047 original size:58 final size:59
Alignment explanation
Indices: 12924--13061 Score: 165
Period size: 58 Copynumber: 2.4 Consensus size: 59
12914 GCTCTCGATT
* **** *
12924 TGATTTTGTAGGTGTTGCAAACCAAGAGAGACTAAAATGATTACACACGTCTTTTTCAT
1 TGATTTTGTAGGTGTTGCAAACCAAGAGAGACTAAAATGATTACACACATCTAAAACAG
* *
12983 TAATTTT-TAGGTGTTGCAAACCAAGAGAGACTAAAATGATTACAGA-ATC-AAAACGACG
1 TGATTTTGTAGGTGTTGCAAACCAAGAGAGACTAAAATGATTACACACATCTAAAAC-A-G
13041 TGATTTTGTAGGTGTTGCAAA
1 TGATTTTGTAGGTGTTGCAAA
13062 ATTAAATTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
56 1 0.01
57 3 0.04
58 44 0.66
59 19 0.28
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (59 bp):
TGATTTTGTAGGTGTTGCAAACCAAGAGAGACTAAAATGATTACACACATCTAAAACAG
Found at i:13091 original size:25 final size:25
Alignment explanation
Indices: 13063--13110 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
13053 TGTTGCAAAA
*
13063 TTAAATTGTTTTTATTGGACGTGAT
1 TTAAATGGTTTTTATTGGACGTGAT
13088 TTAAATGGTTTTTATTGGACGTG
1 TTAAATGGTTTTTATTGGACGTG
13111 TGTAATCACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.50
Consensus pattern (25 bp):
TTAAATGGTTTTTATTGGACGTGAT
Found at i:13487 original size:21 final size:21
Alignment explanation
Indices: 13461--13506 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
13451 AAATCAATTG
13461 AAATTCACTTTTTACCATCAT
1 AAATTCACTTTTTACCATCAT
* *
13482 AAATTCACTTTTTACTATCGT
1 AAATTCACTTTTTACCATCAT
13503 AAAT
1 AAAT
13507 GAATTAACGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (21 bp):
AAATTCACTTTTTACCATCAT
Found at i:18226 original size:24 final size:24
Alignment explanation
Indices: 18191--18249 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
18181 TCAAAAGTTG
* *
18191 CAATGAAAATTATATATATGCATA
1 CAATGAAGATTATATACATGCATA
18215 CAATGAAGATTATATACATGCATA
1 CAATGAAGATTATATACATGCATA
18239 CAATGAAGATT
1 CAATGAAGATT
18250 GCAAGTTGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
CAATGAAGATTATATACATGCATA
Found at i:22481 original size:55 final size:55
Alignment explanation
Indices: 22397--22506 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
22387 GTCGGGTGGC
*
22397 CCAAAAACCCGACCCGACCCATTGACATCCCT-AGCAGACATAGTGCAGCCTTGTA
1 CCAAAAACCCGACACGACCCATTGACATCCCTAAG-AGACATAGTGCAGCCTTGTA
22452 CCAAAAACCCGACACGACCCATTGACATCCCTAAGAGACATAGTGCAGCCTTGTA
1 CCAAAAACCCGACACGACCCATTGACATCCCTAAGAGACATAGTGCAGCCTTGTA
22507 TTAGGCCCCT
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 51 0.96
56 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.16, T:0.16
Consensus pattern (55 bp):
CCAAAAACCCGACACGACCCATTGACATCCCTAAGAGACATAGTGCAGCCTTGTA
Found at i:22911 original size:13 final size:13
Alignment explanation
Indices: 22889--22922 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
22879 GTCAATGAAC
22889 TAAAAAATATT-T
1 TAAAAAATATTAT
22901 TAAATAAATATTAT
1 TAAA-AAATATTAT
22915 TAAAAAAT
1 TAAAAAAT
22923 TATGTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAAAATATTAT
Found at i:31066 original size:21 final size:21
Alignment explanation
Indices: 31040--31118 Score: 77
Period size: 21 Copynumber: 3.8 Consensus size: 21
31030 TCCGCAGTCG
*
31040 TTTCAGATGCCACTACAACCA
1 TTTCAGATGCCACCACAACCA
** * *
31061 TTTCAGATGGTACCGCAACCG
1 TTTCAGATGCCACCACAACCA
***
31082 TTTTTTATGCCACCACAACCA
1 TTTCAGATGCCACCACAACCA
*
31103 TTTCAAATGCCACCAC
1 TTTCAGATGCCACCAC
31119 CGCAGGGTTT
Statistics
Matches: 43, Mismatches: 15, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.27
Consensus pattern (21 bp):
TTTCAGATGCCACCACAACCA
Found at i:31599 original size:43 final size:44
Alignment explanation
Indices: 31519--31638 Score: 215
Period size: 43 Copynumber: 2.8 Consensus size: 44
31509 CGATAGACAT
*
31519 TTTTTATTTATTTTGTTTCTTAATATTTTTATTTAATTATGAAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
*
31563 TTTTTATTTATTTTGTTT-TTAATGTTTTTATTTAATTATGGAC
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
31606 TTTTTATTTATTTTGTTTCTTAATGTTTTTATT
1 TTTTTATTTATTTTGTTTCTTAATGTTTTTATT
31639 ATTTAATTGT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
43 41 0.56
44 32 0.44
ACGTcount: A:0.21, C:0.03, G:0.07, T:0.69
Consensus pattern (44 bp):
TTTTTATTTATTTTGTTTCTTAATGTTTTTATTTAATTATGAAC
Found at i:31682 original size:13 final size:13
Alignment explanation
Indices: 31638--31686 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
31628 ATGTTTTTAT
31638 TATTTAATTGTTTG
1 TATTTAA-TGTTTG
* *
31652 AATTATAACGTTTG
1 TATT-TAATGTTTG
*
31666 TATTTAATGTTTC
1 TATTTAATGTTTG
31679 TATTTAAT
1 TATTTAAT
31687 TATTTTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 15 0.52
14 11 0.38
15 3 0.10
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (13 bp):
TATTTAATGTTTG
Found at i:31757 original size:16 final size:16
Alignment explanation
Indices: 31736--31768 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
31726 TATTTAATTT
*
31736 TCACTTGAGTATTACA
1 TCACTTGAGTATCACA
31752 TCACTTGAGTATCACA
1 TCACTTGAGTATCACA
31768 T
1 T
31769 TAATTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (16 bp):
TCACTTGAGTATCACA
Found at i:42493 original size:25 final size:25
Alignment explanation
Indices: 42465--42524 Score: 84
Period size: 25 Copynumber: 2.4 Consensus size: 25
42455 ATAAATTTTT
42465 ACTAATCTAAAATTTATAAGTCTCG
1 ACTAATCTAAAATTTATAAGTCTCG
* * *
42490 ACTAATTTAAATTTTGTAAGTCTCG
1 ACTAATCTAAAATTTATAAGTCTCG
*
42515 ATTAATCTAA
1 ACTAATCTAA
42525 TAAGAATATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (25 bp):
ACTAATCTAAAATTTATAAGTCTCG
Found at i:42787 original size:16 final size:14
Alignment explanation
Indices: 42748--42795 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 14
42738 TTTTAGTATT
*
42748 TTTTATATTTAATT
1 TTTTATATTTAATA
42762 TTTGTATATTTGAATAA
1 TTT-TATATTT-AAT-A
*
42779 TTTTATATTTAAAA
1 TTTTATATTTAATA
42793 TTT
1 TTT
42796 AAAATAATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 7 0.24
15 9 0.31
16 10 0.34
17 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TTTTATATTTAATA
Found at i:43145 original size:2 final size:2
Alignment explanation
Indices: 43138--43166 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43128 GCATAAATAT
43138 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
43167 GGACATTCAA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:54040 original size:3 final size:3
Alignment explanation
Indices: 54034--54098 Score: 80
Period size: 3 Copynumber: 22.0 Consensus size: 3
54024 TTTTTTTCCG
** *
54034 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54080 TTA TTA TTTA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA
54099 CAATTTTTGC
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.06
3 47 0.89
4 3 0.06
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:54246 original size:25 final size:25
Alignment explanation
Indices: 54217--54338 Score: 192
Period size: 25 Copynumber: 4.9 Consensus size: 25
54207 GCAACCCGTT
*
54217 AGATTAGGGTTTCAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAAC
* *
54242 AGATTAGGGTTTTAAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAAC
*
54267 TGATTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAAC
54292 A-ATTTAGGGTTTCAAACCCTAAAAC
1 AGA-TTAGGGTTTCAAACCCTAAAAC
54317 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
54339 TCCCCTACTC
Statistics
Matches: 90, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
24 1 0.01
25 88 0.98
26 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAAAC
Found at i:55988 original size:14 final size:14
Alignment explanation
Indices: 55971--56001 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55961 ATAGAAATTA
55971 TTTTATTGTTATTT
1 TTTTATTGTTATTT
*
55985 TTTTTTTGTTATTT
1 TTTTATTGTTATTT
55999 TTT
1 TTT
56002 GATTAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.06, T:0.84
Consensus pattern (14 bp):
TTTTATTGTTATTT
Found at i:68767 original size:90 final size:90
Alignment explanation
Indices: 68648--68904 Score: 366
Period size: 90 Copynumber: 2.9 Consensus size: 90
68638 TCAACATTAG
*
68648 GATAACCAGCCGTCCTTATCACGTAGGAACCGAGTTATCACCCTTCCTTTAGATGGCCAGATCTC
1 GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTTTAGATGGCCAGATCTC
68713 TTCATCACGTAAGAGCC-GTCAACCT
66 -TCATCACGTAAGAGCCGGTCAACCT
68738 GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTTTAGATGGCCAGATCTC
1 GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTTTAGATGGCCAGATCTC
68803 TCATCACGT-A-AGCCGTGTCAACCT
66 TCATCACGTAAGAGCCG-GTCAACCT
* * * ** *
68827 -ATAACCAGTCGTCCTCATTACGTAGGAACCGAGTTATCA---TCCCTAAAGATGACCAGATCTC
1 GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTTTAGATGGCCAGATCT-
*
68888 CTCATCACGTAGGAGCC
65 CTCATCACGTAAGAGCC
68905 ATGTCACCCT
Statistics
Matches: 154, Mismatches: 8, Indels: 12
0.89 0.05 0.07
Matches are distributed among these distances:
85 17 0.11
86 10 0.06
87 4 0.03
88 42 0.27
89 17 0.11
90 64 0.42
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (90 bp):
GATAACCAGCCGTCCTCATCACGTAGGAACCGAGTTATCACCCTTCCTTTAGATGGCCAGATCTC
TCATCACGTAAGAGCCGGTCAACCT
Found at i:68910 original size:88 final size:90
Alignment explanation
Indices: 68606--68910 Score: 365
Period size: 90 Copynumber: 3.4 Consensus size: 90
68596 CAACATCAAC
* * *
68606 TGACCAGA-CTTCCTCATCACGTAGGAGTCGTGTCAACATTAGGATAACCAGCCGTCCTTATCAC
1 TGACCAGATC-TCCTCATCACGTAGGAGCCGTGTCAAC-CT--GATAACCAGCCGTCCTCATCAC
68670 GTAGGAACCGAGTTATCACCCTTCCTTTAGA
62 GTAGGAACCGAGTTATCA--CTTCCTTTAGA
* * *
68701 TGGCCAGATCTCTTCATCACGTAAGAGCC--GTCAACCTGATAACCAGCCGTCCTCATCACGTAG
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAG
68764 GAACCGAGTTATCACCCTTCCTTTAGA
66 GAACCGAGTTATCA--CTTCCTTTAGA
* * *
68791 TGGCCAGATCT-CTCATCACGTA--AGCCGTGTCAACCT-ATAACCAGTCGTCCTCATTACGTAG
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAG
* **
68852 GAACCGAGTTATCA-TCCCTAAAGA
66 GAACCGAGTTATCACTTCCTTTAGA
*
68876 TGACCAGATCTCCTCATCACGTAGGAGCCATGTCA
1 TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
68911 CCCTTAGACG
Statistics
Matches: 190, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
85 17 0.09
86 11 0.06
87 4 0.02
88 46 0.24
89 18 0.09
90 63 0.33
92 1 0.01
93 6 0.03
95 23 0.12
96 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (90 bp):
TGACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACCTGATAACCAGCCGTCCTCATCACGTAG
GAACCGAGTTATCACTTCCTTTAGA
Found at i:69369 original size:49 final size:49
Alignment explanation
Indices: 69277--69397 Score: 172
Period size: 49 Copynumber: 2.4 Consensus size: 49
69267 GCAACCCGTT
* * *
69277 AGATTAGGGTTTCAAAACCCTAAATCAGATTAGGGTTTTAACCCTAAATC
1 AGATTAGGGTTTC-AAACCCTAAAACAGATTAGGGTTTAAACCCTAAAAC
* *
69327 TGATTAGGGTTTCAAACCCTAAAACA-TTTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAACAGATTAGGGTTT-AAACCCTAAAAC
69376 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
69398 TCCCTACTCA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
48 9 0.14
49 43 0.67
50 12 0.19
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (49 bp):
AGATTAGGGTTTCAAACCCTAAAACAGATTAGGGTTTAAACCCTAAAAC
Found at i:69388 original size:25 final size:25
Alignment explanation
Indices: 69277--69397 Score: 174
Period size: 24 Copynumber: 4.9 Consensus size: 25
69267 GCAACCCGTT
*
69277 AGATTAGGGTTTCAAAACCCTAAATC
1 AGATTAGGGTTTC-AAACCCTAAAAC
* *
69303 AGATTAGGGTTT-TAACCCTAAATC
1 AGATTAGGGTTTCAAACCCTAAAAC
*
69327 TGATTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAAC
*
69352 A-TTTAGGGTTTCAAACCCTAAAAC
1 AGATTAGGGTTTCAAACCCTAAAAC
69376 AGATTAGGGTTTCAAACCCTAA
1 AGATTAGGGTTTCAAACCCTAA
69398 TCCCTACTCA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
24 45 0.52
25 29 0.34
26 12 0.14
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (25 bp):
AGATTAGGGTTTCAAACCCTAAAAC
Done.