Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006823.1 Hibiscus syriacus cultivar Beakdansim tig00017335_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: 52795
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Found at i:3035 original size:16 final size:17
Alignment explanation
Indices: 3009--3044 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
2999 TCTACTAAAG
3009 CATGATTGGGTAGATAT
1 CATGATTGGGTAGATAT
3026 CATG-TTGGGTAGATAT
1 CATGATTGGGTAGATAT
3042 CAT
1 CAT
3045 ATGAATAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (17 bp):
CATGATTGGGTAGATAT
Found at i:13034 original size:26 final size:25
Alignment explanation
Indices: 13005--13081 Score: 86
Period size: 26 Copynumber: 3.1 Consensus size: 25
12995 ATTTTGCTTG
*
13005 AAAAAAATAATGAAAAAATGAAATAA
1 AAAAAAAGAATGAAAAAATGAAA-AA
**
13031 AAAAGGAGAA--AAAAAATGAAAAA
1 AAAAAAAGAATGAAAAAATGAAAAA
*
13054 GAAAAAAGAATGAAAAAAATGAAAAA
1 AAAAAAAGAATG-AAAAAATGAAAAA
13080 AA
1 AA
13082 GAAGGGTTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 9 0.22
24 11 0.27
26 21 0.51
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (25 bp):
AAAAAAAGAATGAAAAAATGAAAAA
Found at i:13052 original size:9 final size:9
Alignment explanation
Indices: 13040--13081 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
13030 AAAAAGGAGA
13040 AAAAAAATG
1 AAAAAAATG
13049 AAAAAGAA--
1 AAAAA-AATG
*
13057 AAAAGAATG
1 AAAAAAATG
13066 AAAAAAATG
1 AAAAAAATG
13075 AAAAAAA
1 AAAAAAA
13082 GAAGGGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
7 2 0.07
8 4 0.14
9 20 0.71
10 2 0.07
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (9 bp):
AAAAAAATG
Found at i:13058 original size:16 final size:17
Alignment explanation
Indices: 13037--13070 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
13027 ATAAAAAAGG
13037 AGAAAAAA-AATGAAAA
1 AGAAAAAAGAATGAAAA
13053 AGAAAAAAGAATGAAAA
1 AGAAAAAAGAATGAAAA
13070 A
1 A
13071 AATGAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (17 bp):
AGAAAAAAGAATGAAAA
Found at i:14169 original size:55 final size:55
Alignment explanation
Indices: 14084--14705 Score: 947
Period size: 55 Copynumber: 11.3 Consensus size: 55
14074 AGATTTCCCA
* *
14084 ACGATTATTGAAGATTGATCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
14139 GCGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
14194 GCGATTGTTGAAGATTGTTTGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
14249 ACGATTGTTGAAAATTGTTCGAGTCTTATACTCTATGCAGAAATATGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
14304 ACGACTGTTGAAGATTGTTCGAGTCTTATACTCTCTGTAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
14359 ACGATTGATGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * *
14414 ACGATTGATGAAAATTGTTCGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
** * *
14469 ACGACAGTTGAAGATTGTTGGAGTCTTATACTCTCTGCAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
14524 ACGATTGATGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATGGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* *
14579 ACGATTGATGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
1 ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
* * * *
14634 AAGATTTGTTGAAGATTGTTTGGGTCTTATACTCTCTGAGGAAATAGGGAGCAGAC
1 ACGA-TTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
*
14690 ACGATTGATGAAGATT
1 ACGATTGTTGAAGATT
14706 CTTCAAGTTC
Statistics
Matches: 519, Mismatches: 47, Indels: 2
0.91 0.08 0.00
Matches are distributed among these distances:
55 468 0.90
56 51 0.10
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (55 bp):
ACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGAC
Found at i:14791 original size:55 final size:54
Alignment explanation
Indices: 14699--14856 Score: 205
Period size: 55 Copynumber: 2.9 Consensus size: 54
14689 CACGATTGAT
* * *
14699 GAAGATTCTTCAAGTTC-CTACTCCCTAAGAAAGAGGGAGTGAACCCGTT-GACA
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAGTGAACCCGTTCG-CA
* *
14752 GAAGATTGTTCGAGTTCTATACTCCCCGAAGAAAGAGGGAGTGAACTCGTTCGCA
1 GAAGATTGTTCGAGTTCTATACT-CCCTAAGAAAGAGGGAGTGAACCCGTTCGCA
* *
14807 GAAAATTGTTCGAGTTCTATACTCCCTAA-AAATGAGGGAGCGAACCCGTT
1 GAAGATTGTTCGAGTTCTATACTCCCTAAGAAA-GAGGGAGTGAACCCGTT
14857 TTCCGAATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
53 18 0.20
54 24 0.26
55 49 0.53
56 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.24
Consensus pattern (54 bp):
GAAGATTGTTCGAGTTCTATACTCCCTAAGAAAGAGGGAGTGAACCCGTTCGCA
Found at i:15098 original size:2 final size:2
Alignment explanation
Indices: 15093--15159 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
15083 ATAATTATTA
15093 AT AT 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 AT AT
15135 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 A
15160 AGCAGTAAAT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18596 original size:18 final size:18
Alignment explanation
Indices: 18565--18614 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
18555 ATAGAATATG
*
18565 TGATTTTTTCTTTAAAATT
1 TGATTTTAT-TTTAAAATT
*
18584 TGATTTTATTTTAAAGTT
1 TGATTTTATTTTAAAATT
18602 TAGATTATTATTT
1 T-GATT-TTATTT
18615 GATAAATAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (18 bp):
TGATTTTATTTTAAAATT
Found at i:19197 original size:93 final size:92
Alignment explanation
Indices: 19039--19223 Score: 325
Period size: 93 Copynumber: 2.0 Consensus size: 92
19029 TGAGGGTAAG
* **
19039 AGTTAGCACCGTATGAGAGAGTGTGTTAGAGTTATCTAATGTTGTATGGTTCGAACATTACACTT
1 AGTTAGCACCGTATGAGAGAGTGTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTACACTT
19104 CTCTTTTATCTGATGTTGTATGATCTA
66 CTCTTTTATCTGATGTTGTATGATCTA
*
19131 AGTTAGCACCGTATGAGAGAGTCGTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTGCACT
1 AGTTAGCACCGTATGAGAGAGT-GTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTACACT
19196 TCTCTTTTATCTGATGTTGTATGATCTA
65 TCTCTTTTATCTGATGTTGTATGATCTA
19224 GGCATCCATA
Statistics
Matches: 88, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 22 0.25
93 66 0.75
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (92 bp):
AGTTAGCACCGTATGAGAGAGTGTGTAAGAGTTATCTAATGTTGTACAGTTCGAACATTACACTT
CTCTTTTATCTGATGTTGTATGATCTA
Found at i:23241 original size:235 final size:235
Alignment explanation
Indices: 22830--23300 Score: 906
Period size: 235 Copynumber: 2.0 Consensus size: 235
22820 CATGACCTAA
22830 ATCAAGTGCTACCTGCTTAAGGCTTTATTGCTCTATCACTGAAGTAGGGGTCTCACGCTTCCCTT
1 ATCAAGTGCTACCTGCTTAAGGCTTTATTGCTCTATCACTGAAGTAGGGGTCTCACGCTTCCCTT
22895 AATCCCCTACTAAGGGCCTCACCATGAGTACACCTCTAAAGGGTCTCTAACCCTAATGGATGAAC
66 AATCCCCTACTAAGGGCCTCACCATGAGTACACCTCTAAAGGGTCTCTAACCCTAATGGATGAAC
22960 TTTTATGCATTATCTAAATGTGAACTTAACATACTCTGAATTATCTAAATGCAAACATGACATGC
131 TTTTATGCATTATCTAAATGTGAACTTAACATACTCTGAATTATCTAAATGCAAACATGACATGC
*
23025 ATCATCTGGATGCAAACATGACTAGTATCTGGTCTCACAT
196 ATCATCTGGATGCAAACATGACTAGTATATGGTCTCACAT
*
23065 ATCAAGTGCTACCTGCTTAAGGCTTTATTGCTCTATCACTGAAGTAGGGGTCTCACGCTTCCTTT
1 ATCAAGTGCTACCTGCTTAAGGCTTTATTGCTCTATCACTGAAGTAGGGGTCTCACGCTTCCCTT
23130 AATCCCCTACTAAGGGCCTCACCATGAGTACACCTCTAAAGGGTCTCTAACCCTAATGGATGAAC
66 AATCCCCTACTAAGGGCCTCACCATGAGTACACCTCTAAAGGGTCTCTAACCCTAATGGATGAAC
* *
23195 TTTTATGCATTCTCTAAATGTGAACTTAACATACTGTGAATTATCTAAATGCAAACATGACATGC
131 TTTTATGCATTATCTAAATGTGAACTTAACATACTCTGAATTATCTAAATGCAAACATGACATGC
23260 ATCATCTGGATGCAAACATGACTAGTATATGGTCTCACAT
196 ATCATCTGGATGCAAACATGACTAGTATATGGTCTCACAT
23300 A
1 A
23301 ACTCTCAGAC
Statistics
Matches: 232, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
235 232 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (235 bp):
ATCAAGTGCTACCTGCTTAAGGCTTTATTGCTCTATCACTGAAGTAGGGGTCTCACGCTTCCCTT
AATCCCCTACTAAGGGCCTCACCATGAGTACACCTCTAAAGGGTCTCTAACCCTAATGGATGAAC
TTTTATGCATTATCTAAATGTGAACTTAACATACTCTGAATTATCTAAATGCAAACATGACATGC
ATCATCTGGATGCAAACATGACTAGTATATGGTCTCACAT
Found at i:25043 original size:3 final size:3
Alignment explanation
Indices: 25035--25087 Score: 51
Period size: 3 Copynumber: 18.3 Consensus size: 3
25025 GAGAAGATGA
*
25035 AAG AAG AAG AA- ATG AAG AAG AAG AAG AAG AA- AATG AAG AA- AATG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG AA-G
25079 AAG -AG AAG A
1 AAG AAG AAG A
25088 GAAATATGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 7 0.17
3 31 0.74
4 4 0.10
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (3 bp):
AAG
Found at i:25085 original size:26 final size:28
Alignment explanation
Indices: 25024--25096 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
25014 ATAGCTACTT
* *
25024 AGAGAAGATGAAAGAAGAAGAAATGAAGA
1 AGAGAAGAAGAAAGATGAAGAAA-GAAGA
*
25053 AGAAGAAGAAGAAA-ATGAAGAAA-ATGA
1 AG-AGAAGAAGAAAGATGAAGAAAGAAGA
*
25080 AGAGAAG-AGAAATATGA
1 AGAGAAGAAGAAAGATGA
25097 TGAGATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 5 0.13
26 9 0.23
27 5 0.13
29 10 0.26
30 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.29, T:0.08
Consensus pattern (28 bp):
AGAGAAGAAGAAAGATGAAGAAAGAAGA
Found at i:25530 original size:3 final size:3
Alignment explanation
Indices: 25522--25578 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
25512 ATAAAAGTGA
25522 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
25570 AAT AA- AAT A
1 AAT AAT AAT A
25579 GGAATAAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:26190 original size:40 final size:40
Alignment explanation
Indices: 26145--26249 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 40
26135 TTTAAATAGG
** **
26145 ATACTAAAATGAAACAAAAACTAATTTTTTTAATGGCGGA
1 ATACTAAAATGAAACAAAAACTAAAGTTTTTAATAACGGA
* **
26185 ATACTAAAATGAAATC-AAAACCAAAGTTTTTAATAATTGA
1 ATACTAAAATGAAA-CAAAAACTAAAGTTTTTAATAACGGA
* *
26225 GTCCTAAAATGAAACAAAAACTAAA
1 ATACTAAAATGAAACAAAAACTAAA
26250 ATTTAGGTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
39 1 0.02
40 51 0.96
41 1 0.02
ACGTcount: A:0.52, C:0.11, G:0.10, T:0.27
Consensus pattern (40 bp):
ATACTAAAATGAAACAAAAACTAAAGTTTTTAATAACGGA
Found at i:27623 original size:21 final size:21
Alignment explanation
Indices: 27597--27636 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
27587 TGCTGGACTG
27597 GGTCTTACAAGGTCAAGAAAA
1 GGTCTTACAAGGTCAAGAAAA
27618 GGTCTTACAAGGTCAAGAA
1 GGTCTTACAAGGTCAAGAA
27637 GATCAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.15, G:0.25, T:0.20
Consensus pattern (21 bp):
GGTCTTACAAGGTCAAGAAAA
Found at i:27833 original size:2 final size:2
Alignment explanation
Indices: 27826--27903 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
27816 ATCTGCATGC
27826 AT AT 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 AT AT
27868 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
27904 TGTAAGGATG
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28962 original size:16 final size:16
Alignment explanation
Indices: 28941--28972 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28931 TATCTTTATA
28941 AAATGAAAATATATTT
1 AAATGAAAATATATTT
*
28957 AAATGAAAGTATATTT
1 AAATGAAAATATATTT
28973 GATTTATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (16 bp):
AAATGAAAATATATTT
Found at i:29472 original size:20 final size:20
Alignment explanation
Indices: 29440--29492 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
29430 TCATACTAAT
*
29440 ATTTTTGTA-ATTTTTT-TGG
1 ATTTTTTTATATTTTTTCT-G
*
29459 ATTTTTTTCTATTTTTTCTG
1 ATTTTTTTATATTTTTTCTG
29479 ATTTTTTTATATTT
1 ATTTTTTTATATTT
29493 GTAAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 7 0.24
20 21 0.72
21 1 0.03
ACGTcount: A:0.15, C:0.04, G:0.08, T:0.74
Consensus pattern (20 bp):
ATTTTTTTATATTTTTTCTG
Found at i:35585 original size:17 final size:19
Alignment explanation
Indices: 35560--35598 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35550 ATATCTGTAT
35560 TATTAATATTT-TGTTCTA
1 TATTAATATTTATGTTCTA
35578 TATT-ATATTTAATGTTCTA
1 TATTAATATTT-ATGTTCTA
35597 TA
1 TA
35599 AGTTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TATTAATATTTATGTTCTA
Found at i:36937 original size:12 final size:12
Alignment explanation
Indices: 36920--36951 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
36910 CTCATTCAGT
36920 TCGTACTCCCGC
1 TCGTACTCCCGC
36932 TCGTACTCCCGC
1 TCGTACTCCCGC
36944 TCGTACTC
1 TCGTACTC
36952 AGAGTACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.09, C:0.47, G:0.16, T:0.28
Consensus pattern (12 bp):
TCGTACTCCCGC
Found at i:40497 original size:19 final size:19
Alignment explanation
Indices: 40439--40499 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
40429 TCGGTTTTTG
* *
40439 ACCGGTTTGACCGGTCAAA
1 ACCGGGTTGACCGGTCAGA
* *
40458 ACCAGGTTGACCGGTCTGA
1 ACCGGGTTGACCGGTCAGA
*
40477 ACCGGGTTGACCGGTCCGA
1 ACCGGGTTGACCGGTCAGA
40496 ACCG
1 ACCG
40500 ACCTGACCCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.21, C:0.30, G:0.31, T:0.18
Consensus pattern (19 bp):
ACCGGGTTGACCGGTCAGA
Found at i:40506 original size:19 final size:19
Alignment explanation
Indices: 40465--40507 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
40455 AAAACCAGGT
* ***
40465 TGACCGGTCTGAACCGGGT
1 TGACCGGTCCGAACCGACC
40484 TGACCGGTCCGAACCGACC
1 TGACCGGTCCGAACCGACC
40503 TGACC
1 TGACC
40508 CGTTGACCGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.16
Consensus pattern (19 bp):
TGACCGGTCCGAACCGACC
Found at i:41450 original size:14 final size:14
Alignment explanation
Indices: 41427--41456 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
41417 AATTACTATC
*
41427 ATTGGGGGAATATT
1 ATTGGAGGAATATT
41441 ATTGGAGGAATATT
1 ATTGGAGGAATATT
41455 AT
1 AT
41457 CTGCAGGCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.37
Consensus pattern (14 bp):
ATTGGAGGAATATT
Found at i:49671 original size:30 final size:30
Alignment explanation
Indices: 49635--49693 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
49625 ACAAATGAGT
49635 TAATTTCAAATTTTTATAAATGAGACATTA
1 TAATTTCAAATTTTTATAAATGAGACATTA
*
49665 TAATTTCAAATTTTTATAAATGAGTCATT
1 TAATTTCAAATTTTTATAAATGAGACATT
49694 CAGTTAATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.46
Consensus pattern (30 bp):
TAATTTCAAATTTTTATAAATGAGACATTA
Found at i:50707 original size:14 final size:14
Alignment explanation
Indices: 50688--50715 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50678 CGAACGCTCA
50688 CCCCTAGACAAGAT
1 CCCCTAGACAAGAT
50702 CCCCTAGACAAGAT
1 CCCCTAGACAAGAT
50716 TGGTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (14 bp):
CCCCTAGACAAGAT
Done.