Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006039.1 Hibiscus syriacus cultivar Beakdansim tig00014261_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: 79532
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:1173 original size:13 final size:13
Alignment explanation
Indices: 1152--1181 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1142 GGTAGTTTAG
*
1152 GTTTGCTTTAAAT
1 GTTTACTTTAAAT
1165 GTTTACTTTAAAT
1 GTTTACTTTAAAT
1178 GTTT
1 GTTT
1182 GCTAATCTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.07, G:0.13, T:0.57
Consensus pattern (13 bp):
GTTTACTTTAAAT
Found at i:5106 original size:54 final size:54
Alignment explanation
Indices: 5045--5181 Score: 150
Period size: 54 Copynumber: 2.5 Consensus size: 54
5035 TACTATACGA
* *
5045 AAATTCATATACTTAGTATGAATTTCTTAGTTCGCACACATAGTACCCATACAG
1 AAATTCATAAACTTAGTATGAATTTCTTAGTTCACACACATAGTACCCATACAG
* * * * ***
5099 AAATTCATACACTTAGTATGAA-CTCTTTAGTTTACACCCATAGTGTTCATACAG
1 AAATTCATAAACTTAGTATGAATTTC-TTAGTTCACACACATAGTACCCATACAG
** *
5153 AAATTCATAAACAAATTATGAATTTCTTA
1 AAATTCATAAACTTAGTATGAATTTCTTA
5182 ACTTTTTGCA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
53 2 0.03
54 64 0.94
55 2 0.03
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.35
Consensus pattern (54 bp):
AAATTCATAAACTTAGTATGAATTTCTTAGTTCACACACATAGTACCCATACAG
Found at i:5215 original size:57 final size:57
Alignment explanation
Indices: 5146--5425 Score: 405
Period size: 57 Copynumber: 5.0 Consensus size: 57
5136 CCATAGTGTT
* *
5146 CATACAGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACATGAAATGCC
1 CATACTGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACGAAATGCC
*
5203 CATACTGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACGAAGTGCC
1 CATACTGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACGAAATGCC
*
5260 CATAC-GAAAATTCATAAACAAATTATGAATTTCTTAAC-TTTTGCACATGAAATGCC
1 CATACTG-AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACGAAATGCC
5316 C--A-T-AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACAC-AAAGTGGCC
1 CATACTGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACGAAA-T-GCC
* * * *
5370 C-TACGGAAATTCATAAACCAATTATGAATTTATTAACTTTTTGCACACGAAGTGCC
1 CATACTGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACGAAATGCC
5426 TGTACCCCAA
Statistics
Matches: 204, Mismatches: 10, Indels: 19
0.88 0.04 0.08
Matches are distributed among these distances:
52 34 0.17
53 10 0.05
54 5 0.02
55 1 0.00
56 21 0.10
57 131 0.64
58 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.33
Consensus pattern (57 bp):
CATACTGAAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACACGAAATGCC
Found at i:5358 original size:109 final size:113
Alignment explanation
Indices: 5153--5425 Score: 439
Period size: 109 Copynumber: 2.4 Consensus size: 113
5143 GTTCATACAG
5153 AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACATGAAATGCCCATACTGAAATTCAT
1 AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACATGAAATGCCCA-ACTGAAATTCAT
*
5218 AAACAAATTATGAATTTCTTAACTTTTTGCACACGAAGT-GCCCATACGA
65 AAACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGGCCC-TACGA
5267 AAATTCATAAACAAATTATGAATTTCTTAAC-TTTTGCACATGAAATGCCC-A-T-AAATTCATA
1 AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACATGAAATGCCCAACTGAAATTCATA
*
5328 AACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGGCCCTACGG
66 AACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGGCCCTACGA
* * * *
5376 AAATTCATAAACCAATTATGAATTTATTAACTTTTTGCACACGAAGTGCC
1 AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACATGAAATGCC
5426 TGTACCCCAA
Statistics
Matches: 151, Mismatches: 6, Indels: 8
0.92 0.04 0.05
Matches are distributed among these distances:
109 79 0.52
110 21 0.14
111 1 0.01
113 19 0.13
114 31 0.21
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (113 bp):
AAATTCATAAACAAATTATGAATTTCTTAACTTTTTGCACATGAAATGCCCAACTGAAATTCATA
AACAAATTATGAATTTCTTAACTTTTTGCACACAAAGTGGCCCTACGA
Found at i:7753 original size:20 final size:20
Alignment explanation
Indices: 7716--7758 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
7706 TATATTGGGC
* *
7716 TATTTTCTATTGTTTATGGT
1 TATTTTCTATGGTATATGGT
*
7736 TATTTTCTATGGTATATGTT
1 TATTTTCTATGGTATATGGT
7756 TAT
1 TAT
7759 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.14, T:0.63
Consensus pattern (20 bp):
TATTTTCTATGGTATATGGT
Found at i:19625 original size:218 final size:216
Alignment explanation
Indices: 19146--19802 Score: 644
Period size: 218 Copynumber: 3.0 Consensus size: 216
19136 AATTCTGAAA
* ** ** * * * * *
19146 CCCTG-AATAAGAAGAGAGCAGACTTATTTTTTGAATATTTTTCAAGTCCTACACTCCCTGAAAG
1 CCCTGAAAAAAGAA-AGAGCAGACCCATTTTTCAAAAATTGTTCGAGTCCTATACTCCCTAAAAG
* * * * * *
19210 AAAAGGGAGC-GAACCCATTT-TCTGAATATTTTTCAAGTCCTATACTCCCT-GAA-AAAAGAGG
65 AAGAGGGAGCAG-ACACATTTGTC-GAAGATTGTTCGAGTCCTATACTCCTTGGAAGAAAA-A-G
* * *
19271 GAGCACACCCATTTTCTGAAGATT-TTTCAAGTCCTATACTCCCTGAAAAAAGAGGGAGCAACAC
126 GAGCAGA-CCATTTTCTAAAGATTGTTT---GTCCTATACTCCCTGAAAGAAGAGGGAGCAACAC
* **
19335 ATTTTCTGAAGATTGTTTGAGTCCTATACT
187 ATTTTCTAAAGATTGTTCAAGTCCTATACT
* * * * *
19365 CCCTGAAAAAAGAAGGAGCAGACCCATTTTTCGAAGATTGTTCGAGTCTTATACTCCCTAAAATA
1 CCCTGAAAAAAGAAAGAGCAGACCCATTTTTCAAAAATTGTTCGAGTCCTATACTCCCTAAAAGA
* * * *
19430 AGAGGGAGCGGTCACGTTTGTCGAAGATTGTTCGAGTCATATACTCCTTGGAAGAAAAAGGAGCA
66 AGAGGGAGCAGACACATTTGTCGAAGATTGTTCGAGTCCTATACTCCTTGGAAGAAAAAGGAGCA
* *
19495 GATCCATTTTCTAAAGATTGTTTGTCCTTTACTCCCTGAAAGAAGAGGGAGCAGACACGTTTATC
131 GA-CCATTTTCTAAAGATTGTTTGTCCTATACTCCCTGAAAGAAGAGGGAGCA-ACACATTT-TC
*
19560 -AAAGATTGTTCAAGTCCTATGCT
193 TAAAGATTGTTCAAGTCCTATACT
* * * *
19583 CCTTGGAAGAAGAAAGAGCAGACCCGTTTTTCAAAAATTGTTCGAGTCCTATACTCCCTAAAAGA
1 CCCTGAAAAAAGAAAGAGCAGACCCATTTTTCAAAAATTGTTCGAGTCCTATACTCCCTAAAAGA
* * * * *
19648 AGAGGGAGCAGACACATTTTTCGAAGATTGTTCGAGTCCTATATTTCTTGAAAGAAGAAGGAGCA
66 AGAGGGAGCAGACACATTTGTCGAAGATTGTTCGAGTCCTATACTCCTTGGAAGAAAAAGGAGCA
* ** * * ** *
19713 GACTCGTTTTCTAAAGATTGTCCGAGTCCTATACTCCTTGAAAGAAGAAGGAGTGGACCCATTTT
131 GAC-CATTTTCTAAAGATTGT--TTGTCCTATACTCCCTGAAAGAAGAGGGAG-CAACACATTTT
* *
19778 CTAAAGATTGTTCGAGTCATATACT
192 CTAAAGATTGTTCAAGTCCTATACT
19803 ACTTGAAGGA
Statistics
Matches: 363, Mismatches: 62, Indels: 25
0.81 0.14 0.06
Matches are distributed among these distances:
217 29 0.08
218 156 0.43
219 106 0.29
220 68 0.19
221 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (216 bp):
CCCTGAAAAAAGAAAGAGCAGACCCATTTTTCAAAAATTGTTCGAGTCCTATACTCCCTAAAAGA
AGAGGGAGCAGACACATTTGTCGAAGATTGTTCGAGTCCTATACTCCTTGGAAGAAAAAGGAGCA
GACCATTTTCTAAAGATTGTTTGTCCTATACTCCCTGAAAGAAGAGGGAGCAACACATTTTCTAA
AGATTGTTCAAGTCCTATACT
Found at i:19809 original size:55 final size:55
Alignment explanation
Indices: 19146--19802 Score: 589
Period size: 55 Copynumber: 12.0 Consensus size: 55
19136 AATTCTGAAA
* ** * * * * *
19146 CCCTG-AATAAGAAGAGAGCAGACTTATTTTTTGAATATTTTTCAAGTCCTACACT
1 CCCTGAAAGAAGAAG-GAGCAGACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
* * *
19201 CCCTGAAAGAA-AAGGGAGC-GAACCCATTTTCTGAATATTTTTCAAGTCCTATACT
1 CCCTGAAAGAAGAA-GGAGCAG-ACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
* * * * *
19256 CCCTGAAAAAAGAGGGAGCACACCCATTTTCTGAAGATTTTTCAAGTCCTATACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
* * * *
19311 CCCTGAAAAAAGAGGGAGCA-ACACATTTTCTGAAGATTGTTTGAGTCCTATACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
* *
19365 CCCTGAAAAAAGAAGGAGCAGACCCATTTT-TCGAAGATTGTTCGAGTCTTATACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCT-GAAGATTGTTCGAGTCCTATACT
* * * * * * * *
19420 CCCTAAAATAAGAGGGAGCGGTCACGTTTGTC-GAAGATTGTTCGAGTCATATACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTT-TCTGAAGATTGTTCGAGTCCTATACT
* * * * * * *
19475 CCTTGGAAGAAAAAGGAGCAGATCCATTTTCTAAAGATTGTT--TGTCCTTTACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
* * * * * *
19528 CCCTGAAAGAAGAGGGAGCAGACACGTTTATC-AAAGATTGTTCAAGTCCTATGCT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTT-TCTGAAGATTGTTCGAGTCCTATACT
* * * * * *
19583 CCTTGGAAGAAGAAAGAGCAGACCCGTTTT-TCAAAAATTGTTCGAGTCCTATACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCT-GAAGATTGTTCGAGTCCTATACT
* * * *
19638 CCCTAAAAGAAGAGGGAGCAGACACATTTT-TCGAAGATTGTTCGAGTCCTATATT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCT-GAAGATTGTTCGAGTCCTATACT
* * * * * *
19693 TCTTGAAAGAAGAAGGAGCAGACTCGTTTTCTAAAGATTGTCCGAGTCCTATACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
* ** * *
19748 CCTTGAAAGAAGAAGGAGTGGACCCATTTTCTAAAGATTGTTCGAGTCATATACT
1 CCCTGAAAGAAGAAGGAGCAGACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
19803 ACTTGAAGGA
Statistics
Matches: 502, Mismatches: 84, Indels: 32
0.81 0.14 0.05
Matches are distributed among these distances:
53 40 0.08
54 56 0.11
55 398 0.79
56 8 0.02
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (55 bp):
CCCTGAAAGAAGAAGGAGCAGACCCATTTTCTGAAGATTGTTCGAGTCCTATACT
Found at i:21655 original size:5 final size:5
Alignment explanation
Indices: 21645--21669 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
21635 ATTGAATATG
21645 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
21670 ATCCTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:25769 original size:30 final size:29
Alignment explanation
Indices: 25669--25765 Score: 92
Period size: 30 Copynumber: 3.4 Consensus size: 29
25659 TTATTAAAAC
* * *
25669 AAAGGACTAAATAGCAAAAACAACAATTT
1 AAAGGACTAAATAGCACAAACAAAAACTT
* *
25698 ACATGACTAAAATA--ACAAA-AAAAACTT
1 AAAGGACT-AAATAGCACAAACAAAAACTT
*
25725 AAGGGACGTAAATAGCACAAACAAAAACTT
1 AAAGGAC-TAAATAGCACAAACAAAAACTT
*
25755 AAAGTACTAAA
1 AAAGGACTAAA
25766 ATAGAAAAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
27 15 0.28
28 5 0.09
29 15 0.28
30 18 0.34
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.16
Consensus pattern (29 bp):
AAAGGACTAAATAGCACAAACAAAAACTT
Found at i:25777 original size:30 final size:30
Alignment explanation
Indices: 25669--25777 Score: 75
Period size: 30 Copynumber: 3.8 Consensus size: 30
25659 TTATTAAAAC
* * *
25669 AAAGGAC-TAAATAGCAAAAACAACAATTT
1 AAAGGACGTAAATAGAAAAAACAAAAACTT
* * * *
25698 ACATGAC-TAAA-ATAACAAA-AAAAACTT
1 AAAGGACGTAAATAGAAAAAACAAAAACTT
* * *
25725 AAGGGACGTAAATAGCACAAACAAAAACTT
1 AAAGGACGTAAATAGAAAAAACAAAAACTT
*
25755 AAAGTAC-TAAAATAGAAAAAACA
1 AAAGGACGT-AAATAGAAAAAACA
25778 TAACTTTAAA
Statistics
Matches: 60, Mismatches: 16, Indels: 7
0.72 0.19 0.08
Matches are distributed among these distances:
27 10 0.17
28 9 0.15
29 16 0.27
30 25 0.42
ACGTcount: A:0.61, C:0.14, G:0.10, T:0.16
Consensus pattern (30 bp):
AAAGGACGTAAATAGAAAAAACAAAAACTT
Found at i:27193 original size:15 final size:14
Alignment explanation
Indices: 27171--27212 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
27161 ATGTAATATG
27171 TAAATTAATAATAA
1 TAAATTAATAATAA
27185 TAAACTTAATAATAAA
1 TAAA-TTAATAAT-AA
*
27201 TATATT-ATAATA
1 TAAATTAATAATA
27213 GTATTTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.36
15 10 0.40
16 5 0.20
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTAATAATAA
Found at i:27622 original size:133 final size:130
Alignment explanation
Indices: 27410--27670 Score: 334
Period size: 133 Copynumber: 2.0 Consensus size: 130
27400 ATCATCTAAA
** *
27410 GGTGACACGACTCCTACGTGATGAGGAGGTTTGGTCGGTGGATGACACGACTCGTATGTGATGAA
1 GGTGACACGACTCCTACGTGATGAGGAGGACTGGTCGGTGGATGACACGACTCGTAGGTGATGAA
*
27475 GAGTTCTAGACATCTTTAGGAAGGTGATAACACGGTTCCTATGTGATGAGGACGACTGGTTATCT
66 GAGTGCTAGACATCTTTAGG-A--TGATAACACGGTTCCTATGTGATGAGGACGACTGGTTATCT
27540 AGG
128 AGG
* *
27543 GGTGACACGGCTCCTACGTGATGAGGAGGACTGGTCGAG-GGATGACAC-AGTTCGTAGGTGAT-
1 GGTGACACGACTCCTACGTGATGAGGAGGACTGGTCG-GTGGATGACACGA-CTCGTAGGTGATG
* **
27605 AAG-GATGGCATA-CCATCTTTAGGATGATAACACGGTTCCTATGTGATGAGGACGGTTGGTTAT
64 AAGAG-T-GC-TAGACATCTTTAGGATGATAACACGGTTCCTATGTGATGAGGACGACTGGTTAT
27668 CTA
126 CTA
27671 TGTGTGATAA
Statistics
Matches: 114, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
130 40 0.35
131 1 0.01
132 6 0.05
133 64 0.56
134 3 0.03
ACGTcount: A:0.25, C:0.16, G:0.33, T:0.26
Consensus pattern (130 bp):
GGTGACACGACTCCTACGTGATGAGGAGGACTGGTCGGTGGATGACACGACTCGTAGGTGATGAA
GAGTGCTAGACATCTTTAGGATGATAACACGGTTCCTATGTGATGAGGACGACTGGTTATCTAGG
Found at i:27682 original size:46 final size:46
Alignment explanation
Indices: 27629--27723 Score: 145
Period size: 46 Copynumber: 2.1 Consensus size: 46
27619 ATCTTTAGGA
* * * * *
27629 TGATAACACGGTTCCTATGTGATGAGGACGGTTGGTTATCTATGTG
1 TGATAACACGGTTCCCACGTGATGAGAACGGCTGGTTATCTAGGTG
27675 TGATAACACGGTTCCCACGTGATGAGAACGGCTGGTTATCTAGGTG
1 TGATAACACGGTTCCCACGTGATGAGAACGGCTGGTTATCTAGGTG
27721 TGA
1 TGA
27724 CGCAGCTCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.23, C:0.16, G:0.31, T:0.31
Consensus pattern (46 bp):
TGATAACACGGTTCCCACGTGATGAGAACGGCTGGTTATCTAGGTG
Found at i:27712 original size:176 final size:178
Alignment explanation
Indices: 27498--27850 Score: 462
Period size: 176 Copynumber: 2.0 Consensus size: 178
27488 CTTTAGGAAG
* * * *
27498 GTGATAACACGGTTCCTATGTGATGAGGACGACTGGTTATCTAGGGGTGACACGGCTCCTACGTG
1 GTGATAACACGGTTCCCACGTGATGAGAACGACTGGTTATCTAGGGGTGACACAGCTCCTACGTG
* * * *
27563 ATGA-GGAGGAC-TGGTCGAGGGATGACACAGTTCGTAGGTGATAAGGATGGCATACCATCTTTA
66 AT-ATGGAGG-CTTGGTCGAGGGATGACACAGTTCCTAGGTGATAAGGACGGCAGACAATCTTTA
* **
27626 GG-AT-GATAACACGGTTCCTATGTGATGAGGACGGTTGGTTATCTATGT
129 GGAATCGATAACACGGTTCCTACGTGATGAGGACGGCCGGTTATCTATGT
* * *
27674 GTGATAACACGGTTCCCACGTGATGAGAACGGCTGGTTATCTAGGTGTGACGCAGCTCCTACGTG
1 GTGATAACACGGTTCCCACGTGATGAGAACGACTGGTTATCTAGGGGTGACACAGCTCCTACGTG
* * * *
27739 ATATGGAGGCTTGGTCGGGGGATGACACAGTTCCTATGTGATGAGGACGGTAGACAATCTTTAGG
66 ATATGGAGGCTTGGTCGAGGGATGACACAGTTCCTAGGTGATAAGGACGGCAGACAATCTTTAGG
* *
27804 AAATGCGATAACACGGTTCTTACGTGATGAGGATGGCCGGTTATCTA
131 -AAT-CGATAACACGGTTCCTACGTGATGAGGACGGCCGGTTATCTA
27851 GGGGTGACAT
Statistics
Matches: 151, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
175 2 0.01
176 111 0.74
178 2 0.01
180 36 0.24
ACGTcount: A:0.24, C:0.17, G:0.32, T:0.27
Consensus pattern (178 bp):
GTGATAACACGGTTCCCACGTGATGAGAACGACTGGTTATCTAGGGGTGACACAGCTCCTACGTG
ATATGGAGGCTTGGTCGAGGGATGACACAGTTCCTAGGTGATAAGGACGGCAGACAATCTTTAGG
AATCGATAACACGGTTCCTACGTGATGAGGACGGCCGGTTATCTATGT
Found at i:27874 original size:134 final size:134
Alignment explanation
Indices: 27676--27937 Score: 314
Period size: 134 Copynumber: 2.0 Consensus size: 134
27666 ATCTATGTGT
* * * *
27676 GATAACACGGTTCCCACGTGATGAGAACGGCTGGTTATCTAGGTGTGACGCAGCTCCTACGTGAT
1 GATAACACGGTTCCCACGTGATGAGAACGGCCGGTTATCTAGGGGTGACACAGATCCTACGTGAT
* * *
27741 -ATGGAGG-CTTGGTCGGGGGATGACAC-AGTTCCTATGTGATGAGGACGGTAGACAATCTTTAG
66 GA-GGAGGTC-TAGTCGGGGGATGACACGA-TTCCTATGCGATGAGGACGATAGACAATCTTTAG
27803 GAAATGC
128 GAAATGC
** * * **
27810 GATAACACGGTTCTTACGTGATGAGGATGGCCGGTTATCTAGGGGTGACATGGATCCTACGTGAT
1 GATAACACGGTTCCCACGTGATGAGAACGGCCGGTTATCTAGGGGTGACACAGATCCTACGTGAT
* * * * *
27875 GAGGAGGTCTAGTCGGTGGATGACACGATTTCTATGCGATGAGGATGATAGGCCATCTTTAGG
66 GAGGAGGTCTAGTCGGGGGATGACACGATTCCTATGCGATGAGGACGATAGACAATCTTTAGG
27938 GATAATGGTT
Statistics
Matches: 107, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
134 104 0.97
135 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.33, T:0.26
Consensus pattern (134 bp):
GATAACACGGTTCCCACGTGATGAGAACGGCCGGTTATCTAGGGGTGACACAGATCCTACGTGAT
GAGGAGGTCTAGTCGGGGGATGACACGATTCCTATGCGATGAGGACGATAGACAATCTTTAGGAA
ATGC
Found at i:28095 original size:66 final size:64
Alignment explanation
Indices: 27981--28229 Score: 240
Period size: 66 Copynumber: 3.8 Consensus size: 64
27971 GATGCTTAAT
* * ** * * *
27981 GAGAAACTGTCTC-AAGAGATATAAAATTTGTTTCAAGGGAGATGATCTCAAAGATTGGTGTTTC
1 GAGAAACTGTCTCAAAG-GAGACAAAATTCATTTCAAGGGAAACGA-CTCAAAGATTGATGTTTC
28045 A
64 A
* *
28046 CGAGAAACTGTCTCAAAGGAGACAAAATTCATTTCAAGGGAAACAATCTCAAATATAT-ATGTTT
1 -GAGAAACTGTCTCAAAGGAGACAAAATTCATTTCAAGGGAAACGA-CTCAAAGAT-TGATGTTT
*
28110 GTA
63 -CA
* * * *
28113 GAGAAATTGTCTCAATGGAGACAAAATTCGTTTTAAGGGAAACGACTCAAAGA-TGATTGTTTCA
1 GAGAAACTGTCTCAAAGGAGACAAAATTCATTTCAAGGGAAACGACTCAAAGATTGA-TGTTTC-
28177 A
64 A
*
28178 TAGAATA-TGTCTCAAA--AGACAAAATTCATTTCAAGGGAAACGACTCAAAGAT
1 GAGAA-ACTGTCTCAAAGGAGACAAAATTCATTTCAAGGGAAACGACTCAAAGAT
28230 AATTATTATT
Statistics
Matches: 154, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
63 34 0.22
64 1 0.01
65 25 0.16
66 89 0.58
67 5 0.03
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (64 bp):
GAGAAACTGTCTCAAAGGAGACAAAATTCATTTCAAGGGAAACGACTCAAAGATTGATGTTTCA
Found at i:28249 original size:131 final size:132
Alignment explanation
Indices: 27979--28230 Score: 311
Period size: 132 Copynumber: 1.9 Consensus size: 132
27969 ATGATGCTTA
* * * * *
27979 ATGAGAAACTGTCTCAAGAGATATAAAATTTGTTTCAAGGGAGATGATCTCAAAGATTGGTGTTT
1 ATGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATTGGTGTTT
* *
28044 CACGAGAAACTGTCTCAAAGGAGACAAAATTCATTTCAAGGGAAACAATCTCAAATATATATGTT
66 CAAGAGAAACTGTCTCAAA-GAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATATATGTT
28109 TGT
130 TGT
* * *
28112 A-GAGAAATTGTCTCAATG-GAGACAAAATTCGTTTTAAGGGAAACGA-CTCAAAGA-TGATTGT
1 ATGAGAAACTGTCTCAA-GAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATTG-GTGT
* *
28173 TTCAATAGAATA-TGTCTCAAA-AGACAAAATTCATTTCAAGGGAAACGA-CTCAAAGATA
64 TTCAAGAGAA-ACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATA
28231 ATTATTATTT
Statistics
Matches: 104, Mismatches: 12, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
128 9 0.09
129 26 0.25
130 2 0.02
131 28 0.27
132 37 0.36
133 2 0.02
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.27
Consensus pattern (132 bp):
ATGAGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAACGATCTCAAAGATTGGTGTTT
CAAGAGAAACTGTCTCAAAGAGACAAAATTCATTTCAAGGGAAACAATCTCAAAGATATATGTTT
GT
Found at i:29024 original size:29 final size:29
Alignment explanation
Indices: 28829--29022 Score: 142
Period size: 30 Copynumber: 6.5 Consensus size: 29
28819 TTAGTAAAAC
* *
28829 AAAGGACTAAATAGAAAAAATAGCAATTT
1 AAAGGACTAAATAGAAAAAATAGAAACTT
* *
28858 ACAA-GACTAAAGTAGAAAAAACAAAAACTT
1 A-AAGGACTAAA-TAGAAAAAATAGAAACTT
** * * * * *
28888 ATGGGATGTAAATAGCACAAACAAAAACTT
1 AAAGGA-CTAAATAGAAAAAATAGAAACTT
28918 AAAGGACTAAAATAG-AAAAATA-AAACTTT
1 AAAGGACT-AAATAGAAAAAATAGAAAC-TT
* * *
28947 AAACGACTGGAATAGCAAACAAATCGAAACTT
1 AAAGGACT-AAATAG-AAA-AAATAGAAACTT
* *
28979 AAAGGATTAAAATAGTAAAAATAGAAACTT
1 AAAGGACT-AAATAGAAAAAATAGAAACTT
29009 AAAGGACTAAATAG
1 AAAGGACTAAATAG
29023 TAATTACAAA
Statistics
Matches: 130, Mismatches: 25, Indels: 20
0.74 0.14 0.11
Matches are distributed among these distances:
28 4 0.03
29 34 0.26
30 63 0.48
31 8 0.06
32 17 0.13
33 4 0.03
ACGTcount: A:0.57, C:0.10, G:0.14, T:0.19
Consensus pattern (29 bp):
AAAGGACTAAATAGAAAAAATAGAAACTT
Found at i:30351 original size:12 final size:12
Alignment explanation
Indices: 30333--30380 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
30323 CATGTAAATT
30333 AATAATAATAAA
1 AATAATAATAAA
*
30345 CATAATAATAAA
1 AATAATAATAAA
*
30357 AATAAAAAATATAA
1 AAT-AATAATA-AA
*
30371 TATAATAATA
1 AATAATAATA
30381 TTTTTAGTAC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 13 0.45
13 12 0.41
14 4 0.14
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:31382 original size:21 final size:19
Alignment explanation
Indices: 31358--31396 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
31348 AAAACAAGGT
31358 TAAGACAATAGAAAGAAAGAA
1 TAAGACAA-AGAAA-AAAGAA
31379 TAAGACAAAGAAAAAAGA
1 TAAGACAAAGAAAAAAGA
31397 TAATGAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.69, C:0.05, G:0.18, T:0.08
Consensus pattern (19 bp):
TAAGACAAAGAAAAAAGAA
Found at i:43624 original size:60 final size:59
Alignment explanation
Indices: 43535--43648 Score: 156
Period size: 60 Copynumber: 1.9 Consensus size: 59
43525 GAATACACTA
** * * *
43535 AAGGATACCTAGTGTATATGGTGGGCACGACCTTATGTGTCATATTCAGGAATTGTACTT
1 AAGGATACCTAGTACAGATGGAGGACACGACCTTATGTGTCATA-TCAGGAATTGTACTT
* *
43595 AAGGATACCTAGTACAGATGGAGGACACGACCTTTTGTGTTATATCAGGAATTG
1 AAGGATACCTAGTACAGATGGAGGACACGACCTTATGTGTCATATCAGGAATTG
43649 CACTACGGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 10 0.21
60 37 0.79
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (59 bp):
AAGGATACCTAGTACAGATGGAGGACACGACCTTATGTGTCATATCAGGAATTGTACTT
Found at i:43729 original size:20 final size:20
Alignment explanation
Indices: 43694--43749 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
43684 GTCCTCAGGG
*
43694 TTGTTTATTGGGTTATTTTCTA
1 TTGTTTA-T-GGTTATTGTCTA
43716 TTGTTTATGGTTATTGTCTA
1 TTGTTTATGGTTATTGTCTA
* *
43736 TGGTATATGGTTAT
1 TTGTTTATGGTTAT
43750 GGAATAATGG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 23 0.74
21 1 0.03
22 7 0.23
ACGTcount: A:0.16, C:0.04, G:0.21, T:0.59
Consensus pattern (20 bp):
TTGTTTATGGTTATTGTCTA
Found at i:43816 original size:46 final size:45
Alignment explanation
Indices: 43746--43853 Score: 155
Period size: 46 Copynumber: 2.4 Consensus size: 45
43736 TGGTATATGG
* * *
43746 TTATGGAAT-AATGGCAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
43790 TTATGGTGTTAAATGGTAAGTATATTGGTAAAATAAGCTTACTAGC
1 TTATGG-GATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
43836 TTATGGGATAAATGGTAA
1 TTATGGGATAAATGGTAA
43854 AAGATTTTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
44 6 0.11
45 12 0.21
46 38 0.68
ACGTcount: A:0.36, C:0.06, G:0.24, T:0.33
Consensus pattern (45 bp):
TTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:50520 original size:20 final size:20
Alignment explanation
Indices: 50495--50537 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
50485 TATATTGGGG
* *
50495 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
50515 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
50535 TAT
1 TAT
50538 GGAATAATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:55882 original size:2 final size:2
Alignment explanation
Indices: 55875--55900 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55865 CATCAAAAAC
55875 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
55901 GATTCTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:64510 original size:12 final size:12
Alignment explanation
Indices: 64493--64519 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
64483 CTACATCGGG
64493 TATTACTATCAT
1 TATTACTATCAT
64505 TATTACTATCAT
1 TATTACTATCAT
64517 TAT
1 TAT
64520 GTTATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.15, G:0.00, T:0.52
Consensus pattern (12 bp):
TATTACTATCAT
Found at i:65961 original size:17 final size:17
Alignment explanation
Indices: 65940--65983 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
65930 AGAGTTATAT
65940 TAATGAACTAG-TTAAA
1 TAATGAACTAGTTTAAA
*
65956 TGAATGAACTAGTTTAAC
1 T-AATGAACTAGTTTAAA
65974 TAATGAACTA
1 TAATGAACTA
65984 ACTTTATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 19 0.76
18 5 0.20
ACGTcount: A:0.45, C:0.09, G:0.14, T:0.32
Consensus pattern (17 bp):
TAATGAACTAGTTTAAA
Found at i:65989 original size:18 final size:18
Alignment explanation
Indices: 65958--66002 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
65948 TAGTTAAATG
*
65958 AATGAACT-AGTTTAACT
1 AATGAACTAACTTTAACT
**
65975 AATGAACTAACTTTATTT
1 AATGAACTAACTTTAACT
65993 AATGAACTAA
1 AATGAACTAA
66003 GGTGCATGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAACT
Found at i:74463 original size:60 final size:60
Alignment explanation
Indices: 74384--74546 Score: 197
Period size: 59 Copynumber: 2.7 Consensus size: 60
74374 AGAAACTTGG
* * * *
74384 GGACTAAAATAGCAAAAAATTGAAACTTAAGGAACTAAAATAGCGAATTTATACATTTAAA
1 GGACTAAAATAG-AAAAAATAGAAACTTAAGGAACTAAAATAGAGAATATAGACATTTAAA
* * * *
74445 GGATTAAAATAGATAAAATAGAAACTTAAGGGACTAAAATA-ATAATATAGACATTTAAA
1 GGACTAAAATAGAAAAAATAGAAACTTAAGGAACTAAAATAGAGAATATAGACATTTAAA
*
74504 GGACTAAAATA-ACAAAAATAGAAAGTTAAAGGAA-TAAAATAGA
1 GGACTAAAATAGA-AAAAATAGAAACTT-AAGGAACTAAAATAGA
74547 AAAAATATAA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
58 1 0.01
59 43 0.49
60 32 0.37
61 11 0.13
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (60 bp):
GGACTAAAATAGAAAAAATAGAAACTTAAGGAACTAAAATAGAGAATATAGACATTTAAA
Found at i:74483 original size:30 final size:30
Alignment explanation
Indices: 74351--74572 Score: 155
Period size: 30 Copynumber: 7.4 Consensus size: 30
74341 AATACAAAAA
* * **
74351 TAAAGGACCAAAATAGCATTAATAGAAACT
1 TAAAGGACTAAAATAGAAAAAATAGAAACT
** *
74381 T-GGGGACTAAAATAGCAAAAAATTGAAACT
1 TAAAGGACTAAAATAG-AAAAAATAGAAACT
** ** * * *
74411 T-AAGGAACTAAAATAGCGAATTTATACATT
1 TAAAGG-ACTAAAATAGAAAAAATAGAAACT
* *
74441 TAAAGGATTAAAATAGATAAAATAGAAACT
1 TAAAGGACTAAAATAGAAAAAATAGAAACT
* * * * *
74471 TAAGGGACTAAAATA-ATAATATAGACATT
1 TAAAGGACTAAAATAGAAAAAATAGAAACT
*
74500 TAAAGGACTAAAATA-ACAAAAATAGAAAGT
1 TAAAGGACTAAAATAGA-AAAAATAGAAACT
* * *
74530 TAAAGGAATAAAATAGAAAAAATATAAACC
1 TAAAGGACTAAAATAGAAAAAATAGAAACT
*
74560 TAAAGTACTAAAA
1 TAAAGGACTAAAA
74573 CAGTGTTAAC
Statistics
Matches: 146, Mismatches: 41, Indels: 10
0.74 0.21 0.05
Matches are distributed among these distances:
29 37 0.25
30 94 0.64
31 15 0.10
ACGTcount: A:0.56, C:0.08, G:0.14, T:0.22
Consensus pattern (30 bp):
TAAAGGACTAAAATAGAAAAAATAGAAACT
Found at i:76181 original size:19 final size:19
Alignment explanation
Indices: 76157--76195 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
76147 AAATTAATTA
*
76157 ATAATAGTAATAATAAAAT
1 ATAATAATAATAATAAAAT
*
76176 ATAATAATAATGATAAAAT
1 ATAATAATAATAATAAAAT
76195 A
1 A
76196 ATATTTTGTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
ATAATAATAATAATAAAAT
Found at i:76191 original size:22 final size:22
Alignment explanation
Indices: 76146--76199 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
76136 ATAAAAATTG
* *
76146 TAAATTAAT-TAATAATAGTAA
1 TAAAATAATATAATAATAATAA
*
76167 TAATAA-AATATAATAATAATGA
1 TAA-AATAATATAATAATAATAA
76189 TAAAATAATAT
1 TAAAATAATAT
76200 TTTGTGACAC
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (22 bp):
TAAAATAATATAATAATAATAA
Done.