Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007473.1 Hibiscus syriacus cultivar Beakdansim tig00020538_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: 67399
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2016 original size:17 final size:18
Alignment explanation
Indices: 1990--2037 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 18
1980 ATTAGGTTAC
*
1990 AGTAAGAAT-AATATTGT
1 AGTAACAATAAATATTGT
2007 AGTAACAATAAAATATTGT
1 AGTAACAAT-AAATATTGT
* *
2026 AGCAATAATAAA
1 AGTAACAATAAA
2038 CAATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 8 0.31
18 3 0.12
19 15 0.58
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (18 bp):
AGTAACAATAAATATTGT
Found at i:2023 original size:19 final size:19
Alignment explanation
Indices: 1999--2037 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1989 CAGTAAGAAT
*
1999 AATATTGTAGTAACAATAA
1 AATATTGTAGCAACAATAA
*
2018 AATATTGTAGCAATAATAA
1 AATATTGTAGCAACAATAA
2037 A
1 A
2038 CAATATAATT
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:0.54, C:0.05, G:0.10, T:0.31
Consensus pattern (19 bp):
AATATTGTAGCAACAATAA
Found at i:2085 original size:27 final size:26
Alignment explanation
Indices: 2010--2078 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
2000 ATATTGTAGT
**
2010 AACAATAAAATATTGT-AGCAATAATA
1 AACAATAAAATATCATCA-CAATAATA
* * *
2036 AACAATATAATTTCATCAAAATAATA
1 AACAATAAAATATCATCACAATAATA
2062 ATACAATAAAATATCAT
1 A-ACAATAAAATATCAT
2079 TCCAATATCT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (26 bp):
AACAATAAAATATCATCACAATAATA
Found at i:2531 original size:213 final size:209
Alignment explanation
Indices: 2126--2531 Score: 557
Period size: 213 Copynumber: 1.9 Consensus size: 209
2116 AACATAACAG
** *
2126 AAACACATCAAAATAAAATTAGATAAAATTTGTAATCAACTGAGTTAAATAAACAAAATAATTTT
1 AAACACATCAAAATAAAATTAGATAAAATTTGTAATCAACAAAGTTAAATAAACAAAAGAATTTT
* *
2191 TTGTTGAGACTTAAATGACAGTTTCCTTAAGACATATTCATCATCTCATCGATATTTGAGTAGCG
66 TTGTTGAGACTTAAATGACAGTTTCCTTAAGACATATTCATCATCTCATCGATATTTGAGTAACA
* * **
2256 TTGGACGCTCGTCTCCCATGATACAACAAAAAACAATCACAATAGTAAGTACAACAACAATGACT
131 TTGGACGCTAGTCTCCCATGATACAACAAAAAACAATCACAACAGTAAACACAACAACAATGACT
2321 AGTAACATAATAAA
196 AGTAACATAATAAA
2335 AAACACATC-AAA-AAAATTAGAATAAAATTTGTAATCAGACAAAGTTAAATAAACAAAAGAATA
1 AAACACATCAAAATAAAATTAG-ATAAAATTTGTAATCA-ACAAAGTTAAATAAACAAAAGAAT-
* * * * *
2398 ATTTTTGTTGAGACTTATATGAACAGTTTTCTTAAGACATATTCATCATCTC-CCTGGTGCTTTG
63 -TTTTTGTTGAGACTTAAATG-ACAGTTTCCTTAAGACATATTCATCATCTCATC-GAT-ATTTG
* * * * *
2462 ATTAACATTGGACGTTAGTCTCCCATGATACAACAACAAACGATCACAGCAGTAAACACAACAAC
124 AGTAACATTGGACGCTAGTCTCCCATGATACAACAAAAAACAATCACAACAGTAAACACAACAAC
2527 AATGA
189 AATGA
2532 ACAATTGAAT
Statistics
Matches: 171, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
207 8 0.05
208 19 0.11
209 30 0.18
211 20 0.12
212 31 0.18
213 63 0.37
ACGTcount: A:0.44, C:0.17, G:0.12, T:0.28
Consensus pattern (209 bp):
AAACACATCAAAATAAAATTAGATAAAATTTGTAATCAACAAAGTTAAATAAACAAAAGAATTTT
TTGTTGAGACTTAAATGACAGTTTCCTTAAGACATATTCATCATCTCATCGATATTTGAGTAACA
TTGGACGCTAGTCTCCCATGATACAACAAAAAACAATCACAACAGTAAACACAACAACAATGACT
AGTAACATAATAAA
Found at i:2817 original size:35 final size:36
Alignment explanation
Indices: 2766--2833 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
2756 TAAATAAATA
*
2766 TATTTATCAAGTGGCA-TAACTATTATTAACATATC
1 TATTCATCAAGTGGCATTAACTATTATTAACATATC
* *
2801 TATTCATCAAGTGGCATTGATTATTATTAACAT
1 TATTCATCAAGTGGCATTAACTATTATTAACAT
2834 CTATCACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 15 0.52
36 14 0.48
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.41
Consensus pattern (36 bp):
TATTCATCAAGTGGCATTAACTATTATTAACATATC
Found at i:3056 original size:20 final size:21
Alignment explanation
Indices: 3026--3074 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3016 GACTATTAAC
* *
3026 AAAGAATGTTA-TAAAAGTAG
1 AAAGAAGGTTATTAAAAATAG
*
3046 GAAGAAGGTTATTAAAAATAG
1 AAAGAAGGTTATTAAAAATAG
3067 AAAGAAGG
1 AAAGAAGG
3075 CCATTATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.55, C:0.00, G:0.24, T:0.20
Consensus pattern (21 bp):
AAAGAAGGTTATTAAAAATAG
Found at i:3080 original size:21 final size:21
Alignment explanation
Indices: 3037--3080 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3027 AAGAATGTTA
* * **
3037 TAAAAGTAGGAAGAAGGTTAT
1 TAAAAATAGAAAGAAGGCCAT
3058 TAAAAATAGAAAGAAGGCCAT
1 TAAAAATAGAAAGAAGGCCAT
3079 TA
1 TA
3081 TTAATAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.20
Consensus pattern (21 bp):
TAAAAATAGAAAGAAGGCCAT
Found at i:3294 original size:23 final size:23
Alignment explanation
Indices: 3268--3317 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3258 TCGTCAATTC
*
3268 GAGTTCCAAATAGGTATGGAATA
1 GAGTTCCAAATAGCTATGGAATA
*
3291 GAGTTTCAAATAGCTATGGAATA
1 GAGTTCCAAATAGCTATGGAATA
3314 GAGT
1 GAGT
3318 AGATTCTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (23 bp):
GAGTTCCAAATAGCTATGGAATA
Found at i:10367 original size:21 final size:21
Alignment explanation
Indices: 10343--10402 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
10333 ATATGTAATC
*
10343 CTTTGGAACATATATGTGGTT
1 CTTTGGAACATATATGTGGTA
10364 CTTTGAGACACATAT-T-TGGTA
1 CTTTG-GA-ACATATATGTGGTA
*
10385 CTTTGGAATATATATGTG
1 CTTTGGAACATATATGTG
10403 ATCCTTAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 16 0.48
22 3 0.09
23 6 0.18
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.42
Consensus pattern (21 bp):
CTTTGGAACATATATGTGGTA
Found at i:10440 original size:21 final size:21
Alignment explanation
Indices: 10414--10522 Score: 164
Period size: 21 Copynumber: 5.1 Consensus size: 21
10404 TCCTTAAGTA
*
10414 GTGGTCCTTCGGGACATATAT
1 GTGGTCATTCGGGACATATAT
* *
10435 GTGGTCCTTCGGGATATATAT
1 GTGGTCATTCGGGACATATAT
*
10456 GTGGTCATTCGGGACATCTAT
1 GTGGTCATTCGGGACATATAT
10477 GTGGTCATTCGGGACATATAT
1 GTGGTCATTCGGGACATATAT
*
10498 GTGGTCATTCGGGACAAATTAT
1 GTGGTCATTCGGGACATA-TAT
10520 GTG
1 GTG
10523 TGCCCCTAGT
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
21 75 0.93
22 6 0.07
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (21 bp):
GTGGTCATTCGGGACATATAT
Found at i:20593 original size:17 final size:17
Alignment explanation
Indices: 20571--20623 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
20561 AATTAAGAGT
20571 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* *
20588 TAGTTTTATGAATGAAC
1 TAGTTTAATAAATGAAC
* * *
20605 AAGTTTATTTAATGAAC
1 TAGTTTAATAAATGAAC
20622 TA
1 TA
20624 ACATTATTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.40
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:20704 original size:36 final size:36
Alignment explanation
Indices: 20633--20716 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
20623 AACATTATTC
* *
20633 AATGAACT--ATATGCATAAATGAAGTAGCTTACTA
1 AATGAACTAAATATGCATAAATAAACTAGCTTACTA
* *
20667 AATGATCTAAATATGCATAAATAAACTA-CTTCCCTA
1 AATGAACTAAATATGCATAAATAAACTAGCTT-ACTA
*
20703 AATGAACTAGATAT
1 AATGAACTAAATAT
20717 TTTAAATGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 7 0.17
35 3 0.07
36 31 0.76
ACGTcount: A:0.45, C:0.14, G:0.11, T:0.30
Consensus pattern (36 bp):
AATGAACTAAATATGCATAAATAAACTAGCTTACTA
Found at i:22837 original size:28 final size:26
Alignment explanation
Indices: 22799--22851 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
22789 TCCTCTTTAA
22799 AGTTTTTATTTTTTTATTATTTTTTT
1 AGTTTTTATTTTTTTATTATTTTTTT
*
22825 AGTTTTTCGATTTTTTTGTTATTTTTT
1 AGTTTTT--ATTTTTTTATTATTTTTT
22852 ACTAACCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
28 17 0.71
ACGTcount: A:0.13, C:0.02, G:0.08, T:0.77
Consensus pattern (26 bp):
AGTTTTTATTTTTTTATTATTTTTTT
Found at i:31160 original size:699 final size:696
Alignment explanation
Indices: 29816--31265 Score: 2059
Period size: 699 Copynumber: 2.1 Consensus size: 696
29806 TTCCCTCTGG
* * * * *
29816 AGTTGCATATCCTCTTTGGTCTCCCAAGTTGTTTCCTCTGTCCCATGGTTCCTCCATATGACATT
1 AGTTGCATATCCTCTTT-ATGTCCCAAGTTATTTCCTCAGTCCCATGGTTCCTCCACATGACATT
* *
29881 TACTAACGAATTCTGCGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTTATT
65 CACTAACGAATTCTACGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTTATT
* * *
29946 CTTCATAGGTCATATACTGCCTTACTTCAATCTGCTATATTAGAAAGACGGGGAAGGGTCGGAAT
130 CTTCATAGGTCATATACTGCCTTACTTCAATCTGCTATATCAGAAAGACGGAGAAGGGTCAGAAT
* * *
30011 GATACCTCATAAGCATCGATACGTAGAGCACATTATGGATGCCTTCATCTCATGTGGTAAGGCTA
195 GATACCTCATAAGCATCGATACGTAGAACACATTATGGATGCCTCCATCTCAGGTGGTAAGGCTA
** * * * * * * * *
30076 GTCGATAGTTTAGGGGTCCAAGCCTTTCAAGAATCTTATAAGGTCTAATGAAACATTGAACTAGC
260 GTCGATAGGCTACGGGTCAAAGCCTTTCAAGAATCTCACAAGATCTAATCAAACACTGAACTAAC
* * *
30141 TTCCCTTTCCTCTAAAACTAAATCACTCTTTTCCAAGGTGATACTTTTAGGAAAAACTTGTCACC
325 TTCCATTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAACTTGTCACC
*
30206 CACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGATGGTTTCTT
390 CACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGAAGGTTTCTT
* *
30271 GAGTCAATTTTGAATCAATCATACTTTGTCTCTTGTTTAATTTATAAGATTAGGACCAATTCATT
455 GAATCAATTTTGAATCAATCATACTTTGTCTCTTGTTTAATTGATAAGATTAGGACCAATTCATT
* * * * * *
30336 AAGCTCCATCCAACGCAAGGGTTTCCTTCACCTTCGACCGTACAACAACTCAAAATGAATTCCCT
520 AAGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAACCGTAAAACAACTCAAAATGAATTCCCT
* * * * *
30401 CTCGAGTTTACCCAAAACTAGTAACCCGTAGTTTGGGTCGTTACAACTCTCCCCTCCTCGTATGA
585 CTCGAGTTTACCCAAAACTAGTAACCCGTAGTTTAGGCCGTTACAACTCTACCATCCTCGTAAGA
* *
30466 AATTTCATCCTTAAAATTTTTCTAAGTATAAGATATGTCGAAACTGA
650 AATTTCATCCTTAAAATTTTCCTAAGTATAAGATATGGCGAAACTGA
* *
30513 AGTTGCATATCCTCCTTTATGTCCCAATTTATTTCCTCAGTCCCAT-GTTACCTCCACATGACCT
1 AGTTGCATATCCT-CTTTATGTCCCAAGTTATTTCCTCAGTCCCATGGTT-CCTCCACATGACAT
* * ** *
30577 TCACTAATGGAA-TCTACTTGTTCCTTAGGTCTCTAACCTCTCGATCTAAAATCCTTATCGGTTA
64 TCACTAA-CGAATTCTACGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTTA
* * * *
30641 TTCTTCATAGGTCATAT-CTTGGCTTACTTTAATTTGCTCTATCAGAACA-ACGTGAGAAGGGTC
128 TTCTTCATAGGTCATATAC-TGCCTTACTTCAATCTGCTATATCAGAA-AGACG-GAGAAGGGTC
30704 AGAATGATACCTCATAAGCATCGATACGTAGAACACATTATGGATGCACTCCATCTCAGGTGGTA
190 AGAATGATACCTCATAAGCATCGATACGTAGAACACATTATGGATGC-CTCCATCTCAGGTGGTA
* *
30769 AGGCTAGTCCG-TAGGCTACGGGTCAAAGCCTTTCAATAATCTCACAAGATCTAATCAAACGCTG
254 AGGCTAGT-CGATAGGCTACGGGTCAAAGCCTTTCAAGAATCTCACAAGATCTAATCAAACACTG
* *
30833 AGCTAACTTCTATTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAACT
318 AACTAACTTCCATTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAACT
*
30898 TGTCACCCACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGTTTTCTGACGATTGAAG
383 TGTCACCCACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGAAG
* * * **
30963 GTTTCTTGTAAT-GATTTTGAATCAATCATACTTTTTCTTTTGTTTCGTTGATAAGATTAGGACC
448 GTTTCTTG-AATCAATTTTGAATCAATCATACTTTGTCTCTTGTTTAATTGATAAGATTAGGACC
* * * *
31027 AACTT-ATTGAGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAATCGTAAAACAGCTCGAAAT
512 AA-TTCATTAAGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAACCGTAAAACAACTCAAAAT
* * *
31091 GAATTCCCTCTTGAGTTTACCCGAAACTAGTAACCCGTAGTTTAGGCCGTTACAACTCTATCATC
576 GAATTCCCTCTCGAGTTTACCCAAAACTAGTAACCCGTAGTTTAGGCCGTTACAACTCTACCATC
*
31156 CTCGTAAGAAATTTCATCCTTAAAATTTTCCTAAGTATAAGATATGGGGAAACTGA
641 CTCGTAAGAAATTTCATCCTTAAAATTTTCCTAAGTATAAGATATGGCGAAACTGA
* ** *
31212 AGTTGCATATCCTCTTTTTGTCTCCCAAGTTGCTTCCTTAGTCCCATGGTTCCT
1 AGTTGCATATCCTCTTTATG--TCCCAAGTTATTTCCTCAGTCCCATGGTTCCT
31266 GATAACTCTG
Statistics
Matches: 664, Mismatches: 76, Indels: 23
0.87 0.10 0.03
Matches are distributed among these distances:
696 4 0.01
697 144 0.22
698 68 0.10
699 415 0.62
700 30 0.05
701 3 0.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (696 bp):
AGTTGCATATCCTCTTTATGTCCCAAGTTATTTCCTCAGTCCCATGGTTCCTCCACATGACATTC
ACTAACGAATTCTACGTGTTCCTTAACTCTCTAACCTCTCGATATAAAATCCTTATCGGTTATTC
TTCATAGGTCATATACTGCCTTACTTCAATCTGCTATATCAGAAAGACGGAGAAGGGTCAGAATG
ATACCTCATAAGCATCGATACGTAGAACACATTATGGATGCCTCCATCTCAGGTGGTAAGGCTAG
TCGATAGGCTACGGGTCAAAGCCTTTCAAGAATCTCACAAGATCTAATCAAACACTGAACTAACT
TCCATTTCCTCCAAAACTAAATCACTCTTTTCCAAGGTGAGACTTTTAGGAAAAACTTGTCACCC
ACTTTAAATTCTATGTCCTTACGCTTCAAATCAAAATATGATTTCTGACGATTGAAGGTTTCTTG
AATCAATTTTGAATCAATCATACTTTGTCTCTTGTTTAATTGATAAGATTAGGACCAATTCATTA
AGCTCCATCAAACACAAGGGTGTCCTTCACCTCCAACCGTAAAACAACTCAAAATGAATTCCCTC
TCGAGTTTACCCAAAACTAGTAACCCGTAGTTTAGGCCGTTACAACTCTACCATCCTCGTAAGAA
ATTTCATCCTTAAAATTTTCCTAAGTATAAGATATGGCGAAACTGA
Found at i:34181 original size:21 final size:20
Alignment explanation
Indices: 34153--34192 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
34143 CATTACATGA
*
34153 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
34173 ATTTCATGGCTTCAACAAAA
1 ATTT-ATGGCCTCAACAAAA
34193 ACCTTGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:40637 original size:22 final size:22
Alignment explanation
Indices: 40612--40659 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
40602 GTGACATATG
*
40612 GATCCGTGGGAGTGCGATAGCA
1 GATCCGTGGGACTGCGATAGCA
40634 GATCCGTGGGACTGCGATAGCA
1 GATCCGTGGGACTGCGATAGCA
40656 GATC
1 GATC
40660 GTGTTTAGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.38, T:0.19
Consensus pattern (22 bp):
GATCCGTGGGACTGCGATAGCA
Found at i:59258 original size:13 final size:12
Alignment explanation
Indices: 59242--59286 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
59232 TAACGGATTC
59242 TTCTTTTTTATTT
1 TTCTTTTTT-TTT
*
59255 TTCTTTTCTTTT
1 TTCTTTTTTTTT
*
59267 TTCTTTTTTCTAT
1 TTCTTTTTT-TTT
59280 TTCTTTT
1 TTCTTTT
59287 CCTTTCCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 11 0.39
13 17 0.61
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (12 bp):
TTCTTTTTTTTT
Found at i:59267 original size:19 final size:20
Alignment explanation
Indices: 59242--59286 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
59232 TAACGGATTC
*
59242 TTCTTTTTT-ATTTTTCT-T
1 TTCTTTTTTCTTTTTTCTAT
59260 TTCTTTTTTCTTTTTTCTAT
1 TTCTTTTTTCTTTTTTCTAT
59280 TTCTTTT
1 TTCTTTT
59287 CCTTTCCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 9 0.38
19 7 0.29
20 8 0.33
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTCTTTTTTCTTTTTTCTAT
Found at i:59291 original size:19 final size:19
Alignment explanation
Indices: 59252--59291 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
59242 TTCTTTTTTA
*
59252 TTTTTCTTTTCTTTTTTCT
1 TTTTTCTTTTCTTTTTCCT
59271 TTTTTCTATTTC-TTTTCCT
1 TTTTTCT-TTTCTTTTTCCT
59290 TT
1 TT
59292 CCTTTCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTTCCT
Found at i:62641 original size:15 final size:15
Alignment explanation
Indices: 62617--62651 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
62607 TTTGGAAGAT
62617 AAATGAAATGATGGA
1 AAATGAAATGATGGA
* *
62632 AAATGGAATGATTGA
1 AAATGAAATGATGGA
62647 AAATG
1 AAATG
62652 CAAGCAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.26, T:0.23
Consensus pattern (15 bp):
AAATGAAATGATGGA
Done.