Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003243.1 Hibiscus syriacus cultivar Beakdansim tig00006820_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: 71951
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1497 original size:20 final size:18
Alignment explanation
Indices: 1459--1497 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1449 TGATATGGAT
*
1459 GATTTTTGATTTGAATAA
1 GATTTTTGATTTCAATAA
1477 GATTTTTGACTTGTCAATAA
1 GATTTTTGA-TT-TCAATAA
1497 G
1 G
1498 CTAATTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 9 0.50
19 2 0.11
20 7 0.39
ACGTcount: A:0.31, C:0.05, G:0.18, T:0.46
Consensus pattern (18 bp):
GATTTTTGATTTCAATAA
Found at i:1753 original size:21 final size:21
Alignment explanation
Indices: 1711--1753 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1701 TTTTCGGGCT
* *
1711 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
1732 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
1753 A
1 A
1754 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:2454 original size:148 final size:147
Alignment explanation
Indices: 2283--2583 Score: 507
Period size: 149 Copynumber: 2.0 Consensus size: 147
2273 GGGTAGAGGG
* *
2283 TCTACGCGGTTCTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
1 TCTACGCGGTTCTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
*
2348 TTGATCCCTAG-ATATATATATGA-TTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
66 TTGATCCATAGTATATATATAT-ATTTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
2411 ATGGCACTACGGTGCAAT
130 ATGGCACTACGGTGCAAT
2429 TCTACGCGGTTCTTTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTC--TAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
* *
2494 ACTTGATCCATAGTTTATGTATATATTTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
64 ACTTGATCCATAGTATATATATATATTTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
2559 TATGGCACTACGGTGTAAT
129 TATGGCACTACGGTGCAAT
2578 TCTACG
1 TCTACG
2584 GGGCACTTCG
Statistics
Matches: 145, Mismatches: 6, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
146 12 0.08
148 62 0.43
149 71 0.49
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (147 bp):
TCTACGCGGTTCTAGGACATATGTATATCCTTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
TTGATCCATAGTATATATATATATTTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATA
TGGCACTACGGTGCAAT
Found at i:2606 original size:23 final size:23
Alignment explanation
Indices: 2562--2606 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
2552 ATCATTATAT
* *
2562 GGCACTACGGTGTAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
2585 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
2607 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:11828 original size:3 final size:3
Alignment explanation
Indices: 11820--11853 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
11810 ATAGGTTATT
11820 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11854 TGTGAGCCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:13994 original size:60 final size:60
Alignment explanation
Indices: 13916--14031 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
13906 GAACATACGA
* * * * *
13916 ATAGTCGGATGACCATTTTTTAACTTTTAATAGTCAAGAGACTCAATAAAACAATATTCT
1 ATAGTCGAAAGACCATTTTGTAACTTTTAATAATCAACAGACTCAATAAAACAATATTCT
* * *
13976 ATAGTCGAAAGACTATTTTGTAACTTTTAATAATCGACAGACTTAATAAAACAATA
1 ATAGTCGAAAGACCATTTTGTAACTTTTAATAATCAACAGACTCAATAAAACAATA
14032 CCTTATTGTC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (60 bp):
ATAGTCGAAAGACCATTTTGTAACTTTTAATAATCAACAGACTCAATAAAACAATATTCT
Found at i:14457 original size:21 final size:21
Alignment explanation
Indices: 14431--14487 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
14421 TCCATACCTG
14431 TATATATACATATAAATGAAT
1 TATATATACATATAAATGAAT
14452 TATATATACATATAAATGAAT
1 TATATATACATATAAATGAAT
*
14473 TATGTATACATATAA
1 TATATATACATATAA
14488 CGTTTTTGAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
TATATATACATATAAATGAAT
Found at i:19179 original size:21 final size:21
Alignment explanation
Indices: 19153--19192 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
19143 GGTATGACAA
19153 TGAACCGGCTGAAAACCGGGG
1 TGAACCGGCTGAAAACCGGGG
19174 TGAACCGGCTGAAAACCGG
1 TGAACCGGCTGAAAACCGG
19193 CAAAACCGAT
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:0.30, C:0.25, G:0.35, T:0.10
Consensus pattern (21 bp):
TGAACCGGCTGAAAACCGGGG
Found at i:22418 original size:16 final size:16
Alignment explanation
Indices: 22397--22430 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22387 TTACTATTCA
* *
22397 CGTGAATAGTGAATTT
1 CGTGAACAGTGAAATT
22413 CGTGAACAGTGAAATT
1 CGTGAACAGTGAAATT
22429 CG
1 CG
22431 GTCGGCGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (16 bp):
CGTGAACAGTGAAATT
Found at i:26201 original size:20 final size:20
Alignment explanation
Indices: 26176--26220 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
26166 TTGGTGAATC
26176 GAGCTCCATCAACTGCAATA
1 GAGCTCCATCAACTGCAATA
26196 GAGCTCCATCAACTGCAATA
1 GAGCTCCATCAACTGCAATA
26216 GAGCT
1 GAGCT
26221 ATAGACACCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.18, T:0.20
Consensus pattern (20 bp):
GAGCTCCATCAACTGCAATA
Found at i:28283 original size:18 final size:17
Alignment explanation
Indices: 28240--28285 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
28230 ATGGAATTGA
*
28240 ATTCCAATTCCTGACAG
1 ATTCCAATTCCTCACAG
* *
28257 ATTCTAATTCCTTCACAT
1 ATTCCAATTCC-TCACAG
28275 ATTCCAATTCC
1 ATTCCAATTCC
28286 CTCATAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.37
Consensus pattern (17 bp):
ATTCCAATTCCTCACAG
Found at i:31271 original size:20 final size:20
Alignment explanation
Indices: 31246--31319 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
31236 GTATCACAAA
31246 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
* ** *
31266 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
*
31287 ATCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
31307 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
31320 AGTCTACCGT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:31460 original size:5 final size:5
Alignment explanation
Indices: 31438--31472 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
31428 AAGACACGTA
31438 CGACC ACGACC ACGACC CGACC CGACC CGACC CGA
1 CGACC -CGACC -CGACC CGACC CGACC CGACC CGA
31473 GACGAGACGG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.62
6 11 0.38
ACGTcount: A:0.26, C:0.54, G:0.20, T:0.00
Consensus pattern (5 bp):
CGACC
Found at i:34157 original size:15 final size:15
Alignment explanation
Indices: 34137--34173 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
34127 CGCCGCAAGA
34137 AGCGCCGGTGAAACT
1 AGCGCCGGTGAAACT
34152 AGCGCCGGTGAAACT
1 AGCGCCGGTGAAACT
34167 AGCGCCG
1 AGCGCCG
34174 CCAAAGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.24, C:0.30, G:0.35, T:0.11
Consensus pattern (15 bp):
AGCGCCGGTGAAACT
Found at i:34232 original size:45 final size:46
Alignment explanation
Indices: 34181--34289 Score: 163
Period size: 43 Copynumber: 2.5 Consensus size: 46
34171 CCGCCAAAGT
*
34181 TAGCGGCGTTTGT-GAACAAAAAACACCGCAATAGGTCGAGATCTA
1 TAGCGGCGTTTTTGGAACAAAAAACACCGCAATAGGTCGAGATCTA
* *
34226 TAGCGGCGTTTTTGGGAC---AAACGCCGCAATAGGTCGAGATCTA
1 TAGCGGCGTTTTTGGAACAAAAAACACCGCAATAGGTCGAGATCTA
34269 TAGCGGCGTTTTTGGAACAAA
1 TAGCGGCGTTTTTGGAACAAA
34290 CGCCACAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
43 41 0.73
45 12 0.21
46 3 0.05
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
TAGCGGCGTTTTTGGAACAAAAAACACCGCAATAGGTCGAGATCTA
Found at i:34259 original size:43 final size:43
Alignment explanation
Indices: 34201--34338 Score: 197
Period size: 43 Copynumber: 3.2 Consensus size: 43
34191 TGTGAACAAA
* *
34201 AAACACCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
34244 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * * *
34287 AAACGCCACAAAAGGT-TAGATCTATAGCAGCGTTTTTTGATAC
1 AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGA-AC
34330 AAACGCCGC
1 AAACGCCGC
34339 TAATGACCGT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
42 21 0.24
43 65 0.76
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (43 bp):
AAACGCCGCAATAGGTCGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:35487 original size:21 final size:20
Alignment explanation
Indices: 35463--35505 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
35453 AACAAGTAAT
35463 ATTGATAGTATAAAAAACA-AA
1 ATTGAT-GT-TAAAAAACATAA
*
35484 ATTGATGTTAAGAAACATAA
1 ATTGATGTTAAAAAACATAA
35504 AT
1 AT
35506 AGACTAATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
20 6 0.30
21 6 0.30
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
ATTGATGTTAAAAAACATAA
Found at i:37085 original size:42 final size:40
Alignment explanation
Indices: 37019--37169 Score: 128
Period size: 42 Copynumber: 3.6 Consensus size: 40
37009 CATGTTTATA
37019 GCGGCATTTTTACAAAAACGCCACTATATATCTGGGATATT
1 GCGGCATTTTTACAAAAACGCCACTATATATCT-GGATATT
* * * *
37060 GCGGCATTTTATACATAAACGCCACTAAAGTA-CAT-GTTTTT
1 GCGGCATTTT-TACAAAAACGCCACTATA-TATC-TGGATATT
* * *
37101 AGCGGCGTTTTCACAAAAAACGCCGCTATATAT-TCGGATATT
1 -GCGGCATTTTTAC-AAAAACGCCACTATATATCT-GGATATT
* *
37143 GCGGCATTTTTTACATAAATGCCACTA
1 GCGGCA-TTTTTACAAAAACGCCACTA
37170 AAGTACGTAT
Statistics
Matches: 85, Mismatches: 16, Indels: 18
0.71 0.13 0.15
Matches are distributed among these distances:
40 1 0.01
41 33 0.39
42 48 0.56
43 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.32
Consensus pattern (40 bp):
GCGGCATTTTTACAAAAACGCCACTATATATCTGGATATT
Found at i:37095 original size:83 final size:82
Alignment explanation
Indices: 37008--37210 Score: 280
Period size: 83 Copynumber: 2.5 Consensus size: 82
36998 CCAATATTGC
* * *
37008 ACATGTTTATAGCGGCATTTTTACAAAAACGCCACTATATATCTGGGATATTGCGGCATTTTATA
1 ACATGTTTTTAGCGGCGTTTTTACAAAAACGCCACTATATAT-TCGGATATTGCGGCATTTTATA
37073 CATAAACGCCACTAAAGT
65 CATAAACGCCACTAAAGT
* * *
37091 ACATGTTTTTAGCGGCGTTTTCACAAAAAACGCCGCTATATATTCGGATATTGCGGCATTTTTTA
1 ACATGTTTTTAGCGGCGTTTTTAC-AAAAACGCCACTATATATTCGGATATTGCGGCATTTTATA
*
37156 CATAAATGCCACTAAAGT
65 CATAAACGCCACTAAAGT
* * * * *
37174 ACGTATTTTTAGCGGCGTTTGTCCAAAAACACCACTA
1 ACATGTTTTTAGCGGCGTTTTTACAAAAACGCCACTA
37211 AAGTATGTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
82 11 0.10
83 77 0.73
84 17 0.16
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (82 bp):
ACATGTTTTTAGCGGCGTTTTTACAAAAACGCCACTATATATTCGGATATTGCGGCATTTTATAC
ATAAACGCCACTAAAGT
Found at i:37234 original size:83 final size:82
Alignment explanation
Indices: 37055--37236 Score: 199
Period size: 83 Copynumber: 2.2 Consensus size: 82
37045 TATATCTGGG
* * *
37055 ATATTGCGGCATTTTATACATAAACGCCACTAAAGTACATGTTTTTAGCGGCGTTTTCACAAAAA
1 ATATTGCGACATTTTTTACATAAACGCCACTAAAGTACATATTTTTAGCGGCGTTTTCACAAAAA
* * * *
37120 ACGCCGCTATATATTCGG
66 ACACCACTAAATATTC-A
* * *
37138 ATATTGCGGCATTTTTTACATAAATGCCACTAAAGTACGTATTTTTAGCGGCGTTTGTC-C-AAA
1 ATATTGCGACATTTTTTACATAAACGCCACTAAAGTACATATTTTTAGCGGCGTTT-TCACAAAA
37201 AACACCACTAAAGTATGT-A
65 AACACCACTAAA-TAT-TCA
*
37220 ATTTTAGCGACATTTTT
1 ATATT-GCGACATTTTT
37237 GTGAAAACGT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
82 16 0.19
83 66 0.78
84 3 0.04
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (82 bp):
ATATTGCGACATTTTTTACATAAACGCCACTAAAGTACATATTTTTAGCGGCGTTTTCACAAAAA
ACACCACTAAATATTCA
Found at i:45250 original size:16 final size:16
Alignment explanation
Indices: 45238--45279 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
45228 TATATCACCA
45238 AAATAATAAATCAAAG
1 AAATAATAAATCAAAG
*
45254 AAATAATAAAT-AAAT
1 AAATAATAAATCAAAG
45269 AAATGAATAAA
1 AAAT-AATAAA
45280 AAAGTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 7 0.29
16 17 0.71
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (16 bp):
AAATAATAAATCAAAG
Found at i:46300 original size:16 final size:15
Alignment explanation
Indices: 46274--46303 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46264 TGTTGTGTCC
46274 GGTCATCCCGGGATA
1 GGTCATCCCGGGATA
46289 GGTCAGTCCCGGGAT
1 GGTCA-TCCCGGGAT
46304 TTCAGGCCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.27, G:0.37, T:0.20
Consensus pattern (15 bp):
GGTCATCCCGGGATA
Found at i:46528 original size:9 final size:10
Alignment explanation
Indices: 46502--46543 Score: 61
Period size: 9 Copynumber: 4.4 Consensus size: 10
46492 TGCAAAAAGC
46502 ATAAATAATA
1 ATAAATAATA
*
46512 AGAAATAA-A
1 ATAAATAATA
46521 ATAAATAATA
1 ATAAATAATA
46531 AT-AATAATA
1 ATAAATAATA
46540 ATAA
1 ATAA
46544 TACTATATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
9 17 0.61
10 11 0.39
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (10 bp):
ATAAATAATA
Found at i:46653 original size:37 final size:36
Alignment explanation
Indices: 46558--46862 Score: 299
Period size: 37 Copynumber: 8.1 Consensus size: 36
46548 ATATATATAT
* * * *
46558 AAATATTTTCAAAAA-TATGTAATATATAAATTTTCA
1 AAATGTTTT-AAAAACTATATATTATATATATTTTCA
*
46594 AAATGTTTTTTAAAAAACTATATATTATACATATTTTCA
1 AAATG--TTTT-AAAAACTATATATTATATATATTTTCA
* *
46633 AAATCGTTTTAAAAACTATATAATATATATTTTTTTCAA
1 AAAT-GTTTTAAAAACTATATATTATATA-TATTTTC-A
*
46672 AAATGTTTTAAAATCTATATATTATATATATTTTCA
1 AAATGTTTTAAAAACTATATATTATATATATTTTCA
* *
46708 AAATGTTTTTAAAAACTATATAATATATAAATGTTTTCA
1 AAATG-TTTTAAAAACTATAT-AT-TATATATATTTTCA
* *
46747 GAAATGTTTTCAAATCTATATATTATATA-AGTTTTCA
1 -AAATGTTTTAAAAACTATATATTATATATA-TTTTCA
*
46784 AAATGATTTTAAAAACTATATATTATATATATTTTTTA
1 AAATG-TTTTAAAAACTATATATTATATATA-TTTTCA
* * * *
46822 AAATATTTTAAAAATTATATATATTATATGTTTTTTCA
1 AAATGTTTTAAAAA--CTATATATTATATATATTTTCA
46860 AAA
1 AAA
46863 ACCGTTTGCA
Statistics
Matches: 226, Mismatches: 28, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
36 15 0.07
37 78 0.35
38 63 0.28
39 64 0.28
40 6 0.03
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (36 bp):
AAATGTTTTAAAAACTATATATTATATATATTTTCA
Found at i:46782 original size:76 final size:74
Alignment explanation
Indices: 46558--46862 Score: 348
Period size: 76 Copynumber: 4.0 Consensus size: 74
46548 ATATATATAT
* * * *
46558 AAATATTTTCAAAAA-TATGTAATATATAAA-TTTTCAAAATGTTTTTTAAAAAACTATATATTA
1 AAATGTTTTTAAAAACTATATAATATATAAATTTTTCAAAATG--TTTT-AAAATCTATATATTA
*
46621 TACATATTTTCA
63 TATATATTTTCA
**
46633 AAATCG-TTTTAAAAACTATATAATATATATTTTTTTCAAAAATGTTTTAAAATCTATATATTAT
1 AAAT-GTTTTTAAAAACTATATAATATATAAATTTTTC-AAAATGTTTTAAAATCTATATATTAT
46697 ATATATTTTCA
64 ATATATTTTCA
*
46708 AAATGTTTTTAAAAACTATATAATATATAAATGTTTTCAGAAATGTTTTCAAATCTATATATTAT
1 AAATGTTTTTAAAAACTATATAATATATAAAT-TTTTCA-AAATGTTTTAAAATCTATATATTAT
46773 ATA-AGTTTTCA
64 ATATA-TTTTCA
* * * * * *
46784 AAATGATTTTAAAAACTATATATTATATATATTTTTTAAAATATTTTAAAAATTATATATATTAT
1 AAATGTTTTTAAAAACTATATAATATATAAATTTTTCAAAATGTTTT-AAAA-TCTATATATTAT
* *
46849 ATGTTTTTTCA
64 ATATATTTTCA
46860 AAA
1 AAA
46863 ACCGTTTGCA
Statistics
Matches: 200, Mismatches: 19, Indels: 21
0.83 0.08 0.09
Matches are distributed among these distances:
74 9 0.05
75 75 0.38
76 105 0.52
77 5 0.03
78 6 0.03
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.47
Consensus pattern (74 bp):
AAATGTTTTTAAAAACTATATAATATATAAATTTTTCAAAATGTTTTAAAATCTATATATTATAT
ATATTTTCA
Found at i:49195 original size:250 final size:247
Alignment explanation
Indices: 48744--49306 Score: 809
Period size: 250 Copynumber: 2.2 Consensus size: 247
48734 CTTATTCATA
48744 TATTGAATAAAAATATTTTTTTATTATTTCGGGTC--G--GGTTTCTAATTCATATATTCGGGTC
1 TATTGAAT-AAAATATTTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTCGGGTC
* * *
48805 AGGTTGGGTGAAATTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTCGA
65 AGGTTAGGTGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC--G-AGA
* *
48870 GTTCGGGTTTAGGGTAAAAAATACCCGACCCAAAAATATATATAATTTTACCTTATATATTTAGG
127 GTTCGGGTTTAGGGTAAAAAAGACCCAACCCAAAAATATATATAATTTTACCTTATATATTTAGG
*
48935 AATAATTACAATAATACCCCCTCTATATATAATTTTTTTCAATTAAATCACTATTTT
192 AATAATTACAATAATA-CCCCTCTATATATAATTTTTTTCAATTAAATCAATATTTT
48992 TATTGAAT-AAAT-TTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAATATTTTTTTATTATTTCGGGTCGGGTCGG-TTTCTAATTCATATATTCGGGTC
49055 AGGTTAGGTGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTC-AG-GTT
65 AGGTTAGGTGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGAGTT
49118 CGGGTTTAGGGTGAAAAAACCGGACCCAACCCGAAAAATATATATAATTTTACCTTATATATTTA
130 CGGGTTTAGGGT-AAAAAA---GACCCAACCC-AAAAATATATATAATTTTACCTTATATATTTA
* * * *
49183 GGAATAATTACAATAATACCCCTTTATATATATTTTTTTTCAATTAAGTCAATGTTTT
190 GGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAATCAATATTTT
49241 TATTGAATAAAAATAATTTTTTTATTATTTCGTGTTGTGTCGGGTCGGGTTTCTAATTCATATAT
1 TATTGAAT-AAAAT-ATTTTTTTATTATTTC--G--G-GTCGGGTC-GGTTTCTAATTCATATAT
49306 T
58 T
49307 GAATAAAAAT
Statistics
Matches: 285, Mismatches: 10, Indels: 30
0.88 0.03 0.09
Matches are distributed among these distances:
245 35 0.12
246 11 0.04
247 1 0.00
248 8 0.03
249 53 0.19
250 129 0.45
251 4 0.01
253 15 0.05
255 1 0.00
257 1 0.00
258 25 0.09
259 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (247 bp):
TATTGAATAAAATATTTTTTTATTATTTCGGGTCGGGTCGGTTTCTAATTCATATATTCGGGTCA
GGTTAGGTGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGAGTTC
GGGTTTAGGGTAAAAAAGACCCAACCCAAAAATATATATAATTTTACCTTATATATTTAGGAATA
ATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAATCAATATTTT
Found at i:49666 original size:17 final size:18
Alignment explanation
Indices: 49641--49687 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
49631 TATAGAATTG
*
49641 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
49658 GATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
49676 GATTCCAATTCC
1 GATTCCAATTCC
49688 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:50333 original size:15 final size:16
Alignment explanation
Indices: 50313--50346 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
50303 AAAATACAAC
50313 ATTCTC-AGTAATCTT
1 ATTCTCTAGTAATCTT
*
50328 ATTCTCTGGTAATCTT
1 ATTCTCTAGTAATCTT
50344 ATT
1 ATT
50347 ACAATCCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.24, C:0.18, G:0.09, T:0.50
Consensus pattern (16 bp):
ATTCTCTAGTAATCTT
Found at i:63752 original size:59 final size:59
Alignment explanation
Indices: 63660--63773 Score: 185
Period size: 59 Copynumber: 1.9 Consensus size: 59
63650 GAGGTTCATT
*
63660 TTTCATACGAATCGGGAGCTGCACTGGATGAACATTCGAAATGATTA-AATGAATTTGAG
1 TTTCATACGAATCAGGAGCTGCACTGGATGAACATTCGAAATGATTAGAA-GAATTTGAG
* *
63719 TTTCATACGAATCAGGAGGTGCACTGGATGAACATTCGTAATGATTAGAAGAATT
1 TTTCATACGAATCAGGAGCTGCACTGGATGAACATTCGAAATGATTAGAAGAATT
63774 CGAGGTCGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
59 49 0.96
60 2 0.04
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (59 bp):
TTTCATACGAATCAGGAGCTGCACTGGATGAACATTCGAAATGATTAGAAGAATTTGAG
Found at i:71534 original size:3 final size:3
Alignment explanation
Indices: 71526--71575 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
71516 GTAAAAAGAT
71526 ATA ATA ATA ATA ATA A-A ATA ATA ATAA ATA ATA AT- ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
*
71569 AAA ATA A
1 ATA ATA A
71576 AAAATCTTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:71564 original size:23 final size:24
Alignment explanation
Indices: 71519--71576 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
71509 ATTAAAAGTA
71519 AAAAGATATAATAATAATAATAAAAT
1 AAAA-ATA-AATAATAATAATAAAAT
*
71545 AATAATAAATAATAAT-ATAAAAT
1 AAAAATAAATAATAATAATAAAAT
71568 AAAAATAAA
1 AAAAATAAA
71577 AAATCTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 15 0.50
24 9 0.30
25 3 0.10
26 3 0.10
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAAATAAATAATAATAATAAAAT
Done.