Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002229.1 Hibiscus syriacus cultivar Beakdansim tig00004535_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: 64238
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2637 original size:2 final size:2
Alignment explanation
Indices: 2630--2656 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2620 ACAAACTTTC
2630 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2657 CATCTTAGGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3594 original size:15 final size:15
Alignment explanation
Indices: 3576--3613 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
3566 TTAACCGCTC
3576 TCTCTCTTCTCTCAT
1 TCTCTCTTCTCTCAT
3591 TCTCTCTTCTCTCAT
1 TCTCTCTTCTCTCAT
3606 TCTCTCTT
1 TCTCTCTT
3614 TTTTTCAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.05, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTCTCTTCTCTCAT
Found at i:4382 original size:3 final size:3
Alignment explanation
Indices: 4342--4399 Score: 66
Period size: 3 Copynumber: 19.3 Consensus size: 3
4332 GTAAGGGCCT
* *
4342 ATA ATA A-A ATA AAA ATA AAA ATA A-A ATA GATAA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -AT-A ATA ATA ATA ATA
4387 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
4400 CAACCAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 4 0.09
3 38 0.81
4 4 0.09
5 1 0.02
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (3 bp):
ATA
Found at i:8135 original size:67 final size:67
Alignment explanation
Indices: 8027--8158 Score: 264
Period size: 67 Copynumber: 2.0 Consensus size: 67
8017 CAGATGCCCT
8027 GGCAAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAG
1 GGCAAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAG
8092 GA
66 GA
8094 GGCAAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAG
1 GGCAAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAG
8159 AAATTTATAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (67 bp):
GGCAAGTTAATAATAAAAGTAATGCATCTTCGTCCAATTCTAACTCCCTTGAAGCTTCATTGCAG
GA
Found at i:8502 original size:30 final size:30
Alignment explanation
Indices: 8466--8533 Score: 136
Period size: 30 Copynumber: 2.3 Consensus size: 30
8456 ATAGGAGAGA
8466 ATCAAGAAATTTCTCTCCAAGGCACTAAAT
1 ATCAAGAAATTTCTCTCCAAGGCACTAAAT
8496 ATCAAGAAATTTCTCTCCAAGGCACTAAAT
1 ATCAAGAAATTTCTCTCCAAGGCACTAAAT
8526 ATCAAGAA
1 ATCAAGAA
8534 TCTAACAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (30 bp):
ATCAAGAAATTTCTCTCCAAGGCACTAAAT
Found at i:15772 original size:35 final size:35
Alignment explanation
Indices: 15726--15795 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
15716 TCTAAAGAAA
15726 TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
1 TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
*
15761 TGGCGATCTTAAGAGTTTTTGTGATTCCAGAGTCT
1 TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
15796 GAAGAAGAGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.39
Consensus pattern (35 bp):
TGGCGACCTTAAGAGTTTTTGTGATTCCAGAGTCT
Found at i:24475 original size:140 final size:140
Alignment explanation
Indices: 24220--24815 Score: 725
Period size: 140 Copynumber: 4.3 Consensus size: 140
24210 TAAACTAATC
* * * * * *
24220 AACATTTCTAATGGAGAGTTTATAATGAGAAGAAATCATCTGATAGAGGGAGAATAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
* * * * *
24285 TGAGAAGAACTTGATCAACCTTCGCTCGATTCATCGCATCTGGAGTTGAATCAGTGACGCCTCAC
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTCAC
24350 TT-ATGGGATT
131 TTGA-GGGATT
* * *
24360 AATATTTCCAATGGAGAGTTTATAATGAGAGGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
* * * * *
24425 TGAGAAGAACTTGTTCAACATTTTCTCGATTTATTGCATATGGAGTTGAATCAACGAAGCCTCAC
66 TGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTCAC
24490 TTGAGGGATT
131 TTGAGGGATT
* * *
24500 AACATTTCCAAAGGAGAGCTCATAATGAGAAGAACTCATCAGATAGA-AG-GATAAGAAGTTCAT
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGA-AA-AAGTTCAT
* * *
24563 AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCACATATGGAGTTGAATTAGTGAAGCCTC
64 AATGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTC
24628 ACTTGAGGGATT
129 ACTTGAGGGATT
* * * **
24640 AACATTTCCAATGGAGAGATCAAAATGAGAAGAACTCATCCGAT-GAGGGAGAATGAGTTCATAA
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
* * * ** * * * *
24704 TGA-AAAATACTTGTTCAACCTTAGTTTAATTTATCGCATATGGATTTGAATCAAAGATGCCTCA
66 TGAGAAGA-ACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTCA
*
24768 CTTGAGGGATC
130 CTTGAGGGATT
* * * *
24779 AATATTTCTAGTAGAGAGTTCATAATGAGAAGAACTC
1 AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTC
24816 GCAGCTTTAA
Statistics
Matches: 393, Mismatches: 57, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
138 5 0.01
139 104 0.26
140 281 0.72
141 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (140 bp):
AACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGAGAGAAAAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTGCTCGATTCATCGCATATGGAGTTGAATCAATGAAGCCTCAC
TTGAGGGATT
Found at i:25099 original size:23 final size:24
Alignment explanation
Indices: 25056--25100 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
25046 AAACCCGAAT
* *
25056 ACCCAAAGCAAGATCTGACCCAAA
1 ACCCAAACCAAGACCTGACCCAAA
25080 ACCCAAACCAA-ACCTGACCCA
1 ACCCAAACCAAGACCTGACCCA
25101 GAGCCTATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.44, C:0.40, G:0.09, T:0.07
Consensus pattern (24 bp):
ACCCAAACCAAGACCTGACCCAAA
Found at i:28036 original size:130 final size:130
Alignment explanation
Indices: 27759--28164 Score: 425
Period size: 130 Copynumber: 3.1 Consensus size: 130
27749 ACAGTGTTCT
* * ** * *
27759 AGGGTAGATCAGATCTGGAGACTTTGATT-ATTTCACTAATCTTTAGGGAAGATTTAATCGGGGT
1 AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGGGT
* * * *
27823 TGATTTGAC-T-ATTCTTCATA-GAATATCAAATCT-AAATAAATGGATATGCTCTGCTGCGTTC
66 TGATTT-ACTTCACTATTCTTAGGAATATCAAATCTGAAATAAATGGATATGCTCTGCTGCATTC
*
27884 T
130 C
* * * *
27885 AGGGTAGTTTAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCATGCAAGATTGAATCGGGGT
1 AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGGGT
*
27950 TGATTTACTTCACTGTTCCTTAGTGAATATCAAATCTGAAA-AAA-GGATATGCTCCT-CTGCAT
66 TGATTTACTTCACTATT-CTTAG-GAATATCAAATCTGAAATAAATGGATATGCT-CTGCTGCAT
28012 TCC
128 TCC
* * * *
28015 AGGGTAGGTCAAATCTAGAGACTTTGATTCACTTCACTGCTTTTCAGGGAAGATTGAATCAGGGT
1 AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGGGT
* * ** * *
28080 TGATTTGCTTCACTATTCTTCAGGGAAGATCAAATCTGAGGAA-AATATATATATGCTCTTCTTC
66 TGATTTACTTCACTATTCTT-A-GGAATATCAAATCTGA--AATAA-ATGGATATGCTCTGCTGC
*
28144 ATTCT
126 ATTCC
28149 AGGGTAGATCAGATCT
1 AGGGTAGATCAGATCT
28165 GGAAACCTTG
Statistics
Matches: 234, Mismatches: 31, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
126 28 0.12
127 35 0.15
128 4 0.02
129 6 0.03
130 104 0.44
131 19 0.08
132 7 0.03
133 3 0.01
134 28 0.12
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (130 bp):
AGGGTAGATCAGATCTAGAGACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGGGGT
TGATTTACTTCACTATTCTTAGGAATATCAAATCTGAAATAAATGGATATGCTCTGCTGCATTCC
Found at i:29438 original size:7 final size:7
Alignment explanation
Indices: 29428--29475 Score: 53
Period size: 8 Copynumber: 6.6 Consensus size: 7
29418 TTTATATTCT
29428 TTTTTTA
1 TTTTTTA
29435 TTTTTTATA
1 -TTTTT-TA
29444 TTTTTTA
1 TTTTTTA
29451 TTTTTTA
1 TTTTTTA
*
29458 TTCTTTTG
1 TT-TTTTA
29466 TTTTTT-
1 TTTTTTA
29472 TTTT
1 TTTT
29476 ATCTTCAGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 4 0.11
7 15 0.41
8 16 0.43
9 2 0.05
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:29447 original size:16 final size:15
Alignment explanation
Indices: 29427--29475 Score: 64
Period size: 16 Copynumber: 3.3 Consensus size: 15
29417 TTTTATATTC
29427 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
29442 TATTTTTTATTTTTTA
1 T-TTTTTTATTTTTTA
* *
29458 TTCTTTTGTTTTTT-
1 TTTTTTTATTTTTTA
29472 TTTT
1 TTTT
29476 ATCTTCAGGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 3 0.10
15 12 0.40
16 15 0.50
ACGTcount: A:0.10, C:0.02, G:0.02, T:0.86
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:29450 original size:34 final size:35
Alignment explanation
Indices: 29412--29477 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
29402 TTAAACCCCC
29412 TTTTATTTTATATTCTTTT-TTTATTTTTTATATT
1 TTTTATTTTATATTCTTTTGTTTATTTTTTATATT
* *
29446 TTTTATTTTTTATTCTTTTGTTTTTTTTTTAT
1 TTTTATTTTATATTCTTTTGTTTATTTTTTAT
29478 CTTCAGGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 18 0.62
35 11 0.38
ACGTcount: A:0.14, C:0.03, G:0.02, T:0.82
Consensus pattern (35 bp):
TTTTATTTTATATTCTTTTGTTTATTTTTTATATT
Found at i:29464 original size:9 final size:8
Alignment explanation
Indices: 29412--29472 Score: 54
Period size: 7 Copynumber: 7.5 Consensus size: 8
29402 TTAAACCCCC
29412 TTTTATTT
1 TTTTATTT
*
29420 TATATTCTTT
1 T-T-TTATTT
29430 TTTTA-TT
1 TTTTATTT
29437 TTTTATATT
1 TTTTAT-TT
29446 TTTTA-TT
1 TTTTATTT
*
29453 TTTTATTC
1 TTTTATTT
*
29461 TTTTGTTT
1 TTTTATTT
29469 TTTT
1 TTTT
29473 TTTATCTTCA
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
7 14 0.33
8 14 0.33
9 9 0.21
10 6 0.14
ACGTcount: A:0.13, C:0.03, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTATTT
Found at i:36602 original size:13 final size:13
Alignment explanation
Indices: 36584--36608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36574 TATTTTTTAA
36584 TGTTTTCTTTCAC
1 TGTTTTCTTTCAC
36597 TGTTTTCTTTCA
1 TGTTTTCTTTCA
36609 GCCTCAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.08, T:0.64
Consensus pattern (13 bp):
TGTTTTCTTTCAC
Found at i:39629 original size:344 final size:342
Alignment explanation
Indices: 39134--39817 Score: 1023
Period size: 344 Copynumber: 2.0 Consensus size: 342
39124 AATTTAAAAT
**
39134 TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAATTAGTTTTGAAGTTAATTACGCTAGGAA
1 TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAATTAGTTCGGAAGTTAATTACGCTAGGAA
** * * * *
39199 AGGATTAGCACCCCCACAGCGCCCTAAATCGGTACCTAGTCGATTAATTAGTTGTCTTTGCAGTG
66 AGGATTAGCACCCCCACAAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACAATG
*
39264 AATCCTACAAATTCAAATTTAATTTAATTTAAGATTCCTTTTAAAACACATTCCTTGAATTTTAG
131 AATCCTACAAATTCAAATTTAATTTAATTTAAGATCCCTTTTAAAACACATTCCTTGAATTTTAG
*
39329 GAC-GAAACAC-AACAATATTTAATTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAAG
196 GACGGAAA-ACGAA-AATATTTAACTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAAG
* * * * *
39392 CACCCATTTCTTAATCTAATCGAAATAAGGAAATATTACTATTTCGTTCGAAAGTTCATTAATAA
259 CACCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAAGTTCATTAATAA
39457 TTCAAGTTTCAAATGCAAA
324 TTCAAGTTTCAAATGCAAA
* * * *
39476 TTATTCAAACAACATTTTAAGGTATGCGTACCAAAAATTTAGTTCGGCAGTTGATTATGCGTAGG
1 TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAA-TTAGTTCGGAAGTTAATTACGC-TAGG
* *
39541 GAATGATTAGCACCCCCTA-AAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACA
64 AAAGGATTAGCACCCCC-ACAAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACA
* ** * *
39605 ATGAATCTTACATGTTCTAATTTAATTTAATTTAAGATCCCTTTTTAAACACATTCCTTGAATTT
128 ATGAATCCTACAAATTCAAATTTAATTTAATTTAAGATCCCTTTTAAAACACATTCCTTGAATTT
* * *
39670 TAGGACGGAAAACGAAAATATTTAACTATTTCCTATCGAGAAGAAAATGTCTCTCATGCCTTAAA
193 TAGGACGGAAAACGAAAATATTTAACTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAA
*
39735 GCATCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAAGTTCATTAATA
258 GCACCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAAGTTCATTAATA
*
39800 ATTCAAGTTTTAAATGCA
323 ATTCAAGTTTCAAATGCA
39818 TGAAAAATGA
Statistics
Matches: 306, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
342 36 0.12
343 17 0.06
344 246 0.80
345 7 0.02
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (342 bp):
TTATTAAAACAACATTTTAAGGTATGCGTACCAAAAATTAGTTCGGAAGTTAATTACGCTAGGAA
AGGATTAGCACCCCCACAAAGCCCTAAATCGGCACCTAGTCGATTAATTAGTTGTCTCTACAATG
AATCCTACAAATTCAAATTTAATTTAATTTAAGATCCCTTTTAAAACACATTCCTTGAATTTTAG
GACGGAAAACGAAAATATTTAACTATTTCCTATCGAGAAGAAAAAGCCTCTCATGCCGTAAAGCA
CCCATTTCTTAATCCAATCAAAATAAGGAAATATTACTATTCCATTCAAAAGTTCATTAATAATT
CAAGTTTCAAATGCAAA
Found at i:42059 original size:11 final size:12
Alignment explanation
Indices: 42030--42076 Score: 53
Period size: 11 Copynumber: 3.8 Consensus size: 12
42020 AAAGGCCTGT
42030 AATAAAATAGAA
1 AATAAAATAGAA
42042 ACA-AAAATA-AA
1 A-ATAAAATAGAA
42053 AATAAAATAGATA
1 AATAAAATAGA-A
42066 AATAATAATAG
1 AATAA-AATAG
42077 TAGTAGTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
10 1 0.03
11 9 0.30
12 8 0.27
13 7 0.23
14 5 0.17
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.19
Consensus pattern (12 bp):
AATAAAATAGAA
Found at i:47368 original size:32 final size:32
Alignment explanation
Indices: 47308--47400 Score: 93
Period size: 32 Copynumber: 2.9 Consensus size: 32
47298 ATTCACGAGA
* *
47308 GGGA-TTCGCCTGGAATGCATGGCAACACCGTT
1 GGGAGTTCG-CTGGAAAGCATGGCGACACCGTT
*
47340 GGGAG-TCGCTTGGAACAGC-TGGCGACACCTTT
1 GGGAGTTCGC-TGGAA-AGCATGGCGACACCGTT
* *
47372 GGGTGTTGGCTGGAAAGCATGGCGACACC
1 GGGAGTTCGCTGGAAAGCATGGCGACACC
47401 CTTTGGTATC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
31 4 0.08
32 42 0.82
33 5 0.10
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.20
Consensus pattern (32 bp):
GGGAGTTCGCTGGAAAGCATGGCGACACCGTT
Found at i:47418 original size:32 final size:30
Alignment explanation
Indices: 47317--47432 Score: 90
Period size: 32 Copynumber: 3.7 Consensus size: 30
47307 AGGGATTCGC
* * * *
47317 CTGGAATGCATGGCAACACCGTTGGGAGTCG
1 CTGGAAAGCATGGCGACACCTTTGGTA-TCG
* *
47348 CTTGGAACAGC-TGGCGACACCTTTGGGTGTTGG
1 C-TGGAA-AGCATGGCGACACCTTT-GGT-ATCG
47381 CTGGAAAGCATGGCGACACCCTTTGGTATCG
1 CTGGAAAGCATGGCGACA-CCTTTGGTATCG
* *
47412 CATGGAAGGGATGGCGACACC
1 C-TGGAAAGCATGGCGACACC
47433 AATTGTACTG
Statistics
Matches: 68, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
31 9 0.13
32 47 0.69
33 12 0.18
ACGTcount: A:0.22, C:0.23, G:0.34, T:0.21
Consensus pattern (30 bp):
CTGGAAAGCATGGCGACACCTTTGGTATCG
Found at i:49558 original size:31 final size:30
Alignment explanation
Indices: 49504--49610 Score: 169
Period size: 31 Copynumber: 3.5 Consensus size: 30
49494 CTTTTAAAAC
*
49504 TTGCAATATAATCCCCAACATTTAGTCTGT
1 TTGCAATATAGTCCCCAACATTTAGTCTGT
49534 TTGCAATATAGTCCCCTAACATTTAGTCTGT
1 TTGCAATATAGTCCCC-AACATTTAGTCTGT
*
49565 TTGCAATATAGTCCCCCAACATTTAGTCCGT
1 TTGCAATATAGT-CCCCAACATTTAGTCTGT
*
49596 TTGCAATATGGTCCC
1 TTGCAATATAGTCCC
49611 TGACCTAACT
Statistics
Matches: 72, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
30 18 0.25
31 50 0.69
32 4 0.06
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.36
Consensus pattern (30 bp):
TTGCAATATAGTCCCCAACATTTAGTCTGT
Found at i:51536 original size:30 final size:31
Alignment explanation
Indices: 51501--51569 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
51491 TCAGGGACCA
51501 TATTGCAAAC-GACTAAATGTTGG-GAGACTG
1 TATTGCAAACGGACTAAATGTTGGAG-GACTG
*
51531 TATTGCAAACGGACTAAATGTTGGAGGATTG
1 TATTGCAAACGGACTAAATGTTGGAGGACTG
51562 TATTGCAA
1 TATTGCAA
51570 GTTTTAAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 10 0.28
31 25 0.69
32 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (31 bp):
TATTGCAAACGGACTAAATGTTGGAGGACTG
Found at i:53236 original size:17 final size:18
Alignment explanation
Indices: 53201--53241 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
53191 ATTTATTTTT
53201 AAAAATTATTAAAAAATA
1 AAAAATTATTAAAAAATA
* *
53219 ATAAATTA-TAAAATATA
1 AAAAATTATTAAAAAATA
53236 AAAAAT
1 AAAAAT
53242 ATTTCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATTATTAAAAAATA
Found at i:54772 original size:3 final size:3
Alignment explanation
Indices: 54764--54846 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
54754 CTCAGTACCT
54764 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
54812 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
54847 GATGCTTGGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:54923 original size:32 final size:32
Alignment explanation
Indices: 54881--54947 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
54871 AGCACTGGCT
54881 CTACACTAGATTATGCTCTTTACTTGTGGCCA
1 CTACACTAGATTATGCTCTTTACTTGTGGCCA
*
54913 CTACATTAGATTATGCTCTTTACTTGTGGCCA
1 CTACACTAGATTATGCTCTTTACTTGTGGCCA
54945 CTA
1 CTA
54948 TTCATACATG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (32 bp):
CTACACTAGATTATGCTCTTTACTTGTGGCCA
Found at i:55389 original size:16 final size:17
Alignment explanation
Indices: 55359--55390 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55349 ATATTTATTT
55359 ATATAAAATATAATATA
1 ATATAAAATATAATATA
55376 ATATAAAA-ATAATAT
1 ATATAAAATATAATAT
55391 TGAGATCTCG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
ATATAAAATATAATATA
Found at i:55480 original size:17 final size:17
Alignment explanation
Indices: 55460--55492 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
55450 AAAAATTAAA
55460 AAATATTTTA-AATAATT
1 AAAT-TTTTACAATAATT
55477 AAATTTTTACAATAAT
1 AAATTTTTACAATAAT
55493 ATCATTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATTTTTACAATAATT
Found at i:55554 original size:16 final size:16
Alignment explanation
Indices: 55509--55555 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
55499 TATCACCTCA
55509 TAAAATTATAAAATGAT
1 TAAAATTATAAAAT-AT
* *
55526 TAATA-TATTAAATAT
1 TAAAATTATAAAATAT
55541 TAAAATTATAAAATA
1 TAAAATTATAAAATA
55556 ATTTTAACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (16 bp):
TAAAATTATAAAATAT
Done.