Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007766.1 Hibiscus syriacus cultivar Beakdansim tig00110038_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: 442891
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:395209 original size:553 final size:551
Alignment explanation
Indices: 394159--395246 Score: 1743
Period size: 553 Copynumber: 2.0 Consensus size: 551
394149 CAGAAAATTA
* * * *
394159 ATCCCCAGCGGCTAGAAGCGATCACAAACTCTTTCCAACATATAAAAACAAGTTGAGGACACTTG
1 ATCCCCAACGGCTAGAAACGACCACAAACTCATTCCAACATATAAAAACAAGTTGAGGACACTTG
* *
394224 AAGAATGATTTGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATTTATTTCCCT
66 AAGAAGGATTAGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATTTATTTCCCT
*
394289 TTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGTTTTTGTGAGCTA
131 TTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGCTTTTGTGAGCTA
* * *
394354 AATTTTTGTAAACACCGTCCTTTAAGAGGTTTTCTTTTTTACATCTTTCAACATTTGTAAAATAG
196 AATTTTTGTAAACACCGTCCTTTAAGAGGTTTCCTTGTTTACATCTTTCAACATTTGTAAAAGAG
*
394419 GATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTCTTGATCTTGTAAA
261 GATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTATTGATCTTGTAAA
*
394484 AAGAAAGAACAAATTAGTAAATTTGTTAGAAAATCTTAGTGGGGAGCTAAGGTAGTGGATGTAGA
326 AAGAAAGAACAAATTAGTAAATTTGTTAGAAAATCTTAGTGAGGAGCTAAGGTAGTGGATGTAGA
394549 CTTTGTTGAGAAGTCAAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCCTCAC
391 CTTTGTTGAGAAGTCAAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCCTCAC
* *
394614 TCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGGCAAATTATTCAG-TTTTTCAATT-GAGCT
456 TCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGACAAATTATT-AGATTGTTCAATTAG-GCT
394677 TCATCGATAATCCCAACCCAATGGCTCCAAAAC
519 TCATCGATAATCCCAACCCAATGGCTCCAAAAC
* *
394710 ATCCCCAACGGCTAGAAACGGCCACAAACTCATTCCAACATATAAAAACAAGTTGATGACACTTG
1 ATCCCCAACGGCTAGAAACGACCACAAACTCATTCCAACATATAAAAACAAGTTGAGGACACTTG
* * * * * *
394775 AATAAGGATTAGAGCACCTATCCAAGCAATCAAACACAGGATAAGAGCTTTTCATTCTAATTTTC
66 AAGAAGGATTAGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATT-T-ATTTCC
* **
394840 CTTTGTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCCTTATGTTTTGCTTTTGTGAGC
129 CTTTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGCTTTTGTGAGC
* * * *
394905 TAAATTTTTGTAAACACCTTCCTTTAAGAGGTTTCCTTGTTTACATCTTTGAACCTTTGTAACAG
194 TAAATTTTTGTAAACACCGTCCTTTAAGAGGTTTCCTTGTTTACATCTTTCAACATTTGTAAAAG
* *
394970 GGGATTGGTTCTAGCTTAGCCTGTGAAAAGCTAGGGAGTTGTAAAGGTTATCTATTGATCTTGTA
259 AGGATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTATTGATCTTGTA
*
395035 AAAA-AAAGAACAAATTAGTGAATTTGTTAGAAAATCCTTAGTGAGGAGCTAAGGTAGTGGATGT
324 AAAAGAAAGAACAAATTAGTAAATTTGTTAGAAAAT-CTTAGTGAGGAGCTAAGGTAGTGGATGT
* * *
395099 AGAC-TTGATTGAGAAGTCGAACCACTATAAATCCTTGTGCAAATTATCTATCTTTTTATACTCC
388 AGACTTTG-TTGAGAAGTCAAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCC
* * * *
395163 TTACTCCCTAAACTTAAAAAGTCAATTCACCCCCTCTTGACAAATTATTTGATTGTTCAATTAGG
452 TCACTCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGACAAATTATTAGATTGTTCAATTAGG
395228 CTTCATCGATAATCCCAAC
517 CTTCATCGATAATCCCAAC
395247 ATAATGTTAT
Statistics
Matches: 492, Mismatches: 39, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
551 108 0.22
552 35 0.07
553 348 0.71
554 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (551 bp):
ATCCCCAACGGCTAGAAACGACCACAAACTCATTCCAACATATAAAAACAAGTTGAGGACACTTG
AAGAAGGATTAGAACACCTATCAAAGCAATCAAACACAAGAGAAGAGCTTTTCATTTATTTCCCT
TTCTCTTGTAAATATTTGTGTTTTGAGCTTAATTGTATATCAATATGTTTTGCTTTTGTGAGCTA
AATTTTTGTAAACACCGTCCTTTAAGAGGTTTCCTTGTTTACATCTTTCAACATTTGTAAAAGAG
GATTGGTTCTAGCTTAGCCTGTGAAAAGCTAAGGAGTTGTAAAGGTTATCTATTGATCTTGTAAA
AAGAAAGAACAAATTAGTAAATTTGTTAGAAAATCTTAGTGAGGAGCTAAGGTAGTGGATGTAGA
CTTTGTTGAGAAGTCAAACCACTATAAAACCTTGTGCAAACTATCTATCTTTTTATACTCCTCAC
TCCCTAAACTCAAAAAGCCAATTCACCCCCTCTTGACAAATTATTAGATTGTTCAATTAGGCTTC
ATCGATAATCCCAACCCAATGGCTCCAAAAC
Found at i:398968 original size:18 final size:18
Alignment explanation
Indices: 398925--398962 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
398915 GTGAAGTATG
*
398925 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
398943 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
398961 AA
1 AA
398963 GTGTGTAACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:404376 original size:26 final size:26
Alignment explanation
Indices: 404340--404392 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
404330 AGTAAGCCTC
404340 GGGATCCGTCTTGCCTTGGAATGGTG
1 GGGATCCGTCTTGCCTTGGAATGGTG
404366 GGGATCCGTCTTGCCTTGGAATGGTG
1 GGGATCCGTCTTGCCTTGGAATGGTG
404392 G
1 G
404393 AATAGAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.11, C:0.19, G:0.40, T:0.30
Consensus pattern (26 bp):
GGGATCCGTCTTGCCTTGGAATGGTG
Found at i:408168 original size:20 final size:22
Alignment explanation
Indices: 408145--408193 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
408135 AATTTAGTAC
408145 TTAAATTATAAGT-TTT-ATTT
1 TTAAATTATAAGTATTTAATTT
*
408165 TT-AATT-TAATTATTTAATTT
1 TTAAATTATAAGTATTTAATTT
408185 TTAAATTAT
1 TTAAATTAT
408194 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 8 0.33
21 4 0.17
22 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (22 bp):
TTAAATTATAAGTATTTAATTT
Found at i:408203 original size:16 final size:16
Alignment explanation
Indices: 408167--408204 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
408157 TTTTATTTTT
408167 AATTT-AATTATTTAA
1 AATTTAAATTATTTAA
**
408182 TTTTTAAATTATTTAA
1 AATTTAAATTATTTAA
408198 AATTTAA
1 AATTTAA
408205 TCACTTTAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
15 3 0.17
16 15 0.83
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTTAAATTATTTAA
Found at i:414310 original size:3 final size:3
Alignment explanation
Indices: 414302--414327 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
414292 CCTCCTATGA
414302 GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GT
414328 AAGATCCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:414835 original size:18 final size:18
Alignment explanation
Indices: 414808--414842 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
414798 ATATACAAAT
* *
414808 TAAAATATAAATTAATAC
1 TAAAAAATAAATAAATAC
414826 TAAAAAATAAATAAATA
1 TAAAAAATAAATAAATA
414843 ATTCACAATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAAAAATAAATAAATAC
Found at i:415883 original size:26 final size:29
Alignment explanation
Indices: 415854--415908 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
415844 ATATTTTATT
*
415854 AATTTAAT-TT-TAATCTGAAT-ATAATA
1 AATTTAATCTTATAATCTAAATAATAATA
415880 AATTTAATCTTATAATCTAAATAATAATA
1 AATTTAATCTTATAATCTAAATAATAATA
415909 TACCATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
27 2 0.08
28 9 0.36
29 6 0.24
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (29 bp):
AATTTAATCTTATAATCTAAATAATAATA
Found at i:416151 original size:14 final size:13
Alignment explanation
Indices: 416134--416172 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
416124 ACTTATAGTG
416134 TTTAAAAAGATATT
1 TTTAAAAA-ATATT
*
416148 TTTAAATAATATT
1 TTTAAAAAATATT
416161 TTT-AAAAATATT
1 TTTAAAAAATATT
416173 AAAATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 8 0.35
13 8 0.35
14 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:416170 original size:12 final size:12
Alignment explanation
Indices: 416138--416172 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
416128 ATAGTGTTTA
416138 AAAAGATATTTTT
1 AAAA-ATATTTTT
416151 AAATAATATTTTT
1 AAA-AATATTTTT
416164 AAAAATATT
1 AAAAATATT
416173 AAAATATAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.29
13 14 0.67
14 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (12 bp):
AAAAATATTTTT
Found at i:416454 original size:17 final size:18
Alignment explanation
Indices: 416426--416461 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
416416 CACCCACGGG
416426 TCCCTATCCTTTTAAATT
1 TCCCTATCCTTTTAAATT
*
416444 TCCCT-TCCTTTTTAATT
1 TCCCTATCCTTTTAAATT
416461 T
1 T
416462 TATTTGGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (18 bp):
TCCCTATCCTTTTAAATT
Found at i:416799 original size:32 final size:32
Alignment explanation
Indices: 416670--416802 Score: 108
Period size: 32 Copynumber: 4.2 Consensus size: 32
416660 ACATTTCATG
* *
416670 TCATCATTTTTGATTACATGACACATG-CTACA
1 TCATCATTTTTGGTGACATGACACATGTC-ACA
* **
416702 TCATCA-TTTTGGTGACATAACACATGTCATG
1 TCATCATTTTTGGTGACATGACACATGTCACA
* ** * * **
416733 TCATTATTTTTGGTGATGTGGCATATGTTGCA
1 TCATCATTTTTGGTGACATGACACATGTCACA
* * *
416765 TCATCATTTTTGGTGACGTGACATATGACACA
1 TCATCATTTTTGGTGACATGACACATGTCACA
416797 TCATCA
1 TCATCA
416803 ATTGAACATA
Statistics
Matches: 78, Mismatches: 21, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
31 23 0.29
32 55 0.71
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (32 bp):
TCATCATTTTTGGTGACATGACACATGTCACA
Found at i:417309 original size:32 final size:32
Alignment explanation
Indices: 417271--417341 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 32
417261 GTTATCGTCT
* *
417271 ATCATTTTTGGTGATGTGACATATATTACATC
1 ATCATTTTTGGTGACGTGACATATATCACATC
* *
417303 ATCATTTTTGGTGACGTGACATATGTCACGTC
1 ATCATTTTTGGTGACGTGACATATATCACATC
417335 ATCATTT
1 ATCATTT
417342 GAACATATGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
ATCATTTTTGGTGACGTGACATATATCACATC
Found at i:417755 original size:541 final size:536
Alignment explanation
Indices: 416738--417797 Score: 1529
Period size: 541 Copynumber: 2.0 Consensus size: 536
416728 TCATGTCATT
* * *
416738 ATTTTTGGTGATGTGGCATATGTTGCATCATCATTTTTGGTGACGTGACATATGACACATCATCA
1 ATTTTTGGTGATGTGACATATATTACATCATCATTTTTGGTGACGTGACATATGACACATCATCA
* * * * *
416803 ATTGAACATATATGAAAATGTCACATAAATAACATCGGATACCGTTAGTTAACTAAAAATTTTCA
66 ATTGAACATATATGAAAATATCACATAAATAACATCAGATACCGTTAATCAACTAAAAAATTTCA
* **
416868 TCCAACAAGGTCTGTTTAACCAAAAATTGAAAAGTTAGAGAATAATGCTTTAAAAAAGAGAATAA
131 TCCAACAAGGTATGTTTAACCAAAAATTGAAAAGTTAGAGAATAATGCTCCAAAAAAGAGAATAA
416933 AATGACCATTTGTACAAACATTAAGGGTATTTTTTGTTGTATACTATTTTATTTTCCCCAAACTA
196 AATGACCATTTGTACAAACATTAAGGGTATTTTTTGTTGTATACTATTTTATTTTCCCCAAACTA
* * * * *
416998 AAATAAAATATTCTTTTCCTTTTCTTTTTTCTCTCAAACATGTAGTAACCATATGTCCATCATTA
261 AAAGAAAATATTCTTTTCCTTCTCCTTTTTCTCTCAAACATATAGTAACCATATGGCCATCATTA
*
417063 CTGGTCATCATCGTAGAGGACACCGTGTCAACCATTATCATTAACGATGACCGATGATTTTTGAA
326 CTGGTCATCATCGTAGAGGACACCATGTCAACCATTATCATTAACGATGACCGATGATTTTTGAA
* * * * *
417128 AGACACTATCATCCCCATATCGGTCCCCTAAGTTTGAATCATATATTATTTTATCGATAAATGCT
391 ACACACTATCATCCCCATATCGGTCCCATAAGTTTGAATCATATACTACTTTATCAATAAATGCT
*
417193 TCAATTGACGCATATATGGATTATGACTCATCGAATCCATTATTTCAATCTGCCAACACCCATTA
456 TCAATTGACGCATATATGGATTATGACTCATCGAATCCATTATTTCAATATGCCAACACCCATTA
417258 TTAGTTATCGTCTATC
521 TTAGTTATCGTCTATC
* *
417274 ATTTTTGGTGATGTGACATATATTACATCATCATTTTTGGTGACGTGACATATGTCACGTCATCA
1 ATTTTTGGTGATGTGACATATATTACATCATCATTTTTGGTGACGTGACATATGACACATCATCA
* * * * *
417339 TTTGAACATATGTGAAAATATCGC-TCAATAACATCAGATACTGTTAATCAACTAAAAAATTTCA
66 ATTGAACATATATGAAAATATCACATAAATAACATCAGATACCGTTAATCAACTAAAAAATTTCA
**
417403 TTTAACAAGGTATGTTTAACCAAAAATTGAAAAGTTAGAGAATAATGCTCCAAAAAAGAGAATAA
131 TCCAACAAGGTATGTTTAACCAAAAATTGAAAAGTTAGAGAATAATGCTCCAAAAAAGAGAATAA
* * * *
417468 AATGACCATCATTACTTTTTCTTAAACATTGAGGGTA-TTTTTGTTATTATACTA-TTTATTTTC
196 AATGA-C--CA-T--TTGTAC--AAACATTAAGGGTATTTTTTGTT-GTATACTATTTTATTTTC
* * * * *
417531 CCCAAAGTAAAAGAAAGTCTTCTTTTCC-TCTCCTTTTTCTCTTAAACATATAGTTACCA-ATTG
252 CCCAAACTAAAAGAAAATATTCTTTTCCTTCTCCTTTTTCTCTCAAACATATAGTAACCATA-TG
* * * *
417594 GCCATCATTACTGTTCATCGTCGTAGAGGACACCATGTCAACCATTATCATTGACGATGGCCGAT
316 GCCATCATTACTGGTCATCATCGTAGAGGACACCATGTCAACCATTATCATTAACGATGACCGAT
* *
417659 GATTTTTGAAACACACTAT-AGTCCCCATATCGGTCCCATGAGTTTGAATCATATACTACTTTGT
381 GATTTTTGAAACACACTATCA-TCCCCATATCGGTCCCATAAGTTTGAATCATATACTACTTTAT
* *
417723 CAATAAATGCTTCAATTGACGCATATATGGATTATGACTCATCTACTCCATTATTTCAATATGCC
445 CAATAAATGCTTCAATTGACGCATATATGGATTATGACTCATCGAATCCATTATTTCAATATGCC
*
417788 ACCACCCATT
510 AACACCCATT
417798 GTTGGTTGCC
Statistics
Matches: 463, Mismatches: 50, Indels: 17
0.87 0.09 0.03
Matches are distributed among these distances:
535 99 0.21
536 81 0.17
538 2 0.00
539 1 0.00
540 2 0.00
541 217 0.47
542 41 0.09
543 20 0.04
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.35
Consensus pattern (536 bp):
ATTTTTGGTGATGTGACATATATTACATCATCATTTTTGGTGACGTGACATATGACACATCATCA
ATTGAACATATATGAAAATATCACATAAATAACATCAGATACCGTTAATCAACTAAAAAATTTCA
TCCAACAAGGTATGTTTAACCAAAAATTGAAAAGTTAGAGAATAATGCTCCAAAAAAGAGAATAA
AATGACCATTTGTACAAACATTAAGGGTATTTTTTGTTGTATACTATTTTATTTTCCCCAAACTA
AAAGAAAATATTCTTTTCCTTCTCCTTTTTCTCTCAAACATATAGTAACCATATGGCCATCATTA
CTGGTCATCATCGTAGAGGACACCATGTCAACCATTATCATTAACGATGACCGATGATTTTTGAA
ACACACTATCATCCCCATATCGGTCCCATAAGTTTGAATCATATACTACTTTATCAATAAATGCT
TCAATTGACGCATATATGGATTATGACTCATCGAATCCATTATTTCAATATGCCAACACCCATTA
TTAGTTATCGTCTATC
Found at i:421341 original size:13 final size:13
Alignment explanation
Indices: 421323--421356 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
421313 ATTGGGCAAT
421323 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
421336 TTTGAAAACAAGG
1 TTTGAAAACAAGG
421349 TTTGAAAA
1 TTTGAAAA
421357 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 2 0.10
13 18 0.90
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:421855 original size:23 final size:22
Alignment explanation
Indices: 421829--421890 Score: 81
Period size: 23 Copynumber: 2.8 Consensus size: 22
421819 GTCGATTCCT
421829 AAAGGGGGAATCGATTCCCATTC
1 AAAGGGGGAATCGATTCCC-TTC
* *
421852 AAAGGGGAAATCGGTTCCCTTC
1 AAAGGGGGAATCGATTCCCTTC
*
421874 -AAGGGGGCATCGATTCC
1 AAAGGGGGAATCGATTCC
421891 TCATGCACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 14 0.41
22 3 0.09
23 17 0.50
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (22 bp):
AAAGGGGGAATCGATTCCCTTC
Found at i:425990 original size:20 final size:21
Alignment explanation
Indices: 425951--425991 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
425941 TAGATTATTT
425951 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
425972 TCATTTTT-ATATTTT-AAATA
1 TCATTTTTCA-ATTTTGAAATA
425992 ATTTCTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.34, C:0.07, G:0.02, T:0.56
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:434333 original size:2 final size:2
Alignment explanation
Indices: 434326--434375 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
434316 TAAATTATGA
434326 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
434368 AT -T AT AT A
1 AT AT AT AT A
434376 GATTGGGTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:440640 original size:13 final size:13
Alignment explanation
Indices: 440622--440688 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 13
440612 ATGAATCTTA
*
440622 GATGACGCGCATT
1 GATGACACGCATT
*
440635 GATGACATGCATT
1 GATGACACGCATT
* * *
440648 TATGACTCACATT
1 GATGACACGCATT
* *
440661 CATGACACACATT
1 GATGACACGCATT
* *
440674 TATGACGCGCATT
1 GATGACACGCATT
440687 GA
1 GA
440689 GCGTCATTGA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (13 bp):
GATGACACGCATT
Found at i:440660 original size:26 final size:26
Alignment explanation
Indices: 440623--440688 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
440613 TGAATCTTAG
* **
440623 ATGACGCGCATTGATGACATGCATTT
1 ATGACGCACATTGATGACACACATTT
* *
440649 ATGACTCACATTCATGACACACATTT
1 ATGACGCACATTGATGACACACATTT
*
440675 ATGACGCGCATTGA
1 ATGACGCACATTGA
440689 GCGTCATTGA
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (26 bp):
ATGACGCACATTGATGACACACATTT
Done.