Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006162.1 Hibiscus syriacus cultivar Beakdansim tig00014637_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: 100680
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Found at i:689 original size:2 final size:2
Alignment explanation
Indices: 682--720 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
672 TTTATTTAGT
682 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
721 ATGTGTGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:897 original size:2 final size:2
Alignment explanation
Indices: 892--918 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
882 ATATATACAT
892 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
919 TATATAAAGT
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3290 original size:19 final size:18
Alignment explanation
Indices: 3260--3303 Score: 70
Period size: 19 Copynumber: 2.4 Consensus size: 18
3250 TTGCATTTGC
3260 ATTTTATTTTCGCACTGT
1 ATTTTATTTTCGCACTGT
*
3278 ATTTTACTTTTCGCATTGT
1 ATTTTA-TTTTCGCACTGT
3297 ATTTTAT
1 ATTTTAT
3304 CCATGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.18, C:0.14, G:0.09, T:0.59
Consensus pattern (18 bp):
ATTTTATTTTCGCACTGT
Found at i:7002 original size:16 final size:16
Alignment explanation
Indices: 6981--7015 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
6971 GATTCTCATG
6981 TATGTGTATATATATA
1 TATGTGTATATATATA
* *
6997 TATGTGTGTGTATATA
1 TATGTGTATATATATA
7013 TAT
1 TAT
7016 ATATATCCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (16 bp):
TATGTGTATATATATA
Found at i:7006 original size:20 final size:20
Alignment explanation
Indices: 6978--7019 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
6968 ATAGATTCTC
6978 ATGTATGTGTATATATATAT
1 ATGTATGTGTATATATATAT
*
6998 ATGTGTGTGTATATATATAT
1 ATGTATGTGTATATATATAT
7018 AT
1 AT
7020 ATCCTCTCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (20 bp):
ATGTATGTGTATATATATAT
Found at i:10307 original size:24 final size:25
Alignment explanation
Indices: 10280--10329 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
10270 AGAATAAGAG
*
10280 AAAGAACAAAA-AGGGAAAAAATAA
1 AAAGAACAAAATAGAGAAAAAATAA
* *
10304 AAAGAAGAAAATAGAGTAAAAATAA
1 AAAGAACAAAATAGAGAAAAAATAA
10329 A
1 A
10330 TAAAAGGGGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (25 bp):
AAAGAACAAAATAGAGAAAAAATAA
Found at i:12164 original size:2 final size:2
Alignment explanation
Indices: 12157--12189 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
12147 TTTTATTTTC
12157 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12190 CTAGTTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12529 original size:2 final size:2
Alignment explanation
Indices: 12524--12551 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12514 ACACACACAC
12524 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
12552 GCCTAAGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15811 original size:11 final size:11
Alignment explanation
Indices: 15795--15821 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
15785 AAAGGTGGCA
15795 GAGTTTCATAG
1 GAGTTTCATAG
15806 GAGTTTCATAG
1 GAGTTTCATAG
15817 GAGTT
1 GAGTT
15822 GGTGTTGGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.37
Consensus pattern (11 bp):
GAGTTTCATAG
Found at i:17696 original size:18 final size:18
Alignment explanation
Indices: 17673--17716 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
17663 GAATTGTTTT
*
17673 TAAAATAAAAGAT-TAGAA
1 TAAAATAAAAGATAAAG-A
17691 TAAAATAAAAGATAAAGA
1 TAAAATAAAAGATAAAGA
17709 TAAAATAA
1 TAAAATAA
17717 TTAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 22 0.92
19 2 0.08
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.20
Consensus pattern (18 bp):
TAAAATAAAAGATAAAGA
Found at i:17729 original size:44 final size:44
Alignment explanation
Indices: 17675--17769 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
17665 ATTGTTTTTA
* *
17675 AAATAAAAGATTAGAATAAAATAAAAGATAAAGATAAAATAATT
1 AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAATAAAT
* ** *
17719 AAATAAAAGATAAGGATGCAATAAAAGATAAGGATAAAATAAAT
1 AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAATAAAT
17763 AAATAAA
1 AAATAAA
17770 TTCAAAGTAA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.67, C:0.01, G:0.12, T:0.20
Consensus pattern (44 bp):
AAATAAAAGATAAGAATAAAATAAAAGATAAAGATAAAATAAAT
Found at i:17759 original size:18 final size:18
Alignment explanation
Indices: 17719--17761 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
17709 TAAAATAATT
*
17719 AAATAAAAGATAAGGATG
1 AAATAAAAGATAAGGATA
*
17737 CAATAAAAGATAAGGATA
1 AAATAAAAGATAAGGATA
17755 AAATAAA
1 AAATAAA
17762 TAAATAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.65, C:0.02, G:0.16, T:0.16
Consensus pattern (18 bp):
AAATAAAAGATAAGGATA
Found at i:18558 original size:19 final size:20
Alignment explanation
Indices: 18521--18560 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
18511 AAAAACAAGG
*
18521 AAAATATAATTTCTAAAAAT
1 AAAAGATAATTTCTAAAAAT
*
18541 AAAAGATAA-TTCTTAAAAT
1 AAAAGATAATTTCTAAAAAT
18560 A
1 A
18561 TTTAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.33
Consensus pattern (20 bp):
AAAAGATAATTTCTAAAAAT
Found at i:21499 original size:17 final size:17
Alignment explanation
Indices: 21447--21499 Score: 52
Period size: 21 Copynumber: 2.8 Consensus size: 17
21437 ACGATCATTC
*
21447 AAATGAAAAATATATTTT
1 AAAT-AAAAATTTATTTT
21465 AAATAAAATTATAATTATTTT
1 AAATAAAA--AT--TTATTTT
21486 AAATAAAAATTTAT
1 AAATAAAAATTTAT
21500 ATTCATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
17 8 0.27
18 4 0.13
19 4 0.13
21 14 0.47
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
AAATAAAAATTTATTTT
Found at i:30498 original size:3 final size:3
Alignment explanation
Indices: 30490--30531 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
30480 ACATTTTTAA
*
30490 TAT TAT TAT TAT TAAT TAT AAT TATT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT T
30532 TTCAGGCTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:30513 original size:10 final size:10
Alignment explanation
Indices: 30490--30531 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
30480 ACATTTTTAA
30490 TATT-ATTAT
1 TATTAATTAT
30499 TATTAATTAT
1 TATTAATTAT
* *
30509 AATTATTTAT
1 TATTAATTAT
30519 TATT-ATTAT
1 TATTAATTAT
30528 TATT
1 TATT
30532 TTCAGGCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
TATTAATTAT
Found at i:30513 original size:13 final size:13
Alignment explanation
Indices: 30491--30529 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
30481 CATTTTTAAT
30491 ATTATTATTATTA
1 ATTATTATTATTA
* *
30504 ATTATAATTATTT
1 ATTATTATTATTA
30517 ATTATTATTATTA
1 ATTATTATTATTA
30530 TTTTCAGGCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTATTATTATTA
Found at i:30954 original size:13 final size:13
Alignment explanation
Indices: 30920--30954 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
30910 ATTGTTGTTG
*
30920 TTATTATTAATTA
1 TTATTATTTATTA
*
30933 TAATTATTTATTA
1 TTATTATTTATTA
30946 TTATTATTT
1 TTATTATTT
30955 TCAGGCTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATTTATTA
Found at i:31168 original size:422 final size:412
Alignment explanation
Indices: 30388--31226 Score: 1356
Period size: 422 Copynumber: 2.0 Consensus size: 412
30378 AAGATATTTT
*
30388 AAATACAAAATACAATATAAATAATAAAAGTTCATCCTCTTGAAATACTTCTATAAATATTATAT
1 AAATACAAAATACAATATAAATAAGAAAAGTTCATCCTCTTGAAATACTTCTATAAATATTATAT
*
30453 TCATTGTCGACACCCGTTTTCGTATAGACATTTTTAATATTATTATTATTAATTATAATTATTTA
66 TCATTGTCGACACCCATTTTCGTATAGACATTTTTAATATTATTATTATTAATTATAATTATTTA
* *
30518 TTATTATTATTATTTTCAGGCTTTACAAACCTAAATTGGGCCCAGTTACAACTCAACACCCGGGC
131 TTATTATTATTATTTTCAGGCTTTACAAACCCAAATTGGGCCCAGTTACAACTCAACACCCGAGC
30583 CCAGCTACTAAGTGACCTAACCGGCCCGGAACCCGAAGCCCAAACCCAAGCCCAATGCTAACACT
196 CCAGCTACTAAGTGACCTAACCGGCCCGGAACCCGAAGCCCAAACCCAAGCCCAATGCTAACACT
* * * * *
30648 GATCATTTAGGGTTTTTAAACCCTAGTCGTCGCCGCCACCAGAGCCAAGAACTATCATCGCCTTG
261 AATCATTTAGGGTTTTTAAACCCTAGTCATAGCCGCCACCAGAGCCAAGAACTATCACCGCCCTG
* *
30713 GCTACCTGACAGCCGTCGTATGATCGTCAATGTCATCATCTCTCTGCCAAGATCCAAATCAACAT
326 GCTACCTGACAGCCGTCGTATGATCGCCAATGTCATCATCTCTCTGCCAAGACCCAAATCAACAT
30778 GCAATTAAGCAAAAACAGGATAA
391 GCAATTAAGC-AAAACAGGATAA
30801 AAATACAAAATACAATATAAATAAGAAAAGTTCATCCTCTTGAAATACTTCTATAAATATTATAT
1 AAATACAAAATACAATATAAATAAGAAAAGTTCATCCTCTTGAAATACTTCTATAAATATTATAT
* * * *
30866 TCATTGTCGACACCCATTTTCGTATCGACGTTTTTAATATTATTATTGTTGTTGTTATTATTAAT
66 TCATTGTCGACACCCATTTTCGTATAGACATTTTTAATATTATTA---TT-AT-TAATTA-TAAT
30931 TATAATTATTTATTATTATTATTTTCAGGCTTTACAAACCCAAATTGGGCCCAGTTACAACTCAA
125 TAT--TTA-TTATTATTATTATTTTCAGGCTTTACAAACCCAAATTGGGCCCAGTTACAACTCAA
* *
30996 CACCCGAGCCCAGCTACTAAGTGACCTAACCGGCCCGGAACCCGAAGCGCAAACCCAGGCCCAAT
187 CACCCGAGCCCAGCTACTAAGTGACCTAACCGGCCCGGAACCCGAAGCCCAAACCCAAGCCCAAT
* * * *
31061 GCTAACTCTAATCATTTAGGGTTTTTAAACCCTAGTCATAGCCGCCACTAGATCCAAGAACTGTC
252 GCTAACACTAATCATTTAGGGTTTTTAAACCCTAGTCATAGCCGCCACCAGAGCCAAGAACTATC
* *
31126 GCCGCCCCT-GCTACCTGACAGTCGTCGTATGATCGCCAATGTCATCATCTCTCTGCCAAGACCC
317 ACCG-CCCTGGCTACCTGACAGCCGTCGTATGATCGCCAATGTCATCATCTCTCTGCCAAGACCC
*
31190 AAATCAACATGCAATTAAGCAAAAGAGGATAA
381 AAATCAACATGCAATTAAGCAAAACAGGATAA
31222 AAATA
1 AAATA
31227 AACCCCAAAA
Statistics
Matches: 392, Mismatches: 24, Indels: 12
0.92 0.06 0.03
Matches are distributed among these distances:
413 106 0.27
416 2 0.01
417 1 0.00
418 5 0.01
419 7 0.02
421 19 0.05
422 249 0.64
423 3 0.01
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (412 bp):
AAATACAAAATACAATATAAATAAGAAAAGTTCATCCTCTTGAAATACTTCTATAAATATTATAT
TCATTGTCGACACCCATTTTCGTATAGACATTTTTAATATTATTATTATTAATTATAATTATTTA
TTATTATTATTATTTTCAGGCTTTACAAACCCAAATTGGGCCCAGTTACAACTCAACACCCGAGC
CCAGCTACTAAGTGACCTAACCGGCCCGGAACCCGAAGCCCAAACCCAAGCCCAATGCTAACACT
AATCATTTAGGGTTTTTAAACCCTAGTCATAGCCGCCACCAGAGCCAAGAACTATCACCGCCCTG
GCTACCTGACAGCCGTCGTATGATCGCCAATGTCATCATCTCTCTGCCAAGACCCAAATCAACAT
GCAATTAAGCAAAACAGGATAA
Found at i:33284 original size:131 final size:131
Alignment explanation
Indices: 33130--33497 Score: 515
Period size: 131 Copynumber: 2.8 Consensus size: 131
33120 TCGACATTGA
* * * * * *
33130 AAATAGTAATATTTTTTCATTTCGGTTGGAGTAATAAATGAATACTTTAAGGCATGAGATGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* * * *
33195 TTATTCTCGATTGGAAATAATTAGATATTACCATTTTCTCTCGAATCAATATTGATTTTTAAGAC
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCAAATCAATATTAAATTTTAAGAC
33260 G
131 G
* * * ** * *
33261 TAATAGTGATATCTCTTCATTTCGATTGAAGTAATAGATGGTTGCTTTAAGGCATGAAAGGTAAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
* * *
33326 TTATTCTCTATTGGATATCATTAGATATTATCATTTT-TACTCAAATCAATATTAAATTTTAAGA
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCT-CTCAAATCAATATTAAATTTTAAGA
33390 CG
130 CG
*
33392 AAATAGTGATATCTCTTAATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
*
33457 TTATTCTCGATTGGAAATAATTAG-TATTATCGTTTTCTCTC
66 TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTC
33498 TTAGAATTAT
Statistics
Matches: 203, Mismatches: 32, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
130 15 0.07
131 188 0.93
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (131 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCAT
TTATTCTCGATTGGAAATAATTAGATATTATCATTTTCTCTCAAATCAATATTAAATTTTAAGAC
G
Found at i:35257 original size:15 final size:15
Alignment explanation
Indices: 35234--35269 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
35224 ACTAAACTAC
*
35234 ATGCTATACAATGCA
1 ATGCAATACAATGCA
35249 ATGCAATACAATGCA
1 ATGCAATACAATGCA
35264 ATGCAA
1 ATGCAA
35270 GGTACCTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.22
Consensus pattern (15 bp):
ATGCAATACAATGCA
Found at i:37065 original size:5 final size:5
Alignment explanation
Indices: 37055--37079 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
37045 ATAACTGAGT
37055 ATAAA ATAAA ATAAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA
37080 CATTTATATT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:40904 original size:41 final size:40
Alignment explanation
Indices: 40859--40946 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 40
40849 GCCTCGGGTC
* * * *
40859 GGGTTTAGGTTTAATTTGTTTAGGTTGTGTGGGTTCTGGTT
1 GGGTTTAGATTTAATTAGGTT-GGATGTGTGGGTTCTGGTT
* *
40900 GGGTTTTAGATTTAGTTAGGTTGGATGTTTGGGTTCTGGTT
1 GGG-TTTAGATTTAATTAGGTTGGATGTGTGGGTTCTGGTT
40941 GGGTTT
1 GGGTTT
40947 TAGGATTAGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
40 3 0.08
41 23 0.57
42 14 0.35
ACGTcount: A:0.10, C:0.02, G:0.38, T:0.50
Consensus pattern (40 bp):
GGGTTTAGATTTAATTAGGTTGGATGTGTGGGTTCTGGTT
Found at i:40920 original size:37 final size:39
Alignment explanation
Indices: 40878--40964 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 39
40868 TTTAATTTGT
40878 TTAGGTTG-TG-TGGGTTCTGGTTGGGTTTTA-GATTTAG
1 TTAGGTTGATGTTGGGTTCTGGTTGGGTTTTAGGA-TTAG
40915 TTAGGTTGGATGTTTGGGTTCTGGTTGGGTTTTAGGATTAG
1 TTAGGTT-GATG-TTGGGTTCTGGTTGGGTTTTAGGATTAG
*
40956 TTGGGTTGA
1 TTAGGTTGA
40965 AAAATGGTGA
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
37 7 0.16
38 1 0.02
39 2 0.05
40 2 0.05
41 30 0.68
42 2 0.05
ACGTcount: A:0.11, C:0.02, G:0.39, T:0.47
Consensus pattern (39 bp):
TTAGGTTGATGTTGGGTTCTGGTTGGGTTTTAGGATTAG
Found at i:67114 original size:17 final size:16
Alignment explanation
Indices: 67091--67133 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
67081 ATAAATAATA
*
67091 ATTTTATTTTTCCTTT
1 ATTTTATTTTTACTTT
*
67107 ATTTTTATTTTTATTTT
1 A-TTTTATTTTTACTTT
67124 ATTTTATTTT
1 ATTTTATTTT
67134 GTAGATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTATTTTTACTTT
Found at i:72368 original size:39 final size:38
Alignment explanation
Indices: 72314--72446 Score: 203
Period size: 39 Copynumber: 3.4 Consensus size: 38
72304 CATAAGGACT
*
72314 TGCAGTAAGGACTTACCCTGTGCACAAAGCAGAGGAGCC
1 TGCAGTAAGGACTTACCCTGAGCACAAAGC-GAGGAGCC
72353 TGCAGTAAGGACTTACCCTGAGCACAAAGTCGAGGAGCC
1 TGCAGTAAGGACTTACCCTGAGCACAAAG-CGAGGAGCC
**
72392 TGTGGTAAGGACTTACCCTGAGCACAAAGCTGAGGAGCC
1 TGCAGTAAGGACTTACCCTGAGCACAAAGC-GAGGAGCC
*
72431 TGCGGTAAGGACTTAC
1 TGCAGTAAGGACTTAC
72447 AAGTCATAGA
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
38 1 0.01
39 86 0.98
40 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.17
Consensus pattern (38 bp):
TGCAGTAAGGACTTACCCTGAGCACAAAGCGAGGAGCC
Found at i:74475 original size:27 final size:27
Alignment explanation
Indices: 74437--74491 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
74427 GACTAATAAA
74437 ACCGTGAATTTTCTCCTTCTATGGTTT
1 ACCGTGAATTTTCTCCTTCTATGGTTT
74464 ACCGTGAATTTTCTCCTTCTATGGTTT
1 ACCGTGAATTTTCTCCTTCTATGGTTT
74491 A
1 A
74492 GGATTAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.16, C:0.22, G:0.15, T:0.47
Consensus pattern (27 bp):
ACCGTGAATTTTCTCCTTCTATGGTTT
Found at i:77260 original size:42 final size:42
Alignment explanation
Indices: 77206--77312 Score: 160
Period size: 42 Copynumber: 2.5 Consensus size: 42
77196 CCCTAAAATC
* *
77206 TTCATGTAATTCGTTTTCCGGAAAATGTTTTCCCGTGTTTGT
1 TTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGT
*
77248 TTCACGTAATTCGTTTTCCAGAAAATATTTTCCCGTGTTTGT
1 TTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGT
* * *
77290 TTTACGTAATTCATTTTCTGGAA
1 TTCACGTAATTCGTTTTCCGGAA
77313 TGTAATTCAT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 58 1.00
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.47
Consensus pattern (42 bp):
TTCACGTAATTCGTTTTCCGGAAAATATTTTCCCGTGTTTGT
Found at i:77525 original size:12 final size:12
Alignment explanation
Indices: 77486--77539 Score: 56
Period size: 12 Copynumber: 4.5 Consensus size: 12
77476 TTTTCATCAA
77486 AATATTATTTATT
1 AATA-TATTTATT
* *
77499 AAAATATTTA-A
1 AATATATTTATT
77510 AATATATTTATT
1 AATATATTTATT
* *
77522 AATATTTTTAAT
1 AATATATTTATT
77534 AATATA
1 AATATA
77540 ATATTATATT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
11 9 0.27
12 21 0.64
13 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
AATATATTTATT
Found at i:77542 original size:29 final size:27
Alignment explanation
Indices: 77510--77682 Score: 86
Period size: 29 Copynumber: 6.0 Consensus size: 27
77500 AAATATTTAA
77510 AATATATTTATTAATATTTTTAATAATAT
1 AATATATTTATT-ATA-TTTTAATAATAT
* * *
77539 AATATTATATTTTTA-ATATTATATAAAAT
1 AATA-TAT-TTATTATATTTTA-ATAATAT
* *
77568 AATCA-ATTATATTATA-ATAATATAATAT
1 AAT-ATATT-TATTATATTTTA-ATAATAT
* *
77596 AAGATATTATATTTTTATTTTAATAATAT
1 AATATATT-TA-TTATATTTTAATAATAT
*
77625 -ATAATAATTTTTTATATATTTAATAATGAAT
1 AAT-AT-ATTTATTATAT-TTTAATAAT--AT
*
77656 AATATTATTTA-TATATTTAAATAATAT
1 AATA-TATTTATTATATTTTAATAATAT
77683 TTTAGTAAAG
Statistics
Matches: 113, Mismatches: 15, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
27 4 0.04
28 34 0.30
29 46 0.41
30 15 0.13
31 11 0.10
32 3 0.03
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (27 bp):
AATATATTTATTATATTTTAATAATAT
Found at i:77548 original size:22 final size:24
Alignment explanation
Indices: 77486--77563 Score: 81
Period size: 23 Copynumber: 3.3 Consensus size: 24
77476 TTTTCATCAA
* * *
77486 AATATTATTTATTAAAATATTTAA-
1 AATA-TATATATTAATATTTTTAAT
*
77510 AATATATTTATTAATATTTTTAAT
1 AATATATATATTAATATTTTTAAT
77534 AATATA-ATATT-ATATTTTTAAT
1 AATATATATATTAATATTTTTAAT
*
77556 ATTATATA
1 AATATATA
77564 AAATAATCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
22 16 0.33
23 22 0.46
24 10 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATATATATTAATATTTTTAAT
Found at i:77636 original size:26 final size:28
Alignment explanation
Indices: 77589--77682 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 28
77579 TTATAATAAT
*
77589 ATAATATA-AGATATTATATTTTTAT-TTTA
1 ATAATATATA-ATATT-T-TTTATATATTTA
77618 ATAATATATAATAATTTTTTATATATTTA
1 ATAATATATAAT-ATTTTTTATATATTTA
*
77647 ATAATGA-ATAATATTATTTATATATTTAA
1 ATAAT-ATATAATATTTTTTATATATTT-A
77676 ATAATAT
1 ATAATAT
77683 TTTAGTAAAG
Statistics
Matches: 57, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
28 21 0.37
29 31 0.54
30 5 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
ATAATATATAATATTTTTTATATATTTA
Found at i:77810 original size:90 final size:86
Alignment explanation
Indices: 77698--77867 Score: 200
Period size: 90 Copynumber: 1.9 Consensus size: 86
77688 TAAAGATATT
* * * * * *
77698 TAAAATATACTAATTAATATTTTTA-AAATATAA-TATAACACTATTACTTTAATAAATAATTAA
1 TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATA-TTTAAT-AATAAATAA
77761 TATAATTTATAATATTTTATTTCAC
64 -ATAATTT-TAATATTTTATTTCAC
*
77786 TAAAATATAACAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTAATAATAAATAA
1 TAAAATAT-ACAA-ATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAA
*
77851 ATTATTTTAATATTTTA
64 ATAATTTTAATATTTTA
77868 AAATAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
88 18 0.26
89 9 0.13
90 21 0.30
91 12 0.17
92 10 0.14
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (86 bp):
TAAAATATACAAATTAATATTTTTATAAATAAAATTATAAAAATAATATTTAATAATAAATAAAT
AATTTTAATATTTTATTTCAC
Found at i:78058 original size:15 final size:15
Alignment explanation
Indices: 78034--78105 Score: 85
Period size: 15 Copynumber: 4.9 Consensus size: 15
78024 ATAATTCATT
78034 TTCCAG-AATTTC-AA
1 TTCCAGTAA-TTCAAA
**
78048 TTCCAGTAATTCATT
1 TTCCAGTAATTCAAA
*
78063 TTCCATTAATTCAAA
1 TTCCAGTAATTCAAA
78078 TTCCAGTAATTCAAA
1 TTCCAGTAATTCAAA
*
78093 TTACAGTAATTCA
1 TTCCAGTAATTCA
78106 TTTTCCGGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
14 9 0.18
15 40 0.82
ACGTcount: A:0.36, C:0.19, G:0.06, T:0.39
Consensus pattern (15 bp):
TTCCAGTAATTCAAA
Found at i:78058 original size:29 final size:30
Alignment explanation
Indices: 78025--78090 Score: 100
Period size: 29 Copynumber: 2.2 Consensus size: 30
78015 TCCAGAAATA
78025 TAATTCATTTTCCA-GAATTTC-AATTCCAG
1 TAATTCATTTTCCATGAA-TTCAAATTCCAG
*
78054 TAATTCATTTTCCATTAATTCAAATTCCAG
1 TAATTCATTTTCCATGAATTCAAATTCCAG
78084 TAATTCA
1 TAATTCA
78091 AATTACAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.42
Consensus pattern (30 bp):
TAATTCATTTTCCATGAATTCAAATTCCAG
Found at i:78813 original size:8 final size:7
Alignment explanation
Indices: 78794--78826 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
78784 TTGTATAATC
78794 TAAAAAT
1 TAAAAAT
78801 TAAAAAT
1 TAAAAAT
78808 TAAAAA-
1 TAAAAAT
78814 TAAAAAT
1 TAAAAAT
78821 ATAAAA
1 -TAAAA
78827 TTACAACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.25
7 13 0.54
8 5 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
TAAAAAT
Found at i:78837 original size:20 final size:20
Alignment explanation
Indices: 78793--78837 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
78783 ATTGTATAAT
78793 CTAAAAATTAAAAATTAAAA
1 CTAAAAATTAAAAATTAAAA
* *
78813 ATAAAAA-TATAAAATTACAA
1 CTAAAAATTA-AAAATTAAAA
78833 CTAAA
1 CTAAA
78838 TTTAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (20 bp):
CTAAAAATTAAAAATTAAAA
Found at i:83283 original size:22 final size:22
Alignment explanation
Indices: 83258--83305 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
83248 CATGATCTCT
83258 TTTCCCTAGTGTAGACACTCAA
1 TTTCCCTAGTGTAGACACTCAA
83280 TTTCCCTAGTGTAGACACTCAA
1 TTTCCCTAGTGTAGACACTCAA
83302 TTTC
1 TTTC
83306 ATTCAGGCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.27, G:0.12, T:0.35
Consensus pattern (22 bp):
TTTCCCTAGTGTAGACACTCAA
Found at i:85243 original size:45 final size:45
Alignment explanation
Indices: 85175--85408 Score: 389
Period size: 45 Copynumber: 5.2 Consensus size: 45
85165 TGAATAAAAT
85175 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
*
85220 AATGCATATGGGTGCATTCTTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
*
85265 AATGCATATGGGTGCATTCTTGGCATGAAAGGATGTCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
* *
85310 AATGCATATGGGTGCATTATTGGCATGAAAGGATGACATAATTTA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
* *
85355 AATGCATATGGGTACATTATTGGCATGAAATGATG-CTATAATTGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGTC-ATAATTG-A
85401 AATGCATA
1 AATGCATA
85409 ATGATGCATT
Statistics
Matches: 180, Mismatches: 7, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
44 1 0.01
45 170 0.94
46 9 0.05
ACGTcount: A:0.34, C:0.10, G:0.25, T:0.31
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGTCATAATTGA
Found at i:91512 original size:22 final size:22
Alignment explanation
Indices: 91481--91554 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
91471 CTAAAAAAGG
*
91481 AGTATTGATACCATAGTATGGT
1 AGTATCGATACCATAGTATGGT
* ** *
91503 GGTATCGATA-CA-AAAAAGG-
1 AGTATCGATACCATAGTATGGT
91522 AGTATCGATACCATAGTATGGT
1 AGTATCGATACCATAGTATGGT
*
91544 AGTATCAATAC
1 AGTATCGATAC
91555 TGAGAAAAGG
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 9 0.23
20 6 0.15
21 6 0.15
22 18 0.46
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (22 bp):
AGTATCGATACCATAGTATGGT
Found at i:91532 original size:41 final size:42
Alignment explanation
Indices: 91460--91576 Score: 166
Period size: 41 Copynumber: 2.8 Consensus size: 42
91450 AATTTCAAAA
* *
91460 TGGTATTGATACTAAAAAAGGAGTATTGATACCATAGTATGG
1 TGGTATCGATACTAAAAAAGGAGTATCGATACCATAGTATGG
91502 TGGTATCGATAC-AAAAAAGGAGTATCGATACCATAGTATGG
1 TGGTATCGATACTAAAAAAGGAGTATCGATACCATAGTATGG
* * *
91543 TAGTATCAATACTGAGAAAAGG-GTATCGATACCA
1 TGGTATCGATACT-AAAAAAGGAGTATCGATACCA
91577 GGAAACACAA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
41 38 0.56
42 23 0.34
43 7 0.10
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.26
Consensus pattern (42 bp):
TGGTATCGATACTAAAAAAGGAGTATCGATACCATAGTATGG
Found at i:92121 original size:22 final size:22
Alignment explanation
Indices: 92096--92166 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 22
92086 TGGGTGTATT
92096 ATTGGCATGAAAGGATTCCATA
1 ATTGGCATGAAAGGATTCCATA
* * * *
92118 ATTGGAATGAATATGG-GTGCATT
1 ATTGGCATGAA-A-GGATTCCATA
* *
92141 CTTGGCATGAAAGGATGCCATA
1 ATTGGCATGAAAGGATTCCATA
92163 ATTG
1 ATTG
92167 AAATGCATAT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 2 0.06
22 17 0.49
23 14 0.40
24 2 0.06
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.30
Consensus pattern (22 bp):
ATTGGCATGAAAGGATTCCATA
Found at i:92147 original size:45 final size:45
Alignment explanation
Indices: 92078--92323 Score: 368
Period size: 45 Copynumber: 5.4 Consensus size: 45
92068 TGAATAAAAT
* * *
92078 AATGCATATGGGTGTATTATTGGCATGAAAGGATTCCATAATTGG
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* *
92123 AATGAATATGGGTGCATTCTTGGCATGAAAGGATGCCATAATTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* *
92168 AATGCATATGGGTGCATTATTGGCATGAAAGAATGCCATAATTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
* * *
92213 AATGCATATGGGTGCATTATTGGCATGAACGGATTCCATAATTAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
*
92258 AATGCATATAGGTGCATTATTGGCATGAAAGGATGCCATAATTGAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTG-A
92304 AATGCATAAT-GGTGCATTAT
1 AATGCAT-ATGGGTGCATTAT
92324 AAGTATGAAT
Statistics
Matches: 183, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
45 163 0.89
46 18 0.10
47 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAATTGA
Found at i:92150 original size:23 final size:23
Alignment explanation
Indices: 92078--92241 Score: 79
Period size: 23 Copynumber: 7.3 Consensus size: 23
92068 TGAATAAAAT
* *
92078 AATGCATATGGGTGTATTATTGG
1 AATGAATATGGGTGCATTATTGG
* * * *
92101 CATGAA-A-GGATTCCATAATTGG
1 AATGAATATGG-GTGCATTATTGG
*
92123 AATGAATATGGGTGCATTCTTGG
1 AATGAATATGGGTGCATTATTGG
* * * *
92146 CATGAA-A-GGATGCCATAATTGA
1 AATGAATATGGGTG-CATTATTGG
*
92168 AATGCATATGGGTGCATTATTGG
1 AATGAATATGGGTGCATTATTGG
* ** * **
92191 CATGAA-A-GAATGCCATAATTAA
1 AATGAATATGGGTG-CATTATTGG
*
92213 AATGCATATGGGTGCATTATTGG
1 AATGAATATGGGTGCATTATTGG
*
92236 CATGAA
1 AATGAA
92242 CGGATTCCAT
Statistics
Matches: 95, Mismatches: 37, Indels: 18
0.63 0.25 0.12
Matches are distributed among these distances:
21 9 0.09
22 36 0.38
23 41 0.43
24 9 0.09
ACGTcount: A:0.34, C:0.10, G:0.26, T:0.30
Consensus pattern (23 bp):
AATGAATATGGGTGCATTATTGG
Found at i:92965 original size:3 final size:3
Alignment explanation
Indices: 92945--93022 Score: 81
Period size: 3 Copynumber: 26.3 Consensus size: 3
92935 GCTTAAAAAA
* *
92945 TAT TAT ATAT TA- TAT TAT TAT GAT TAT GAT TAT TA- TATT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
* *
92990 TAT GAT TAT TAT TAT TAT TAT TAT CAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
93023 TCATTTTTGG
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
2 6 0.10
3 51 0.82
4 5 0.08
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Done.