Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004709.1 Hibiscus syriacus cultivar Beakdansim tig00010601_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: 61388
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1470 original size:18 final size:19
Alignment explanation
Indices: 1430--1470 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1420 GAATAAATGA
1430 AAATAAATATACATACAAC
1 AAATAAATATACATACAAC
1449 -AATAAATAATA-ATA-AAC
1 AAATAAAT-ATACATACAAC
1466 AAATA
1 AAATA
1471 TACATGCGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.15
18 14 0.70
19 3 0.15
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.22
Consensus pattern (19 bp):
AAATAAATATACATACAAC
Found at i:3416 original size:38 final size:38
Alignment explanation
Indices: 3369--3442 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
3359 AGAAAATGAG
* *
3369 AAAATTCACTAATGTCAAGAAAATAAAAATACAAAAAA
1 AAAACTCACTAATGTCAAGAAAAGAAAAATACAAAAAA
* * *
3407 AAAACTCACTAATGTCGAGAGAAGAAGAATACAAAA
1 AAAACTCACTAATGTCAAGAAAAGAAAAATACAAAA
3443 GAAACTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.61, C:0.12, G:0.11, T:0.16
Consensus pattern (38 bp):
AAAACTCACTAATGTCAAGAAAAGAAAAATACAAAAAA
Found at i:4713 original size:2 final size:2
Alignment explanation
Indices: 4706--4742 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4696 ATGCAATTGA
4706 AT AT 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 AT AT A
4743 GTTAGGATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4954 original size:2 final size:2
Alignment explanation
Indices: 4947--4987 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
4937 ACTAATATGC
4947 AT AT AT AT AT A- AT AT AT AT AT AT AT -T 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
4987 A
1 A
4988 ATTTAGTGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4967 original size:15 final size:15
Alignment explanation
Indices: 4947--4989 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
4937 ACTAATATGC
4947 ATATATATATAATAT
1 ATATATATATAATAT
*
4962 ATATATATATTATAT
1 ATATATATATAATAT
4977 ATATATATATAAT
1 ATATATATATAAT
4990 TTAGTGTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATAATAT
Found at i:8945 original size:6 final size:6
Alignment explanation
Indices: 8934--8961 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
8924 AATTTATATC
8934 ATATAA ATATAA ATATAA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATAT
8962 TTTTATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:10319 original size:21 final size:22
Alignment explanation
Indices: 10288--10328 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
10278 ATAACAGGTA
10288 AAAATATGATAAAACCGGTATC
1 AAAATATGATAAAACCGGTATC
10310 AAAA-ATGATAAAACCGGTA
1 AAAATATGATAAAACCGGTA
10329 AAATGATACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.54, C:0.12, G:0.15, T:0.20
Consensus pattern (22 bp):
AAAATATGATAAAACCGGTATC
Found at i:12579 original size:21 final size:21
Alignment explanation
Indices: 12532--12596 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
12522 AAGACAATCA
* *
12532 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
12554 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
12574 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
12595 AG
1 AG
12597 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:12672 original size:33 final size:33
Alignment explanation
Indices: 12630--12695 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
12620 AAATAGATGG
*
12630 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
12663 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
12696 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:14514 original size:18 final size:19
Alignment explanation
Indices: 14470--14517 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
14460 AATGTAGGGT
14470 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
14489 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
14508 T-ATTTTGTAT
1 TAATTTTGTAT
14518 GTGAATATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:15300 original size:196 final size:197
Alignment explanation
Indices: 14641--15977 Score: 2373
Period size: 196 Copynumber: 6.8 Consensus size: 197
14631 GGCCAAAAGG
14641 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
14705 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTT-TTTCCAGAATGAATGGAAAACAGGGTGCACCC
14770 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
14835 AAT
195 AAT
* * *
14838 ATGTAATTTTTCAATCTAACCGGTATAATTATATCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
*
14903 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCAAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA--TTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
14968 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
129 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
15033 T-A-
194 TAAT
*
15035 ATGTAATGTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCT-AA-AAT
1 ATGTAAT-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
15098 GTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
65 GTGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCAGAATGAATGGAAAACAGGGTGCACCC
15163 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
15228 AAT
195 AAT
15231 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
15295 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA-CC
66 TGTCGACACTAATATAGTTTGTGTCGATATTT-TTTCCAGAATGAATGGAAAACAGGGTGCACCC
15359 ATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
15423 AAT
195 AAT
*
15426 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
15491 TGTCGACACTAATATAG--T-T-TCGATATTTTTTCCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTTGTGTCGATATTTTTT-CCAGAATGAATGGAAAACAGGGTGCACCC
15552 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
15616 AAT
195 AAT
*
15619 ATGTAATTTTTCAATCTAACCGGTACAATTATA-C-TTTTTATGAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
15682 TGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAATGGAAAACAGGGTGCACC
66 TGTCGACACTAATATAGTTTGTGTCGATA-TT-TTTTCCAGAATGAATGGAAAACAGGGTGCACC
15747 CATAAAGTGTCGATCCATATAT-AAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
129 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
15811 TAAT
194 TAAT
***
15815 ATGTAATTTTTCAATCTATACCGGTACAATTATACTTATTTTATGAGAGAATATGTCTAAATAAT
1 ATGTAATTTTTCAATCTA-ACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
15880 GTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAATGGAAAACAGGGTGCAC
65 GTGTCGACACTAATATAGTTTGTGTCGATA-TT-TTTTCCAGAATGAATGGAAAACAGGGTGCAC
15945 CCATAAAGTGTCGATCCATATATAAAAAGTGTC
128 CCATAAAGTGTCGATCCATATATAAAAAGTGTC
15978 TGCAAACAAG
Statistics
Matches: 1103, Mismatches: 13, Indels: 45
0.95 0.01 0.04
Matches are distributed among these distances:
191 47 0.04
192 36 0.03
193 75 0.07
194 147 0.13
195 150 0.14
196 229 0.21
197 63 0.06
198 133 0.12
199 211 0.19
200 12 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (197 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTCCAGAATGAATGGAAAACAGGGTGCACCCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
AT
Found at i:15752 original size:389 final size:393
Alignment explanation
Indices: 14641--15977 Score: 2358
Period size: 389 Copynumber: 3.4 Consensus size: 393
14631 GGCCAAAAGG
14641 ATGTAA-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
14705 TGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAG-TTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCC
14770 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
* * *
14835 AATATGTAATTTTTCAATCTAACCGGTATAATTATATCGGTTTTATGTGAGAATATGTCTAAATA
195 AATATGTAATTTTTCAATCTAACCGGTACAATTATA-CCGTTTTATGAGAGAATATGTCTAAATA
*
14900 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCAAGAATGAATGGAAAACAGGGTGC
259 ATGTGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATGGAAAACAGGGTGC
14965 ACCCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
323 ACCCATAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
15030 ATGT-A-
387 ATGTAAT
*
15035 ATGTAATGTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCT-AA-AAT
1 ATGTAAT-TTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
15098 GTGTCGACACTAATATAGTTTGTGTCGATATTT-TTTCCAGAATGAATGGAAAACAGGGTGCACC
65 GTGTCGACACTAATATAG-TTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACC
15162 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
129 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
15227 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTATGAGAGAATATGTCTAAATA
194 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGAGAGAATATGTCTAAATA
*
15292 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCA
259 ATGTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCA
15357 -CCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
324 CCCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
15421 GTAAT
389 GTAAT
*
15426 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGTGAGAATATGTCTAAATAATG
1 ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
15491 TGTCGACACTAATATAG-T-T-TCGATATTT-TTTCCCAGAATGAATGGAAAACAGGGTGCACCC
66 TGTCGACACTAATATAGTTGTGTCGATATTTATTT-CCAGAATGAATGGAAAACAGGGTGCACCC
15552 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTATAATGT
130 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
*
15616 AATATGTAATTTTTCAATCTAACCGGTACAATTATA-CTTTTTATGAGAGAATATGTCTAAATAA
195 AATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGAGAGAATATGTCTAAATAA
15680 TGTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAATGGAAAACAGGGTGCA
260 TGTGTCGACACTAATATAGTTTGTGTCGATATTT-TTTTCCAGAATGAATGGAAAACAGGGTGCA
*
15745 CCCATAAAGTGTCGATCCATATATAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
324 CCCATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
15810 GTAAT
389 GTAAT
***
15815 ATGTAATTTTTCAATCTATACCGGTACAATTATACTTATTTTATGAGAGAATATGTCTAAATAAT
1 ATGTAATTTTTCAATCTA-ACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAAT
*
15880 GTGTCGACACTAATATAGTTTGTGTCGATATTTGTTTTCCAGAATGAATGGAAAACAGGGTGCAC
65 GTGTCGACACTAATATAG-TTGTGTCGATATTT-ATTTCCAGAATGAATGGAAAACAGGGTGCAC
15945 CCATAAAGTGTCGATCCATATATAAAAAGTGTC
128 CCATAAAGTGTCGATCCATATATAAAAAGTGTC
15978 TGCAAACAAG
Statistics
Matches: 912, Mismatches: 15, Indels: 31
0.95 0.02 0.03
Matches are distributed among these distances:
387 60 0.07
388 92 0.10
389 209 0.23
390 134 0.15
391 40 0.04
392 79 0.09
393 133 0.15
394 51 0.06
395 62 0.07
396 52 0.06
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (393 bp):
ATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATATGTCTAAATAATG
TGTCGACACTAATATAGTTGTGTCGATATTTATTTCCAGAATGAATGGAAAACAGGGTGCACCCA
TAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGTA
ATATGTAATTTTTCAATCTAACCGGTACAATTATACCGTTTTATGAGAGAATATGTCTAAATAAT
GTGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATGGAAAACAGGGTGCACC
CATAAAGTGTCGATCCATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AAT
Found at i:17920 original size:183 final size:183
Alignment explanation
Indices: 17385--18267 Score: 1567
Period size: 183 Copynumber: 4.8 Consensus size: 183
17375 TTTCAACATA
** * * * *
17385 TTATAATAAAATAGGTAAATTTGCAATATAACCGGTAT-AATATACCGGTTTTATGCGTGAATAG
1 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
17449 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
17514 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
131 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
17567 TTATAATGTAATAGATAATTTTGTAATATAACCGGTAT-AA-ATACC-GTTTTATGCGCGAATAG
1 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
* * * *
17629 GTCTACTACCTATCTCAACACTTTATAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
17694 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
131 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
*
17747 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCACGAATAG
1 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
*
17812 GTCTACAACATATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
* * *
17877 ATGTGTCGATACGATTTAAAAAAGTGTCGACATTTACACATCGGAACCCATAA
131 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
*
17930 TTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
1 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
17995 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
*
18060 ATGTGTTGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
131 ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
18113 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
1 TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
*
18178 GTCTACAACATATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
66 GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
*
18243 ATGTGTCGATACCATTTAAAAAAGT
131 ATGTGTCGATACGATTTAAAAAAGT
18268 GTCGGTAATT
Statistics
Matches: 668, Mismatches: 30, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
180 168 0.25
181 7 0.01
182 40 0.06
183 453 0.68
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
TTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAG
GTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAA
ATGTGTCGATACGATTTAAAAAAGTATCGACATTTACACATCGGAACCCAGAT
Found at i:18979 original size:25 final size:25
Alignment explanation
Indices: 18945--19009 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
18935 TTATCATTAA
18945 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
18970 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
18995 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
19010 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:19277 original size:21 final size:22
Alignment explanation
Indices: 19231--19277 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
19221 AAATTACATA
19231 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* * *
19253 -CTTTTTATAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
19273 ACTTT
1 ACTTT
19278 CAATATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:19362 original size:23 final size:22
Alignment explanation
Indices: 19317--19364 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
19307 AGGTAGCCCT
*
19317 TATAATTAATAGGTATCGTTTA
1 TATAATTAATAGGTATCGGTTA
19339 TATAATGTAATAGGTAGT-GGTTA
1 TATAAT-TAATAGGTA-TCGGTTA
19362 TAT
1 TAT
19365 TGTAAAGTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 16 0.70
24 1 0.04
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (22 bp):
TATAATTAATAGGTATCGGTTA
Found at i:19582 original size:25 final size:25
Alignment explanation
Indices: 19548--19598 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
19538 ACAACAAATC
*
19548 AATTAAACATTGTTGTGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
*
19573 AATTGAACATTGTTATGGGTACATT
1 AATTAAACATTGTTATGGGTACATT
19598 A
1 A
19599 TTTGGAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (25 bp):
AATTAAACATTGTTATGGGTACATT
Found at i:20005 original size:18 final size:18
Alignment explanation
Indices: 19984--20020 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
19974 GTAATTGGAG
19984 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
20002 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
20020 T
1 T
20021 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:20028 original size:24 final size:24
Alignment explanation
Indices: 19976--20022 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
19966 TTTCATATGT
* *
19976 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
20000 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
20023 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:20324 original size:38 final size:38
Alignment explanation
Indices: 20281--20359 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
20271 ATGCTCATCA
*
20281 AAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAAATC
1 AAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAATC
*
20319 AAATCCAAATCTCATATGATGCCAAGCAAAAGGAAATC
1 AAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAATC
20357 AAA
1 AAA
20360 ATCTACAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.48, C:0.20, G:0.15, T:0.16
Consensus pattern (38 bp):
AAATCCAAAGCTCATATGATGCCAAGCAAAAGGAAATC
Found at i:20779 original size:20 final size:22
Alignment explanation
Indices: 20754--20829 Score: 68
Period size: 23 Copynumber: 3.5 Consensus size: 22
20744 ACTTTCAATA
*
20754 TAATAGGTA-AAC-ATATGATG
1 TAATAGGTAGAACTATATAATG
*
20774 TAATAGGTAGCACTTATATAATG
1 TAATAGGTAGAAC-TATATAATG
**
20797 TAATAGGTATCG-TTTATATAATG
1 TAATAGGTA--GAACTATATAATG
20820 TAATAGGTAG
1 TAATAGGTAG
20830 TGGTTATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
20 9 0.19
21 3 0.06
23 34 0.72
25 1 0.02
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (22 bp):
TAATAGGTAGAACTATATAATG
Found at i:20797 original size:23 final size:23
Alignment explanation
Indices: 20766--20829 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
20756 ATAGGTAAAC
*
20766 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCACTT
* **
20789 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCACTT
20812 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
20830 TGGTTATATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.05, G:0.20, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCACTT
Found at i:20836 original size:23 final size:23
Alignment explanation
Indices: 20766--20838 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
20756 ATAGGTAAAC
* **
20766 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGTGCTT
*
20789 ATATAATGTAATAGGTA-TCGTTT
1 ATATAATGTAATAGGTAGT-GCTT
*
20812 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGTGCTT
20835 ATAT
1 ATAT
20839 TGTAAAGTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 42 0.98
24 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGTGCTT
Found at i:22847 original size:39 final size:39
Alignment explanation
Indices: 22741--22852 Score: 125
Period size: 39 Copynumber: 2.9 Consensus size: 39
22731 AAATATGAAG
* * * * * * *
22741 ACTCCACGACTGCATGGAGTCTTCAGGCAAATAGAGAAG
1 ACTCCACGAATGCACGGTGTCTTCAGGCCAATGGAAAAA
* *
22780 ACTCCAGGAATGCACGGTGTCTTAAGGCCAATGGAAAAA
1 ACTCCACGAATGCACGGTGTCTTCAGGCCAATGGAAAAA
* *
22819 ACTCCACGAGTGCACGGTGTATTCAGGCCAATGG
1 ACTCCACGAATGCACGGTGTCTTCAGGCCAATGG
22853 GGGAAGACAC
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (39 bp):
ACTCCACGAATGCACGGTGTCTTCAGGCCAATGGAAAAA
Found at i:23306 original size:108 final size:109
Alignment explanation
Indices: 23135--23437 Score: 311
Period size: 106 Copynumber: 2.8 Consensus size: 109
23125 TTTAGTGTAA
* * *
23135 ATTTTATTG-TTTCATTTTAAAT-ATAAATTAATTAGATTAATTTATTTTGATTTTACAGATTAA
1 ATTTT-TTGTTTTTATTTTAAATAATAAATTAATTAGACTAATTTATTTTAATTTTACAGATT-A
*
23198 AAT-GTATTCG-GTTGGTTTGGTAAGTTTAATTTAAATTTTTATTGTTT-
64 AATCGTATTCGAG-TGG--TGGTAAGTTTAATGTAAA-TTTTATTGTTTC
* * *
23245 ATTTTTTGTTTTTATTTTAAATAAT-TATTAA-TAGACT-ATTTATTTTAATTTTATATATTAAA
1 ATTTTTTGTTTTTATTTTAAATAATAAATTAATTAGACTAATTTATTTTAATTTTACAGATTAAA
* *
23307 TCGTATTTGAGTGGTGGTAAGTTTAGTGTAAATTTTATTGTTTC
66 TCGTATTCGAGTGGTGGTAAGTTTAATGTAAATTTTATTGTTTC
* * * * * * *
23351 ATTTTTTGTTTTTATTTTCAAT-ATAAAGTAATTATA-TTATTTATTTTGATTGTATAGATTAAA
1 ATTTTTTGTTTTTATTTTAAATAATAAATTAATTAGACTAATTTATTTTAATTTTACAGATTAAA
* *
23414 TCGTATTTGAGTGTTTGGTAAGTT
66 TCGTATTCGAGTG-GTGGTAAGTT
23438 GATTTTAATT
Statistics
Matches: 167, Mismatches: 17, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
105 13 0.08
106 42 0.25
107 42 0.25
108 37 0.22
109 9 0.05
110 22 0.13
111 2 0.01
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.55
Consensus pattern (109 bp):
ATTTTTTGTTTTTATTTTAAATAATAAATTAATTAGACTAATTTATTTTAATTTTACAGATTAAA
TCGTATTCGAGTGGTGGTAAGTTTAATGTAAATTTTATTGTTTC
Found at i:23448 original size:107 final size:105
Alignment explanation
Indices: 23135--23449 Score: 345
Period size: 107 Copynumber: 2.9 Consensus size: 105
23125 TTTAGTGTAA
* *
23135 ATTTTATTG-TTTCATTTTAAATATAAATTAATTAGATTAATTTATTTTGATTTTACAGATTAAA
1 ATTTT-TTGTTTTTATTTT-AATATAAATTAATTAGATT-ATTTATTTTGATTTTATAGATT-AA
*
23199 AT-GTATTCG-GTTGGTTTGGTAAGTTTAATTTAAATTTTTATTGTTT
62 ATCGTATTTGAG-T-GTTTGGTAAG-TTAATTTAAA-TTTTATTGTTT
* * *
23245 ATTTTTTGTTTTTATTTTAA-ATAATTATTAA-TAGACTATTTATTTTAATTTTATATATTAAAT
1 ATTTTTTGTTTTTATTTTAATATAA--ATTAATTAGATTATTTATTTTGATTTTATAGATTAAAT
* * *
23308 CGTATTTGAGTG-GTGGTAAGTTTAGTGTAAATTTTATTGTTT
64 CGTATTTGAGTGTTTGGTAAG-TTAATTTAAATTTTATTGTTT
* * *
23350 CATTTTTTGTTTTTATTTTCAATATAAAGTAATTATATTATTTATTTTGATTGTATAGATTAAAT
1 -ATTTTTTGTTTTTATTTT-AATATAAATTAATTAGATTATTTATTTTGATTTTATAGATTAAAT
* *
23415 CGTATTTGAGTGTTTGGTAAGTTGATTTTAATTTT
64 CGTATTTGAGTGTTTGGTAAGTTAATTTAAATTTT
23450 TCTTTAATTA
Statistics
Matches: 175, Mismatches: 20, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
105 11 0.06
106 38 0.22
107 56 0.32
108 41 0.23
109 11 0.06
110 18 0.10
ACGTcount: A:0.30, C:0.03, G:0.12, T:0.56
Consensus pattern (105 bp):
ATTTTTTGTTTTTATTTTAATATAAATTAATTAGATTATTTATTTTGATTTTATAGATTAAATCG
TATTTGAGTGTTTGGTAAGTTAATTTAAATTTTATTGTTT
Found at i:26034 original size:12 final size:12
Alignment explanation
Indices: 26017--26050 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
26007 TTTTACAAGC
26017 AAATGACGTTAG
1 AAATGACGTTAG
*
26029 AAATGACATTAG
1 AAATGACGTTAG
26041 AAATGACGTT
1 AAATGACGTT
26051 GGAGAACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (12 bp):
AAATGACGTTAG
Found at i:28353 original size:19 final size:20
Alignment explanation
Indices: 28331--28368 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
28321 TTACATCTCC
*
28331 AAATCCTGC-TAACATCATT
1 AAATCCTGCAAAACATCATT
*
28350 AAATCTTGCAAAACATCAT
1 AAATCCTGCAAAACATCAT
28369 CACATTCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.42, C:0.24, G:0.05, T:0.29
Consensus pattern (20 bp):
AAATCCTGCAAAACATCATT
Found at i:34480 original size:55 final size:54
Alignment explanation
Indices: 34419--34803 Score: 345
Period size: 55 Copynumber: 7.0 Consensus size: 54
34409 AGACTTGAAA
* * *
34419 AATCTTCGAATGACGGGTCTGCTCCCTATCCCTTCAGGGAGTATAAGACTCGATC
1 AATCTTC-AATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
*
34474 AATCTTCAGCA-AACGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
1 AATCTTCA--ATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
* * * *
34529 AATCTTCAACAAACGTGTCTGCTCCCTATTCATTTAGGGAGTATAAGACTCAATC
1 AATCTTCAA-TAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
* * *
34584 AATCTTCAATAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAAC
1 AATCTTCAAT-AACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAG-ACTCGATC
* ** * * * *
34639 AATCTTCATAAAACGGGTCCCCTCTCTATTC-TACCAGAGAGTAT-AGAACTCGAAC
1 AATCTTCA-ATAACGGGTCTGCTCCCTATTCAT-TCAGGGAGTATAAG-ACTCGATC
* * * * *
34694 AATCTTCAATAAACGAGTCCGCTCCCTATTC-TACCAGAGAGTAT-AGAACTCGAAC
1 AATCTTCAAT-AACGGGTCTGCTCCCTATTCAT-TCAGGGAGTATAAG-ACTCGATC
* * *
34749 AATCTTCACCA-AACGAGTCTGCTCCCTATTC-TACCAGAGAGTATAAGACTCGATC
1 AATCTTCA--ATAACGGGTCTGCTCCCTATTCAT-TCAGGGAGTATAAGACTCGATC
34804 TTCATAAAAT
Statistics
Matches: 294, Mismatches: 24, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
53 1 0.00
54 5 0.02
55 283 0.96
56 4 0.01
57 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (54 bp):
AATCTTCAATAACGGGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGATC
Found at i:34738 original size:165 final size:165
Alignment explanation
Indices: 34431--34801 Score: 414
Period size: 165 Copynumber: 2.2 Consensus size: 165
34421 TCTTCGAATG
* * * * **
34431 ACGGGTCTGCTCCCTATCCCTTCAGGGAGTATAAGACTCGATCAATCTTCAGCAAACGTGTCTGC
1 ACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAGAAAACGGGTCCCC
* * * * *
34496 TCCCTATTCATTCAGGGAGTATAAGACTCGATCAATCTTCAACAAACGTGTCTGCTCCCTATTCA
66 TCCCTATTCATCCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCA
** * *
34561 TTTAGGGAGTATA-AGACTC-AATCAATCTTCAATAA
131 TCCAGAGAGTATAGA-ACTCGAA-CAATCTTCAACAA
* * *
34596 ACGGGTCCGCTCCCTATTCGTTCAGGGAGTAT-AGAACTCGAACAATCTTCATAAAACGGGTCCC
1 ACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCAGAAAACGGGTCCC
* *
34660 CTCTCTATTC-TACCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAACGAGTCCGCTCCCTAT
65 CTCCCTATTCAT-CCAGAGAGTATAAG-ACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTAT
*
34723 TC-TACCAGAGAGTATAGAACTCGAACAATCTTCACCAA
128 TCAT-CCAGAGAGTATAGAACTCGAACAATCTTCAACAA
* * *
34761 ACGAGTCTGCTCCCTATT-CTACCAGAGAGTATAAGACTCGA
1 ACGGGTCTGCTCCCTATTCCT-TCAGGGAGTATAAGACTCGA
34802 TCTTCATAAA
Statistics
Matches: 172, Mismatches: 26, Indels: 16
0.80 0.12 0.07
Matches are distributed among these distances:
164 7 0.04
165 160 0.93
166 5 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (165 bp):
ACGGGTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAGAAAACGGGTCCCC
TCCCTATTCATCCAGAGAGTATAAGACTCGAACAATCTTCAACAAACGAGTCCGCTCCCTATTCA
TCCAGAGAGTATAGAACTCGAACAATCTTCAACAA
Found at i:34800 original size:110 final size:110
Alignment explanation
Indices: 34435--34801 Score: 417
Period size: 110 Copynumber: 3.3 Consensus size: 110
34425 CGAATGACGG
* * * * ** * *
34435 GTCTGCTCCCTATCCCT-TCAGGGAGTATAAGACTCGATCAATCTTCAGCAAACGTGTCTGCTCC
1 GTCTGCTCCCTAT-TCTACCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGAGTCCGCTCC
* *
34499 CTATTC-ATTCAGGGAGTATA-AGACTCGATCAATCTTCAACAAACGT
65 CTATTCTA-TCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGA
** * *
34545 GTCTGCTCCCTATTC-ATTTAGGGAGTATAAGACTC-AATCAATCTTCAATAAACGGGTCCGCTC
1 GTCTGCTCCCTATTCTA-CCAGAGAGTATAAGACTCGAA-CAATCTTCAATAAACGAGTCCGCTC
*
34608 CCTATTCGT-TCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGG
64 CCTATTC-TATCAGGGAGTATAGAACTCGAACAATCTTCA-ACAAACGA
** *
34655 GTCCCCTCTCTATTCTACCAGAGAGTAT-AGAACTCGAACAATCTTCAATAAACGAGTCCGCTCC
1 GTCTGCTCCCTATTCTACCAGAGAGTATAAG-ACTCGAACAATCTTCAATAAACGAGTCCGCTCC
* * *
34719 CTATTCTACCAGAGAGTATAGAACTCGAACAATCTTCACCAAACGA
65 CTATTCTATCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGA
34765 GTCTGCTCCCTATTCTACCAGAGAGTATAAGACTCGA
1 GTCTGCTCCCTATTCTACCAGAGAGTATAAGACTCGA
34802 TCTTCATAAA
Statistics
Matches: 221, Mismatches: 23, Indels: 26
0.82 0.09 0.10
Matches are distributed among these distances:
109 5 0.02
110 209 0.95
111 7 0.03
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (110 bp):
GTCTGCTCCCTATTCTACCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGAGTCCGCTCCC
TATTCTATCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGA
Found at i:36179 original size:12 final size:13
Alignment explanation
Indices: 36139--36186 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
36129 TTTCTCTTTT
36139 TTTCATTTTTCTC
1 TTTCATTTTTCTC
**
36152 TTTTTGTTTTTCTC
1 -TTTCATTTTTCTC
36166 TTTCATTTTT-TC
1 TTTCATTTTTCTC
*
36178 TTCCATTTT
1 TTTCATTTT
36187 CCATTTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 10 0.34
13 8 0.28
14 11 0.38
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (13 bp):
TTTCATTTTTCTC
Found at i:36235 original size:16 final size:16
Alignment explanation
Indices: 36209--36263 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
36199 CTTTTTTTTC
36209 TTTTCGTTTTTCCATCAT
1 TTTTC-TTTTTCC-TCAT
*
36227 TTTTCTTTTTTCTCAT
1 TTTTCTTTTTCCTCAT
*
36243 TTTTC-TTTTCTTC-T
1 TTTTCTTTTTCCTCAT
36257 TTTTCTT
1 TTTTCTT
36264 CTTCTCGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 6 0.18
15 7 0.21
16 9 0.27
17 6 0.18
18 5 0.15
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTCTTTTTCCTCAT
Found at i:36252 original size:44 final size:43
Alignment explanation
Indices: 36137--36254 Score: 114
Period size: 44 Copynumber: 2.6 Consensus size: 43
36127 TATTTCTCTT
* * *
36137 TTTTTCATTTTTCTCTTTTTGTTTTTCTCTTTCATTTTTTCTTCCA
1 TTTTTCTTTTTTCTC-TTTT-TTTTTCT-TTTCATTTTTCCATCCA
* *
36183 TTTTCCATTTTTTCT-TCTTTTTTTTCTTTTCGTTTTTCCAT-CA
1 TTTTTC-TTTTTTCTCT-TTTTTTTTCTTTTCATTTTTCCATCCA
36226 TTTTTCTTTTTTCTCATTTTTCTTTTCTT
1 TTTTTCTTTTTTCTC-TTTTT-TTTTCTT
36255 CTTTTTCTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
42 8 0.13
43 11 0.18
44 19 0.31
45 8 0.13
46 8 0.13
47 7 0.11
ACGTcount: A:0.06, C:0.19, G:0.02, T:0.73
Consensus pattern (43 bp):
TTTTTCTTTTTTCTCTTTTTTTTTCTTTTCATTTTTCCATCCA
Found at i:36253 original size:14 final size:14
Alignment explanation
Indices: 36223--36269 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 14
36213 CGTTTTTCCA
36223 TCATTTTTCTTTTTTC
1 TCATTTTTC--TTTTC
36239 TCATTTTTCTTTTC
1 TCATTTTTCTTTTC
36253 TTC-TTTTTCTTCTTC
1 -TCATTTTTCTT-TTC
36268 TC
1 TC
36270 GGTTTTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
14 15 0.52
15 5 0.17
16 9 0.31
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (14 bp):
TCATTTTTCTTTTC
Found at i:36256 original size:17 final size:16
Alignment explanation
Indices: 36197--36256 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
36187 CCATTTTTTC
*
36197 TTCTTTTTTTTC--TT
1 TTCTTTTTTCTCATTT
*
36211 TTCGTTTTTCCATCATTT
1 TTC-TTTTTTC-TCATTT
36229 TTCTTTTTTCTCATTT
1 TTCTTTTTTCTCATTT
36245 TTCTTTTCTTCT
1 TTCTTTT-TTCT
36257 TTTTCTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.08
15 5 0.13
16 15 0.39
17 10 0.26
18 5 0.13
ACGTcount: A:0.05, C:0.20, G:0.02, T:0.73
Consensus pattern (16 bp):
TTCTTTTTTCTCATTT
Found at i:46020 original size:45 final size:47
Alignment explanation
Indices: 45952--46040 Score: 146
Period size: 45 Copynumber: 1.9 Consensus size: 47
45942 TGTTTTGTTA
45952 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
* *
45999 TTCA-AAAAATAAA-CCTAACCGCATGATATTTAGTTCGCATGC
1 TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
46041 ATTTATTCGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 27 0.68
46 9 0.22
47 4 0.10
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.29
Consensus pattern (47 bp):
TTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGCTTG
Found at i:57818 original size:20 final size:22
Alignment explanation
Indices: 57793--57837 Score: 67
Period size: 20 Copynumber: 2.1 Consensus size: 22
57783 GGTAAAAAAA
*
57793 TTACCTAAAATATT-AT-TTTT
1 TTACCTAAAACATTAATGTTTT
57813 TTACCTAAAACATTAATGTTTT
1 TTACCTAAAACATTAATGTTTT
57835 TTA
1 TTA
57838 ACATTTCCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.59
21 2 0.09
22 7 0.32
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (22 bp):
TTACCTAAAACATTAATGTTTT
Found at i:58064 original size:13 final size:13
Alignment explanation
Indices: 58046--58071 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
58036 CATAGTTTAA
58046 CAGTCTTCATATG
1 CAGTCTTCATATG
58059 CAGTCTTCATATG
1 CAGTCTTCATATG
58072 TGCGTATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
CAGTCTTCATATG
Done.