Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005147.1 Hibiscus syriacus cultivar Beakdansim tig00011593_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: 70043
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:805 original size:3 final size:3
Alignment explanation
Indices: 797--852 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
787 GGGTTCTCAA
*
797 ATT ATT ATT ATT CTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
845 ATT ATT AT
1 ATT ATT AT
853 AACAACACTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:9556 original size:21 final size:20
Alignment explanation
Indices: 9528--9566 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9518 CATTGCAGGA
*
9528 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
9548 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
9567 GACCTTGATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:12020 original size:417 final size:417
Alignment explanation
Indices: 11239--12064 Score: 1454
Period size: 417 Copynumber: 2.0 Consensus size: 417
11229 AATCATGAAG
*
11239 AAGGTATTCATGAAGGAAATTATAAAATGGTTGGATGCAAGAGTGATTTATCCTATATCCGATAG
1 AAGGTAGTCATGAAGGAAATTATAAAATGGTTGGATGCAAGAGTGATTTATCCTATATCCGATAG
*
11304 TTCATGGCTCAACCCGGTGTAGTGTGTGCCAAAGAAGGGTAGTGTGACCGTGGTTAAAAGCAAAC
66 TTCATGGCTCAACCCGGTGTAGTGTGTGCCAAAGAAGGGTAGTGTGACAGTGGTTAAAAGCAAAC
* *
11369 ATGATGAACTCCTCACCACCAGAACAATCACGGGCTGGCGTATATGTATGGATTACAGGAAGCTT
131 ATGACGAACTCCTCACCACCAGAACAATCACGGGCTGGCGTATATGTATGGATTACAAGAAGCTT
*
11434 AATAAAGCAACAAATAAAGATCATTTTCCCCTCCCTTTTATCGACCAAATGCTTGATAGGTTAGC
196 AATAAAGCAACAAATAAAGATCATTTTCCCCTCCATTTTATCGACCAAATGCTTGATAGGTTAGC
* *
11499 GGGAAAAGCATTCTATTGCTTCCTTAATGGATACTCAGGATATAATCAAATAGCCATAGCACCGG
261 GGGAAAAGCATTCTATTGATTCCTTAATGGATACTCAGGATATAATCAAATAGCCATAGCACCAG
11564 AGGATCAAGAGAAAACCACTTTCACATGCCCTTATGGTACCTATGCATTTAGACGAATGTCGTTC
326 AGGATCAAGAGAAAACCACTTTCACATGCCCTTATGGTACCTATGCATTTAGACGAATGTCGTTC
11629 GGGCTGTGTAATACTCCAGTCATAAAT
391 GGGCTGTGTAATACTCCAGTCATAAAT
* ** *
11656 AAGGTAGTCATGAAGTAAATTATAAAATGGTTGGATGCGTGAGTGATTTATCCTATATCCTATAG
1 AAGGTAGTCATGAAGGAAATTATAAAATGGTTGGATGCAAGAGTGATTTATCCTATATCCGATAG
* * * *
11721 TTCATGGGTCAGCCCGGTGTAGTGTGTGCCAAAGAAGGGTGGTGTGACAGTGGTTAAAAGCGAAC
66 TTCATGGCTCAACCCGGTGTAGTGTGTGCCAAAGAAGGGTAGTGTGACAGTGGTTAAAAGCAAAC
* *
11786 ATGACGAACTCCTCACCACTAGAACAATCACGGGCTGTCGTATATGTATGGATTACAAGAAGCTT
131 ATGACGAACTCCTCACCACCAGAACAATCACGGGCTGGCGTATATGTATGGATTACAAGAAGCTT
* * *
11851 AATAAAGCCACAAATAAAGGTCATTTTCCCCTCCATTTTATCGATCAAATGCTTGATAGGTTAGC
196 AATAAAGCAACAAATAAAGATCATTTTCCCCTCCATTTTATCGACCAAATGCTTGATAGGTTAGC
*
11916 GGGAATAGCATTCTATTGATTCCTTAATGGATACTCAGGATATAATCAAATAGCCATAGCACCAG
261 GGGAAAAGCATTCTATTGATTCCTTAATGGATACTCAGGATATAATCAAATAGCCATAGCACCAG
11981 AGGATCAAGAGAAAACCACTTTCACATGCCCTTATGGTACCTATGCATTTAGACGAATGTCGTTC
326 AGGATCAAGAGAAAACCACTTTCACATGCCCTTATGGTACCTATGCATTTAGACGAATGTCGTTC
*
12046 GGGCTGTGTAATGCTCCAG
391 GGGCTGTGTAATACTCCAG
12065 CTACCTTCCA
Statistics
Matches: 387, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
417 387 1.00
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (417 bp):
AAGGTAGTCATGAAGGAAATTATAAAATGGTTGGATGCAAGAGTGATTTATCCTATATCCGATAG
TTCATGGCTCAACCCGGTGTAGTGTGTGCCAAAGAAGGGTAGTGTGACAGTGGTTAAAAGCAAAC
ATGACGAACTCCTCACCACCAGAACAATCACGGGCTGGCGTATATGTATGGATTACAAGAAGCTT
AATAAAGCAACAAATAAAGATCATTTTCCCCTCCATTTTATCGACCAAATGCTTGATAGGTTAGC
GGGAAAAGCATTCTATTGATTCCTTAATGGATACTCAGGATATAATCAAATAGCCATAGCACCAG
AGGATCAAGAGAAAACCACTTTCACATGCCCTTATGGTACCTATGCATTTAGACGAATGTCGTTC
GGGCTGTGTAATACTCCAGTCATAAAT
Found at i:19302 original size:3 final size:3
Alignment explanation
Indices: 19294--19330 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
19284 GAGTTCTCAA
19294 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19331 ACACTTTACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:23600 original size:24 final size:26
Alignment explanation
Indices: 23573--23625 Score: 67
Period size: 24 Copynumber: 2.1 Consensus size: 26
23563 ACTCAATTTA
23573 TTTTTATTTATTTT-AT-TTTA-ATAT
1 TTTTTATTT-TTTTCATATTTATATAT
*
23597 TTTTTCTTTTTTTCATATTTATATAT
1 TTTTTATTTTTTTCATATTTATATAT
23623 TTT
1 TTT
23626 GTAATTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 4 0.16
24 10 0.40
25 4 0.16
26 7 0.28
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTATTTTTTTCATATTTATATAT
Found at i:26208 original size:99 final size:99
Alignment explanation
Indices: 26088--26268 Score: 326
Period size: 99 Copynumber: 1.8 Consensus size: 99
26078 TTATAATATT
* *
26088 ATATGTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAATGCCCCAAATTTATGG
1 ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAAATTTATGG
26153 ATAAGATTCAGCTAGCCTCATAAAGGTGATTATA
66 ATAAGATTCAGCTAGCCTCATAAAGGTGATTATA
* *
26187 ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTATGG
1 ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAAATTTATGG
26252 ATAAGATTCAGCTAGCC
66 ATAAGATTCAGCTAGCC
26269 AGACAATGGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
99 78 1.00
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (99 bp):
ATATCTATACAATAAAGCTTGAGCTGTCCCTCTAGAGCAATTGGTTAAACGCCCCAAATTTATGG
ATAAGATTCAGCTAGCCTCATAAAGGTGATTATA
Found at i:28240 original size:83 final size:83
Alignment explanation
Indices: 28099--28403 Score: 439
Period size: 83 Copynumber: 3.6 Consensus size: 83
28089 TACGGAATAA
* * *
28099 CTCAAGGCGAGAAGGGTTATCTGTCAACAAACCTTCGAGTTAAATAACATTCAACTCAAGGGCAT
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCAT
28164 ATCAAATTTATAGCATAG
66 ATCAAATTTATAGCATAG
* *
28182 CTCAAGGCGAGAAGGGTTATCTATCAACAAACCTTCGAGTTCGATTACATTCAGCTCAAGGGCAT
1 CTCAAGGCGAGAAGGGTTATCTGTCAACAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCAT
28247 ATCAAATTTATAGCATAG
66 ATCAAATTTATAGCATAG
* ** * * *
28265 CTCAAGGCGAGAACGACTATCTGTCAAAAAAACCTTCTAGTTCAATTTCATTCAGCTCAAGGGCA
1 CTCAAGGCGAGAAGGGTTATCTGTC-AACAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCA
* *
28330 TATCAAATTTACAGCATAA
65 TATCAAATTTATAGCATAG
* * *
28349 CTCAAGGAGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTCCATTCA
1 CTCAAGGCGAGAAGGGTTATCTGTCAAC--AAACCTTCGAGTTCAATTACATTCA
28404 ACTCGATGAC
Statistics
Matches: 196, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
83 101 0.52
84 73 0.37
85 22 0.11
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (83 bp):
CTCAAGGCGAGAAGGGTTATCTGTCAACAAACCTTCGAGTTCAATTACATTCAGCTCAAGGGCAT
ATCAAATTTATAGCATAG
Found at i:28378 original size:167 final size:167
Alignment explanation
Indices: 28099--28403 Score: 459
Period size: 167 Copynumber: 1.8 Consensus size: 167
28089 TACGGAATAA
* ** *
28099 CTCAAGGCGAGAAGGGTTATCTGTCAACAAACCTTCGAGTTAAATAACATTCAACTCAAGGGCAT
1 CTCAAGGCGAGAACGACTATCTGTCAAAAAACCTTCGAGTTAAATAACATTCAACTCAAGGGCAT
* * *
28164 ATCAAATTTATAGCATAGCTCAAGGCGAGAAGGGTTATCTATCAAC-AAACCTTCGAGTTCGATT
66 ATCAAATTTACAGCATAACTCAAGGAGAGAAGGGTTATCTATCAACAAAACCTTCGAGTTCGATT
28228 ACATTCAGCTCAAGGGCATATCAAATTTATAGCATAG
131 ACATTCAGCTCAAGGGCATATCAAATTTATAGCATAG
* * ** *
28265 CTCAAGGCGAGAACGACTATCTGTCAAAAAAACCTTCTAGTTCAATTTCATTCAGCTCAAGGGCA
1 CTCAAGGCGAGAACGACTATCTGTC-AAAAAACCTTCGAGTTAAATAACATTCAACTCAAGGGCA
*
28330 TATCAAATTTACAGCATAACTCAAGGAGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGA
65 TATCAAATTTACAGCATAACTCAAGGAGAGAAGGGTTATCTATCAAC-AAAACCTTCGAGTTCGA
*
28395 TTCCATTCA
129 TTACATTCA
28404 ACTCGATGAC
Statistics
Matches: 122, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
166 22 0.18
167 76 0.62
169 24 0.20
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (167 bp):
CTCAAGGCGAGAACGACTATCTGTCAAAAAACCTTCGAGTTAAATAACATTCAACTCAAGGGCAT
ATCAAATTTACAGCATAACTCAAGGAGAGAAGGGTTATCTATCAACAAAACCTTCGAGTTCGATT
ACATTCAGCTCAAGGGCATATCAAATTTATAGCATAG
Found at i:29093 original size:18 final size:18
Alignment explanation
Indices: 29047--29086 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 18
29037 TTTTTTATTT
29047 ATTTATTAT-TTATTATA
1 ATTTATTATCTTATTATA
29064 ATTTATTATCTTATTATA
1 ATTTATTATCTTATTATA
29082 TATTT
1 -ATTT
29087 TTCTCTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.43
18 8 0.38
19 4 0.19
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTATTATCTTATTATA
Found at i:30376 original size:24 final size:26
Alignment explanation
Indices: 30347--30404 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
30337 TTTTTACTCA
30347 ATATATTTTTTATTTATTTT-AT-TTT
1 ATATATTTTTTATTT-TTTTCATATTT
*
30372 A-ATATTTTTTCTTTTTTTCATATTT
1 ATATATTTTTTATTTTTTTCATATTT
30397 ATATATTT
1 ATATATTT
30405 CACAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.14
24 14 0.48
25 5 0.17
26 6 0.21
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.72
Consensus pattern (26 bp):
ATATATTTTTTATTTTTTTCATATTT
Found at i:33086 original size:16 final size:15
Alignment explanation
Indices: 33062--33095 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
33052 AACTCTTGCT
*
33062 TTCTTATCTTCTTTC
1 TTCTTATCTTCTTCC
33077 TTCTTCATCTTCTTCC
1 TTCTT-ATCTTCTTCC
33093 TTC
1 TTC
33096 AACCAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.06, C:0.32, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCTTATCTTCTTCC
Found at i:39311 original size:15 final size:15
Alignment explanation
Indices: 39291--39320 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39281 TATATTTTCC
39291 TCAATTACTTATTCT
1 TCAATTACTTATTCT
*
39306 TCAATTATTTATTCT
1 TCAATTACTTATTCT
39321 CCTGCCCCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (15 bp):
TCAATTACTTATTCT
Found at i:40604 original size:23 final size:23
Alignment explanation
Indices: 40575--40629 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
40565 GGATTGAGTT
40575 GTTCAGCTATTAGCTAACGAAAA
1 GTTCAGCTATTAGCTAACGAAAA
40598 GTTCAGCTATTAGCTAACGAAAA
1 GTTCAGCTATTAGCTAACGAAAA
*
40621 GTTTAGCTA
1 GTTCAGCTA
40630 AGCATGGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.29
Consensus pattern (23 bp):
GTTCAGCTATTAGCTAACGAAAA
Found at i:40885 original size:23 final size:22
Alignment explanation
Indices: 40859--40901 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
40849 TCTAACGAAC
*
40859 TAAAAATCCTAATTAATAAATAT
1 TAAAAATCCTAAATAA-AAATAT
40882 TAAAAATCCTAAATAAAAAT
1 TAAAAATCCTAAATAAAAAT
40902 TCTATGCAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAATCCTAAATAAAAATAT
Found at i:47424 original size:32 final size:34
Alignment explanation
Indices: 47378--47446 Score: 124
Period size: 32 Copynumber: 2.1 Consensus size: 34
47368 TGTTATTGAG
47378 TTGGTCTCGGGTGATATGGTTGTTGAGGAGGCTT
1 TTGGTCTCGGGTGATATGGTTGTTGAGGAGGCTT
47412 TTGGT-TC-GGTGATATGGTTGTTGAGGAGGCTT
1 TTGGTCTCGGGTGATATGGTTGTTGAGGAGGCTT
47444 TTG
1 TTG
47447 TTTCTGCGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 28 0.80
33 2 0.06
34 5 0.14
ACGTcount: A:0.12, C:0.07, G:0.41, T:0.41
Consensus pattern (34 bp):
TTGGTCTCGGGTGATATGGTTGTTGAGGAGGCTT
Found at i:50695 original size:23 final size:23
Alignment explanation
Indices: 50652--50695 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
50642 TCTAACAAAC
* * *
50652 TAAAAATCTTAATTAATAATTGT
1 TAAAAATCCTAAATAAAAATTGT
50675 TAAAAATCCTAAATAAAAATT
1 TAAAAATCCTAAATAAAAATT
50696 CTATGCAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAAAATCCTAAATAAAAATTGT
Found at i:57176 original size:5 final size:6
Alignment explanation
Indices: 57161--57203 Score: 68
Period size: 6 Copynumber: 7.0 Consensus size: 6
57151 GCTCGATCAA
*
57161 AAAAAT AAAAAT AAAAAT AAAAACG AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAA-T AAAAAT AAAAAT AAAAAT
57204 GTAACAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:64589 original size:28 final size:28
Alignment explanation
Indices: 64552--64707 Score: 88
Period size: 27 Copynumber: 5.9 Consensus size: 28
64542 ATATTTTAAT
64552 ATATT-TATTAATATTTATAATAATATA
1 ATATTATATTAATATTTATAATAATATA
64579 ATATTATATT-ATA---ATAAT-ATA-A
1 ATATTATATTAATATTTATAATAATATA
**
64601 GATATTATATTTTTATTTTATAA-ATATATA
1 -ATATTATATTAATA-TTTATAATA-ATATA
* * * *
64631 ATATTTTTTTATATATTAATAATGA-ATA
1 ATATTATATTA-ATATTTATAATAATATA
*
64659 GTATTAT-TTATATATTTA-ATATAATATA
1 ATATTATATTA-ATATTTATA-ATAATATA
*
64687 ATA--ATTTTAATATTT-TAATAA
1 ATATTATATTAATATTTATAATAA
64708 AGATATTTAA
Statistics
Matches: 101, Mismatches: 12, Indels: 34
0.69 0.08 0.23
Matches are distributed among these distances:
22 1 0.01
23 13 0.13
24 7 0.07
25 4 0.04
26 10 0.10
27 24 0.24
28 21 0.21
29 18 0.18
30 3 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
ATATTATATTAATATTTATAATAATATA
Found at i:64590 original size:21 final size:22
Alignment explanation
Indices: 64548--64611 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 22
64538 TAAAATATTT
**
64548 TAATATATTTATTAATATTTATAA
1 TAATATAGATATT-ATA-TTATAA
64572 TAATATA-ATATTATATTATAA
1 TAATATAGATATTATATTATAA
64593 TAATATAAGATATTATATT
1 TAATAT-AGATATTATATT
64612 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
21 12 0.32
22 4 0.11
23 14 0.38
24 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TAATATAGATATTATATTATAA
Found at i:64893 original size:22 final size:22
Alignment explanation
Indices: 64856--64914 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
64846 TTTTAATAAT
* *
64856 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAA-ATTTTA
64879 AAAT-AATAATATTAAATTTTA
1 AAATAAATAATATTAAATTTTA
**
64900 TGATAAATAATATTA
1 AAATAAATAATATTA
64915 TTTATTGTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 8 0.26
22 19 0.61
23 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATAAATAATATTAAATTTTA
Found at i:65138 original size:30 final size:29
Alignment explanation
Indices: 65086--65162 Score: 136
Period size: 30 Copynumber: 2.6 Consensus size: 29
65076 TTCTAGAAAT
65086 GTAATTCATTTTCCAGAATTCAAATTCCA
1 GTAATTCATTTTCCAGAATTCAAATTCCA
*
65115 GTAATTCATTTTCTAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAG-AATTCAAATTCCA
65145 GTAATTCATTTTCCAGAA
1 GTAATTCATTTTCCAGAA
65163 AATCAATTAC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 17 0.38
30 28 0.62
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (29 bp):
GTAATTCATTTTCCAGAATTCAAATTCCA
Found at i:65158 original size:15 final size:15
Alignment explanation
Indices: 65086--65160 Score: 98
Period size: 15 Copynumber: 5.1 Consensus size: 15
65076 TTCTAGAAAT
65086 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
65101 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
*
65115 GTAATTCATTTTCTA
1 GTAATTCATTTTCCA
**
65130 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
65145 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
65160 G
1 G
65161 AAAATCAATT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
14 12 0.24
15 37 0.76
ACGTcount: A:0.32, C:0.19, G:0.08, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:68512 original size:16 final size:16
Alignment explanation
Indices: 68488--68522 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
68478 ATTTATAAAC
*
68488 ATTATTTTAAAATTAA
1 ATTAATTTAAAATTAA
*
68504 ATTAATTTAAATTTAA
1 ATTAATTTAAAATTAA
68520 ATT
1 ATT
68523 GTCTTATATC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTAATTTAAAATTAA
Found at i:69512 original size:22 final size:23
Alignment explanation
Indices: 69469--69513 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
69459 GGCATGTCCA
*
69469 TGTTAAAAGTCTAATTTGCAGCT
1 TGTTAAAAGTCTAAATTGCAGCT
69492 TGTT-AAAGTC-AAATTGCCAGCT
1 TGTTAAAAGTCTAAATTG-CAGCT
69514 AAAAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (23 bp):
TGTTAAAAGTCTAAATTGCAGCT
Done.