Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005825.1 Hibiscus syriacus cultivar Beakdansim tig00013647_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: 82724
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:2890 original size:16 final size:16
Alignment explanation
Indices: 2866--2907 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
2856 TGAAACAAAA
*
2866 TTTCCTTTTAGATTTT
1 TTTCATTTTAGATTTT
2882 TTTCATTTTAGATTTT
1 TTTCATTTTAGATTTT
2898 TTTCATTTTA
1 TTTCATTTTA
2908 TGAGACTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (16 bp):
TTTCATTTTAGATTTT
Found at i:11857 original size:6 final size:6
Alignment explanation
Indices: 11833--11873 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
11823 GCTATAGTAG
* *
11833 AAGAAA AA-TAA ATGAAA AAGAAA AAGAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
11874 GCAAAGATAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 3 0.10
6 27 0.90
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:12115 original size:2 final size:2
Alignment explanation
Indices: 12108--12133 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
12098 CAGAAACTTC
12108 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
12134 ACACTTGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:14070 original size:26 final size:24
Alignment explanation
Indices: 14024--14094 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 24
14014 ATGTTATGAT
*
14024 GATGAATTTTTAAAATCTTAAGAAGAG
1 GATGAA-TTTTAAAATTTTAAG-AG-G
*
14051 GATGAATTTTGAAATTTTAAGAGG
1 GATGAATTTTAAAATTTTAAGAGG
14075 GATGAGATTTTAAAAATTTT
1 GATGA-ATTTT-AAAATTTT
14095 GGGAAGGACA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
24 6 0.15
25 7 0.18
26 20 0.51
27 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.20, T:0.38
Consensus pattern (24 bp):
GATGAATTTTAAAATTTTAAGAGG
Found at i:28106 original size:2 final size:2
Alignment explanation
Indices: 28099--28139 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
28089 TCAATCTACA
28099 AT AT 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 AT AT A
28140 ATTTACGACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:28314 original size:13 final size:13
Alignment explanation
Indices: 28296--28338 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
28286 AATGACGCGC
28296 AATGAGCTTCATA
1 AATGAGCTTCATA
*
28309 AATGAGCGTCATA
1 AATGAGCTTCATA
*
28322 AATGCG-TGTCATA
1 AATGAGCT-TCATA
28335 AATG
1 AATG
28339 CGCGTCATCT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (13 bp):
AATGAGCTTCATA
Found at i:28339 original size:13 final size:13
Alignment explanation
Indices: 28304--28346 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
28294 GCAATGAGCT
*
28304 TCATAAATGAGCG
1 TCATAAATGCGCG
*
28317 TCATAAATGCGTG
1 TCATAAATGCGCG
28330 TCATAAATGCGCG
1 TCATAAATGCGCG
28343 TCAT
1 TCAT
28347 CTTAAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (13 bp):
TCATAAATGCGCG
Found at i:31795 original size:597 final size:598
Alignment explanation
Indices: 30103--33091 Score: 5718
Period size: 597 Copynumber: 5.0 Consensus size: 598
30093 AATTTAGGGG
30103 TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
1 TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
30168 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
66 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
30233 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
131 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
* *
30298 TAACGTCTCAATGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGATGTTTATGG
196 TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
30363 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
261 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
*
30428 ATAATTATAAT-AAAATATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
326 ATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
30492 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
391 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
30557 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
456 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
*
30622 TATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGTGGTTGG
521 TATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
30687 TTTGAAACTACTA
586 TTTGAAACTACTA
*
30700 CTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
1 TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
30765 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
66 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
30830 TTTAAGGGCTCAAAT-AAAATTCAAAC-TTTTACTAACGTGCCACATCATCCAACTCACGACAGC
131 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
30893 TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
196 TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
*
30958 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACAAACTCTGCATTTTACCCCAAAAT
261 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
31023 ATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
326 ATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
31088 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
391 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
31153 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
456 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
31218 TATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
521 TATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
31283 TTTGAAACTACTA
586 TTTGAAACTACTA
31296 TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
1 TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
31361 GA-TTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
66 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
31425 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
131 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
31490 TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
196 TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
31555 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
261 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
31620 ATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
326 ATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
31685 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
391 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
31750 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
456 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
*
31815 TATATTTCCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
521 TATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
31880 TTTGAAACTACTA
586 TTTGAAACTACTA
* * *
31893 TTTGATTTTAGGGATTTTTCATTTCTGATTTGGGAATAAAATATACGAGGGAAAGAGGGTTAATT
1 TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
31958 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
66 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
32023 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
131 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
*
32088 TAACGCCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
196 TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
32153 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
261 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
*
32218 ATAATTATAAT-AAAATATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
326 ATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
32282 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
391 TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
32347 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
456 TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
* *
32412 TATATTTGCTTCCAAAACATAAAGTTAAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
521 TATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
32477 TTTGAAACTACTA
586 TTTGAAACTACTA
* * *
32490 TTTGATTTTAGGGATTTTTCATTTCTAATTTGGGAATAAAATATATGAGGGAAAGAGGGTTAATT
1 TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
32555 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
66 GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
*
32620 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAGCTCACGACAGC
131 TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
* *
32685 TAACGTCTCAGTGATCACATCTTAATTAAAGCGAAACAAAAGTGACCAAGTATTGACGTTTATGG
196 TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
* *
32750 ATCGAGTGACTATAGGTTTAAAAGAAAGAAACAAAAGTGACAAACTCTGCATTTTACCCCCAAAA
261 ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTA-CCCCAAAA
*
32815 CATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAA
325 TATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAA
32880 TTTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTA
390 TTTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTA
32945 TTAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAA
455 TTAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAA
*
33010 TTATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGGAATCATAGTTTTTGCGGTTG
520 TTATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTG
33075 GTTTGAAACTACTA
585 GTTTGAAACTACTA
33089 TTT
1 TTT
33092 TCACCGTATT
Statistics
Matches: 2356, Mismatches: 30, Indels: 10
0.98 0.01 0.00
Matches are distributed among these distances:
595 252 0.11
596 347 0.15
597 1211 0.51
598 286 0.12
599 260 0.11
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.34
Consensus pattern (598 bp):
TTTGATTTTAGGGATTTTCCATTTCTGATTTGGGAATAAAACATATGAGGGAAAGAGGGTTAATT
GATTTTTTTATCCCTGAATTATTTTAGATTTACAAAAAGACCCATAATGAGTAATTTATCTCAAG
TTTAAGGGCTCAAATAAAAATTCAAACTTTTTACTAACGTGCCACATCATCCAACTCACGACAGC
TAACGTCTCAGTGACCACATCTTAATTAAAACGAAACAAAAGTGACCAAGTATTGACGTTTATGG
ATCGAGTGACTATAGGTTTAAAAGAATGAAACAAAAGTGACCAACTCTGCATTTTACCCCAAAAT
ATAATTATAATAAAAACATATTTTATATAACTCACTACTAATATTTTAATATATAAATCATAAAT
TTTATTTACTTTTAAATAATTAAAATAAATTATTAAAAGTAATAAATTTTTAAGGATGTTAGTAT
TAAATTATTAAAATAAAATATAAATACATAATTGAGTGAAACACATGCATTAGTAAAGGTAAAAT
TATATTTGCTTCCAAAACGTAAAGTTGAAAATGAAAAAGCTAGAAATCATAGTTTTTGCGGTTGG
TTTGAAACTACTA
Found at i:38859 original size:10 final size:10
Alignment explanation
Indices: 38846--38877 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
38836 ATCATTTCCC
38846 ATAATTTTTA
1 ATAATTTTTA
38856 ATAATTTTTAA
1 ATAATTTTT-A
38867 ATAATTTTTA
1 ATAATTTTTA
38877 A
1 A
38878 AGGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:38869 original size:11 final size:11
Alignment explanation
Indices: 38846--38878 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
38836 ATCATTTCCC
38846 ATAATTTTT-A
1 ATAATTTTTAA
38856 ATAATTTTTAA
1 ATAATTTTTAA
38867 ATAATTTTTAA
1 ATAATTTTTAA
38878 A
1 A
38879 GGTAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATAATTTTTAA
Found at i:40451 original size:21 final size:23
Alignment explanation
Indices: 40425--40476 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
40415 AGTCACTGGT
40425 ATAATTTACCTTTT-A-TTTTAA
1 ATAATTTACCTTTTAATTTTTAA
*
40446 ATAATTTATCTTTTAATTTTTAA
1 ATAATTTACCTTTTAATTTTTAA
*
40469 TTAATTTA
1 ATAATTTA
40477 TAATTATACG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 13 0.48
22 1 0.04
23 13 0.48
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.60
Consensus pattern (23 bp):
ATAATTTACCTTTTAATTTTTAA
Found at i:40473 original size:23 final size:21
Alignment explanation
Indices: 40425--40477 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 21
40415 AGTCACTGGT
*
40425 ATAATTTACCTTTTATTTTAA
1 ATAATTTATCTTTTATTTTAA
40446 ATAATTTATCTTTTAATTTTTAA
1 ATAATTTATCTTTT-A-TTTTAA
*
40469 TTAATTTAT
1 ATAATTTAT
40478 AATTATACGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 13 0.46
22 1 0.04
23 14 0.50
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (21 bp):
ATAATTTATCTTTTATTTTAA
Found at i:42151 original size:34 final size:33
Alignment explanation
Indices: 42069--42164 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
42059 TGGCAAGTTC
*
42069 GAAAATTCATCTTGGTTGGTGGCCAACTTATTG
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTA
*
42102 GAAATTTCATCTTGGTTGGTGGCCAACTTATTA
1 GAAAATTCATCTTGGTTGGTGGCCAACTTATTA
*
42135 GAAAATTCATCTTTGGTAGGTGGCCAACTT
1 GAAAATTCATC-TTGGTTGGTGGCCAACTT
42165 TGCACATGGG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 41 0.71
34 17 0.29
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.36
Consensus pattern (33 bp):
GAAAATTCATCTTGGTTGGTGGCCAACTTATTA
Found at i:46685 original size:33 final size:34
Alignment explanation
Indices: 46643--46708 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
46633 ATTTGGCAAG
* *
46643 TTGGAAAATTCATCTT-GGTTGGTGGTCAACTTA
1 TTGGAAAATTCATCTTAGGTAGGTGGCCAACTTA
46676 TTGGAAAATTCATCTTAGGTAGGTGGCCAACTT
1 TTGGAAAATTCATCTTAGGTAGGTGGCCAACTT
46709 TGCACATGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 16 0.53
34 14 0.47
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (34 bp):
TTGGAAAATTCATCTTAGGTAGGTGGCCAACTTA
Found at i:62871 original size:59 final size:59
Alignment explanation
Indices: 62746--62881 Score: 152
Period size: 59 Copynumber: 2.3 Consensus size: 59
62736 GAGTTTAAGA
* * * * *
62746 GACCATTTTGTAACTTTTAATAGTCGGGGACTCAACAAAATAACATGCTATAGTTAGAG
1 GACCATTTTGTAACTTTAAATAGTCAGAGACTCAACAAAACAACATCCTATAGTTAGAG
* * *
62805 GATCATTTTGTAACTTTAAATTA-TCTAGAGACTCAATAAAGCAACATCCTATAGTTAG-G
1 GACCATTTTGTAACTTTAAA-TAGTC-AGAGACTCAACAAAACAACATCCTATAGTTAGAG
62864 GACCATTTATGT-ACTTTA
1 GACCATTT-TGTAACTTTA
62882 CCCTTAATTA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
59 34 0.52
60 31 0.48
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (59 bp):
GACCATTTTGTAACTTTAAATAGTCAGAGACTCAACAAAACAACATCCTATAGTTAGAG
Found at i:65860 original size:19 final size:19
Alignment explanation
Indices: 65836--65890 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
65826 GCTTCTTGGA
*
65836 GAGAGAGAAAAGAAATAAG
1 GAGAGAGAAAAGAAAGAAG
*
65855 GAGAGAGAAAAAGAAAGAGG
1 GAGAGAG-AAAAGAAAGAAG
65875 GAGA-AG-AAAGAAAGAA
1 GAGAGAGAAAAGAAAGAA
65891 AGAAAGAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 9 0.28
19 9 0.28
20 14 0.44
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (19 bp):
GAGAGAGAAAAGAAAGAAG
Found at i:65871 original size:4 final size:4
Alignment explanation
Indices: 65864--65911 Score: 53
Period size: 4 Copynumber: 11.8 Consensus size: 4
65854 GGAGAGAGAA
**
65864 AAAG AAAG AGGG AGAAG AAAG AAAG AAAG AAAG AAAG -AAG TAAAG AAA
1 AAAG AAAG AAAG A-AAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAA
65912 AATGTGGGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
4 29 0.78
5 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:69052 original size:26 final size:26
Alignment explanation
Indices: 69019--69077 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
69009 CCTATAAAGT
*
69019 AGATTTTCTACATAGAAGGAAAAGGA
1 AGATTTTCTACATAAAAGGAAAAGGA
*
69045 AGATTTTCTACATAAAAGTAAAAGGA
1 AGATTTTCTACATAAAAGGAAAAGGA
*
69071 AAATTTT
1 AGATTTT
69078 TACTTTTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.29
Consensus pattern (26 bp):
AGATTTTCTACATAAAAGGAAAAGGA
Found at i:74844 original size:20 final size:20
Alignment explanation
Indices: 74811--74865 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
74801 ACAGTGTTAG
* *
74811 AAGTTTCGATACTTTC-TCA
1 AAGTTTTGAAACTTTCATCA
74830 ATAGTTTTGAAACTTTCATCA
1 A-AGTTTTGAAACTTTCATCA
74851 AAGTTTTGAAACTTT
1 AAGTTTTGAAACTTT
74866 TAAAAATAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 27 0.84
21 4 0.12
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (20 bp):
AAGTTTTGAAACTTTCATCA
Found at i:77172 original size:21 final size:21
Alignment explanation
Indices: 77148--77193 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
77138 CAAATTATTG
*
77148 TAAAATGGTCATTATATGTTA
1 TAAAATAGTCATTATATGTTA
* * *
77169 TAAAATAGTGATTATTTTTTA
1 TAAAATAGTCATTATATGTTA
77190 TAAA
1 TAAA
77194 TTTAAAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (21 bp):
TAAAATAGTCATTATATGTTA
Found at i:77235 original size:31 final size:32
Alignment explanation
Indices: 77184--77243 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
77174 TAGTGATTAT
*
77184 TTTTTATAAATTTAAAGAATATTTTTTAATCA
1 TTTTTATAAATTTAAAGAATAATTTTTAATCA
* *
77216 TTTTT-TAACTTTAATGAATAATTTTTAA
1 TTTTTATAAATTTAAAGAATAATTTTTAA
77244 AATTATAGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 20 0.80
32 5 0.20
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTTTATAAATTTAAAGAATAATTTTTAATCA
Done.