Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002714.1 Hibiscus syriacus cultivar Beakdansim tig00005600_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: 54298
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:17291 original size:31 final size:31
Alignment explanation
Indices: 17253--17328 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
17243 TGTCCAAGGT
* *
17253 GAAGAAGAGGAAGAAA-AACTGTATAGAAGAA
1 GAAGAAGAAGAA-AAAGAACGGTATAGAAGAA
*
17284 GAAGAAGAAGAAAAAGAACGGTATAGAGGAA
1 GAAGAAGAAGAAAAAGAACGGTATAGAAGAA
* *
17315 AAAGAACAAGAAAA
1 GAAGAAGAAGAAAA
17329 CACGCTAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 3 0.08
31 36 0.92
ACGTcount: A:0.62, C:0.04, G:0.28, T:0.07
Consensus pattern (31 bp):
GAAGAAGAAGAAAAAGAACGGTATAGAAGAA
Found at i:17409 original size:2 final size:2
Alignment explanation
Indices: 17402--17426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17392 TCTTCAAAAT
17402 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17427 TAACGGTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18029 original size:3 final size:3
Alignment explanation
Indices: 18023--18076 Score: 63
Period size: 3 Copynumber: 18.0 Consensus size: 3
18013 TTCATTTTTT
* * * * *
18023 TTA TTA TTA TAA ATA TTA TTA TTA ATA TTA TTT TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
18071 TTA TTA
1 TTA TTA
18077 CAAACATGTC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:18075 original size:15 final size:15
Alignment explanation
Indices: 18023--18076 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
18013 TTCATTTTTT
18023 TTATTATTA-TAA-A
1 TTATTATTATTAATA
18036 -TATTATTATTAATA
1 TTATTATTATTAATA
*
18050 TTATTTTTATTAATA
1 TTATTATTATTAATA
18065 TTATTATTATTA
1 TTATTATTATTA
18077 CAAACATGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
12 8 0.22
13 3 0.08
14 1 0.03
15 24 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTATTATTATTAATA
Found at i:19414 original size:27 final size:26
Alignment explanation
Indices: 19381--19456 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 26
19371 ATATAGTTCT
19381 AATTTTATTTTTATTATTGATTATTTA
1 AATTTTATTTTTATTATTGA-TATTTA
** * * *
19408 TGTTTTACTTTTACTTGTTTATATTTA
1 AATTTTATTTTTA-TTATTGATATTTA
*
19435 AATATTATTTTTATTATT-ATAT
1 AATTTTATTTTTATTATTGATAT
19457 AGTCATATAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 4 0.11
26 4 0.11
27 25 0.66
28 5 0.13
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.66
Consensus pattern (26 bp):
AATTTTATTTTTATTATTGATATTTA
Found at i:30972 original size:8 final size:8
Alignment explanation
Indices: 30955--31003 Score: 62
Period size: 8 Copynumber: 5.9 Consensus size: 8
30945 ATTATGCTTG
*
30955 AAGAAGAA
1 AAGAAAAA
30963 AAGAAAAA
1 AAGAAAAA
30971 AAGAAAAAA
1 AAG-AAAAA
*
30980 AAAAGAAAA
1 AAGA-AAAA
30989 AAGAAAAA
1 AAGAAAAA
30997 AAGAAAA
1 AAGAAAA
31004 GAAAAGGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
8 22 0.61
9 14 0.39
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:30985 original size:19 final size:21
Alignment explanation
Indices: 30958--31008 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
30948 ATGCTTGAAG
30958 AAGAAAAGAAAAAAAG-AAAA
1 AAGAAAAGAAAAAAAGAAAAA
30978 AA-AAAAG-AAAAAAGAAAAA
1 AAGAAAAGAAAAAAAGAAAAA
30997 AAGAAAAGAAAA
1 AAGAAAAGAAAA
31009 GGGGGTCAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 7 0.25
19 11 0.39
20 7 0.25
21 3 0.11
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (21 bp):
AAGAAAAGAAAAAAAGAAAAA
Found at i:30993 original size:26 final size:27
Alignment explanation
Indices: 30955--31008 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
30945 ATTATGCTTG
30955 AAGAAGAAAAGAAAAAAAGAAAAAAAA
1 AAGAAGAAAAGAAAAAAAGAAAAAAAA
*
30982 AAGAA-AAAAGAAAAAAAGAAAAGAAA
1 AAGAAGAAAAGAAAAAAAGAAAAAAAA
31008 A
1 A
31009 GGGGGTCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (27 bp):
AAGAAGAAAAGAAAAAAAGAAAAAAAA
Found at i:31404 original size:19 final size:17
Alignment explanation
Indices: 31362--31410 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
31352 TATTTTCTCT
31362 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
31378 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
31396 AAAATTCAACTTATT
1 -AAATTCAATTTATT
31411 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:31908 original size:114 final size:114
Alignment explanation
Indices: 31702--31927 Score: 344
Period size: 114 Copynumber: 2.0 Consensus size: 114
31692 AAGTGCTACG
* *
31702 TTCTCGTAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATC
* * * * * *
31767 TGATTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATT
66 TGATTCGGTAAGAACCACAAAACCAATCATTGGAATTAAAAGATGAATT
* *
31816 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTTTTCTTTGAGTCATCTGATC
1 TTCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATC
* *
31881 TGGTTCGGTAAGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
66 TGATTCGGTAAGAACCACAAAACCAATCATTGGAATTAAAAGATGAA
31928 CTGCATGATC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 100 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.31
Consensus pattern (114 bp):
TTCTCATAGTAAAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTCATCTGATC
TGATTCGGTAAGAACCACAAAACCAATCATTGGAATTAAAAGATGAATT
Found at i:33064 original size:113 final size:108
Alignment explanation
Indices: 32690--33408 Score: 826
Period size: 113 Copynumber: 6.4 Consensus size: 108
32680 TAATAAGAAG
*
32690 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGAT
* * * * *
32755 TAGCTTTTCCAGAGAAAATTCATAATGAGAAGAACTCATCTGAA
66 CAACATTGCCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAA
* * * *
32799 GAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGA
1 GAA-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGA
32864 TCAACATTGCCAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
65 TCAACATTGCCAGGAA-AGTTCATAATGAGAAGAA--C-TCATCTGAA
* * *
32912 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGAT
* * *
32977 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAACAA
66 CAACATTGCCAG-GAAAGTTCATAATGAGAAGAACTCATCTG---AA
* * ** *
33024 GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTTATCATTTGATGGA
1 -GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGA
*
33089 TCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAA
65 TCAACATTGCCAGG-AAAGTTCATAATGAGAAGAA--C-TCATCTGAA
* * * *
33137 GAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGA
1 GAA-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGA
*
33202 TCAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAA
65 TCAACATTGCCAGG-AAAGTTCATAATGAGAAGAACTCATCTGAA
* ** * * *
33247 GAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAATGAGA
1 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCAC----T----
* * * *
33312 TAGATTAGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
58 T-GA-T-GGATCAACATTGCCAG-GAAAGTTCATAATGAGAAGAACTCATCTGAA
**
33367 GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTG
1 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
33409 AATGACTCTA
Statistics
Matches: 534, Mismatches: 49, Indels: 43
0.85 0.08 0.07
Matches are distributed among these distances:
109 56 0.10
110 95 0.18
111 1 0.00
112 89 0.17
113 198 0.37
115 1 0.00
116 7 0.01
117 1 0.00
118 2 0.00
119 1 0.00
120 82 0.15
121 1 0.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (108 bp):
GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATCCATCACTTGATGGAT
CAACATTGCCAGGAAAGTTCATAATGAGAAGAACTCATCTGAA
Found at i:33140 original size:222 final size:221
Alignment explanation
Indices: 32690--33288 Score: 911
Period size: 222 Copynumber: 2.7 Consensus size: 221
32680 TAATAAGAAG
*
32690 GAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
* *
32755 TAGCTTTTCCAGAGAAAATTCATAATGAGAAGAACTCATCTG--AAGAAGGAAGAAGTTCATAAT
66 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGAA-GAAGAAGTTCATAAT
32818 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAG
130 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAG
32883 TTCATAATGAGAAGAACTCGTCATCTGAA
195 TTCATAATGAGAAGAACTCGTCATCT--A
*
32912 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTACTCAAATCCATCACTTGATGGAT
1 GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
32977 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAACAAGGAAGAAGAAGTTCATAA
66 CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA-AA-GAAGAAGAAGTTCATAA
* *
33042 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTTATCATTTGATGGATCAACATTGCCAGGTAGA
129 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGA
33107 GTTCATAATGAGAAGAACTCGTCATCTGAA
194 GTTCATAATGAGAAGAACTCGTCATCT--A
* * ** * *
33137 GAAGGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGA
1 GAA-GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGA
* * * * *
33202 TCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG--AAGAAGAAGAAGTTCACAA
65 TCAGCTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAAAGAAGAAGAAGTTCATAA
**
33264 TGAGAAGAGCTTGTTCAACCTTTTG
129 TGAGAAGAATTTGTTCAACCTTTTG
33289 CATAATTCTA
Statistics
Matches: 351, Mismatches: 20, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
222 142 0.40
223 2 0.01
225 113 0.32
226 94 0.27
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (221 bp):
GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGAT
CAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAAAGAAGAAGAAGTTCATAATG
AGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGT
TCATAATGAGAAGAACTCGTCATCTA
Found at i:33371 original size:120 final size:118
Alignment explanation
Indices: 33219--33487 Score: 378
Period size: 120 Copynumber: 2.3 Consensus size: 118
33209 TGCCAGGTAG
33219 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACC
* * * * * * **
33284 TTTTGCATAATTCTATCACAGAATGAGATAGATTAGCATCAGCTTTTCCAG-AGAA
66 TTTTGAATAACTCTATCACAGAAGGAAATAGATCA--AT-AGCATCCCCAGCAGAA
*
33339 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACC
* * * * *
33404 TTTTGAATGACTCTATCACATAAGGAAATAGGTCAATATCATCCCCAGCGGAA
66 TTTTGAATAACTCTATCACAGAAGGAAATAGATCAATAGCATCCCCAGCAGAA
33457 AGTTCATAATGAGAAGAACTCATCTGAAGAA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA
33488 AGAGAAGAAT
Statistics
Matches: 134, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
117 7 0.05
118 36 0.27
120 91 0.68
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (118 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCAACC
TTTTGAATAACTCTATCACAGAAGGAAATAGATCAATAGCATCCCCAGCAGAA
Found at i:33411 original size:338 final size:328
Alignment explanation
Indices: 32687--33411 Score: 985
Period size: 335 Copynumber: 2.1 Consensus size: 328
32677 TCATAATAAG
32687 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATG
1 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG----AATCCATCACTTGATG
* * * *
32752 GATTAGCTTTTCCAGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGTTCATAA
62 GATCAACATTGCCAGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGTTCATAA
32817 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGA
127 TGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGA
* *
32882 GTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA
192 GTTCATAATGAGAAGAAC-CGTCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCAA
*
32947 CCTTTTACTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
256 CCTTTTACTCAAATCCATCACTTGATGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAAC
33012 TCATCTGAA
321 TCATCTG-A
** *
33021 CAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTTATCATTTGAT
1 -AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC---T-TTTGAATCCATCACTTGAT
* *
33086 GGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGTT
61 GGATCAACATTGCCAGAG-AAAATTCATAATGAGAAGAA--C-TCATCTGAAGAAGGAAGAAGTT
33150 CATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG
122 CATAATGAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAG
* * *
33215 GTAGAGTTCATAATGAGAAGAA-C-TCATCTGAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGT
187 GAAGAGTTCATAATGAGAAGAACCGTCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGT
* * *
33278 TCAACCTTTTGCAT-AATTCTATCACAGAATGAGATAGATTAGCATCAGCTTTTCCAGAGAAAGT
252 TCAACCTTTTAC-TCAAATCCATCAC----T----T-GA-T-GCATCAGCTTTTCCAGAGAAAGT
33342 TCATAATGAGAAGAACTCATCTG-
305 TCATAATGAGAAGAACTCATCTGA
**
33365 AA-GAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGAAT
1 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGAAT
33412 GACTCTATCA
Statistics
Matches: 350, Mismatches: 20, Indels: 37
0.86 0.05 0.09
Matches are distributed among these distances:
334 1 0.00
335 138 0.39
336 2 0.01
337 1 0.00
338 116 0.33
339 6 0.02
342 35 0.10
343 3 0.01
344 2 0.01
345 1 0.00
346 45 0.13
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (328 bp):
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGAATCCATCACTTGATGGATC
AACATTGCCAGAGAAAATTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGTTCATAATGAG
AAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATCAACATTGCCAGGAAGAGTTC
ATAATGAGAAGAACCGTCATCTGAAGAAGAAGAAATTCACAATGAGAAGAACTTGTTCAACCTTT
TACTCAAATCCATCACTTGATGCATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC
TGA
Found at i:33643 original size:3 final size:3
Alignment explanation
Indices: 33637--33678 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
33627 TTCATTTTTT
* * *
33637 TTA TTA TTA TTA TAA ATA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
33679 CAAACATGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:34422 original size:11 final size:11
Alignment explanation
Indices: 34406--34441 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
34396 TCCCTCCGAT
34406 GAGGGAAGCTA
1 GAGGGAAGCTA
34417 GAGGGAAGCTA
1 GAGGGAAGCTA
* *
34428 GAGAGAAGCCA
1 GAGGGAAGCTA
34439 GAG
1 GAG
34442 AGAACTCTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.44, T:0.06
Consensus pattern (11 bp):
GAGGGAAGCTA
Found at i:34442 original size:11 final size:11
Alignment explanation
Indices: 34410--34445 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
34400 TCCGATGAGG
*
34410 GAAGCTAGAGG
1 GAAGCTAGAGA
34421 GAAGCTAGAGA
1 GAAGCTAGAGA
*
34432 GAAGCCAGAGA
1 GAAGCTAGAGA
34443 GAA
1 GAA
34446 CTCTGGCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.44, C:0.11, G:0.39, T:0.06
Consensus pattern (11 bp):
GAAGCTAGAGA
Found at i:35029 original size:27 final size:26
Alignment explanation
Indices: 34996--35071 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 26
34986 ATATAGTTCT
34996 AATTTTATTTTTATTATTGATTATTTA
1 AATTTTATTTTTATTATTGA-TATTTA
** * * *
35023 TGTTTTAATTTTACTTGTTTATATTTA
1 AATTTTATTTTTA-TTATTGATATTTA
*
35050 AATATTATTTTTATTATT-ATAT
1 AATTTTATTTTTATTATTGATAT
35072 AGTCATATAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
25 4 0.11
26 4 0.11
27 25 0.66
28 5 0.13
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (26 bp):
AATTTTATTTTTATTATTGATATTTA
Found at i:37433 original size:32 final size:31
Alignment explanation
Indices: 37392--37483 Score: 105
Period size: 31 Copynumber: 2.9 Consensus size: 31
37382 CTAACATGGC
* *
37392 TGAGGGACTAAAATCGAATGAGAGTCTATGAT-
1 TGAGGGACTAAAATCGAATG-GA-TCGATAATG
37424 TGAGGGACTAAAATCGAATGGATCGATAATG
1 TGAGGGACTAAAATCGAATGGATCGATAATG
* * * *
37455 TTAGGGACTAAAATCAAACGGATTGATAA
1 TGAGGGACTAAAATCGAATGGATCGATAA
37484 CGTTAGAGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 6 0.11
31 27 0.51
32 20 0.38
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (31 bp):
TGAGGGACTAAAATCGAATGGATCGATAATG
Found at i:39933 original size:2 final size:2
Alignment explanation
Indices: 39926--39987 Score: 108
Period size: 2 Copynumber: 31.5 Consensus size: 2
39916 CCGTCCAAAT
39926 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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 TA
*
39968 TA TA TA TA TA -A TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
39988 TTATTCTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41121 original size:27 final size:28
Alignment explanation
Indices: 41091--41154 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
41081 TTTCATTGTA
*
41091 TTATTATATATATATTATTATTATT-TT
1 TTATTATATATATATCATTATTATTATT
*
41118 TTA-TACTATATCTATCATTATTATTATT
1 TTATTA-TATATATATCATTATTATTATT
*
41146 TAATTATAT
1 TTATTATAT
41155 TTTTCTATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 2 0.06
27 20 0.65
28 7 0.23
29 2 0.06
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (28 bp):
TTATTATATATATATCATTATTATTATT
Found at i:41162 original size:30 final size:30
Alignment explanation
Indices: 41095--41153 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
41085 ATTGTATTAT
* *
41095 TATATATAT-ATTATTATTATTTTTTATAC
1 TATATCTATCATTATTATTATTTATTATAC
41124 TATATCTATCATTATTATTATTTAATTATA
1 TATATCTATCATTATTATTATTT-ATTATA
41154 TTTTTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (30 bp):
TATATCTATCATTATTATTATTTATTATAC
Found at i:41185 original size:21 final size:22
Alignment explanation
Indices: 41141--41185 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
41131 ATCATTATTA
* *
41141 TTATTTAATTATATTTTTCTAT
1 TTATTTAACTATATTTCTCTAT
41163 TTATTT-ACTATATTTCTCTAT
1 TTATTTAACTATATTTCTCTAT
41184 TT
1 TT
41186 TTGTCTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTTAACTATATTTCTCTAT
Found at i:41276 original size:23 final size:25
Alignment explanation
Indices: 41237--41298 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
41227 CTCATTATTT
* *
41237 ATATTTAGCTATATTTTT-TCATGT-
1 ATATTTA-TTATATTTTTCTTATGTA
41261 AT-TTTATTATATTTTTCTTATGTA
1 ATATTTATTATATTTTTCTTATGTA
41285 CATATTTATTATAT
1 -ATATTTATTATAT
41299 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 9 0.28
23 9 0.28
24 2 0.06
25 2 0.06
26 10 0.31
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.61
Consensus pattern (25 bp):
ATATTTATTATATTTTTCTTATGTA
Found at i:46715 original size:17 final size:16
Alignment explanation
Indices: 46693--46726 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
46683 TAAAAACAGT
46693 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
46710 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
46726 A
1 A
46727 TCCTCACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:50566 original size:19 final size:20
Alignment explanation
Indices: 50544--50587 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
50534 GAGAAAAGGT
50544 AAAAGTTAA-AATGAAAGAG
1 AAAAGTTAATAATGAAAGAG
* *
50563 AAAAATTAATAATGAAAGAT
1 AAAAGTTAATAATGAAAGAG
50583 AAAAG
1 AAAAG
50588 AAAAAGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.16, T:0.18
Consensus pattern (20 bp):
AAAAGTTAATAATGAAAGAG
Done.