Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004483.1 Hibiscus syriacus cultivar Beakdansim tig00009878_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: 95792
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:323 original size:24 final size:23
Alignment explanation
Indices: 267--329 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 23
257 GCGACCTACC
* * *
267 CCTCGGATGGCCTCTGTTGGATG
1 CCTCGGATGCCCTCGGTCGGATG
*
290 CGCTCAGATGCCCTCGGTCGGATGG
1 C-CTCGGATGCCCTCGGTCGGAT-G
*
315 CCTCGGATGCTCTCG
1 CCTCGGATGCCCTCG
330 CATAGCTCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
23 1 0.03
24 29 0.91
25 2 0.06
ACGTcount: A:0.10, C:0.32, G:0.33, T:0.25
Consensus pattern (23 bp):
CCTCGGATGCCCTCGGTCGGATG
Found at i:2351 original size:22 final size:21
Alignment explanation
Indices: 2316--2365 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
2306 TTTATAATTT
* *
2316 ATTATTAATTTAAAGCCCTAA
1 ATTATAAATTTAAAGCCCAAA
* *
2337 ATTATAAATCTTAAATCTCAAA
1 ATTATAAAT-TTAAAGCCCAAA
2359 ATTATAA
1 ATTATAA
2366 CCTTGAACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 8 0.33
22 16 0.67
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTATAAATTTAAAGCCCAAA
Found at i:10441 original size:19 final size:20
Alignment explanation
Indices: 10412--10450 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10402 AAAGGAAATC
10412 GGGGCTAAAATTGAA-TTTAA
1 GGGGCTAAAA-TGAACTTTAA
10432 GGGG-TAAAATGAACTTTAA
1 GGGGCTAAAATGAACTTTAA
10451 AATAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.41, C:0.05, G:0.26, T:0.28
Consensus pattern (20 bp):
GGGGCTAAAATGAACTTTAA
Found at i:16164 original size:23 final size:24
Alignment explanation
Indices: 16137--16182 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
16127 GGATTTTTTA
*
16137 GTATTGCTCTTGTAT-TTTCTTGC
1 GTATTGCTCTGGTATCTTTCTTGC
*
16160 GTATTTCTCTGGTATCTTTCTTG
1 GTATTGCTCTGGTATCTTTCTTG
16183 TCCTTTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.09, C:0.17, G:0.17, T:0.57
Consensus pattern (24 bp):
GTATTGCTCTGGTATCTTTCTTGC
Found at i:19151 original size:42 final size:44
Alignment explanation
Indices: 19099--19182 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 44
19089 GTGTCTTTTT
*
19099 TGGCATCTATTATCGATCGAATTG-A-ATATATACTCTGTCATA
1 TGGCATCTATTATCAATCGAATTGAATATATATACTCTGTCATA
* * *
19141 TGGCTTCTATTATTAATTGAATTGAATATATATACTCTGTCA
1 TGGCATCTATTATCAATCGAATTGAATATATATACTCTGTCA
19183 CAATCCTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 20 0.56
43 1 0.03
44 15 0.42
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (44 bp):
TGGCATCTATTATCAATCGAATTGAATATATATACTCTGTCATA
Found at i:20627 original size:30 final size:30
Alignment explanation
Indices: 20468--20629 Score: 102
Period size: 30 Copynumber: 5.5 Consensus size: 30
20458 CTTAATAAAA
* * *
20468 TAAGGGACT-AAATAGTAATAACAGAAATT
1 TAAGGGACTAAAATAGAAAAAACAGAAACT
*
20497 TACA-GGACTAAAACA-ACAAAAACA-ACAACT
1 TA-AGGGACTAAAATAGA-AAAAACAGA-AACT
* * * * *
20527 TAAAGGACCAAAATAGCAAAAA-ATAAACC
1 TAAGGGACTAAAATAGAAAAAACAGAAACT
* * * * *
20556 CAAAGGACTAATATAGAAAAAAGAGAAAGT
1 TAAGGGACTAAAATAGAAAAAACAGAAACT
* *
20586 TAAAGTG-CTAAAATAGAAAAAGCAGAAACT
1 T-AAGGGACTAAAATAGAAAAAACAGAAACT
20616 TAAGGGACTAAAAT
1 TAAGGGACTAAAAT
20630 GGTATTAATA
Statistics
Matches: 100, Mismatches: 23, Indels: 19
0.70 0.16 0.13
Matches are distributed among these distances:
29 35 0.35
30 62 0.62
31 3 0.03
ACGTcount: A:0.57, C:0.12, G:0.15, T:0.15
Consensus pattern (30 bp):
TAAGGGACTAAAATAGAAAAAACAGAAACT
Found at i:24089 original size:322 final size:322
Alignment explanation
Indices: 23597--24250 Score: 1073
Period size: 322 Copynumber: 2.0 Consensus size: 322
23587 TTTTAACGGT
*
23597 GTTAAAATAGAGTTGACATCAGTAAACTTTTCTAAACATTGGTTGTTACTTAAAGGAACGCAAAA
1 GTTAAAATACAGTTGACATCAGTAAACTTTTCTAAACATTGGTTGTTACTTAAAGGAACGCAAAA
*
23662 TAAATGTAGTTAGACGATTTTTTTTAAAGGGAAATTTTATATTGTATTTGAGACACAACTACAAA
66 TAAATGTAGTTAGACAATTTTTTTTAAAGGGAAATTTTATATTGTATTTGAGACACAACTACAAA
23727 ACAAATAAAGATGGAGACTTATGCCTCATTAAAAAAACATTTCTGATCTTAAATGAAAGAAAAAG
131 ACAAATAAAGATGGAGACTTATGCCTCATTAAAAAAACATTTCTGATCTTAAATGAAAGAAAAAG
*
23792 AGTGTGCCGCAGAACATGGACATATAACTAGATTTTG-C-C-CCT-AACTGACACCCGACCAACT
196 AGTGTGCCACAGAACATGGACATATAACTAGATTTTGCCACACCTGAACTGACACCCGACCAACT
23853 TTTCAAACTAACTATACCCCCTAGATCAGTATACGTTACTACACCATATTAATAAGGGAACC
261 TTTCAAACTAACTATACCCCCTAGATCAGTATACGTTACTACACCATATTAATAAGGGAACC
* *
23915 GTTAAAATACAGTTGATATCAGTAAACTTTTCTAAACATTGGTTGTTACTTAAATGAACGCAAAA
1 GTTAAAATACAGTTGACATCAGTAAACTTTTCTAAACATTGGTTGTTACTTAAAGGAACGCAAAA
*
23980 TAAATGTAGTTAGACAATTTTTTTTTTTGAAAGGGAAATTTTGTATTGTATTTGAGACACAACTA
66 TAAATGTAGTTAGACAA---TTTTTTTT-AAAGGGAAATTTTATATTGTATTTGAGACACAACTA
*
24045 CAAAACAAATAAAGATGGAGACTTATGCCTCATTAAAAAAACATTTTTGATCTTAAATGAAAGAA
127 CAAAACAAATAAAGATGGAGACTTATGCCTCATTAAAAAAACATTTCTGATCTTAAATGAAAGAA
*
24110 AAAGAGTGTGCCACGGAACATGGACATATAACTAGATTTTGCCCCTCACAATGATCCTAGGAACT
192 AAAGAGTGTGCCACAGAACATGGACATATAACTAGATTTTG---C-CAC----A-CCT--GAACT
24175 GACACCCGACCAACTTTTCAAACTAACTATACCCCCTAGATCAGTATACGTTACTACACCATATT
246 GACACCCGACCAACTTTTCAAACTAACTATACCCCCTAGATCAGTATACGTTACTACACCATATT
24240 AATAAGGGAAC
311 AATAAGGGAAC
24251 ACAACAAAAG
Statistics
Matches: 309, Mismatches: 8, Indels: 19
0.92 0.02 0.06
Matches are distributed among these distances:
318 78 0.25
321 8 0.03
322 138 0.45
327 1 0.00
328 1 0.00
334 3 0.01
337 80 0.26
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (322 bp):
GTTAAAATACAGTTGACATCAGTAAACTTTTCTAAACATTGGTTGTTACTTAAAGGAACGCAAAA
TAAATGTAGTTAGACAATTTTTTTTAAAGGGAAATTTTATATTGTATTTGAGACACAACTACAAA
ACAAATAAAGATGGAGACTTATGCCTCATTAAAAAAACATTTCTGATCTTAAATGAAAGAAAAAG
AGTGTGCCACAGAACATGGACATATAACTAGATTTTGCCACACCTGAACTGACACCCGACCAACT
TTTCAAACTAACTATACCCCCTAGATCAGTATACGTTACTACACCATATTAATAAGGGAACC
Found at i:29663 original size:38 final size:38
Alignment explanation
Indices: 29610--29688 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
29600 CTATGAATGA
* *
29610 CTCGGCAGTAATCAAGGCTTTGGCAAGGTCTTTGACTC
1 CTCGGCAGTAATCAAGGCTTTGGCAAGATCCTTGACTC
* * *
29648 CTCGGCGGTAGTCAAGGCTTTGGCGAGATCCTTGACTC
1 CTCGGCAGTAATCAAGGCTTTGGCAAGATCCTTGACTC
29686 CTC
1 CTC
29689 AACGTTCTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.28
Consensus pattern (38 bp):
CTCGGCAGTAATCAAGGCTTTGGCAAGATCCTTGACTC
Found at i:31090 original size:21 final size:21
Alignment explanation
Indices: 31064--31106 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
31054 ATTCTGTCGT
31064 GGGCTTGGCGTGCTTTGGGGC
1 GGGCTTGGCGTGCTTTGGGGC
*
31085 GGGCTTGGTGTGCTTTGGGGC
1 GGGCTTGGCGTGCTTTGGGGC
31106 G
1 G
31107 AGCCTCAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.30
Consensus pattern (21 bp):
GGGCTTGGCGTGCTTTGGGGC
Found at i:34097 original size:13 final size:13
Alignment explanation
Indices: 34068--34102 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
34058 ATAACTAATA
*
34068 ATATTAAAT-ATT
1 ATATTAAATAAAT
34080 ATATTAAATAAAT
1 ATATTAAATAAAT
34093 ATATTAAATA
1 ATATTAAATA
34103 TATTATGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:37098 original size:8 final size:8
Alignment explanation
Indices: 37085--37125 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
37075 CTCATTTTCA
37085 GAGAATTT
1 GAGAATTT
37093 GAGAATTT
1 GAGAATTT
*
37101 -AGAGTTT
1 GAGAATTT
*
37108 GGGAATTT
1 GAGAATTT
37116 GAGAATTT
1 GAGAATTT
37124 GA
1 GA
37126 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:37418 original size:126 final size:126
Alignment explanation
Indices: 37193--37799 Score: 1142
Period size: 126 Copynumber: 4.8 Consensus size: 126
37183 CTATAATCGG
*
37193 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGTGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
37258 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
37319 TTCACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
37384 TCATTGCCCTACTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
37445 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCTCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
37510 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
37571 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
37636 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
37697 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATA--T
37762 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
64 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
37800 ATAACTTAAA
Statistics
Matches: 470, Mismatches: 9, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
126 431 0.92
128 39 0.08
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:37879 original size:33 final size:32
Alignment explanation
Indices: 37841--37913 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
37831 AACAAGTTAA
* *
37841 GAATAACTTAAATTAAAACGTTATGTGA-AATTT
1 GAATAAATTAAA-TAAAACGTTATG-GATAAATT
* *
37874 GAATAAATTAGATAAAATGTTATGGATAAATT
1 GAATAAATTAAATAAAACGTTATGGATAAATT
37906 GAATAAAT
1 GAATAAAT
37914 GTGAAGTGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 2 0.06
32 23 0.66
33 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.34
Consensus pattern (32 bp):
GAATAAATTAAATAAAACGTTATGGATAAATT
Found at i:38240 original size:26 final size:27
Alignment explanation
Indices: 38177--38234 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
38167 ATTAAGTTGA
*
38177 AATTT-AATGTTAAATTTCGAATACTAT
1 AATTTAAAT-TTAAATTTCGAATAATAT
38204 AATTTAAATTTAAATTT-GAATAATAT
1 AATTTAAATTTAAATTTCGAATAATAT
*
38230 TATTT
1 AATTT
38235 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 12 0.43
27 13 0.46
28 3 0.11
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.48
Consensus pattern (27 bp):
AATTTAAATTTAAATTTCGAATAATAT
Found at i:38249 original size:33 final size:34
Alignment explanation
Indices: 38212--38275 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
38202 ATAATTTAAA
* *
38212 TTTAAATTT-GAATAATATTATTTTTATTTTTAT
1 TTTAAATTTCGAATAATATAATTTGTATTTTTAT
38245 TTTAAATTTCGAATAATATAATTTGTATTTT
1 TTTAAATTTCGAATAATATAATTTGTATTTT
38276 AAAACATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 9 0.32
34 19 0.68
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (34 bp):
TTTAAATTTCGAATAATATAATTTGTATTTTTAT
Found at i:38824 original size:21 final size:21
Alignment explanation
Indices: 38800--38883 Score: 125
Period size: 21 Copynumber: 4.0 Consensus size: 21
38790 ATAAAACCCT
*
38800 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
38821 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
38842 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
*
38863 GCGGGCTCGGAATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
38884 CGGAGATGGC
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.20, C:0.24, G:0.37, T:0.19
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:40692 original size:34 final size:31
Alignment explanation
Indices: 40654--40735 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
40644 AATTCTAAAT
40654 AATAATAATTATATAAATATTATTTTAATAAAAA
1 AATAATAATTATATAAATA-TA--TTAATAAAAA
* * *
40688 AATAATATTTACATAAATATATTAATATAAA
1 AATAATAATTATATAAATATATTAATAAAAA
* *
40719 AATAATAACTATTTAAA
1 AATAATAATTATATAAA
40736 AAATACTAAC
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
31 22 0.54
33 2 0.05
34 17 0.41
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
AATAATAATTATATAAATATATTAATAAAAA
Found at i:40750 original size:32 final size:34
Alignment explanation
Indices: 40650--40755 Score: 96
Period size: 34 Copynumber: 3.2 Consensus size: 34
40640 TAATAATTCT
* * * *
40650 AAATAATAATAATTATATAAATATTATTTTA-ATAA
1 AAATAATAATATTTACATAAATA-TA-CTAACATAA
* *
40685 AAA-AATAATATTTACATAAATATATTAATATAA
1 AAATAATAATATTTACATAAATATACTAACATAA
40718 AAATAATAACTATTTA-A-AAA-ATACTAACATAA
1 AAATAATAA-TATTTACATAAATATACTAACATAA
40750 AAATAA
1 AAATAA
40756 ATTTCTTACC
Statistics
Matches: 63, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
32 19 0.30
33 12 0.19
34 23 0.37
35 9 0.14
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (34 bp):
AAATAATAATATTTACATAAATATACTAACATAA
Found at i:43995 original size:7 final size:7
Alignment explanation
Indices: 43979--44019 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
43969 TTCATTTTTA
43979 TGGA-AG
1 TGGAGAG
43985 TGGAGAG
1 TGGAGAG
43992 TGGAGAG
1 TGGAGAG
43999 TGGAGAG
1 TGGAGAG
44006 TGGAGAG
1 TGGAGAG
44013 TTGGAGA
1 -TGGAGA
44020 TTGTTCTGCT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 4 0.12
7 23 0.70
8 6 0.18
ACGTcount: A:0.29, C:0.00, G:0.54, T:0.17
Consensus pattern (7 bp):
TGGAGAG
Found at i:45407 original size:31 final size:30
Alignment explanation
Indices: 45372--45458 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
45362 TCAATAAAGT
45372 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAAAATTATAAAATA-TTATTAAATTTA
* *
45403 TTAAAAGATTATAAAATTATTAATAAATTTA
1 TTAAAAAATTATAAAA-TATTATTAAATTTA
* *
45434 TCT-AAATACTATAAAATAATTATTA
1 T-TAAAAAATTATAAAAT-ATTATTA
45459 TATTATCGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 44 0.92
32 3 0.06
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (30 bp):
TTAAAAAATTATAAAATATTATTAAATTTA
Found at i:45434 original size:20 final size:20
Alignment explanation
Indices: 45367--45434 Score: 54
Period size: 19 Copynumber: 3.5 Consensus size: 20
45357 TTTCGTCAAT
*
45367 AAAG-TTTAAAAAATTA-TA
1 AAAGATTTATAAAATTATTA
* * *
45385 AAATACTTATTAAATTTATTA
1 AAAGATTTA-TAAAATTATTA
45406 AAAGA-TTATAAAATTATTA
1 AAAGATTTATAAAATTATTA
45425 ATAA-ATTTAT
1 A-AAGATTTAT
45435 CTAAATACTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 3 0.08
19 15 0.38
20 15 0.38
21 6 0.15
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (20 bp):
AAAGATTTATAAAATTATTA
Found at i:46644 original size:13 final size:13
Alignment explanation
Indices: 46626--46670 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
46616 TTCAATCAAA
46626 AAATATCTGAACT
1 AAATATCTGAACT
*
46639 AAATATCTTAA-T
1 AAATATCTGAACT
46651 GAAATATCTGAACT
1 -AAATATCTGAACT
46665 AAATAT
1 AAATAT
46671 TTTCTTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 1 0.04
13 26 0.93
14 1 0.04
ACGTcount: A:0.49, C:0.11, G:0.07, T:0.33
Consensus pattern (13 bp):
AAATATCTGAACT
Found at i:47061 original size:91 final size:90
Alignment explanation
Indices: 46953--47123 Score: 254
Period size: 91 Copynumber: 1.9 Consensus size: 90
46943 AGAAAATTTC
* * *
46953 CTCTTAAATTAGAATATGAAATTTAATTTTATCCACTTAGTAATTT-TGTTAACGATGTTACTTT
1 CTCTTAAATTAGAATATGAAATTTAATTTTATCCACTTAAT-ATTTCCGTTAACGATGTTACCTT
47017 TTAAATAAATAATAATATAATATATGA
65 TT-AATAAATAATAATATAATATATGA
* * *
47044 CTCTTAAATTAGAATATGAAATTTAATTTTATCCGCTTAATATTTCCGTTAATGATGTTTCCTTT
1 CTCTTAAATTAGAATATGAAATTTAATTTTATCCACTTAATATTTCCGTTAACGATGTTACCTTT
*
47109 TAATAAATGATAATA
66 TAATAAATAATAATA
47124 AAGTATCTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
90 17 0.24
91 55 0.76
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.44
Consensus pattern (90 bp):
CTCTTAAATTAGAATATGAAATTTAATTTTATCCACTTAATATTTCCGTTAACGATGTTACCTTT
TAATAAATAATAATATAATATATGA
Found at i:49840 original size:36 final size:36
Alignment explanation
Indices: 49786--49861 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
49776 ATTCGATAGG
* * *
49786 TTAATTAATTGAATTGTTAAGATTAAATGGTTTTAA
1 TTAATTAACTGAACTGTTAAGATTAAACGGTTTTAA
*
49822 TTAATTAACTGAACTGTTAAGATTAAACGGTTTTGA
1 TTAATTAACTGAACTGTTAAGATTAAACGGTTTTAA
49858 TTAA
1 TTAA
49862 CCAAACCGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.43
Consensus pattern (36 bp):
TTAATTAACTGAACTGTTAAGATTAAACGGTTTTAA
Found at i:57543 original size:29 final size:29
Alignment explanation
Indices: 57472--57533 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
57462 GAGTGCTTAG
*
57472 GGTCTCC-ATTTTTTCATCCTTGTAATTA
1 GGTCTCCTATTTTTTCATCCTTATAATTA
*
57500 GGTCTCCTATTTTTTCATCTTTATAATTA
1 GGTCTCCTATTTTTTCATCCTTATAATTA
57529 GGTCT
1 GGTCT
57534 TTAATTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.18, C:0.19, G:0.11, T:0.52
Consensus pattern (29 bp):
GGTCTCCTATTTTTTCATCCTTATAATTA
Found at i:57756 original size:44 final size:43
Alignment explanation
Indices: 57561--57921 Score: 247
Period size: 44 Copynumber: 8.3 Consensus size: 43
57551 ATTTTTCACT
* * * * *
57561 TTTATAATTGAGG-TCCTAATATTATTCAATCTAACATTT-TATC
1 TTTATAATTGAGGCCCCT-ATTTTTTTCAATCTCAC-TTTCTACC
* * * *
57604 TTTATAATTGAAGTCTCTATTTTTTTCTAATC-C-CTGTTTTACC
1 TTTATAATTGAGGCCCCTATTTTTTTC-AATCTCACT-TTCTACC
* * * * * *
57647 TTTA-AATTTAGGCACCTAATTTTGT-AATCTTACTTT-TAAC
1 TTTATAATTGAGGCCCCTATTTTTTTCAATCTCACTTTCTACC
*** *
57687 TTTATAATTGAGGCTTTTAAGTTTTTTCAATCTCACTTTCTACC
1 TTTATAATTGAGGCCCCT-ATTTTTTTCAATCTCACTTTCTACC
* * * *
57731 TTT-TCAATTGAGTCCTCTATCTTTTTCCAATCTCAATTTCTACC
1 TTTAT-AATTGAGGCCCCTAT-TTTTTTCAATCTCACTTTCTACC
* * * *
57775 TTTATAATTGAGACCCCCAATTTTTTT-AATCTCACTTTTTTAAC
1 TTTATAATTGAG-GCCCCTATTTTTTTCAATCTCAC-TTTCTACC
* *
57819 TTTATAATTGAGGCCCTTAAGTTTTTTT-AATCTCACTTTCTAAC
1 TTTATAATTGAGGCCCCT-A-TTTTTTTCAATCTCACTTTCTACC
* * *
57863 TTTCTAATTGAGGCCCCTATTTTTTTTTAATCTCAATTTCTACC
1 TTTATAATTGAGGCCCCTA-TTTTTTTCAATCTCACTTTCTACC
*
57907 TTTATAATTAAGGCC
1 TTTATAATTGAGGCC
57922 TTTAATTTTT
Statistics
Matches: 252, Mismatches: 48, Indels: 35
0.75 0.14 0.10
Matches are distributed among these distances:
40 11 0.04
41 12 0.05
42 25 0.10
43 56 0.22
44 127 0.50
45 21 0.08
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.48
Consensus pattern (43 bp):
TTTATAATTGAGGCCCCTATTTTTTTCAATCTCACTTTCTACC
Found at i:57929 original size:132 final size:129
Alignment explanation
Indices: 57518--57931 Score: 405
Period size: 132 Copynumber: 3.2 Consensus size: 129
57508 ATTTTTTCAT
* * * * * *
57518 CTTTATAATTAGGTCTTTAATTTTTTAAATTTTA-TTTTTCACTTTTATAATTGAGGTCC-TAA-
1 CTTTATAATTAGGCCTCTAATTTTTTTAATCTTACTTTTTAAC-TTTATAATTGAGGCCCTTAAG
* * * * * * **
57580 TATTATTCAATCTAACATTT-TATCTTTATAATTGAAGTCTCTATTTTTTTCTAATCCCTGTTT-
65 T-TTTTTCAATCTCAC-TTTCTAACTTT-TAATTGAGGCCTCTATTTTTTTCTAATCTCAATTTC
57643 TAC
127 TAC
* **
57646 CTTTA-AATTTAGGCAC-CTAA-TTTTGTAATCTTAC-TTTTAACTTTATAATTGAGGCTTTTAA
1 CTTTATAA-TTAGGC-CTCTAATTTTTTTAATCTTACTTTTTAACTTTATAATTGAGGCCCTTAA
* * * *
57707 GTTTTTTCAATCTCACTTTCTACCTTTTCAATTGAGTCCTCTATCTTTTTCCAATCTCAATTTCT
64 GTTTTTTCAATCTCACTTTCTAACTTTT-AATTGAGGCCTCTATTTTTTTCTAATCTCAATTTCT
57772 AC
128 AC
* * * *
57774 CTTTATAATTGAGACCCCCAATTTTTTTAATCTCACTTTTTTAACTTTATAATTGAGGCCCTTAA
1 CTTTATAATT-AGGCCTCTAATTTTTTTAATCTTAC-TTTTTAACTTTATAATTGAGGCCCTTAA
* * *
57839 GTTTTTTTAATCTCACTTTCTAACTTTCTAATTGAGGCCCCTATTTTTTTTTAATCTCAATTTCT
64 GTTTTTTCAATCTCACTTTCTAACTTT-TAATTGAGGCCTCTATTTTTTTCTAATCTCAATTTCT
57904 AC
128 AC
*
57906 CTTTATAATTAAGGCCTTTAATTTTT
1 CTTTATAATT-AGGCCTCTAATTTTT
57932 CACAATTTTA
Statistics
Matches: 233, Mismatches: 38, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
126 17 0.07
127 65 0.28
128 25 0.11
129 9 0.04
130 12 0.05
132 104 0.45
133 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (129 bp):
CTTTATAATTAGGCCTCTAATTTTTTTAATCTTACTTTTTAACTTTATAATTGAGGCCCTTAAGT
TTTTTCAATCTCACTTTCTAACTTTTAATTGAGGCCTCTATTTTTTTCTAATCTCAATTTCTAC
Found at i:59093 original size:2 final size:2
Alignment explanation
Indices: 59086--59130 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
59076 AATTGATCAT
59086 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
59128 TA T
1 TA T
59131 CATTCATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63860 original size:57 final size:57
Alignment explanation
Indices: 63767--63877 Score: 186
Period size: 57 Copynumber: 1.9 Consensus size: 57
63757 GTTTTGTAAC
*
63767 TTATAATTCTCAAGTGAAACAATGAAGTAGAGGCTTATAAATAAATAGACTTGTCAT
1 TTATAATTCTCAAGTAAAACAATGAAGTAGAGGCTTATAAATAAATAGACTTGTCAT
* * *
63824 TTATGATTCTCAAGTAAAACAATGAAGTAGAGGCTTATAAATGAATAGATTTGT
1 TTATAATTCTCAAGTAAAACAATGAAGTAGAGGCTTATAAATAAATAGACTTGT
63878 AAAAAGGATG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.32
Consensus pattern (57 bp):
TTATAATTCTCAAGTAAAACAATGAAGTAGAGGCTTATAAATAAATAGACTTGTCAT
Found at i:64255 original size:19 final size:19
Alignment explanation
Indices: 64220--64257 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
64210 TGAAATAGCC
*
64220 ATTGCATGCCTTCTGATTT
1 ATTGCATGCATTCTGATTT
64239 ATTGCCATGCATT-TGATTT
1 ATTG-CATGCATTCTGATTT
64258 GCATTATCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (19 bp):
ATTGCATGCATTCTGATTT
Found at i:66362 original size:29 final size:29
Alignment explanation
Indices: 66305--66369 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
66295 TTTTGTCTTT
* **
66305 TGTGGTATTTATATTTTCAAAATGTCTAA
1 TGTGGTGTTTATATTTTCAAAATACCTAA
* *
66334 TGTGGTGTTTATATTTTTAAATTACCTAA
1 TGTGGTGTTTATATTTTCAAAATACCTAA
*
66363 AGTGGTG
1 TGTGGTG
66370 CATGAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.06, G:0.18, T:0.48
Consensus pattern (29 bp):
TGTGGTGTTTATATTTTCAAAATACCTAA
Found at i:74486 original size:75 final size:75
Alignment explanation
Indices: 74390--74540 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
74380 TTAAATATTG
74390 AAATAAAAAAAATTAATCTTATTAAGTTAGACCATATCATAAAAATAATAATTTTTATATTAAAT
1 AAATAAAAAAAATTAATCTTATTAAGTTAGACCATATCATAAAAATAATAATTTTTATATTAAAT
74455 ATTTAATTTT
66 ATTTAATTTT
*
74465 AAATTAAAAAAATTAATCTTATTAAGTTAGACCATATCATAAAAATAATAATTTTTATATTAAAT
1 AAATAAAAAAAATTAATCTTATTAAGTTAGACCATATCATAAAAATAATAATTTTTATATTAAAT
74530 ATTTAATTTT
66 ATTTAATTTT
74540 A
1 A
74541 TTGTATTTTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (75 bp):
AAATAAAAAAAATTAATCTTATTAAGTTAGACCATATCATAAAAATAATAATTTTTATATTAAAT
ATTTAATTTT
Found at i:74509 original size:35 final size:35
Alignment explanation
Indices: 74395--74509 Score: 83
Period size: 35 Copynumber: 3.1 Consensus size: 35
74385 TATTGAAATA
74395 AAAAAAATTAATCTTATTAAGTTAGACCATATCAT
1 AAAAAAATTAATCTTATTAAGTTAGACCATATCAT
* * ** * *
74430 AAAAATAA-TAATTTTTATATTAAATATTTA--ATTTTAAATT
1 AAAAA-AATTAA--TCT-TATTAAGT-TAGACCA-TAT-CA-T
74470 AAAAAAATTAATCTTATTAAGTTAGACCATATCAT
1 AAAAAAATTAATCTTATTAAGTTAGACCATATCAT
74505 AAAAA
1 AAAAA
74510 TAATAATTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 22
0.63 0.13 0.24
Matches are distributed among these distances:
35 14 0.25
36 5 0.09
37 12 0.21
38 12 0.21
39 5 0.09
40 9 0.16
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.38
Consensus pattern (35 bp):
AAAAAAATTAATCTTATTAAGTTAGACCATATCAT
Found at i:77135 original size:21 final size:20
Alignment explanation
Indices: 77099--77137 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
77089 GTAATTTTGG
77099 AAACTGAAAATGAATATGGA
1 AAACTGAAAATGAATATGGA
77119 AAACATGAATAAT-AATATG
1 AAAC-TGAA-AATGAATATG
77138 CTTAAAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 10 0.59
22 3 0.18
ACGTcount: A:0.56, C:0.05, G:0.15, T:0.23
Consensus pattern (20 bp):
AAACTGAAAATGAATATGGA
Found at i:77750 original size:211 final size:211
Alignment explanation
Indices: 77371--77764 Score: 531
Period size: 211 Copynumber: 1.9 Consensus size: 211
77361 CCTAACATTA
* *
77371 GTTTGAGTTGGACATTAACATGCGAACTGAGATATGACAATATTTTGAGATTATGGGATCAAATT
1 GTTTGAGCTAGACATTAACATGCGAACTGAGATATGACAATATTTTGAGATTATGGGATCAAATT
** * * * *
77436 TTATCATAACTTAATCAATAGGTTAATGATCAGCTCAGACTACAATCATTTTTTAATAGAAAATG
66 TTATCATAACCCAATCAATAGGTTAATGACCAGCTCAAACTACAATAATTTTTTAATAAAAAATG
* * * * *
77501 ACGAGTTTGAAATATATGAATAGTCGAGTGACCATTTTATAACTTTTAATAGTGACTCAACAAAG
131 ACGAGTTTGAAACATACGAATAATCGAGTAACCATTTTACAACTTTTAATAGTGACTCAACAAAG
77566 TAATACCCTAACGGTC
196 TAATACCCTAACGGTC
* * * *
77582 GTTTGAGCTAGACGTTAACATGCCG-ACTGAGATATGACAATGTTTTGAGATTCTGTGATCAAAT
1 GTTTGAGCTAGACATTAACATG-CGAACTGAGATATGACAATATTTTGAGATTATGGGATCAAAT
** * * * *
77646 TTTATCATGTCCCAATTAATAGGTTAA-GACCATCTTAAACTACAGTAAATTTTTTAATAAAAAA
65 TTTATCATAACCCAATCAATAGGTTAATGACCAGCTCAAACTACAAT-AATTTTTTAATAAAAAA
* *
77710 TGATGAGTTTGAAACATACGAATAATCGAGTAATCATTTTACAACTTTTAATAGT
129 TGACGAGTTTGAAACATACGAATAATCGAGTAACCATTTTACAACTTTTAATAGT
77765 TGGGGGACTC
Statistics
Matches: 156, Mismatches: 25, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
210 14 0.09
211 140 0.90
212 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (211 bp):
GTTTGAGCTAGACATTAACATGCGAACTGAGATATGACAATATTTTGAGATTATGGGATCAAATT
TTATCATAACCCAATCAATAGGTTAATGACCAGCTCAAACTACAATAATTTTTTAATAAAAAATG
ACGAGTTTGAAACATACGAATAATCGAGTAACCATTTTACAACTTTTAATAGTGACTCAACAAAG
TAATACCCTAACGGTC
Found at i:84717 original size:13 final size:14
Alignment explanation
Indices: 84699--84985 Score: 85
Period size: 13 Copynumber: 19.8 Consensus size: 14
84689 CAAAAATTAT
84699 ATTATAATA-AATA
1 ATTATAATATAATA
84712 ATTATAATAATAAGTA
1 ATTATAAT-ATAA-TA
*
84728 ATAATATTAAT-TATTA
1 AT--TA-TAATATAATA
*
84744 AATATAATA-AATA
1 ATTATAATATAATA
*
84757 ATTAAAATATAATA
1 ATTATAATATAATA
84771 ATATATCAATATAATA
1 AT-TAT-AATATAATA
* *
84787 ATTAAAATAGAA-A
1 ATTATAATATAATA
* * *
84800 TTTATAAAAAAATA
1 ATTATAATATAATA
* *
84814 ATTATGATAT-ATT
1 ATTATAATATAATA
* * *
84827 TTGTAAAATTTGAAATA
1 AT-TATAATAT--AATA
* * * *
84844 ATGAAAATTTTAT-
1 ATTATAATATAATA
84857 ATTATAATA-AATA
1 ATTATAATATAATA
*
84870 AATA-AACTATTAATA
1 ATTATAA-TA-TAATA
84885 ATTAATAATATTAATTATAA
1 ATT-ATAATA-T-A--AT-A
*
84905 AATATAATA-AATA
1 ATTATAATATAATA
*
84918 ATTAAAATATAATA
1 ATTATAATATAATA
*
84932 ATATATAAATATAGTA
1 AT-TAT-AATATAATA
84948 ATTA-AA-ATAGATA
1 ATTATAATATA-ATA
* *
84961 TTTTATAA-AAAATA
1 -ATTATAATATAATA
84975 ATTATAATATA
1 ATTATAATATA
84986 TTTTGTAAAA
Statistics
Matches: 201, Mismatches: 41, Indels: 63
0.66 0.13 0.21
Matches are distributed among these distances:
12 7 0.03
13 63 0.31
14 45 0.22
15 20 0.10
16 41 0.20
17 8 0.04
18 2 0.01
19 12 0.06
20 3 0.01
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.39
Consensus pattern (14 bp):
ATTATAATATAATA
Found at i:84723 original size:16 final size:16
Alignment explanation
Indices: 84702--84818 Score: 60
Period size: 16 Copynumber: 7.9 Consensus size: 16
84692 AAATTATATT
84702 ATAATAAATAATTATA
1 ATAATAAATAATTATA
* *
84718 ATAATAAGTAATAATA
1 ATAATAAATAATTATA
* * *
84734 TTAATTATTAA--AT-
1 ATAATAAATAATTATA
*
84747 ATAATAAATAATTAAA
1 ATAATAAATAATTATA
84763 AT-AT-AATAA-TAT-
1 ATAATAAATAATTATA
*
84775 ATCAATATAATAATTAAA
1 AT-AATA-AATAATTATA
*
84793 AT-AGAAAT--TTATA
1 ATAATAAATAATTATA
84806 A-AA-AAATAATTAT
1 ATAATAAATAATTAT
84819 GATATATTTT
Statistics
Matches: 76, Mismatches: 13, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
12 6 0.08
13 16 0.21
14 13 0.17
15 6 0.08
16 31 0.41
17 2 0.03
18 2 0.03
ACGTcount: A:0.61, C:0.01, G:0.02, T:0.37
Consensus pattern (16 bp):
ATAATAAATAATTATA
Found at i:84773 original size:26 final size:26
Alignment explanation
Indices: 84744--84942 Score: 106
Period size: 30 Copynumber: 7.5 Consensus size: 26
84734 TTAATTATTA
84744 AATATAATAAATAATTAAAATATAAT
1 AATATAATAAATAATTAAAATATAAT
*
84770 AATATATCAATATAATAATTAAAATAGAA-
1 -A-ATAT-AATA-AATAATTAAAATATAAT
* * ** *
84799 ATTTATAAAAAAATAATTATGATATATTT
1 A-ATAT-AATAAATAATTAAAATATA-AT
** * * * *
84828 TGTAAAATTTGAAATAATGAAAATTTTAT
1 AATATAA--T-AAATAATTAAAATATAAT
* * *
84857 ATTATAATAAATAAATAAACTATTAAT
1 AATATAATAAATAATTAAAATA-TAAT
*
84884 AAT-TAAT-AAT-ATT-AATTATAA-
1 AATATAATAAATAATTAAAATATAAT
84905 AATATAATAAATAATTAAAATATAAT
1 AATATAATAAATAATTAAAATATAAT
84931 AATAT-ATAAATA
1 AATATAATAAATA
84943 TAGTAATTAA
Statistics
Matches: 128, Mismatches: 30, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
21 3 0.02
22 7 0.05
23 7 0.05
24 5 0.04
25 17 0.13
26 19 0.15
27 21 0.16
28 14 0.11
29 9 0.07
30 26 0.20
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (26 bp):
AATATAATAAATAATTAAAATATAAT
Found at i:84898 original size:16 final size:15
Alignment explanation
Indices: 84866--84956 Score: 71
Period size: 16 Copynumber: 5.9 Consensus size: 15
84856 TATTATAATA
* *
84866 AATAAATAAACTATT
1 AATAATTAAAATATT
84881 AATAATTAATAATATT
1 AATAATTAA-AATATT
*
84897 AATTA-TAAAATATAAT
1 AATAATTAAAATAT--T
84913 AAATAATTAAAATA-T
1 -AATAATTAAAATATT
84928 AATAATATATAAATA-T
1 AATAAT-TA-AAATATT
*
84944 AGTAATTAAAATA
1 AATAATTAAAATA
84957 GATATTTTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
14 16 0.25
15 16 0.25
16 21 0.33
17 4 0.06
18 7 0.11
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (15 bp):
AATAATTAAAATATT
Found at i:84919 original size:20 final size:18
Alignment explanation
Indices: 84859--84932 Score: 63
Period size: 18 Copynumber: 4.4 Consensus size: 18
84849 AATTTTATAT
* *
84859 TATAATAAATAAATAAAC
1 TATAATAAATAATTAAAA
84877 TAT--T-AATAATTAATAA
1 TATAATAAATAATTAA-AA
*
84893 TAT--T-AATTA-TAAAA
1 TATAATAAATAATTAAAA
84907 TATAATAAATAATTAAAA
1 TATAATAAATAATTAAAA
84925 TATAATAA
1 TATAATAA
84933 TATATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 5 0.11
15 11 0.23
16 11 0.23
17 4 0.09
18 16 0.34
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.36
Consensus pattern (18 bp):
TATAATAAATAATTAAAA
Found at i:85130 original size:159 final size:154
Alignment explanation
Indices: 84690--85151 Score: 646
Period size: 161 Copynumber: 2.9 Consensus size: 154
84680 CGCACCATTC
* *
84690 AAAAATTATATTATAATAAATAATT-ATAATAATAAGTAATAATATTAATTATTAAATATAATAA
1 AAAAATTATATTATAATAAATAATTAATAATAATAATTAATAATATTAATTATAAAATATAATAA
* *
84754 ATAATTAAAATATAATAATATATCAATATAATAATTAAAATAGA-AATTTATAAAAAAATAATTA
66 ATAATTAAAATATAAT-ATATA--AATATAGTAATTAAAATAGATATTTTAT-AAAAAATAATTA
*
84818 TGATATATTTTGTAAAATTTGAAATAATG
127 TAATATATTTTGTAAAA-TTGAAATAATG
* * *
84847 AAAATTTTATATTATAATAAATAAATAAACTATTAATAATTAATAATATTAATTATAAAATATAA
1 AAAA-ATTATATTATAATAAAT-AATTAA-TAATAATAATTAATAATATTAATTATAAAATATAA
84912 TAAATAATTAAAATATAATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAAT
63 TAAATAATT-AAA-AT-ATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAAT
84977 TATAATATATTTTGTAAAATTGAAATAATG
125 TATAATATATTTTGTAAAATTGAAATAATG
* * * *
85007 AAAAATTATATTATAATAAATGATTGTAATAATAATAATTCATAATATTAATTATCAAATAGAAT
1 AAAAATTATATTATAATAAAT-AAT-TAATAATAATAATTAATAATATTAATTATAAAATATAAT
*
85072 AAATAATTAAAATAT-ATATATAAATATAGTAATCAAAATAGATATTTTATATAAAAA-AATTAT
64 AAATAATTAAAATATAATATATAAATATAGTAATTAAAATAGATATTTTATA-AAAAATAATTAT
85135 AATATATTTTG-AAAATT
128 AATATATTTTGTAAAATT
85152 TTGAAATTTA
Statistics
Matches: 278, Mismatches: 17, Indels: 23
0.87 0.05 0.07
Matches are distributed among these distances:
154 6 0.02
155 52 0.19
156 7 0.03
157 6 0.02
158 19 0.07
159 61 0.22
160 18 0.06
161 88 0.32
162 9 0.03
163 7 0.03
164 5 0.02
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (154 bp):
AAAAATTATATTATAATAAATAATTAATAATAATAATTAATAATATTAATTATAAAATATAATAA
ATAATTAAAATATAATATATAAATATAGTAATTAAAATAGATATTTTATAAAAAATAATTATAAT
ATATTTTGTAAAATTGAAATAATG
Found at i:95513 original size:13 final size:13
Alignment explanation
Indices: 95495--95519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
95485 TTCCAACCTG
95495 ACCCGACCCGTTT
1 ACCCGACCCGTTT
95508 ACCCGACCCGTT
1 ACCCGACCCGTT
95520 GACCGATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.16, T:0.20
Consensus pattern (13 bp):
ACCCGACCCGTTT
Done.