Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005542.1 Hibiscus syriacus cultivar Beakdansim tig00012830_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: 66672
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:6808 original size:133 final size:134
Alignment explanation
Indices: 6315--6910 Score: 702
Period size: 133 Copynumber: 4.5 Consensus size: 134
6305 ATAAGTGATT
* * * * * * *
6315 TGCTCCACTATTTTTGTAGGGTAGATCAGA-TCGAG-AAACTTTGATTCA-TTCCACTGTTCTTC
1 TGCTCCACTACTCTT-TAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTT-CGCTGCTCTTC
* * * * * * *
6377 AGGAAAAATTGAATCGGAATCAATTTCCTTCACTACTCTTCAGAAAGACCAAATCTGAAAGAAGA
64 AGGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGA
6442 AGAATA
129 AGAATA
* *
6448 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTTGATCCACTTTGCTGGTCTTCA
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAA-TTTGATCCACTTCGCTGCTCTTCA
* * *
6513 GGGAAGATTGAATCAGAATAGATTTGCTTCACTGCTCTTTAGGAAGACCAAATTTGAAAGAAGAA
65 GGGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAA
* *
6578 AAATT
130 GAATA
* * ** * * *
6583 TGCTCCACTACTCTTTAGGGGAGACCAGACTCGATAAATTTTTTATCCAGTTCGCTGGTCTTCAG
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCGCTGCTCTTCAG
* * *
6648 GGAAGATTGAATCAGAATCGATTTGCTTTAATGCTCTTCAGGAAGACCAAATCTGAAAGAACAAG
66 GGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
*
6713 AATC
131 AATA
** * * *
6717 TAATCCACTACTC-TTAGGGGAGATCAGACTCCAGAAAAATTAGATCCACTTCACTGCTCTTCAG
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCGCTGCTCTTCAG
* * *
6781 GGAAGATT-AATTC-GAAATCGATCTGCTTCACTGTTCTTTAGGAAGACCAAATCTGAAAGAAGA
66 GGAAGATTGAA-TCAG-AATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGA
6844 AGAATA
129 AGAATA
* * * *
6850 TGCTCCACTACTCTTTAGAGGAGATCATACTCGAG-AAACTTTGATCCACTTCGCTTCTCTT
1 TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCGCTGCTCTT
6911 TAGAGATTAT
Statistics
Matches: 393, Mismatches: 63, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
132 16 0.04
133 149 0.38
134 115 0.29
135 111 0.28
136 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (134 bp):
TGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTGATCCACTTCGCTGCTCTTCAG
GGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
AATA
Found at i:6840 original size:267 final size:269
Alignment explanation
Indices: 6372--6883 Score: 735
Period size: 267 Copynumber: 1.9 Consensus size: 269
6362 ATTCCACTGT
* *
6372 TCTTCAGGAAAAATTGAATCGGAATCAATTTCCTTCACTACTCTTCAGAAAGACCAAATCTGAAA
1 TCTTCAGGAAAAATTGAATCAGAATCAATTTCCTTCAATACTCTTCAGAAAGACCAAATCTGAAA
* ** * * *
6437 GAAGAAGAATATGCTCCACTACTCTTTAGGGGAGATCAGACTCGAGAAAAATTTTGATCCACTTT
66 GAACAAGAATATAATCCACTACTCTTTAGGGGAGATCAGACTCCAGAAAAATTTAGATCCACTTC
* * * *
6502 GCTGGTCTTCAGGGAAGATTGAATCAGAATAGATTTGCTTCACTGCTCTTTAGGAAGACCAAATT
131 ACTGCTCTTCAGGGAAGATTGAATCAGAATAGATCTGCTTCACTGCTCTTTAGGAAGACCAAATC
* *
6567 TGAAAGAAGAAAAATTTGCTCCACTACTCTTTAGGGGAGACCAGACTCGATAAATTTTTTATCCA
196 TGAAAGAAGAAAAATATGCTCCACTACTCTTTAGAGGAGACCAGACTCGATAAATTTTTTATCCA
6632 GTTCGCTGG
261 GTTCGCTGG
* * * * * * *
6641 TCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTTAATGCTCTTCAGGAAGACCAAATCTGAAA
1 TCTTCAGGAAAAATTGAATCAGAATCAATTTCCTTCAATACTCTTCAGAAAGACCAAATCTGAAA
*
6706 GAACAAGAATCTAATCCACTACTC-TTAGGGGAGATCAGACTCCAGAAAAA-TTAGATCCACTTC
66 GAACAAGAATATAATCCACTACTCTTTAGGGGAGATCAGACTCCAGAAAAATTTAGATCCACTTC
* *
6769 ACTGCTCTTCAGGGAAGATT-AATTC-GAAATCGATCTGCTTCACTGTTCTTTAGGAAGACCAAA
131 ACTGCTCTTCAGGGAAGATTGAA-TCAG-AATAGATCTGCTTCACTGCTCTTTAGGAAGACCAAA
* * *
6832 TCTGAAAGAAGAAGAATATGCTCCACTACTCTTTAGAGGAGATCATACTCGA
194 TCTGAAAGAAGAAAAATATGCTCCACTACTCTTTAGAGGAGACCAGACTCGA
6884 GAAACTTTGA
Statistics
Matches: 214, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
266 3 0.01
267 110 0.51
268 25 0.12
269 76 0.36
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.28
Consensus pattern (269 bp):
TCTTCAGGAAAAATTGAATCAGAATCAATTTCCTTCAATACTCTTCAGAAAGACCAAATCTGAAA
GAACAAGAATATAATCCACTACTCTTTAGGGGAGATCAGACTCCAGAAAAATTTAGATCCACTTC
ACTGCTCTTCAGGGAAGATTGAATCAGAATAGATCTGCTTCACTGCTCTTTAGGAAGACCAAATC
TGAAAGAAGAAAAATATGCTCCACTACTCTTTAGAGGAGACCAGACTCGATAAATTTTTTATCCA
GTTCGCTGG
Found at i:9092 original size:21 final size:20
Alignment explanation
Indices: 9064--9102 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
9054 AATTGCAAGA
*
9064 ATTTATGGCCTCCACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
9084 ATTTCATGGCTTCAACAAA
1 ATTT-ATGGCCTCAACAAA
9103 GACCTTGATA
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:0.23, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:15517 original size:20 final size:20
Alignment explanation
Indices: 15492--15543 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
15482 ATTGTTGTGG
*
15492 GTATCGCTACTAAGAGGAAT
1 GTATCGATACTAAGAGGAAT
15512 GTATCGATACTAAGAGGAAT
1 GTATCGATACTAAGAGGAAT
15532 GTATCGATACTA
1 GTATCGATACTA
15544 TGAATTCCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (20 bp):
GTATCGATACTAAGAGGAAT
Found at i:18864 original size:54 final size:54
Alignment explanation
Indices: 18800--19442 Score: 820
Period size: 54 Copynumber: 12.0 Consensus size: 54
18790 TGATTACCAA
*
18800 ACAA-CACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAATAACCGT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
* * * *
18853 ACAAGTACTATGTGTACAACCCACGA-AAATCATCATATATTGATG---AACCGT
1 ACAAGCACTATGTGTGCAACCCAC-ATAATTCATCATATGTTGATGAACAACCGT
* *
18904 AC-AGACACTATGTGTACAACCCAAAT-ATTCATCATATGTTGATGAACAACCGT
1 ACAAG-CACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
* ** ** *
18957 ACAAGCAGTATGTGTGCAACCCACGGAATTCATTGTATGTTGATGAACAGCCGT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
** * * *
19011 ACAAGCACTATGTGTGCAACCCACGGAATTCATCTTATATTGATGAACAACCAT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
* * *
19065 ACAGGCACTATGTGTGTAACCCACATAATTCATCATATTTTGATGAACAACCGT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
* * * ** *
19119 TCATGCACTATGTGTACAACCCACGGAATTCATCATAAGTTGATGAACAACCGT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
*
19173 ACAAGCACTATGTGTGCAACCCACATAATTCATCAAATGTTGATGAACAACCGT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
* * *
19227 ACAGGCACTATGTGTGCAACCTACGA-AATTCATCATATGTTGATGAACAACCAT
1 ACAAGCACTATGTGTGCAACCCAC-ATAATTCATCATATGTTGATGAACAACCGT
* * **
19281 ATATGCACTATGTGTGCAACCCA-GGAATTCATCATATGTTGATGAACAACCGT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
* * *
19334 ACATGCACTATGTGTGCAACCTACATAATTCATCAAATGTTGATGAACAACCGT
1 ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
* *
19388 ACATGCACTATGTGTGCAACCCACGA-AATTCATCATAGGTTGATGAACAACCGT
1 ACAAGCACTATGTGTGCAACCCAC-ATAATTCATCATATGTTGATGAACAACCGT
19442 A
1 A
19443 TAGACACTAC
Statistics
Matches: 516, Mismatches: 61, Indels: 25
0.86 0.10 0.04
Matches are distributed among these distances:
50 19 0.04
51 25 0.05
53 76 0.15
54 393 0.76
55 3 0.01
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.26
Consensus pattern (54 bp):
ACAAGCACTATGTGTGCAACCCACATAATTCATCATATGTTGATGAACAACCGT
Found at i:36238 original size:10 final size:9
Alignment explanation
Indices: 36220--36275 Score: 58
Period size: 10 Copynumber: 5.8 Consensus size: 9
36210 TTTGATCGAT
36220 TTTGAACCGG
1 TTTG-ACCGG
36230 CTTTGACCGG
1 -TTTGACCGG
36240 TTTGACCGG
1 TTTGACCGG
36249 TTTCGACCGG
1 TTT-GACCGG
*
36259 TCTGAACCGG
1 TTTG-ACCGG
*
36269 TCTGACC
1 TTTGACC
36276 CGACCCGACC
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
9 16 0.38
10 22 0.52
11 4 0.10
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (9 bp):
TTTGACCGG
Found at i:36256 original size:19 final size:19
Alignment explanation
Indices: 36220--36275 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
36210 TTTGATCGAT
36220 TTTGAACCGGCTTTGACCGG
1 TTTGAACCGG-TTTGACCGG
36240 TTTG-ACCGGTTTCGACCGG
1 TTTGAACCGGTTT-GACCGG
* *
36259 TCTGAACCGGTCTGACC
1 TTTGAACCGGTTTGACC
36276 CGACCCGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 3 0.09
19 18 0.56
20 11 0.34
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (19 bp):
TTTGAACCGGTTTGACCGG
Found at i:38655 original size:33 final size:34
Alignment explanation
Indices: 38577--38663 Score: 140
Period size: 35 Copynumber: 2.6 Consensus size: 34
38567 CTCGAAGGTC
* *
38577 TTTGTGTTTCAAGAGGAACATTTTCAAAGGGTTT
1 TTTGTGTTTCAAGAGAAACAATTTCAAAGGGTTT
38611 TCTTGTGTTTCAAGAGAAACAATTTCAAA-GGTTT
1 T-TTGTGTTTCAAGAGAAACAATTTCAAAGGGTTT
38645 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTTCAAGAGAAAC
38664 TGTCTCCAGG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
33 18 0.36
34 7 0.14
35 25 0.50
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (34 bp):
TTTGTGTTTCAAGAGAAACAATTTCAAAGGGTTT
Found at i:38708 original size:70 final size:67
Alignment explanation
Indices: 38616--39324 Score: 248
Period size: 72 Copynumber: 10.2 Consensus size: 67
38606 GGTTTTCTTG
* * * *
38616 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTGTGTTTCAAGAGAAACTGTCTCCAGGGAGGCAA
1 TGTTTCAAGAGAAACAATTTCAAAGG---TTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
*
38681 AAGTT
63 AACTT
*
38686 TTTTTCAAGAGAAAC-ATATTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACAAT-TTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
38750 CTT
65 CTT
* ** * * * *
38753 TGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAATT--TGGTTCAAGAGAAATTGTCTCAAGAGA
1 TGTTTCAAGAGAAACAATTTCAA-AG-------GTTGGTGTTTCAAGAGAAACTGTCTCAAGAGA
38816 GACAAAA-TT
58 GACAAAACTT
* * **** * * ** *
38825 TGTTTAAAGAGAAAC-TTTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAGGCTGTCTCAAGGGA
1 TGTTTCAAGAGAAACAATT-TCAA-AG-G----TTGGT-GTTTCAAGAGAAACTGTCTCAAGAGA
38889 GACAAAA-TT
58 GACAAAACTT
* * * *
38898 TGTTTCAAGCA-AAAC-ATATTCAAAGATT-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAA
1 TGTTTCAAG-AGAAACAAT-TTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
38960 A-TT
64 ACTT
* * ** * * *
38963 TGTTTCAAGGGAATCTGTCTCAAGAGAGACAAAATT--TGGTTCAAGAGAAACTGTTTCAAGAGA
1 TGTTTCAAGAGAAACAATTTCAA-AG-G------TTGGTGTTTCAAGAGAAACTGTCTCAAGAGA
39026 GACAAAA-TT
58 GACAAAACTT
* * * * * *
39035 TGTTTCAAG-GAAA-ACATATTCAAAGATT-TTGTTTAAAGGGAATCTGTCTCAAGAGATACAAA
1 TGTTTCAAGAGAAACA-AT-TTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
39097 A-TT
64 ACTT
*** * * *
39100 TGTTTCAAGAGAAATTGTCTCAAGAGAGACCAAATT--TGTTTCAAGAGAAACTGTCTAAAGAGG
1 TGTTTCAAGAGAAACAATTTCAA-AG-G------TTGGTGTTTCAAGAGAAACTGTCTCAAGAGA
*
39163 GA-AAAAATT
58 GACAAAACTT
* ** * * *
39172 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT--TGTTTCAAAAAGAAACTGTCTCAAGGG
1 TGTTTCAAGAGAAACAATTTCAA-AG-G------TTGGTGTTTC-AAGAGAAACTGTCTCAAGAG
39235 AGACAAAA-TT
57 AGACAAAACTT
* * *
39245 TGTTTCAAG-GAAA-ACATATTCAAAGATT-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 TGTTTCAAGAGAAACA-AT-TTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAA
39307 A-TT
64 ACTT
*
39310 TGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAAC
39325 TGTCTCATGA
Statistics
Matches: 505, Mismatches: 83, Indels: 105
0.73 0.12 0.15
Matches are distributed among these distances:
64 2 0.00
65 125 0.25
66 23 0.05
67 53 0.10
68 3 0.01
69 2 0.00
70 22 0.04
71 11 0.02
72 141 0.28
73 115 0.23
74 6 0.01
75 2 0.00
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.28
Consensus pattern (67 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTGGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
TT
Found at i:38808 original size:36 final size:36
Alignment explanation
Indices: 38716--39424 Score: 725
Period size: 36 Copynumber: 20.2 Consensus size: 36
38706 CAAAGGTTGG
38716 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
38753 TGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
38789 TGGTTCAAGAGAAATTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
38825 TGTTTAAAGAGAAACTTTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * ** *
38862 AGTTCCAAAAGAGGCTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
38898 TGTTTCAAGCA-AAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAG-AGAAAC-TGTCTCAAGAGAGACAAAATT
* *
38927 TGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
38963 TGTTTCAAGGGAATCTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
38999 TGGTTCAAGAGAAACTGTTTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
39035 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
* * * *
39064 TGTTTAAAGGGAATCTGTCTCAAGAGATACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
39100 TGTTTCAAGAGAAATTGTCTCAAGAGAGACCAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
39136 TGTTTCAAGAGAAACTGTCTAAAGAGGGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
39172 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
39208 TGTTTCAAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTC-AAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
39245 TGTTTCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
39274 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
39310 TGTTTCAAGGGAAACTGTCTCATGAGAGAAAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
*
39346 TGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
39382 TGTTTAAAAAAGAAACTGTTTCAAGGGAGACGAAATT
1 TGTTT-CAAGAGAAACTGTCTCAAGAGAGACAAAATT
39419 TGTTTC
1 TGTTTC
39425 GACGGAAACA
Statistics
Matches: 556, Mismatches: 80, Indels: 73
0.78 0.11 0.10
Matches are distributed among these distances:
28 6 0.01
29 52 0.09
30 5 0.01
31 3 0.01
32 5 0.01
33 6 0.01
34 1 0.00
35 5 0.01
36 342 0.62
37 131 0.24
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:38942 original size:174 final size:174
Alignment explanation
Indices: 38751--39424 Score: 848
Period size: 174 Copynumber: 3.9 Consensus size: 174
38741 GAGACAAAAC
* * *
38751 TTTGTTTCAAGGGAAACTGTCTCAAGAGAAACAAAATTTGGTTCAAGAGAAATTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * * * * * **
38816 GACAAAATTTGTTTAAAGAGAAACTTTCTCAAGAGAGACAAAACTTAG-TTCCAAAAGAGGCTGT
66 GAAAAAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAAAAGAAACTGT
*
38880 CTCAAGGGAGACAAAATTTGTTTCAAGCAAAACATATTCAAAGAT
130 CTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGAT
* * *
38925 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAATCTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* * ** *
38990 GACAAAATTTGGTTCAAGAGAAACTGTTTCAAGAGAGACAAAATTTGTTTCAAGGA-AAACATAT
66 GAAAAAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAAGAAAC-TGT
* * * * *
39054 -TCAA---AG----ATTTTGTTTAAAGGGAATC-TGTCTCAAGAGAT
130 CTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATAT-TCAA-AGAT
* * * *
39092 ACAAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGACCAAATTTGTTTCAAGAGAAACTGTCTA
1 ------TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTC
* * *
39157 AAGAGGGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAAGAA
60 AAGAGAGAAAAAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAAGAA
39222 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGAT
125 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGAT
* *
39272 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCATGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
* *
39337 GAAAAAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAAAAGAAACTGTT
66 GAAAAAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAAGAAACTGTC
*
39402 TCAAGGGAGACGAAATTTGTTTC
131 TCAAGGGAGACAAAATTTGTTTC
39425 GACGGAAACA
Statistics
Matches: 426, Mismatches: 54, Indels: 40
0.82 0.10 0.08
Matches are distributed among these distances:
165 2 0.00
166 18 0.04
167 4 0.01
170 2 0.00
173 119 0.28
174 254 0.60
177 2 0.00
180 4 0.01
181 19 0.04
182 2 0.00
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.27
Consensus pattern (174 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
GAAAAAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAAAGAAACTGTC
TCAAGGGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGAT
Found at i:39040 original size:21 final size:20
Alignment explanation
Indices: 38946--39043 Score: 63
Period size: 21 Copynumber: 5.2 Consensus size: 20
38936 GGAAACTGTC
38946 TCAAGAGAGACTAAATTTGTT
1 TCAAGAGAGAC-AAATTTGTT
* *
38967 TCAAG-G-G---AATCTGTC
1 TCAAGAGAGACAAATTTGTT
*
38982 TCAAGAGAGACAAAATTTGGT
1 TCAAGAGAGAC-AAATTTGTT
*
39003 TC-A-AGAG--AAA-CTGTT
1 TCAAGAGAGACAAATTTGTT
39018 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGAC-AAATTTGTT
39039 TCAAG
1 TCAAG
39044 GAAAACATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 24
0.64 0.09 0.27
Matches are distributed among these distances:
15 16 0.28
16 5 0.09
17 5 0.09
19 5 0.09
20 5 0.09
21 21 0.37
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (20 bp):
TCAAGAGAGACAAATTTGTT
Found at i:39067 original size:137 final size:137
Alignment explanation
Indices: 38719--39386 Score: 586
Period size: 137 Copynumber: 4.8 Consensus size: 137
38709 AGGTTGGTGT
* *
38719 TTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAAC-TGTCTCAAGAGAAAC
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGAAAACATAT-TCAA-AG----
* * * * * * * *
38783 AAAATTTGGTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTTTCTCAA
59 --ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAATCTGTCTCAA
* *
38848 GAGAGACAAAACTTAG
122 GAGAGACAAAATTTGG
* ** * *
38864 TTCCAAAAGAGGCTGTCTCAAGGGAGACAAAATTTGTTTCAAGCAAAACATATTCAAAGATTTTG
1 TT-CAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTG
*
38929 TTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAATCTGTCTCAAGAGAGACA
65 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAATCTGTCTCAAGAGAGACA
38994 AAATTTGG
130 AAATTTGG
*
39002 TTCAAGAGAAACTGTTTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGT
* * * * *
39067 TTAAAGGGAATCTGTCTCAAGAGATACAAAATTTGTTTCAAGAGAAAT-TGTCTCAAGAGAGACC
66 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAG-GGAATCTGTCTCAAGAGAGACA
*
39131 AAATTTGT
130 AAATTTGG
* * * * *
39139 TTCAAGAGAAACTGTCTAAAGAGGGAAAAAATTTGTTTCAAGGGAAAC-TGTCTCAAGAGAGACA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATAT-TC-A-A-AG---
* ** * * * *
39203 AAATTTGTTTCAAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATAT-TC-
59 -ATTTTGTTTC-AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAATC-TGTCTCA
* *
39266 A-A-AG----ATTTTGT
121 AGAGAGACAAAATTTGG
* * *
39277 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC-TGTCTCATGAGAGAAA
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATAT-TCA--A-AG---
* * *
39341 AAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
59 -ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTT
39387 AAAAAAGAAA
Statistics
Matches: 453, Mismatches: 55, Indels: 38
0.83 0.10 0.07
Matches are distributed among these distances:
136 2 0.00
137 196 0.43
138 148 0.33
139 1 0.00
140 2 0.00
142 2 0.00
143 1 0.00
144 15 0.03
145 57 0.13
146 29 0.06
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (137 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATTCAAAGATTTTGT
TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAATCTGTCTCAAGAGAGACAA
AATTTGG
Found at i:39109 original size:21 final size:19
Alignment explanation
Indices: 39083--39148 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 19
39073 GGAATCTGTC
39083 TCAAGAGATACAAAATTTGTT
1 TCAAGAGA-AC-AAATTTGTT
*
39104 TCAAGAG---AAA-TTGTC
1 TCAAGAGAACAAATTTGTT
39119 TCAAGAGAGACCAAATTTGTT
1 TCAAGAGA-A-CAAATTTGTT
39140 TCAAGAGAA
1 TCAAGAGAA
39149 ACTGTCTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 11 0.30
16 3 0.08
20 4 0.11
21 19 0.51
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (19 bp):
TCAAGAGAACAAATTTGTT
Found at i:39251 original size:347 final size:349
Alignment explanation
Indices: 38652--39386 Score: 1127
Period size: 347 Copynumber: 2.1 Consensus size: 349
38642 TTTTTTGTGT
* * * * *
38652 TTCAAGAGAAACTGTCTCCAGGGAGGCAAAAGTTTTTTTCAAGAGAAACATATTCAAAGGTTGGT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGAGAAACATATTCAAAGATTGGT
* *
38717 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTCAAGAGAAA
65 GTTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAAA
* * * *
38782 CAAAATTTGGTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTAAAGAGAAACTTTCTCA
130 CAAAATTTGGTTCAAGAGAAACTGTCTAAAGAGAGAAAAAATTTGTTTAAAGAGAAACTGTCTCA
* **
38847 AGAGAGACAAAACTTAGTTCCAAAAGAGGCTGTCTCAAGGGAGACAAAATTTGTTTCAAGCAAAA
195 AGAGAGACAAAACTTAGTTCAAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGCAAAA
* *
38912 CATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAAT
260 CATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
*
38977 CTGTCTCAAGAGAGACAAAATTTGG
325 CTGTCTCAAGAGAGAAAAAATTTGG
* *
39002 TTCAAGAGAAACTGTTTCAAGAGAGACAAAATTTGTTTCAAG-GAAAACATATTCAAAGATT-TT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAG-AAACATATTCAAAGATTGGT
* * * * *
39065 GTTTAAAGGGAATCTGTCTCAAGAGATACAAAA-TTTGTTTCAAGAGAAATTGTCTCAAGAGAGA
65 GTTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAAA
* * * * *
39129 CCAAATTTGTTTCAAGAGAAACTGTCTAAAGAGGGAAAAAATTTGTTTCAAGGGAAACTGTCTCA
130 CAAAATTTGGTTCAAGAGAAACTGTCTAAAGAGAGAAAAAATTTGTTTAAAGAGAAACTGTCTCA
* *
39194 AGAGAGACAAAA-TTTGTTTCAAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAA
195 AGAGAGACAAAACTTAG-TTCAAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGCAAA
39258 ACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAA
259 ACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAA
*
39323 ACTGTCTCATGAGAGAAAAAATTTGG
324 ACTGTCTCAAGAGAGAAAAAATTTGG
39349 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
1 TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
39387 AAAAAAGAAA
Statistics
Matches: 350, Mismatches: 33, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
346 3 0.01
347 263 0.75
348 31 0.09
349 26 0.07
350 27 0.08
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (349 bp):
TTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACATATTCAAAGATTGGTG
TTTAAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACTGTCTCAAGAGAAAC
AAAATTTGGTTCAAGAGAAACTGTCTAAAGAGAGAAAAAATTTGTTTAAAGAGAAACTGTCTCAA
GAGAGACAAAACTTAGTTCAAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGCAAAAC
ATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAAC
TGTCTCAAGAGAGAAAAAATTTGG
Found at i:39294 original size:210 final size:209
Alignment explanation
Indices: 38925--39424 Score: 757
Period size: 210 Copynumber: 2.4 Consensus size: 209
38915 ATTCAAAGAT
* * *
38925 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGGGAATCTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* * *
38990 GACAAAATTTGGTTCAAGAGAAACTGTTTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATT
66 GACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATT
* * *
39055 CAAAGATTTTGTTTAAAGGGAATCTGTCTCAAGAGATACAAAATTTGTTTCAAGAGAAATTGTCT
131 CAAAGATTTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCT
**
39120 CAAGAGAGACCAAA
196 CAAGAGAGAAAAAA
* * *
39134 TTTGTTTCAAGAGAAACTGTCTAAAGAGGGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
*
39199 GACAAAATTTGTTTCAAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATAT
66 GACAAAATTTGTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATAT
* *
39264 TCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTC
130 TCAAAGATTTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTC
*
39329 TCATGAGAGAAAAAA
195 TCAAGAGAGAAAAAA
* * ** * *
39344 TTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTAAAAAAGAAACTGTTTCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT-CAAGGGAAACTGTCTCAAGAG
*
39409 AGACGAAATTTGTTTC
65 AGACAAAATTTGTTTC
39425 GACGGAAACA
Statistics
Matches: 261, Mismatches: 28, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
209 73 0.28
210 157 0.60
211 31 0.12
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (209 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
GACAAAATTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATT
CAAAGATTTTGTTTAAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCT
CAAGAGAGAAAAAA
Found at i:39299 original size:138 final size:137
Alignment explanation
Indices: 39134--39386 Score: 416
Period size: 138 Copynumber: 1.8 Consensus size: 137
39124 AGAGACCAAA
*
39134 TTTGTTTCAAGAGAAACTGTCTAAAGAGGGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTAAAGAGAGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
* * *
39199 GACAAAATTTGTTTCAAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAAACATAT
66 GAAAAAATTTGGTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATAT
39264 TCAAAGAT
130 TCAAAGAT
* * * *
39272 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCATGAGA
1 TTTGTTTCAAGAGAAACTGTCTAAAGAGAGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
*
39337 GAAAAAATTTGGTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
66 GAAAAAATTTGGTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTT
39387 AAAAAAGAAA
Statistics
Matches: 106, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
137 33 0.31
138 73 0.69
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (137 bp):
TTTGTTTCAAGAGAAACTGTCTAAAGAGAGAAAAAATTTGTTTCAAGGGAAACTGTCTCAAGAGA
GAAAAAATTTGGTTCAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAACATATT
CAAAGAT
Found at i:40929 original size:95 final size:95
Alignment explanation
Indices: 40676--40929 Score: 314
Period size: 95 Copynumber: 2.6 Consensus size: 95
40666 GGCTAGCTGG
* * * **
40676 ATCCATAAAGCCGGGGTATTTTAACCAATTGCTCTAGAGGGACAGCTCAATATTATTATATAG-A
1 ATCCATAAAGCCAGGGCA-TTTAACCAATTGCTCTAGAGGGACAACTCAA-GCT-TTAT-T-GTA
* * *
40740 TATTATAATCACCTTTATCATGCTAGCTGAATATT
61 CACTATAATCACCTTTATCAGGCTAGCTGAATATT
* * *
40775 ATCCATAAAGTCAGGGCGTTTAACCAATTGCTCTATAGGGACAACTCAAGCTTCT-TTGTACACT
1 ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTT-TATTGTACACT
*
40839 ATAATCACCTTTATCAGGCTAGCTGAATCTT
65 ATAATCACCTTTATCAGGCTAGCTGAATATT
* *
40870 ATCCATAAAGCCAGGGCATTTAACCAATTGCTTTAGAGGGACACCTCAAGCTTTATTGTA
1 ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTA
40930 TATATATATT
Statistics
Matches: 135, Mismatches: 17, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
94 2 0.01
95 86 0.64
96 2 0.01
97 2 0.01
98 29 0.21
99 14 0.10
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.32
Consensus pattern (95 bp):
ATCCATAAAGCCAGGGCATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTACACTA
TAATCACCTTTATCAGGCTAGCTGAATATT
Found at i:44691 original size:6 final size:7
Alignment explanation
Indices: 44680--44722 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
44670 TTTATTTGCG
44680 AAAA-TT
1 AAAATTT
44686 AAAATTT
1 AAAATTT
44693 AAAA-TT
1 AAAATTT
44699 AAAATTT
1 AAAATTT
44706 AAAA-TT
1 AAAATTT
44712 AAAATTT
1 AAAATTT
44719 AAAA
1 AAAA
44723 ACCGATTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
6 16 0.47
7 18 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
AAAATTT
Found at i:44698 original size:13 final size:13
Alignment explanation
Indices: 44680--44722 Score: 86
Period size: 13 Copynumber: 3.3 Consensus size: 13
44670 TTTATTTGCG
44680 AAAATTAAAATTT
1 AAAATTAAAATTT
44693 AAAATTAAAATTT
1 AAAATTAAAATTT
44706 AAAATTAAAATTT
1 AAAATTAAAATTT
44719 AAAA
1 AAAA
44723 ACCGATTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAATTAAAATTT
Found at i:51340 original size:26 final size:26
Alignment explanation
Indices: 51304--51389 Score: 145
Period size: 26 Copynumber: 3.3 Consensus size: 26
51294 AGGACACTAA
*
51304 GTGTATTATGGTAGGCACGACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
*
51330 GTGTATTATGGTGGGCACGACTTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
*
51356 GTGTATTATGGTGGGCACAACCTTAT
1 GTGTATTATGGTGGGCACGACCTTAT
51382 GTGTATTA
1 GTGTATTA
51390 AAACTTTGGT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (26 bp):
GTGTATTATGGTGGGCACGACCTTAT
Found at i:61589 original size:19 final size:19
Alignment explanation
Indices: 61565--61610 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
61555 ACTGGCAGCA
* **
61565 GAGGCGGTTGGAAGCTGTT
1 GAGGCGGTTGGAAACCATT
*
61584 GAGGCGGCTGGAAACCATT
1 GAGGCGGTTGGAAACCATT
61603 GAGGCGGT
1 GAGGCGGT
61611 GGCACACGGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.15, G:0.46, T:0.20
Consensus pattern (19 bp):
GAGGCGGTTGGAAACCATT
Found at i:61746 original size:3 final size:3
Alignment explanation
Indices: 61733--61821 Score: 117
Period size: 3 Copynumber: 30.0 Consensus size: 3
61723 TTAATGTATT
* *
61733 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
61780 TAA TAA TTA TAA TAA TGA TAA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61822 ATTAATATGG
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:62121 original size:42 final size:40
Alignment explanation
Indices: 62074--62182 Score: 191
Period size: 42 Copynumber: 2.7 Consensus size: 40
62064 GAATAAGCTC
62074 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCGCTT
1 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTT--CTT
62116 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
1 TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
*
62156 TCGATGAGTTCTTCTCATTATGAACTT
1 TTGATGAGTTCTTCTCATTATGAACTT
62183 TCTCTAGAAA
Statistics
Matches: 66, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
40 29 0.44
42 37 0.56
ACGTcount: A:0.18, C:0.22, G:0.12, T:0.48
Consensus pattern (40 bp):
TTGATGAGTTCTTCTCATTATGAACTTCTTCATCCTTCTT
Found at i:62441 original size:113 final size:113
Alignment explanation
Indices: 62233--62656 Score: 611
Period size: 113 Copynumber: 3.8 Consensus size: 113
62223 TAGAATTATG
* ** * ** *
62233 CAAAAAGTTGAACAAGCTCTTCTTATTATGAACTTCTTCTT-CTTC-AGATGACGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA-GATGAGTTCTTCTC
* * * * * *
62296 ATTATGAACTCTAC-CTGGCAATGTTAATCCATCAAATGATGAATTTAAA
65 ATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
* * *
62345 CAAAAGGTTGAAAAAATTATTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
62410 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
*
62458 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
* * *
62523 TTATGAACTTCCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAA
66 TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
*
62571 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTTCAGATGAGTTCTTCTC
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TTCTTCAGATGAGTTCTTCTC
62636 ATTATGAACTTTCTCTGGAAA
65 ATTATGAACTTTCTCTGGAAA
62657 TGTCAATCTA
Statistics
Matches: 282, Mismatches: 26, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
112 36 0.13
113 206 0.73
114 40 0.14
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTTAAA
Found at i:63545 original size:83 final size:83
Alignment explanation
Indices: 63390--64109 Score: 1294
Period size: 83 Copynumber: 8.8 Consensus size: 83
63380 GTAGTTCCTA
* * *
63390 CCAAACCAGATCAGATAACTCAAAGAACACTTCCA-AAGATGCTATGAGCAAATTCATCTTCTAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
63454 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
63472 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTTCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
63537 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
63555 CCAAATGAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCATCTTCC-A
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
*
63619 GTT-AATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
63636 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
63701 ATTCAATGATTGG-TCTG
66 ATTCAATGATTGGTTCTG
63718 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA-TCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
63782 ATTCAA-GATTGGTTCTG
66 ATTCAATGATTGGTTCTG
63799 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
63864 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
63882 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
63947 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
63965 CCAAATCAGATCAGATAACTCAAAGAACACTTCC-GAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
64029 ATTCAATGA-TGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
64046 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCA
64110 GTTAAGGTTT
Statistics
Matches: 618, Mismatches: 13, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
80 6 0.01
81 191 0.31
82 181 0.29
83 240 0.39
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (83 bp):
CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:63669 original size:164 final size:165
Alignment explanation
Indices: 63390--64109 Score: 1274
Period size: 164 Copynumber: 4.4 Consensus size: 165
63380 GTAGTTCCTA
* * *
63390 CCAAACCAGATCAGATAACTCAAAGAACACTTCCA-AAGATGCTATGAGCAAATTCATCTTCTAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTC-CA
*
63454 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
65 ATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
*
63519 AGCAAATTCATCTTTCAAATTCAATGATTGGTTCTG
130 AGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG
* * *
63555 CCAAATGAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCATCTTCCAG
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
63620 TT-AATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
66 TTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
63684 GCAAATTCATCTTCCAAATTCAATGATTGG-TCTG
131 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG
63718 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA-TCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCC-A
63782 ATTCAA-GATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
65 ATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
63846 AGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG
130 AGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG
63882 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCC-A
63947 ATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCC-GAAGATGCTATT
65 ATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
64011 AGCAAATTCATCTTCCAAATTCAATGA-TGGTTCTG
130 AGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG
* *
64046 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCA
64110 GTTAAGGTTT
Statistics
Matches: 536, Mismatches: 13, Indels: 14
0.95 0.02 0.02
Matches are distributed among these distances:
162 9 0.02
163 148 0.28
164 218 0.41
165 92 0.17
166 69 0.13
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (165 bp):
CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
TTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTA
GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG
Found at i:65136 original size:1 final size:1
Alignment explanation
Indices: 65126--65208 Score: 67
Period size: 1 Copynumber: 83.0 Consensus size: 1
65116 TTGATCTCCC
* * * * * * * * * *
65126 TTTTTCTTTTTTCTTTTTCTCTTTTTTTTTTTTCTCTTTTTTTCTTTTCTTTTTTCTTTTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
65191 TTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTT
65209 CTTCAAGCAT
Statistics
Matches: 60, Mismatches: 22, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 60 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:65150 original size:15 final size:15
Alignment explanation
Indices: 65126--65204 Score: 90
Period size: 15 Copynumber: 5.3 Consensus size: 15
65116 TTGATCTCCC
65126 TTTT-TCTTTTTTCT
1 TTTTCTCTTTTTTCT
*
65140 TTTTCTCTTTTTTTT
1 TTTTCTCTTTTTTCT
65155 TTTTCTCTTTTTT-T
1 TTTTCTCTTTTTTCT
* *
65169 CTTTTCTTTTTTCTTTT
1 -TTTTCTCTTTT-TTCT
*
65186 TTTTCTTTTTTTTCT
1 TTTTCTCTTTTTTCT
65201 TTTT
1 TTTT
65205 TTTTCTTCAA
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
14 5 0.09
15 39 0.67
16 13 0.22
17 1 0.02
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (15 bp):
TTTTCTCTTTTTTCT
Found at i:65165 original size:10 final size:9
Alignment explanation
Indices: 65125--65207 Score: 89
Period size: 9 Copynumber: 9.0 Consensus size: 9
65115 CTTGATCTCC
65125 CTTTTTCTTT
1 CTTTTT-TTT
65135 -TTTCTTTTT
1 CTTT-TTTTT
*
65144 CTCTTTTTT
1 CTTTTTTTT
*
65153 -TTTTTTCT
1 CTTTTTTTT
65161 CTTTTTTTCT
1 CTTTTTTT-T
*
65171 TTTCTTTTTT
1 CTT-TTTTTT
65181 CTTTTTTTT
1 CTTTTTTTT
65190 CTTTTTTTT
1 CTTTTTTTT
65199 CTTTTTTTT
1 CTTTTTTTT
65208 TCTTCAAGCA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
8 6 0.10
9 41 0.66
10 10 0.16
11 5 0.08
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:65169 original size:38 final size:38
Alignment explanation
Indices: 65126--65206 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
65116 TTGATCTCCC
*
65126 TTTTTCTTTTTTCTTTTTCTCTTTTTT-TTTTTTCTCTT
1 TTTTTCTTTTCT-TTTTTCTCTTTTTTCTTTTTTCTCTT
* *
65164 TTTTTCTTTTCTTTTTTCTTTTTTTTCTTTTTTTTCTT
1 TTTTTCTTTTCTTTTTTCTCTTTTTTCTTTTTTCTCTT
65202 TTTTT
1 TTTTT
65207 TTCTTCAAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
37 13 0.33
38 26 0.67
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (38 bp):
TTTTTCTTTTCTTTTTTCTCTTTTTTCTTTTTTCTCTT
Found at i:65170 original size:31 final size:31
Alignment explanation
Indices: 65132--65204 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
65122 TCCCTTTTTC
65132 TTTTTTCTTTTTCTCTTTT-TTTTTTTTCTCT
1 TTTTTTCTTTTTCTCTTTTCTTTTTTTTCT-T
*
65163 TTTTTTC-TTTTCTTTTTTCTTTTTTTTCTT
1 TTTTTTCTTTTTCTCTTTTCTTTTTTTTCTT
65193 TTTTTTCTTTTT
1 TTTTTTCTTTTT
65205 TTTTCTTCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 18 0.46
31 21 0.54
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (31 bp):
TTTTTTCTTTTTCTCTTTTCTTTTTTTTCTT
Found at i:65207 original size:13 final size:13
Alignment explanation
Indices: 65126--65208 Score: 105
Period size: 14 Copynumber: 6.2 Consensus size: 13
65116 TTGATCTCCC
65126 TTTTTCTTTTTTCT
1 TTTTTCTTTTTT-T
65140 TTTTCTCTTTTTTT
1 TTTT-TCTTTTTTT
65154 TTTTTCTCTTTTTT
1 TTTTTCT-TTTTTT
*
65168 TCTTTTCTTTTTTC
1 T-TTTTCTTTTTTT
*
65182 TTTTT-TTTCTTT
1 TTTTTCTTTTTTT
65194 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
65207 TT
1 TT
65209 CTTCAAGCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
12 10 0.16
13 15 0.25
14 22 0.36
15 14 0.23
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTCTTTTTTT
Done.