Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006962.1 Hibiscus syriacus cultivar Beakdansim tig00017910_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: 87999
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:11409 original size:32 final size:32
Alignment explanation
Indices: 11372--11438 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
11362 AGGCTTCATA
11372 GAAGAAGACAAGAAAAACCTAGTATGCAGGTT
1 GAAGAAGACAAGAAAAACCTAGTATGCAGGTT
11404 GAAGAAGACAAGAAAAACCTAGTATGCAGGTT
1 GAAGAAGACAAGAAAAACCTAGTATGCAGGTT
11436 GAA
1 GAA
11439 AAACCTAGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.48, C:0.12, G:0.25, T:0.15
Consensus pattern (32 bp):
GAAGAAGACAAGAAAAACCTAGTATGCAGGTT
Found at i:11458 original size:18 final size:19
Alignment explanation
Indices: 11415--11458 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
11405 AAGAAGACAA
11415 GAAAAACCTAGTATGCAGGTT
1 GAAAAACCTAGTAT--AGGTT
11436 GAAAAACCTAGTAT-GGTT
1 GAAAAACCTAGTATAGGTT
*
11454 TAAAA
1 GAAAA
11459 CAAGCTCCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
21 14 0.64
ACGTcount: A:0.43, C:0.11, G:0.20, T:0.25
Consensus pattern (19 bp):
GAAAAACCTAGTATAGGTT
Found at i:20617 original size:34 final size:34
Alignment explanation
Indices: 20574--20647 Score: 139
Period size: 34 Copynumber: 2.2 Consensus size: 34
20564 TTTCATTATC
20574 CTGAAAACATGATACTCTCAATGTTTCCTATGAA
1 CTGAAAACATGATACTCTCAATGTTTCCTATGAA
*
20608 CTGAAAACATGGTACTCTCAATGTTTCCTATGAA
1 CTGAAAACATGATACTCTCAATGTTTCCTATGAA
20642 CTGAAA
1 CTGAAA
20648 TCTTCATGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (34 bp):
CTGAAAACATGATACTCTCAATGTTTCCTATGAA
Found at i:24739 original size:31 final size:31
Alignment explanation
Indices: 24680--24744 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
24670 GATTCTTTTA
* *
24680 TTACAAATAGATAACGTTAGTGATCAATTTG
1 TTACAAATAGATAACATTAGTGACCAATTTG
*
24711 TTACAAATAGATAACATTAGTGGCCAATTTG
1 TTACAAATAGATAACATTAGTGACCAATTTG
24742 TTA
1 TTA
24745 TTTTTGAAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (31 bp):
TTACAAATAGATAACATTAGTGACCAATTTG
Found at i:31220 original size:106 final size:106
Alignment explanation
Indices: 30588--31688 Score: 1713
Period size: 106 Copynumber: 10.5 Consensus size: 106
30578 CATTGTTCCA
* * * ** * * *
30588 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGGTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* * * *
30653 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
30694 AGTCCAACATCCTTCGTTGTGAAGTTGAAATTGATTCTG-AA-TGA-AA--T-TTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
30753 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
30794 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
30858 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTCTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * **
30899 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAA--AATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
30962 CAGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** *
31003 AGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAA--AATTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
31066 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
31107 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* **
31172 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCAAG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
31213 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTG-TTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
31277 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
31318 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
31383 CAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGA
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
31424 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAGTTGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
31489 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
31530 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
31595 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
31636 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTG
31689 GTTGAGGTGT
Statistics
Matches: 928, Mismatches: 57, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
100 83 0.09
101 2 0.00
102 2 0.00
103 4 0.00
104 196 0.21
105 202 0.22
106 439 0.47
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:31472 original size:317 final size:314
Alignment explanation
Indices: 30588--31687 Score: 1764
Period size: 317 Copynumber: 3.5 Consensus size: 314
30578 CATTGTTCCA
* * **
30588 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGGTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT-GTTGTTGACAA
* * * * *
30652 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAACATCCTTCGTTGTGAA
64 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
** * *
30717 GTTGAAATTGATTCTG-AA-TGA-AA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTG
129 GTTGAAATTGGCTCTGAAATTGAGAAGTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
30778 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAA
194 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTGAGAA
* * *
30843 GTTG-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTCTCTGG
258 GTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
*
30899 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAAT-TTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
* * *
30963 AGCGGTCCCTTCGTCGTGAAGTTGAACATACGTTGTCTGGAGTCCAATATCCTTCGATGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* **
31028 TGAAATTGGCTCTGAAATTGGGAAAATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 TGAAATTGGCTCTGAAATTGAGAAGTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
31093 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGT
196 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-AATTGAGAAGT
**
31158 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCAAG
260 TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* *
31213 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
31278 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
31343 TGAAATTGGCTCTGAAATTGAGAAGTTGGTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTG
131 TGAAATTGGCTCTGAAATTGAGAAGTT--TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTG
*
31408 AACTTGCGTTGTCTGAAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAA
194 AACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAA-TTGAGAA
*
31473 GTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
258 GTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
* *
31530 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG-TTGTTGACAAC
* *
31595 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTATGGAGTCCAATATCCTTCGCTGTGAAG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG
31660 TTGAAATTGGCTCTGAAATTGAGAAGTT
130 TTGAAATTGGCTCTGAAATTGAGAAGTT
31688 GGTTGAGGTG
Statistics
Matches: 734, Mismatches: 43, Indels: 17
0.92 0.05 0.02
Matches are distributed among these distances:
309 81 0.11
310 2 0.00
311 47 0.06
312 3 0.00
313 101 0.14
314 97 0.13
315 98 0.13
316 2 0.00
317 201 0.27
318 102 0.14
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (314 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTGTTGACAACC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
TGAAATTGGCTCTGAAATTGAGAAGTTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTGAGAAGTT
GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
Found at i:43032 original size:351 final size:351
Alignment explanation
Indices: 42389--43089 Score: 1402
Period size: 351 Copynumber: 2.0 Consensus size: 351
42379 TTAAATTCTT
42389 CTTGCTTCTCGACTTTGATCTACCATATTTGTGACTGCTGCTTTGGCCACATTCTGTTGATCTCC
1 CTTGCTTCTCGACTTTGATCTACCATATTTGTGACTGCTGCTTTGGCCACATTCTGTTGATCTCC
42454 CTCTCATCGTTGACAACGCTTCTACTTGTTGGAGATTTACTTGTCTGTCTTCTCTTGTGCCGATT
66 CTCTCATCGTTGACAACGCTTCTACTTGTTGGAGATTTACTTGTCTGTCTTCTCTTGTGCCGATT
42519 TTCTTCTTGTAGAACAACAGCTTCAACATCATCGAATACTAGACTAGTGGCATTACTGTTTGTCA
131 TTCTTCTTGTAGAACAACAGCTTCAACATCATCGAATACTAGACTAGTGGCATTACTGTTTGTCA
42584 AGTTGATGATGAGTTGATCATATGAATCAGGTAGACTTTGAAGTAGAAGTTCAGCACGTTCTTGT
196 AGTTGATGATGAGTTGATCATATGAATCAGGTAGACTTTGAAGTAGAAGTTCAGCACGTTCTTGT
42649 TCTCCTATTATATATCTTAAGGATGTAAGCTGAGAAAATAAAGTTTCAGTGAGTTTAAGTGCTCC
261 TCTCCTATTATATATCTTAAGGATGTAAGCTGAGAAAATAAAGTTTCAGTGAGTTTAAGTGCTCC
42714 GTCACTGAAGTAGATTCTAGAATCTA
326 GTCACTGAAGTAGATTCTAGAATCTA
42740 CTTGCTTCTCGACTTTGATCTACCATATTTGTGACTGCTGCTTTGGCCACATTCTGTTGATCTCC
1 CTTGCTTCTCGACTTTGATCTACCATATTTGTGACTGCTGCTTTGGCCACATTCTGTTGATCTCC
42805 CTCTCATCGTTGACAACGCTTCTACTTGTTGGAGATTTACTTGTCTGTCTTCTCTTGTGCCGATT
66 CTCTCATCGTTGACAACGCTTCTACTTGTTGGAGATTTACTTGTCTGTCTTCTCTTGTGCCGATT
42870 TTCTTCTTGTAGAACAACAGCTTCAACATCATCGAATACTAGACTAGTGGCATTACTGTTTGTCA
131 TTCTTCTTGTAGAACAACAGCTTCAACATCATCGAATACTAGACTAGTGGCATTACTGTTTGTCA
42935 AGTTGATGATGAGTTGATCATATGAATCAGGTAGACTTTGAAGTAGAAGTTCAGCACGTTCTTGT
196 AGTTGATGATGAGTTGATCATATGAATCAGGTAGACTTTGAAGTAGAAGTTCAGCACGTTCTTGT
43000 TCTCCTATTATATATCTTAAGGATGTAAGCTGAGAAAATAAAGTTTCAGTGAGTTTAAGTGCTCC
261 TCTCCTATTATATATCTTAAGGATGTAAGCTGAGAAAATAAAGTTTCAGTGAGTTTAAGTGCTCC
43065 GTCACTGAAGTAGATTCTAGAATCT
326 GTCACTGAAGTAGATTCTAGAATCT
43090 GGAGTGTACA
Statistics
Matches: 350, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
351 350 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (351 bp):
CTTGCTTCTCGACTTTGATCTACCATATTTGTGACTGCTGCTTTGGCCACATTCTGTTGATCTCC
CTCTCATCGTTGACAACGCTTCTACTTGTTGGAGATTTACTTGTCTGTCTTCTCTTGTGCCGATT
TTCTTCTTGTAGAACAACAGCTTCAACATCATCGAATACTAGACTAGTGGCATTACTGTTTGTCA
AGTTGATGATGAGTTGATCATATGAATCAGGTAGACTTTGAAGTAGAAGTTCAGCACGTTCTTGT
TCTCCTATTATATATCTTAAGGATGTAAGCTGAGAAAATAAAGTTTCAGTGAGTTTAAGTGCTCC
GTCACTGAAGTAGATTCTAGAATCTA
Found at i:44500 original size:15 final size:15
Alignment explanation
Indices: 44462--44492 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
44452 TTATCCGATG
*
44462 TAAATATATATCAAA
1 TAAATATATATAAAA
44477 TAAATATATATAAAA
1 TAAATATATATAAAA
44492 T
1 T
44493 GATTATATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
TAAATATATATAAAA
Found at i:45170 original size:40 final size:41
Alignment explanation
Indices: 45108--45186 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 41
45098 TAATATTAAC
45108 ATTCAAGGACTAAAATAATTAGGTTAACTATTTAAAAATAT
1 ATTCAAGGACTAAAATAATTAGGTTAACTATTTAAAAATAT
* *
45149 ATTCAA-GTCTAAAATATTTAGGTTAACTATTTAAAAAT
1 ATTCAAGGACTAAAATAATTAGGTTAACTATTTAAAAAT
45187 CAAATTATCT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 30 0.83
41 6 0.17
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.37
Consensus pattern (41 bp):
ATTCAAGGACTAAAATAATTAGGTTAACTATTTAAAAATAT
Found at i:49726 original size:15 final size:15
Alignment explanation
Indices: 49706--49734 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49696 ATATGATCCC
49706 TTTCTTTCTTCTAGT
1 TTTCTTTCTTCTAGT
49721 TTTCTTTCTTCTAG
1 TTTCTTTCTTCTAG
49735 CCAACTATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.21, G:0.07, T:0.66
Consensus pattern (15 bp):
TTTCTTTCTTCTAGT
Found at i:57541 original size:31 final size:31
Alignment explanation
Indices: 57505--57564 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
57495 AACTTAAAAG
*
57505 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
57536 AGTTTTACAATATTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
57565 CATACAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:58068 original size:20 final size:20
Alignment explanation
Indices: 58020--58081 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
58010 AACTTAAATC
*
58020 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
58040 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
58058 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
58077 AAAAT
1 AAAAT
58082 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:58114 original size:63 final size:59
Alignment explanation
Indices: 58046--58178 Score: 135
Period size: 63 Copynumber: 2.1 Consensus size: 59
58036 ATATAAAATT
58046 TTAATAA-TATATAAAATAATTTATATGATATAAAATTAAATATCTATAATAGAATATT-AAAAA
1 TTAATAATTATATAAAA-AA-TTA-AT-AT-TAAAATT-AATATCTATAATAGAATATTAAAAAA
* *
58109 TTAATATTTAATTTATTTAAAAAATTAATATTAAAATTAATATCTATAATATAATATTAAAAAA
1 TT-A-A--TAA-TTATATAAAAAATTAATATTAAAATTAATATCTATAATAGAATATTAAAAAA
58173 TTAATA
1 TTAATA
58179 TTTAATTTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 17
0.76 0.03 0.21
Matches are distributed among these distances:
60 2 0.03
62 1 0.02
63 22 0.36
64 15 0.25
65 3 0.05
66 2 0.03
67 6 0.10
68 2 0.03
69 8 0.13
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (59 bp):
TTAATAATTATATAAAAAATTAATATTAAAATTAATATCTATAATAGAATATTAAAAAA
Found at i:58145 original size:64 final size:64
Alignment explanation
Indices: 58076--58235 Score: 242
Period size: 64 Copynumber: 2.6 Consensus size: 64
58066 TTATATGATA
*
58076 TAAAATTAAATATCTATAATAGAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
58140 TAAAATT-AATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTAAAACATTAATAT
1 TAAAATTAAATATCTATAATATAATATT-AAAAATTAATATTTAATTTATTTAAAAAATTAATAT
*
58204 TAATATTAAA-ATC-A-AATATAATA-T-AAAATTAA
1 TAAAATTAAATATCTATAATATAATATTAAAAATTAA
58236 ATATAAAACC
Statistics
Matches: 91, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
59 8 0.09
61 1 0.01
62 9 0.10
63 20 0.22
64 51 0.56
65 2 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (64 bp):
TAAAATTAAATATCTATAATATAATATTAAAAATTAATATTTAATTTATTTAAAAAATTAATAT
Found at i:58175 original size:40 final size:37
Alignment explanation
Indices: 58098--58180 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 37
58088 TCTATAATAG
*
58098 AATATTAAAAATTAATATTTAATTTATTTAAAAAATT
1 AATATTAAAAATTAATATTTAATTAATTTAAAAAATT
58135 AATATT-AAAATTAATATCTATAATATAATATTAAAAAATT
1 AATATTAAAAATTAATAT-T-TAAT-TAAT-TTAAAAAATT
58175 AATATT
1 AATATT
58181 TAATTTATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 11 0.27
37 7 0.17
38 4 0.10
39 3 0.07
40 16 0.39
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (37 bp):
AATATTAAAAATTAATATTTAATTAATTTAAAAAATT
Found at i:58179 original size:28 final size:25
Alignment explanation
Indices: 58131--58204 Score: 82
Period size: 24 Copynumber: 3.0 Consensus size: 25
58121 TTATTTAAAA
58131 AATTAATATT--AAAATTAATATCTAT
1 AATTAATATTAAAAAATTAATAT-T-T
58156 AATATAATATTAAAAAATTAATATTT
1 AAT-TAATATTAAAAAATTAATATTT
* *
58182 AATTTAT-TTAAAACATTAATATT
1 AATTAATATTAAAAAATTAATATT
58205 AATATTAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 15 0.34
25 6 0.14
26 11 0.25
27 1 0.02
28 11 0.25
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTAATATTAAAAAATTAATATTT
Found at i:58232 original size:17 final size:18
Alignment explanation
Indices: 58199--58241 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
58189 TTAAAACATT
58199 AATATTAATATTAAAATCA
1 AATA-TAATATTAAAATCA
*
58218 AATATAATA-TAAAATTA
1 AATATAATATTAAAATCA
58235 AATATAA
1 AATATAA
58242 AACCTCTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.61
18 5 0.22
19 4 0.17
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AATATAATATTAAAATCA
Found at i:60491 original size:10 final size:10
Alignment explanation
Indices: 60476--60531 Score: 51
Period size: 10 Copynumber: 5.4 Consensus size: 10
60466 GGGTCTCCAA
60476 CGTTTATGTT
1 CGTTTATGTT
60486 CGTTTATGTT
1 CGTTTATGTT
60496 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
60507 ATGTTCGTGTT
1 -CGTTTATGTT
60518 CGTTTATGTT
1 CGTTTATGTT
60528 CGTT
1 CGTT
60532 CATTTATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
10 25 0.69
11 7 0.19
12 4 0.11
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:60507 original size:16 final size:16
Alignment explanation
Indices: 60482--60538 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
60472 CCAACGTTTA
*
60482 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
60498 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
60514 TGTTCGTTTATGTTC-
1 TGTTCATTTATGTTCG
60529 -GTTCATTTAT
1 TGTTCATTTAT
60539 TAAGTGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 9 0.24
16 29 0.76
ACGTcount: A:0.11, C:0.12, G:0.19, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:64763 original size:190 final size:190
Alignment explanation
Indices: 64440--64784 Score: 525
Period size: 190 Copynumber: 1.8 Consensus size: 190
64430 AAGATAAAAC
*
64440 TCCTTTTACCATTCAAACTTAAATATATATTATTTTAATTTGAAACATACAAAAGTATATAATTA
1 TCCTTTTACCATTCAAACTTAAACATATATTATTTTAATTTGAAACATACAAAAGTATATAATTA
* * * *
64505 TCTTTAACATTCAAAGTTAAAAAAGATAATAAATATCTTTTTAAATTGATACATTCAAAGAGTAA
66 TCTTTAACATTCAAAATTAAAAAAGATAACAAATACCTTTTTAAATTGATACATTAAAAGAGTAA
64570 TTATCCTACTAATAATCAAATTAAATAATATATTTAATTTAGAATGGTCAAAAGGTAAAT
131 TTATCCTACTAATAATCAAATTAAATAATATATTTAATTTAGAATGGTCAAAAGGTAAAT
* * *
64630 TCCTTTTACTATTCAAACTTAAACATATATTATTTTAATTTGAAATATATAAAAGTATATAATTA
1 TCCTTTTACCATTCAAACTTAAACATATATTATTTTAATTTGAAACATACAAAAGTATATAATTA
* * *
64695 TCTTTTAATATTTAAAATT-AAAAATATAACAAATACCTTTTTAAATT-A-ACTTATTAAAAGAG
66 TC-TTTAACATTCAAAATTAAAAAAGATAACAAATACCTTTTTAAATTGATAC--ATTAAAAGAG
* *
64757 TAATTATCCTATTAATATTCAAATTAAA
128 TAATTATCCTACTAATAATCAAATTAAA
64785 AATCATCTTT
Statistics
Matches: 139, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
188 2 0.01
189 1 0.01
190 123 0.88
191 13 0.09
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.40
Consensus pattern (190 bp):
TCCTTTTACCATTCAAACTTAAACATATATTATTTTAATTTGAAACATACAAAAGTATATAATTA
TCTTTAACATTCAAAATTAAAAAAGATAACAAATACCTTTTTAAATTGATACATTAAAAGAGTAA
TTATCCTACTAATAATCAAATTAAATAATATATTTAATTTAGAATGGTCAAAAGGTAAAT
Found at i:65734 original size:21 final size:23
Alignment explanation
Indices: 65710--65758 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 23
65700 TATTCGACTC
65710 AAATTAATTGATCAA-TATA-T-A
1 AAATTAATTGAT-AATTATACTAA
65731 AAA-T-ATTGATAATTATACTAA
1 AAATTAATTGATAATTATACTAA
65752 AAATTAA
1 AAATTAA
65759 CATATAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
18 2 0.09
19 10 0.43
20 2 0.09
21 7 0.30
22 1 0.04
23 1 0.04
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (23 bp):
AAATTAATTGATAATTATACTAA
Found at i:67392 original size:16 final size:16
Alignment explanation
Indices: 67358--67406 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
67348 TCCGTATCCG
* *
67358 ATCCAAAAAAATCGAAT
1 ATCC-AAAAATTCGGAT
67375 ATCCAAAAATTCGGAT
1 ATCCAAAAATTCGGAT
* *
67391 ATCCGAAATTTCGGAT
1 ATCCAAAAATTCGGAT
67407 TGGATATCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 24 0.86
17 4 0.14
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (16 bp):
ATCCAAAAATTCGGAT
Found at i:70750 original size:19 final size:21
Alignment explanation
Indices: 70716--70759 Score: 74
Period size: 19 Copynumber: 2.2 Consensus size: 21
70706 TAAAAATTTA
70716 AAAATTTTATTTTTAAAAAAT
1 AAAATTTTATTTTTAAAAAAT
70737 AAAA-TTTA-TTTTAAAAAAT
1 AAAATTTTATTTTTAAAAAAT
70756 AAAA
1 AAAA
70760 AAATTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 15 0.65
20 4 0.17
21 4 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
AAAATTTTATTTTTAAAAAAT
Found at i:70765 original size:18 final size:19
Alignment explanation
Indices: 70726--70765 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
70716 AAAATTTTAT
**
70726 TTTTAAAAAATAAAATTTA
1 TTTTAAAAAATAAAATAAA
70745 TTTTAAAAAATAAAA-AAA
1 TTTTAAAAAATAAAATAAA
70763 TTT
1 TTT
70766 CTTAAATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAAAAAATAAAATAAA
Found at i:70808 original size:166 final size:169
Alignment explanation
Indices: 70493--70819 Score: 446
Period size: 166 Copynumber: 1.9 Consensus size: 169
70483 TTTAAGTGTA
* * *
70493 TGTCAGTTAAATTTGACTGCTAATTGACATATGTTAAATTTATAAAAAATTTAAAAAATTTATTT
1 TGTCAGTTAAATTTGACTGCTAATTGACACATATCAAATTTATAAAAAATTTAAAAAATTTATTT
* ** **
70558 TAAAATAAAAAATAAAAATTCTTTTAAAAAAATTTAAATTTTTCTTAAATCTAAAAAACACAAAA
66 T---ATAAAAAATAAAAATTATTTTAAAAAAATAAAAAAATTTCTTAAATCTAAAAAACACAAAA
*
70623 ATCTAAAATCCCTAATTCCAAATCTTTTTACCTACATTGATC
128 ATCTAAAATCCCTAATTCCAAATCCTTTTACCTACATTGATC
* * *
70665 TGTC-GTTAAATTTGATTGTTAATTGACACATATCAAATTTAT-AAAAATTTAAAAATTTTATTT
1 TGTCAGTTAAATTTGACTGCTAATTGACACATATCAAATTTATAAAAAATTTAAAAAATTTATTT
* * **
70728 T-TAAAAAATAAAATTTATTTT-AAAAAATAAAAAAATTTCTTAAATCTAAAAACACTCAAATTT
66 TATAAAAAATAAAAATTATTTTAAAAAAATAAAAAAATTTCTTAAATCTAAAAA-ACACAAAAAT
70791 CTAAAATCCCTAATTCCAAATCCTTTTAC
130 CTAAAATCCCTAATTCCAAATCCTTTTAC
70820 TTACGTTTGA
Statistics
Matches: 138, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
165 27 0.20
166 53 0.38
170 21 0.15
171 33 0.24
172 4 0.03
ACGTcount: A:0.46, C:0.12, G:0.04, T:0.39
Consensus pattern (169 bp):
TGTCAGTTAAATTTGACTGCTAATTGACACATATCAAATTTATAAAAAATTTAAAAAATTTATTT
TATAAAAAATAAAAATTATTTTAAAAAAATAAAAAAATTTCTTAAATCTAAAAAACACAAAAATC
TAAAATCCCTAATTCCAAATCCTTTTACCTACATTGATC
Found at i:71909 original size:20 final size:22
Alignment explanation
Indices: 71884--71923 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
71874 TGTTGTATAT
71884 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
71904 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
71924 TCTACTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:72411 original size:21 final size:21
Alignment explanation
Indices: 72387--72426 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
72377 ATGTTTAATG
72387 AAAAAGATACCAATTGTTAAC
1 AAAAAGATACCAATTGTTAAC
* *
72408 AAAATGATATCAATTGTTA
1 AAAAAGATACCAATTGTTA
72427 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (21 bp):
AAAAAGATACCAATTGTTAAC
Found at i:75115 original size:34 final size:32
Alignment explanation
Indices: 75057--75126 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
75047 ACCTTACAAC
* *
75057 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTTACGGGATAAACTAGAACCTT
75089 TCCCTAGCTTTTATACGGGATAAACTAGAACCTT
1 TCCCTAG-TTTT-TACGGGATAAACTAGAACCTT
75123 TCCC
1 TCCC
75127 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 4 0.12
34 23 0.68
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTTACGGGATAAACTAGAACCTT
Found at i:75367 original size:20 final size:22
Alignment explanation
Indices: 75342--75381 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
75332 TGTTGTATAT
75342 AGCCG-TAGGGGATG-TTTTGG
1 AGCCGTTAGGGGATGATTTTGG
*
75362 AGCCGTTTGGGGATGATTTT
1 AGCCGTTAGGGGATGATTTT
75382 TATACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.40, T:0.35
Consensus pattern (22 bp):
AGCCGTTAGGGGATGATTTTGG
Found at i:75615 original size:21 final size:21
Alignment explanation
Indices: 75543--75645 Score: 111
Period size: 21 Copynumber: 4.9 Consensus size: 21
75533 CATTCGAAAT
*
75543 GGAGTGCATGGATGCACTCCA
1 GGAGTGCATGGATGCACTGCA
* * * *
75564 TG-GTGCATCGATGAACTAG-T
1 GGAGTGCATGGATGCACT-GCA
75584 GGTAGGTGCATGGATGCACTGCA
1 GG-A-GTGCATGGATGCACTGCA
75607 GGAGTGCATGGATGCACTGCA
1 GGAGTGCATGGATGCACTGCA
*
75628 GGGGTGCATGGATGCACT
1 GGAGTGCATGGATGCACT
75646 TTGACACCAT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
20 14 0.21
21 36 0.54
22 2 0.03
23 15 0.22
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.22
Consensus pattern (21 bp):
GGAGTGCATGGATGCACTGCA
Found at i:76581 original size:223 final size:223
Alignment explanation
Indices: 76014--76985 Score: 812
Period size: 247 Copynumber: 4.2 Consensus size: 223
76004 GTTTCACCCG
* *
76014 ACCCGACCCGAAATAATAAGAAA-ATTATTTTTATTTAATATAAACAGTGACTTAATTGAAAATA
1 ACCCGACCCGAAATAATAA-AAATATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAA-A
* *
76078 TATATATATATATAGAGGTAGTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATT
64 AAT-TATATATA-AGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATA--
* **
76143 TTTGGGTCGGGTCGGGTCGTGTATTTTTCACCCTAAACCCGAACCCGACCCGACCAAAATAAAGT
125 TTT---TCGGGTC--G--G-GTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAAT--A--
** **** * *
76208 TTCAC-CCGACTCGACTCGACCCGACACGAATATATGAATTAGAAATCC
178 -TCACACTTAAAAAAATCGACCCGACCCGAATATATGAATTAGAAA--C
*
76256 GACCCGACCCGAAATAATGAAAAAT-TTATTTTTATTCAATAAAAACAATGACTTAATTG-AAAA
1 -ACCCGACCCGAAATAAT-AAAAATATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAA
*
76319 AATTATATAT-AGAGGAATATTATTATAATTATTCCTAAATATATAAGGTAAAATTATATATATT
64 AATTATATATAAGAGG--TATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATT
76383 TTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAA
127 TTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAA
*
76448 ATTGACCCGACCCGAATATATGAATTAG-AA-
192 ATCGACCCGACCCGAATATATGAATTAGAAAC
* *
76478 ACCCGACCTGAAATAATAAAAATATTATATTTATTCAATAAAAACAGTGACTTAATTGGAAAAAA
1 ACCCGACCCGAAATAATAAAAATATTATTTTTATTCAATAAAAACAGTGACTTAATT-GAAAAAA
*
76543 ATTATATATAAAGAGGTATTATTGTAATTATTCCTAAATATATAAGATAAAATTATATATATTTT
65 ATTATATAT-AAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTT
* *
76608 CGGGTCGGGTATTTTTCACCCTAAACCCTAA-T----TCGACCCGAATATCACACTTAAAAAAAC
129 CGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAA-
* * * ** **
76668 CCGACCCGACCCGACCA-AAATAAAGTTTCACCC
193 TCGACCCGACCCGA--ATATATGAA-TTAGAAAC
* * *** *
76701 GACCCGACCCGAATATATTAATTAGAA-ACTCGATCCGAAATAAT-AATAAAATATTTTTATTCA
1 -ACCCGACCCGAA-ATAATAA--A-AATA-T-TAT---TTTTATTCAAT-AAA-A-----A--CA
* * * * * * *
76764 ATAAAAACAATGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTATAATTATTCCTAAAT
47 GT---GAC--TTAATTGA---AAAAAATTATATATA-AGAGGTATTATTGTAATTATTCCTAAAT
* * * *
76829 ATATAAGGTAAAATTATATATATTTTCGTGTTGGGTATTTTTTACCCTAAACCCAAACTCGACCC
103 ATATAAGGTAAAATTATATATATTTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCC
* *
76894 GACCTGAATATCACACTT-AAAAAACCGACCCGACCCGAATATATGAATTAG-AA-
168 GACCCGAATATCACACTTAAAAAAATCGACCCGACCCGAATATATGAATTAGAAAC
* * *
76947 ACCCGACCCAAAATAA-AAAAAAAATATTTTTATTCAATA
1 ACCCGACCCGAAATAATAAAAATATTATTTTTATTCAATA
76986 TATGAATAAG
Statistics
Matches: 610, Mismatches: 67, Indels: 111
0.77 0.09 0.14
Matches are distributed among these distances:
218 26 0.04
219 12 0.02
220 11 0.02
221 50 0.08
222 2 0.00
223 91 0.15
224 11 0.02
225 17 0.03
226 28 0.05
227 2 0.00
228 4 0.01
229 2 0.00
230 37 0.06
231 4 0.01
232 7 0.01
233 2 0.00
235 7 0.01
236 4 0.01
237 3 0.00
238 9 0.01
239 2 0.00
240 55 0.09
241 5 0.01
242 3 0.00
243 55 0.09
244 6 0.01
245 15 0.02
246 1 0.00
247 92 0.15
248 4 0.01
249 5 0.01
250 14 0.02
251 6 0.01
252 18 0.03
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (223 bp):
ACCCGACCCGAAATAATAAAAATATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
TTATATATAAGAGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCG
GGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAATCG
ACCCGACCCGAATATATGAATTAGAAAC
Found at i:76953 original size:31 final size:31
Alignment explanation
Indices: 76883--76955 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
76873 CCCTAAACCC
* * *
76883 AAACTCGACCCGACCTGAATATCACACTTAA
1 AAACCCGACCCGACCCGAATATCACAATTAA
* * *
76914 AAAACCGACCCGACCCGAATAT-ATGAATTAG
1 AAACCCGACCCGACCCGAATATCA-CAATTAA
76945 AAACCCGACCC
1 AAACCCGACCC
76956 AAAATAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.40, C:0.33, G:0.12, T:0.15
Consensus pattern (31 bp):
AAACCCGACCCGACCCGAATATCACAATTAA
Found at i:80957 original size:35 final size:35
Alignment explanation
Indices: 80910--80976 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
80900 AGAGAGTTGG
* * *
80910 AATTTGTCTTTAACTCTAAATATATTTTAATGTAT
1 AATTTGTCTTTAACCCTAAATAGAGTTTAATGTAT
*
80945 AATTTGTTTTTAACCCTAAATAGAGTTTAATG
1 AATTTGTCTTTAACCCTAAATAGAGTTTAATG
80977 CCTTTAACCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (35 bp):
AATTTGTCTTTAACCCTAAATAGAGTTTAATGTAT
Done.