Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000626.1 Hibiscus syriacus cultivar Beakdansim tig00001214_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: 70215
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3133 original size:19 final size:19
Alignment explanation
Indices: 3099--3136 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3089 CAACTCTAGC
*
3099 CAAAGTCAACATGTCGGGT
1 CAAAGTCAACAGGTCGGGT
*
3118 CAAAGTCAACGGGTCGGGT
1 CAAAGTCAACAGGTCGGGT
3137 TGACTATGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.32, T:0.18
Consensus pattern (19 bp):
CAAAGTCAACAGGTCGGGT
Found at i:8839 original size:24 final size:23
Alignment explanation
Indices: 8812--8860 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
8802 TAAATGAAAG
* *
8812 AAAAATAATAATAATAATAAAATA
1 AAAAATAACAAAAAT-ATAAAATA
*
8836 AAAAATAACAAAAATATTAAATA
1 AAAAATAACAAAAATATAAAATA
8859 AA
1 AA
8861 TCAGAAGGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (23 bp):
AAAAATAACAAAAATATAAAATA
Found at i:8861 original size:27 final size:28
Alignment explanation
Indices: 8797--8861 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 28
8787 AAAATTAATG
* *
8797 TTAAATAAATGAAAGAAAAATAATAATA
1 TTAAATAAATGAAAGAAAAACAAAAATA
*
8825 AT-AATAAAAT-AAA-AAATAACAAAAATA
1 TTAAAT-AAATGAAAGAAA-AACAAAAATA
8852 TTAAATAAAT
1 TTAAATAAAT
8862 CAGAAGGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
26 3 0.10
27 19 0.63
28 8 0.27
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.25
Consensus pattern (28 bp):
TTAAATAAATGAAAGAAAAACAAAAATA
Found at i:11400 original size:80 final size:80
Alignment explanation
Indices: 11093--12489 Score: 1527
Period size: 80 Copynumber: 17.2 Consensus size: 80
11083 CTGAATAGAG
* * * * * *
11093 TCGAACTCGAAGATCTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGACG
1 TCGAACTCGAAGGTC-TT-TGGA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA-T-GATG
*
11158 TGCCTTTGACCTGAGTGTAA
61 TGCCTTTGAGCTGAGTGTAA
* * *
11178 TCGAACTTGAAGGTCTTTGTTGACAGATAACCC-TCTAGCCTTGAGTTATGCTGTAAATTTGATA
1 TCGAACTCGAAGGTCTTTG--GA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA--TGATG
*
11242 TGCCTTTGAGCTGAATGTAA
61 TGCCTTTGAGCTGAGTGTAA
* * * * * **
11262 ACAAACCCGAAGGTCTTTGTTGGCAGATAACCCTTGTAGCCTTGAGTTATGCTGCAAATGATGCA
1 TCGAACTCGAAGGTC--T-TTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
11327 CCTTTGAGCTGAGTGTAA
63 CCTTTGAGCTGAGTGTAA
* * * * *
11345 TCGAACTCAAAGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
*
11410 TTAAGCTGAGTGTAA
66 TTGAGCTGAGTGTAA
* * *
11425 TCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTG--GA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
11490 CCTTTGAGCTGAGTGTAA
63 CCTTTGAGCTGAGTGTAA
* * * * * * *
11508 TCGATCCCGAAGGTCTTTGGCAGATAGCCCTTCTTGCCTT-ATGCTACGCTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGA-GTTATGCTGCAAATGATGTGCC
*
11572 -TTGAGTTGAGTGTAA
65 TTTGAGCTGAGTGTAA
* * * * **
11587 TCAAACTCGATGGACTTTGGCAGATAACCCTTCTAGGTTTGAGTTATGCTGCAAATGATGTGCC-
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
11651 TTGAGCTGAGTGTAA
66 TTGAGCTGAGTGTAA
* * * * *
11666 TCGAACTCGCATGTCTTTGGAAGATAACCCTTCTTGCCTTAAGCTATG-TCGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCT-GCAAATGATGTGCC
11730 TTTGAGCTGAGTGTAA
65 TTTGAGCTGAGTGTAA
* * ** *
11746 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCCAGCCTTTAGTTATATTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTG--GA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
*
11811 CTTTTGAGCTGAGTGTAA
63 CCTTTGAGCTGAGTGTAA
* * * * *
11829 TCGAACTCGAAGGTCTTTGGCAGATAGA-CCTTCTTGCCTTAAGCTATGCTGCAAATGATGTACC
1 TCGAACTCGAAGGTCTTTGGAAGATA-ACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
11893 -TTGAGCTGAGTGTAA
65 TTTGAGCTGAGTGTAA
* * *
11908 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTT
1 TCGAACTCGAAGGTCTTTG--GA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
* * *
11973 TCTTTAAGTTGAGTGTAA
63 CCTTTGAGCTGAGTGTAA
* * * *
11991 TCGAACTCAAAGTTCTTTGGAGGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCC-
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
12055 TTGAGCTGAGTGTAA
66 TTGAGCTGAGTGTAA
* * * * * * * * * *
12070 TCGAACTCGAAGGTCTTTGGCATATAGCCCTTATTGTCGTAAGCTATGTTGCAAATGATGTGCC-
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
*
12134 TTGAACTGAGTGTAA
66 TTGAGCTGAGTGTAA
* *
12149 TCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTG--GA-AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG
12214 CCTTTGAGCTGAGTGTAA
63 CCTTTGAGCTGAGTGTAA
* * * * * *
12232 TTGAACTTGAAGGTCTTTGGCAA-ATAATCATTCTAGCCTTAAGTTATACTGCAAATGATGTGCC
1 TCGAACTCGAAGGTCTTTGG-AAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCC
12296 TTTGAGCTGAGTGTAA
65 TTTGAGCTGAGTGTAA
* * * * *
12312 TCGAGCTCGAAGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
12377 TTGAGCTGAGTGTAA
66 TTGAGCTGAGTGTAA
* * * * * ** **
12392 TCGAACTCGAAGGTCTTTGGCAGGTAGCCCTTCTTGCCTTGTGCAATTATGCAAATGATGTGCCT
1 TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
* * *
12457 CTGACCTGAATGTAA
66 TTGAGCTGAGTGTAA
*
12472 TCGAACTCAAAGGTCTTT
1 TCGAACTCGAAGGTCTTT
12490 TTTGAAGGTG
Statistics
Matches: 1114, Mismatches: 168, Indels: 65
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.00
79 265 0.24
80 414 0.37
81 11 0.01
82 73 0.07
83 231 0.21
84 65 0.06
85 50 0.04
86 1 0.00
87 3 0.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (80 bp):
TCGAACTCGAAGGTCTTTGGAAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCT
TTGAGCTGAGTGTAA
Found at i:11699 original size:321 final size:325
Alignment explanation
Indices: 11093--12489 Score: 1709
Period size: 321 Copynumber: 4.3 Consensus size: 325
11083 CTGAATAGAG
* * * * *
11093 TCGAACTCGAAGATCTTTATTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTAAATTGGACG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAA-T-GATG
* *
11158 TGCCTTTGACCTGAGTGTAATCGAACTTGAAGGTCTTTGTTGACAGATAACCC-TCTAGCCTTGA
64 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTAGCCTTGA
* * * * * *
11222 GTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGTAAACAAACCCGAAGGTCTTTGTTGGCA
128 GCTATGCTGCAAA--TGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTC--T-TTGGCA
* * **
11287 GATAACCCTTGTAGCCTTGAGTTATGCTGCAAATGATGCACCTTTGAGCTGAGTGTAATCGAACT
188 GATAACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACT
* * *
11352 CAAAGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTAAGCT
253 CGAAGGTCTTTGGAAGATAACCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCT
11417 GAGTGTAA
318 GAGTGTAA
* *
11425 TCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTG
* * * *
11490 CCTTTGAGCTGAGTGTAATCGATCCCGAAGGTCTTTG-G-CAGATAGCCCTTCTTGCCTT-ATGC
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATAACCCTTCTAGCCTTGA-GC
* * * *
11552 TACGCTGCAAATGATGTGCC-TTGAGTTGAGTGTAATCAAACTCGATGGACTTTGGCAGATAACC
130 TATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAACC
** * * *
11616 CTTCTAGGTTTGAGTTATGCTGCAAATGATGTGCC-TTGAGCTGAGTGTAATCGAACTCGCATGT
195 CTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
11680 CTTTGGAAGATAACCCTTCTTGCCTTAAGCTATG-TCGCAAATGATGTGCCTTTGAGCTGAGTGT
260 CTTTGGAAGATAACCCTTCTTGCCTTAAGCTATGCT-GCAAATGATGTGCCTTTGAGCTGAGTGT
11744 AA
324 AA
* *
11746 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCCAGCCTTTAGTTATATTGTAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTG
* * *
11811 CTTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-G-CAGATAGA-CCTTCTTGCCTTAAGC
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATA-ACCCTTCTAGCCTTGAGC
* *
11873 TATGCTGCAAATGATGTACC-TTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATA
130 TATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTG--G-CAGATA
* ** * * *
11937 ACCCTTCTAGCCTTGAGTTATACTGTAAATGATGTTTCTTTAAGTTGAGTGTAATCGAACTCAAA
192 ACCCTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
* * * * * *
12002 GTTCTTTGGAGGATAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGCC-TTGAGCTGAGT
257 GGTCTTTGGAAGATAACCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
12066 GTAA
322 GTAA
* * * * * * * * * *
12070 TCGAACTCGAAGGTCTTTG--G-CATATAGCCCTTATTGTCGTAAGCTATGTTGCAAATGATGTG
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTG
* * *
12132 CC-TTGAACTGAGTGTAATCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTAGCCTTGAGT
66 CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTAGCCTTGAGC
* * ** * * *
12196 TATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATTGAACTTGAAGGTCTTTGGCAAATAATC
130 TATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAACC
* * *
12261 ATTCTAGCCTTAAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAGCTCGAAGGT
195 CTTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGT
*
12326 CTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
260 CTTTGGAAGATAACCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTA
12391 A
325 A
* * * * ** *
12392 TCGAACTCGAAGGTCTTTG--G-CAGGTAGCCCTTCTTGCCTTGTGCAAT-TATGCAAATGATGT
1 TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATAT-TGTAAATGATGT
* * * *
12453 GCCTCTGACCTGAATGTAATCGAACTCAAAGGTCTTT
65 GCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT
12490 TTTGAAGGTG
Statistics
Matches: 932, Mismatches: 115, Indels: 45
0.85 0.11 0.04
Matches are distributed among these distances:
320 34 0.04
321 391 0.42
322 117 0.13
323 66 0.07
324 104 0.11
325 91 0.10
326 9 0.01
327 10 0.01
328 19 0.02
330 38 0.04
331 1 0.00
332 52 0.06
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (325 bp):
TCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATATTGTAAATGATGTG
CCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATAACCCTTCTAGCCTTGAGCT
ATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGGCAGATAACCC
TTCTAGCCTTGAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC
TTTGGAAGATAACCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGTGTAA
Found at i:12149 original size:483 final size:485
Alignment explanation
Indices: 11157--12489 Score: 1785
Period size: 483 Copynumber: 2.8 Consensus size: 485
11147 TAAATTGGAC
* *
11157 GTGCCTTTGACCTGAGTGTAATCGAACTTGAAGGTCTTTGTTGACAGATAACCC-TCTAGCCTTG
1 GTGCC-TTGAACTGAGTGTAATCGAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTAGCCTTG
* * * * *
11221 AGTTATG-CTGTAAATTTGATATGCCTTTGAGCTGAATGTAAACAAACCCGAAGGTCTTTGTTGG
64 AGTTATGTC-GTAAA--TGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTT-G
* * * **
11285 CAGATAACCCTTGTAGCCTTGAGTTATGCTGCAAATGATGCACCTTTGAGCTGAGTGTAATCGAA
125 CAGATAACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAA
* *
11350 CTCAAAGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTAAG
190 CTCGAAGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAG
*
11415 CTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACATATAACCCTTCTAGCCTTGAGTTATACTGT
255 CTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGT
* * * * *
11480 AAATGATGTGCCTTTGAGCTGAGTGTAATCGATCCCGAAGGTCTTTGGCAGATAGCCCTTCTTGC
320 AAATGATGTGCCTTTAAGCTGAGTGTAATCGAACCCAAAGGTCTTTGGCAGATAACCCTTCTAGC
* *
11545 CTTATGCTACGCTGCAAATGATGTGCCTTGAGTTGAGTGTAATCAAACTCGATGGACTTTGGCAG
385 CTTATGCTACGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATCAAACTCGAAGGACTTTGGCAG
* * * *
11610 ATAACCCTTCTAGGTTTGAGTTATGCTGCAAATGAT
450 ATAACCCTTATAGGTGTAAGCTATGCTGCAAATGAT
* * * * *
11646 GTGCCTTGAGCTGAGTGTAATCGAACTCGCATGTCTTTG-GA-AGATAACCCTTCTTGCCTTAAG
1 GTGCCTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATAACCCTTCTAGCCTTGAG
* *
11709 CTATGTCGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGAT
66 TTATGTCGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTG-CAGAT
* * * * *
11774 AACCCTTCCAGCCTTTAGTTATATTGTAAATGATGTGCTTTTGAGCTGAGTGTAATCGAACTCGA
130 AACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
* * *
11839 AGGTCTTTGGCAGATAGACCTTCTTGCCTTAAGCTATGCTGCAAATGATGTACC-TTGAGCTGAG
195 AGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
11903 TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATG
260 TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATG
** * * *
11968 ATGTTTCTTTAAGTTGAGTGTAATCGAACTCAAAGTTCTTTGG-AGGATAACCCTTCTAGCCTTG
325 ATGTGCCTTTAAGCTGAGTGTAATCGAACCCAAAGGTCTTTGGCA-GATAACCCTTCTAGCCTT-
* * * * * *
12032 A-GTTATGTTGCAAATGATGTGCCTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGCATATA
388 ATGCTACGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATCAAACTCGAAGGACTTTGGCAGATA
* * *
12096 GCCCTTAT-TGTCGTAAGCTATGTTGCAAATGAT
453 ACCCTTATAGGT-GTAAGCTATGCTGCAAATGAT
*
12129 GTGCCTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTAGCCTTGA
1 GTGCCTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTG-TGACAGATAACCCTTCTAGCCTTGA
* * * *
12194 GTTATGTTGTAAATGATGTGCCTTTGAGCTGAGTGTAATTGAACTTGAAGGTCTTTG--GCAAAT
65 GTTATGTCGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGCAGAT
* * *
12257 AATCATTCTAGCCTTAAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAGCTCGA
130 AACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGA
12322 AGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
195 AGGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAG
* * * * ** *
12387 TGTAATCGAACTCGAAGGTCTTTG--G-CAGGTAGCCCTTCTTGCCTTGTGCAATTA-TGCAAAT
260 TGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTA-TACTGTAAAT
* * * * *
12448 GATGTGCCTCTGACCTGAATGTAATCGAACTCAAAGGTCTTT
324 GATGTGCCTTTAAGCTGAGTGTAATCGAACCCAAAGGTCTTT
12490 TTTGAAGGTG
Statistics
Matches: 743, Mismatches: 90, Indels: 30
0.86 0.10 0.03
Matches are distributed among these distances:
481 60 0.08
482 6 0.01
483 351 0.47
484 188 0.25
485 11 0.01
486 91 0.12
487 1 0.00
488 30 0.04
489 5 0.01
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.33
Consensus pattern (485 bp):
GTGCCTTGAACTGAGTGTAATCGAACTCGAAGGTCTTTGTGACAGATAACCCTTCTAGCCTTGAG
TTATGTCGTAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGCAGATA
ACCCTTCTAGCCTTAAGTTATACTGCAAATGATGTGCCTTTGAGCTGAGTGTAATCGAACTCGAA
GGTCTTTGGAAGATAGCCCTTCTTGCCTTAAGCTATGCTGCAAATGATGTGCCTTTGAGCTGAGT
GTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGA
TGTGCCTTTAAGCTGAGTGTAATCGAACCCAAAGGTCTTTGGCAGATAACCCTTCTAGCCTTATG
CTACGCTGCAAATGATGTGCCTTGAGCTGAGTGTAATCAAACTCGAAGGACTTTGGCAGATAACC
CTTATAGGTGTAAGCTATGCTGCAAATGAT
Found at i:13464 original size:95 final size:95
Alignment explanation
Indices: 13267--13529 Score: 339
Period size: 95 Copynumber: 2.7 Consensus size: 95
13257 GGCTAGCTGA
* * * **
13267 ATCCATAAAGCCGAGGCGTTCAACCAATTGCTCTAGAGGGACAACTTAATATCATTGTA-TAAAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA-A-C-TT-TATTGTAT
13331 ATTATAATCACCTTTATCAGGCTAGCTAAATATT
62 ATTATAATCACCTTTATCAGGCTAGCTAAATATT
* * *
13365 ATCCATAAAGCCGGGGCATTTAACCAATTGCTCTATAGGGATAACTCAAACTTTATTGTATATTA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAACTTTATTGTATATTA
* * * * *
13430 TAATTACCTTTATCATGTTAGCTGAATCTT
66 TAATCACCTTTATCAGGCTAGCTAAATATT
* *
13460 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATATAT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAACTTTATTGTATAT-T
13525 ATAAT
65 ATAAT
13530 ATTATAATCT
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
94 2 0.01
95 92 0.63
96 7 0.05
97 1 0.01
98 43 0.30
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAACTTTATTGTATATTA
TAATCACCTTTATCAGGCTAGCTAAATATT
Found at i:18251 original size:15 final size:15
Alignment explanation
Indices: 18231--18262 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18221 AATCATAAGG
*
18231 AATAATAATACTAAA
1 AATAATAATAATAAA
18246 AATAATAATAATAAA
1 AATAATAATAATAAA
18261 AA
1 AA
18263 ATGAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAATAATAATAAA
Found at i:19078 original size:90 final size:89
Alignment explanation
Indices: 18922--19096 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
18912 CCTAACACAC
* * *
18922 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
*
18987 ATTTAATTAATTAGAATTTAATAAT
66 ATTTAATTAATT-GAAATTAATAAT
* *
19012 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
19077 ATTTAATTAATTGAAATTAA
66 ATTTAATTAATTGAAATTAA
19097 ATATTCGGGA
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 7 0.09
90 72 0.91
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAATAAT
Found at i:25121 original size:90 final size:90
Alignment explanation
Indices: 24968--25145 Score: 286
Period size: 90 Copynumber: 2.0 Consensus size: 90
24958 CCTAACACAC
* * *
24968 CCTTTTATAGCCAATTTACCCTAGTCATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
* *
25033 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
25058 CCTTTTATATCCAAGTTACCCTAATCATA-TATGGGATTTTATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTA-GGGATTTTATTATTTCAAATTAATTAAATCTA
25122 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
25146 TTCGGGATTA
Statistics
Matches: 81, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 2 0.02
90 79 0.98
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:30901 original size:54 final size:55
Alignment explanation
Indices: 30795--30901 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 55
30785 CCAAAAACAG
* *
30795 AATACATTATTAAAAAATGCCAATTCTGTTTGCTTGGACAGCACTACAAATCTGA
1 AATACATTATTAAAAAATGCCAATTCTGTTTGCTTGAACAACACTACAAATCTGA
* * * *
30850 AATACATTA-TAAAAAATGTCAGTTCTGTTTGCTTGAACAACATTACCAATCT
1 AATACATTATTAAAAAATGCCAATTCTGTTTGCTTGAACAACACTACAAATCT
30902 ATCAACAGTC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
54 37 0.80
55 9 0.20
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (55 bp):
AATACATTATTAAAAAATGCCAATTCTGTTTGCTTGAACAACACTACAAATCTGA
Found at i:32491 original size:17 final size:17
Alignment explanation
Indices: 32469--32502 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
32459 CTTTTCATGT
32469 TGATATGATATGTTATA
1 TGATATGATATGTTATA
32486 TGATATGATATGTTATA
1 TGATATGATATGTTATA
32503 CAACTTTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
TGATATGATATGTTATA
Found at i:33460 original size:30 final size:30
Alignment explanation
Indices: 33424--33488 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
33414 GTGGTAGTTG
33424 TGAAAGTGGT-GTTGTAGAAATGGATAATGC
1 TGAAAGTGGTAG-TGTAGAAATGGATAATGC
* *
33454 TGAAAGTGGTAGTGTAGAAATGGATATTGT
1 TGAAAGTGGTAGTGTAGAAATGGATAATGC
33484 TGAAA
1 TGAAA
33489 TAGATATTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.35, C:0.02, G:0.32, T:0.31
Consensus pattern (30 bp):
TGAAAGTGGTAGTGTAGAAATGGATAATGC
Found at i:33473 original size:15 final size:15
Alignment explanation
Indices: 33409--33466 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
33399 AGGGTATAAC
33409 TGAAAGTGGTAGTTG
1 TGAAAGTGGTAGTTG
33424 TGAAAGTGGT-GTTG
1 TGAAAGTGGTAGTTG
*
33438 TAGAAA-TGGATA-ATG
1 T-GAAAGTGG-TAGTTG
33453 CTGAAAGTGGTAGT
1 -TGAAAGTGGTAGT
33467 GTAGAAATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
14 8 0.23
15 23 0.66
16 4 0.11
ACGTcount: A:0.31, C:0.02, G:0.36, T:0.31
Consensus pattern (15 bp):
TGAAAGTGGTAGTTG
Found at i:33488 original size:15 final size:15
Alignment explanation
Indices: 33435--33503 Score: 68
Period size: 15 Copynumber: 4.6 Consensus size: 15
33425 GAAAGTGGTG
*
33435 TTGTAGAAATGGATA
1 TTGTTGAAATGGATA
* *
33450 ATGCTGAAAGTGG-TA
1 TTGTTGAAA-TGGATA
* *
33465 GTGTAGAAATGGATA
1 TTGTTGAAATGGATA
*
33480 TTGTTGAAATAGATA
1 TTGTTGAAATGGATA
33495 TTGTTGAAA
1 TTGTTGAAA
33504 GGGACAGTGA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
14 3 0.07
15 37 0.86
16 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.28, T:0.33
Consensus pattern (15 bp):
TTGTTGAAATGGATA
Found at i:33489 original size:45 final size:45
Alignment explanation
Indices: 33408--33504 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 45
33398 AAGGGTATAA
* *
33408 CTGAAAGTGGTAGTTGTGAAAGTGGTGTTGTAGAAATGGATAATG
1 CTGAAAGTGGTAGTTGTGAAAGTGGTATTGTAGAAATAGATAATG
* *
33453 CTGAAAGTGGTAG-TGTAGAAA-TGGATATTGTTGAAATAGATATTG
1 CTGAAAGTGGTAGTTGT-GAAAGTGG-TATTGTAGAAATAGATAATG
*
33498 TTGAAAG
1 CTGAAAG
33505 GGACAGTGAG
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
44 6 0.13
45 39 0.87
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (45 bp):
CTGAAAGTGGTAGTTGTGAAAGTGGTATTGTAGAAATAGATAATG
Found at i:36627 original size:111 final size:111
Alignment explanation
Indices: 36433--37220 Score: 1209
Period size: 111 Copynumber: 7.1 Consensus size: 111
36423 CCCATGAAAT
* ** * *
36433 ATTGAATC-GAGGCAGACTTGTTCCATTGTCACTCATGGAATATCAAATCTTGAAAGAGAGAGAT
1 ATTGAATCAG-GGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGAT
* * *
36497 ATGTTCCGCTTCTTCTGAGGGAATATCAGATCTAGGAAAGTTGATCC
65 ATGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
*
36544 ATTGAATCAGGGTAGACTTGTTCCGCTGCCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
* *
36609 TGTTTCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTT
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
*
36655 ATTGAATCAGGGTAGACTTTTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
*
36720 TGTTCCGCTTCCTCGGAGGGAATATCAGATCTGGGAAAGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
*
36766 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGAGATA
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
* ** * *
36831 TGTTCTGCTTTTTCTGAGGGAATGTCAGATCTGGGAAAGTTGATCC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
** *
36877 ATTGAATCAGGGTAGACTTGTTCCATTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
* *
36942 TGTTCCACTTCCTCTGAGGGAATATCATATCTGGGAAAGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
* *
36988 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGTATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
* ** * * *
37053 TATTCCATTTCCTCTAAGGGAATATCAGATCTAGGAATGTTGATTC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
*
37099 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATC
1 ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
* ** * * *
37164 TATTTTGCTTCTTCTGAGGGAATATAAGATCTGGGAAAGTTGATCC
66 TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
37210 ATTGAATCAGG
1 ATTGAATCAGG
37221 ATCAAACCTG
Statistics
Matches: 621, Mismatches: 55, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
111 620 1.00
112 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (111 bp):
ATTGAATCAGGGTAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATCTTGAAAGAGAGGGATA
TGTTCCGCTTCCTCTGAGGGAATATCAGATCTGGGAAAGTTGATTC
Found at i:38409 original size:10 final size:10
Alignment explanation
Indices: 38394--38442 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
38384 TCATTTTATG
38394 TTTTCTATTT
1 TTTTCTATTT
38404 TTTTCTA-TT
1 TTTTCTATTT
38413 TTTTC-ATTCT
1 TTTTCTATT-T
38423 TTTTACT-TTT
1 TTTT-CTATTT
38433 TTTT-TATTT
1 TTTTCTATTT
38442 T
1 T
38443 AGGCAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
8 2 0.06
9 12 0.35
10 17 0.50
11 3 0.09
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTCTATTT
Found at i:38425 original size:18 final size:19
Alignment explanation
Indices: 38394--38434 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
38384 TCATTTTATG
*
38394 TTTTCTATTTTTTTCTA-TT
1 TTTTCTATTCTTTT-TACTT
38413 TTTTC-ATTCTTTTTACTT
1 TTTTCTATTCTTTTTACTT
38431 TTTT
1 TTTT
38435 TTTATTTTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 2 0.10
18 13 0.65
19 5 0.25
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCTATTCTTTTTACTT
Found at i:38425 original size:19 final size:19
Alignment explanation
Indices: 38394--38442 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
38384 TCATTTTATG
38394 TTTTCTATTTTTTT-CTATT
1 TTTTCTATTTTTTTACT-TT
38413 TTTTC-ATTCTTTTTACTTT
1 TTTTCTATT-TTTTTACTTT
*
38432 TTTTTTATTTT
1 TTTTCTATTTT
38443 AGGCAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 3 0.12
19 18 0.69
20 5 0.19
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTATTTTTTTACTTT
Found at i:41104 original size:11 final size:11
Alignment explanation
Indices: 41084--41124 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
41074 TGGTGTAGCA
41084 AATGGAAATGC
1 AATGGAAATGC
*
41095 AATGGCAATG-
1 AATGGAAATGC
41105 -ATGGAAATGC
1 AATGGAAATGC
*
41115 AATGGCAATG
1 AATGGAAATG
41125 AAAAATGCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 8 0.32
11 17 0.68
ACGTcount: A:0.41, C:0.10, G:0.29, T:0.20
Consensus pattern (11 bp):
AATGGAAATGC
Found at i:41110 original size:20 final size:20
Alignment explanation
Indices: 41085--41125 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
41075 GGTGTAGCAA
41085 ATGGAAATGCAATGGCAATG
1 ATGGAAATGCAATGGCAATG
41105 ATGGAAATGCAATGGCAATG
1 ATGGAAATGCAATGGCAATG
41125 A
1 A
41126 AAAATGCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.29, T:0.20
Consensus pattern (20 bp):
ATGGAAATGCAATGGCAATG
Found at i:41162 original size:16 final size:16
Alignment explanation
Indices: 41143--41175 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41133 TAAAAACAGT
41143 AAAT-AAAAGATAAATA
1 AAATGAAAAGA-AAATA
41159 AAATGAAAAGAAAATA
1 AAATGAAAAGAAAATA
41175 A
1 A
41176 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATGAAAAGAAAATA
Found at i:41695 original size:24 final size:24
Alignment explanation
Indices: 41650--41699 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
41640 ATAAAGAACC
*
41650 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
41674 AAAATAAAGCTTAGACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
41698 AA
1 AA
41700 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.56, C:0.14, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:51206 original size:37 final size:37
Alignment explanation
Indices: 51154--51257 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
51144 CTTTTCGTCT
*
51154 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * * *
51191 TGCTAGGATTCAAACTCCTAAAAATATGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
* * *
51228 TACTATGATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
51258 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAAAATTC
Found at i:51984 original size:17 final size:15
Alignment explanation
Indices: 51962--52010 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 15
51952 TATACTTTTA
51962 TATTTGATTTATATATT
1 TATTTG-TTTATAT-TT
51979 TATTTGTTT-T-TTT
1 TATTTGTTTATATTT
*
51992 TATTTGTTTATATTA
1 TATTTGTTTATATTT
52007 TATT
1 TATT
52011 ATATTTTCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 11 0.38
14 2 0.07
15 7 0.24
16 3 0.10
17 6 0.21
ACGTcount: A:0.22, C:0.00, G:0.06, T:0.71
Consensus pattern (15 bp):
TATTTGTTTATATTT
Found at i:52017 original size:27 final size:28
Alignment explanation
Indices: 51939--52023 Score: 73
Period size: 30 Copynumber: 2.9 Consensus size: 28
51929 TATAAGCCAA
51939 TTATCATTATATGTATACTTTTATATTTGAT
1 TTAT-ATTATAT-TATA-TTTTATATTTGAT
* * * *
51970 TTATATATTTATTTGTTTTTTTTATTTG-T
1 TTATAT-TATA-TTATATTTTATATTTGAT
51999 TTATATTATATTATATTTTCATATT
1 TTATATTATATTATATTTT-ATATT
52024 ACTATCATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
27 7 0.16
28 7 0.16
29 7 0.16
30 12 0.28
31 9 0.21
32 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.05, T:0.66
Consensus pattern (28 bp):
TTATATTATATTATATTTTATATTTGAT
Found at i:56696 original size:8 final size:8
Alignment explanation
Indices: 56692--56751 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
56682 GGGAAAAAAC
56692 AAAAAAGA
1 AAAAAAGA
*
56700 AAAGAAGA
1 AAAAAAGA
56708 AAAAAAGA
1 AAAAAAGA
56716 AGAAAAA-A
1 A-AAAAAGA
*
56724 AAGAAAGA
1 AAAAAAGA
*
56732 ACAAAAA-T
1 A-AAAAAGA
*
56740 CAAAAAGA
1 AAAAAAGA
56748 AAAA
1 AAAA
56752 GGGACAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
7 9 0.22
8 22 0.55
9 9 0.22
ACGTcount: A:0.82, C:0.03, G:0.13, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:57429 original size:22 final size:22
Alignment explanation
Indices: 57355--57440 Score: 109
Period size: 22 Copynumber: 3.9 Consensus size: 22
57345 GCTACCCCAT
*
57355 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
* * *
57377 CAAACCTATGAGCATCACATAC
1 CAAACCTTTGAGCATCAAATGC
*
57399 CAAACCTTTGAGCATCAAATGT
1 CAAACCTTTGAGCATCAAATGC
*
57421 CAAACCTTTGACCATACAAA
1 CAAACCTTTGAGCAT-CAAA
57441 ATAACCTAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 50 0.93
23 4 0.07
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:58467 original size:106 final size:106
Alignment explanation
Indices: 58270--59313 Score: 1446
Period size: 106 Copynumber: 9.9 Consensus size: 106
58260 CAAGAAAACA
* * * * *
58270 CAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAA-CAACAATTTTCCAATTTCAGAGCAA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
58334 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
58375 TAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAATAAACAATTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
* * * *
58440 ATTGT-AACTTCACAGCGAAAGATATTGGACTCAAGATAACG
66 ATT-TCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
58481 CAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
*
58546 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* *
58587 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTT-CCAATTTTAGAGCC
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCCCAATTTCAGAGCC
* *
58651 AATTTCAACTTCACAACGAAAGATATTGGACTCAAGACAACG
65 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
58693 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
58758 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* * * * *
58799 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTCAATTTTAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
*
58864 ATTTTAACTTCACAACGAAGGATATTGGACTCCAGACAACG
66 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
58905 CAAGTTCAACTTCACGACGATGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAG-CA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
** * *
58969 TATTTCAACTTCACGGCGTAGGATATTGGACTCAAGACAACG
66 -ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
*
59011 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCCAATTTCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
* * * * * *
59076 ATTTCAACTTCTCAGCGAATGATCTTGGAC-CCAAGATAACA
66 ATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACG
* * * * * *
59117 CAAGCTCAACTTCACGACGAAGGGGA-GGCTGATTATCAA-CAA-AATTT--C-A-TTCAGAGTC
1 CAAGTTCAACTTCACGACGAA-GGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
* * * * *
59175 AATTTTAACTTCACAACGAATGATATTGGACTCGAGATAACA
65 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
* ** * ** *
59217 CAAGTTCAACTTCACAACGAAGGGATGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
1 CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
* *
59282 ATTTCAACTTCACGACGGAGGATATTGGACTC
66 ATTTCAACTTCACAACGAAGGATATTGGACTC
59314 GGAACAATGC
Statistics
Matches: 842, Mismatches: 80, Indels: 33
0.88 0.08 0.03
Matches are distributed among these distances:
99 4 0.00
100 73 0.09
101 4 0.00
102 6 0.01
104 5 0.01
105 43 0.05
106 698 0.83
107 9 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
CAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCA
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACG
Found at i:60097 original size:37 final size:37
Alignment explanation
Indices: 60044--60148 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
60034 CCTTTTGGTC
60044 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * *
60081 TTGCTAGGATTCAAACTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
60118 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
60149 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:60664 original size:22 final size:21
Alignment explanation
Indices: 60639--60679 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
60629 ACATATATTT
60639 TTATTTATTT-ATATTGATTTGG
1 TTATTT-TTTAATATT-ATTTGG
60661 TTATTTTTTAATATTATTT
1 TTATTTTTTAATATTATTT
60680 ATATATATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TTATTTTTTAATATTATTTGG
Found at i:60975 original size:2 final size:2
Alignment explanation
Indices: 60968--60996 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60958 TTTTACTCAT
60968 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
60997 TTCATTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:61582 original size:16 final size:16
Alignment explanation
Indices: 61563--61595 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61553 TAGAAGTAGT
61563 AAAT-AAAAGATAAATA
1 AAATGAAAAGA-AAATA
61579 AAATGAAAAGAAAATA
1 AAATGAAAAGAAAATA
61595 A
1 A
61596 TCCTCACATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATGAAAAGAAAATA
Found at i:62080 original size:24 final size:24
Alignment explanation
Indices: 62035--62084 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
62025 ATAAAGAACC
*
62035 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
62059 AAAATAAAGCTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
62083 AA
1 AA
62085 TCAACCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 16 0.67
25 8 0.33
ACGTcount: A:0.58, C:0.14, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:67354 original size:21 final size:21
Alignment explanation
Indices: 67328--67388 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
67318 CTTCAGAGGT
67328 AATACCAATAGTTGGAGCTGA
1 AATACCAATAGTTGGAGCTGA
67349 AATACCAATAGTTGGAGCTGA
1 AATACCAATAGTTGGAGCTGA
*
67370 AATACCAATAGTTGAAGCT
1 AATACCAATAGTTGGAGCT
67389 TTTCCACGAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (21 bp):
AATACCAATAGTTGGAGCTGA
Done.