Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001824.1 Hibiscus syriacus cultivar Beakdansim tig00003692_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: 82403
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:12043 original size:2 final size:2
Alignment explanation
Indices: 11973--12023 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
11963 TAATTTTGTT
11973 TA TA TA TA TA TA TA TA TA T- TCA TA TA T- TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
12013 TA TA TA TA TA T
1 TA TA TA TA TA T
12024 GTGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.07
2 41 0.91
3 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:12192 original size:32 final size:31
Alignment explanation
Indices: 12123--12195 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 31
12113 TAAGTATATA
* *
12123 TTATATAGTTTTTGAAAACGTTTTTAAAATAT
1 TTATATA-TTTTTGAAAACATTTTTAAAACAT
*
12155 ATATATATTTTTGAAAA-ATATTTTGAAAACAT
1 TTATATATTTTTGAAAACAT-TTTT-AAAACAT
12187 TTATATATT
1 TTATATATT
12196 ATATAGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
30 1 0.03
31 14 0.40
32 20 0.57
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (31 bp):
TTATATATTTTTGAAAACATTTTTAAAACAT
Found at i:12216 original size:38 final size:38
Alignment explanation
Indices: 12151--12395 Score: 222
Period size: 38 Copynumber: 6.7 Consensus size: 38
12141 CGTTTTTAAA
*
12151 ATAT-ATATATA-TTTTTGAAAAATATTTTGAAAACATTT
1 ATATAATATATAGTTTTT--AAAACATTTTGAAAACATTT
* *
12189 ATATATTATATAGTTTTTAAAACATTTTG-AAA-ATAT
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACATTT
*
12225 ATATAATATATAGTTTTTAAAACATTTT-AAAA-A--C
1 ATATAATATATAGTTTTTAAAACATTTTGAAAACATTT
12259 ATAT-AT-TATA-----TAAAACATTTTTGAAAACATTT
1 ATATAATATATAGTTTTTAAAACA-TTTTGAAAACATTT
*
12291 ATATAATATATAGTTTTTAAAATCATTTTG-AAAC-CTT
1 ATATAATATATAGTTTTTAAAA-CATTTTGAAAACATTT
*
12328 ATATAATATATAGTTTTTGAAAATATTTTTGAAAAC--TT
1 ATATAATATATAGTTTTT-AAAACA-TTTTGAAAACATTT
*
12366 ATATAATATATAATTTTTTAAAAACATTTT
1 ATATAATATAT-AGTTTTT-AAAACATTTT
12396 TTAAAACTAT
Statistics
Matches: 176, Mismatches: 11, Indels: 40
0.78 0.05 0.18
Matches are distributed among these distances:
27 7 0.04
28 4 0.02
29 4 0.02
30 1 0.01
32 8 0.05
33 4 0.02
34 8 0.05
36 34 0.19
37 24 0.14
38 44 0.25
39 31 0.18
40 7 0.04
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (38 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAACATTT
Found at i:12407 original size:38 final size:38
Alignment explanation
Indices: 12270--12410 Score: 187
Period size: 38 Copynumber: 3.7 Consensus size: 38
12260 TATATTATAT
12270 AAAACATTTTTGAAAACATTTATATAATATATAGTTTTTA
1 AAAACATTTTTGAAAAC--TTATATAATATATAGTTTTTA
* * *
12310 AAATCA-TTTTGAAACCTTATATAATATATAGTTTTTG
1 AAAACATTTTTGAAAACTTATATAATATATAGTTTTTA
* *
12347 AAAATATTTTTGAAAACTTATATAATATATAATTTTTTA
1 AAAACATTTTTGAAAACTTATATAATATAT-AGTTTTTA
*
12386 AAAACATTTTTTAAAAC-TATATAAT
1 AAAACATTTTTGAAAACTTATATAAT
12411 TTTGAAAACA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
37 24 0.27
38 30 0.34
39 30 0.34
40 5 0.06
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAACATTTTTGAAAACTTATATAATATATAGTTTTTA
Found at i:12418 original size:29 final size:30
Alignment explanation
Indices: 12372--12440 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
12362 ACTTATATAA
12372 TATATAATTTTTTAAAAACATTTTTT-AAAAC
1 TATATAA--TTTTAAAAACATTTTTTAAAAAC
* *
12403 TATATAATTTTGAAAACATTTTTTAAAAAG
1 TATATAATTTTAAAAACATTTTTTAAAAAC
12433 TATATAAT
1 TATATAAT
12441 ATATAATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
29 16 0.46
30 12 0.34
31 7 0.20
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.46
Consensus pattern (30 bp):
TATATAATTTTAAAAACATTTTTTAAAAAC
Found at i:12473 original size:36 final size:35
Alignment explanation
Indices: 12403--12496 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 35
12393 TTTTTAAAAC
* *
12403 TATATAATTTTGAAAACATTTTTTAAAAAGTATAT
1 TATATAATTTTGAAAATATTTTTGAAAAAGTATAT
*
12438 AATATATAATTTT-AAAATATTTTTGAAATTA-TATAT
1 --TATATAATTTTGAAAATATTTTTGAAA-AAGTATAT
12474 TATAT-ATTTTGGAAAATATTTTT
1 TATATAATTTT-GAAAATATTTTT
12497 TATATATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
33 5 0.10
34 5 0.10
35 11 0.22
36 18 0.35
37 12 0.24
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (35 bp):
TATATAATTTTGAAAATATTTTTGAAAAAGTATAT
Found at i:12480 original size:23 final size:23
Alignment explanation
Indices: 12454--12503 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
12444 TAATTTTAAA
* *
12454 ATATTTTTGAAATTATATATTAT
1 ATATTTTGGAAAATATATATTAT
* *
12477 ATATTTTGGAAAATATTTTTTAT
1 ATATTTTGGAAAATATATATTAT
12500 ATAT
1 ATAT
12504 AATATATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (23 bp):
ATATTTTGGAAAATATATATTAT
Found at i:19695 original size:84 final size:84
Alignment explanation
Indices: 19563--20547 Score: 953
Period size: 84 Copynumber: 11.9 Consensus size: 84
19553 GCTCAAGACA
* * * *
19563 AGAAGGGTTATTTGCCAACCAAAGACCTTCGAGTTCTACTACGATCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
19628 TACAGCATAACTTAAGTCT
66 TACAGCATAACTTAAGTCT
* * ** * * * * * * *
19647 AGAAGGGTTGTCTGCCAACAAAATACCCCCAAGTTCGATTACACTCAGCGCCGAGGGTATATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCAT
* *
19712 TTACAGCATAACTCAAGGCT
65 TTACAGCATAACTTAAGTCT
* * * * *
19732 AGAAGGGTTATCTGTC-ACCAAAGGCCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
19796 TGCA-TACAACTTAAGTCT
66 TACAGCATAACTTAAGTCT
* ** * * * * *
19814 AGAAGGGTTGTCTGCCAACAAAAGACCCCCGAGTTCGATTACACTCAACGCT-GAGGGCATATCA
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTC-A-GCTCCAAGGCACATCA
* * *
19878 TTTACAGTATAACTCAAGGCT
64 TTTACAGCATAACTTAAGTCT
* * * *
19899 AGAAGAGTTATCTACCAACCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
19964 TGCAGCATAACTTAAGTCG
66 TACAGCATAACTTAAGTCT
* * * * * * *
19983 AGAAGAGTTATCT----ACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * *
20044 TTACAGTATAACTCAAGGCT
65 TTACAGCATAACTTAAGTCT
* * * *
20064 AGAAGGGTTATTTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * *
20129 TGCATCATAACTTAAGTCA
66 TACAGCATAACTTAAGTCT
* * *
20148 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
20213 TGCAGTATAGCTTAAGTCG
66 TACAGCATAACTTAAGTCT
* * ** * * * *
20232 AGAAGGGTTATCTGCC-A-AAGA-ACC-TCGAGTTCGATTACATTCAGCTTCGAGGGAACATTAT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* *
20293 TTACAGCATAACTCAAGGCT
65 TTACAGCATAACTTAAGTCT
* * * * * *
20313 AGAAGGGTTATCAGTC-ACCAAAGACCTTCGAGTTCAACTACGCTCAGTTCCCAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
20377 TGCAGTATAGCTTAAGTCG
66 TACAGCATAACTTAAGTCT
** *
20396 AGAAGGCCTATCTG-C--CAAAA-ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
20457 TGCAGCATAACTTAAGTCA
66 TACAGCATAACTTAAGTCT
* * *
20476 AGAAGGGTTATCTACCAAC-AGAGACCTTTGAGTTCGACTAC-CTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
20539 TACAGCATA
66 TACAGCATA
20548 GCCCAAGGCA
Statistics
Matches: 722, Mismatches: 160, Indels: 40
0.78 0.17 0.04
Matches are distributed among these distances:
80 109 0.15
81 87 0.12
82 60 0.08
83 96 0.13
84 251 0.35
85 119 0.16
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TACAGCATAACTTAAGTCT
Found at i:20049 original size:165 final size:164
Alignment explanation
Indices: 19540--20571 Score: 1010
Period size: 165 Copynumber: 6.2 Consensus size: 164
19530 TTTGAGGTAA
* * * * * *
19540 CATTTGCAATATAGCTCAAGACAAGAAGGGTTATTTGCCAACCAAAGACCTTCGAGTTCTACTAC
1 CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
* * * *
19605 GATCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAA
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCT--C-ACCAAA
* * * * * * *
19670 TACCCCCAAGTTCGATTACACTCAGCGCCGAGGGTATAT
127 GACCCTCGAGTTCGACTACACTCAGC-TCGAGGGCACAT
* * * * *
19709 CATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGGCCTTTGAGTTCGACTACG
1 CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* * * * *
19774 CTCAGCTCCAAGGCATATCATTTGCA-TACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCT--C-ACCAAAG
* * *
19838 ACCCCCGAGTTCGATTACACTCAACGCT-GAGGGCATAT
128 ACCCTCGAGTTCGACTACACTC-A-GCTCGAGGGCACAT
* * * *
19876 CATTTACAGTATAACTCAAGGCTAGAAGAGTTATCTACCAACCAAAGACCTTCGAGTTCGACTAT
1 CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTGCC-ACCAAAGACCTTCGAGTTCGACTAC
* *
19941 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGAGTTATCT-ACCAAAGAC
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTCACCAAAGAC
*
20005 CCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
130 CCTCGAGTTCGACTACACTCAGC-TCGAGGGCACAT
* * *
20041 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTGCCACC-AAAGACCTTCGAGTTCGACTAC
* * *
20106 GCTCAGCTCCAAGGCATATCATTTGCATCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAAA
65 GCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCT--C-ACCAAA
* * * * *
20171 GACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACAT
127 GACCCTCGAGTTCGACTACACTCAGCTCGAGGGCACAT
* * * * *
20209 CATTTGCAGTATAGCTTAAGTCGAGAAGGGTTATCTG---CCAAAGAACC-TCGAGTTCGATTAC
1 CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTGCCACCAAAG-ACCTTCGAGTTCGACTAC
** * * * * * * *
20270 ATTCAGCTTCGAGGGAACATTATTTACAGCATAACTCAAGGCTAGAAGGGTTATCAGTCACCAAA
65 GCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATC--TCACCAAA
* * * * *
20335 GACCTTCGAGTTCAACTACGCTCAGTTCCCA-GGCACAT
127 GACCCTCGAGTTCGACTACACTCAGCT-CGAGGGCACAT
* * * * **
20373 CATTTGCAGTATAGCTTAAGTCGAGAAGGCCTATCTGCCA--AAA-ACCTTCGAGTTCGACTACG
1 CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
* *
20435 CTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCT-ACCAACAGAG
66 CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTCACC-A-A-AG
* * * *
20499 ACCTTTGAGTTCGACTAC-CTCAGCTCCAAGGCACAT
128 ACCCTCGAGTTCGACTACACTCAGCTCGAGGGCACAT
* * * *
20535 CATTTACAGCATAGCCCAAGGCAAGAAGGGCTATCTG
1 CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTG
20572 TCAATAAAAT
Statistics
Matches: 741, Mismatches: 98, Indels: 55
0.83 0.11 0.06
Matches are distributed among these distances:
160 3 0.00
161 5 0.01
162 44 0.06
163 61 0.08
164 117 0.16
165 191 0.26
167 101 0.14
168 136 0.18
169 83 0.11
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (164 bp):
CATTTACAGTATAGCTCAAGGCTAGAAGGGTTATCTGCCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTCACCAAAGACC
CTCGAGTTCGACTACACTCAGCTCGAGGGCACAT
Found at i:20168 original size:249 final size:247
Alignment explanation
Indices: 19540--20574 Score: 1078
Period size: 249 Copynumber: 4.2 Consensus size: 247
19530 TTTGAGGTAA
* * * * * * * *
19540 CATTTGCAATATAGCTCAAGACAAGAAGGGTTATTTGCCAACCAAAGACCTTCGAGTTCTACTAC
1 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
* * * *
19605 GATCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAA
65 GCTCAGCTCCAAGGCACATCATTTACAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAA
* ** * * * * * * * * * * *
19670 TACCCCCAAGTTCGATTACACTCAGCGCCGAGGGTATATCATTTACAGCATAACTCAAGGCTAGA
130 GACCTTCGAGTTCGACTACGCTCAGCTCC-AAGGCACATCATTTGCAGCATAACTTAAGTCGAGA
* * * * *
19735 AGGGTTATCTGTCACCAAAGGCCTTTGAGTTCGACTACGCTCAGCTCCAAGGCATAT
194 AGGGTTATC--T-ACCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * * * * * * ** *
19792 CATTTGCA-TACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCCCCGAGTTCGATTAC
1 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTAC
* * * * * * * *
19856 ACTCAACGCT-GAGGGCATATCATTTACAGTATAACTCAAGGCTAGAAGAGTTATCTACCAACCA
65 GCTC-A-GCTCCAAGGCACATCATTTACAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACCA
*
19920 AAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
128 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAG
* * * *
19985 AAGAGTTATCTACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
193 AAGGGTTATCTACCAAAGACCCTCGAGTTCGACTACACTCAGC-TCCAAGGCACAT
*
20041 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATTTGTCACCAAAAGACCTTCGAGTTCGACTAC
1 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACCTTCGAGTTCGACTAC
* * *
20106 GCTCAGCTCCAAGGCATATCATTTGCA-TCATAACTTAAGTCAAGAAGGGTTATCTGCCAACCAA
65 GCTCAGCTCCAAGGCACATCATTTACAGT-ATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAA
* * * *
20170 AGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGA
129 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGA
* * * * * * *
20235 AGGGTTATCTGCCAAAGAACCTCGAGTTCGATTACATTCAGCTTCGAGGGAACAT
194 AGGGTTATCTACCAAAGACCCTCGAGTTCGACTACACTCAGC-TCCAAGGCACAT
* * * *
20290 TATTTACAGCATAACTCAAGGCTAGAAGGGTTATCAGTCACCAAAGACCTTCGAGTTCAACTACG
1 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * * * * **
20355 CTCAGTTCCCAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGCCTATCTGCC-A--AAA-
66 CTCAGCTCCAAGGCACATCATTTACAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAG
* *
20416 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCAAGAAG
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
* *
20481 GGTTATCTACCAACAGAGACCTTTGAGTTCGACTAC-CTCAGCTCCAAGGCACAT
196 GGTTATCTACC-A-A-AGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
* * * * *
20535 CATTTACAGCATAGCCCAAGGCAAGAAGGGCTATCTGTCA
1 CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCA
20575 ATAAAATTGT
Statistics
Matches: 661, Mismatches: 111, Indels: 29
0.83 0.14 0.04
Matches are distributed among these distances:
244 69 0.10
245 47 0.07
246 6 0.01
247 17 0.03
248 101 0.15
249 214 0.32
250 46 0.07
251 82 0.12
252 76 0.11
253 3 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (247 bp):
CATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCCAAGGCACATCATTTACAGTATAACTTAAGTCTAGAAGGGTTATCTGCCAACCAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAG
GGTTATCTACCAAAGACCCTCGAGTTCGACTACACTCAGCTCCAAGGCACAT
Found at i:21142 original size:2 final size:2
Alignment explanation
Indices: 21135--21219 Score: 147
Period size: 2 Copynumber: 43.5 Consensus size: 2
21125 TAATTTTGTT
21135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
21177 TA TA TA TA TA TA TA TA TA TA TA TA TA -A T- TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
21217 TA T
1 TA T
21220 GTGTGTGTAT
Statistics
Matches: 80, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
1 2 0.03
2 78 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21319 original size:76 final size:76
Alignment explanation
Indices: 21234--21419 Score: 186
Period size: 76 Copynumber: 2.4 Consensus size: 76
21224 GTGTATAGTA
21234 ATATAGTTTTTGAAAATGTTTGAAAAAATATA-AT-GTATAAT-TTTCGGAAAACGAT-TTTTGA
1 ATATAGTTTTTGAAAATGTTTGAAAAAATATATATAGTAT-ATGTTT-GGAAAA--ATATTTTGA
*
21295 AAATAAGTATATATT
62 AAACAAGTATATATT
* ** *
21310 ATATAGTTTTTGAAAACGTTT-TTAAAATATATATAGTATATGGTTTTGAAAAATATTTTGAAAA
1 ATATAGTTTTTGAAAATGTTTGAAAAAATATATATAGTATAT-GTTTGGAAAAATATTTTGAAAA
**
21374 CATTTATATATT
65 CAAGTATATATT
* **
21386 ATATAGTTTTTAAAACAT-TTTGAAAGTATATATA
1 ATATAGTTTTTGAAA-ATGTTTGAAAAAATATATA
21420 ATATATAGTT
Statistics
Matches: 90, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
75 10 0.11
76 59 0.66
77 18 0.20
78 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (76 bp):
ATATAGTTTTTGAAAATGTTTGAAAAAATATATATAGTATATGTTTGGAAAAATATTTTGAAAAC
AAGTATATATT
Found at i:21350 original size:37 final size:38
Alignment explanation
Indices: 21234--21600 Score: 287
Period size: 36 Copynumber: 9.9 Consensus size: 38
21224 GTGTATAGTA
*
21234 ATATAGTTTTTG-AAA-ATGTTTGAAAA-A-ATATAAT
1 ATATAGTTTTTGAAAACATTTTTGAAAATATATATAAT
* * * *
21268 GTATAATTTTCGGAAAACGATTTTTGAAAATAAGTATATATT
1 ATATAGTTTT-TGAAAAC-ATTTTTGAAAAT-A-TATATAAT
* *
21310 ATATAGTTTTTGAAAACGTTTTT-AAAATATATATAGT
1 ATATAGTTTTTGAAAACATTTTTGAAAATATATATAAT
* * *
21347 ATAT-GGTTTTGAAAA-ATATTTTGAAAACATTTATATATT
1 ATATAGTTTTTGAAAACAT-TTTTG-AAA-ATATATATAAT
*
21386 ATATAGTTTTT-AAAACA-TTTTGAAAGTATATATAAT
1 ATATAGTTTTTGAAAACATTTTTGAAAATATATATAAT
*
21422 ATATAGTTTTT-AAAACATTTTT--AAA-ACATAT-AT
1 ATATAGTTTTTGAAAACATTTTTGAAAATATATATAAT
*
21455 -TATA-----T-AAAACATTTTTGAAAACATTTATATAAT
1 ATATAGTTTTTGAAAACATTTTTG-AAA-ATATATATAAT
21488 ATATAGTTTTT-AAAATCA-TTTTGAAAACT-TATATAAT
1 ATATAGTTTTTGAAAA-CATTTTTGAAAA-TATATATAAT
*
21525 ATATAGTTTTTGAAAATATTTTTGAAAACTTATATATAAT
1 ATATAGTTTTTGAAAACATTTTTGAAAA--TATATATAAT
* *
21565 ATATAATTTTTTAAAAACATTTTTGAAAACTATATA
1 ATAT-AGTTTTTGAAAACATTTTTGAAAA-TATATA
21601 ATTGAAAACA
Statistics
Matches: 271, Mismatches: 28, Indels: 62
0.75 0.08 0.17
Matches are distributed among these distances:
27 12 0.04
30 2 0.01
31 1 0.00
32 8 0.03
33 4 0.01
34 17 0.06
35 4 0.01
36 42 0.15
37 39 0.14
38 36 0.13
39 33 0.12
40 32 0.12
41 27 0.10
42 14 0.05
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (38 bp):
ATATAGTTTTTGAAAACATTTTTGAAAATATATATAAT
Found at i:21389 original size:39 final size:37
Alignment explanation
Indices: 21302--21600 Score: 210
Period size: 37 Copynumber: 8.1 Consensus size: 37
21292 TGAAAATAAG
* * ** * *
21302 TATATATTATATAGTTTTTGAAAACGTTTTTAAAA-TA
1 TATATAATATATAG-TTTTAAAAATATTTTGAAAACTT
* *
21339 TATATAGTATATGGTTTTGAAAAATATTTTGAAAACATT
1 TATATAATATATAGTTTT-AAAAATATTTTGAAAAC-TT
* * * * *
21378 TATATATTATATAGTTTTTAAAACATTTTG-AAAGTA
1 TATATAATATATAGTTTTAAAAATATTTTGAAAACTT
* * *
21414 TATATAATATATAGTTTTTAAAACATTTTTAAAAC--
1 TATATAATATATAGTTTTAAAAATATTTTGAAAACTT
21449 -ATAT-AT-TATA----TAAAACAT-TTTTGAAAACATT
1 TATATAATATATAGTTTTAAAA-ATATTTTGAAAAC-TT
*
21480 TATATAATATATAGTTTTTAAAATCATTTTGAAAAC-T
1 TATATAATATATAGTTTTAAAAAT-ATTTTGAAAACTT
*
21517 TATATAATATATAGTTTTTGAAAATATTTTTGAAAACTT
1 TATATAATATATAG-TTTTAAAAATA-TTTTGAAAACTT
* * *
21556 ATATATAATATATAATTTTTTAAAAACATTTTTGAAAACTA
1 -TATATAATATAT-A-GTTTTAAAAATA-TTTTGAAAACTT
21597 TATA
1 TATA
21601 ATTGAAAACA
Statistics
Matches: 214, Mismatches: 25, Indels: 43
0.76 0.09 0.15
Matches are distributed among these distances:
28 13 0.06
29 1 0.00
32 8 0.04
33 4 0.02
34 8 0.04
36 33 0.15
37 48 0.22
38 33 0.15
39 28 0.13
40 16 0.07
41 22 0.10
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
TATATAATATATAGTTTTAAAAATATTTTGAAAACTT
Found at i:21477 original size:12 final size:11
Alignment explanation
Indices: 21428--21480 Score: 52
Period size: 11 Copynumber: 4.3 Consensus size: 11
21418 TAATATATAG
21428 TTTTTAAAACA
1 TTTTTAAAACA
21439 TTTTTAAAACATA
1 TTTTTAAAAC--A
21452 TATTATATAAAACA
1 T-TT-T-TAAAACA
21466 TTTTTGAAAACA
1 TTTTT-AAAACA
21478 TTT
1 TTT
21481 ATATAATATA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
11 11 0.31
12 10 0.28
13 4 0.11
14 4 0.11
15 1 0.03
16 6 0.17
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (11 bp):
TTTTTAAAACA
Found at i:21550 original size:38 final size:38
Alignment explanation
Indices: 21460--21688 Score: 177
Period size: 37 Copynumber: 6.3 Consensus size: 38
21450 TATATTATAT
*
21460 AAAACATTTTTGAAAACATTTATATAATATATAGTTTTT-
1 AAAATATTTTTGAAAAC--TTATATAATATATAGTTTTTG
21499 AAAATCA-TTTTGAAAACTTATATAATATATAGTTTTTG
1 AAAAT-ATTTTTGAAAACTTATATAATATATAGTTTTTG
* *
21537 AAAATATTTTTGAAAACTTATATATAATATATAATTTTTTA
1 AAAATATTTTTGAAAAC-T-TATATAATATAT-AGTTTTTG
*
21578 AAAACATTTTTGAAAAC-----T-ATATA-A----TTG
1 AAAATATTTTTGAAAACTTATATAATATATAGTTTTTG
* * ** *
21605 AAAACATTTTTTAAAAAGTATATAATATATAA-TTTT-
1 AAAATATTTTTGAAAACTTATATAATATATAGTTTTTG
* *
21641 AAAATATTTTTG-AAA-TTATATATTATATAGGTTTTGG
1 AAAATATTTTTGAAAACTTATATAATATATA-GTTTTTG
21678 AAAATATTTTT
1 AAAATATTTTT
21689 TATATATAAT
Statistics
Matches: 158, Mismatches: 13, Indels: 40
0.75 0.06 0.19
Matches are distributed among these distances:
27 17 0.11
31 1 0.01
32 1 0.01
33 10 0.06
34 14 0.09
35 3 0.02
36 13 0.08
37 34 0.22
38 15 0.09
39 15 0.09
40 13 0.08
41 22 0.14
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (38 bp):
AAAATATTTTTGAAAACTTATATAATATATAGTTTTTG
Found at i:21575 original size:40 final size:37
Alignment explanation
Indices: 21459--21602 Score: 184
Period size: 38 Copynumber: 3.7 Consensus size: 37
21449 ATATATTATA
21459 TAAAACATTTTTGAAAACATTTATATAATATATAGTTTT
1 TAAAACATTTTTGAAAAC--TTATATAATATATAGTTTT
21498 TAAAATCA-TTTTGAAAACTTATATAATATATAGTTTT
1 TAAAA-CATTTTTGAAAACTTATATAATATATAGTTTT
* *
21535 TGAAAATATTTTTGAAAACTTATATATAATATATAATTTTT
1 T-AAAACATTTTTGAAAAC-T-TATATAATATAT-AGTTTT
21576 TAAAAACATTTTTGAAAAC-TATATAAT
1 T-AAAACATTTTTGAAAACTTATATAAT
21603 TGAAAACATT
Statistics
Matches: 95, Mismatches: 4, Indels: 13
0.85 0.04 0.12
Matches are distributed among these distances:
37 21 0.22
38 22 0.23
39 16 0.17
40 14 0.15
41 22 0.23
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (37 bp):
TAAAACATTTTTGAAAACTTATATAATATATAGTTTT
Found at i:21611 original size:27 final size:28
Alignment explanation
Indices: 21578--21630 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
21568 TAATTTTTTA
*
21578 AAAACA-TTTTTGAAAACTATATAATTG
1 AAAACATTTTTTAAAAACTATATAATTG
*
21605 AAAACATTTTTTAAAAAGTATATAAT
1 AAAACATTTTTTAAAAACTATATAAT
21631 ATATAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.38
Consensus pattern (28 bp):
AAAACATTTTTTAAAAACTATATAATTG
Found at i:21675 original size:25 final size:25
Alignment explanation
Indices: 21647--21694 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
21637 TTTTAAAATA
* *
21647 TTTTTGAAATTATATATTATATAGG
1 TTTTGGAAAATATATATTATATAGG
* *
21672 TTTTGGAAAATATTTTTTATATA
1 TTTTGGAAAATATATATTATATA
21695 TAATATATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.54
Consensus pattern (25 bp):
TTTTGGAAAATATATATTATATAGG
Found at i:23923 original size:84 final size:83
Alignment explanation
Indices: 23822--24103 Score: 302
Period size: 84 Copynumber: 3.4 Consensus size: 83
23812 AAGGGCTATC
* * *
23822 TACCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACAGCATAATTCAA
1 TACCAAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGCATATCATTTACAGCATAATTCAA
*
23887 GGCTAGAAGGGTTATATG
66 GGCTAGAAGGGTTATCTG
* ** * * * * * *
23905 TCACCAAAGACCTTCGAGTTCGACTACGTTCAGC-TCCAAGGTATATAATTTGCAGCATAGCTT-
1 T-ACCAAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGCATATCATTTACAGCATA-ATTC
* * *
23968 AAGTCGAGAAGGGCTATCTG
64 AAGGCTAGAAGGGTTATCTG
* * * *
23988 --CCAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAA
1 TACCAAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGCATATCATTTACAGCATAATTCAA
*
24051 GGCTAGAAGGGTTATCTAT
66 GGCTAGAAGGGTTATCT-G
* *
24070 TACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
1 TACCAAAGACCCTCGAGTTCGACTACACTCAGCT
24104 CCAAGGAACA
Statistics
Matches: 154, Mismatches: 38, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
80 26 0.17
81 36 0.23
83 35 0.23
84 57 0.37
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (83 bp):
TACCAAAGACCCTCGAGTTCGACTACACTCAGCTTCGAGGGCATATCATTTACAGCATAATTCAA
GGCTAGAAGGGTTATCTG
Found at i:24059 original size:164 final size:164
Alignment explanation
Indices: 23772--24144 Score: 557
Period size: 164 Copynumber: 2.3 Consensus size: 164
23762 CATTTGTTCA
* * * * *
23772 AGCTCTAAGGCACATCATTTGCAGTATAGCTTAAGTCGATAAGGGCTATCTACCAAAGACCCTCG
1 AGCTCCAAGGAACATAATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCG
*
23837 AGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACAGCATAATTCAAGGCTAGAAGGGTTAT
66 AGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
* *
23902 ATGTCACCAAAGACCTTCGAGTTCGACTACGTTC
131 ATATCACCAAAGACCTTCGAGTTCGACTACGCTC
* * * *
23936 AGCTCCAAGGTATATAATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCG
1 AGCTCCAAGGAACATAATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCG
* * *
24001 AGTTTGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
66 AGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
* *
24066 CTATTACCAAAGACCTTCGAGTTCGACTACGCTC
131 ATATCACCAAAGACCTTCGAGTTCGACTACGCTC
* * * *
24100 AGCTCCAAGGAACATCATTTGCAGTATACCCTAAGTTGAGAAGGG
1 AGCTCCAAGGAACATAATTTGCAGTATAGCTTAAGTCGAGAAGGG
24145 ACACTAATTT
Statistics
Matches: 186, Mismatches: 23, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
164 186 1.00
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (164 bp):
AGCTCCAAGGAACATAATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCG
AGTTCGATTACACTCAGCTTCGAGGGCACACCATTTACAGCATAACTCAAGGCTAGAAGGGTTAT
ATATCACCAAAGACCTTCGAGTTCGACTACGCTC
Found at i:24258 original size:37 final size:36
Alignment explanation
Indices: 24205--24346 Score: 196
Period size: 37 Copynumber: 3.8 Consensus size: 36
24195 TTGAAAATGG
*
24205 TTTTTGGAAATTATATAATATATAGTTTTTAAAACA
1 TTTTTGAAAATTATATAATATATAGTTTTTAAAACA
24241 TTCTTTGAAAATTATATAATATATAGTTTTTGAAAACA
1 TT-TTTGAAAATTATATAATATATAGTTTTT-AAAACA
* *
24279 TTTTTAAAAATTATATAATATATAGTTTTAAAAACA
1 TTTTTGAAAATTATATAATATATAGTTTTTAAAACA
*
24315 -TTTTGAAAACAATTATATATTATATAGTTTTT
1 TTTTTG--AA-AATTATATAATATATAGTTTTT
24347 TTTTAAAAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
35 4 0.04
36 8 0.08
37 55 0.58
38 28 0.29
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (36 bp):
TTTTTGAAAATTATATAATATATAGTTTTTAAAACA
Found at i:25497 original size:22 final size:21
Alignment explanation
Indices: 25434--25499 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
25424 TTGATCCCTA
* * *
25434 AATTCTTATTTTATTTTATTT
1 AATTATTATTATATTTTTTTT
* **
25455 ATTTATTATTATCATGCTTTTT
1 AATTATTATTAT-ATTTTTTTT
25477 AATTATTATTAGTATTTTTTTT
1 AATTATTATTA-TATTTTTTTT
25499 A
1 A
25500 CCTTATATTG
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
21 9 0.26
22 24 0.71
23 1 0.03
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (21 bp):
AATTATTATTATATTTTTTTT
Found at i:25581 original size:16 final size:16
Alignment explanation
Indices: 25557--25590 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
25547 TTAATACTTC
*
25557 TTTATTTTTTA-TTTA
1 TTTAATTTTTATTTTA
25572 TTTAATTTTTATTTTA
1 TTTAATTTTTATTTTA
25588 TTT
1 TTT
25591 CTTTGGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTAATTTTTATTTTA
Found at i:30631 original size:17 final size:18
Alignment explanation
Indices: 30609--30650 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
30599 CTTTAGTTTA
*
30609 TTTATTTAATTATT-TTT
1 TTTATTTAATTATTATCT
*
30626 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
30644 TTTATTT
1 TTTATTT
30651 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:30942 original size:50 final size:51
Alignment explanation
Indices: 30859--30965 Score: 146
Period size: 50 Copynumber: 2.1 Consensus size: 51
30849 TTATTTTCTG
* **
30859 AAATTTAATATTTTCTTCATTTATTTTATTTTTTCTTTTAACTTTT-TTTA
1 AAATTTAATATTTCCTTCATTTATTTTATTTTTTAATTTAACTTTTATTTA
* *
30909 AAATTTAATATTTCCTTCATTTA-TTTATTTTTTTAATTTAATTTTTATTTG
1 AAATTTAATATTTCCTTCATTTATTTTA-TTTTTTAATTTAACTTTTATTTA
30960 AAATTT
1 AAATTT
30966 CTTTTATTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 4 0.08
50 37 0.74
51 9 0.18
ACGTcount: A:0.27, C:0.07, G:0.01, T:0.65
Consensus pattern (51 bp):
AAATTTAATATTTCCTTCATTTATTTTATTTTTTAATTTAACTTTTATTTA
Found at i:36268 original size:42 final size:42
Alignment explanation
Indices: 35965--36268 Score: 126
Period size: 42 Copynumber: 7.1 Consensus size: 42
35955 GAACCATCTG
*
35965 AAGAATATACCACATGACTTTCCCGTGAAGGAGAGTCATCCA
1 AAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCA
* * * ** **
36007 AAG-ATCAT-CTAACATG-GTTCAGACCCGTGAAGGGGAACCA-CTTG
1 AAGAAT-ATAC-CACATGACTT---TCCCGTGAAGGGGAGTCATC-CA
*
36051 AAGAATATACCACATGACTTTCCCTTGAAGGGGAGTCATCCA
1 AAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCA
** * * * * ** ** *
36093 AAG-ATCATTTCACCTG-GTTCAGACCCGCGAACTGGAACCA-CCTG
1 AAGAAT-ATACCACATGACTT---TCCCGTGAAGGGGAGTCATCC-A
36137 AAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCA
1 AAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCA
* * * * * **
36179 AAG-ATCAT-CTAACCTG-GTTTAGACCCGCGAAGGGAAACCA-CCTA
1 AAGAAT-ATAC-CACATGACTTT---CCCGTGAAGGGGAGTCATCC-A
*
36223 AAGAATATACCACATGACTTTCCCGTAAAGGGGAGTCATCCA
1 AAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCA
36265 AAGA
1 AAGA
36269 TCATCTCATC
Statistics
Matches: 180, Mismatches: 54, Indels: 56
0.62 0.19 0.19
Matches are distributed among these distances:
41 15 0.08
42 72 0.40
43 10 0.06
44 68 0.38
45 15 0.08
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.21
Consensus pattern (42 bp):
AAGAATATACCACATGACTTTCCCGTGAAGGGGAGTCATCCA
Found at i:36354 original size:86 final size:86
Alignment explanation
Indices: 35889--36346 Score: 664
Period size: 86 Copynumber: 5.3 Consensus size: 86
35879 AAGAACATCT
* * * * * *
35889 CACATGAATTTCCCATGAAGGGGAGTAATCCAAAGATAATCTCACCTGGTTCAGACCCACGTAGG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
* *
35954 AGAACCATCTGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
* * * *
35975 CACATGACTTTCCCGTGAAGGAGAGTCATCCAAAGATCATCTAACATGGTTCAGACCCGTGAAGG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
*
36040 GGAACCACTTGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
* * **
36061 CACATGACTTTCCCTTGAAGGGGAGTCATCCAAAGATCATTTCACCTGGTTCAGACCCGCGAACT
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
36126 GGAACCACCTGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
* *
36147 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTAACCTGGTTTAGACCCGCGAAGG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
* *
36212 GAAACCACCTAAAGAATATAC
66 GGAACCACCTGAAGAATATAC
* * *
36233 CACATGACTTTCCCGTAAAGGGGAGTCATCCAAAGATCATCTCATCTGGTTCAGACCCGTGAAGG
1 CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
36298 GGAACCACCTGAAGAATATAC
66 GGAACCACCTGAAGAATATAC
** * *
36319 CATTTGGCTTTCCCGTGAAGGGGGGTCA
1 CACATGACTTTCCCGTGAAGGGGAGTCA
36347 ACTAAAGAAT
Statistics
Matches: 330, Mismatches: 42, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
86 330 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.21
Consensus pattern (86 bp):
CACATGACTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACCTGGTTCAGACCCGCGAAGG
GGAACCACCTGAAGAATATAC
Found at i:36892 original size:199 final size:197
Alignment explanation
Indices: 36552--37143 Score: 783
Period size: 199 Copynumber: 3.0 Consensus size: 197
36542 TATTTAAGTC
* * * *
36552 ATTAGCAACAAGGAACTATCTCCCAGCCAAATTTACAGCATAGCTCAAGGAGAAAATGGTTATCT
1 ATTAGCAACAAGGAACTATCT-CCAGCCGAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCT
* * ** **
36617 ATCAACAAAACTTTCGAGTTCGATTTCATTCAGCTTGAAAACATATCAATTGCATGGTAGCAACG
65 GTCAACAAAACTTTCGAGTTCGATTTCATTCAGCTCGAAGGCATATCAACCGCATGGTAGCAACG
36682 AGGAACTACTTTCCGGTTGAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGC
130 AGGAACTACTTT-CGGTTGAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGC
36747 TGCG
194 TGCG
* *
36751 ATTAGCAACAAGGAACTATCTCTCAGCCGAATTTACAGCATAACTCAAGGCGAGAAGGGTTATTT
1 ATTAGCAACAAGGAACTATCTC-CAGCCGAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCT
* *
36816 GTCAACAAAACTTTCGAGTTCGATTTCATTTATCTCGAAGGCATATCAACCGCATGGTAGCAACG
65 GTCAACAAAACTTTCGAGTTCGATTTCATTCAGCTCGAAGGCATATCAACCGCATGGTAGCAACG
* *
36881 AGGAACTACTTTTCGGTTGAAGTTTAAACTGGGGTCTTTAAGTCAAGAAGTAGACCTAGGTTGGC
130 AGGAACTAC-TTTCGGTTGAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGC
36946 TGCG
194 TGCG
* * * *
36950 ATTTAGCAACAAAGAACTATATCCTA-ACGAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATC
1 A-TTAGCAACAAGGAACTATCTCC-AGCCGAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATC
* * * * ** *
37014 TGTCATAAAAAACCTTCGAGTTTGATTTCATTCAGCTCGAGGGCATATCAACCATATGGTAGCAT
64 TGTCA-ACAAAACTTTCGAGTTCGATTTCATTCAGCTCGAAGGCATATCAACCGCATGGTAGCAA
* * * ** * *
37079 CGAGGAACTCCTTTCGGTTTAATTTTCAAA-TCGAGGTCTTTAAACCGAGAAGAAGACCAAGGTT
128 CGAGGAACTACTTTCGGTTGAAGTTT-AAACT-GAGGTCTTTAAGTCAAGAAGAAGACCTAGGTT
37143 G
191 G
37144 ACTATGCTTT
Statistics
Matches: 346, Mismatches: 40, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
198 1 0.00
199 232 0.67
200 113 0.33
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (197 bp):
ATTAGCAACAAGGAACTATCTCCAGCCGAATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTG
TCAACAAAACTTTCGAGTTCGATTTCATTCAGCTCGAAGGCATATCAACCGCATGGTAGCAACGA
GGAACTACTTTCGGTTGAAGTTTAAACTGAGGTCTTTAAGTCAAGAAGAAGACCTAGGTTGGCTG
CG
Found at i:38008 original size:41 final size:41
Alignment explanation
Indices: 37962--38090 Score: 135
Period size: 40 Copynumber: 3.2 Consensus size: 41
37952 ACTACCATTA
*
37962 TTTATTATTTTATTTAACTCTTTCCTTTTTA-TTTATTTTGT
1 TTTATT-TTTTATTTAACTCATTCCTTTTTATTTTATTTTGT
* *
38003 TTTATTTTTAAATTTAAC-AATT-CTTGTTTATTTTATTTTGT
1 TTTATTTTT-TATTTAACTCATTCCTT-TTTATTTTATTTTGT
* *
38044 TTTA-TTTTTATTT-TCTCACTTCTTTTTTATTTTATTTTGT
1 TTTATTTTTTATTTAACTCA-TTCCTTTTTATTTTATTTTGT
38084 TTT-TTTT
1 TTTATTTT
38091 ATTTTTATTT
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
38 1 0.01
39 8 0.11
40 36 0.49
41 29 0.39
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (41 bp):
TTTATTTTTTATTTAACTCATTCCTTTTTATTTTATTTTGT
Found at i:38039 original size:5 final size:5
Alignment explanation
Indices: 38029--38103 Score: 55
Period size: 5 Copynumber: 14.0 Consensus size: 5
38019 ACAATTCTTG
*
38029 TTTAT TTTAT TTTGT TTTATT TTTATT TTCTCACT TCTT-T TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTA-T TTTA-T TT-T-A-T T-TTAT TTTAT TTTAT
*
38079 TTTGT TTT-T TTTATT TTTAT TTTAT
1 TTTAT TTTAT TTTA-T TTTAT TTTAT
38104 CTTTTAACAT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
4 6 0.10
5 33 0.56
6 14 0.24
7 1 0.02
8 4 0.07
9 1 0.02
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:38067 original size:40 final size:40
Alignment explanation
Indices: 37989--38095 Score: 139
Period size: 40 Copynumber: 2.7 Consensus size: 40
37979 CTCTTTCCTT
*
37989 TTTA-TTTATTTTGTTTTATTTTTAAATTTAACAATTCTTG
1 TTTATTTTATTTTGTTTTATTTTT-ATTTTAACAATTCTTG
** * *
38029 TTTATTTTATTTTGTTTTATTTTTATTTTCTCACTTCTTT
1 TTTATTTTATTTTGTTTTATTTTTATTTTAACAATTCTTG
38069 TTTATTTTATTTTG-TTT-TTTTTATTTT
1 TTTATTTTATTTTGTTTTATTTTTATTTT
38096 TATTTTATCT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
38 10 0.16
39 3 0.05
40 29 0.48
41 19 0.31
ACGTcount: A:0.17, C:0.06, G:0.04, T:0.74
Consensus pattern (40 bp):
TTTATTTTATTTTGTTTTATTTTTATTTTAACAATTCTTG
Found at i:38132 original size:17 final size:16
Alignment explanation
Indices: 38066--38134 Score: 54
Period size: 17 Copynumber: 4.2 Consensus size: 16
38056 TTCTCACTTC
38066 TTTTTTATTTTATT-T
1 TTTTTTATTTTATTAT
*
38081 TGTTTT-TTTTATT-T
1 TTTTTTATTTTATTAT
**
38095 TTATTTTATCTTTTAACAT
1 TT-TTTTA--TTTTATTAT
38114 TTTTTATATTTTATTAT
1 TTTTT-TATTTTATTAT
38131 TTTT
1 TTTT
38135 CTTTTCTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
14 9 0.21
15 9 0.21
17 11 0.26
18 8 0.19
19 5 0.12
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTTATTAT
Found at i:38241 original size:50 final size:51
Alignment explanation
Indices: 38143--38242 Score: 143
Period size: 51 Copynumber: 2.0 Consensus size: 51
38133 TTCTTTTCTG
* * *
38143 AAATTTAATATTTTCTTCATTTATTTTATTTTTTTATTTTAACATTTTTTT
1 AAATTTAATATTTCCTTCATTGATTTTATTTTTTTAATTTAACATTTTTTT
*
38194 AAATTTAATATTTCCTTCCTTGA-TTTATTTTTTTAATTT-A-ATTTTTTT
1 AAATTTAATATTTCCTTCATTGATTTTATTTTTTTAATTTAACATTTTTTT
38242 A
1 A
38243 TATATTTCTT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
48 9 0.20
49 1 0.02
50 15 0.33
51 20 0.44
ACGTcount: A:0.26, C:0.07, G:0.01, T:0.66
Consensus pattern (51 bp):
AAATTTAATATTTCCTTCATTGATTTTATTTTTTTAATTTAACATTTTTTT
Found at i:41238 original size:140 final size:140
Alignment explanation
Indices: 40986--41266 Score: 553
Period size: 140 Copynumber: 2.0 Consensus size: 140
40976 AGAAGGCATC
40986 GCCATATCATTGAACTAGCTCTTTTGCTAATGGCTTAAGCCTCTCTTCCCTTCGGGTTTTGGTCA
1 GCCATATCATTGAACTAGCTCTTTTGCTAATGGCTTAAGCCTCTCTTCCCTTCGGGTTTTGGTCA
41051 TATGCAGTAAGCTCAGCTGTGTACCTCATCAACCGGTTGCCTACACAAGTTTTGCAAGGAAAATC
66 TATGCAGTAAGCTCAGCTGTGTACCTCATCAACCGGTTGCCTACACAAGTTTTGCAAGGAAAATC
41116 ACCATTTGAA
131 ACCATTTGAA
*
41126 GCCATATCATTGAACTAGCTCTTTTGCTAATGGCTTAAGCCTTTCTTCCCTTCGGGTTTTGGTCA
1 GCCATATCATTGAACTAGCTCTTTTGCTAATGGCTTAAGCCTCTCTTCCCTTCGGGTTTTGGTCA
41191 TATGCAGTAAGCTCAGCTGTGTACCTCATCAACCGGTTGCCTACACAAGTTTTGCAAGGAAAATC
66 TATGCAGTAAGCTCAGCTGTGTACCTCATCAACCGGTTGCCTACACAAGTTTTGCAAGGAAAATC
41256 ACCATTTGAA
131 ACCATTTGAA
41266 G
1 G
41267 TCTTCTATAA
Statistics
Matches: 140, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
140 140 1.00
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (140 bp):
GCCATATCATTGAACTAGCTCTTTTGCTAATGGCTTAAGCCTCTCTTCCCTTCGGGTTTTGGTCA
TATGCAGTAAGCTCAGCTGTGTACCTCATCAACCGGTTGCCTACACAAGTTTTGCAAGGAAAATC
ACCATTTGAA
Found at i:47650 original size:15 final size:15
Alignment explanation
Indices: 47632--47661 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
47622 CCACGGTGCT
47632 CCCGAAATCCTGCGC
1 CCCGAAATCCTGCGC
*
47647 CCCGGAATCCTGCGC
1 CCCGAAATCCTGCGC
47662 GATTGTGATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (15 bp):
CCCGAAATCCTGCGC
Found at i:54181 original size:2 final size:2
Alignment explanation
Indices: 54174--54206 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54164 ATTATATCGT
54174 TA TA 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 TA TA T
54207 TAATGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64548 original size:36 final size:36
Alignment explanation
Indices: 64501--64573 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
64491 CGAGCTTCAC
64501 TTAGAGCACAATGCGAATCTTGATATGGTTCCATTA
1 TTAGAGCACAATGCGAATCTTGATATGGTTCCATTA
64537 TTAGAGCACAATGCGAATCTTGATATGGTTCCATTA
1 TTAGAGCACAATGCGAATCTTGATATGGTTCCATTA
64573 T
1 T
64574 GACATTGAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (36 bp):
TTAGAGCACAATGCGAATCTTGATATGGTTCCATTA
Found at i:65418 original size:17 final size:14
Alignment explanation
Indices: 65388--65435 Score: 62
Period size: 14 Copynumber: 3.3 Consensus size: 14
65378 TTGGCCCGTT
65388 TTAT-TTTTTATTA
1 TTATATTTTTATTA
65401 TTATAATTATTATATTA
1 TTAT-ATT-TT-TATTA
65418 TTATATTTTTATTA
1 TTATATTTTTATTA
65432 TTAT
1 TTAT
65436 TAATCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.13
14 9 0.29
15 4 0.13
16 5 0.16
17 9 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTTTTATTA
Found at i:65436 original size:17 final size:17
Alignment explanation
Indices: 65388--65437 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 17
65378 TTGGCCCGTT
65388 TTAT-TTTTTATTATTA
1 TTATATTTTTATTATTA
*
65404 -TA-ATTATTA-TATTA
1 TTATATTTTTATTATTA
65418 TTATATTTTTATTATTA
1 TTATATTTTTATTATTA
65435 TTA
1 TTA
65438 ATCAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 5 0.18
15 9 0.32
16 6 0.21
17 8 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTTTTATTATTA
Found at i:65455 original size:3 final size:3
Alignment explanation
Indices: 65395--65437 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
65385 GTTTTATTTT
* *
65395 TTA TTA TTA TAA TTA TTA -TA TTA TTA -TA TTT TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
65438 ATCAAAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:67214 original size:146 final size:145
Alignment explanation
Indices: 66931--67224 Score: 371
Period size: 146 Copynumber: 2.0 Consensus size: 145
66921 TCATATTTTT
*
66931 ATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGTCATTTTCTGA
1 ATATTTATTTATTTTTTAATATTAAGAAATGGACTGTCTTAAAGCACCTAGAAGTCATTTTCTGA
* * * * * *
66996 TATTCTCAAAAAAAAAATATCATATTTTTATAAATTATATATATTAATTTATTTTAATTATTTTT
66 TATTCTCAAAAAAAAAATATCATATTTATATAAAATAAAGATATTAATATATATTAATTATTTTT
*
67061 AGAAAAATGTTTATTA
131 AGAAAAAT-TATATTA
* *
67077 ATATTTATTTATTTTTTAATATTAAGAAATTGACTGTCTTAAAGCACCTAGAAGTCCTTTTCTGA
1 ATATTTATTTATTTTTTAATATTAAGAAATGGACTGTCTTAAAGCACCTAGAAGTCATTTTCTGA
* * *
67142 TATT-TCTAAGTAAATAAATATCTTATTTATA-AAAATAAAGATA-T-ATATATATTAATATATA
66 TATTCTC-AA-AAAAAAAATATCATATTTATATAAAATAAAGATATTAATATATATTAAT-TAT-
***
67203 TTTTCTTAAAATTATATTA
127 TTTTAGAAAAATTATATTA
67222 ATA
1 ATA
67225 AATTTGAAAT
Statistics
Matches: 128, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
144 10 0.08
145 15 0.12
146 86 0.67
147 17 0.13
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (145 bp):
ATATTTATTTATTTTTTAATATTAAGAAATGGACTGTCTTAAAGCACCTAGAAGTCATTTTCTGA
TATTCTCAAAAAAAAAATATCATATTTATATAAAATAAAGATATTAATATATATTAATTATTTTT
AGAAAAATTATATTA
Found at i:68316 original size:46 final size:49
Alignment explanation
Indices: 68242--68332 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 49
68232 TTTTCTTTTC
* *
68242 TTTTTCCTAAATAAATGCATGCGAACTAGAAATCATGCA-GTTAGGTTAA
1 TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATG-AGGTTAGGTTAA
68291 TTTTTCC-AAACAAA-GCATG-GAACTAGAAAGCATGAGGTTAGG
1 TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGG
68333 ATTTATACCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 1 0.03
46 20 0.51
47 5 0.13
48 6 0.15
49 7 0.18
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (49 bp):
TTTTTCCTAAACAAATGCATGCGAACTAGAAAGCATGAGGTTAGGTTAA
Found at i:69159 original size:43 final size:43
Alignment explanation
Indices: 69088--69172 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 43
69078 GGCTTTAGAA
* *
69088 AAGTTAGGAGGGAAAGTTATCCCATATATGTAAAGTTTTGTTG
1 AAGTTAGGACGGAAAGATATCCCATATATGTAAAGTTTTGTTG
* * * *
69131 AAGTTAGGACTGAAAGATGTCCCCTATATTTAAAGTTTTGTT
1 AAGTTAGGACGGAAAGATATCCCATATATGTAAAGTTTTGTT
69173 TGATGCACGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.36
Consensus pattern (43 bp):
AAGTTAGGACGGAAAGATATCCCATATATGTAAAGTTTTGTTG
Found at i:69277 original size:27 final size:26
Alignment explanation
Indices: 69247--69300 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
69237 TTTTCATACA
69247 TGCATTTACATTTTACATCTTTGCATT
1 TGCATTTACA-TTTACATCTTTGCATT
* * *
69274 TGCATTTTCATTTGCATCTTTTCATT
1 TGCATTTACATTTACATCTTTGCATT
69300 T
1 T
69301 TTATGTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 15 0.62
27 9 0.38
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.56
Consensus pattern (26 bp):
TGCATTTACATTTACATCTTTGCATT
Found at i:69297 original size:14 final size:14
Alignment explanation
Indices: 69262--69300 Score: 55
Period size: 12 Copynumber: 2.9 Consensus size: 14
69252 TTACATTTTA
*
69262 CATCTTTGCATTTG
1 CATCTTTTCATTTG
69276 CA--TTTTCATTTG
1 CATCTTTTCATTTG
69288 CATCTTTTCATTT
1 CATCTTTTCATTT
69301 TTATGTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
12 11 0.50
14 11 0.50
ACGTcount: A:0.15, C:0.21, G:0.08, T:0.56
Consensus pattern (14 bp):
CATCTTTTCATTTG
Found at i:71794 original size:20 final size:21
Alignment explanation
Indices: 71771--71810 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
71761 TAAATTATAA
71771 TATAAA-ATGATCTTTAAAAT
1 TATAAATATGATCTTTAAAAT
* *
71791 TATAAATATTATTTTTAAAA
1 TATAAATATGATCTTTAAAA
71811 AATTTTCATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TATAAATATGATCTTTAAAAT
Found at i:76402 original size:16 final size:16
Alignment explanation
Indices: 76381--76416 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
76371 CCCCTTTTGA
76381 TTTTATTAAGAGTAGG
1 TTTTATTAAGAGTAGG
*
76397 TTTTATTAAGATTAGG
1 TTTTATTAAGAGTAGG
76413 TTTT
1 TTTT
76417 CTTTTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (16 bp):
TTTTATTAAGAGTAGG
Found at i:78489 original size:2 final size:2
Alignment explanation
Indices: 78482--78547 Score: 100
Period size: 2 Copynumber: 33.5 Consensus size: 2
78472 TTATTCTATC
*
78482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
78524 AT -T AT -T AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT -AT AT AT A
78548 CATGGAGTAC
Statistics
Matches: 59, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 2 0.03
2 55 0.93
3 2 0.03
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79974 original size:21 final size:23
Alignment explanation
Indices: 79930--79976 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
79920 AACATATAAT
*
79930 TAAATTAGTTGAAAATTTAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
*
79953 TAAATTA-TTTAAAA-TAAAAGG
1 TAAATTAGTTGAAAATTAAAAGG
79974 TAA
1 TAA
79977 GCTATACCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 6 0.27
23 7 0.32
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (23 bp):
TAAATTAGTTGAAAATTAAAAGG
Done.