Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004673.1 Hibiscus syriacus cultivar Beakdansim tig00010477_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: 60723
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:12026 original size:5 final size:5
Alignment explanation
Indices: 12009--12125 Score: 71
Period size: 5 Copynumber: 23.4 Consensus size: 5
11999 AATTTTCAAA
* * *
12009 AAAAT AAACT AAAAT AAACT AAAAT AAAGT AAAAT AAAAAT AAAAAT AAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT -AAAAT
* * * * ** *
12062 AAAA- AACA- CAAAT AAAAT -AAAC AAAAT -ACAT AAACG AACAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
*
12108 AAAACA AAAAT AAAAT AA
1 AAAA-T AAAAT AAAAT AA
12126 TGGGATCAAA
Statistics
Matches: 85, Mismatches: 22, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
4 11 0.13
5 53 0.62
6 21 0.25
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:12050 original size:6 final size:6
Alignment explanation
Indices: 12039--12066 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
12029 AAAATAAAGT
12039 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
12067 ACACAAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:12066 original size:13 final size:13
Alignment explanation
Indices: 12039--12078 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
12029 AAAATAAAGT
12039 AAAATAAAAAT-A
1 AAAATAAAAATAA
12051 AAAATAAAAATAA
1 AAAATAAAAATAA
* *
12064 AAAACACAAATAA
1 AAAATAAAAATAA
12077 AA
1 AA
12079 TAAACAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAATAAAAATAA
Found at i:12078 original size:18 final size:17
Alignment explanation
Indices: 12019--12082 Score: 62
Period size: 18 Copynumber: 3.8 Consensus size: 17
12009 AAAATAAACT
*
12019 AAAATAAACT-AAAAT-
1 AAAATAAAATAAAAATA
*
12034 AAAGTAAAATAAAAATA
1 AAAATAAAATAAAAATA
12051 AAAATAAAAATAAAAA-A
1 AAAAT-AAAATAAAAATA
12068 CACAAATAAAATAAA
1 -A-AAATAAAATAAA
12083 CAAAATACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
15 8 0.20
16 5 0.12
17 5 0.12
18 19 0.46
19 4 0.10
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:12372 original size:14 final size:15
Alignment explanation
Indices: 12346--12376 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
12336 TAACAGAAAA
12346 AAATAATAAATAAAT
1 AAATAATAAATAAAT
12361 AAATAA-AAATAAAT
1 AAATAATAAATAAAT
12375 AA
1 AA
12377 TATATGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATAATAAATAAAT
Found at i:14420 original size:85 final size:85
Alignment explanation
Indices: 14296--15450 Score: 1465
Period size: 85 Copynumber: 13.7 Consensus size: 85
14286 AGATGAATAG
* * * ** *
14296 AATCGAACTCGACA-GTTTTTGTTGATAGATAGCCTTTCTCAACTTAAGCTATGCTGTAAATTTG
1 AATCGAACTCGA-AGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
* * *
14360 ATATGCCTTTGAGATGAATGG
65 ATATGCCCTTGAGCTGAATGT
* * * * * * * *
14381 AATCGATCTCGGAGGTATTTGTTGACGGATAACCCTTCTCGCCTTGAGTTATGCTATAAATTTTA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
14446 TATGCCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * * * *
14466 AATTGAACTCGAAGGTCTTTGTTGATAGATACCCCTTCTCACCTTGAGATATGTTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
14531 TATGCCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * *
14551 AATCGAACTTGAGGGTCTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGCTGTAAATTTCA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
14616 TATGCCTTTGAGCTGAATAT
66 TATGCCCTTGAGCTGAATGT
* * * * * * * *
14636 AATCGAACTTGAAGG-CTTTTGTTAACAGATGGTCCTTCTCACCTTGAGCTATGTTGTATATTTA
1 AATCGAACTCGAAGGTC-TTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTG
* *
14700 ATATGCCTTTGAGCTGAATAT
65 ATATGCCCTTGAGCTGAATGT
* * *
14721 AATCGAACTCAAAGGTCTTTTTTGACATATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
*
14786 TATGCCCTTGAACTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * *
14806 AATCGAACTCGAA--TGTTTGTTGGCAGATAGCCCTTCTCGCCTTGAGCTATGCTGCAAA-TAGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
14868 TATGCCCTTGAGTTAAATGT
66 TATGCCCTTGAGCTGAATGT
* *
14888 AATCGAACTCGAAGATCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
14953 TGTGCCTTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
14973 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
15038 TATGCCTTTGAGCTGAATAT
66 TATGCCCTTGAGCTGAATGT
* *
15058 AATTGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAG-TAATACTGTAAATTTG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCT-ATGCTGTAAATTTG
15122 ATATGCCCTTGAGCTGAATGT
65 ATATGCCCTTGAGCTGAATGT
* * * * * * *
15143 AATTGAAATCGAAGG--TTTGTTGGCAGATAGCCCTTCTCGCCTTGAGTTATGCTGCATA-TAGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
* *
15205 TATGCCTTTGAGTTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * * *
15225 AATCAAACTAGAAGGTCTTTGTTGACAGATAACCCTTTTCGCCTTGAGTTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
15290 TATGCCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
** * * *
15310 AATCGAACTCGAAGG--TTTGTTGGTAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAA-TAGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
15372 TATGCCCTTGAGCTGAATGT
66 TATGCCCTTGAGCTGAATGT
* * * *
15392 AATCGAACTTGAAGG--TTTGTTGGCAGATAGCCCTTCTCACCTTGAGCTATGCTGCAAAT
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAAT
15451 AGTTCCTTTA
Statistics
Matches: 934, Mismatches: 124, Indels: 26
0.86 0.11 0.02
Matches are distributed among these distances:
82 142 0.15
83 113 0.12
84 83 0.09
85 595 0.64
86 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (85 bp):
AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
TATGCCCTTGAGCTGAATGT
Found at i:14978 original size:337 final size:336
Alignment explanation
Indices: 14296--15450 Score: 1539
Period size: 337 Copynumber: 3.4 Consensus size: 336
14286 AGATGAATAG
* * * * * *
14296 AATCGAACTCGACAGTTTTTGTTGATAGATAGCCTTTCTCAACTTAAGCTATGCTGTAAATTTGA
1 AATCGAACTCGA-AGGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTAA
* ** * * * * *
14361 TATGCCTTTGAGATGAATGGAATCGATCTCGGAGGTATTTGTTGACGGATAACCCTTCTCGCCTT
65 TATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
* * * * *
14426 GAGTTATGCTATAAATTTTATATGCCCTTGAGCTGAATGTAATTGAACTCGAAGGTCTTTGTTGA
130 GAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAA--TGTTTGTTGG
* * * * * * *
14491 TAGATACCCCTTCTCACCTTGAGATATGTTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCG
193 CAGATAGCCCTTCTCGCCTTGAGATATGCTGCAAA-TAGATATGCCCTTGAGTTGAATGTAATCG
* * * *
14556 AACTTGAGGGTCTTTGTTGACAGATAGCCCTTCTCGTCTTGAGCTATGCTGTAAATTTCATATGC
257 AACTAGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGC
*
14621 CTTTGAGCTGAATAT
322 CTTTGAGCTGAATGT
* * * * * *
14636 AATCGAACTTGAAGGCTTTTGTTAACAGATGGTCCTTCTCACCTTGAGCTATGTTGTATATTTAA
1 AATCGAACTCGAAGG-TTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTAA
* * *
14701 TATGCCTTTGAGCTGAATATAATCGAACTCAAAGGTCTTTTTTGACATATAGCCCTTCTCGCCTT
65 TATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
* *
14766 GAGCTATGCTGTAAATTTGATATGCCCTTGAACTGAATGTAATCGAACTCGAATGTTTGTTGGCA
130 GAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAATGTTTGTTGGCA
* *
14831 GATAGCCCTTCTCGCCTTGAGCTATGCTGCAAATAGATATGCCCTTGAGTTAAATGTAATCGAAC
195 GATAGCCCTTCTCGCCTTGAGATATGCTGCAAATAGATATGCCCTTGAGTTGAATGTAATCGAAC
* * * *
14896 TCGAAGATCTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTGATGTGCCTT
260 TAGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTT
14961 TGAGCTGAATGT
325 TGAGCTGAATGT
* *
14973 AATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGA
1 AATCGAACTCGAAGGT-TTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTAA
*
15038 TATGCCTTTGAGCTGAATATAATTGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
65 TATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
* * *
15103 GAG-TAATACTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAAATCGAAGGTTTGTTGGC
130 GAGCT-ATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAATGTTTGTTGGC
* * * *
15167 AGATAGCCCTTCTCGCCTTGAGTTATGCTGCATATAGATATGCCTTTGAGTTGAATGTAATCAAA
194 AGATAGCCCTTCTCGCCTTGAGATATGCTGCAAATAGATATGCCCTTGAGTTGAATGTAATCGAA
* * * *
15232 CTAGAAGGTCTTTGTTGACAGATAACCCTTTTCGCCTTGAGTTATGCTGTAAATTTGATATGCCC
259 CTAGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCT
15297 TTGAGCTGAATGT
324 TTGAGCTGAATGT
** * * *
15310 AATCGAACTCGAAGG-TTTGTTGGTAGATAGCCCTTCTCGCCTTGAGCTATACTGCAAA--TAGA
1 AATCGAACTCGAAGGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTA-A
* * * * *
15372 TATGCCCTTGAGCTGAATGTAATCGAACTTGAAGG--TTTGTTGGCAGATAGCCCTTCTCACCTT
65 TATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTT
*
15435 GAGCTATGCTGCAAAT
130 GAGCTATGCTGTAAAT
15451 AGTTCCTTTA
Statistics
Matches: 720, Mismatches: 90, Indels: 18
0.87 0.11 0.02
Matches are distributed among these distances:
332 38 0.05
333 2 0.00
334 32 0.04
335 39 0.05
336 2 0.00
337 416 0.58
338 37 0.05
339 2 0.00
340 152 0.21
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (336 bp):
AATCGAACTCGAAGGTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTATGCTGTAAATTTAAT
ATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTG
AGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATTGAACTCGAATGTTTGTTGGCAG
ATAGCCCTTCTCGCCTTGAGATATGCTGCAAATAGATATGCCCTTGAGTTGAATGTAATCGAACT
AGAAGGTCTTTGTTGACAGATAGCCCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCTTT
GAGCTGAATGT
Found at i:16806 original size:84 final size:86
Alignment explanation
Indices: 16703--16929 Score: 278
Period size: 95 Copynumber: 2.6 Consensus size: 86
16693 GGCTAGCTGG
*
16703 ATCCATAAAGTAGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCA-G-TATTATAATCACCT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCATGATATTATAATCACCT
* *
16766 TTATCAGGCTAGTTGAATCTT
66 TTATCAGGCCAGCTGAATCTT
* *
16787 ATCCATATAGTCGGGGCGTTTAACTAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACT----C---A-TG-ATATTA
16852 TAATCACCTTTATCAGGCCAGCTGAATCTT
57 TAATCACCTTTATCAGGCCAGCTGAATCTT
* * * *
16882 ATCCATAAAGTCAGGGTGTTTAACCAATTGCTTTGGAGGGACAACTCA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCA
16930 AGCTTTATTA
Statistics
Matches: 121, Mismatches: 11, Indels: 18
0.81 0.07 0.12
Matches are distributed among these distances:
84 43 0.36
88 2 0.02
91 2 0.02
93 1 0.01
95 73 0.60
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (86 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCATGATATTATAATCACCT
TTATCAGGCCAGCTGAATCTT
Found at i:16921 original size:95 final size:95
Alignment explanation
Indices: 16752--16938 Score: 302
Period size: 95 Copynumber: 2.0 Consensus size: 95
16742 GACAACTCAG
* * * * *
16752 TATTATAATCACCTTTATCAGGCTAGTTGAATCTTATCCATATAGTCGGGGCGTTTAACTAATTG
1 TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
16817 CTCTAGAGGGACAACTCAAGCTTTATTGTA
66 CTCTAGAGGGACAACTCAAGCTTTATTGTA
*
16847 TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGTGTTTAACCAATTG
1 TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
* *
16912 CTTTGGAGGGACAACTCAAGCTTTATT
66 CTCTAGAGGGACAACTCAAGCTTTATT
16939 ATAATCTGGG
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (95 bp):
TATTATAATCACCTTTATCAGGCCAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
CTCTAGAGGGACAACTCAAGCTTTATTGTA
Found at i:21368 original size:4 final size:4
Alignment explanation
Indices: 21359--21389 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
21349 CATTTCATAT
21359 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
21390 CATAGTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:22033 original size:2 final size:2
Alignment explanation
Indices: 22028--22062 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22018 CTAAGAAGAA
22028 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22063 AACATGATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22285 original size:31 final size:30
Alignment explanation
Indices: 22222--22290 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
22212 TAATGGAATT
*
22222 AAAT-AAAAAAGGAGAAAAGAAACAAAATA
1 AAATAAAAAAAAGAGAAAAGAAACAAAATA
**
22251 AAATAGAAAAAAAGAGAAAAGAATAGGAAA-A
1 AAATA-AAAAAAAGAGAAAAGAA-ACAAAATA
22282 AAATAAAAA
1 AAATAAAAA
22291 TAGAATATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
29 4 0.12
30 4 0.12
31 22 0.65
32 4 0.12
ACGTcount: A:0.77, C:0.01, G:0.14, T:0.07
Consensus pattern (30 bp):
AAATAAAAAAAAGAGAAAAGAAACAAAATA
Found at i:22295 original size:22 final size:21
Alignment explanation
Indices: 22245--22297 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
22235 GAAAAGAAAC
*
22245 AAAATAAAATAGAAAAAAAGA
1 AAAATAGAATAGAAAAAAAGA
* *
22266 GAAA-AGAATAGGAAAAAAATA
1 AAAATAGAATA-GAAAAAAAGA
22287 AAAATAGAATA
1 AAAATAGAATA
22298 TATATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 5 0.19
21 15 0.58
22 6 0.23
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.11
Consensus pattern (21 bp):
AAAATAGAATAGAAAAAAAGA
Found at i:22475 original size:3 final size:3
Alignment explanation
Indices: 22467--22503 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
22457 AGTAACAGAA
22467 AAT AAT AAT AAT AAT AAT AAT AAAT AA- AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AA
22504 ACATATACGC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:22519 original size:6 final size:6
Alignment explanation
Indices: 22508--22666 Score: 318
Period size: 6 Copynumber: 26.5 Consensus size: 6
22498 AAATAAACAT
22508 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
1 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
22556 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
1 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
22604 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
1 ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC ATACGC
22652 ATACGC ATACGC ATA
1 ATACGC ATACGC ATA
22667 TACATATACA
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 153 1.00
ACGTcount: A:0.34, C:0.33, G:0.16, T:0.17
Consensus pattern (6 bp):
ATACGC
Found at i:24745 original size:30 final size:30
Alignment explanation
Indices: 24699--24755 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
24689 TAAAAATATC
* *
24699 TTTTGTTTTTGTTTTAACTTATTAAATGTA
1 TTTTATTTTTGGTTTAACTTATTAAATGTA
24729 TTTTATTTTTGGTTTAACTTATTAAAT
1 TTTTATTTTTGGTTTAACTTATTAAAT
24756 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.63
Consensus pattern (30 bp):
TTTTATTTTTGGTTTAACTTATTAAATGTA
Found at i:24770 original size:25 final size:29
Alignment explanation
Indices: 24699--24764 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
24689 TAAAAATATC
* *
24699 TTTTGTTTTTGTTTTAACTTATTAAATGTA
1 TTTTATTTTTGATTTAACTTATTAAA-GTA
*
24729 TTTTATTTTTGGTTTAACTTATTAAA-TA
1 TTTTATTTTTGATTTAACTTATTAAAGTA
24757 TTTT-TTTT
1 TTTTATTTT
24765 ATTTAATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 4 0.12
28 6 0.18
30 24 0.71
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (29 bp):
TTTTATTTTTGATTTAACTTATTAAAGTA
Found at i:24864 original size:15 final size:15
Alignment explanation
Indices: 24833--24888 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
24823 TCTTATTTTC
**
24833 TAAAATATATT-TTT
1 TAAAATATATTAAAT
*
24847 TAAAATATCTTAAAT
1 TAAAATATATTAAAT
*
24862 TAAAATATATTTAAT
1 TAAAATATATTAAAT
24877 TATAAATTATAT
1 TA-AAA-TATAT
24889 ATTTTATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 10 0.29
15 16 0.47
16 3 0.09
17 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATATATTAAAT
Found at i:24894 original size:46 final size:48
Alignment explanation
Indices: 24833--24927 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
24823 TCTTATTTTC
*
24833 TAAAATATATTTTTTA-AAATATCTTAAATT-AAAATATATTTAATTA
1 TAAAATATATATTTTATAAATATCTTAAATTAAAAATATATTTAATTA
* * * * * *
24879 TAAATTATATATTTTATTATTATCTTCATTTAAAAATATATTTTATTA
1 TAAAATATATATTTTATAAATATCTTAAATTAAAAATATATTTAATTA
24927 T
1 T
24928 TATTTTCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 14 0.35
47 10 0.25
48 16 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (48 bp):
TAAAATATATATTTTATAAATATCTTAAATTAAAAATATATTTAATTA
Found at i:24941 original size:136 final size:131
Alignment explanation
Indices: 24749--25010 Score: 289
Period size: 136 Copynumber: 2.0 Consensus size: 131
24739 GGTTTAACTT
*
24749 ATTAAATATTTTTTTTATTTAATGTAAAAATATATTTTATCTTCATCTTCACTTAAA-AATAGA-
1 ATTAAATATTTTTTTTATTTAATGTAAAAATATATTTTATCTTCATCTTCAATTAAAGAATAGAT
** *
24812 TTTTATTCCTATCTTATTTTCTAAAATATATTTT-TTAAAATATCTTAAATTAAAATATATTTAA
66 TTTTA-T--TATCTTAACTTC-AAAATATATTTTACTAAAATATCTTAAATTAAAATAT-TTTAA
24876 TTATAA
126 TTATAA
* * * * *
24882 ATTATATATTTTATTATTATCTTCATTTAAAAATATATTTTAT-TATTATTTTCAATTAAAGAAT
1 ATTAAATATTTT-TT-TTAT-TTAATGTAAAAATATATTTTATCT-TCATCTTCAATTAAAGAAT
* * * *
24946 ATATTTTTATTATCTTAACTTCAAAATATATTTTAACTAATATATTTTAAGTTAAAATATTTTAA
62 AGATTTTTATTATCTTAACTTCAAAATATATTTT-ACTAAAATATCTTAAATTAAAATATTTTAA
25011 AAACATCTTT
Statistics
Matches: 108, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
133 11 0.10
134 14 0.13
135 20 0.19
136 52 0.48
137 6 0.06
138 5 0.05
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (131 bp):
ATTAAATATTTTTTTTATTTAATGTAAAAATATATTTTATCTTCATCTTCAATTAAAGAATAGAT
TTTTATTATCTTAACTTCAAAATATATTTTACTAAAATATCTTAAATTAAAATATTTTAATTATA
A
Found at i:24956 original size:28 final size:29
Alignment explanation
Indices: 24885--24980 Score: 126
Period size: 29 Copynumber: 3.3 Consensus size: 29
24875 ATTATAAATT
*
24885 ATATATTTTATTATTATCTTCATTTAAAA
1 ATATATTTTATTATTATCTTCAATTAAAA
*
24914 ATATATTTTATTATTATTTTCAATTAAAGA
1 ATATATTTTATTATTATCTTCAATTAAA-A
*
24944 ATATA-TTT-TTATTATCTT-AACTTCAAA
1 ATATATTTTATTATTATCTTCAA-TTAAAA
24971 ATATATTTTA
1 ATATATTTTA
24981 ACTAATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
27 8 0.14
28 16 0.27
29 29 0.49
30 6 0.10
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (29 bp):
ATATATTTTATTATTATCTTCAATTAAAA
Found at i:24989 original size:14 final size:15
Alignment explanation
Indices: 24970--25010 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
24960 TTAACTTCAA
24970 AATATATTTTAA-CT
1 AATATATTTTAAGCT
*
24984 AATATATTTTAAGTT
1 AATATATTTTAAGCT
*
24999 AAAATATTTTAA
1 AATATATTTTAA
25011 AAACATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATATTTTAAGCT
Found at i:25119 original size:30 final size:29
Alignment explanation
Indices: 25052--25119 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
25042 ATATATATAT
* *
25052 ATATATATATAAAGTTAAAATAAGAGAAA
1 ATATATATTTAAAGTGAAAATAAGAGAAA
* *
25081 A-ATATATTTAAAGTGAAGATAAGATTAAA
1 ATATATATTTAAAGTGAAAATAAGA-GAAA
25110 ATATATATTT
1 ATATATATTT
25120 TTATATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 20 0.61
29 5 0.15
30 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (29 bp):
ATATATATTTAAAGTGAAAATAAGAGAAA
Found at i:28875 original size:2 final size:2
Alignment explanation
Indices: 28870--28922 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
28860 CTAAGAAGAA
28870 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28912 AT AT AT AT AT A
1 AT AT AT AT AT A
28923 AACATGAACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29171 original size:4 final size:4
Alignment explanation
Indices: 29162--29188 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
29152 CAGTTCATAT
29162 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
29189 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:29831 original size:2 final size:2
Alignment explanation
Indices: 29826--29870 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
29816 CTAAGAAGAA
29826 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29868 AT A
1 AT A
29871 AACATGATCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29984 original size:21 final size:21
Alignment explanation
Indices: 29923--30007 Score: 59
Period size: 21 Copynumber: 4.0 Consensus size: 21
29913 ATTTTCAAAA
*
29923 AAAATAAAAAACAACACAAAT-
1 AAAATAAAAAACAA-ATAAATG
*
29944 AAAATAAACAAAATAAATAAATG
1 AAAAT-AA-AAAACAAATAAATG
*
29967 AAAATAAAATAA-AAAT-AAGG
1 AAAATAAAA-AACAAATAAATG
* *
29987 AAAAGAAAAAGAAAAATAAAT
1 AAAATAAAAA-ACAAATAAAT
30008 TAAATAATGG
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
19 1 0.02
20 12 0.23
21 15 0.29
22 13 0.25
23 11 0.21
ACGTcount: A:0.76, C:0.05, G:0.06, T:0.13
Consensus pattern (21 bp):
AAAATAAAAAACAAATAAATG
Found at i:30272 original size:3 final size:3
Alignment explanation
Indices: 30264--30289 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
30254 AGTAACAGAA
30264 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
30290 ATAAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:30309 original size:6 final size:6
Alignment explanation
Indices: 30300--30806 Score: 950
Period size: 6 Copynumber: 84.5 Consensus size: 6
30290 ATAAAATTAA
30300 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30348 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30396 ATACAT ATACAT ATACAT ACATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT --ATACAT ATACAT ATACAT ATACAT ATACAT
30446 ATACATAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATAC--AT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30496 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC-- ATACAT ATAC--
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30540 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30588 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30636 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30684 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30732 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT ATACAT
30780 ATACAT ATACAT ATACAT ATACAT ATA
1 ATACAT ATACAT ATACAT ATACAT ATA
30807 ATAAAAGAAT
Statistics
Matches: 493, Mismatches: 0, Indels: 16
0.97 0.00 0.03
Matches are distributed among these distances:
4 8 0.02
6 473 0.96
8 12 0.02
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATACAT
Found at i:32890 original size:31 final size:30
Alignment explanation
Indices: 32822--32878 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
32812 TAAAAATATC
* *
32822 TTTTGTTTTTGTTTTAACTTATTAAATGTA
1 TTTTATTTTTGGTTTAACTTATTAAATGTA
32852 TTTTATTTTTGGTTTAACTTATTAAAT
1 TTTTATTTTTGGTTTAACTTATTAAAT
32879 ATTTTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.25, C:0.04, G:0.09, T:0.63
Consensus pattern (30 bp):
TTTTATTTTTGGTTTAACTTATTAAATGTA
Found at i:32986 original size:15 final size:15
Alignment explanation
Indices: 32955--33010 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
32945 TCTTATTTTC
**
32955 TAAAATATATT-TTT
1 TAAAATATATTAAAT
*
32969 TAAAATATCTTAAAT
1 TAAAATATATTAAAT
*
32984 TAAAATATATTTAAT
1 TAAAATATATTAAAT
32999 TATAAATTATAT
1 TA-AAA-TATAT
33011 ATTTTATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 10 0.29
15 16 0.47
16 3 0.09
17 5 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATATATTAAAT
Found at i:33016 original size:46 final size:48
Alignment explanation
Indices: 32955--33049 Score: 113
Period size: 48 Copynumber: 2.0 Consensus size: 48
32945 TCTTATTTTC
*
32955 TAAAATATATTTTTTA-AAATATCTTAAATT-AAAATATATTTAATTA
1 TAAAATATATATTTTATAAATATCTTAAATTAAAAATATATTTAATTA
* * * * * *
33001 TAAATTATATATTTTATTATTATCTTCATTTAAAAATATATTTTATTA
1 TAAAATATATATTTTATAAATATCTTAAATTAAAAATATATTTAATTA
33049 T
1 T
33050 TATTTTCAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
46 14 0.35
47 10 0.25
48 16 0.40
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (48 bp):
TAAAATATATATTTTATAAATATCTTAAATTAAAAATATATTTAATTA
Found at i:33078 original size:28 final size:29
Alignment explanation
Indices: 33007--33102 Score: 126
Period size: 29 Copynumber: 3.3 Consensus size: 29
32997 ATTATAAATT
*
33007 ATATATTTTATTATTATCTTCATTTAAAA
1 ATATATTTTATTATTATCTTCAATTAAAA
*
33036 ATATATTTTATTATTATTTTCAATTAAAGA
1 ATATATTTTATTATTATCTTCAATTAAA-A
*
33066 ATATA-TTT-TTATTATCTT-AACTTCAAA
1 ATATATTTTATTATTATCTTCAA-TTAAAA
33093 ATATATTTTA
1 ATATATTTTA
33103 ACTAATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
27 8 0.14
28 16 0.27
29 29 0.49
30 6 0.10
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (29 bp):
ATATATTTTATTATTATCTTCAATTAAAA
Found at i:33111 original size:14 final size:15
Alignment explanation
Indices: 33092--33132 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
33082 TTAACTTCAA
33092 AATATATTTTAA-CT
1 AATATATTTTAAGCT
*
33106 AATATATTTTAAGTT
1 AATATATTTTAAGCT
*
33121 AAAATATTTTAA
1 AATATATTTTAA
33133 AAACATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AATATATTTTAAGCT
Found at i:33239 original size:30 final size:29
Alignment explanation
Indices: 33172--33239 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
33162 CAATATATAT
* *
33172 ATATATATATAAAGTTAAAATAAGAGAAA
1 ATATATATTTAAAGTGAAAATAAGAGAAA
* *
33201 A-ATATATTTAAAGTGAAGATAAGATTAAA
1 ATATATATTTAAAGTGAAAATAAGA-GAAA
33230 ATATATATTT
1 ATATATATTT
33240 TTATATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 20 0.61
29 5 0.15
30 8 0.24
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (29 bp):
ATATATATTTAAAGTGAAAATAAGAGAAA
Found at i:39748 original size:19 final size:20
Alignment explanation
Indices: 39716--39759 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
39706 GGGGTACATA
39716 ATGCGGTCTGATGCGAT-CCG
1 ATGCGGTCTGATGCG-TGCCG
39736 ATGCGGT-TGATGCGTGCCG
1 ATGCGGTCTGATGCGTGCCG
39755 ATGCG
1 ATGCG
39760 TTTAGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.04
19 15 0.65
20 7 0.30
ACGTcount: A:0.14, C:0.23, G:0.39, T:0.25
Consensus pattern (20 bp):
ATGCGGTCTGATGCGTGCCG
Found at i:47302 original size:16 final size:16
Alignment explanation
Indices: 47283--47313 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
47273 TTTTAATTTA
47283 TTTTAATATTTTTAAT
1 TTTTAATATTTTTAAT
*
47299 TTTTAATGTTTTTAA
1 TTTTAATATTTTTAA
47314 AATCATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTTTAATATTTTTAAT
Found at i:47311 original size:25 final size:24
Alignment explanation
Indices: 47260--47314 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
47250 ATCTTTAATA
*
47260 TTTAAATTATTAATTTTAATTTAT
1 TTTAAATTATTAATTTTAATGTAT
*
47284 TTTAATATTTTTAATTTTTAATGT-T
1 TTTAA-ATTATTAA-TTTTAATGTAT
47309 TTTAAA
1 TTTAAA
47315 ATCATATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 13 0.48
26 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (24 bp):
TTTAAATTATTAATTTTAATGTAT
Found at i:51454 original size:41 final size:41
Alignment explanation
Indices: 51409--51596 Score: 143
Period size: 41 Copynumber: 4.7 Consensus size: 41
51399 ATCTTGGAAT
* * * **
51409 CATGCACTAATTCACAATTCTATTCTGTTCAATCATAATAA
1 CATGCAATAATTCACAATTCGACTCAATTCAATCATAATAA
* * *
51450 CATGCAATAATTCACCATTCGACTCAATTCGATCATGATAA
1 CATGCAATAATTCACAATTCGACTCAATTCAATCATAATAA
* * * *** *
51491 CATGCAATAATTCACAATTTGATTTAATTCAATCATGGCAG
1 CATGCAATAATTCACAATTCGACTCAATTCAATCATAATAA
* * *
51532 TATGCAATAATTCACAA-T----TCAATTCAATCATGACAA
1 CATGCAATAATTCACAATTCGACTCAATTCAATCATAATAA
* * * *
51568 CATGAAATAATTCATAATTCAACTTAATT
1 CATGCAATAATTCACAATTCGACTCAATT
51597 TGATCATGGC
Statistics
Matches: 118, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
36 29 0.25
37 1 0.01
40 1 0.01
41 87 0.74
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (41 bp):
CATGCAATAATTCACAATTCGACTCAATTCAATCATAATAA
Found at i:51563 original size:36 final size:36
Alignment explanation
Indices: 51473--51589 Score: 108
Period size: 36 Copynumber: 3.1 Consensus size: 36
51463 ACCATTCGAC
* * *
51473 TCAATTCGATCATGATAACATGCAATAATTCACAATTTGAT
1 TCAATTCAATCATGACAACATGAAATAATTCAC-A----AT
* * ** *
51514 TTAATTCAATCATGGCAGTATGCAATAATTCACAAT
1 TCAATTCAATCATGACAACATGAAATAATTCACAAT
*
51550 TCAATTCAATCATGACAACATGAAATAATTCATAAT
1 TCAATTCAATCATGACAACATGAAATAATTCACAAT
51586 TCAA
1 TCAA
51590 CTTAATTTGA
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
36 36 0.56
40 1 0.02
41 27 0.42
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.32
Consensus pattern (36 bp):
TCAATTCAATCATGACAACATGAAATAATTCACAAT
Found at i:51595 original size:77 final size:77
Alignment explanation
Indices: 51473--51619 Score: 204
Period size: 77 Copynumber: 1.9 Consensus size: 77
51463 ACCATTCGAC
* * * ** * *
51473 TCAATTCGATCATGATAACATGCAATAATTCACAATTTGATTTAATTCAATCATGGCAGTATGCA
1 TCAATTCAATCATGACAACATGAAATAATTCACAATTCAACTTAATTCAATCATGGCAGCATGCA
51538 ATAATTCACAAT
66 ATAATTCACAAT
* **
51550 TCAATTCAATCATGACAACATGAAATAATTCATAATTCAACTTAATTTGATCATGGCAGCATGCA
1 TCAATTCAATCATGACAACATGAAATAATTCACAATTCAACTTAATTCAATCATGGCAGCATGCA
51615 ATAAT
66 ATAAT
51620 CCATAATTGA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
77 60 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (77 bp):
TCAATTCAATCATGACAACATGAAATAATTCACAATTCAACTTAATTCAATCATGGCAGCATGCA
ATAATTCACAAT
Found at i:51846 original size:41 final size:41
Alignment explanation
Indices: 51788--51880 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 41
51778 GCTTTTCTTT
* * * *
51788 CAATTCAATTTGGTCATGGCAACATGCATTTATTCACAAAC
1 CAATTCAATTAGATCATGACAACATGCATTAATTCACAAAC
* * *
51829 CAATTCAATTAGATCATGATAACATGTATTAATTCACAATC
1 CAATTCAATTAGATCATGACAACATGCATTAATTCACAAAC
*
51870 CAATACAATTA
1 CAATTCAATTA
51881 AAATCAACGC
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (41 bp):
CAATTCAATTAGATCATGACAACATGCATTAATTCACAAAC
Found at i:59957 original size:123 final size:121
Alignment explanation
Indices: 59745--59974 Score: 311
Period size: 123 Copynumber: 1.9 Consensus size: 121
59735 AGTTCGATCT
* * *
59745 TGGCAACATGCACTAATTCACAATTCGATTAGTTCAATCATAGCAACATGCAATAATTCACCATT
1 TGGCAACATGCAATAATTCACAATTCGATTAATTCAATCATAGCAACA-GCAATAATTCACAATT
* *
59810 CGACTCAATTCGAACATGAGAGCATGCAATAATTCACAATTCGATTCAATTCAATCA
65 CAACTCAATTCGAACATGAGAGCATGCAATAATCCACAATTCGATTCAATTCAATCA
* *
59867 TGGCAACATGCAATAATTCACAATTCGATTCAATTCAATCATGGTTCCACA-CAATAATTCACAA
1 TGGCAACATGCAATAATTCACAATTCGATT-AATTCAATCATAG--CAACAGCAATAATTCACAA
* * *
59931 TTCAACTTAATTCGATCATG-GCAGCATGCAATAATCCATAATTC
63 TTCAACTCAATTCGAACATGAG-AGCATGCAATAATCCACAATTC
59975 AATCATGGAA
Statistics
Matches: 94, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
122 30 0.32
123 60 0.64
125 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (121 bp):
TGGCAACATGCAATAATTCACAATTCGATTAATTCAATCATAGCAACAGCAATAATTCACAATTC
AACTCAATTCGAACATGAGAGCATGCAATAATCCACAATTCGATTCAATTCAATCA
Found at i:59976 original size:41 final size:40
Alignment explanation
Indices: 59745--59974 Score: 252
Period size: 41 Copynumber: 5.7 Consensus size: 40
59735 AGTTCGATCT
* *
59745 TGGCAACATGCACTAATTCACAATTCGATTAGTTCAATCA
1 TGGCAACATGCAATAATTCACAATTCGATTAATTCAATCA
* * *
59785 TAGCAACATGCAATAATTCACCATTCGACTCAATTCGAA-CA
1 TGGCAACATGCAATAATTCACAATTCGA-TTAATTC-AATCA
*
59826 TGAG-AGCATGCAATAATTCACAATTCGATTCAATTCAATCA
1 TG-GCAACATGCAATAATTCACAATTCGATT-AATTCAATCA
59867 TGGCAACATGCAATAATTCACAATTCGATTCAATTCAATCA
1 TGGCAACATGCAATAATTCACAATTCGATT-AATTCAATCA
* * *
59908 TGGTTCCACA--CAATAATTCACAATTCAACTTAATTCGATCA
1 TGG--CAACATGCAATAATTCACAATTCGA-TTAATTCAATCA
* * *
59949 TGGCAGCATGCAATAATCCATAATTC
1 TGGCAACATGCAATAATTCACAATTC
59975 AATCATGGAA
Statistics
Matches: 162, Mismatches: 17, Indels: 21
0.81 0.09 0.10
Matches are distributed among these distances:
39 3 0.02
40 29 0.18
41 121 0.75
42 5 0.03
43 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.11, T:0.29
Consensus pattern (40 bp):
TGGCAACATGCAATAATTCACAATTCGATTAATTCAATCA
Done.