Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004131.1 Hibiscus syriacus cultivar Beakdansim tig00009037_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: 101932
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:12 original size:7 final size:7
Alignment explanation
Indices: 11--101 Score: 148
Period size: 7 Copynumber: 12.7 Consensus size: 7
1 AAGAAGAAAG
11 AAGAAGA
1 AAGAAGA
18 AAGAAGGA
1 AAGAA-GA
26 GAA-AAGAA
1 -AAGAAG-A
34 AAGAAGA
1 AAGAAGA
41 AAGAAGA
1 AAGAAGA
48 AAGAAGA
1 AAGAAGA
55 AAGAAGA
1 AAGAAGA
62 AAGAAGA
1 AAGAAGA
69 AAGAAGA
1 AAGAAGA
76 AAGAAGA
1 AAGAAGA
83 AAGAAGA
1 AAGAAGA
90 AAGAAGA
1 AAGAAGA
97 AAGAA
1 AAGAA
102 AATCGATCAA
Statistics
Matches: 80, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
7 70 0.88
8 8 0.10
9 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (7 bp):
AAGAAGA
Found at i:1711 original size:39 final size:39
Alignment explanation
Indices: 1667--1789 Score: 117
Period size: 39 Copynumber: 3.2 Consensus size: 39
1657 TTTTACTCGG
1667 AAGAAGACATTTTATTTCATTCAAGATTGTTTTTCTTAA
1 AAGAAGACATTTTATTTCATTCAAGATTGTTTTTCTTAA
* * * * * * *
1706 AAGAAGA-A-TTTATCTCGCTTGAGACAAT-TTTTACTTGA
1 AAGAAGACATTTTATTTC-ATTCA-AGATTGTTTTTCTTAA
* *
1744 AAGAAGACATTTCATTTCACTCAAGATTGTTTTTCTTAA
1 AAGAAGACATTTTATTTCATTCAAGATTGTTTTTCTTAA
*
1783 AACAAGA
1 AAGAAGA
1790 TTTGTCTCAC
Statistics
Matches: 62, Mismatches: 17, Indels: 10
0.70 0.19 0.11
Matches are distributed among these distances:
37 7 0.11
38 22 0.35
39 27 0.44
40 6 0.10
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (39 bp):
AAGAAGACATTTTATTTCATTCAAGATTGTTTTTCTTAA
Found at i:1813 original size:36 final size:36
Alignment explanation
Indices: 1696--1880 Score: 93
Period size: 39 Copynumber: 4.9 Consensus size: 36
1686 TTCAAGATTG
* * *
1696 TTTTTCTTAAAAGAAGAATTTATCTCGCTTGAGACAA
1 TTTTTCTTAAAACAAG-ATTTATCTCACTTGAGAAAA
* * * ** ***
1733 TTTTTACTTGAAAGAAGACATTTCATTTCACTCAAGATTG
1 TTTTT-CTTAAAACAAG--ATTT-ATCTCACTTGAGAAAA
*
1773 TTTTTCTTAAAACAAGATTTGTCTCACTTGAGAAAA
1 TTTTTCTTAAAACAAGATTTATCTCACTTGAGAAAA
* * * * ** **
1809 TTTTTACTCGAAAA-AGACATTACATTTCACTCAAGATTA
1 TTTTT-CT-TAAAACA-AGATT-TATCTCACTTGAGAAAA
*
1848 TTTTTCTTAAAACAAGATTTTTCTCACTTGAGA
1 TTTTTCTTAAAACAAGATTTATCTCACTTGAGA
1881 CAGTTTTTAC
Statistics
Matches: 106, Mismatches: 34, Indels: 17
0.68 0.22 0.11
Matches are distributed among these distances:
36 23 0.22
37 20 0.19
38 21 0.20
39 28 0.26
40 14 0.13
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.39
Consensus pattern (36 bp):
TTTTTCTTAAAACAAGATTTATCTCACTTGAGAAAA
Found at i:1843 original size:75 final size:76
Alignment explanation
Indices: 1523--1968 Score: 587
Period size: 77 Copynumber: 5.9 Consensus size: 76
1513 ATACAAAAAA
* * * *
1523 TTCATTTTACTCAAGATTGTTTTTCTTAAAACAAGATTTGCCTCGTTTGAGACAATTTTTACTTG
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCG
1588 AAAGAAGACAT
66 AAAGAAGACAT
* * * *
1599 TTCATTTCACTAAAGATTTTTTTTTCCTTAAAATAAGATTTGTCTTGCTTGAGACAATTTTTACT
1 TTCATTTCACTCAAGA-TTGTTTTT-CTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACT
*
1664 CGGAAGAAGACAT
64 CGAAAGAAGACAT
* * * * *
1677 TTTATTTCATTCAAGATTGTTTTTCTTAAAAGAAGAATTTATCTCGCTTGAGACAATTTTTACTT
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAG-ATTTGTCTCGCTTGAGACAATTTTTACTC
1742 GAAAGAAGACAT
65 GAAAGAAGACAT
* *
1754 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGAAAATTTTTACTCG
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCG
1819 AAA-AAGACAT
66 AAAGAAGACAT
* * * * *
1829 TACATTTCACTCAAGATTATTTTTCTTAAAACAAGATTTTTCTCACTTGAGACAGTTTTTACTCG
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCG
*
1894 AAAGAAGATAT
66 AAAGAAGACAT
* * * * *
1905 TTCATTTTACTCAAGA-T-TATTT-TTAAAACAAGATTTATCTCGCTTGAGATAA-TTTCACTCG
1 TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCG
1966 AAA
66 AAA
1969 CAGAAGATTT
Statistics
Matches: 327, Mismatches: 39, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
72 11 0.03
73 26 0.08
74 4 0.01
75 71 0.22
76 73 0.22
77 83 0.25
78 59 0.18
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.41
Consensus pattern (76 bp):
TTCATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACAATTTTTACTCG
AAAGAAGACAT
Found at i:1983 original size:39 final size:39
Alignment explanation
Indices: 1934--2620 Score: 920
Period size: 39 Copynumber: 17.7 Consensus size: 39
1924 TTTTTAAAAC
*
1934 AAGA-TTTATCTCGCTTGAGATAATTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
1972 AAGATTTTATCTCACTTGATATAGTTTCATTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
2011 AAGATTTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
1 AAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
2051 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
2090 --GATTTTATCTCGCTTGAGATAGTTTCACTC-ATAACAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGA-AACAG
* *
2127 AAGA-TTGATCT-GCTTGAGATTGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
2164 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * *
2203 AAGATTTTATCTCTCTTGAGATAGTTTCATTCGAAAAAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * * *
2242 AAGATTTTATCTCTCTTAAGATATTTTTACTCGAAATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * *
2281 AAGATTTTATCTCGCTTTAGATGGTTTCACTTGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
*
2320 AAGATTTTTATCTCGCTTGAGATAATTTCACTCGAAACAG
1 AAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
2360 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
2399 AAGATTTTATCTTGCTTGAGATAGTTTTACTTGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
2438 AAGATTTTATATCGCTTGAGATAGTTTCACTTGATATAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* * * *
2477 AAGATTTTTCTCTCTCTTAAGATAGTTTCACTTGAAACAG
1 AAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
2517 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAGAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* **
2556 AAGATTTTATCTCGCTTGAGATAGTTTCTCTTTAAACAG
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
* *
2595 AAGA-TTTATCTCACTTGAGATTGTTT
1 AAGATTTTATCTCGCTTGAGATAGTTT
2621 TTCTTAAAAC
Statistics
Matches: 572, Mismatches: 67, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
36 1 0.00
37 59 0.10
38 37 0.06
39 372 0.65
40 103 0.18
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
Found at i:2070 original size:118 final size:117
Alignment explanation
Indices: 1934--2620 Score: 913
Period size: 118 Copynumber: 5.9 Consensus size: 117
1924 TTTTTAAAAC
* * *
1934 AAGA-TTTATCTCGCTTGAGATAATTTCACTCGAAACAGAAGATTTTATCTCACTTGATATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
1998 TCATTTGAAACAGAAGATTTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
66 TCATTTGAAACAGAAGA-TTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
*
2051 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAATAG--GATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* * * * * *
2114 TCA-CTCATAACATAAGA-TTGATCT-GCTTGAGATTGTTTCACTCGAAACAG
66 TCATTTGA-AACAGAAGATTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
*
2164 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCTCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* * * * * *
2229 TCATTCGAAAAAGAAGATTTTATCTCTCTTAAGATATTTTTACTCGAAATAG
66 TCATTTGAAACAGAAGATTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
* * * *
2281 AAGATTTTATCTCGCTTTAGATGGTTTCACTTGAAACAGAAGATTTTTATCTCGCTTGAGATAAT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTTATCTCGCTTGAGATAGT
* * *
2346 TTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAG
65 TTCATTTGAAACAGAAGATTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
* * * * *
2399 AAGATTTTATCTTGCTTGAGATAGTTTTACTTGAAACAAAAGATTTTATATCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* * * * * *
2464 TCACTTGATATAGAAGATTTTTCTCTCTCTTAAGATAGTTTCACTTGAAACAG
66 TCATTTGAAACAGAAGA-TTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
* *
2517 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAAGAAAAGATTTTATCTCGCTTGAGATAGTT
1 AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
* * *
2582 TC-TCTTTAAACAGAAGA-TTTATCTCACTTGAGATTGTTT
66 TCAT-TTGAAACAGAAGATTTTATCTCTCTTGAGATAGTTT
2621 TTCTTAAAAC
Statistics
Matches: 497, Mismatches: 63, Indels: 21
0.86 0.11 0.04
Matches are distributed among these distances:
113 62 0.12
114 6 0.01
115 35 0.07
116 58 0.12
117 98 0.20
118 238 0.48
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (117 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGATAGTT
TCATTTGAAACAGAAGATTTTATCTCTCTTGAGATAGTTTCACTCGAAACAG
Found at i:2366 original size:19 final size:19
Alignment explanation
Indices: 2344--2405 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
2334 GCTTGAGATA
2344 ATTTCACTCGAAACAGAAG
1 ATTTCACTCGAAACAGAAG
* ****
2363 ATTTTATCTCGCTTGAGATAG
1 ATTTCA-CTCGAAACAGA-AG
2384 -TTTCACTCGAAACAGAAG
1 ATTTCACTCGAAACAGAAG
2402 ATTT
1 ATTT
2406 TATCTTGCTT
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 2 0.07
19 15 0.50
20 11 0.37
21 2 0.07
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTTCACTCGAAACAGAAG
Found at i:2367 original size:157 final size:157
Alignment explanation
Indices: 1929--2620 Score: 961
Period size: 157 Copynumber: 4.5 Consensus size: 157
1919 GATTATTTTT
* * * *
1929 AAAACAAGA-TTTATCTCGCTTGAGATAATTTCACTCGAAACAGAAGATTTTATCTCACTTGATA
1 AAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGA
* *
1993 TAGTTTCATTTGAAACAGAAGATTTTTATCTCTCTTGAGATAGTTTCACTCGAAACAGAAGATTT
66 TAGTTTCACTTGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
2058 TATCTCGCTTGAGATAGTTTCACTCGA
131 TATCTCGCTTGAGATAGTTTCACTCGA
* * *
2085 AATAG--GATTTTATCTCGCTTGAGATAGTTTCACTC-ATAACATAAGA-TTGATCT-GCTTGAG
1 AAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGA-AACAGAAGATTTTATCTCGCTTGAG
* *
2145 ATTGTTTCACTCGAAACAGAAGA-TTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
65 ATAGTTTCACTTGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATT
* *
2209 TTATCTCTCTTGAGATAGTTTCATTCGA
130 TTATCTCGCTTGAGATAGTTTCACTCGA
* * * * * *
2237 AAAAGAAGATTTTATCTCTCTTAAGATATTTTTACTCGAAATAGAAGATTTTATCTCGCTTTAGA
1 AAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGA
* *
2302 TGGTTTCACTTGAAACAGAAGATTTTTATCTCGCTTGAGATAATTTCACTCGAAACAGAAGATTT
66 TAGTTTCACTTGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
2367 TATCTCGCTTGAGATAGTTTCACTCGA
131 TATCTCGCTTGAGATAGTTTCACTCGA
* * * * * *
2394 AACAGAAGATTTTATCTTGCTTGAGATAGTTTTACTTGAAACAAAAGATTTTATATCGCTTGAGA
1 AAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGA
* * * * * *
2459 TAGTTTCACTTGATATAGAAGATTTTTCTCTCTCTTAAGATAGTTTCACTTGAAACAGAAGATTT
66 TAGTTTCACTTGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
2524 TATCTCGCTTGAGATAGTTTCACTCGA
131 TATCTCGCTTGAGATAGTTTCACTCGA
* ** *
2551 AAGAA-AAGATTTTATCTCGCTTGAGATAGTTTCTCTTTAAACAGAAGA-TTTATCTCACTTGAG
1 AA-AAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAG
*
2614 ATTGTTT
65 ATAGTTT
2621 TTCTTAAAAC
Statistics
Matches: 473, Mismatches: 54, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
152 70 0.15
153 25 0.05
154 42 0.09
155 41 0.09
156 49 0.10
157 245 0.52
158 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (157 bp):
AAAAGAAGATTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGA
TAGTTTCACTTGAAACAGAAGATTTTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTT
TATCTCGCTTGAGATAGTTTCACTCGA
Found at i:10427 original size:20 final size:20
Alignment explanation
Indices: 10390--10427 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10380 ATGTTTCAAG
*
10390 GGTATCGATACCATCCTTCA
1 GGTATCGATACCACCCTTCA
*
10410 GGTATCGATACTACCCTT
1 GGTATCGATACCACCCTT
10428 TATAGTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.32
Consensus pattern (20 bp):
GGTATCGATACCACCCTTCA
Found at i:21506 original size:18 final size:19
Alignment explanation
Indices: 21475--21510 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
21465 ACATGCTTTG
*
21475 AATAGAAAATAAAACAGCA
1 AATAGAAAACAAAACAGCA
21494 AATA-AAAACAAAACAGC
1 AATAGAAAACAAAACAGC
21511 CTAGGGTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.14, G:0.08, T:0.08
Consensus pattern (19 bp):
AATAGAAAACAAAACAGCA
Found at i:23686 original size:9 final size:8
Alignment explanation
Indices: 23672--23731 Score: 63
Period size: 9 Copynumber: 7.5 Consensus size: 8
23662 GGACCTACAA
23672 AAAATAAAT
1 AAAAT-AAT
23681 AAAATAAT
1 AAAATAAT
23689 AAAATAAT
1 AAAATAAT
23697 --AATAAT
1 AAAATAAT
23703 AATAATAAT
1 AA-AATAAT
23712 AAATATAAT
1 AAA-ATAAT
*
23721 ATAAT-AT
1 AAAATAAT
23728 AAAA
1 AAAA
23732 AATTTTGTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
6 6 0.13
7 5 0.11
8 14 0.31
9 20 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:23691 original size:12 final size:12
Alignment explanation
Indices: 23670--23731 Score: 60
Period size: 12 Copynumber: 5.3 Consensus size: 12
23660 ATGGACCTAC
23670 AAAA-AATAAAT
1 AAAATAATAAAT
23681 AAAATAATAAA-
1 AAAATAATAAAT
*
23692 ATAATAAT-AAT
1 AAAATAATAAAT
23703 AATAATAATAAAT
1 AA-AATAATAAAT
*
23716 ATAAT-ATAATAT
1 AAAATAATAA-AT
23728 AAAA
1 AAAA
23732 AATTTTGTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
10 2 0.05
11 16 0.38
12 20 0.48
13 4 0.10
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:23697 original size:3 final size:3
Alignment explanation
Indices: 23678--23726 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
23668 ACAAAAAATA
23678 AAT AA- AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AA- ATAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
23721 -AT AAT A
1 AAT AAT A
23727 TAAAAAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 7 0.17
3 33 0.80
4 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:24399 original size:84 final size:84
Alignment explanation
Indices: 24311--24929 Score: 691
Period size: 84 Copynumber: 7.5 Consensus size: 84
24301 GTTTGCCTCT
* * * * * * * *
24311 GAGCTGAGTGTAATCAAACTCGAAGGTCTTCGGTTGGCAGATAGCTCTTCTAGTCTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
24376 CTGCAAATGATGTACCTTG
66 CTGCAAATGATGTGCCTTG
* * * *
24395 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
24459 CTGTAAATGATGTGCCCTCG
66 CTGCAAATGATGTG-CCTTG
* * * * * * * * *
24479 AAGCTGAGTGTAATCAAACTCG-AGG-GTAT--TTGGCAGATAGCCCTTCTCGACTTAAGCTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
24540 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
*
24559 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
24624 TTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * * * *
24643 GACCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
24707 TTGTAAATGATGTGCCCTCG
66 CTGCAAATGATGTG-CCTTG
* * * * * * * *
24727 AAGCTTAGTGCAATCGAACTTGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
24788 CTGCAAATGATGTGCCTTG
66 CTGCAAATGATGTGCCTTG
* * *
24807 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTATCGACTTAAGTTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
*
24872 CTGCAAATGATGTGCTTTG
66 CTGCAAATGATGTGCCTTG
** * * *
24891 GAAATGAGCGTAGTCAAACTCGAAGGCCTTTGGTGGGCA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCA
24930 CGATTCCCTT
Statistics
Matches: 444, Mismatches: 79, Indels: 24
0.81 0.14 0.04
Matches are distributed among these distances:
80 47 0.11
81 78 0.18
82 6 0.01
83 80 0.18
84 233 0.52
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (84 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTG
Found at i:24567 original size:164 final size:164
Alignment explanation
Indices: 24304--24925 Score: 651
Period size: 164 Copynumber: 3.8 Consensus size: 164
24294 AAATTTGGTT
* * * * *
24304 TGCCTCTGAGCTGAGTGTAATCAAACTCGAAGGTCTTCGGTTGGCAGATAGCTCTTCTAGTCTTA
1 TGCCTCGGAGCTGAGCGTAATCAAACTCGAAGGT-TT--GTTGGCAGATAACCCTTCTAGACTTA
* *
24369 AGTTATGCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
63 AGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
* * * *
24434 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATG
128 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * * * *
24471 TGCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGTAT-TTGGCAGATAGCCCTTCTCGACTTAAG
1 TG-CCTCGGAGCTGAGCGTAATCAAACTCGAAGGTTTGTTGGCAGATAACCCTTCTAGACTTAAG
*
24535 CTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGA-AG
65 TTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T-GACAG
*
24599 ATAACCCTTCTCGACTTAAGTTATGTTGCAAATGATG
128 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * * * * * *
24636 TGCCTTGGACCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGA
1 TGCCTCGGAGCTGAGCGTAATCAAACTCGAAGG--TTTGTTGGCAGATAACCCTTCTAGACTTAA
** * * * * * * * * *
24701 GTTATGTTGTAAATGATGTGCCCTCGAAGCTTAGTGCAATCGAACTTGAGGGTCTTT-G-G-CAG
64 GTTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAG
*
24763 ATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATG
128 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* * * * * *
24800 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTATCGACTTA
1 TGCCTCGGAGCTGAGCGTAATCAAACTCGAAGG--TTT-GTTGGCAGATAACCCTTCTAGACTTA
* ** * *
24865 AGTTATACTGCAAATGATGTGCTTTGGAAATGAGCGTAGTCAAACTCGAAGGCCTTTGGTG
63 AGTTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG
24926 GGCACGATTC
Statistics
Matches: 377, Mismatches: 67, Indels: 23
0.81 0.14 0.05
Matches are distributed among these distances:
164 200 0.53
165 75 0.20
166 5 0.01
167 40 0.11
168 57 0.15
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (164 bp):
TGCCTCGGAGCTGAGCGTAATCAAACTCGAAGGTTTGTTGGCAGATAACCCTTCTAGACTTAAGT
TATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATA
ACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
Found at i:24761 original size:248 final size:248
Alignment explanation
Indices: 24311--24925 Score: 987
Period size: 248 Copynumber: 2.5 Consensus size: 248
24301 GTTTGCCTCT
* * * * * * *
24311 GAGCTGAGTGTAATCAAACTCGAAGGTCTTCGGTTGGCAGATAGCTCTTCTAGTCTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTAAGTTATG
* *
24376 CTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCC
66 CTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCC
*
24441 TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGT
131 TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCAAACTCGAGGGT
24506 ATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
196 ATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
* *
24559 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGAAGATAACCCTTCTCGACTTAAGTTATG
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTAAGTTATG
* *
24624 TTGCAAATGATGTGCCTTGGACCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCC
66 CTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCC
* * * *
24689 TTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTTAGTGCAATCGAACTTGAGGGT
131 TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCAAACTCGAGGGT
* * *
24754 CTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTG
196 ATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
* *
24807 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTATCGACTTAAGTTATA
1 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTAAGTTATG
* * * *
24872 CTGCAAATGATGTGCTTTGGAAATGAGCGTAGTCAAACTCGAAGGCCTTTGGTG
66 CTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTGGTG
24926 GGCACGATTC
Statistics
Matches: 337, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
248 337 1.00
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (248 bp):
GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACTCTTCTCGACTTAAGTTATG
CTGCAAATGATGTGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCC
TTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGCAATCAAACTCGAGGGT
ATTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
Found at i:25954 original size:110 final size:110
Alignment explanation
Indices: 25759--26922 Score: 1959
Period size: 110 Copynumber: 10.6 Consensus size: 110
25749 TAAATTTTCC
* * * *
25759 TATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAACTAAAAAGTTGTTTGTTGACAGTCAA
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
* * *
25824 TCGCCCCTTCTCTGTAAAGTTGAGCTTGTGTTGTCCCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* * *
25869 TATCCATCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTGTTTGTTGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
*
25934 TCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
*
25979 TATCCTTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
**
26044 TTTCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* *
26089 TATCCTTCGCTGTGAAGTTGAAATTGACTATAAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
26154 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* *
26199 TATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
*
26264 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCCCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* * *
26309 TATCCATCGCTGTGAAGTTGAAATTGACTCTGAATAAAACTGAAAAGTTGTTTGTTGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
*
26374 TCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
*
26419 TATCCTTCGCTGTGAAGTTGAAATTGACTTTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
*
26484 TTGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* * *
26529 TATCATTCGCTGTGAAGTTGAAATTGACTATAAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
*
26594 TTGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* *
26639 TATCATTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
*
26704 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTATCTCGAGTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* * *
26749 TATCCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGACAGTCAG
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
*
26814 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGATTCCAA
66 TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
* * * *
26859 TATCCTTTGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAATTTGTTTATTGACAGTC
1 TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTG-AAAAGTTGTTTGTAGACAGTC
26923 GCCTCTTTGC
Statistics
Matches: 995, Mismatches: 58, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
110 977 0.98
111 18 0.02
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (110 bp):
TATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAGACAGTCAG
TCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAA
Found at i:27487 original size:15 final size:16
Alignment explanation
Indices: 27449--27485 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
27439 CAAAATGTCA
*
27449 TTTTTTGCAACATGTT
1 TTTTTTGTAACATGTT
27465 TTTTTTGTAACATGTT
1 TTTTTTGTAACATGTT
27481 TTTTT
1 TTTTT
27486 GTTTGGCATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.08, G:0.11, T:0.65
Consensus pattern (16 bp):
TTTTTTGTAACATGTT
Found at i:31784 original size:36 final size:36
Alignment explanation
Indices: 31734--31812 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
31724 AAGAGGAAAT
*
31734 GACGTTGCTGGGAGTGTGGTGGTAGTTGAGGTTATG
1 GACGTTGCTAGGAGTGTGGTGGTAGTTGAGGTTATG
31770 GACGTTGCTAGGAGTGTGGTGGTAGTTGAGGTTATG
1 GACGTTGCTAGGAGTGTGGTGGTAGTTGAGGTTATG
31806 GACGTTG
1 GACGTTG
31813 TGGAATGGTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.15, C:0.06, G:0.46, T:0.33
Consensus pattern (36 bp):
GACGTTGCTAGGAGTGTGGTGGTAGTTGAGGTTATG
Found at i:31964 original size:18 final size:19
Alignment explanation
Indices: 31935--31973 Score: 71
Period size: 18 Copynumber: 2.1 Consensus size: 19
31925 ATAAATAATA
31935 ATAATAATAATAAAAAAAT
1 ATAATAATAATAAAAAAAT
31954 ATAAT-ATAATAAAAAAAT
1 ATAATAATAATAAAAAAAT
31972 AT
1 AT
31974 TTGTAGACCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
ATAATAATAATAAAAAAAT
Found at i:32705 original size:83 final size:82
Alignment explanation
Indices: 32549--32803 Score: 282
Period size: 84 Copynumber: 3.1 Consensus size: 82
32539 GTTTGCCTCT
* *
32549 GAGCTGAGTGTAATCGAACTCGAAGGTCTTCGGTTGGCAGATAGCTCTTCTAGTCC-TAAGCTAT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGG-T-GCAGATAGCCCTTCTAG-CCTTAAGCTAT
32613 GCTGCAAATGATGTACCTTG
63 GCTGCAAATGATGTACCTTG
* * * * * *
32633 GAGCTGAGCGTAGTCGAACGCGAAGGTCTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTG-CAGATAGCCCTTCTAGCCTTAAGCTATGC
* * *
32698 TGTAAATGATGTGCCCTCG
65 TGCAAATGATGT-ACCTTG
* * *** *
32717 AAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-GCAGATAGCCCTTCTCTACTTAAGCTATACT
1 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTAGCCTTAAGCTATGCT
*
32780 GCAAATGATGTGCCTTG
66 GCAAATGATGTACCTTG
32797 GAGCTGA
1 GAGCTGA
32804 AATGAGGGAA
Statistics
Matches: 141, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
80 10 0.07
81 33 0.23
82 4 0.03
83 35 0.25
84 59 0.42
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.29
Consensus pattern (82 bp):
GAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTGCAGATAGCCCTTCTAGCCTTAAGCTATGCT
GCAAATGATGTACCTTG
Found at i:33257 original size:10 final size:9
Alignment explanation
Indices: 33242--33286 Score: 54
Period size: 10 Copynumber: 4.7 Consensus size: 9
33232 ACAAAAAATA
33242 AAAAATAATT
1 AAAAATAA-T
33252 AAAAATAAT
1 AAAAATAAT
*
33261 AATAATAAT
1 AAAAATAAT
33270 AAAATATAAT
1 AAAA-ATAAT
33280 ATAAAAT
1 A-AAAAT
33287 TTTTTTAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 12 0.39
10 16 0.52
11 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATAAT
Found at i:33264 original size:16 final size:16
Alignment explanation
Indices: 33234--33285 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
33224 ATGGACCTAC
*
33234 AAAAAATAAAAAATAAT
1 AAAAAAT-AATAATAAT
*
33251 TAAAAATAATAATAAT
1 AAAAAATAATAATAAT
33267 AATAAAAT-ATAAT-AT
1 AA-AAAATAATAATAAT
33282 AAAA
1 AAAA
33286 TTTTTTTAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 2 0.06
15 4 0.13
16 14 0.45
17 11 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAAATAATAATAAT
Found at i:33267 original size:19 final size:17
Alignment explanation
Indices: 33235--33280 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
33225 TGGACCTACA
33235 AAAAATAA-AAAATAATT
1 AAAAATAATAAAATAA-T
33252 AAAAATAATAATAATAAT
1 AAAAATAATAA-AATAAT
33270 AAAATATAATA
1 AAAA-ATAATA
33281 TAAAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 8 0.31
18 7 0.27
19 11 0.42
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAATAATAAAATAAT
Found at i:34669 original size:20 final size:22
Alignment explanation
Indices: 34629--34670 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
34619 GGATTAAATT
*
34629 AAAAATATTAAATTTGTATTTA
1 AAAAATATTAAATTTGAATTTA
34651 AAAAATATT-AA-TTGAATTTA
1 AAAAATATTAAATTTGAATTTA
34671 CATAGTGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
AAAAATATTAAATTTGAATTTA
Found at i:38046 original size:2 final size:2
Alignment explanation
Indices: 38039--38078 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
38029 AAATTAATTA
38039 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
38079 TATTTTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39853 original size:50 final size:51
Alignment explanation
Indices: 39768--39893 Score: 166
Period size: 50 Copynumber: 2.5 Consensus size: 51
39758 AGCAGTAAAG
* *
39768 CGCGCCCCCTGAATCGCGCTATACGCTGATTTGGCGCCACGTGGGTATA-A
1 CGCGCCCCCTGAACCGCGCTATACGCTGATATGGCGCCACGTGGGTATAGA
** * *
39818 CGCGCCCCCTGCCCCGCGATATACGGTGATATGGCGCCACGTGGGTATAGA
1 CGCGCCCCCTGAACCGCGCTATACGCTGATATGGCGCCACGTGGGTATAGA
* *
39869 -GTGCCCCCTGATCCGCGCTATACGC
1 CGCGCCCCCTGAACCGCGCTATACGC
39894 CACGTAGGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 63 0.98
51 1 0.02
ACGTcount: A:0.17, C:0.35, G:0.29, T:0.20
Consensus pattern (51 bp):
CGCGCCCCCTGAACCGCGCTATACGCTGATATGGCGCCACGTGGGTATAGA
Found at i:42308 original size:18 final size:18
Alignment explanation
Indices: 42285--42324 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
42275 AAAGGCGATG
42285 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
42303 GCGGCATCATATATGGCT
1 GCGGCATCATATATGGCT
42321 GCGG
1 GCGG
42325 TGGCTGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.25
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:44028 original size:111 final size:111
Alignment explanation
Indices: 43831--44163 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
43821 ATTACAAAAA
*
43831 TTAATTCTTACTCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* * *
43896 AATTAAAAAGTTAAAACGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
43942 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
44007 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
*
44053 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
* *
44118 AATTAAAACGTTAAAATGTTACTGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
44164 ATGATTTTCA
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.45, C:0.11, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACTGTATCAGCAAAGTGTCGAGATAT
Found at i:44501 original size:50 final size:50
Alignment explanation
Indices: 44442--44566 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
44432 GATACCCATG
* * * *
44442 TATAGCGCGGATCAGGGGGCGCGTTATACCCATGTGGCGCCAGATCACCA
1 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACCA
* ** * * *
44492 TATATCGCGGGGCAGGAGGCGCGCTATACCCACGTGGCACCAAATCAGCG
1 TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACCA
*
44542 TATAGCGCGGTTCAGGGGGCGCGCT
1 TATAGCGCGGATCAGGGGGCGCGCT
44567 TTACTGCTAC
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
50 61 1.00
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.17
Consensus pattern (50 bp):
TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCACCAAATCACCA
Found at i:46036 original size:22 final size:22
Alignment explanation
Indices: 46023--46075 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
46013 ATGTTTATGA
46023 TTAGGGATATTAATGCTTACTG
1 TTAGGGATATTAATGCTTACTG
*
46045 TTAGGGATATTAATGGTTACTG
1 TTAGGGATATTAATGCTTACTG
46067 TTAGGGATA
1 TTAGGGATA
46076 GACCAAGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.28, C:0.06, G:0.26, T:0.40
Consensus pattern (22 bp):
TTAGGGATATTAATGCTTACTG
Found at i:46785 original size:27 final size:28
Alignment explanation
Indices: 46735--46799 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
46725 AGAAATTACA
*
46735 CACTTTTTCATTAGCCTATAAAAAGTGG
1 CACTTTTCCATTAGCCTATAAAAAGTGG
46763 CACTTTTCCATTAGCCTATAAAAAGTGG
1 CACTTTTCCATTAGCCTATAAAAAGTGG
46791 CACTTTTCC
1 CACTTTTCC
46800 CCCTTTTTGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (28 bp):
CACTTTTCCATTAGCCTATAAAAAGTGG
Found at i:50464 original size:24 final size:25
Alignment explanation
Indices: 50414--50467 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
50404 GTTTTATGTT
* * * *
50414 TTATATATTTATTTTGTTTGTATTA
1 TTATATATTTACTTTGTATATAATA
50439 TTATATA-TTACTTTGTATATAATA
1 TTATATATTTACTTTGTATATAATA
50463 TTATA
1 TTATA
50468 GCATGATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
TTATATATTTACTTTGTATATAATA
Found at i:63768 original size:104 final size:104
Alignment explanation
Indices: 63508--64012 Score: 785
Period size: 104 Copynumber: 4.8 Consensus size: 104
63498 AAATCCACTG
*
63508 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
*
63573 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATCCACC
66 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
* *
63612 ACAGAAGGAGGTGACCCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAGA
1 -CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGA
* *
63677 AGGTTCATAATAAGAAGAGCATGTTCCTTTCAAATTCACC
65 AGGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
* *
63717 CAGAAGGAGGTGAACCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
* *
63782 GGTTCGTAATGAGAAGAGCCTGTTCCTTTTAAATTCACC
66 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
* *
63821 CAGAAGGAGGTGAACCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
* * *
63886 GGTTTGTAATGAGAAGAACTTGTTCCTTTCAAATTCACCC
66 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCA-CC
* *
63926 CAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAACAAAAGGA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCAT-C--CTAAAGGA
*
63991 GAAGAAGTTCATAATGAGAAGA
63 GAAG--GTTCGTAATGAGAAGA
64013 ACTTGTTCAA
Statistics
Matches: 368, Mismatches: 26, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
104 192 0.52
105 150 0.41
106 1 0.00
108 11 0.03
110 14 0.04
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.21
Consensus pattern (104 bp):
CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAA
GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATTCACC
Found at i:63930 original size:209 final size:209
Alignment explanation
Indices: 63508--63980 Score: 786
Period size: 209 Copynumber: 2.3 Consensus size: 209
63498 AAATCCACTG
* *
63508 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAA
*
63573 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATCCACCACAGAAGGAGGTGACCCAACATTTCC
66 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAACATTTCC
*
63638 AGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAGAAGGTTCATAATAAGAAGAGCATGTTC
131 AGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAGAAGGTTCATAATAAGAAGAACATGTTC
63703 CTTTCAAATTCACC
196 CTTTCAAATTCACC
*
63717 CAGAAGGAGGTGAACCGACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAA
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAA
* * * *
63782 GGTTCGTAATGAGAAGAGCCTGTTCCTTTTAAATTCACC-CAGAAGGAGGTGAACCGACATTTCC
66 GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAACATTTCC
* * ** * *
63846 AGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAGGTTTGTAATGAGAAGAACTTGTTC
131 AGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAGAAGGTTCATAATAAGAAGAACATGTTC
63911 CTTTCAAATTCACCC
196 CTTTCAAATTCA-CC
*
63926 CAGAAGGAGGTGAATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCC
1 CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCC
63981 AACAAAAGGA
Statistics
Matches: 246, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
208 93 0.38
209 153 0.62
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.22
Consensus pattern (209 bp):
CAGAAGGAGGTGAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGAAGAA
GGTTCGTAATGAGAAGAGCATGTTCCTTTCAAATCCACCACAGAAGGAGGTGAACCAACATTTCC
AGAAGAGTTCATAATGAGAAGAACTCATCCAAAAGGAGAAGGTTCATAATAAGAAGAACATGTTC
CTTTCAAATTCACC
Found at i:64266 original size:136 final size:134
Alignment explanation
Indices: 63939--64436 Score: 529
Period size: 136 Copynumber: 3.7 Consensus size: 134
63929 AAGGAGGTGA
* * * *
63939 ATCAACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCCAACAAAAGGAGAAGAAGTTCAT
1 ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCAT
**
64003 AATGAGAAGAACTTGTTCAACCT-TAGCTCGATTCATCGCATATGGAGTTGAATCAACAACACCT
66 AATGAGAAGAACTTGTTCAACCTATA-CTCGATTCATAACAT-T----TTGAATCAACAACACCT
*
64067 CACTTGAGGG
125 CGCTTGAGGG
* * *
64077 ATCAACACTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAAAGGGAGAAGAAGTTTA
1 ATCAACATTTC-AATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCA
* * * * * *** *
64142 TAATGATAAGAGCTTGTTCGACCTATCACTTGATTCATTACATTTTGAATCAGTGACGCCTCGCT
65 TAATGAGAAGAACTTGTTCAACCTAT-ACTCGATTCATAACATTTTGAATCAACAACACCTCGCT
64207 TGAGGG
129 TGAGGG
* * *
64213 AAT-GACATTTCATATGGAGAGTTCATAATGAGAAGAACTCATCTGACAGAGGGAGAAGAAGTTC
1 -ATCAACATTTCA-ATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTC
* * * * * * *
64277 ATAATGAGAAGAGCTTGTTCGACCTATTGCTCGATTCACAACACTTCGAATCAACAATACCTCGC
64 ATAATGAGAAGAACTTGTTCAACCTA-TACTCGATTCATAACATTTTGAATCAACAACACCTCGC
*
64342 TTGAAGG
128 TTGAGGG
* * **
64349 ATCAACATTTTCAGTGGAGAGTTCATAATGAGAAGAACTTATCCGA-TGAGAGGA-AAGAAGTTC
1 ATCAACA-TTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAG-GGAGAAGAAGTTC
*
64412 GTAATGAGAAGAACTTGTTCAACCT
64 ATAATGAGAAGAACTTGTTCAACCT
64437 TAACTTGTTT
Statistics
Matches: 305, Mismatches: 45, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
135 37 0.12
136 168 0.55
137 8 0.03
138 10 0.03
139 1 0.00
140 67 0.22
141 13 0.04
142 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (134 bp):
ATCAACATTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAAAGGGAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACCTATACTCGATTCATAACATTTTGAATCAACAACACCTCGCTTG
AGGG
Found at i:66066 original size:24 final size:25
Alignment explanation
Indices: 66016--66069 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
66006 GTTTTATGTT
* * * *
66016 TTATATATTTATTTTGTTTGTATTA
1 TTATATATTTACTTTGTATATAATA
66041 TTATATA-TTACTTTGTATATAATA
1 TTATATATTTACTTTGTATATAATA
66065 TTATA
1 TTATA
66070 GCATGATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
TTATATATTTACTTTGTATATAATA
Found at i:68262 original size:20 final size:20
Alignment explanation
Indices: 68237--68278 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
68227 AGCTGTGCAT
*
68237 CATATCCAATC-TTATACGTG
1 CATAT-CAATCGTTATACATG
68257 CATATCAATCGTTATACATG
1 CATATCAATCGTTATACATG
68277 CA
1 CA
68279 AACCATCAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.33
Consensus pattern (20 bp):
CATATCAATCGTTATACATG
Found at i:70170 original size:2 final size:2
Alignment explanation
Indices: 70163--70222 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
70153 ACCATATAAG
70163 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
70205 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
70223 CTTCATATTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76132 original size:15 final size:13
Alignment explanation
Indices: 76099--76123 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76089 ACTTGATTTG
76099 AATTTTATGTTTC
1 AATTTTATGTTTC
76112 AATTTTATGTTT
1 AATTTTATGTTT
76124 ATCAATTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (13 bp):
AATTTTATGTTTC
Found at i:83497 original size:27 final size:25
Alignment explanation
Indices: 83458--83508 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
83448 AACCAACACA
83458 TAAATGTTAATATTATTCATAATTTTTT
1 TAAATGTTAATA-TATT-AT-ATTTTTT
83486 TAAAT-TTAATATATTATATTTTT
1 TAAATGTTAATATATTATATTTTT
83509 GAGTTGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 6 0.26
25 2 0.09
26 4 0.17
27 6 0.26
28 5 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TAAATGTTAATATATTATATTTTTT
Found at i:83529 original size:20 final size:20
Alignment explanation
Indices: 83504--83554 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
83494 ATATATTATA
* *
83504 TTTTTGAGTTGCTCACGAAC
1 TTTTTGAATCGCTCACGAAC
*
83524 TTTTTGAATCGCTCACGAGC
1 TTTTTGAATCGCTCACGAAC
83544 TTTTTGAATCG
1 TTTTTGAATCG
83555 AGTATCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TTTTTGAATCGCTCACGAAC
Found at i:84044 original size:243 final size:244
Alignment explanation
Indices: 83615--84275 Score: 1009
Period size: 244 Copynumber: 2.7 Consensus size: 244
83605 AACAGTTGGC
* * *
83615 ATAATTACATATCTAACCACTGACACTTGCATATTATTTTAATTTGTTCATAATTTTAATAAATT
1 ATAATTACACATCTAATCACTGACACTTACATATTATTTTAATTTGTTCATAATTTTAATAAATT
* * * * * *
83680 AAAATAAATTTTAATTATTGAATCAAATGAAACCTTGTGTCATCATTCAATTGAAGGAATAATTA
66 AAAATAAA-TTTAATCATCGAATCAGATGAAATCATGTGTCATCATCCAATTGAAGGAATAATTA
* * *
83745 TATTTTAATTTATTTTTAATTCAATATACTTTCAATCAATCATAGGGTGACATGTGTCATCC-GA
130 TATTTTAATTTATTTTTAATTCAATATACTTTCAACCAATCATAGGGTGACATGTGTCACCCTAA
* *
83809 GGTGGAAAGAAAATAAAGCACATCAAATGTAAGCAAAAGGGTTCAAACTT
195 GGTGGAAAGAAAATAAAACACATCAAATGTAAGCAAAAGGGTTCAAACCT
* *
83859 ATAATTACACGTCTAATCACTGACACTTATATATTATTTTAATTTGTTCATAATTTTAATAAATT
1 ATAATTACACATCTAATCACTGACACTTACATATTATTTTAATTTGTTCATAATTTTAATAAATT
* *
83924 AAAATAAATTTAATCATCGAATCAGATGAAGTCATGTGTCCTCATCCAATTGAAGGAATAATTAT
66 AAAATAAATTTAATCATCGAATCAGATGAAATCATGTGTCATCATCCAATTGAAGGAATAATTAT
**
83989 ATTTTAATTTATTTTTAATTTGATATACTTTCAACCAATCATAGGGTGACATGTGTCACCCTAAG
131 ATTTTAATTTATTTTTAATTCAATATACTTTCAACCAATCATAGGGTGACATGTGTCACCCTAAG
* *
84054 GTGGAAAGAAAATAAAACACATCAAATGTAAGCAAATGGGTTCGAACCT
196 GTGGAAAGAAAATAAAACACATCAAATGTAAGCAAAAGGGTTCAAACCT
* * * *
84103 ATAATTACACATCTAATCACTGACATTTACATATTATTTTAACTTGGTCATAATTTTAACAAATT
1 ATAATTACACATCTAATCACTGACACTTACATATTATTTTAATTTGTTCATAATTTTAATAAATT
* * * * *
84168 TAAATAAATTTTATCATCAAATTAGATGAAATCATGTGTCATCATCGAATTGAAGGAATAATTAT
66 AAAATAAATTTAATCATCGAATCAGATGAAATCATGTGTCATCATCCAATTGAAGGAATAATTAT
* *
84233 ATTTTAATTTATTTTTAATTCAATACACTTTTAACCAATCATA
131 ATTTTAATTTATTTTTAATTCAATATACTTTCAACCAATCATA
84276 TGTCACCCTG
Statistics
Matches: 377, Mismatches: 39, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
243 106 0.28
244 271 0.72
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.37
Consensus pattern (244 bp):
ATAATTACACATCTAATCACTGACACTTACATATTATTTTAATTTGTTCATAATTTTAATAAATT
AAAATAAATTTAATCATCGAATCAGATGAAATCATGTGTCATCATCCAATTGAAGGAATAATTAT
ATTTTAATTTATTTTTAATTCAATATACTTTCAACCAATCATAGGGTGACATGTGTCACCCTAAG
GTGGAAAGAAAATAAAACACATCAAATGTAAGCAAAAGGGTTCAAACCT
Found at i:84529 original size:30 final size:30
Alignment explanation
Indices: 84492--84647 Score: 171
Period size: 30 Copynumber: 5.4 Consensus size: 30
84482 TAACATTTAA
* *
84492 AAAATATATTTTATTTTTATCTTAACTTAT
1 AAAATATATTTTACTTTTATTTTAACTTAT
* * *
84522 TAAATATATTTTATTTTTATTTTAGCTTA-
1 AAAATATATTTTACTTTTATTTTAACTTAT
* * *
84551 AAAATATATTTTAATCTTATTTTAGC-T-T
1 AAAATATATTTTACTTTTATTTTAACTTAT
* *
84579 AAAA-GTATTTTACTTTTATCTTAACTTAT
1 AAAATATATTTTACTTTTATTTTAACTTAT
84608 AAAATATATTTTACTTTTATTTTAA-TT-T
1 AAAATATATTTTACTTTTATTTTAACTTAT
*
84636 AAGATATATTTT
1 AAAATATATTTT
84648 TATAAGTTAA
Statistics
Matches: 108, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
27 16 0.15
28 18 0.17
29 30 0.28
30 44 0.41
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (30 bp):
AAAATATATTTTACTTTTATTTTAACTTAT
Found at i:84767 original size:2 final size:2
Alignment explanation
Indices: 84755--84787 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
84745 TTACACAGTG
84755 AT AT A- 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
84788 GAAAGTACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85125 original size:35 final size:35
Alignment explanation
Indices: 85085--85154 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 35
85075 CAAGACCCTT
85085 TTTCGTAAAATATC-TACTACTAATACAATACAATA
1 TTTCGTAAAATATCGT-CTACTAATACAATACAATA
* *
85120 TTTCGTAAAATCTCGTCTACTAATACAATAGAATA
1 TTTCGTAAAATATCGTCTACTAATACAATACAATA
85155 AGTTTCTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 31 0.97
36 1 0.03
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (35 bp):
TTTCGTAAAATATCGTCTACTAATACAATACAATA
Found at i:85535 original size:54 final size:54
Alignment explanation
Indices: 85476--85585 Score: 202
Period size: 54 Copynumber: 2.0 Consensus size: 54
85466 TATTTTAATT
*
85476 TATTAAAATTAAGATTAAATTAATATAATATGTAAGTATCAATTATTAGATGTG
1 TATTAAAATTAAGATTAAATTAATATAATATGTAAGTATCAATGATTAGATGTG
*
85530 TATTAAAATTAGGATTAAATTAATATAATATGTAAGTATCAATGATTAGATGTG
1 TATTAAAATTAAGATTAAATTAATATAATATGTAAGTATCAATGATTAGATGTG
85584 TA
1 TA
85586 ATTATACTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.45, C:0.02, G:0.13, T:0.40
Consensus pattern (54 bp):
TATTAAAATTAAGATTAAATTAATATAATATGTAAGTATCAATGATTAGATGTG
Found at i:85858 original size:63 final size:63
Alignment explanation
Indices: 85791--85916 Score: 191
Period size: 63 Copynumber: 2.0 Consensus size: 63
85781 TTCAAACTAA
* * * * *
85791 ACCGAATTCGATCTTTTTATAT-GAAAAATGCTTCAACTCTGTAAAATTAAATCAAATTAAAAT
1 ACCGAATTCAATCTCTTTATATAGAAAAA-ACTTCAACTCTCTAAAATTAAATCAAATCAAAAT
85854 ACCGAATTCAATCTCTTTATATAGAAAAAACTTCAACTCTCTAAAATTAAATCAAATCAAAAT
1 ACCGAATTCAATCTCTTTATATAGAAAAAACTTCAACTCTCTAAAATTAAATCAAATCAAAAT
85917 TTAATAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
63 51 0.89
64 6 0.11
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.33
Consensus pattern (63 bp):
ACCGAATTCAATCTCTTTATATAGAAAAAACTTCAACTCTCTAAAATTAAATCAAATCAAAAT
Found at i:87434 original size:29 final size:29
Alignment explanation
Indices: 87349--87434 Score: 131
Period size: 28 Copynumber: 3.0 Consensus size: 29
87339 TAGGATTATA
* *
87349 TTTTTCACACTTAGGTCCCTAGACTTTAA
1 TTTTTTACACTTAGGTCCCTAGACTTTAG
87378 TTTTTTACA-TATAGG-CCCTAGACTTTAG
1 TTTTTTACACT-TAGGTCCCTAGACTTTAG
87406 TTTTTTACACTTAGGTCCCTAGACTTTAG
1 TTTTTTACACTTAGGTCCCTAGACTTTAG
87435 AGTTCTCACA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
28 26 0.50
29 26 0.50
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (29 bp):
TTTTTTACACTTAGGTCCCTAGACTTTAG
Found at i:93353 original size:29 final size:29
Alignment explanation
Indices: 93300--93393 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
93290 TAGTTCTGCC
* *
93300 ATTCTGCATAGGACTTTGTTTCCCATTCTG
1 ATTCTGCATGGGACTTT-TTTCCCATCCTG
* *
93330 ATTTTGTATGGGACTTTTTTCCCATCCTG
1 ATTCTGCATGGGACTTTTTTCCCATCCTG
* * *
93359 ATTCTGCATGAGATTTTTTTCCCTGTCCTG
1 ATTCTGCATGGGACTTTTTTCCC-ATCCTG
93389 ATTCT
1 ATTCT
93394 TCATCAATAT
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 30 0.56
30 24 0.44
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (29 bp):
ATTCTGCATGGGACTTTTTTCCCATCCTG
Found at i:93406 original size:29 final size:30
Alignment explanation
Indices: 93345--93410 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
93335 GTATGGGACT
* *
93345 TTTTTCCC-ATCCTGATTCTGCATGAGATT
1 TTTTTCCCTATCCTGATTCTGCATCAGATA
* *
93374 TTTTTCCCTGTCCTGATTCTTCATCA-ATA
1 TTTTTCCCTATCCTGATTCTGCATCAGATA
93403 -TTTTCCCT
1 TTTTTCCCT
93411 TCTCTGTTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 8 0.25
29 10 0.31
30 14 0.44
ACGTcount: A:0.15, C:0.27, G:0.09, T:0.48
Consensus pattern (30 bp):
TTTTTCCCTATCCTGATTCTGCATCAGATA
Found at i:93492 original size:28 final size:28
Alignment explanation
Indices: 93412--93479 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
93402 ATTTTCCCTT
*
93412 CTCTGTTCTGTACGAGATTTGTTCCCCG
1 CTCTGTTCTGTACGAGATTTGTTCCCCA
*
93440 CTCTGTTCTGTACAAGATTTGTTCCCCA
1 CTCTGTTCTGTACGAGATTTGTTCCCCA
*
93468 CTCTGTTATGTA
1 CTCTGTTCTGTA
93480 TGGGATTCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.15, C:0.26, G:0.18, T:0.41
Consensus pattern (28 bp):
CTCTGTTCTGTACGAGATTTGTTCCCCA
Found at i:95013 original size:24 final size:23
Alignment explanation
Indices: 94966--95013 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
94956 ATTAAATAGA
**
94966 TATTTTATTTATATTTTATGATT
1 TATTTTATTTATATTTTAAAATT
94989 TATTTTATTTTATATTTTAAAATT
1 TATTTTA-TTTATATTTTAAAATT
95013 T
1 T
95014 TATATTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTTATTTATATTTTAAAATT
Found at i:95768 original size:23 final size:23
Alignment explanation
Indices: 95717--95780 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 23
95707 CAATTTGTAT
* *
95717 TTTTTAAAA-ATAATTAAAAATA
1 TTTTTAAAATAAAATTTAAAATA
**
95739 -TAGTAAAATAAAATTTAAAATA
1 TTTTTAAAATAAAATTTAAAATA
* *
95761 TTTTTAAAATTAAATCTAAA
1 TTTTTAAAATAAAATTTAAA
95781 CCGGACTGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
21 6 0.19
22 11 0.34
23 15 0.47
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTTTAAAATAAAATTTAAAATA
Found at i:96326 original size:19 final size:19
Alignment explanation
Indices: 96284--96327 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
96274 GTATTAATAT
* *
96284 AAAATTGTTTACAAAGTAA
1 AAAATTATTTACAAACTAA
*
96303 AAAATTATTTACAATCTAA
1 AAAATTATTTACAAACTAA
*
96322 TAAATT
1 AAAATT
96328 TTATTTATGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (19 bp):
AAAATTATTTACAAACTAA
Found at i:96837 original size:12 final size:12
Alignment explanation
Indices: 96817--96855 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
96807 TTTGGTGTTG
*
96817 AAAACAAGATTA
1 AAAATAAGATTA
96829 AAAATAAGATTA
1 AAAATAAGATTA
96841 AAAA-AAGA-TA
1 AAAATAAGATTA
96851 AAAAT
1 AAAAT
96856 TTGCAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
10 6 0.24
11 4 0.16
12 15 0.60
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (12 bp):
AAAATAAGATTA
Done.