Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 121 of 226
Found at i:40956825 original size:40 final size:40
Alignment explanation
Indices: 40956741--40956894 Score: 158
Period size: 39 Copynumber: 3.9 Consensus size: 40
40956731 AAGGAGAGGG
*
40956741 AAAGAAAGAAAGAAAG-AAA-GAAAGGAG-AG-GAAAGAAA
1 AAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA-AAA
*
40956778 GAA-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
1 AAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
* *
40956817 AAAGAAAGAAAGAAGAAGAAGAAAAGGAAAAGAGAAGA-AAAAAG
1 AAAGAAAG-AAG--G-A-AAGAAAAGGAAAGGAGAAGAGAAAAAA
* *
40956861 AAAGAAAGAAGGAAAGAAAAGAAAAGAAGAAGAG
1 AAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAG
40956895 GGAAGGAATG
Statistics
Matches: 98, Mismatches: 8, Indels: 19
0.78 0.06 0.15
Matches are distributed among these distances:
36 11 0.11
37 5 0.05
38 8 0.08
39 24 0.24
40 9 0.09
41 4 0.04
43 4 0.04
44 14 0.14
45 19 0.19
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (40 bp):
AAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAAAA
Found at i:40956886 original size:18 final size:17
Alignment explanation
Indices: 40956740--40956889 Score: 116
Period size: 18 Copynumber: 8.8 Consensus size: 17
40956730 GAAGGAGAGG
*
40956740 GAAAG-AAAGAAAGAAA
1 GAAAGAAAAGAAGGAAA
*
40956756 GAAAGAAAGGAGAGGAAA
1 GAAAGAAAAGA-AGGAAA
40956774 GAAAGAAAAAGAAGGAAA
1 GAAAG-AAAAGAAGGAAA
* *
40956792 GAAAAGGAAAGGA-GAAGA
1 G-AAAGAAAAGAAGGAA-A
40956810 GAAA-AAAA-AA-GAAA
1 GAAAGAAAAGAAGGAAA
*
40956824 GAAAGAAGAAGAAGAAAA
1 GAAAGAA-AAGAAGGAAA
* *
40956842 GGAAAAGAGAAGAA-AAAA
1 -G-AAAGAAAAGAAGGAAA
40956860 GAAAG-AAAGAAGGAAA
1 GAAAGAAAAGAAGGAAA
40956876 GAAAAGAAAAGAAG
1 G-AAAGAAAAGAAG
40956890 AAGAGGGAAG
Statistics
Matches: 109, Mismatches: 11, Indels: 26
0.75 0.08 0.18
Matches are distributed among these distances:
14 5 0.05
15 11 0.10
16 18 0.17
17 17 0.16
18 38 0.35
19 15 0.14
20 5 0.05
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAGAAGGAAA
Found at i:40963563 original size:3 final size:3
Alignment explanation
Indices: 40963555--40963580 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40963545 TCTTAATACT
40963555 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
40963581 TAATAATAAT
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:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:40963895 original size:27 final size:27
Alignment explanation
Indices: 40963839--40963896 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
40963829 CCAAACAATA
***
40963839 TGGCACCATTGGTGCCGCCAATGGTTT
1 TGGCACCATTGGTGCCGCCAATGCCAT
*
40963866 TGGCACCTTTGGTGCCGCCAATGCCAT
1 TGGCACCATTGGTGCCGCCAATGCCAT
40963893 TGGC
1 TGGC
40963897 GTGACCAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGCACCATTGGTGCCGCCAATGCCAT
Found at i:40963980 original size:27 final size:29
Alignment explanation
Indices: 40963944--40964014 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 29
40963934 TGTTTTTTTG
40963944 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
40963971 ATATATTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
40964000 A-ATATTTTGGTAAAT
1 ATATATTTTGGTAAAT
40964015 TTTTATTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 16 0.38
28 21 0.50
29 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:40966759 original size:41 final size:41
Alignment explanation
Indices: 40966710--40966880 Score: 211
Period size: 41 Copynumber: 4.2 Consensus size: 41
40966700 AAAATGAGCA
*
40966710 TTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTAGTCT
* * * * * *
40966751 TTAGCGGCGTTTTTGAAGAAGTGCCGCGAAAGACCCAAG-CA
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATG-CTCTAGTCT
*
40966792 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTAGTCT
* * *
40966833 TTAGCGGCGTTTTTAAAGAAGCGCTGCTAATGCTC-AGGGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTA-GTCT
40966874 TTAGCGG
1 TTAGCGG
40966881 ATTTTTTTTA
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
40 3 0.03
41 102 0.94
42 4 0.04
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTAGTCT
Found at i:40966903 original size:82 final size:82
Alignment explanation
Indices: 40966706--40966856 Score: 266
Period size: 82 Copynumber: 1.8 Consensus size: 82
40966696 GCTAAAAATG
*
40966706 AGCATTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTGAAGAA
1 AGCATTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTAAAGAA
*
40966771 GTGCCGCGAAAGACCCA
66 GCGCCGCGAAAGACCCA
* *
40966788 AGCATTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCTGGTCTTTAGCGGCGTTTTTAAAGAA
1 AGCATTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTAAAGAA
40966853 GCGC
66 GCGC
40966857 TGCTAATGCT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (82 bp):
AGCATTAGCGGCGTTTTTTAAGAAGCGCCGCTAATGCTCTAGTCTTTAGCGGCGTTTTTAAAGAA
GCGCCGCGAAAGACCCA
Found at i:40967223 original size:14 final size:15
Alignment explanation
Indices: 40967190--40967240 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
40967180 AGGGTTTTTA
*
40967190 GTTTAGGGAGTATGG
1 GTTTAAGGAGTATGG
*
40967205 GTTTAAGGATTAT-G
1 GTTTAAGGAGTATGG
40967219 GTTTAAGG-GT-TGG
1 GTTTAAGGAGTATGG
40967232 GATTTAAGG
1 G-TTTAAGG
40967241 TTTAAGAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 1 0.03
13 3 0.10
14 16 0.52
15 11 0.35
ACGTcount: A:0.24, C:0.00, G:0.39, T:0.37
Consensus pattern (15 bp):
GTTTAAGGAGTATGG
Found at i:40967274 original size:15 final size:16
Alignment explanation
Indices: 40967248--40967290 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
40967238 AGGTTTAAGA
40967248 GTTAGAGGGTTAGAGGT
1 GTTAG-GGGTTAGAGGT
*
40967265 -TTAGGGGTTAGATGT
1 GTTAGGGGTTAGAGGT
40967280 GTTAGGGGTTA
1 GTTAGGGGTTA
40967291 AAAGTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (16 bp):
GTTAGGGGTTAGAGGT
Found at i:40967494 original size:15 final size:15
Alignment explanation
Indices: 40967474--40967505 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40967464 TATTTTAAGG
40967474 TTTAGGGAGTATGGA
1 TTTAGGGAGTATGGA
*
40967489 TTTAGGGATTATGGA
1 TTTAGGGAGTATGGA
40967504 TT
1 TT
40967506 AGCAATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.34, T:0.41
Consensus pattern (15 bp):
TTTAGGGAGTATGGA
Found at i:40970540 original size:15 final size:17
Alignment explanation
Indices: 40970506--40970543 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
40970496 TAATTTATTT
40970506 ATTTTTATTATTTTAGA
1 ATTTTTATTATTTTAGA
*
40970523 ATTTTTA-TA-TTTATA
1 ATTTTTATTATTTTAGA
40970538 ATTTTT
1 ATTTTT
40970544 TTTCCTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTTATTATTTTAGA
Found at i:40971656 original size:27 final size:27
Alignment explanation
Indices: 40971626--40971681 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
40971616 AATTTCGAGG
*
40971626 TTTACAATTTT-TAATTTTTATTAATTA
1 TTTAC-ATTTTCTAACTTTTATTAATTA
* *
40971653 TTTACGTTTTCTCACTTTTATTAATTA
1 TTTACATTTTCTAACTTTTATTAATTA
40971680 TT
1 TT
40971682 ATTATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (27 bp):
TTTACATTTTCTAACTTTTATTAATTA
Found at i:40974743 original size:21 final size:21
Alignment explanation
Indices: 40974705--40974745 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40974695 CTAAGGTCTC
*
40974705 ATTATTTAAGAATTAAATAAA
1 ATTATTTAAGAATAAAATAAA
40974726 ATTATTTACA-AATAAAATAA
1 ATTATTTA-AGAATAAAATAA
40974746 TACATCAGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATTATTTAAGAATAAAATAAA
Found at i:40975820 original size:14 final size:14
Alignment explanation
Indices: 40975801--40975828 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40975791 GAAGATAACC
40975801 ATATTATACCACAT
1 ATATTATACCACAT
40975815 ATATTATACCACAT
1 ATATTATACCACAT
40975829 GGACATCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATTATACCACAT
Found at i:40978197 original size:148 final size:148
Alignment explanation
Indices: 40977929--40978207 Score: 461
Period size: 148 Copynumber: 1.9 Consensus size: 148
40977919 ATAAAAGCAT
*
40977929 TGGCAGACAATAACCAAACACTTTAGTAAAACCTAGGCAATGACAGACAATAACCAATACAAAAA
1 TGGCAGACAATAACCAAACACTTTAATAAAACCTAGGCAATGACAGACAATAACCAATACAAAAA
* * *
40977994 CAATTTAATATAAACAAATCCAATTTTTTCATGTACAATAACCAAATAATTTAATACAAACAAAT
66 CAATTTAATAGAAACAAATACAATTTTTTCATGTACAATAACCAAACAATTTAATACAAACAAAT
40978059 CCATTTTTGTTATACACA
131 CCATTTTTGTTATACACA
* *
40978077 TGGCAGACAATAACCAAACACTTTAATACAACCTAGGCAATGGCAGACAATAACCAATACAAAAA
1 TGGCAGACAATAACCAAACACTTTAATAAAACCTAGGCAATGACAGACAATAACCAATACAAAAA
***
40978142 CAATTTAATAGATTGAAATAC-ATTTTTGTCATGTACAATAACCAAACAATTTAATACAAACAAA
66 CAATTTAATAGAAACAAATACAATTTTT-TCATGTACAATAACCAAACAATTTAATACAAACAAA
40978206 TC
130 TC
40978208 TAAAACAATG
Statistics
Matches: 121, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
147 6 0.05
148 115 0.95
ACGTcount: A:0.48, C:0.19, G:0.08, T:0.25
Consensus pattern (148 bp):
TGGCAGACAATAACCAAACACTTTAATAAAACCTAGGCAATGACAGACAATAACCAATACAAAAA
CAATTTAATAGAAACAAATACAATTTTTTCATGTACAATAACCAAACAATTTAATACAAACAAAT
CCATTTTTGTTATACACA
Found at i:40985803 original size:30 final size:29
Alignment explanation
Indices: 40985740--40985815 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
40985730 GGTATGTGTA
* * * *
40985740 TATATACAATATATATTCGTGGGTTTTAT
1 TATATATAACATATATGCGTGGGTTTGAT
*
40985769 TATATATGACATATATGCGTGGGTCTTGAT
1 TATATATAACATATATGCGTGGGT-TTGAT
*
40985799 TATATATAATATATATG
1 TATATATAACATATATG
40985816 TATATATGGG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 20 0.51
30 19 0.49
ACGTcount: A:0.33, C:0.07, G:0.16, T:0.45
Consensus pattern (29 bp):
TATATATAACATATATGCGTGGGTTTGAT
Found at i:40986821 original size:17 final size:17
Alignment explanation
Indices: 40986779--40986830 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
40986769 TATGATGTGG
*
40986779 TATGAATGAATTGTTA-
1 TATGAATGAACTGTTAT
40986795 TATTGAATGAACTGTTAT
1 TA-TGAATGAACTGTTAT
* *
40986813 TATGCATGAACTATTAT
1 TATGAATGAACTGTTAT
40986830 T
1 T
40986831 TCATATGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.06
17 27 0.87
18 2 0.06
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (17 bp):
TATGAATGAACTGTTAT
Found at i:40987921 original size:29 final size:29
Alignment explanation
Indices: 40987884--40987977 Score: 172
Period size: 29 Copynumber: 3.3 Consensus size: 29
40987874 TTATTGTTTG
40987884 CTTCTTAGCATGCCAATTTTTGACTATTT
1 CTTCTTAGCATGCCAATTTTTGACTATTT
*
40987913 CTTCTTAGCACGCCAATTTTTGACTATTT
1 CTTCTTAGCATGCCAATTTTTGACTATTT
40987942 CTTCTTAGCATGCCAATTTTTGACTATTT
1 CTTCTTAGCATGCCAATTTTTGACTATTT
40987971 CTT-TTAG
1 CTTCTTAG
40987978 GTTTGTGGCG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
28 4 0.06
29 59 0.94
ACGTcount: A:0.20, C:0.21, G:0.11, T:0.48
Consensus pattern (29 bp):
CTTCTTAGCATGCCAATTTTTGACTATTT
Found at i:40998796 original size:41 final size:41
Alignment explanation
Indices: 40998751--40998939 Score: 252
Period size: 41 Copynumber: 4.6 Consensus size: 41
40998741 CAAGTGAGAT
* *
40998751 AATTCAGACTCTATGTCTAGTAGGCTGGATGCCGGTGAAAC
1 AATTCAGACTTTATGTCTAGCAGGCTGGATGCCGGTGAAAC
* * *
40998792 AATTCAAACTCTAAGTCTAGCAGGCTGGATGCCGGTGAAAC
1 AATTCAGACTTTATGTCTAGCAGGCTGGATGCCGGTGAAAC
* * *
40998833 AATTCAGACTTTATGTCTAGCAAGCTTGATGCTGGTGAAAC
1 AATTCAGACTTTATGTCTAGCAGGCTGGATGCCGGTGAAAC
* * *
40998874 AATTTAGACTTTATGTCTAGCAGGCTTGATGCTGGTGAAAC
1 AATTCAGACTTTATGTCTAGCAGGCTGGATGCCGGTGAAAC
* * *
40998915 ATTTCGGACTTTAAGTCTAGCAGGC
1 AATTCAGACTTTATGTCTAGCAGGC
40998940 CAAAAGCCGG
Statistics
Matches: 133, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (41 bp):
AATTCAGACTTTATGTCTAGCAGGCTGGATGCCGGTGAAAC
Found at i:41011303 original size:15 final size:16
Alignment explanation
Indices: 41011275--41011304 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41011265 GTTTATGTTA
41011275 AGTAAATGAAATGGAC
1 AGTAAATGAAATGGAC
41011291 AGTAAAT-AAATGGA
1 AGTAAATGAAATGGA
41011305 ATGATAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.20
Consensus pattern (16 bp):
AGTAAATGAAATGGAC
Found at i:41012355 original size:14 final size:13
Alignment explanation
Indices: 41012334--41012380 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
41012324 TTTAGAAATG
41012334 TATGTTTTTAAGT
1 TATGTTTTTAAGT
*
41012347 TATGTTTTTACAAT
1 TATGTTTTTA-AGT
*
41012361 AATGCTTTTTAAGT
1 TATG-TTTTTAAGT
41012375 TATGTT
1 TATGTT
41012381 CTTACAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 12 0.43
14 10 0.36
15 6 0.21
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (13 bp):
TATGTTTTTAAGT
Found at i:41012370 original size:28 final size:28
Alignment explanation
Indices: 41012338--41012394 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
41012328 GAAATGTATG
*
41012338 TTTTTAAGTTATGTTTTTACAATAATGC
1 TTTTTAAGTTATGTTCTTACAATAATGC
41012366 TTTTTAAGTTATGTTCTTACAATAATGC
1 TTTTTAAGTTATGTTCTTACAATAATGC
41012394 T
1 T
41012395 CCGTAACCCT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.53
Consensus pattern (28 bp):
TTTTTAAGTTATGTTCTTACAATAATGC
Found at i:41018590 original size:12 final size:12
Alignment explanation
Indices: 41018573--41018601 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41018563 ATACATTTGG
41018573 GCCTTAAATCAA
1 GCCTTAAATCAA
41018585 GCCTTAAATCAA
1 GCCTTAAATCAA
41018597 GCCTT
1 GCCTT
41018602 CGAGGCCCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.34, C:0.28, G:0.10, T:0.28
Consensus pattern (12 bp):
GCCTTAAATCAA
Found at i:41019858 original size:23 final size:23
Alignment explanation
Indices: 41019828--41019873 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
41019818 ACTATATTAA
41019828 CATGCTATACCAATTCATTCATT
1 CATGCTATACCAATTCATTCATT
41019851 CATGCTATACCAATTCATTCATT
1 CATGCTATACCAATTCATTCATT
41019874 ACCCATACTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.39
Consensus pattern (23 bp):
CATGCTATACCAATTCATTCATT
Found at i:41020423 original size:21 final size:21
Alignment explanation
Indices: 41020370--41020458 Score: 61
Period size: 21 Copynumber: 4.2 Consensus size: 21
41020360 AGACTGCATA
* * * *
41020370 GAAGCACATAAGTGCTAAATG
1 GAAGCCCATAAGGGTTAAACG
* *
41020391 GAAACCCGTAAGGGTTAAACG
1 GAAGCCCATAAGGGTTAAACG
** * * *
41020412 GAAGGTCATAAGAGCTGAACG
1 GAAGCCCATAAGGGTTAAACG
* *
41020433 GAAACCCATAAGGGTTAAACT
1 GAAGCCCATAAGGGTTAAACG
41020454 GAAGC
1 GAAGC
41020459 TCAAAAGAGA
Statistics
Matches: 47, Mismatches: 21, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.27, T:0.16
Consensus pattern (21 bp):
GAAGCCCATAAGGGTTAAACG
Found at i:41020436 original size:42 final size:42
Alignment explanation
Indices: 41020370--41020505 Score: 139
Period size: 42 Copynumber: 3.2 Consensus size: 42
41020360 AGACTGCATA
* * * *
41020370 GAAGCACATAAGTGCTAAATGGAAACCCGTAAGGGTTAAACG
1 GAAGCTCATAAGAGCTGAACGGAAACCCGTAAGGGTTAAACG
* * *
41020412 GAAGGTCATAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACGGAAACCCGTAAGGGTTAAACG
* * ** *
41020454 GAAGCTCAAAAGAGATGAACTAAAACCCAG-AAGGGTTAAACT
1 GAAGCTCATAAGAGCTGAACGGAAACCC-GTAAGGGTTAAACG
*
41020496 GAAACTCATA
1 GAAGCTCATA
41020506 TGAGTTAACT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
42 78 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (42 bp):
GAAGCTCATAAGAGCTGAACGGAAACCCGTAAGGGTTAAACG
Found at i:41020500 original size:21 final size:21
Alignment explanation
Indices: 41020433--41020500 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
41020423 GAGCTGAACG
*
41020433 GAAACCCATAAGGGTTAAACT
1 GAAACCCAAAAGGGTTAAACT
* * * * *
41020454 GAAGCTCAAAAGAGATGAACT
1 GAAACCCAAAAGGGTTAAACT
* *
41020475 AAAACCCAGAAGGGTTAAACT
1 GAAACCCAAAAGGGTTAAACT
41020496 GAAAC
1 GAAAC
41020501 TCATATGAGT
Statistics
Matches: 33, Mismatches: 14, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (21 bp):
GAAACCCAAAAGGGTTAAACT
Found at i:41034914 original size:29 final size:27
Alignment explanation
Indices: 41034838--41034926 Score: 74
Period size: 29 Copynumber: 3.2 Consensus size: 27
41034828 CGAAATAGAG
41034838 TAAGTCCGCT-GGACTAGTAAACACAGA
1 TAAGTCCGCTGGGAC-AGTAAACACAGA
* * ** *
41034865 T-AGTACGCCGAAACAATAAACACGAGA
1 TAAGTCCGCTGGGACAGTAAACAC-AGA
*
41034892 TAAAGTCCGCTGGGACAGTAAACACAAGG
1 T-AAGTCCGCTGGGACAGTAAACAC-AGA
41034921 TAAGTC
1 TAAGTC
41034927 GAAAGGGACG
Statistics
Matches: 46, Mismatches: 12, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
26 14 0.30
27 7 0.15
28 5 0.11
29 20 0.43
ACGTcount: A:0.40, C:0.21, G:0.22, T:0.16
Consensus pattern (27 bp):
TAAGTCCGCTGGGACAGTAAACACAGA
Found at i:41040115 original size:21 final size:21
Alignment explanation
Indices: 41040098--41040146 Score: 73
Period size: 20 Copynumber: 2.3 Consensus size: 21
41040088 ACCAAAAATT
41040098 TATTTTAAAAA-TAAAAAAAG
1 TATTTTAAAAATTAAAAAAAG
*
41040118 TATTTTAAAAATTAAAAAAAA
1 TATTTTAAAAATTAAAAAAAG
41040139 TATATTTA
1 TAT-TTTA
41040147 TTATATTCAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 11 0.42
21 11 0.42
22 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TATTTTAAAAATTAAAAAAAG
Found at i:41043029 original size:75 final size:74
Alignment explanation
Indices: 41042935--41043106 Score: 202
Period size: 75 Copynumber: 2.3 Consensus size: 74
41042925 CCGCAGAGGA
* * * * *
41042935 GTTTGCGCCCAGCGCTAGTCTG-GTTAACCGACAATATTGAAAGTGAGCCTAGCTCTAGTTGGAT
1 GTTTGCGCCCAGCGCTAGTC-GAGAT-ACCGACAATAATAAAAGTGAGCCCAACTCTAGTTGGAT
41042999 AAACCAACAAT
64 AAACCAACAAT
* * * *
41043010 GTTTGTGCCCAGCGCTAGTCGAAGATACTGACGATAATAAAAGTGAGCCCAACTCTAGTTGGATG
1 GTTTGCGCCCAGCGCTAGTCG-AGATACCGACAATAATAAAAGTGAGCCCAACTCTAGTTGGATA
**
41043075 AACCAACGGT
65 AACCAACAAT
*
41043085 GTTTGCGCCCAACGCTAGTCGA
1 GTTTGCGCCCAGCGCTAGTCGA
41043107 ATAAACCGAC
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
74 2 0.02
75 78 0.95
76 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.24
Consensus pattern (74 bp):
GTTTGCGCCCAGCGCTAGTCGAGATACCGACAATAATAAAAGTGAGCCCAACTCTAGTTGGATAA
ACCAACAAT
Found at i:41045057 original size:19 final size:16
Alignment explanation
Indices: 41045016--41045046 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41045006 ATTTTCAATA
41045016 AATTTTTATAATTAAT
1 AATTTTTATAATTAAT
*
41045032 AGTTTTTATAATTAA
1 AATTTTTATAATTAA
41045047 AAATAATTTT
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
AATTTTTATAATTAAT
Found at i:41048065 original size:129 final size:128
Alignment explanation
Indices: 41047828--41048069 Score: 315
Period size: 129 Copynumber: 1.9 Consensus size: 128
41047818 GTAACAACGA
* * *
41047828 AGCTTGTTGAGTCATCAGAGGGGCTTCCACCCAAGGAAGAGGTGAGTTATGCATCAAACTTAGAG
1 AGCTTGTTGAGTCATCAGAGAGGCTTCCACCCAAGGAAAAGGTGAGTTATACATCAAACTTAGAG
* * * * *
41047893 GAAATAGTAGTGATGCAAACATTGAAGCTAGGACCAATGAGGCTCAATTCGGGGAAAGTGATAG
66 GAAAAAGTAGGGATGAAAACATTAAAGCTAGGACCAATAAGGCT-AATTCGGGGAAAGTGATAG
* * * * *
41047957 AGCTTGTTGTGTCATC-GTAGAGGCTTCCACCCAAGGAAAATGTGAGTTGTACATCAGACTTTGA
1 AGCTTGTTGAGTCATCAG-AGAGGCTTCCACCCAAGGAAAAGGTGAGTTATACATCAAACTTAGA
* * *
41048021 GGAAAAAGTAGGGATGAAAATATTAAAGTTAGGATCAATAAGGCTAATT
65 GGAAAAAGTAGGGATGAAAACATTAAAGCTAGGACCAATAAGGCTAATT
41048070 TCTGTTGAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
128 5 0.05
129 91 0.95
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.24
Consensus pattern (128 bp):
AGCTTGTTGAGTCATCAGAGAGGCTTCCACCCAAGGAAAAGGTGAGTTATACATCAAACTTAGAG
GAAAAAGTAGGGATGAAAACATTAAAGCTAGGACCAATAAGGCTAATTCGGGGAAAGTGATAG
Found at i:41050783 original size:56 final size:56
Alignment explanation
Indices: 41050722--41050859 Score: 145
Period size: 56 Copynumber: 2.5 Consensus size: 56
41050712 TGTCTGGGTT
* * * *
41050722 CGCCTTAGGTCGCGAAGCCAACTT-GCACATACTT-TTCAAAAAACTCGAACAAGGTC
1 CGCCTTAGGTCGCAAAACCAA-TTCGCACATACTTATT-AAAAAACACAAACAAGGTC
* * *
41050778 CGCCTTAGGTCGCAAAACCGATTCGCACATACTTATTAGAAAACACAAACATGGTC
1 CGCCTTAGGTCGCAAAACCAATTCGCACATACTTATTAAAAAACACAAACAAGGTC
* * * *
41050834 TGCCTTAGGTTGCAAGACCAGTTCGC
1 CGCCTTAGGTCGCAAAACCAATTCGC
41050860 TTATCAAAAT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
55 2 0.03
56 64 0.94
57 2 0.03
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (56 bp):
CGCCTTAGGTCGCAAAACCAATTCGCACATACTTATTAAAAAACACAAACAAGGTC
Found at i:41051788 original size:17 final size:17
Alignment explanation
Indices: 41051754--41051800 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
41051744 GTAAAATTAA
41051754 CTAGATGCAAATAT-TAAT
1 CTAGATGC-AAT-TCTAAT
**
41051772 CTCTATGCAATTCTAAT
1 CTAGATGCAATTCTAAT
41051789 CTAGATGCAATT
1 CTAGATGCAATT
41051801 TACGTAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 1 0.04
17 17 0.71
18 6 0.25
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (17 bp):
CTAGATGCAATTCTAAT
Found at i:41052498 original size:36 final size:36
Alignment explanation
Indices: 41052449--41052546 Score: 160
Period size: 36 Copynumber: 2.7 Consensus size: 36
41052439 TTAGTTAAGC
* *
41052449 AGCCTTTCAGATCTATTCTGACTGATTCAGTTTAGT
1 AGCCTTTCGGATCTATTCTGACTGATTCAGTTCAGT
* *
41052485 AGCCTTTTGGATCTATTCTGACTGATTCTGTTCAGT
1 AGCCTTTCGGATCTATTCTGACTGATTCAGTTCAGT
41052521 AGCCTTTCGGATCTATTCTGACTGAT
1 AGCCTTTCGGATCTATTCTGACTGAT
41052547 GCGCTCCTCC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 57 1.00
ACGTcount: A:0.19, C:0.20, G:0.18, T:0.42
Consensus pattern (36 bp):
AGCCTTTCGGATCTATTCTGACTGATTCAGTTCAGT
Found at i:41066153 original size:20 final size:21
Alignment explanation
Indices: 41066121--41066162 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
41066111 TCCACTCAAA
41066121 ATTAGCATCTAGG-TGTTCAC
1 ATTAGCATCTAGGTTGTTCAC
41066141 ATTAGTCAT-TAGGTTGTTCAC
1 ATTAG-CATCTAGGTTGTTCAC
41066162 A
1 A
41066163 CAGAAAGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (21 bp):
ATTAGCATCTAGGTTGTTCAC
Found at i:41067983 original size:25 final size:24
Alignment explanation
Indices: 41067935--41067986 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
41067925 TTTTAATAAG
*
41067935 ATTTAATATTAAATTTAATCTAAT
1 ATTTAATATTAAATTAAATCTAAT
* *
41067959 ATTTATATATTAGATTAAATTTAAT
1 ATTTA-ATATTAAATTAAATCTAAT
41067984 ATT
1 ATT
41067987 AAAGTGATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (24 bp):
ATTTAATATTAAATTAAATCTAAT
Found at i:41081067 original size:23 final size:23
Alignment explanation
Indices: 41081029--41081079 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
41081019 CGACGATATT
*
41081029 TGTAATATCCTAAAAATTACTAC
1 TGTAATACCCTAAAAATTACTAC
*
41081052 TGTAATACCCTGAAAATTACTAC
1 TGTAATACCCTAAAAATTACTAC
*
41081075 AGTAA
1 TGTAA
41081080 GAAAGTAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
TGTAATACCCTAAAAATTACTAC
Found at i:41083816 original size:13 final size:13
Alignment explanation
Indices: 41083798--41083823 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41083788 ACCAAGTCTA
41083798 TCTAGTAATGCCT
1 TCTAGTAATGCCT
41083811 TCTAGTAATGCCT
1 TCTAGTAATGCCT
41083824 CATACCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.38
Consensus pattern (13 bp):
TCTAGTAATGCCT
Found at i:41084273 original size:524 final size:524
Alignment explanation
Indices: 41083285--41084323 Score: 1862
Period size: 524 Copynumber: 2.0 Consensus size: 524
41083275 AAATGTATGT
* *
41083285 CTTCTAGTAATGCCTCGTACCCTATTCCGGCGTCGAATACGAGTGAGGGGTGTTACAATGTGACA
1 CTTCTAGTAATGCCTCATACCCTATTCCGGCGTCGAATACGAGTGAGGGGTGTTACAATGTAACA
* * * * * *
41083350 TCGCCAGATTCGGTCATAACGTTTAGACCGGGTTTGGGGTGTTACAAGATTGGTCTATAAGATTA
66 GCGCCAGATTAGGTCATAACATTTAGACCGAGTTTGGGGAGTTACAAGATTGGTCCATAAGATTA
41083415 GATGATGCTTTATGGGCTTACAGAACAACATACAAGACACTGTTAGGGATGTCACCCTATAGGTT
131 GATGATGCTTTATGGGCTTACAGAACAACATACAAGACACTGTTAGGGATGTCACCCTATAGGTT
*
41083480 GGTTTTTGGGAAAGCTTGCCATCTACCATTTGAGTTAGAGCACAAAGCTTACTAGGCTCTTCAAC
196 GGTTTTTGGGAAAGCCTGCCATCTACCATTTGAGTTAGAGCACAAAGCTTACTAGGCTCTTCAAC
* *
41083545 AACTTAATTTGGATCCTAAGCTCGCGAAAGAAAAATGGATGTTCCAACTCAATGAGTTAGAAGAG
261 AACTTAATTTGGATCCTAAGCTCGCCAAAGAAAAACGGATGTTCCAACTCAATGAGTTAGAAGAG
*
41083610 TTCCGAATGTTCTCTTATGAAAAAGCCAAATTACTTAAAGAAAGACTCAAGAAATGGCATGACAA
326 TTCCGAATGTTCTCATATGAAAAAGCCAAATTACTTAAAGAAAGACTCAAGAAATGGCATGACAA
* *
41083675 CCACATTCGCGTTCGAGAATTTGAAGCAGGTCAGCAAGTCTTGTTGTTCAATTTCAGATTGAAGT
391 CCACATTCGAGTTCGAGAATTTGAAGCAGGTCAGCAAGTCTTGTTGTTCAATTCCAGATTGAAGT
* *
41083740 TCTTTCCAGGTAAGCTAAAATCACGTTGGTCCAGTCCATTTATGATTCACCAAGTCTATCTAGTA
456 TCTTTCCAGGTAAGCTAAAATCACATTGGTCCAGTCCATTTACGATTCACCAAGTCTATCTAGTA
41083805 ATGC
521 ATGC
41083809 CTTCTAGTAATGCCTCATACCCTATTCCGGCGTCGAATACGAGTGAGGGGTGTTACAATGTAACA
1 CTTCTAGTAATGCCTCATACCCTATTCCGGCGTCGAATACGAGTGAGGGGTGTTACAATGTAACA
41083874 GCGCCAGATTAGGTCATAACATTTAGACCGAGTTTGGGGAGTTACAAGATTGGTCCATAAGATTA
66 GCGCCAGATTAGGTCATAACATTTAGACCGAGTTTGGGGAGTTACAAGATTGGTCCATAAGATTA
* *
41083939 GATGATGCTTTATGGGCTTACAGAACAGCATACAAGACACTGTTAGGGATGTTACCCTATAGGTT
131 GATGATGCTTTATGGGCTTACAGAACAACATACAAGACACTGTTAGGGATGTCACCCTATAGGTT
41084004 GGTTTTTGGGAAAGCCTGCCATCTACCATTTGAGTTAGAGCACAAAGCTTACTAGGCTCTTCAAC
196 GGTTTTTGGGAAAGCCTGCCATCTACCATTTGAGTTAGAGCACAAAGCTTACTAGGCTCTTCAAC
*
41084069 AACTTAATTTGGATCCTAAGCTTGCCAAAGAAAAACGGATGTTCCAACTCAATGAGTTAGAAGAG
261 AACTTAATTTGGATCCTAAGCTCGCCAAAGAAAAACGGATGTTCCAACTCAATGAGTTAGAAGAG
*
41084134 TTCCGAATGTTCTCATATGAAAATGCCAAATTACTTAAAGAAAGACTCAAGAAATGGCATGACAA
326 TTCCGAATGTTCTCATATGAAAAAGCCAAATTACTTAAAGAAAGACTCAAGAAATGGCATGACAA
*
41084199 CCACATTCGAGTTTGAGAATTTGAAGCAGGTCAGCAAGTCTTGTTGTTCAATTCCAGATTGAAGT
391 CCACATTCGAGTTCGAGAATTTGAAGCAGGTCAGCAAGTCTTGTTGTTCAATTCCAGATTGAAGT
* * *
41084264 TTTTTCCAGGTAAGCTAAAATGACATTGGTCCGGTCCATTTACGATTCACCAAGTCTATC
456 TCTTTCCAGGTAAGCTAAAATCACATTGGTCCAGTCCATTTACGATTCACCAAGTCTATC
41084324 CATAAAGATT
Statistics
Matches: 491, Mismatches: 24, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
524 491 1.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (524 bp):
CTTCTAGTAATGCCTCATACCCTATTCCGGCGTCGAATACGAGTGAGGGGTGTTACAATGTAACA
GCGCCAGATTAGGTCATAACATTTAGACCGAGTTTGGGGAGTTACAAGATTGGTCCATAAGATTA
GATGATGCTTTATGGGCTTACAGAACAACATACAAGACACTGTTAGGGATGTCACCCTATAGGTT
GGTTTTTGGGAAAGCCTGCCATCTACCATTTGAGTTAGAGCACAAAGCTTACTAGGCTCTTCAAC
AACTTAATTTGGATCCTAAGCTCGCCAAAGAAAAACGGATGTTCCAACTCAATGAGTTAGAAGAG
TTCCGAATGTTCTCATATGAAAAAGCCAAATTACTTAAAGAAAGACTCAAGAAATGGCATGACAA
CCACATTCGAGTTCGAGAATTTGAAGCAGGTCAGCAAGTCTTGTTGTTCAATTCCAGATTGAAGT
TCTTTCCAGGTAAGCTAAAATCACATTGGTCCAGTCCATTTACGATTCACCAAGTCTATCTAGTA
ATGC
Found at i:41084870 original size:15 final size:16
Alignment explanation
Indices: 41084835--41084871 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
41084825 TTGATAAACT
41084835 TTATTATATAATTATA
1 TTATTATATAATTATA
41084851 TTATT-TATAATT-TA
1 TTATTATATAATTATA
41084865 TATATTA
1 T-TATTA
41084872 ATTTTTATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 3 0.16
15 11 0.58
16 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTATATAATTATA
Found at i:41091409 original size:69 final size:69
Alignment explanation
Indices: 41091333--41091520 Score: 322
Period size: 69 Copynumber: 2.7 Consensus size: 69
41091323 CAGCATTGAC
* *
41091333 TTGTACCAAAAATGGACAACATTTAAGCACTAATTTGGACAACATTAATAACAAACGGACAACAT
1 TTGTACCAAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATAACAAACAGACAACAT
41091398 AGAT
66 AGAT
* **
41091402 TTGTACCAAAAATGGACAGCATTTAAGCACTAATTTGGACAGCATTAATAACATTCAGACAACAT
1 TTGTACCAAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATAACAAACAGACAACAT
41091467 AGAT
66 AGAT
*
41091471 TTGTACCAAAAATGGACAGTATTTAAGCACTAATTTGGACAACATTAATA
1 TTGTACCAAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATA
41091521 TGCTAAAAAA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 112 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (69 bp):
TTGTACCAAAAATGGACAGCATTTAAGCACTAATTTGGACAACATTAATAACAAACAGACAACAT
AGAT
Found at i:41091438 original size:34 final size:34
Alignment explanation
Indices: 41091400--41091507 Score: 82
Period size: 34 Copynumber: 3.1 Consensus size: 34
41091390 GACAACATAG
41091400 ATTTGTACCAAAAATGGACAGCATTTAAGCACTA
1 ATTTGTACCAAAAATGGACAGCATTTAAGCACTA
* ** *
41091434 ATTTGGACAGCATTAAT--A-A-CA-TTCAGACAACATA
1 ATTTGTAC--CAAAAATGGACAGCATTTAAG-C-AC-TA
*
41091468 GATTTGTACCAAAAATGGACAGTATTTAAGCACTA
1 -ATTTGTACCAAAAATGGACAGCATTTAAGCACTA
41091503 ATTTG
1 ATTTG
41091508 GACAACATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 22
0.64 0.11 0.26
Matches are distributed among these distances:
31 4 0.07
32 3 0.06
33 8 0.15
34 15 0.28
35 10 0.19
36 8 0.15
37 2 0.04
38 4 0.07
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.29
Consensus pattern (34 bp):
ATTTGTACCAAAAATGGACAGCATTTAAGCACTA
Found at i:41092432 original size:42 final size:43
Alignment explanation
Indices: 41092380--41092465 Score: 138
Period size: 42 Copynumber: 2.0 Consensus size: 43
41092370 ACATGTTATA
*
41092380 ATATATCGATGCCACTGTCCCAGACAGGGTCTTACACGAAATC
1 ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
* *
41092423 ATATA-CGATGCCAATGTCCCAGACATGGTCTTACATGAAATC
1 ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
41092465 A
1 A
41092466 CACCTCAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 35 0.88
43 5 0.12
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (43 bp):
ATATATCGATGCCAATGTCCCAGACAGGGTCTTACACGAAATC
Found at i:41095065 original size:28 final size:27
Alignment explanation
Indices: 41095036--41095131 Score: 77
Period size: 28 Copynumber: 3.4 Consensus size: 27
41095026 GCCTAGCTCG
* *
41095036 ATACAGTAACAGCATGAACCTTAGCCCG
1 ATACAGTAACAG-ATGGACCTTAGCCCA
* * *
41095064 ATGCAGCAATAGAGTGGGA-CTTAGCCCA
1 ATACAGTAACAGA-T-GGACCTTAGCCCA
* * *
41095092 ATACAGTAATAGTGTGGGCCTTAGCCCA
1 ATACAGTAACAG-ATGGACCTTAGCCCA
41095120 ATACAGTAACAG
1 ATACAGTAACAG
41095132 TACAGTGCCA
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
27 3 0.06
28 49 0.91
29 2 0.04
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
ATACAGTAACAGATGGACCTTAGCCCA
Found at i:41095490 original size:27 final size:27
Alignment explanation
Indices: 41095457--41095544 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 27
41095447 AGGTATAACA
*
41095457 GTCATTTTACCTTATGGGGGTATTTAG
1 GTCATTTTACCCTATGGGGGTATTTAG
* * **
41095484 GTTATTTTACCCTATGAGGGTATTTCT
1 GTCATTTTACCCTATGGGGGTATTTAG
* * *
41095511 GTCATTTTACCCTATAGGAGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTAG
41095538 GTCATTT
1 GTCATTT
41095545 ATTGACCGCT
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.19, C:0.14, G:0.20, T:0.47
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTAG
Found at i:41102848 original size:28 final size:28
Alignment explanation
Indices: 41102817--41102871 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
41102807 AATGTAAGCC
* *
41102817 TTAGCCCAATATAGTAATAGAGTGGGCG
1 TTAGCCCAATACAATAATAGAGTGGGCG
*
41102845 TTAGCCCAATACAATAATAGTGTGGGC
1 TTAGCCCAATACAATAATAGAGTGGGC
41102872 CTCAATACAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.25
Consensus pattern (28 bp):
TTAGCCCAATACAATAATAGAGTGGGCG
Found at i:41118513 original size:34 final size:34
Alignment explanation
Indices: 41118474--41118573 Score: 96
Period size: 36 Copynumber: 2.9 Consensus size: 34
41118464 CTACAAAAAA
41118474 TGGACAACATTTATACATGCAAAGCAACCACATT
1 TGGACAACATTTATACATGCAAAGCAACCACATT
* *
41118508 TGGACAACA-TTATAACATGTAAAAAGCAGCCACATT
1 TGGACAACATTTAT-ACATG--CAAAGCAACCACATT
* * * *
41118544 TGGATATCATTGTA-ATATGCAAAACAACCA
1 TGGACAACATT-TATACATGCAAAGCAACCA
41118574 TACTTTAATA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
33 4 0.08
34 22 0.42
36 24 0.45
37 1 0.02
38 2 0.04
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.24
Consensus pattern (34 bp):
TGGACAACATTTATACATGCAAAGCAACCACATT
Found at i:41119396 original size:42 final size:43
Alignment explanation
Indices: 41119326--41119416 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 43
41119316 TCCTAGATAT
** *
41119326 GGTCTTACATGTTATAATATATCGATGCCACTGTCCCAGACAG
1 GGTCTTACATGAAATAATATATCGATGCCAATGTCCCAGACAG
* * *
41119369 GGTCTTACATGAAATCATATA-CTATGCCAATGTCCCAGACAT
1 GGTCTTACATGAAATAATATATCGATGCCAATGTCCCAGACAG
41119411 GGTCTT
1 GGTCTT
41119417 TCAAAAAATC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 24 0.57
43 18 0.43
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
GGTCTTACATGAAATAATATATCGATGCCAATGTCCCAGACAG
Found at i:41123747 original size:10 final size:10
Alignment explanation
Indices: 41123728--41123766 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
41123718 CTATTTTTAC
41123728 AAAAATTTCA
1 AAAAATTTCA
*
41123738 AAAAAATTCA
1 AAAAATTTCA
*
41123748 AAAATTTTCA
1 AAAAATTTCA
41123758 AAAACATTT
1 AAAA-ATTT
41123767 TTCTTGTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
10 21 0.88
11 3 0.12
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAATTTCA
Found at i:41125696 original size:25 final size:25
Alignment explanation
Indices: 41125642--41125696 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
41125632 TTTTCTTTTT
***
41125642 ATTTTTCTTTTCATTTTTAGTTTAG
1 ATTTTTCTTTTCATTTTTAAAATAG
*
41125667 GTTTTCTCTTTTC-TTTTTAAAATAG
1 ATTTT-TCTTTTCATTTTTAAAATAG
41125692 ATTTT
1 ATTTT
41125697 ATTCTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.18, C:0.09, G:0.07, T:0.65
Consensus pattern (25 bp):
ATTTTTCTTTTCATTTTTAAAATAG
Found at i:41136259 original size:20 final size:20
Alignment explanation
Indices: 41136234--41136272 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
41136224 TGAGTTATTT
41136234 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
41136254 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
41136273 GAACATGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:41142762 original size:12 final size:12
Alignment explanation
Indices: 41142747--41142774 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41142737 TACTTACTCT
41142747 CTTACTTGTTTA
1 CTTACTTGTTTA
41142759 CTTACTTGTTTA
1 CTTACTTGTTTA
41142771 CTTA
1 CTTA
41142775 AATAACTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.07, T:0.57
Consensus pattern (12 bp):
CTTACTTGTTTA
Found at i:41143117 original size:50 final size:49
Alignment explanation
Indices: 41143063--41143260 Score: 198
Period size: 50 Copynumber: 3.9 Consensus size: 49
41143053 ACATGAGAGT
* * * **
41143063 TCTCATATCGGTGCCCATGCCATGTCCCAGACACAGTCTTACGGGGAACC
1 TCTCATATCGGTACCAACGCCATGTCCCAGACATGGTCTTACGGGG-ACC
* *
41143113 TCTCATCTCGGTACCAACGCCATGTCCCTGACATGGTCTTACGGGGGACC
1 TCTCATATCGGTACCAACGCCATGTCCCAGACATGGTCTTAC-GGGGACC
* * *
41143163 TCTCATCTTGGTACCAACGCCATGTCCCAGACATGGTCTTACATGGGACC
1 TCTCATATCGGTACCAACGCCATGTCCCAGACATGGTCTTAC-GGGGACC
** *
41143213 TCTCATAATCTCAATAATGCCAATGCCATGTCCCAGACATGGTCTTAC
1 TCTCAT-A--TCGGT-A--CCAACGCCATGTCCCAGACATGGTCTTAC
41143261 ATGGGGTTTC
Statistics
Matches: 125, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
50 90 0.72
51 4 0.03
53 2 0.02
54 1 0.01
56 28 0.22
ACGTcount: A:0.23, C:0.32, G:0.20, T:0.25
Consensus pattern (49 bp):
TCTCATATCGGTACCAACGCCATGTCCCAGACATGGTCTTACGGGGACC
Found at i:41143852 original size:27 final size:27
Alignment explanation
Indices: 41143821--41143878 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
41143811 TTTCACTTAA
41143821 AATTGCCTAGCAAAAGTTGTTTAACAT
1 AATTGCCTAGCAAAAGTTGTTTAACAT
41143848 AATTGCCTAGCAAAAGTTGTTTAACAT
1 AATTGCCTAGCAAAAGTTGTTTAACAT
41143875 AATT
1 AATT
41143879 TAAAACTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (27 bp):
AATTGCCTAGCAAAAGTTGTTTAACAT
Found at i:41145716 original size:21 final size:21
Alignment explanation
Indices: 41145686--41145752 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
41145676 CTGTTGTTGG
**
41145686 GAAAGAAGTTGCTGCTGCAGAA
1 GAAA-AAGTTGCTGCTAAAGAA
* *
41145708 GAGAAAGTTGTTGCTAAAGAA
1 GAAAAAGTTGCTGCTAAAGAA
*
41145729 GAAAAAGTT-CT--TAAAAAA
1 GAAAAAGTTGCTGCTAAAGAA
41145747 GAAAAA
1 GAAAAA
41145753 TAAAATTTTG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
18 12 0.32
20 1 0.03
21 22 0.58
22 3 0.08
ACGTcount: A:0.49, C:0.07, G:0.24, T:0.19
Consensus pattern (21 bp):
GAAAAAGTTGCTGCTAAAGAA
Found at i:41147814 original size:790 final size:792
Alignment explanation
Indices: 41146244--41147822 Score: 2472
Period size: 790 Copynumber: 2.0 Consensus size: 792
41146234 GGGGAATGCA
*
41146244 CATGGGACTTGGAAATGCACCTACATTTCAATTTTTTTTTCTTTCAGTAATGAAGCATGAAAGGT
1 CATGGGACTTGGAAATGCACCCACATTTCAATTTTTTTTTCTTTCAGTAATGAAGCATGAAAGGT
* * *
41146309 TTAATTATAGTTAATGAAAATTATTTGAAATTTTTTTGTTACATTCGATGCTTAATTCTTGAATC
66 TTAATTATAGTTAATGAAAATTATTAGAAATATTTATGTTACATTCGATGCTTAATTCTTGAATC
* * * * * * *
41146374 ATGTGAATTATCAATGATTGAGTTGGATAATTTTGACAGAATGTTGTAGCTTTAATTCTTTAATG
131 ATGTGAATTATCAATGAATGAGCTGGATAAATTTGACAGAAGGTTGTAGATTCAATTATTTAATG
*
41146439 AATGGATTAGGTTGCATTAGTAGTGGATAACTACTATCATTCCTTAAATCTTGAATGAATCTGCT
196 AATGGATTAGGTTGCATTAGTAGTGGATAACTACTATCATTCCTTAAATCTTGAATGAATCTACT
* * * *
41146504 TTTTACAGCTGCTTATATATGTATATATAGTTATAAGTTAGAGACACTCCAAAGTGGGTGTAGTA
261 TTTTACAGCTGCTTATATATGTATATATAGTTATAAATTACAAACACTCCAAAGTAGGTGTAGTA
* * *
41146569 TGGAATGTTAAAAGGGGAACACTCCAATACAAGCGTTAGAAAAATCAATCTGGTCAAAGGTTGTC
326 TGGAATGTTAAAAAGGGAACACTCCAATACAAGCGTTAAAAAAATCAATCTGGCCAAAGGTTGTC
* * *
41146634 ACTGCATGAGTGTGTGTCAGCAGAATTACGTACTCCCTAGGGGTTTGTTGCGCCCCATCGTTACT
391 ACTGCATCAGTGTATGTCAGCAGAATTACGTACTCCCTAGGGGTTTGTTGCACCCCATCGTTACT
* * *
41146699 TCTTAGTAACAACGGTACAGTAATGCAACGATATCCCTTATTCTGAAAAAAACGTATATATAATA
456 TCTCAGTAACAACGGTACAATAATGAAACGATATCCCTTATTCTG-AAAAAAC--ATATATAATA
* *
41146764 TATAAATACTTAGTATTGTACAATAAATGATGTAATGGTAGATAAAACTTAAGGTTTGAAGCATG
518 TATAAATACTTAGTATTGTACAATAAATGATATAATGGTAGATAAAACTTAAGGTATGAAGCATG
* *
41146829 ATGCTGGCATTGATGAAGTTGCAACCTTATTCATTCATGCTTATGAATTGTCGATGCAATATTCT
583 ATGCTAGCATTGATGAAGTTGCAACCTTATTCATTCATGCTTATGAATTGTCGATCCAATATTCT
* * *
41146894 TTCATCTAAATGTGATTCATCTATTGGCAATTTAGAGGGTTCAAGTTTCTAGAATGATCATTTGC
648 TTCATCTAAATGTGATGCATCCATTGGCAATTTAGAGGGTTCAAGTTGCTAGAATGATCATTTGC
*
41146959 CTTAGTAAAATTTTTGTAGCCTTGCTAGTTTATGATTTACTTGAGGACAAGTAAAAACTCAAGTT
713 CTTAGTAAAATTTTTGTAGCCTTACTAGTTTATGATTTACTTGAGGACAAGTAAAAACTCAAGTT
*
41147024 TGGGGGTGTAATGTG
778 TAGGGGTGTAATGTG
* *
41147039 CATGGGGCTTGGAAATGCACCCACATTTCAA-TTTTTTTTCTTTCAGTAATGAAGCATGCAAGGT
1 CATGGGACTTGGAAATGCACCCACATTTCAATTTTTTTTTCTTTCAGTAATGAAGCATGAAAGGT
*
41147103 TTAATTATAGTTAATGAAAATTGTTAGAAA-ATTTATGTTACATTCGATGCTTAATTCTTGAATC
66 TTAATTATAGTTAATGAAAATTATTAGAAATATTTATGTTACATTCGATGCTTAATTCTTGAATC
*
41147167 ATGTGAATTATCAATGAATGAGCTGGATAAATTTGACAGAAGGTTGTAGATTCAATTATTTGATG
131 ATGTGAATTATCAATGAATGAGCTGGATAAATTTGACAGAAGGTTGTAGATTCAATTATTTAATG
*
41147232 AATGGATTAGGTTGCATTAGTAGTGGATGACTGA-TATCATTCCTTAAATCTTGAATGAATCTAC
196 AATGGATTAGGTTGCATTAGTAGTGGATAACT-ACTATCATTCCTTAAATCTTGAATGAATCTAC
*
41147296 TTTTTACAGCTGCTTATATATGTATATATAGTTATAAATTACAAACACTCCAAAGTAGGTGTATT
260 TTTTTACAGCTGCTTATATATGTATATATAGTTATAAATTACAAACACTCCAAAGTAGGTGTAGT
* * * *
41147361 GTGGAATGTTAAAAAGGGAGCACTCCAATACAAGCATTTTAAAAAAATCAATCTTGCCAAAGGTT
325 ATGGAATGTTAAAAAGGGAACACTCCAATACAAGC--GTTAAAAAAATCAATCTGGCCAAAGGTT
* *
41147426 GTCGCTGCATCAGTGTATGTCAGC-GCAATTACGTACTCCTTAGGGGTTTGTTGCACCCCATCGT
388 GTCACTGCATCAGTGTATGTCAGCAG-AATTACGTACTCCCTAGGGGTTTGTTGCACCCCATCGT
* *
41147490 TACTTCTCAGTAATAAGGGTACAATAATGAAACGATATCCCTTATTCTG-AAAAA-ATATATAAT
452 TACTTCTCAGTAACAACGGTACAATAATGAAACGATATCCCTTATTCTGAAAAAACATATATAAT
* * **
41147553 ATATAAATACTTAGTATTGTACAATAAATGTTATAATGGTAGATAGAACTTGGGGTATGAAGCAT
517 ATATAAATACTTAGTATTGTACAATAAATGATATAATGGTAGATAAAACTTAAGGTATGAAGCAT
* * * * * *
41147618 TATTCTAGCATTGATGAAGTTGTAACCTTTTTCATTCATGCTTATGAATTGTTGGTCCAATATTC
582 GATGCTAGCATTGATGAAGTTGCAACCTTATTCATTCATGCTTATGAATTGTCGATCCAATATTC
*
41147683 TTTCATCTGAATGTGATGCATCCATTAGG-AATTTAGAGGGTTCAAGTTGCTAGAATGATCATTT
647 TTTCATCTAAATGTGATGCATCCATT-GGCAATTTAGAGGGTTCAAGTTGCTAGAATGATCATTT
* *
41147747 GCCTTAGTAAAATTTTTTTAGCCTTACTAGTTTCT-ATTCTACTTGAGGACAAGTAAAAACTCAA
711 GCCTTAGTAAAATTTTTGTAGCCTTACTAGTTTATGATT-TACTTGAGGACAAGTAAAAACTCAA
41147811 GTTTAGGGGTGT
775 GTTTAGGGGTGT
41147823 GATAGCACTA
Statistics
Matches: 717, Mismatches: 61, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
789 3 0.00
790 250 0.35
791 2 0.00
793 246 0.34
794 62 0.09
795 154 0.21
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (792 bp):
CATGGGACTTGGAAATGCACCCACATTTCAATTTTTTTTTCTTTCAGTAATGAAGCATGAAAGGT
TTAATTATAGTTAATGAAAATTATTAGAAATATTTATGTTACATTCGATGCTTAATTCTTGAATC
ATGTGAATTATCAATGAATGAGCTGGATAAATTTGACAGAAGGTTGTAGATTCAATTATTTAATG
AATGGATTAGGTTGCATTAGTAGTGGATAACTACTATCATTCCTTAAATCTTGAATGAATCTACT
TTTTACAGCTGCTTATATATGTATATATAGTTATAAATTACAAACACTCCAAAGTAGGTGTAGTA
TGGAATGTTAAAAAGGGAACACTCCAATACAAGCGTTAAAAAAATCAATCTGGCCAAAGGTTGTC
ACTGCATCAGTGTATGTCAGCAGAATTACGTACTCCCTAGGGGTTTGTTGCACCCCATCGTTACT
TCTCAGTAACAACGGTACAATAATGAAACGATATCCCTTATTCTGAAAAAACATATATAATATAT
AAATACTTAGTATTGTACAATAAATGATATAATGGTAGATAAAACTTAAGGTATGAAGCATGATG
CTAGCATTGATGAAGTTGCAACCTTATTCATTCATGCTTATGAATTGTCGATCCAATATTCTTTC
ATCTAAATGTGATGCATCCATTGGCAATTTAGAGGGTTCAAGTTGCTAGAATGATCATTTGCCTT
AGTAAAATTTTTGTAGCCTTACTAGTTTATGATTTACTTGAGGACAAGTAAAAACTCAAGTTTAG
GGGTGTAATGTG
Found at i:41154531 original size:29 final size:30
Alignment explanation
Indices: 41154496--41154566 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
41154486 CTATCAAATT
41154496 ATGAAAACGGATGGTGACGACCATCAA-CA
1 ATGAAAACGGATGGTGACGACCATCAAGCA
* * *
41154525 ATGAAAATGGATGGTTACGACCATCAAGTA
1 ATGAAAACGGATGGTGACGACCATCAAGCA
*
41154555 ATGAAAAGGGAT
1 ATGAAAACGGAT
41154567 AGCTTCGGCT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.18
Consensus pattern (30 bp):
ATGAAAACGGATGGTGACGACCATCAAGCA
Found at i:41156598 original size:14 final size:14
Alignment explanation
Indices: 41156581--41156609 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41156571 TGTATGAAGC
41156581 AACACTGATTTAAA
1 AACACTGATTTAAA
41156595 AACACTGATTTAAA
1 AACACTGATTTAAA
41156609 A
1 A
41156610 GCAACATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.14, G:0.07, T:0.28
Consensus pattern (14 bp):
AACACTGATTTAAA
Found at i:41160547 original size:18 final size:18
Alignment explanation
Indices: 41160524--41160568 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
41160514 CATAGAGTCG
41160524 TAATATCATAATACAACA
1 TAATATCATAATACAACA
41160542 TAATATCATAATACAACA
1 TAATATCATAATACAACA
41160560 TAATATCAT
1 TAATATCAT
41160569 TTAATTTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (18 bp):
TAATATCATAATACAACA
Found at i:41161532 original size:17 final size:18
Alignment explanation
Indices: 41161506--41161539 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41161496 ATACGACACT
*
41161506 ACTAACATGTT-GTAAAC
1 ACTAAAATGTTAGTAAAC
41161523 ACTAAAATGTTAGTAAA
1 ACTAAAATGTTAGTAAA
41161540 ATAATTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (18 bp):
ACTAAAATGTTAGTAAAC
Found at i:41165471 original size:19 final size:17
Alignment explanation
Indices: 41165447--41165493 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
41165437 TTTTAATTAA
41165447 ATAAATATTACTTTTATAT
1 ATAAATATTA-TTTTAT-T
*
41165466 ATAAATATGATTTTATT
1 ATAAATATTATTTTATT
*
41165483 TTAAATATTAT
1 ATAAATATTAT
41165494 AATTATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
19 9 0.36
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATAAATATTATTTTATT
Found at i:41165489 original size:17 final size:19
Alignment explanation
Indices: 41165447--41165490 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41165437 TTTTAATTAA
*
41165447 ATAAATATTACTTTTATAT
1 ATAAATATGACTTTTATAT
41165466 ATAAATATGA-TTTTAT-T
1 ATAAATATGACTTTTATAT
*
41165483 TTAAATAT
1 ATAAATAT
41165491 TATAATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 8 0.35
18 6 0.26
19 9 0.39
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATAAATATGACTTTTATAT
Found at i:41167546 original size:24 final size:24
Alignment explanation
Indices: 41167519--41167568 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
41167509 ATTAGATCAT
41167519 ATATATT-TTTAAAAAATTATAAAA
1 ATATATTATTTAAAAAATT-TAAAA
* *
41167543 ATATATTATTTGATAAATTTAAAA
1 ATATATTATTTAAAAAATTTAAAA
41167567 AT
1 AT
41167569 TCCAGCACAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
ATATATTATTTAAAAAATTTAAAA
Found at i:41170778 original size:44 final size:45
Alignment explanation
Indices: 41170691--41170849 Score: 153
Period size: 44 Copynumber: 3.6 Consensus size: 45
41170681 TTCGATCTAA
* * * *** *
41170691 TCCACTACAACTTCAGGGAGATAGGA-TTATCGAATTCAATCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTCTTCTTCAGTCTGC
* *
41170735 TCCACTGCAACCTCAGGGAGATAAGATTTG-CTTCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTCTTCTTCAGTCTGC
* * ** * *
41170779 CCCATTGTGACTTCAGGGGGATAAGACTTGTTTTCTT-AGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTCTTCTTCAGTCTGC
*
41170823 TCCGCTGCAACTTCAGGGAGATAAGAC
1 TCCACTGCAACTTCAGGGAGATAAGAC
41170850 CCGATGCGAT
Statistics
Matches: 91, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
44 84 0.92
45 7 0.08
ACGTcount: A:0.25, C:0.24, G:0.22, T:0.29
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTCTTCTTCAGTCTGC
Found at i:41171247 original size:87 final size:87
Alignment explanation
Indices: 41171095--41171339 Score: 409
Period size: 87 Copynumber: 2.8 Consensus size: 87
41171085 GCTAGTGCTT
* * * *
41171095 AAGAAAGCAAGATCTGCTATCTTTAACCAGCTCCACTACAACTGATGGAGGCAAGGCTTTGTTTT
1 AAGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
41171160 CGATCTACTTCGCTGTTAACGC
66 CGATCTACTTCGCTGTTAACGC
* *
41171182 AGGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGTTTTGTTTT
1 AAGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
* *
41171247 CGGTCTGCTTCGCTGTTAACGC
66 CGATCTACTTCGCTGTTAACGC
*
41171269 AAGTAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
1 AAGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
41171334 CGATCT
66 CGATCT
41171340 GTTGATCTGT
Statistics
Matches: 146, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
87 146 1.00
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.29
Consensus pattern (87 bp):
AAGAAGGCAAGATCTGTTATCTTTAACCAGCTCCACTGCAACCGATGGAGGCAAGGCTTTGTTTT
CGATCTACTTCGCTGTTAACGC
Found at i:41172623 original size:12 final size:12
Alignment explanation
Indices: 41172608--41172679 Score: 51
Period size: 12 Copynumber: 6.1 Consensus size: 12
41172598 TGACCTTGAT
41172608 TTTTTATTTTTC
1 TTTTTATTTTTC
*
41172620 TTTTT-TTTTTGA
1 TTTTTATTTTT-C
* * *
41172632 TATTGATTTTGC
1 TTTTTATTTTTC
41172644 TTTTCT-TTTTT-
1 TTTT-TATTTTTC
* *
41172655 TGTTTATTTTTA
1 TTTTTATTTTTC
41172667 TTTTTATTTTTC
1 TTTTTATTTTTC
41172679 T
1 T
41172680 CTCTTTTCCC
Statistics
Matches: 44, Mismatches: 11, Indels: 10
0.68 0.17 0.15
Matches are distributed among these distances:
10 1 0.02
11 13 0.30
12 26 0.59
13 4 0.09
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.79
Consensus pattern (12 bp):
TTTTTATTTTTC
Found at i:41172676 original size:29 final size:29
Alignment explanation
Indices: 41172603--41172676 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 29
41172593 CATTTTGACC
41172603 TTGATTTTTTATTTTTCTTTTTTTTTTGATA
1 TTGA-TTTTTA-TTTTCTTTTTTTTTTGATA
** *
41172634 TTGATTTTGCTTTTCTTTTTTTGTTT-ATT
1 TTGATTTTTATTTTCTTTTTTT-TTTGATA
*
41172663 TTTATTTTTATTTT
1 TTGATTTTTATTTT
41172677 TCTCTCTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 25 0.69
30 7 0.19
31 4 0.11
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (29 bp):
TTGATTTTTATTTTCTTTTTTTTTTGATA
Found at i:41176052 original size:98 final size:98
Alignment explanation
Indices: 41175873--41176064 Score: 303
Period size: 98 Copynumber: 2.0 Consensus size: 98
41175863 ATACAATAAA
* * *
41175873 ACTTTAAAGGAACATCCACTCATCTAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
41175938 CCTTTAAAATCCCAAACTTGGAATATTTCTTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCTTTT
* * *
41175971 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAATTCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
* *
41176036 CCTTTAGAATCTCAAACTCGGAATATTTC
66 CCTTTAAAATCCCAAACTCGGAATATTTC
41176065 CTTCATGATT
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
98 85 1.00
ACGTcount: A:0.36, C:0.23, G:0.11, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAAAATCCCAAACTCGGAATATTTCTTTT
Found at i:41179513 original size:30 final size:30
Alignment explanation
Indices: 41179479--41179570 Score: 85
Period size: 40 Copynumber: 2.7 Consensus size: 30
41179469 AAAATCAATA
41179479 ATATATAAAAGTTTAGAATAATAAATACAC
1 ATATATAAAAGTTTAGAATAATAAATACAC
*
41179509 ATATATATGAAAGTATACATACAAAGAAAAATAAATACAC
1 ATATATA--AAAGT-T---T----AGAATAATAAATACAC
41179549 ATATATAAAAGTTTAGAATAAT
1 ATATATAAAAGTTTAGAATAAT
41179571 TCGAAATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 20
0.69 0.03 0.28
Matches are distributed among these distances:
30 14 0.28
32 5 0.10
33 1 0.02
34 1 0.02
36 1 0.02
37 1 0.02
38 5 0.10
40 22 0.44
ACGTcount: A:0.58, C:0.07, G:0.08, T:0.28
Consensus pattern (30 bp):
ATATATAAAAGTTTAGAATAATAAATACAC
Found at i:41189440 original size:25 final size:25
Alignment explanation
Indices: 41189412--41189460 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
41189402 TATAGTCTAT
* * *
41189412 CTATAGTAGTCTCAGTATTTACTAC
1 CTATAGCAGTCTCAGGATATACTAC
*
41189437 CTATAGCAGTTTCAGGATATACTA
1 CTATAGCAGTCTCAGGATATACTA
41189461 TCAAAAACAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (25 bp):
CTATAGCAGTCTCAGGATATACTAC
Found at i:41189815 original size:18 final size:18
Alignment explanation
Indices: 41189794--41189838 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
41189784 CATTCGTTTC
41189794 CAAAACATTATT-CATTT
1 CAAAACATTATTCCATTT
* *
41189811 ACAAATCGTTATTCCATTT
1 -CAAAACATTATTCCATTT
41189830 CAAAACATT
1 CAAAACATT
41189839 TTTTATTGCG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (18 bp):
CAAAACATTATTCCATTT
Found at i:41197050 original size:26 final size:26
Alignment explanation
Indices: 41197021--41197091 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
41197011 TCTCATCTCT
* *
41197021 ATTTTTCCCTTAGCAAAATTTTGACA
1 ATTTTACCCTTAGTAAAATTTTGACA
*
41197047 ATTTTACCCTTGGTAAAATTTTGACA
1 ATTTTACCCTTAGTAAAATTTTGACA
* *
41197073 ATTTTGCCCCTAGTAAAAT
1 ATTTTACCCTTAGTAAAAT
41197092 CTCAAGAAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (26 bp):
ATTTTACCCTTAGTAAAATTTTGACA
Found at i:41197271 original size:6 final size:6
Alignment explanation
Indices: 41197257--41197296 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
41197247 ATATTTTCAT
*
41197257 TTTC-A TTTCCA TTTCTA TTTCTA TTTCTA TTTCTA TTTCT
1 TTTCTA TTTCTA TTTCTA TTTCTA TTTCTA TTTCTA TTTCT
41197297 GGAAACCTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.15, C:0.20, G:0.00, T:0.65
Consensus pattern (6 bp):
TTTCTA
Found at i:41197276 original size:18 final size:19
Alignment explanation
Indices: 41197251--41197294 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
41197241 TCATTTATAT
41197251 TTTC-ATTTTC-ATTTCCA
1 TTTCTATTTTCTATTTCCA
*
41197268 TTTCTA-TTTCTATTTCTA
1 TTTCTATTTTCTATTTCCA
41197286 TTTCTATTT
1 TTTCTATTT
41197295 CTGGAAACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 8 0.35
18 13 0.57
19 2 0.09
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (19 bp):
TTTCTATTTTCTATTTCCA
Found at i:41197277 original size:12 final size:12
Alignment explanation
Indices: 41197242--41197296 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
41197232 GCAAATGAAT
* *
41197242 CATTTATATTTT
1 CATTTCTATTTC
41197254 CATTT-TCATTTC
1 CATTTCT-ATTTC
41197266 CATTTCTATTTC
1 CATTTCTATTTC
*
41197278 TATTTCTATTTC
1 CATTTCTATTTC
*
41197290 TATTTCT
1 CATTTCT
41197297 GGAAACCTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
11 1 0.03
12 37 0.95
13 1 0.03
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (12 bp):
CATTTCTATTTC
Found at i:41203118 original size:25 final size:26
Alignment explanation
Indices: 41203090--41203150 Score: 88
Period size: 25 Copynumber: 2.4 Consensus size: 26
41203080 TTCCCATAGC
*
41203090 AAAATTTTGACGATTTTACCC-AGGT
1 AAAATTTTGACGAATTTACCCTAGGT
* *
41203115 AAAATTTTGACGAATTTGCCCTTGGT
1 AAAATTTTGACGAATTTACCCTAGGT
41203141 AAAATTTTGA
1 AAAATTTTGA
41203151 GAAAATATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
25 19 0.59
26 13 0.41
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (26 bp):
AAAATTTTGACGAATTTACCCTAGGT
Found at i:41213597 original size:12 final size:14
Alignment explanation
Indices: 41213575--41213613 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
41213565 GAGAAAAACT
*
41213575 TAATAATAATATAAA
1 TAATAAT-ATATACA
*
41213590 TGATAATATATACA
1 TAATAATATATACA
41213604 TAATAATATA
1 TAATAATATA
41213614 CAAAAGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATAATATATACA
Found at i:41214120 original size:31 final size:31
Alignment explanation
Indices: 41214059--41214120 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
41214049 TATATCAAAA
* * *
41214059 AATAAGAACTAATTAGATTTAAAATTAAAGT
1 AATAAAAACTAATTAGAATTAAAATCAAAGT
*
41214090 AATAAAAACTAAATTAGAATTGAAA-CAAAGT
1 AATAAAAACT-AATTAGAATTAAAATCAAAGT
41214121 TAAAAGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.58, C:0.05, G:0.10, T:0.27
Consensus pattern (31 bp):
AATAAAAACTAATTAGAATTAAAATCAAAGT
Found at i:41215545 original size:18 final size:18
Alignment explanation
Indices: 41215517--41215569 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
41215507 CGACAGACTA
41215517 TTTG-CCTTTTTCTTTAT
1 TTTGACCTTTTTCTTTAT
* *
41215534 TTTTAGCTTTTTCTTTAT
1 TTTGACCTTTTTCTTTAT
41215552 TTTGACCTTTTTCTTTAT
1 TTTGACCTTTTTCTTTAT
41215570 ATATAAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
17 3 0.10
18 28 0.90
ACGTcount: A:0.09, C:0.15, G:0.06, T:0.70
Consensus pattern (18 bp):
TTTGACCTTTTTCTTTAT
Found at i:41217609 original size:50 final size:50
Alignment explanation
Indices: 41217528--41217759 Score: 338
Period size: 50 Copynumber: 4.6 Consensus size: 50
41217518 TGAAATAGAT
* *
41217528 ATGAGAGGTCCCATGTAAGACCATGCCTGGGACATGGCGTTGGCACCAAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* *
41217578 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATTGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
41217628 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
*** * * * *
41217678 ATGAGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCATCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
** *
41217728 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGA
41217760 TATGAAATTG
Statistics
Matches: 163, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 163 1.00
ACGTcount: A:0.26, C:0.22, G:0.31, T:0.21
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:41220692 original size:63 final size:63
Alignment explanation
Indices: 41220538--41220791 Score: 184
Period size: 63 Copynumber: 4.1 Consensus size: 63
41220528 TGCTAAGCCA
* * ** * *
41220538 TGTAACTCACTGA-TTGTGATTTAA-AGTCACACGGACC-AGGAACACATACGTGTCTTCAGGCC
1 TGTAACTCACT-ATTTGTGA-TTAAGAGTCACAAGGGCCAAGG-ACACGGACGTGTGTCCAGGCC
*
41220600 A
63 G
* *
41220601 TGTAACACACTATTTGTGATTTAA-AGTCACATGGGCCAAGGACACGGACGTGTGTCCAGGCCG
1 TGTAACTCACTATTTGTGA-TTAAGAGTCACAAGGGCCAAGGACACGGACGTGTGTCCAGGCCG
* * * * * * * **
41220664 TGTAACTCACTGTTTAT-ACTTAAGAGTCACACGAGCCAGGGACAC-CAGCTTGTGTCCAGGTTG
1 TGTAACTCACTATTTGTGA-TTAAGAGTCACAAGGGCCAAGGACACGGA-CGTGTGTCCAGGCCG
* * * *
41220727 AGTAACTCACTATTTGTGA-TATAGGGTCACAAGGGCCAAGGACATGG-CGTGTG-CCAAGCCG
1 TGTAACTCACTATTTGTGATTA-AGAGTCACAAGGGCCAAGGACACGGACGTGTGTCCAGGCCG
41220788 TGTA
1 TGTA
41220792 TGGCATTAAA
Statistics
Matches: 151, Mismatches: 33, Indels: 16
0.75 0.17 0.08
Matches are distributed among these distances:
61 8 0.05
62 14 0.09
63 125 0.83
64 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.25
Consensus pattern (63 bp):
TGTAACTCACTATTTGTGATTAAGAGTCACAAGGGCCAAGGACACGGACGTGTGTCCAGGCCG
Found at i:41221432 original size:22 final size:22
Alignment explanation
Indices: 41221387--41221433 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
41221377 TAGGAAACTA
*
41221387 CATTTGTATCTGATCTGTTATG
1 CATTTGTATCTGATCTATTATG
* *
41221409 CATTTGTATCTGGTCTATTCTG
1 CATTTGTATCTGATCTATTATG
41221431 CAT
1 CAT
41221434 CTTACCTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.49
Consensus pattern (22 bp):
CATTTGTATCTGATCTATTATG
Found at i:41227463 original size:109 final size:109
Alignment explanation
Indices: 41227265--41227489 Score: 436
Period size: 109 Copynumber: 2.1 Consensus size: 109
41227255 TTGTCCTAGT
41227265 ACATAGG--GTGTCACAGCAAAGAATTGAAGTGGACATGGCAAAAATAAAAGTGATCAAAAATTT
1 ACATAGGATGTGTCACAGCAAAGAATTGAAGTGGACATGGCAAAAATAAAAGTGATCAAAAATTT
41227328 GCCACCACCCACCAATGTTAAGGTTATTAGAAGTTTTCTAAGAC
66 GCCACCACCCACCAATGTTAAGGTTATTAGAAGTTTTCTAAGAC
41227372 ACATAGGATGTGTCACAGCAAAGAATTGAAGTGGACATGGCAAAAATAAAAGTGATCAAAAATTT
1 ACATAGGATGTGTCACAGCAAAGAATTGAAGTGGACATGGCAAAAATAAAAGTGATCAAAAATTT
41227437 GCCACCACCCACCAATGTTAAGGTTATTAGAAGTTTTCTAAGAC
66 GCCACCACCCACCAATGTTAAGGTTATTAGAAGTTTTCTAAGAC
41227481 ACATAGGAT
1 ACATAGGAT
41227490 TTTAAAAAGA
Statistics
Matches: 116, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 7 0.06
109 109 0.94
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (109 bp):
ACATAGGATGTGTCACAGCAAAGAATTGAAGTGGACATGGCAAAAATAAAAGTGATCAAAAATTT
GCCACCACCCACCAATGTTAAGGTTATTAGAAGTTTTCTAAGAC
Found at i:41230503 original size:23 final size:23
Alignment explanation
Indices: 41230473--41230525 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
41230463 TTCAAGCATC
41230473 CCAGCACAATCAAGCTTCCCCTA
1 CCAGCACAATCAAGCTTCCCCTA
*
41230496 CCAGCACAATCAAGCTTCCTCTA
1 CCAGCACAATCAAGCTTCCCCTA
41230519 CCA-CACA
1 CCAGCACA
41230526 TCTCCGGCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.14
23 25 0.86
ACGTcount: A:0.32, C:0.43, G:0.08, T:0.17
Consensus pattern (23 bp):
CCAGCACAATCAAGCTTCCCCTA
Found at i:41239198 original size:63 final size:62
Alignment explanation
Indices: 41239099--41239269 Score: 200
Period size: 63 Copynumber: 2.7 Consensus size: 62
41239089 CGCGGGACAG
* * * * *
41239099 GCCGTATAACTCACTGTTTGTGATTTAGAATCACACGGGCTAGGGACATGGGC-GTTTGTCCAA
1 GCCGTGTAACTCACTGTTTGTGCTTAAGAGTCACACGGGCTAGGGACACGGGCAGTTT-T-CAA
* * *
41239162 GCCGTGTAACTCACTGTTTATGCTTAAGAGTCACACGGGTTAGGGACACGGGCATGTTTTCAG
1 GCCGTGTAACTCACTGTTTGTGCTTAAGAGTCACACGGGCTAGGGACACGGGCA-GTTTTCAA
* * * *
41239225 GCTGTGTAACTCACTGTTTGTTCTTAAGAGTTACACGGGCCAGGG
1 GCCGTGTAACTCACTGTTTGTGCTTAAGAGTCACACGGGCTAGGG
41239270 CCACAAGCAT
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
63 87 0.95
64 1 0.01
65 4 0.04
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (62 bp):
GCCGTGTAACTCACTGTTTGTGCTTAAGAGTCACACGGGCTAGGGACACGGGCAGTTTTCAA
Found at i:41244240 original size:13 final size:14
Alignment explanation
Indices: 41244214--41244244 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
41244204 ATTTAAAATC
41244214 ATTATGTATGAATA
1 ATTATGTATGAATA
41244228 ATTATGT-TGAATA
1 ATTATGTATGAATA
41244241 ATTA
1 ATTA
41244245 AGAGATTAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (14 bp):
ATTATGTATGAATA
Found at i:41244560 original size:22 final size:21
Alignment explanation
Indices: 41244532--41244609 Score: 93
Period size: 22 Copynumber: 3.6 Consensus size: 21
41244522 AAGTATGAGA
*
41244532 ACCTATATGTTGATATATGTG
1 ACCTATATGTTAATATATGTG
41244553 ACCATATATGTTAATATATGTG
1 ACC-TATATGTTAATATATGTG
* *
41244575 AACCTAAATGTTTATATATGTG
1 -ACCTATATGTTAATATATGTG
*
41244597 ATTCTATATGTTA
1 A-CCTATATGTTA
41244610 TACCATGCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
21 4 0.08
22 41 0.85
23 3 0.06
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (21 bp):
ACCTATATGTTAATATATGTG
Found at i:41244876 original size:25 final size:26
Alignment explanation
Indices: 41244848--41244898 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
41244838 CCCCTAGGTG
41244848 TGCG-AACACTAGGTATGCGAACCCC
1 TGCGAAACACTAGGTATGCGAACCCC
* *
41244873 TGCGCAAACACTCGGTATGTGAACCC
1 TGCG-AAACACTAGGTATGCGAACCC
41244899 TAGGTGTGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
27 18 0.82
ACGTcount: A:0.27, C:0.31, G:0.24, T:0.18
Consensus pattern (26 bp):
TGCGAAACACTAGGTATGCGAACCCC
Found at i:41244948 original size:14 final size:14
Alignment explanation
Indices: 41244931--41244959 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41244921 GTGACCCTAC
41244931 ATGTGCAAACCCCT
1 ATGTGCAAACCCCT
41244945 ATGTGCAAACCCCT
1 ATGTGCAAACCCCT
41244959 A
1 A
41244960 GGTGTGAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.14, T:0.21
Consensus pattern (14 bp):
ATGTGCAAACCCCT
Found at i:41244969 original size:14 final size:14
Alignment explanation
Indices: 41244933--41244963 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
41244923 GACCCTACAT
*
41244933 GTGCAAACCCCTAT
1 GTGCAAACCCCTAG
41244947 GTGCAAACCCCTAG
1 GTGCAAACCCCTAG
41244961 GTG
1 GTG
41244964 TGAACCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.26, C:0.32, G:0.23, T:0.19
Consensus pattern (14 bp):
GTGCAAACCCCTAG
Found at i:41245299 original size:11 final size:12
Alignment explanation
Indices: 41245272--41245303 Score: 57
Period size: 11 Copynumber: 2.8 Consensus size: 12
41245262 CACCAACAAG
41245272 CTTGTTTATGAA
1 CTTGTTTATGAA
41245284 CTTGTTTATG-A
1 CTTGTTTATGAA
41245295 CTTGTTTAT
1 CTTGTTTAT
41245304 TTACTATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.19, C:0.09, G:0.16, T:0.56
Consensus pattern (12 bp):
CTTGTTTATGAA
Found at i:41245572 original size:23 final size:24
Alignment explanation
Indices: 41245527--41245585 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
41245517 ATTGTCCGTG
*
41245527 AACATGTTCAATTATATGTTCATA
1 AACATGTTCGATTATATGTTCATA
* *
41245551 AACATGTTCGTTTA-ATGTTCATG
1 AACATGTTCGATTATATGTTCATA
41245574 AACATGTTCGAT
1 AACATGTTCGAT
41245586 CAAGTTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 19 0.61
24 12 0.39
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.41
Consensus pattern (24 bp):
AACATGTTCGATTATATGTTCATA
Found at i:41247090 original size:13 final size:14
Alignment explanation
Indices: 41247068--41247100 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
41247058 CTAGAGTAAT
41247068 AAAAAA-ATTGA-A
1 AAAAAAGATTGAGA
41247080 AAAAAAGATTGAGA
1 AAAAAAGATTGAGA
41247094 AAAAAAG
1 AAAAAAG
41247101 GAGAAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 5 0.26
14 8 0.42
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (14 bp):
AAAAAAGATTGAGA
Found at i:41247447 original size:19 final size:19
Alignment explanation
Indices: 41247394--41247447 Score: 81
Period size: 21 Copynumber: 2.7 Consensus size: 19
41247384 CTATCAAGTT
41247394 AAAACTATTTTAATAGGTG
1 AAAACTATTTTAATAGGTG
*
41247413 AAAAATATAATTTAATAGGTG
1 AAAACTAT--TTTAATAGGTG
41247434 AAAACTATTTTAAT
1 AAAACTATTTTAAT
41247448 GAGTATTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 13 0.42
21 18 0.58
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (19 bp):
AAAACTATTTTAATAGGTG
Found at i:41253484 original size:14 final size:14
Alignment explanation
Indices: 41253459--41253500 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
41253449 TGTGATTATT
41253459 ATGATGATTGATATG
1 ATGAT-ATTGATATG
41253474 ATGATATTGATATG
1 ATGATATTGATATG
*
41253488 ATGAGATTGATAT
1 ATGATATTGATAT
41253501 CTTGATATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (14 bp):
ATGATATTGATATG
Found at i:41254122 original size:27 final size:27
Alignment explanation
Indices: 41254091--41254148 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
41254081 GACATTTTTA
*
41254091 GTGGGTTTAGTGGGTTAAACCGGAGGC
1 GTGGGTTTAGTGGGTTAAACCAGAGGC
* *
41254118 GTGGGTTTAGTTGGTTACACCAGAGGC
1 GTGGGTTTAGTGGGTTAAACCAGAGGC
41254145 GTGG
1 GTGG
41254149 CCTCTGAGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.17, C:0.12, G:0.43, T:0.28
Consensus pattern (27 bp):
GTGGGTTTAGTGGGTTAAACCAGAGGC
Found at i:41268770 original size:134 final size:135
Alignment explanation
Indices: 41268539--41268784 Score: 302
Period size: 134 Copynumber: 1.8 Consensus size: 135
41268529 CGATACCAAG
* * * * *
41268539 GAAATTCTATCGATACCAAATATAAGCTATCGATATCGTATCGATACTTGATAAATCCTTTGGAA
1 GAAATTCTATCGATACCAAACAAAAGCTATCGATATCGTATCGATACCTGATAAATACTTTGAAA
** *
41268604 GTCAGAATACCAATTTCGTACCGATACTGAAAAAAT-TATTGATAAAAGTATATCATTATTGATA
66 AACAGAATACCAATTTCGTACCGATACTG-AAAAATGTATCGATAAAAGTATATCATTATTGATA
41268668 CTTGAA
130 CTTGAA
* * *
41268674 GAAATT-TATTGATACCCAACAAAAGGTATCGATA-CTGTATCGATACCTGATAAATACTTTGAA
1 GAAATTCTATCGATACCAAACAAAAGCTATCGATATC-GTATCGATACCTGATAAATACTTTGAA
* * * *
41268737 AAACATAATATC-ATTCTGGTATCGATACTGAAAAATGTATCGATAAAA
65 AAACAGAATACCAATT-TCGTACCGATACTGAAAAATGTATCGATAAAA
41268785 TTTTGAATCT
Statistics
Matches: 93, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
133 10 0.11
134 77 0.83
135 6 0.06
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (135 bp):
GAAATTCTATCGATACCAAACAAAAGCTATCGATATCGTATCGATACCTGATAAATACTTTGAAA
AACAGAATACCAATTTCGTACCGATACTGAAAAATGTATCGATAAAAGTATATCATTATTGATAC
TTGAA
Found at i:41270145 original size:24 final size:25
Alignment explanation
Indices: 41270118--41270164 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
41270108 AAAACTCTTC
* *
41270118 TAAAATAAAACTTAAA-AAAATTCT
1 TAAAAAAAAACTCAAAGAAAATTCT
41270142 TAAAAAAAAACTCAAAGAAAATT
1 TAAAAAAAAACTCAAAGAAAATT
41270165 TTATTAACTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (25 bp):
TAAAAAAAAACTCAAAGAAAATTCT
Found at i:41274099 original size:26 final size:26
Alignment explanation
Indices: 41274066--41274118 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
41274056 AAACTCTTCT
*
41274066 AAAAGAAAACTCAATAGAA-ATTCTTA
1 AAAAGAAAACTCAA-AGAATACTCTTA
41274092 AAAAGAAAACTCAAAGAATACTCTTA
1 AAAAGAAAACTCAAAGAATACTCTTA
41274118 A
1 A
41274119 GTATATCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (26 bp):
AAAAGAAAACTCAAAGAATACTCTTA
Found at i:41284147 original size:30 final size:30
Alignment explanation
Indices: 41284111--41284182 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
41284101 GTTGCATCAT
41284111 ACATGCTCCAAATATTATCTCAAAAAAGAG
1 ACATGCTCCAAATATTATCTCAAAAAAGAG
41284141 ACATGCTCCAAATATTATCTCAAAAAAGAG
1 ACATGCTCCAAATATTATCTCAAAAAAGAG
41284171 ACATGCTCCAAA
1 ACATGCTCCAAA
41284183 AATAATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (30 bp):
ACATGCTCCAAATATTATCTCAAAAAAGAG
Found at i:41295658 original size:22 final size:21
Alignment explanation
Indices: 41295605--41295661 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 21
41295595 TAAATATGAG
41295605 ATTTTAATTAAATTTATTTAT
1 ATTTTAATTAAATTTATTTAT
* *
41295626 ATTTAAGATTAATTTTAATTT-T
1 ATTTTA-ATTAAATTT-ATTTAT
41295648 AATTTTAATTAAAT
1 -ATTTTAATTAAAT
41295662 AATGCAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 5 0.17
22 15 0.52
23 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTAATTAAATTTATTTAT
Found at i:41295955 original size:12 final size:12
Alignment explanation
Indices: 41295934--41295971 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
41295924 ATATTATTTA
41295934 ATTAAATTTTCT
1 ATTAAATTTTCT
*
41295946 ATT-AATTTTTT
1 ATTAAATTTTCT
41295957 AATTAAATTTTCT
1 -ATTAAATTTTCT
41295970 AT
1 AT
41295972 AAAAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
11 7 0.32
12 8 0.36
13 7 0.32
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (12 bp):
ATTAAATTTTCT
Found at i:41295958 original size:24 final size:25
Alignment explanation
Indices: 41295921--41295971 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
41295911 AATAAATGAA
41295921 ATTATATTATTTAATTAAATTTTCT
1 ATTATATTATTTAATTAAATTTTCT
*
41295946 ATTA-ATTTTTTAATTAAATTTTCT
1 ATTATATTATTTAATTAAATTTTCT
41295970 AT
1 AT
41295972 AAAAAAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTATATTATTTAATTAAATTTTCT
Found at i:41295965 original size:13 final size:13
Alignment explanation
Indices: 41295920--41295967 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
41295910 GAATAAATGA
* *
41295920 AATTATATTATTT
1 AATTAAATTTTTT
*
41295933 AATTAAATTTTCT
1 AATTAAATTTTTT
41295946 -ATT-AATTTTTT
1 AATTAAATTTTTT
41295957 AATTAAATTTT
1 AATTAAATTTT
41295968 CTATAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
11 7 0.24
12 6 0.21
13 16 0.55
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (13 bp):
AATTAAATTTTTT
Found at i:41298365 original size:21 final size:21
Alignment explanation
Indices: 41298318--41298365 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
41298308 ATTGTTTTGT
* * *
41298318 TGTTTTTCCATGTTTTGCTAC
1 TGTTTTCCCATGTTTTCCCAC
* *
41298339 TATTTTCCCATTTTTTCCCAC
1 TGTTTTCCCATGTTTTCCCAC
41298360 TGTTTT
1 TGTTTT
41298366 GCTACCATAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.10, C:0.23, G:0.08, T:0.58
Consensus pattern (21 bp):
TGTTTTCCCATGTTTTCCCAC
Found at i:41301591 original size:46 final size:46
Alignment explanation
Indices: 41301524--41302028 Score: 594
Period size: 51 Copynumber: 10.6 Consensus size: 46
41301514 TTTGAGTACT
*
41301524 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
41301570 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
41301616 TATGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
* *
41301662 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTATACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
41301708 TCTGATC-AGTGACAAGTGGAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
41301759 TCTGATCAAGTG-GAAAGTGATGAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
41301804 TCTGATC-AGTGACAAGTGGAAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
* * *
41301855 TCTGATCAAGTG-GAAAGTGATGAGTGATAGCTTCGGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
*
41301900 TCTGATC-AGTGACAAGTGGAAAGTGGTAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGAC------AAAGTGATAAGTGATAGCTTCAGCTACACTTA
41301951 TCTGATC-AGTGACAAGTGACAAGTGATAAGTGATAGCTTCAGCTACACTTA
1 TCTGATCAAGTGAC-----A-AAGTGATAAGTGATAGCTTCAGCTACACTTA
*
41302002 TCTGATC-AGGGAC-AAGTGATAAGTGAT
1 TCTGATCAAGTGACAAAGTGATAAGTGAT
41302029 CATACGCAAG
Statistics
Matches: 407, Mismatches: 29, Indels: 48
0.84 0.06 0.10
Matches are distributed among these distances:
44 22 0.05
45 80 0.20
46 136 0.33
50 3 0.01
51 158 0.39
52 8 0.02
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:41301592 original size:39 final size:39
Alignment explanation
Indices: 41301546--41301684 Score: 134
Period size: 46 Copynumber: 3.2 Consensus size: 39
41301536 ACAAAGTGAT
41301546 AAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA
1 AAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA
* *
41301585 AAGTGATAAGTGGTAGTTTTAGCTACACTTATATGATCAAGTGACAAAGTGA
1 AAGTG---A----TAGCTTTAGCTACACTTATCTGATCAAGTGAC------A
41301637 TAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA
1 -AAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA
41301677 AAGTGATA
1 AAGTGATA
41301685 AGTGATAGCT
Statistics
Matches: 82, Mismatches: 4, Indels: 28
0.72 0.04 0.25
Matches are distributed among these distances:
39 13 0.16
40 1 0.01
42 1 0.01
46 60 0.73
50 1 0.01
52 1 0.01
53 5 0.06
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (39 bp):
AAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA
Found at i:41301816 original size:96 final size:97
Alignment explanation
Indices: 41301538--41302028 Score: 705
Period size: 96 Copynumber: 5.1 Consensus size: 97
41301528 ATCAAGTGAC
* * * *
41301538 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGTT
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGATAGCT
** *
41301603 TTAGCTACACTTATATGATCAAGTGAC------
66 TCGGCTACACTTATCTGATC-AGTGACAAGTGG
* *
41301630 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGATAGCT
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGATAGCT
*
41301695 TCGGCTATACTTATCTGATCAGTGACAAGTGG
66 TCGGCTACACTTATCTGATCAGTGACAAGTGG
*
41301727 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTG-GAAAGTGATGAGTGATAGCT
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGATAGCT
41301791 TCGGCTACACTTATCTGATCAGTGACAAGTGG
66 TCGGCTACACTTATCTGATCAGTGACAAGTGG
*
41301823 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTG-GAAAGTGATGAGTGATAGCT
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGATAGCT
41301887 TCGGCTACACTTATCTGATCAGTGACAAGTGG
66 TCGGCTACACTTATCTGATCAGTGACAAGTGG
*
41301919 AAAGTGGTAAGTGATAGCTTCAGCTACACTTATCTGATC-AGTGACAAGTGACAAGTGATAAGTG
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTG---A--GA-AAGTGATAAGTG
* *
41301983 ATAGCTTCAGCTACACTTATCTGATCAGGGACAAGT-G
60 ATAGCTTCGGCTACACTTATCTGATCAGTGACAAGTGG
41302020 ATAAGTGAT
1 A-AAGTGAT
41302029 CATACGCAAG
Statistics
Matches: 370, Mismatches: 15, Indels: 18
0.92 0.04 0.04
Matches are distributed among these distances:
91 6 0.02
92 79 0.21
95 4 0.01
96 183 0.49
97 43 0.12
101 4 0.01
102 51 0.14
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (97 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGATAGCT
TCGGCTACACTTATCTGATCAGTGACAAGTGG
Found at i:41301933 original size:147 final size:146
Alignment explanation
Indices: 41301538--41302028 Score: 615
Period size: 147 Copynumber: 3.4 Consensus size: 146
41301528 ATCAAGTGAC
* * * *
41301538 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTGGTAGTT
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTG-GAAAGTGATAAGTGATAGCT
* * *
41301603 TTAGCTACACTTATATGATCAAGTGAC------AAAGTGATAAGTGATAGCTTTAGCTACACTTA
65 TCAGCTACACTTATCTGATC-AGTGACAAGTGGAAAGTGATAAGTGATAGCTTCAGCTACACTTA
41301662 TCTGATCAAGTGAC-----
129 TCTGATC-AGTGACAAGTG
* *
41301676 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAGTGACAAGTGGAAAGTGATAAGTGA
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTG---A-T--CAAGTGGAAAGTGATAAGTGA
* *
41301741 TAGCTTCAGCTACACTTATCTG---A-T--CAAGTGGAAAGTGATGAGTGATAGCTTCGGCTACA
60 TAGCTTCAGCTACACTTATCTGATCAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCAGCTACA
41301800 CTTATCTGATCAGTGACAAGTGG
125 CTTATCTGATCAGTGACAAGT-G
*
41301823 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGGAAAGTGATGAGTGATAGCTT
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGGAAAGTGATAAGTGATAGCTT
* *
41301888 CGGCTACACTTATCTGATCAGTGACAAGTGGAAAGTGGTAAGTGATAGCTTCAGCTACACTTATC
66 CAGCTACACTTATCTGATCAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCAGCTACACTTATC
41301953 TGATCAGTGACAAGTG
131 TGATCAGTGACAAGTG
41301969 ACAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATC-AG-GGACAAGTGATAAGTGAT
1 A-AAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGGA-AAGTGATAAGTGAT
41302029 CATACGCAAG
Statistics
Matches: 308, Mismatches: 19, Indels: 44
0.83 0.05 0.12
Matches are distributed among these distances:
136 1 0.00
138 34 0.11
139 1 0.00
141 48 0.16
142 37 0.12
143 33 0.11
144 8 0.03
145 4 0.01
146 17 0.06
147 125 0.41
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (146 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGGAAAGTGATAAGTGATAGCTT
CAGCTACACTTATCTGATCAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCAGCTACACTTATC
TGATCAGTGACAAGTG
Found at i:41305460 original size:11 final size:11
Alignment explanation
Indices: 41305444--41305479 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
41305434 AGCATTCTAG
41305444 TTTCTTTTTTT
1 TTTCTTTTTTT
*
41305455 TTTCTTTTCTT
1 TTTCTTTTTTT
*
41305466 CTTCTTTTTTT
1 TTTCTTTTTTT
41305477 TTT
1 TTT
41305480 GTCATATACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:41305818 original size:21 final size:21
Alignment explanation
Indices: 41305776--41305819 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41305766 AAAGTTTTGA
* * **
41305776 TTTTTAAGAAAAATAGTGATT
1 TTTTTAAAAAAAAGAGAAATT
41305797 TTTTTAAAAAAAAGAGAAATT
1 TTTTTAAAAAAAAGAGAAATT
41305818 TT
1 TT
41305820 AGATTTTTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (21 bp):
TTTTTAAAAAAAAGAGAAATT
Found at i:41305891 original size:147 final size:147
Alignment explanation
Indices: 41305647--41305922 Score: 421
Period size: 147 Copynumber: 1.9 Consensus size: 147
41305637 AAAAATTGAT
*
41305647 TTTTTTTAAAAAAAAAGAGAGTTTAGATTTTTAAAATAAAAATCTATTTTTTAGTCATATTAAAG
1 TTTTTTTAAAAAAAAAGAAAGTTTAGATTTTTAAAATAAAAA-CTATTTTTTAGTCATATTAAAG
* * *
41305712 GAAAAATTTAAATTTTTAAAACAAAATTTTGATCTTTTTCAACTATTTCAAAATAAAGTTTTGAT
65 GAAAAATTTAAATTTTTAAAACAAAATTTTGATCTTGTCCAACTATTTCAAAATAAAGCTTTGAT
41305777 TTTTAAGAAAAATAGTGA
130 TTTTAAGAAAAATAGTGA
* * *
41305795 TTTTTTTAAAAAAAAGAGAAATTTTAGATTTTTAAAATAAAAA-TA-TTTTTAGTCATTTTTAAG
1 TTTTTTTAAAAAAAA-AGAAAGTTTAGATTTTTAAAATAAAAACTATTTTTTAGTCATATTAAAG
* * *
41305858 GAAAATTTTAAATTTTTTAAAACAAAGTTTTGATCTTGTCCAACTATTTCGAAATAAAGCTTTGA
65 GAAAAATTTAAA-TTTTTAAAACAAAATTTTGATCTTGTCCAACTATTTCAAAATAAAGCTTTGA
41305923 AGAAAAGTAG
Statistics
Matches: 116, Mismatches: 10, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
146 27 0.23
147 49 0.42
148 15 0.13
149 25 0.22
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.42
Consensus pattern (147 bp):
TTTTTTTAAAAAAAAAGAAAGTTTAGATTTTTAAAATAAAAACTATTTTTTAGTCATATTAAAGG
AAAAATTTAAATTTTTAAAACAAAATTTTGATCTTGTCCAACTATTTCAAAATAAAGCTTTGATT
TTTAAGAAAAATAGTGA
Found at i:41307499 original size:23 final size:23
Alignment explanation
Indices: 41307473--41307548 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
41307463 ATAAGTGCAA
41307473 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
41307496 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
41307519 CACTGGA-ATGTAGCCGAAGCTAC
1 CACT-GATATGTAGCCGAAGCTAC
41307542 CACTGAT
1 CACTGAT
41307549 CAATAACACT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.04
23 46 0.94
24 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:41308360 original size:16 final size:16
Alignment explanation
Indices: 41308341--41308376 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41308331 GTAGAAACAT
* *
41308341 GAAATTCAAGCATCAA
1 GAAAATCAAGAATCAA
41308357 GAAAATCAAGAATCAA
1 GAAAATCAAGAATCAA
41308373 GAAA
1 GAAA
41308377 CATGAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.14, G:0.14, T:0.14
Consensus pattern (16 bp):
GAAAATCAAGAATCAA
Found at i:41309528 original size:28 final size:30
Alignment explanation
Indices: 41309496--41309551 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
41309486 TTAGGACTTA
41309496 TCTTTT-AATT-T-CTTGCTGTCAATTTTTT
1 TCTTTTAAATTCTGCTTG-TGTCAATTTTTT
41309524 TCTTTTAAATTCTGCTTGTGTCAATTTT
1 TCTTTTAAATTCTGCTTGTGTCAATTTT
41309552 ATTTAATCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 6 0.24
29 4 0.16
30 11 0.44
31 4 0.16
ACGTcount: A:0.16, C:0.14, G:0.09, T:0.61
Consensus pattern (30 bp):
TCTTTTAAATTCTGCTTGTGTCAATTTTTT
Found at i:41318907 original size:70 final size:72
Alignment explanation
Indices: 41318833--41319074 Score: 260
Period size: 70 Copynumber: 3.5 Consensus size: 72
41318823 TCAAATAATA
* * * * * *
41318833 TCAAAATATTCAAAATATTTGTA-CAAATTAATTAATC-TC-ATGTTATTACATCAAATAATATC
1 TCAAAATATTCAAAATATTT-TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATC
41318895 AAAATAAC
65 AAAATAAC
41318903 TCAAAA-A---AAATTATATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATAT
1 TCAAAATATTCAAA--ATATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATAT
41318964 CAAAATAAC
64 CAAAATAAC
*
41318973 TCAAAAAAATTTC----TATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATAT
1 TC-AAAATA-TTCAAAATATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATAT
41319034 CAAAATAAC
64 CAAAATAAC
* *
41319043 TCAAAATATT---TATATTTTATTACATAAAATAA
1 TCAAAATATTCAAAATATTTTATTACATCAAATAA
41319075 TATCAAAATA
Statistics
Matches: 151, Mismatches: 8, Indels: 27
0.81 0.04 0.15
Matches are distributed among these distances:
66 3 0.02
67 2 0.01
68 17 0.11
69 27 0.18
70 97 0.64
71 4 0.03
72 1 0.01
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.38
Consensus pattern (72 bp):
TCAAAATATTCAAAATATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCA
AAATAAC
Found at i:41318931 original size:25 final size:25
Alignment explanation
Indices: 41318903--41319030 Score: 133
Period size: 25 Copynumber: 5.3 Consensus size: 25
41318893 TCAAAATAAC
* *
41318903 TCAAAAAAAATTATATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
*
41318928 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
* ** *
41318953 TCAAATAATA-TC-A--AAATAAC-
1 TCAAATAAAATTCTATTTTATTACA
41318973 TCAAA-AAAATTTCTATTTTATTACA
1 TCAAATAAAA-TTCTATTTTATTACA
*
41318998 TCAAATAAACTTCTATTTTATTACA
1 TCAAATAAAATTCTATTTTATTACA
41319023 TCAAATAA
1 TCAAATAA
41319031 TATCAAAATA
Statistics
Matches: 83, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
19 3 0.04
20 5 0.06
21 6 0.07
22 1 0.01
23 1 0.01
24 6 0.07
25 58 0.70
26 3 0.04
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (25 bp):
TCAAATAAAATTCTATTTTATTACA
Found at i:41319062 original size:44 final size:43
Alignment explanation
Indices: 41319011--41319096 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 43
41319001 AATAAACTTC
*
41319011 TATTTTATTACATCAAATAATATCAAAATAACTCAAAATATTTA
1 TATTTTATTACATAAAATAATATCAAAAT-ACTCAAAATATTTA
*
41319055 TATTTTATTACATAAAATAATATCAAAATATTCAAAATATTT
1 TATTTTATTACATAAAATAATATCAAAATACTCAAAATATTT
41319097 GTACAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 12 0.30
44 28 0.70
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (43 bp):
TATTTTATTACATAAAATAATATCAAAATACTCAAAATATTTA
Found at i:41320203 original size:7 final size:7
Alignment explanation
Indices: 41320193--41320218 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41320183 TTATATACAT
41320193 AATACTA
1 AATACTA
41320200 AATACTA
1 AATACTA
41320207 AATACTA
1 AATACTA
41320214 AATAC
1 AATAC
41320219 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Done.