Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014870.1 Kokia drynarioides strain JFW-HI SEQ_129913, 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: 345502
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Warning! 6 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:262 original size:111 final size:111
Alignment explanation
Indices: 83--301 Score: 429
Period size: 111 Copynumber: 2.0 Consensus size: 111
73 TCCCATGTCC
83 TTGAAAATAATTTTCCTTGAGAATCCAGTTCATAGTACTTCAACCTAGAGTCATCAGAATACTCA
1 TTGAAAATAATTTTCCTTGAGAATCCAGTTCATAGTACTTCAACCTAGAGTCATCAGAATACTCA
148 TAAGTGAAATAGTACATTTGTTGTCGATTATCTGCAAACACATTTG
66 TAAGTGAAATAGTACATTTGTTGTCGATTATCTGCAAACACATTTG
194 TTGAAAATAATTTTCCTTGAGAATCCAGTTCATAGTACTTCAACCTAGAGTCATCAGAATACTCA
1 TTGAAAATAATTTTCCTTGAGAATCCAGTTCATAGTACTTCAACCTAGAGTCATCAGAATACTCA
*
259 TAAGTGAAATAGTACATTTGTTGTCGATTATCTGCAACCACAT
66 TAAGTGAAATAGTACATTTGTTGTCGATTATCTGCAAACACAT
302 GAAACCCATC
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (111 bp):
TTGAAAATAATTTTCCTTGAGAATCCAGTTCATAGTACTTCAACCTAGAGTCATCAGAATACTCA
TAAGTGAAATAGTACATTTGTTGTCGATTATCTGCAAACACATTTG
Found at i:1692 original size:15 final size:15
Alignment explanation
Indices: 1649--1697 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1639 AGGGTGTTGA
*
1649 AGAAGAAAAGAAAAG
1 AGAAGAAAAGGAAAG
* *
1664 AGAATAAAAAGAAAG
1 AGAAGAAAAGGAAAG
* *
1679 AGAAGAGAAGGAAAA
1 AGAAGAAAAGGAAAG
1694 AGAA
1 AGAA
1698 AAAGAAGACG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.71, C:0.00, G:0.27, T:0.02
Consensus pattern (15 bp):
AGAAGAAAAGGAAAG
Found at i:1703 original size:21 final size:21
Alignment explanation
Indices: 1651--1710 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
1641 GGTGTTGAAG
* *
1651 AAGAAAAGAAAAGAGAA-TAAA
1 AAGAAAA-AGAAGAGAAGGAAA
*
1672 AAGAAAGAGAAGAGAAGGAAA
1 AAGAAAAAGAAGAGAAGGAAA
1693 AAGAAAAAGAAGACGAAG
1 AAGAAAAAGAAGA-GAAG
1711 TTGTTCTCAC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 8 0.24
21 21 0.64
22 4 0.12
ACGTcount: A:0.70, C:0.02, G:0.27, T:0.02
Consensus pattern (21 bp):
AAGAAAAAGAAGAGAAGGAAA
Found at i:2131 original size:17 final size:17
Alignment explanation
Indices: 2109--2156 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
2099 ATTTATCTAG
2109 TTGTCATTACATTTTAA
1 TTGTCATTACATTTTAA
* * *
2126 TTGTCACTGCATTTTAC
1 TTGTCATTACATTTTAA
* *
2143 TTGTTATCACATTT
1 TTGTCATTACATTT
2157 GCATTGTAGT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.23, C:0.17, G:0.08, T:0.52
Consensus pattern (17 bp):
TTGTCATTACATTTTAA
Found at i:7021 original size:47 final size:47
Alignment explanation
Indices: 6960--7059 Score: 191
Period size: 47 Copynumber: 2.1 Consensus size: 47
6950 GATTAAAGGA
6960 CCATCTATAAAGCATGGAAAATATGGAATGTAATCTTCGAAGATATT
1 CCATCTATAAAGCATGGAAAATATGGAATGTAATCTTCGAAGATATT
7007 CCATCTATAAAGCATGGAAAATATGGAATGTAATCTTCGAAGATATT
1 CCATCTATAAAGCATGGAAAATATGGAATGTAATCTTCGAAGATATT
*
7054 CAATCT
1 CCATCT
7060 TAGATATTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (47 bp):
CCATCTATAAAGCATGGAAAATATGGAATGTAATCTTCGAAGATATT
Found at i:11015 original size:14 final size:14
Alignment explanation
Indices: 10996--11024 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
10986 CATGTTTCCT
10996 TCAATTTAAAATCC
1 TCAATTTAAAATCC
11010 TCAATTTAAAATCC
1 TCAATTTAAAATCC
11024 T
1 T
11025 TTTATAAATT
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:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (14 bp):
TCAATTTAAAATCC
Found at i:11834 original size:25 final size:25
Alignment explanation
Indices: 11762--11836 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 25
11752 GAATTTTCTT
* *
11762 GAAATTTTATCTAGAGTAAAATCATC
1 GAAATTTTA-CTAGGGTAAAATTATC
* * *
11788 AAAATTTTACAAAGGGTAAAATTGTC
1 GAAATTTTAC-TAGGGTAAAATTATC
11814 GAAATTTTACTAGGGTAAAATTA
1 GAAATTTTACTAGGGTAAAATTA
11837 GGATGAAAGA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
25 12 0.30
26 28 0.70
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (25 bp):
GAAATTTTACTAGGGTAAAATTATC
Found at i:25636 original size:146 final size:146
Alignment explanation
Indices: 25372--25664 Score: 586
Period size: 146 Copynumber: 2.0 Consensus size: 146
25362 AAATAGTTTT
25372 TAAGGAAAATCAATATTGAAGGCAATCAGCGTCCAGAAGAAGCCAAAACTATTTTCTAGTACATT
1 TAAGGAAAATCAATATTGAAGGCAATCAGCGTCCAGAAGAAGCCAAAACTATTTTCTAGTACATT
25437 GCAGGTGGCAAGTGAATTCTACAATAGAATAGACTCAACTGGAAGTGATGTGGGGTACTCTGGTC
66 GCAGGTGGCAAGTGAATTCTACAATAGAATAGACTCAACTGGAAGTGATGTGGGGTACTCTGGTC
25502 GATGGACAAGGCAGTC
131 GATGGACAAGGCAGTC
25518 TAAGGAAAATCAATATTGAAGGCAATCAGCGTCCAGAAGAAGCCAAAACTATTTTCTAGTACATT
1 TAAGGAAAATCAATATTGAAGGCAATCAGCGTCCAGAAGAAGCCAAAACTATTTTCTAGTACATT
25583 GCAGGTGGCAAGTGAATTCTACAATAGAATAGACTCAACTGGAAGTGATGTGGGGTACTCTGGTC
66 GCAGGTGGCAAGTGAATTCTACAATAGAATAGACTCAACTGGAAGTGATGTGGGGTACTCTGGTC
25648 GATGGACAAGGCAGTC
131 GATGGACAAGGCAGTC
25664 T
1 T
25665 TAACTACCCC
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 147 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (146 bp):
TAAGGAAAATCAATATTGAAGGCAATCAGCGTCCAGAAGAAGCCAAAACTATTTTCTAGTACATT
GCAGGTGGCAAGTGAATTCTACAATAGAATAGACTCAACTGGAAGTGATGTGGGGTACTCTGGTC
GATGGACAAGGCAGTC
Found at i:25925 original size:17 final size:17
Alignment explanation
Indices: 25903--25938 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
25893 GTTCCCTGTA
25903 TAAAAAATTT-TAATAAT
1 TAAAAAATTTATAA-AAT
25920 TAAAAAATTTATAAAAT
1 TAAAAAATTTATAAAAT
25937 TA
1 TA
25939 TTTAATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.83
18 3 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAAAATTTATAAAAT
Found at i:26151 original size:37 final size:37
Alignment explanation
Indices: 26110--26184 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
26100 AAGCATTGTA
26110 ATATACTTCTATTGATCAATAAAATATGATTTCTCTT
1 ATATACTTCTATTGATCAATAAAATATGATTTCTCTT
*
26147 ATATACTTCTATTGATCAATAAAATATGTTTTCTCTT
1 ATATACTTCTATTGATCAATAAAATATGATTTCTCTT
26184 A
1 A
26185 GCTCTCTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (37 bp):
ATATACTTCTATTGATCAATAAAATATGATTTCTCTT
Found at i:38263 original size:42 final size:42
Alignment explanation
Indices: 38198--38285 Score: 113
Period size: 42 Copynumber: 2.1 Consensus size: 42
38188 GTGAGTTGTA
*
38198 TAGGCAAGCAGTGCATACAAGCTATGAACTGCAAGCCCCATG
1 TAGGCAAGCAATGCATACAAGCTATGAACTGCAAGCCCCATG
* * * ** *
38240 TAGGCAAGCAATGCATGCGAGCTATGGACTGTGAGCTCCATG
1 TAGGCAAGCAATGCATACAAGCTATGAACTGCAAGCCCCATG
38282 TAGG
1 TAGG
38286 TGAGTAGTGC
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.28, T:0.19
Consensus pattern (42 bp):
TAGGCAAGCAATGCATACAAGCTATGAACTGCAAGCCCCATG
Found at i:48605 original size:47 final size:48
Alignment explanation
Indices: 48544--48635 Score: 168
Period size: 47 Copynumber: 1.9 Consensus size: 48
48534 GATGATATAA
48544 TTTTCAATAATGTAATTAATGCAAA-TAATATTATTCAAAATAAATAC
1 TTTTCAATAATGTAATTAATGCAAAGTAATATTATTCAAAATAAATAC
*
48591 TTTTTAATAATGTAATTAATGCAAAGTAATATTATTCAAAATAAA
1 TTTTCAATAATGTAATTAATGCAAAGTAATATTATTCAAAATAAA
48636 ACTAATAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 24 0.56
48 19 0.44
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (48 bp):
TTTTCAATAATGTAATTAATGCAAAGTAATATTATTCAAAATAAATAC
Found at i:49702 original size:332 final size:332
Alignment explanation
Indices: 49098--49758 Score: 1105
Period size: 332 Copynumber: 2.0 Consensus size: 332
49088 ATAAAAACCA
*
49098 TTTATATAATAAATTATATAATTGATTATTTATAAAATTATACACATGAAATATAAAGTTATTTA
1 TTTATATAATAAATTATATAATTGATTATTTATAAAATTATAAACATGAAATATAAAGTTATTTA
49163 ATATATAAATAATTAAATTTTAATATTTAAAACTAAAGTAATATTTTTTACTTTTTTAATTAATG
66 ATATATAAATAATTAAATTTTAATATTTAAAACTAAAGTAATATTTTTTACTTTTTTAATTAATG
*
49228 AAACATAATACTTTAAAGATAAAATAATTCTATATAAATTTTAACCTTTTGTAAATAATTATATA
131 AAACATAATACTTTAAAGATAAAATAACTCTATATAAATTTTAACCTTTTGTAAATAATTATATA
*
49293 AATTCATTTAACAAAAGTGTTTTAAAAAATCAAAATGCTTATTTATAAATATGATAAAATTTATA
196 AATTCATGTAACAAAAGTGTTTTAAAAAATCAAAATGCTTATTTATAAATATGATAAAATTTATA
*
49358 TATAATAAAAAATATTTAAAATGAC-A-AATAATACAATCAACAATGAAGGATATATTTACTAGT
261 AATAATAAAAAATATTTAAAATGACAACAATAATACAATCAACAATGAAGGATATATTTACTAGT
49421 TCAAATG
326 TCAAATG
49428 TTTATATAATAAATTATATAAATT-ATTATTTATAAAATTATAAACATGAAATATAAAGTTATTT
1 TTTATATAATAAATTATAT-AATTGATTATTTATAAAATTATAAACATGAAATATAAAGTTATTT
* *
49492 ATTATATAAATAATTAAATTTTAATATTTAAAATTAAAGTAATATATTTTTTACTTTTTTAATTA
65 AATATATAAATAATTAAATTTTAATATTTAAAACTAAAGT-A-ATATTTTTTACTTTTTTAATTA
* * * *
49557 CTTAAACATAATACTTTAAAGATAAAATAACTCTATATAAATTTTAACCTTTTTTAAATTATTAT
128 ATGAAACATAATACTTTAAAGATAAAATAACTCTATATAAATTTTAACCTTTTGTAAATAATTAT
* * ** * *
49622 ATAAATTCATGTGACAGAAGTGTTTTAAAAGAATCTGAATTCTTATTTTTAAATATGAT-AAATT
193 ATAAATTCATGTAACAAAAGTGTTTTAAAA-AATCAAAATGCTTATTTATAAATATGATAAAATT
*
49686 TATAAATAATAAAAAATATTTAAAATGACAACAATAATATAATCAACAATGAAGGATATATTTAC
257 TATAAATAATAAAAAATATTTAAAATGACAACAATAATACAATCAACAATGAAGGATATATTTAC
49751 TAGTTCAA
322 TAGTTCAA
49759 TAGTTTCTTC
Statistics
Matches: 308, Mismatches: 17, Indels: 8
0.92 0.05 0.02
Matches are distributed among these distances:
330 96 0.31
331 5 0.02
332 142 0.46
333 25 0.08
334 40 0.13
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (332 bp):
TTTATATAATAAATTATATAATTGATTATTTATAAAATTATAAACATGAAATATAAAGTTATTTA
ATATATAAATAATTAAATTTTAATATTTAAAACTAAAGTAATATTTTTTACTTTTTTAATTAATG
AAACATAATACTTTAAAGATAAAATAACTCTATATAAATTTTAACCTTTTGTAAATAATTATATA
AATTCATGTAACAAAAGTGTTTTAAAAAATCAAAATGCTTATTTATAAATATGATAAAATTTATA
AATAATAAAAAATATTTAAAATGACAACAATAATACAATCAACAATGAAGGATATATTTACTAGT
TCAAATG
Found at i:57205 original size:27 final size:27
Alignment explanation
Indices: 57175--57235 Score: 95
Period size: 27 Copynumber: 2.3 Consensus size: 27
57165 GTTAGGGGTT
*
57175 TATAAATTAAATTTGTGAAAATTATGA
1 TATAAATTAAATTTATGAAAATTATGA
* *
57202 TATAAATTAAATTTATGGAAATTATGG
1 TATAAATTAAATTTATGAAAATTATGA
57229 TATAAAT
1 TATAAAT
57236 AAAAATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (27 bp):
TATAAATTAAATTTATGAAAATTATGA
Found at i:59286 original size:15 final size:15
Alignment explanation
Indices: 59266--59306 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
59256 ATAGATCGAC
59266 TACATGCAAATTCAA
1 TACATGCAAATTCAA
*
59281 TACATGTAAATTCAA
1 TACATGCAAATTCAA
59296 TACATGACAAA
1 TACATG-CAAA
59307 CATTCTTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (15 bp):
TACATGCAAATTCAA
Found at i:61008 original size:37 final size:36
Alignment explanation
Indices: 60950--61113 Score: 161
Period size: 37 Copynumber: 4.4 Consensus size: 36
60940 GCACGATGGA
* *
60950 TTGCTAGGCATAAAGCCCGATAACATCGGCATAAAGC
1 TTGCTAGGCATAAAGCTCGATAACAT-GGCACAAAGC
* * * *
60987 TTACTAGGCACATAGCTCGATAACAGTGGCACGAAGGC
1 TTGCTAGGCATAAAGCTCGATAACA-TGGCAC-AAAGC
* *
61025 CTGCTAGGCATAAAGCTCAATAACATAGGCACAAAGGC
1 TTGCTAGGCATAAAGCTCGATAACAT-GGCACAAA-GC
61063 TTGCTAGGCAT-AAGCTCGATAACACCT-GCACAAAGGC
1 TTGCTAGGCATAAAGCTCGATAACA--TGGCACAAA-GC
*
61100 CTGCTAGGCATAAA
1 TTGCTAGGCATAAA
61114 ACCCAATAAC
Statistics
Matches: 105, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
37 60 0.57
38 44 0.42
39 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.18
Consensus pattern (36 bp):
TTGCTAGGCATAAAGCTCGATAACATGGCACAAAGC
Found at i:61042 original size:38 final size:38
Alignment explanation
Indices: 60933--61153 Score: 191
Period size: 38 Copynumber: 5.9 Consensus size: 38
60923 TATCCCATTG
* * *
60933 AACACTGGCACGATGGATTGCTAGGCATAAAGCCCGAT
1 AACACTGGCACGAAGGCTTGCTAGGCATAAAGCTCGAT
* * * * *
60971 AACA-TCGGCA-TAAAGCTTACTAGGCACATAGCTCGAT
1 AACACT-GGCACGAAGGCTTGCTAGGCATAAAGCTCGAT
* * *
61008 AACAGTGGCACGAAGGCCTGCTAGGCATAAAGCTCAAT
1 AACACTGGCACGAAGGCTTGCTAGGCATAAAGCTCGAT
*
61046 AACA-TAGGCACAAAGGCTTGCTAGGCAT-AAGCTCGAT
1 AACACT-GGCACGAAGGCTTGCTAGGCATAAAGCTCGAT
* * * * *
61083 AACACCT-GCACAAAGGCCTGCTAGGCATAAAACCCAAT
1 AACA-CTGGCACGAAGGCTTGCTAGGCATAAAGCTCGAT
* * * *
61121 AACACTGGAACGAAGGCATACTATGCATAAAGC
1 AACACTGGCACGAAGGCTTGCTAGGCATAAAGC
61154 CTGATATCAC
Statistics
Matches: 147, Mismatches: 28, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
37 63 0.43
38 83 0.56
39 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.17
Consensus pattern (38 bp):
AACACTGGCACGAAGGCTTGCTAGGCATAAAGCTCGAT
Found at i:61137 original size:75 final size:75
Alignment explanation
Indices: 60951--61184 Score: 246
Period size: 75 Copynumber: 3.1 Consensus size: 75
60941 CACGATGGAT
* * * * *
60951 TGCTAGGCATAAAGCCCGATAACATCGGCATAAA-GCTTACTAGGCACATAGCTCGATAACA-GT
1 TGCTAGGCATAAAGCCCAATAACATAGGCACAAAGGCTTACTAGGCATA-AGCTCGATAACACCT
*
61014 GGCACGAAGGCC
65 -GCACAAAGGCC
* *
61026 TGCTAGGCATAAAGCTCAATAACATAGGCACAAAGGCTTGCTAGGCATAAGCTCGATAACACCTG
1 TGCTAGGCATAAAGCCCAATAACATAGGCACAAAGGCTTACTAGGCATAAGCTCGATAACACCTG
61091 CACAAAGGCC
66 CACAAAGGCC
* * * * * *
61101 TGCTAGGCATAAAACCCAATAACACT-GGAACGAAGGCATACTATGCATAAAGC-CTGATATCAC
1 TGCTAGGCATAAAGCCCAATAACA-TAGGCACAAAGGCTTACTAGGCAT-AAGCTC-GATAACAC
61164 C-GACACAAA-GCC
63 CTG-CACAAAGGCC
61176 TGCTAGGCA
1 TGCTAGGCA
61185 CATAGCCCGA
Statistics
Matches: 137, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
75 105 0.77
76 32 0.23
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (75 bp):
TGCTAGGCATAAAGCCCAATAACATAGGCACAAAGGCTTACTAGGCATAAGCTCGATAACACCTG
CACAAAGGCC
Found at i:64267 original size:36 final size:36
Alignment explanation
Indices: 64215--64286 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
64205 CGTCCCTCTT
64215 GAAGCAATTTCAACCTAGAACGAAAACAACTAAATC
1 GAAGCAATTTCAACCTAGAACGAAAACAACTAAATC
*
64251 GAAGTAATTTCAACCTAGAACGAAAACAACTAAATC
1 GAAGCAATTTCAACCTAGAACGAAAACAACTAAATC
64287 AGTAACCCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (36 bp):
GAAGCAATTTCAACCTAGAACGAAAACAACTAAATC
Found at i:64274 original size:21 final size:20
Alignment explanation
Indices: 64215--64274 Score: 51
Period size: 21 Copynumber: 3.1 Consensus size: 20
64205 CGTCCCTCTT
64215 GAAGCAATTTCAACCTAGAAC
1 GAAG-AATTTCAACCTAGAAC
64236 GAA-AA---CAA-CTA-AATC
1 GAAGAATTTCAACCTAGAA-C
64251 GAAGTAATTTCAACCTAGAAC
1 GAAG-AATTTCAACCTAGAAC
64272 GAA
1 GAA
64275 AACAACTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 16
0.66 0.00 0.34
Matches are distributed among these distances:
14 2 0.06
15 7 0.23
16 3 0.10
17 2 0.06
19 2 0.06
20 3 0.10
21 10 0.32
22 2 0.06
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.18
Consensus pattern (20 bp):
GAAGAATTTCAACCTAGAAC
Found at i:66476 original size:21 final size:21
Alignment explanation
Indices: 66452--66492 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
66442 ATATTATTTC
*
66452 AAATTATATTTGA-ATTTAAAG
1 AAATTA-AATTGATATTTAAAG
66473 AAATTAAATTGATATTTAAA
1 AAATTAAATTGATATTTAAA
66493 TACTGTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (21 bp):
AAATTAAATTGATATTTAAAG
Found at i:72530 original size:17 final size:18
Alignment explanation
Indices: 72504--72540 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
72494 ACACAAGGTC
72504 CACCACCTTCT-GAATAT
1 CACCACCTTCTGGAATAT
*
72521 CACCAGCTTCTGGAATAT
1 CACCACCTTCTGGAATAT
72539 CA
1 CA
72541 GATGTTGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.30, C:0.32, G:0.11, T:0.27
Consensus pattern (18 bp):
CACCACCTTCTGGAATAT
Found at i:76535 original size:21 final size:21
Alignment explanation
Indices: 76511--76553 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
76501 ATCATGAACT
**
76511 TTAAACCGTAAATTTTAGACC
1 TTAAACCGTAAACATTAGACC
*
76532 TTAAACCTTAAACATTAGACC
1 TTAAACCGTAAACATTAGACC
76553 T
1 T
76554 CAAATATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAACCGTAAACATTAGACC
Found at i:76553 original size:14 final size:14
Alignment explanation
Indices: 76540--76586 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
76530 CCTTAAACCT
76540 TAAACATTAGACC-
1 TAAACATTAGACCA
*
76553 TCAAATATTAGACCA
1 T-AAACATTAGACCA
*
76568 TAAACTTTAGACCA
1 TAAACATTAGACCA
76582 TAAAC
1 TAAAC
76587 CCCTAAGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 1 0.03
14 27 0.93
15 1 0.03
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (14 bp):
TAAACATTAGACCA
Found at i:76670 original size:14 final size:14
Alignment explanation
Indices: 76653--76735 Score: 51
Period size: 14 Copynumber: 5.9 Consensus size: 14
76643 TATAAGGTCT
*
76653 AGGTTTAGGGTACA
1 AGGTTTAGGGTTCA
* * *
76667 AGGTCTATGGTTTA
1 AGGTTTAGGGTTCA
*
76681 AGGTTT-GGGGTCTA
1 AGGTTTAGGGTTC-A
* * *
76695 TGGTTTAGGATTTA
1 AGGTTTAGGGTTCA
*
76709 AGGTTTAGGGTCTTA
1 AGGTTTAGGGT-TCA
*
76724 AGGTTTAAGGTT
1 AGGTTTAGGGTT
76736 TAGGTTCTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
13 3 0.06
14 32 0.63
15 16 0.31
ACGTcount: A:0.22, C:0.05, G:0.34, T:0.40
Consensus pattern (14 bp):
AGGTTTAGGGTTCA
Found at i:76680 original size:21 final size:21
Alignment explanation
Indices: 76593--76734 Score: 115
Period size: 21 Copynumber: 6.8 Consensus size: 21
76583 AAACCCCTAA
* **
76593 GTTTAGGGTTCAAGGTCTAAA
1 GTTTAGGGTTTAAGGTCTATG
** *
76614 GTTTAGGGTTTAAAATCCATG
1 GTTTAGGGTTTAAGGTCTATG
* *
76635 GTTTAGGATATAAGGTCTA-G
1 GTTTAGGGTTTAAGGTCTATG
**
76655 GTTTAGGGTACAAGGTCTATG
1 GTTTAGGGTTTAAGGTCTATG
* **
76676 GTTTAAGGTTTGGGGTCTATG
1 GTTTAGGGTTTAAGGTCTATG
* * *
76697 GTTTAGGATTTAAGGTTTAGG
1 GTTTAGGGTTTAAGGTCTATG
*
76718 GTCTTAAGGTTTAAGGT
1 GT-TTAGGGTTTAAGGT
76735 TTAGGTTCTT
Statistics
Matches: 93, Mismatches: 26, Indels: 3
0.76 0.21 0.02
Matches are distributed among these distances:
20 18 0.19
21 63 0.68
22 12 0.13
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (21 bp):
GTTTAGGGTTTAAGGTCTATG
Found at i:76715 original size:7 final size:7
Alignment explanation
Indices: 76675--76741 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
76665 CAAGGTCTAT
76675 GGTTTAA
1 GGTTTAA
**
76682 GGTTTGG
1 GGTTTAA
* *
76689 GGTCTAT
1 GGTTTAA
76696 GGTTT-A
1 GGTTTAA
76702 GGATTTAA
1 GG-TTTAA
*
76710 GGTTTAG
1 GGTTTAA
76717 GGTCTTAA
1 GGT-TTAA
76725 GGTTTAA
1 GGTTTAA
76732 GGTTT-A
1 GGTTTAA
76738 GGTT
1 GGTT
76742 CTTAGGTCTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
6 7 0.15
7 32 0.67
8 9 0.19
ACGTcount: A:0.19, C:0.03, G:0.34, T:0.43
Consensus pattern (7 bp):
GGTTTAA
Found at i:80694 original size:41 final size:41
Alignment explanation
Indices: 80606--80686 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
80596 ATTATTTCTC
* *
80606 ATTCTTATCCCGAGACATAAGTCTTCCTTTAATATAATCTA
1 ATTCTCATCCCGAGACATAAGTCTTCCTTTAATATAATCGA
* *
80647 ATTCTCATCTCGAGACATGAGTCTTCCATTTAA-AT-ATCGA
1 ATTCTCATCCCGAGACATAAGTCTTCC-TTTAATATAATCGA
80687 GTTTCTCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 4 0.11
41 26 0.74
42 5 0.14
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (41 bp):
ATTCTCATCCCGAGACATAAGTCTTCCTTTAATATAATCGA
Found at i:82458 original size:18 final size:18
Alignment explanation
Indices: 82435--82469 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
82425 AGAGAGCAGT
*
82435 TTTGGTATCGATTTTGAC
1 TTTGGTATCGATATTGAC
82453 TTTGGTATCGATATTGA
1 TTTGGTATCGATATTGA
82470 AGGCTTGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.49
Consensus pattern (18 bp):
TTTGGTATCGATATTGAC
Found at i:89948 original size:18 final size:18
Alignment explanation
Indices: 89925--89959 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
89915 AGAGAGCAAT
*
89925 TTTGGTATCGATTTTGAC
1 TTTGGTATCGATATTGAC
89943 TTTGGTATCGATATTGA
1 TTTGGTATCGATATTGA
89960 AGGCTCGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.09, G:0.23, T:0.49
Consensus pattern (18 bp):
TTTGGTATCGATATTGAC
Found at i:94029 original size:30 final size:29
Alignment explanation
Indices: 93994--94087 Score: 91
Period size: 30 Copynumber: 3.1 Consensus size: 29
93984 ATTTGGCCAA
93994 AAATTTTAATAAAAGCTCAATTTAGTCCCT
1 AAATTTTAATAAAA-CTCAATTTAGTCCCT
* * *
94024 AAATTTCACTAAAATCACAATTTAGTCCCT
1 AAATTTTAATAAAA-CTCAATTTAGTCCCT
* * *
94054 AAA-TGTAACTAAAATTCTAATTTAGTCCTT
1 AAATTTTAA-TAAAACTC-AATTTAGTCCCT
94084 AAAT
1 AAAT
94088 CCATTGAACT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
29 3 0.06
30 48 0.94
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (29 bp):
AAATTTTAATAAAACTCAATTTAGTCCCT
Found at i:94135 original size:30 final size:30
Alignment explanation
Indices: 94011--94145 Score: 98
Period size: 30 Copynumber: 4.5 Consensus size: 30
94001 AATAAAAGCT
* *
94011 CAATTTAGTCCCTAAATTTCACTAAAA-TC
1 CAATTTAGACCTTAAATTTCACTAAAATTC
* * * *
94040 ACAATTTAGTCCCTAAATGTAACTAAAATTC
1 -CAATTTAGACCTTAAATTTCACTAAAATTC
* * * * * * *
94071 TAATTTAGTCCTTAAA-TCCATTGAACTTA
1 CAATTTAGACCTTAAATTTCACTAAAATTC
94100 CAATTTA-ACCTTTAAATTTCACTAAAATTC
1 CAATTTAGACC-TTAAATTTCACTAAAATTC
94130 CAATTTA-ATCCTTAAA
1 CAATTTAGA-CCTTAAA
94146 CTAAAATTAA
Statistics
Matches: 83, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
28 2 0.02
29 17 0.20
30 60 0.72
31 4 0.05
ACGTcount: A:0.39, C:0.20, G:0.04, T:0.37
Consensus pattern (30 bp):
CAATTTAGACCTTAAATTTCACTAAAATTC
Found at i:101152 original size:3 final size:3
Alignment explanation
Indices: 101144--101183 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
101134 CTAATTTTAT
101144 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
101184 AAATAAATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:101272 original size:39 final size:39
Alignment explanation
Indices: 101218--101343 Score: 227
Period size: 39 Copynumber: 3.2 Consensus size: 39
101208 AAACAAAATA
101218 CAAACCCAATTTTATCTACCCAAAGCTCAAATACACCTT
1 CAAACCCAATTTTATCTACCCAAAGCTCAAATACACCTT
*
101257 CAAACCCAATTTTATCTACCCAAAGCCCAAATACACCTT
1 CAAACCCAATTTTATCTACCCAAAGCTCAAATACACCTT
101296 CAAACCCAATTTTATCTACCCAAAG-TCCAAATACACCTT
1 CAAACCCAATTTTATCTACCCAAAGCT-CAAATACACCTT
101335 CAAACCCAA
1 CAAACCCAA
101344 ACCTAATTAC
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
39 84 1.00
ACGTcount: A:0.40, C:0.35, G:0.02, T:0.23
Consensus pattern (39 bp):
CAAACCCAATTTTATCTACCCAAAGCTCAAATACACCTT
Found at i:101382 original size:78 final size:78
Alignment explanation
Indices: 101218--101363 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 78
101208 AAACAAAATA
** *
101218 CAAACCCAATTTTATCTACCCAAAGCTCAAATACACCTTCAAACCCAATTTTATCTACCCAAAGC
1 CAAACCCAATTTTATCTACCCAAAGCTCAAATACACCTTCAAACCCAACCTAATCTACCCAAAGC
101283 CCAAATACACCTT
66 CCAAATACACCTT
*
101296 CAAACCCAATTTTATCTACCCAAAG-TCCAAATACACCTTCAAACCCAAACCTAAT-TA-CCTAA
1 CAAACCCAATTTTATCTACCCAAAGCT-CAAATACACCTTCAAACCC-AACCTAATCTACCCAAA
101358 GCCCAA
64 GCCCAA
101364 GTTACAAGCC
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
77 11 0.18
78 46 0.74
79 5 0.08
ACGTcount: A:0.40, C:0.35, G:0.03, T:0.23
Consensus pattern (78 bp):
CAAACCCAATTTTATCTACCCAAAGCTCAAATACACCTTCAAACCCAACCTAATCTACCCAAAGC
CCAAATACACCTT
Found at i:102308 original size:29 final size:29
Alignment explanation
Indices: 102192--102350 Score: 118
Period size: 29 Copynumber: 5.6 Consensus size: 29
102182 ACTTTATTTT
* * * *
102192 AAAATT-ATTTTGACCCCAAAACTTTCTA
1 AAAATTCAATTTGACCCCTAAATTTTCCA
* *
102220 AAAATCCAAATTTGA-CCCTAAACTTTCC-
1 AAAATTC-AATTTGACCCCTAAATTTTCCA
*
102248 AAAATTAGAATTTGACCCCTAAAATTTT-CA
1 AAAATT-CAATTTGACCCCT-AAATTTTCCA
102278 AAAATTCAATTTGACCCCTAAATTTTCCA
1 AAAATTCAATTTGACCCCTAAATTTTCCA
* * *
102307 AATATT---TTTGA-CCCTCGAATTTCCCA
1 AAAATTCAATTTGACCCCT-AAATTTTCCA
*
102333 AAAATTCAAATTTAACCC
1 AAAATTC-AATTTGACCC
102351 GGTTTTAATG
Statistics
Matches: 105, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
25 4 0.04
26 18 0.17
28 24 0.23
29 35 0.33
30 22 0.21
31 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAATTCAATTTGACCCCTAAATTTTCCA
Found at i:103851 original size:5 final size:5
Alignment explanation
Indices: 103827--103861 Score: 52
Period size: 5 Copynumber: 6.6 Consensus size: 5
103817 ATAAAAATAC
103827 AAAAT CAAAAT AATAAT AAAAT AAAAT AAAAT AAA
1 AAAAT -AAAAT AA-AAT AAAAT AAAAT AAAAT AAA
103862 CTAAGTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:104917 original size:25 final size:26
Alignment explanation
Indices: 104889--104938 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
104879 TTTCTCGAAA
*
104889 AAAGTTAATGGTCAA-AGTCAAAGTT
1 AAAGTCAATGGTCAACAGTCAAAGTT
*
104914 AAAGTCAATGGTCAACGGTCAAAGT
1 AAAGTCAATGGTCAACAGTCAAAGT
104939 CAACGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (26 bp):
AAAGTCAATGGTCAACAGTCAAAGTT
Found at i:104942 original size:13 final size:13
Alignment explanation
Indices: 104924--104948 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104914 AAAGTCAATG
104924 GTCAACGGTCAAA
1 GTCAACGGTCAAA
104937 GTCAACGGTCAA
1 GTCAACGGTCAA
104949 TGAGCTTGTC
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:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:113537 original size:31 final size:31
Alignment explanation
Indices: 113502--113566 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
113492 TTGCATATGT
113502 ATTCATAAAATTTTGCAGT-GCATTTTCATGC
1 ATTCATAAAATTTTGCA-TCGCATTTTCATGC
*
113533 ATTCATAAAGTTTTGCATCGCATTTTCATGC
1 ATTCATAAAATTTTGCATCGCATTTTCATGC
113564 ATT
1 ATT
113567 AAATTTTCGA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 1 0.03
31 31 0.97
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.43
Consensus pattern (31 bp):
ATTCATAAAATTTTGCATCGCATTTTCATGC
Found at i:117937 original size:52 final size:52
Alignment explanation
Indices: 117874--118098 Score: 279
Period size: 52 Copynumber: 4.3 Consensus size: 52
117864 ACTCTATGTT
117874 ATCGTGAGTATATGAATCCCTTACGGATTAAAAGGTCCGATGACTAAGTGTC
1 ATCGTGAGTATATGAATCCCTTACGGATTAAAAGGTCCGATGACTAAGTGTC
* * *
117926 ATCGTGAGTATATGAATCCTTTACGAATTAAAAGGTGCGATGACTAAGTGTC
1 ATCGTGAGTATATGAATCCCTTACGGATTAAAAGGTCCGATGACTAAGTGTC
* ** **
117978 ATCGTGAGTATACGAATCTTTTACGGATTAAAAGGTCCGATGACTCTGTGTC
1 ATCGTGAGTATATGAATCCCTTACGGATTAAAAGGTCCGATGACTAAGTGTC
** *** * * * * *
118030 ATCGTGAGTATACAAATCCCTTGTAGATTATAAGGTCCGGTGGCTATGGGTC
1 ATCGTGAGTATATGAATCCCTTACGGATTAAAAGGTCCGATGACTAAGTGTC
*
118082 ATCATGAGTATATGAAT
1 ATCGTGAGTATATGAAT
118099 GAAGTGAAAT
Statistics
Matches: 150, Mismatches: 23, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 150 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.31
Consensus pattern (52 bp):
ATCGTGAGTATATGAATCCCTTACGGATTAAAAGGTCCGATGACTAAGTGTC
Found at i:119075 original size:13 final size:13
Alignment explanation
Indices: 119057--119082 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
119047 TAATGATAAG
119057 ATGAACAGTAAAA
1 ATGAACAGTAAAA
119070 ATGAACAGTAAAA
1 ATGAACAGTAAAA
119083 CATCATAAAT
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:0.62, C:0.08, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAACAGTAAAA
Found at i:120010 original size:52 final size:52
Alignment explanation
Indices: 119924--120032 Score: 173
Period size: 52 Copynumber: 2.1 Consensus size: 52
119914 GAGGACTCTA
* * **
119924 TGTCATCGTGAATATATGAATCCTTTACGGATTAAAAGGTCCGATGACTAAG
1 TGTCAGCGTGAATATATGAATCCCTTACAAATTAAAAGGTCCGATGACTAAG
*
119976 TGTCAGCGTGAGTATATGAATCCCTTACAAATTAAAAGGTCCGATGACTAAG
1 TGTCAGCGTGAATATATGAATCCCTTACAAATTAAAAGGTCCGATGACTAAG
120028 TGTCA
1 TGTCA
120033 TCGTCCTTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (52 bp):
TGTCAGCGTGAATATATGAATCCCTTACAAATTAAAAGGTCCGATGACTAAG
Found at i:120114 original size:52 final size:52
Alignment explanation
Indices: 120036--120142 Score: 144
Period size: 52 Copynumber: 2.1 Consensus size: 52
120026 AGTGTCATCG
* *
120036 TCCTTTACGGATTAAAAGGTCTGATGACTAAGAGTCATCGTGAGTATATGAA
1 TCCTTTACGGATTAAAAGGTCCGATGACTAAGAGTCATCGTGAGTATACGAA
** * *
120088 TCCTTTACGGA-TAAAGAGGTCCGATGACTCTGTGTTATCGTGAGTATACGAA
1 TCCTTTACGGATTAAA-AGGTCCGATGACTAAGAGTCATCGTGAGTATACGAA
120140 TCC
1 TCC
120143 CTTGTGGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
51 4 0.08
52 44 0.92
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (52 bp):
TCCTTTACGGATTAAAAGGTCCGATGACTAAGAGTCATCGTGAGTATACGAA
Found at i:120128 original size:92 final size:92
Alignment explanation
Indices: 119944--120116 Score: 276
Period size: 92 Copynumber: 1.9 Consensus size: 92
119934 AATATATGAA
*
119944 TCCTTTACGGATTAAAAGGTCCGATGACTAAGTGTCAGCGTGAGTATATGAATCCCTTACAAATT
1 TCCTTTACGGATTAAAAGGTCCGATGACTAAGAGTCAGCGTGAGTATATGAATCCCTTACAAATT
120009 AAAAGGTCCGATGACTAAGTGTCATCG
66 AAAAGGTCCGATGACTAAGTGTCATCG
* * * **
120036 TCCTTTACGGATTAAAAGGTCTGATGACTAAGAGTCATCGTGAGTATATGAATCCTTTACGGA-T
1 TCCTTTACGGATTAAAAGGTCCGATGACTAAGAGTCAGCGTGAGTATATGAATCCCTTACAAATT
120100 AAAGAGGTCCGATGACT
66 AAA-AGGTCCGATGACT
120117 CTGTGTTATC
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
91 4 0.05
92 70 0.95
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (92 bp):
TCCTTTACGGATTAAAAGGTCCGATGACTAAGAGTCAGCGTGAGTATATGAATCCCTTACAAATT
AAAAGGTCCGATGACTAAGTGTCATCG
Found at i:120157 original size:20 final size:20
Alignment explanation
Indices: 120132--120175 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
120122 TTATCGTGAG
120132 TATACGAATCCCTTGTGGAT
1 TATACGAATCCCTTGTGGAT
120152 TATACGAATCCCTTGTGGAT
1 TATACGAATCCCTTGTGGAT
120172 TATA
1 TATA
120176 AGGTCAGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (20 bp):
TATACGAATCCCTTGTGGAT
Found at i:120824 original size:21 final size:21
Alignment explanation
Indices: 120800--120850 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
120790 AGAGTATTTA
120800 GTATCGATAGAT-GTATGACAT
1 GTATCGATAGATAGTAT-ACAT
* * *
120821 GTATCGGTAGATATTATACTT
1 GTATCGATAGATAGTATACAT
120842 GTATCGATA
1 GTATCGATA
120851 AAACTAGTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (21 bp):
GTATCGATAGATAGTATACAT
Found at i:122602 original size:50 final size:50
Alignment explanation
Indices: 122539--122653 Score: 160
Period size: 50 Copynumber: 2.3 Consensus size: 50
122529 ATCCTATACC
*
122539 CCTAAAGCTGTAGAGGAACGGATTGAAGCCGCAATGGAAAATCTCATAT-A
1 CCTAAAGCTGTAGAGGAACAGATTGAAGCCGCAATGGAAAATCTCAT-TCA
** * **
122589 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCGCATTGGCGAATCTCATTCA
1 CCTAAAGCTGTAGAGGAACAGATTGAAGCCGCAATGGAAAATCTCATTCA
122639 CCTAAAGCTGTAGAG
1 CCTAAAGCTGTAGAG
122654 TAGATTAAAG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 1 0.02
50 57 0.98
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGAACAGATTGAAGCCGCAATGGAAAATCTCATTCA
Found at i:122809 original size:40 final size:40
Alignment explanation
Indices: 122755--123045 Score: 211
Period size: 39 Copynumber: 7.4 Consensus size: 40
122745 GATTGAAGTA
* * *
122755 ATCCAAACTTTTACCCTAACCAGAAGGCAGATTGAAGACC
1 ATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACC
* ** * *
122795 ATCCACTCTCTTACCCCGACCATG-GGGCAGATTAAAG-CA
1 ATCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACC
* * * *
122834 ATCCAATCTTTTATCCTAACTAGAGGGTAGATTGAAGACC
1 ATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACC
* * *
122874 ATCCGATCTCTTACCCCAACCATG-GGGCAGATTGAAGA-A
1 ATCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACC
* * * *
122913 ATCCAATCTTTTACCCTAACTAGAGGGAAAATTGAAGACC
1 ATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACC
** * * ** *
122953 ATCTGATCTATTATCCC-GACCATGA-GATAGATTGAAG-CA
1 ATCCAATCTCTTA-CCCTAACCA-GAGGGCAGATTGAAGACC
* * *
122992 ATCCAATCTTTTACCTTAACCAGAGGGCAGATTG-AGACA
1 ATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACC
* *
123031 ATCTAATCTATTACC
1 ATCCAATCTCTTACC
123046 AATAAAGTTA
Statistics
Matches: 191, Mismatches: 49, Indels: 23
0.73 0.19 0.09
Matches are distributed among these distances:
38 8 0.04
39 95 0.50
40 81 0.42
41 7 0.04
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.25
Consensus pattern (40 bp):
ATCCAATCTCTTACCCTAACCAGAGGGCAGATTGAAGACC
Found at i:122866 original size:79 final size:78
Alignment explanation
Indices: 122732--123026 Score: 383
Period size: 79 Copynumber: 3.7 Consensus size: 78
122722 TATTTTATCT
* * * *
122732 CGACCATGGGGTAGATTGAAGTAATCCAAACTTTTACCCTAACCAGAAGGCAGATTGAAGACCAT
1 CGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCAT
122797 CCACTCTCTTACCC
66 CCA-TCTCTTACCC
* * * *
122811 CGACCATGGGGCAGATTAAAGCAATCCAATCTTTTATCCTAACTAGAGGGTAGATTGAAGACCAT
1 CGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCAT
122876 CCGATCTCTTACCC
66 CC-ATCTCTTACCC
* * * * *
122890 CAACCATGGGGCAGATTGAAGAAATCCAATCTTTTACCCTAACTAGAGGGAAAATTGAAGACCAT
1 CGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCAT
* * *
122955 CTGATCTATTATCC
66 C-CATCTCTTACCC
* ** *
122969 CGACCATGAGATAGATTGAAGCAATCCAATCTTTTACCTTAACCAGAGGGCAGATTGA
1 CGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGA
123027 GACAATCTAA
Statistics
Matches: 188, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
79 187 0.99
80 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (78 bp):
CGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAGAGGGCAGATTGAAGACCAT
CCATCTCTTACCC
Found at i:124531 original size:30 final size:30
Alignment explanation
Indices: 124495--124593 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 30
124485 ATTTTAAAAA
* *
124495 TTGACCCTTGAACTTTCTAAAAATCTATAT
1 TTGACCCTTGAACTTTCCAAAAATCTAAAT
* *
124525 TTGACCCCTAAACTTTCCAAAAAT-TCAAAT
1 TTGACCCTTGAACTTTCCAAAAATCT-AAAT
* * *
124555 TTAACCCTCGAATCTTTCCAAAAATTCAAAAT
1 TTGACCCTTGAA-CTTTCCAAAAA-TCTAAAT
124587 TTGACCC
1 TTGACCC
124594 CTAATTTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
29 1 0.02
30 32 0.58
31 11 0.20
32 11 0.20
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (30 bp):
TTGACCCTTGAACTTTCCAAAAATCTAAAT
Found at i:124575 original size:31 final size:31
Alignment explanation
Indices: 124537--124683 Score: 97
Period size: 30 Copynumber: 4.8 Consensus size: 31
124527 GACCCCTAAA
124537 CTTTCCAAAAATTCAAATTTAACCCTCGAAT
1 CTTTCCAAAAATTCAAATTTAACCCTCGAAT
* *
124568 CTTTCCAAAAATTCAAAATTTGACCC-CTAAT
1 CTTTCCAAAAATTC-AAATTTAACCCTCGAAT
** * * *
124599 -TTTTTAAAAATTCCATTTTAACACCT--AAA
1 CTTTCCAAAAATTCAAATTTAAC-CCTCGAAT
* *** * *
124628 CTTTCCAAATATTTTGATTTGACCCTTGAA-
1 CTTTCCAAAAATTCAAATTTAACCCTCGAAT
* * *
124658 GTTCCCAAAAGTTCAAATTTAACCCT
1 CTTTCCAAAAATTCAAATTTAACCCT
124684 GTTTTAATGT
Statistics
Matches: 86, Mismatches: 24, Indels: 13
0.70 0.20 0.11
Matches are distributed among these distances:
29 11 0.13
30 45 0.52
31 20 0.23
32 10 0.12
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (31 bp):
CTTTCCAAAAATTCAAATTTAACCCTCGAAT
Found at i:124610 original size:30 final size:29
Alignment explanation
Indices: 124523--124611 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 29
124513 AAAAATCTAT
*
124523 ATTTGACCCCTAAACTTTCCAAAAATTCAA
1 ATTTGACCCCT-AATTTTCCAAAAATTCAA
* *
124553 ATTTAACCCTCGAATCTTTCCAAAAATTCAAA
1 ATTTGACCC-CTAAT-TTTCCAAAAATTC-AA
**
124585 ATTTGACCCCTAATTTTTTAAAAATTC
1 ATTTGACCCCTAATTTTCCAAAAATTC
124612 CATTTTAACA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
30 21 0.43
31 18 0.37
32 10 0.20
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (29 bp):
ATTTGACCCCTAATTTTCCAAAAATTCAA
Found at i:138020 original size:52 final size:52
Alignment explanation
Indices: 137941--138204 Score: 321
Period size: 52 Copynumber: 5.1 Consensus size: 52
137931 ATAAACGAAG
** *
137941 AGGTCCGATGACTCTGTATCATCGTGAGTATATGAATCCCTTACGGATTAAA
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTAAA
* * *
137993 AGGTCCGATGACTAAGTGTCATTGTGAGTATATAAATCCCTTACGAATTAAA
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTAAA
* * *
138045 AGGTCCAATGACTAAGTGTTATCGTGAGTATATGAATCCTTTACGGATTAAA
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTAAA
* * ** * * *
138097 AGGTCCAATGACTAAGAGTCATCGAAAGTATATGGATCCTTTACGGATTAAG
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTAAA
** * * * * *
138149 AGGTCCGATGACTTTGTCTCGTCGTGAGTATACGAATCCCTTGCGGATTATA
1 AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTAAA
138201 AGGT
1 AGGT
138205 TCGGTCGTGA
Statistics
Matches: 180, Mismatches: 32, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 180 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (52 bp):
AGGTCCGATGACTAAGTGTCATCGTGAGTATATGAATCCCTTACGGATTAAA
Found at i:141006 original size:50 final size:49
Alignment explanation
Indices: 140884--141016 Score: 153
Period size: 49 Copynumber: 2.7 Consensus size: 49
140874 ATCCTATACC
* *
140884 CCTAAAGTTGTAGAGGAACAGATTGAAGCCGTAATTGCAAATCTCATCA
1 CCTAAAGCTGTAGAGGAGCAGATTGAAGCCGTAATTGCAAATCTCATCA
* **
140933 CCTAAAGCTGTAGATGG-GCAGATTGAAGCCG-CATTGGTGAATCTCATTCA
1 CCTAAAGCTGTAGA-GGAGCAGATTGAAGCCGTAATT-GCAAATCTCA-TCA
* * *
140983 CCTAAAGCTGTAGAGGAGTAGATTAAAGTCGTAA
1 CCTAAAGCTGTAGAGGAGCAGATTGAAGCCGTAA
141017 GGACGAATCT
Statistics
Matches: 70, Mismatches: 9, Indels: 8
0.80 0.10 0.09
Matches are distributed among these distances:
48 3 0.04
49 36 0.51
50 30 0.43
51 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (49 bp):
CCTAAAGCTGTAGAGGAGCAGATTGAAGCCGTAATTGCAAATCTCATCA
Found at i:141156 original size:40 final size:40
Alignment explanation
Indices: 141087--141318 Score: 211
Period size: 39 Copynumber: 5.9 Consensus size: 40
141077 CTCGACCATG
*
141087 GGGCAGATTGAAG-CAATCCAATCTTTTACCTTAACCAAA
1 GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
* * * ** **
141126 GGGTAGATTGAAGACCATCCGATCTTTTACCCCGACCATG
1 GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
*
141166 GGGCAGATTGAA-ACAAGCCAATCTTTTACCCTAACCAAA
1 GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
* * * * * * * * *
141205 AGGCAGATTAAAGACTATCCGATCTCTTATCTTGACCATA
1 GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
* * * *
141245 GGACAGATTGAAG-CAATTCAATCTTTTACCCTAACTAGA
1 GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
* *
141284 GGACAGATTG-AGACAATCTAATCTTTTACCACTAA
1 GGGCAGATTGAAGACAATCCAATCTTTTACC-CTAA
141319 AGTTATAGAG
Statistics
Matches: 149, Mismatches: 40, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
38 2 0.01
39 84 0.56
40 63 0.42
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (40 bp):
GGGCAGATTGAAGACAATCCAATCTTTTACCCTAACCAAA
Found at i:141167 original size:79 final size:79
Alignment explanation
Indices: 141071--141279 Score: 292
Period size: 79 Copynumber: 2.6 Consensus size: 79
141061 ACCCCGAGTA
* * * *
141071 TTTTACCTCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCTTAACCAAAGGGTAGATTG
1 TTTTACCTCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAAGGCAGATTA
141136 AAGACCATCCGATC
66 AAGACCATCCGATC
* * *
141150 TTTTACCCCGACCATGGGGCAGATTGAAACAAGCCAATCTTTTACCCTAACCAAAAGGCAGATTA
1 TTTTACCTCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAAGGCAGATTA
*
141215 AAGACTATCCGATC
66 AAGACCATCCGATC
* * * * * *
141229 TCTTATCTTGACCATAGGACAGATTGAAGCAATTCAATCTTTTACCCTAAC
1 TTTTACCTCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAAC
141280 TAGAGGACAG
Statistics
Matches: 113, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 113 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (79 bp):
TTTTACCTCGACCATGGGGCAGATTGAAGCAATCCAATCTTTTACCCTAACCAAAAGGCAGATTA
AAGACCATCCGATC
Found at i:141405 original size:30 final size:30
Alignment explanation
Indices: 141371--141430 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
141361 ACCTCTAAAG
141371 TAATAGAGGGGCAGATCAAAACTCACAGTA
1 TAATAGAGGGGCAGATCAAAACTCACAGTA
141401 TAATAGAGGGGCAGATCAAAACTCACAGTA
1 TAATAGAGGGGCAGATCAAAACTCACAGTA
141431 ACAGACCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (30 bp):
TAATAGAGGGGCAGATCAAAACTCACAGTA
Found at i:141809 original size:4 final size:4
Alignment explanation
Indices: 141802--141837 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
141792 TTATTATTTT
*
141802 ATAA ATAA ATAA ATAA ACAA ATAA ATAA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
141838 ATTAAAAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 26 0.90
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:142819 original size:30 final size:29
Alignment explanation
Indices: 142776--142867 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 29
142766 GAACTTTCTG
*
142776 AAAATCCACATTTGACACCTAAACTTTCCAA
1 AAAAT-CAAATTTGAC-CCTAAACTTTCCAA
* * *
142807 AAAATCAAATTTGTCCCTCGAATTTTCCAA
1 AAAATCAAATTTGACCCT-AAACTTTCCAA
* * *
142837 AAATTCCATTTTGATCCCTAAACTTTCCAA
1 AAAATCAAATTTGA-CCCTAAACTTTCCAA
142867 A
1 A
142868 TATTTCGATT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
29 3 0.06
30 37 0.76
31 9 0.18
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAATCAAATTTGACCCTAAACTTTCCAA
Found at i:169607 original size:21 final size:20
Alignment explanation
Indices: 169583--169634 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
169573 TGTCAGTCTT
*
169583 ATGAATAGTGAGGTCAAGTCC
1 ATGAATAGTGAGGTCAAAT-C
* * *
169604 ATGAACAATGGGGTCAAATC
1 ATGAATAGTGAGGTCAAATC
169624 ATGAATAGTGA
1 ATGAATAGTGA
169635 TAATATATAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (20 bp):
ATGAATAGTGAGGTCAAATC
Found at i:170011 original size:14 final size:15
Alignment explanation
Indices: 169992--170022 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
169982 TGTTTCACTG
169992 AAAATAA-TTTTAGA
1 AAAATAATTTTTAGA
170006 AAAATAATTTTTAGA
1 AAAATAATTTTTAGA
170021 AA
1 AA
170023 TAATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.44
15 9 0.56
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
AAAATAATTTTTAGA
Found at i:170023 original size:13 final size:14
Alignment explanation
Indices: 169991--170028 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
169981 TTGTTTCACT
169991 GAAAATAA-TTTTA
1 GAAAATAATTTTTA
170004 GAAAAATAATTTTTA
1 G-AAAATAATTTTTA
170019 G-AAATAATTT
1 GAAAATAATTT
170029 ATTTTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.43
14 7 0.30
15 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (14 bp):
GAAAATAATTTTTA
Found at i:170461 original size:23 final size:27
Alignment explanation
Indices: 170434--170488 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 27
170424 TTATTTAAAC
170434 AAATACTCAT-A-TTTATA-TA-ATTA
1 AAATACTCATAATTTTATACTAGATTA
*
170457 AAATAGTCATAATTTTATACTAGATTA
1 AAATACTCATAATTTTATACTAGATTA
170484 AAATA
1 AAATA
170489 TGTCATAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 9 0.33
24 1 0.04
25 6 0.22
26 2 0.07
27 9 0.33
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (27 bp):
AAATACTCATAATTTTATACTAGATTA
Found at i:170485 original size:27 final size:26
Alignment explanation
Indices: 170445--170496 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
170435 AATACTCATA
170445 TTTATATAATTAAAATA-GTCATAAT
1 TTTATATAATTAAAATATGTCATAAT
170470 TTTATACTAGATTAAAATATGTCATAA
1 TTTATA-TA-ATTAAAATATGTCATAA
170497 GTCCTTGTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 6 0.25
26 2 0.08
27 9 0.38
28 7 0.29
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (26 bp):
TTTATATAATTAAAATATGTCATAAT
Found at i:170871 original size:15 final size:16
Alignment explanation
Indices: 170850--170905 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 16
170840 TATACTACAA
170850 AATATTTATTATTAAT
1 AATATTTATTATTAAT
*
170866 -ATATTTATAATTGTAAT
1 AATATTTATTA-T-TAAT
170883 AAATATTTATTATTTAA-
1 -AATATTTATTA-TTAAT
170900 AATATT
1 AATATT
170906 AATATTGAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 9 0.26
16 7 0.21
17 4 0.12
18 3 0.09
19 11 0.32
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AATATTTATTATTAAT
Found at i:174911 original size:44 final size:44
Alignment explanation
Indices: 174848--174935 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
174838 TGTTTTTAGT
*
174848 GATTTTTATGTTTTTGAGTCTGTGATAGCTTAATCTAGCTAATC
1 GATTTTTATGTTTTTGAGTCCGTGATAGCTTAATCTAGCTAATC
174892 GATTTTTATGTTTTTGAGTCCGTGATAGCTTAATCTAGCTAATC
1 GATTTTTATGTTTTTGAGTCCGTGATAGCTTAATCTAGCTAATC
174936 TAAGTACTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.23, C:0.12, G:0.18, T:0.47
Consensus pattern (44 bp):
GATTTTTATGTTTTTGAGTCCGTGATAGCTTAATCTAGCTAATC
Found at i:187361 original size:18 final size:18
Alignment explanation
Indices: 187340--187379 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
187330 CAAATGCAGA
187340 CACATATCCAGATGCAAT
1 CACATATCCAGATGCAAT
187358 CACATATCCAGATGCAAT
1 CACATATCCAGATGCAAT
187376 CACA
1 CACA
187380 AGCTAGAATG
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:0.40, C:0.30, G:0.10, T:0.20
Consensus pattern (18 bp):
CACATATCCAGATGCAAT
Found at i:191657 original size:14 final size:14
Alignment explanation
Indices: 191626--191656 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
191616 TAATTTTTAC
191626 TTTTACTTTTCATT
1 TTTTACTTTTCATT
191640 TTTTA-TTTTCATT
1 TTTTACTTTTCATT
191653 TTTT
1 TTTT
191657 TCCTTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTACTTTTCATT
Found at i:196707 original size:42 final size:42
Alignment explanation
Indices: 196633--196742 Score: 112
Period size: 42 Copynumber: 2.5 Consensus size: 42
196623 TATTTTTAAT
* *
196633 AAAATATATGTTTATAAAATAGATAACAATATATATGTATAA
1 AAAATATATGTATATAAAATAGATAACAATATATATATATAA
* *
196675 AAAATATATGTATATAAAATAGTTATGTATATATATATATATATAA
1 AAAATATATGTATATAAAATAG--AT-AACA-ATATATATATATAA
* * *
196721 AACAGTATATATGTATAAAATA
1 AA-AATATATGTATATAAAATA
196743 TACAATTTGT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
42 21 0.38
44 2 0.04
45 2 0.04
46 15 0.27
47 16 0.29
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (42 bp):
AAAATATATGTATATAAAATAGATAACAATATATATATATAA
Found at i:196743 original size:29 final size:29
Alignment explanation
Indices: 196685--196744 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
196675 AAAATATATG
* * *
196685 TATATAAAATAGTTATGTATATATATATA
1 TATATAAAACAGTTATATATATATAAATA
*
196714 TATATAAAACAG-TATATATGTATAAA-A
1 TATATAAAACAGTTATATATATATAAATA
196741 TATA
1 TATA
196745 CAATTTGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 5 0.19
28 11 0.41
29 11 0.41
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.40
Consensus pattern (29 bp):
TATATAAAACAGTTATATATATATAAATA
Found at i:197049 original size:16 final size:17
Alignment explanation
Indices: 197028--197065 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
197018 GAATATGACA
*
197028 AAAAGT-GTTTTTTTTT
1 AAAAGTAGTTTTCTTTT
197044 AAAAGTAGGTTTTCTTTT
1 AAAAGTA-GTTTTCTTTT
197062 AAAA
1 AAAA
197066 ACATGTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
18 13 0.68
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (17 bp):
AAAAGTAGTTTTCTTTT
Found at i:197347 original size:24 final size:26
Alignment explanation
Indices: 197309--197356 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
197299 AAAACATGCA
*
197309 TAAAACAAAACAAGTGTCCAAGAATG
1 TAAAACAAAACAAGTGTACAAGAATG
*
197335 TAAAA-AAAA-AAGTTTACAAGAA
1 TAAAACAAAACAAGTGTACAAGAA
197357 GCTTATGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 11 0.55
25 4 0.20
26 5 0.25
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.17
Consensus pattern (26 bp):
TAAAACAAAACAAGTGTACAAGAATG
Found at i:207251 original size:21 final size:21
Alignment explanation
Indices: 207227--207288 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
207217 ATTATATTTA
207227 TAACTCTTCTCATAATGTTTG
1 TAACTCTTCTCATAATGTTTG
*
207248 TAACTCTCCTCATAA-GTTTTG
1 TAACTCTTCTCATAATG-TTTG
*
207269 TAACTC-TCATCATTATGTTT
1 TAACTCTTC-TCATAATGTTT
207289 ATTTTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 2 0.06
21 32 0.91
22 1 0.03
ACGTcount: A:0.24, C:0.21, G:0.08, T:0.47
Consensus pattern (21 bp):
TAACTCTTCTCATAATGTTTG
Found at i:207667 original size:19 final size:19
Alignment explanation
Indices: 207643--207688 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
207633 TAAAGTATAC
* *
207643 TTATTATTTATTTTTAAAT
1 TTATTATTTAATTTAAAAT
*
207662 TTATTATTAAATTTAAAAT
1 TTATTATTTAATTTAAAAT
207681 TTA-TATTT
1 TTATTATTT
207689 TTTATATACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATTATTTAATTTAAAAT
Found at i:215093 original size:6 final size:6
Alignment explanation
Indices: 215084--215204 Score: 66
Period size: 6 Copynumber: 19.3 Consensus size: 6
215074 AGTGCATAAT
* * * * * *
215084 AAAATA AAAATA AAAATA AAAATA AAAATG AACATG AACATG AACATGA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A
* * *
215133 AAATTGA AAAATTA AAAATTA AAAA-A ATAAA-A AACAATGA AAATTG
1 AAAAT-A AAAA-TA AAAA-TA AAAATA A-AAATA AA-AAT-A AAAATA
* *
215179 AAAATG AAAATG AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AA
215205 TGTACTAATT
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
5 3 0.03
6 70 0.71
7 22 0.22
8 4 0.04
ACGTcount: A:0.71, C:0.03, G:0.07, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:215152 original size:15 final size:15
Alignment explanation
Indices: 215132--215165 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
215122 CATGAACATG
* *
215132 AAAATTGAAAAATTA
1 AAAATTAAAAAAATA
215147 AAAATTAAAAAAATA
1 AAAATTAAAAAAATA
215162 AAAA
1 AAAA
215166 ACAATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (15 bp):
AAAATTAAAAAAATA
Found at i:218090 original size:21 final size:20
Alignment explanation
Indices: 218073--218124 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
218063 GCGAAATTTT
* *
218073 AAAATATAAAAATTAAATTA
1 AAAATAAAAAAAATAAATTA
*
218093 AAAATAAAAAAAATAAAAAATA
1 AAAATAAAAAAAAT--AAATTA
218115 AAAATAAAAA
1 AAAATAAAAA
218125 TGGCTAAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 12 0.44
22 15 0.56
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAATAAAAAAAATAAATTA
Found at i:218102 original size:6 final size:6
Alignment explanation
Indices: 218072--218125 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
218062 AGCGAAATTT
* * *
218072 TAAAATA TAAAAA TTAAAT TAAAAA TAAAAA -AAATA -AAAAA TAAAAA
1 TAAAA-A TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
218119 TAAAAA T
1 TAAAAA T
218126 GGCTAAAGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
5 8 0.20
6 27 0.68
7 5 0.12
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:227786 original size:4 final size:4
Alignment explanation
Indices: 227755--227798 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
227745 TGTGTTGAGA
* *
227755 AATT AATA AATT AATT AGTT AATCT AATT AATT AAATT AATT AA
1 AATT AATT AATT AATT AATT AAT-T AATT AATT -AATT AATT AA
227799 ATAAATAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 26 0.76
5 8 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (4 bp):
AATT
Found at i:227792 original size:9 final size:9
Alignment explanation
Indices: 227754--227800 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
227744 TTGTGTTGAG
227754 AAATTAA-T
1 AAATTAATT
227762 AAATTAATT
1 AAATTAATT
*
227771 -AGTTAATCT
1 AAATTAAT-T
227780 -AATTAATT
1 AAATTAATT
227788 AAATTAATT
1 AAATTAATT
227797 AAAT
1 AAAT
227801 AAATAATATT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
8 14 0.41
9 20 0.59
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (9 bp):
AAATTAATT
Found at i:227795 original size:13 final size:13
Alignment explanation
Indices: 227755--227804 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
227745 TGTGTTGAGA
227755 AATTAA-TAAATT
1 AATTAATTAAATT
*
227767 AATTAGTT-AATCT
1 AATTAATTAAAT-T
227780 AATTAATTAAATT
1 AATTAATTAAATT
*
227793 AATTAAATAAAT
1 AATTAATTAAAT
227805 AATATTTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
12 8 0.25
13 21 0.66
14 3 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (13 bp):
AATTAATTAAATT
Found at i:234059 original size:18 final size:18
Alignment explanation
Indices: 234032--234074 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
234022 ATAAGAAAAA
*
234032 AAATAAAATAAAATAAAT
1 AAATATAATAAAATAAAT
* *
234050 AAATATAATATAATATAT
1 AAATATAATAAAATAAAT
*
234068 ATATATA
1 AAATATA
234075 TATATATATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATATAATAAAATAAAT
Found at i:234069 original size:2 final size:2
Alignment explanation
Indices: 234052--234083 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
234042 AAATAAATAA
234052 AT AT A- AT AT A- 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
234084 GTATTATAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:236861 original size:9 final size:9
Alignment explanation
Indices: 236849--236874 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
236839 TCTAAAAGGT
236849 TTGGGCTTG
1 TTGGGCTTG
236858 TTGGGCTTG
1 TTGGGCTTG
236867 TTGGGCTT
1 TTGGGCTT
236875 CATGGGGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.42, T:0.46
Consensus pattern (9 bp):
TTGGGCTTG
Found at i:236951 original size:14 final size:14
Alignment explanation
Indices: 236913--236953 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 14
236903 TTTAGTTTAA
*
236913 GGTAAATGGGTTAT
1 GGTAAATGGGTTAG
*
236927 GGAAAATTGGGTTAG
1 GGTAAA-TGGGTTAG
236942 GGTAAATGGGTT
1 GGTAAATGGGTT
236954 GTTTGGTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.29, C:0.00, G:0.39, T:0.32
Consensus pattern (14 bp):
GGTAAATGGGTTAG
Found at i:239448 original size:21 final size:22
Alignment explanation
Indices: 239411--239453 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
239401 ACTTTCATCA
*
239411 TTAAGCTTTAGTTAACC-ATTT
1 TTAACCTTTAGTTAACCTATTT
239432 TTAACCTTTA-TTAAACCTATTT
1 TTAACCTTTAGTT-AACCTATTT
239454 ATAATCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 2 0.11
21 13 0.68
22 4 0.21
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.49
Consensus pattern (22 bp):
TTAACCTTTAGTTAACCTATTT
Found at i:243711 original size:17 final size:18
Alignment explanation
Indices: 243682--243739 Score: 59
Period size: 17 Copynumber: 3.2 Consensus size: 18
243672 ATAGAAAACA
243682 TTTT-TTTTCTTCTTTT-C
1 TTTTCTTTT-TTCTTTTAC
243699 TTTTCTTTTTTCTTTTAC
1 TTTTCTTTTTTCTTTTAC
*
243717 -TTTCTTTTTCTCGTTTTCC
1 TTTTCTTTTT-TC-TTTTAC
243736 TTTT
1 TTTT
243740 TCAAGTGACT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
17 20 0.57
18 7 0.20
19 5 0.14
20 3 0.09
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTCTTTTTTCTTTTAC
Found at i:253721 original size:37 final size:37
Alignment explanation
Indices: 253671--253741 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
253661 TATTGAGAAC
* *
253671 GTTTACAAAAGGAGATAGGATTGGTTCACCCAATCAT
1 GTTTACAAAAGGAGATAGAATTGATTCACCCAATCAT
253708 GTTTACAAAAGGAGATAGAATTGATTCACCCAAT
1 GTTTACAAAAGGAGATAGAATTGATTCACCCAAT
253742 TTTGTCCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (37 bp):
GTTTACAAAAGGAGATAGAATTGATTCACCCAATCAT
Found at i:254096 original size:25 final size:25
Alignment explanation
Indices: 254067--254118 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
254057 CTCGTTTATT
*
254067 TATT-AATGATATTTTTTTATAAAAA
1 TATTAAATAATATTTTTTT-TAAAAA
254092 TATTAAAATAATATTTTTTTTAAAAA
1 TATT-AAATAATATTTTTTTTAAAAA
254118 T
1 T
254119 TAAGTGGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 7 0.29
27 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TATTAAATAATATTTTTTTTAAAAA
Found at i:255334 original size:20 final size:20
Alignment explanation
Indices: 255309--255351 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
255299 CTCATTTAGA
*
255309 TTGGTGAGCAACGAACACAT
1 TTGGTGAACAACGAACACAT
* *
255329 TTGGTGAATAACGAACATAT
1 TTGGTGAACAACGAACACAT
255349 TTG
1 TTG
255352 ATAAGCTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (20 bp):
TTGGTGAACAACGAACACAT
Found at i:256486 original size:322 final size:322
Alignment explanation
Indices: 255901--256549 Score: 1253
Period size: 322 Copynumber: 2.0 Consensus size: 322
255891 TTCTCACCAC
255901 TTTCACTGTTTGTGTTCAATGACAAAATTTATGATATTTGGGATGTCAAGATTAAGACCTGCATG
1 TTTCACTGTTTGTGTTCAATGACAAAATTTATGATATTTGGGATGTCAAGATTAAGACCTGCATG
255966 CAAGCTTTTGACTTGTGGGAGGTTGTGAATACTAATGTCGAGCCAGCTTCATTAAGTGACAACGC
66 CAAGCTTTTGACTTGTGGGAGGTTGTGAATACTAATGTCGAGCCAGCTTCATTAAGTGACAACGC
256031 GATAATTGCTCAGATTAAACACCATAGTGACGAGTAAGCTAAAGGATATAAGGCAATGTCCTCCA
131 GATAATTGCTCAGATTAAACACCATAGTGACGAGTAAGCTAAAGGATATAAGGCAATGTCCTCCA
*
256096 TTCAGAATTGTGTCTCAGACATAATATTCACACGTATTATGACCTGTGAGACTCCGAAAAAAGCT
196 TTCAGAATTGTGTCTCAGACATAATATTCACACGTATTATGACCTGTGAAACTCCGAAAAAAGCT
*
256161 TGAGATAAGCTAAATGATGAGTTTCAAGGATCGAACAAGACTCGACAACAATAACTCATTAA
261 TGAGATAAGCTAAATGATGAGTTTCAAGGATCAAACAAGACTCGACAACAATAACTCATTAA
256223 TTTCACTGTTTGTGTTCAATGACAAAATTTATGATATTTGGGATGTCAAGATTAAGACCTGCATG
1 TTTCACTGTTTGTGTTCAATGACAAAATTTATGATATTTGGGATGTCAAGATTAAGACCTGCATG
* *
256288 CAAGCTTTTGACTTGTGGGAGGTTGTGACTACTGATGTCGAGCCAGCTTCATTAAGTGACAACGC
66 CAAGCTTTTGACTTGTGGGAGGTTGTGAATACTAATGTCGAGCCAGCTTCATTAAGTGACAACGC
*
256353 GATAATTGCTCAGATTAAACACCATAGTGACGAGTAAGCTAAAGGATATAAGGTAATGTCCTCCA
131 GATAATTGCTCAGATTAAACACCATAGTGACGAGTAAGCTAAAGGATATAAGGCAATGTCCTCCA
256418 TTCAGAATTGTGTCTCAGACATAATATTCACACGTATTATGACCTGTGAAACTCCGAAAAAAGCT
196 TTCAGAATTGTGTCTCAGACATAATATTCACACGTATTATGACCTGTGAAACTCCGAAAAAAGCT
256483 TGAGATAAGCTAAATGATGAGTTTCAAGGATCAAACAAGACTCGACAACAATAACTCATTAA
261 TGAGATAAGCTAAATGATGAGTTTCAAGGATCAAACAAGACTCGACAACAATAACTCATTAA
256545 TTTCA
1 TTTCA
256550 GGAGAGATTT
Statistics
Matches: 322, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
322 322 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (322 bp):
TTTCACTGTTTGTGTTCAATGACAAAATTTATGATATTTGGGATGTCAAGATTAAGACCTGCATG
CAAGCTTTTGACTTGTGGGAGGTTGTGAATACTAATGTCGAGCCAGCTTCATTAAGTGACAACGC
GATAATTGCTCAGATTAAACACCATAGTGACGAGTAAGCTAAAGGATATAAGGCAATGTCCTCCA
TTCAGAATTGTGTCTCAGACATAATATTCACACGTATTATGACCTGTGAAACTCCGAAAAAAGCT
TGAGATAAGCTAAATGATGAGTTTCAAGGATCAAACAAGACTCGACAACAATAACTCATTAA
Found at i:258434 original size:41 final size:40
Alignment explanation
Indices: 258357--258455 Score: 101
Period size: 41 Copynumber: 2.4 Consensus size: 40
258347 TTTTTAACTA
* *
258357 GCTAAAAGCCTGCTATGCAATAGCTTGATTCATTTCATTG
1 GCTAAAAGCCTGCTAGGCAATAGCTTGAATCATTTCATTG
* * **
258397 GCTAGAAGCCTGCTAGGCCAA-AGGCTTGAATCGTTTCACCG
1 GCTAAAAGCCTGCTAGG-CAATA-GCTTGAATCATTTCATTG
*
258438 GCTAAAAAGCCTACTAGG
1 GCT-AAAAGCCTGCTAGG
258456 TCGTAACCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 16 0.33
41 20 0.42
42 12 0.25
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.26
Consensus pattern (40 bp):
GCTAAAAGCCTGCTAGGCAATAGCTTGAATCATTTCATTG
Found at i:263747 original size:21 final size:21
Alignment explanation
Indices: 263723--263763 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
263713 AACTCAAAAA
*
263723 GTCAAAGGTTAACGATCAACG
1 GTCAAAGGTCAACGATCAACG
* *
263744 GTCAATGGTCAACGGTCAAC
1 GTCAAAGGTCAACGATCAAC
263764 TATCAACTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (21 bp):
GTCAAAGGTCAACGATCAACG
Found at i:263755 original size:14 final size:14
Alignment explanation
Indices: 263736--263798 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 14
263726 AAAGGTTAAC
263736 GATCAACGGTCAAT
1 GATCAACGGTCAAT
*
263750 GGTCAACGGTCAACT
1 GATCAACGGTCAA-T
*
263765 -ATCAACTGTCAAT
1 GATCAACGGTCAAT
**
263778 GATCAGTGGTCAAT
1 GATCAACGGTCAAT
*
263792 GGTCAAC
1 GATCAAC
263799 AGTTAACGGG
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
13 1 0.03
14 36 0.95
15 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (14 bp):
GATCAACGGTCAAT
Found at i:271884 original size:110 final size:112
Alignment explanation
Indices: 271679--271899 Score: 299
Period size: 110 Copynumber: 2.0 Consensus size: 112
271669 AAATAAAGAA
** *
271679 CATTTATCGATTTTTAAATAGGATGTTCAATTATTACTTAGGTTCAAAGAAAAACCATACTCAAT
1 CATTTATCGATTTTTAAATAGGATACTCAATTATTA-TTAGGTTCAAAGAAAAACCATACCCAAT
* * *
271744 ACGTTAGGACACGATTTTTCGAGTCTCCTAAAATAACAGAACATTGAG
65 ACGTTAGGACACAATTTCTCGAGTCTCCTAAAATAAAAGAACATTGAG
271792 CATTTATCGA-TTTTAAATAGGATACTCAATTATT-TT-GGTTCAAAGAAAAAACCATACCCAAT
1 CATTTATCGATTTTTAAATAGGATACTCAATTATTATTAGGTTCAAAG-AAAAACCATACCCAAT
* *
271854 ACGTTAGGGA-ATAATTTCTCGGATTC-CCTAAAATAAAAGAACATTG
65 ACGTTA-GGACACAATTTCTC-GAGTCTCCTAAAATAAAAGAACATTG
271900 CCTTTACTTT
Statistics
Matches: 97, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
109 9 0.09
110 49 0.51
111 7 0.07
112 22 0.23
113 10 0.10
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (112 bp):
CATTTATCGATTTTTAAATAGGATACTCAATTATTATTAGGTTCAAAGAAAAACCATACCCAATA
CGTTAGGACACAATTTCTCGAGTCTCCTAAAATAAAAGAACATTGAG
Found at i:272299 original size:34 final size:32
Alignment explanation
Indices: 272251--272328 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 32
272241 AAATGACATG
* * *
272251 GAAAATAATAAATGATTAAATAAAATAAAATAAT
1 GAAAACAATAAATGAAT-AA-AAAATAAAAAAAT
*
272285 GAAAACAATGAATGAATAAAAAATAAAAAAAT
1 GAAAACAATAAATGAATAAAAAATAAAAAAAT
* *
272317 AAAAATAATAAA
1 GAAAACAATAAA
272329 ACATACATAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
32 21 0.57
33 2 0.05
34 14 0.38
ACGTcount: A:0.72, C:0.01, G:0.06, T:0.21
Consensus pattern (32 bp):
GAAAACAATAAATGAATAAAAAATAAAAAAAT
Found at i:272477 original size:31 final size:31
Alignment explanation
Indices: 272439--272499 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
272429 GATGGGCAAA
*
272439 TTTTAAAACA-ATGAAAAAAAGAATTTAATTT
1 TTTTAAAAAACAT-AAAAAAAGAATTTAATTT
* *
272470 TTTTAAAAAACATAACAAAAGGATTTAATT
1 TTTTAAAAAACATAAAAAAAGAATTTAATT
272500 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.54, C:0.05, G:0.07, T:0.34
Consensus pattern (31 bp):
TTTTAAAAAACATAAAAAAAGAATTTAATTT
Found at i:279573 original size:7 final size:7
Alignment explanation
Indices: 279561--279595 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
279551 GAAATTACCT
279561 GAGGATG
1 GAGGATG
279568 GAGGATG
1 GAGGATG
279575 GAGGATG
1 GAGGATG
279582 GAGGATG
1 GAGGATG
279589 GAGGATG
1 GAGGATG
279596 AGTAAGCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.29, C:0.00, G:0.57, T:0.14
Consensus pattern (7 bp):
GAGGATG
Found at i:280074 original size:16 final size:16
Alignment explanation
Indices: 280050--280084 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
280040 TTCACCTATT
*
280050 TAATTTTTTT-ATATA
1 TAATTTTTTTAAAATA
280065 TAATTTTTTTAAAATA
1 TAATTTTTTTAAAATA
280081 TAAT
1 TAAT
280085 ACATGACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTTTTTTAAAATA
Found at i:281378 original size:19 final size:20
Alignment explanation
Indices: 281354--281399 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
281344 GAAGGAGAAG
*
281354 TGAGAGTAAATAAAA-GTTT
1 TGAGAGAAAATAAAATGTTT
281373 TGAGAGAAAATAAAATGTTT
1 TGAGAGAAAATAAAATGTTT
281393 TGAGAGA
1 TGAGAGA
281400 TTTGAGGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (20 bp):
TGAGAGAAAATAAAATGTTT
Found at i:292795 original size:20 final size:23
Alignment explanation
Indices: 292772--292822 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
292762 TTAAGCTAAG
292772 TTAATTAA-A-GT-TTAATTTAA
1 TTAATTAAGATGTATTAATTTAA
*
292792 TTAATTAAGATTTATTAATTTAA
1 TTAATTAAGATGTATTAATTTAA
292815 TCTAATTA
1 T-TAATTA
292823 TAAAAGTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 1 0.04
22 1 0.04
23 10 0.38
24 6 0.23
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (23 bp):
TTAATTAAGATGTATTAATTTAA
Found at i:297842 original size:25 final size:27
Alignment explanation
Indices: 297791--297854 Score: 87
Period size: 26 Copynumber: 2.4 Consensus size: 27
297781 TGGTGAACAT
* *
297791 GAGTTCGCTAGGTAAGTTGCGAACTGG
1 GAGTTCGCCAGTTAAGTTGCGAACTGG
297818 G-GTTCGCCAGTTAAG-TGCGAACTGG
1 GAGTTCGCCAGTTAAGTTGCGAACTGG
*
297843 GAGTTTGCCAGT
1 GAGTTCGCCAGT
297855 CAAAGAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 11 0.33
26 21 0.64
27 1 0.03
ACGTcount: A:0.20, C:0.17, G:0.36, T:0.27
Consensus pattern (27 bp):
GAGTTCGCCAGTTAAGTTGCGAACTGG
Found at i:300477 original size:2 final size:2
Alignment explanation
Indices: 300470--300494 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
300460 TATGAAAAAG
300470 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
300495 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:311819 original size:26 final size:26
Alignment explanation
Indices: 311779--311997 Score: 192
Period size: 26 Copynumber: 8.5 Consensus size: 26
311769 TCAAAGTTTA
311779 GCTCTTACGTA-CCCAGACAGTATATC
1 GCTCTTACG-AGCCCAGACAGTATATC
* * * * *
311805 TCTTTTATGAGCCCAAATAGTATATC
1 GCTCTTACGAGCCCAGACAGTATATC
* * * * *
311831 ACTCTTACAAGCCCAAACAATATATT
1 GCTCTTACGAGCCCAGACAGTATATC
* * *
311857 GCTCTTGCGAG-CCAGTCAGAATATC
1 GCTCTTACGAGCCCAGACAGTATATC
* *
311882 ACTCTTACGAGCCTAGACAGTATATC
1 GCTCTTACGAGCCCAGACAGTATATC
* *
311908 GCTCTTACGAG-CCAGTCAGAATATC
1 GCTCTTACGAGCCCAGACAGTATATC
* *
311933 GCTCTTACGAGCCTATACAGTATATC
1 GCTCTTACGAGCCCAGACAGTATATC
* * *
311959 GCTCTTATGAGCCCAAACAATATATC
1 GCTCTTACGAGCCCAGACAGTATATC
* *
311985 ACTATTACGAGCC
1 GCTCTTACGAGCC
311998 AGTTAAAATA
Statistics
Matches: 150, Mismatches: 40, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
25 41 0.27
26 109 0.73
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (26 bp):
GCTCTTACGAGCCCAGACAGTATATC
Found at i:311886 original size:25 final size:25
Alignment explanation
Indices: 311852--312033 Score: 161
Period size: 25 Copynumber: 7.2 Consensus size: 25
311842 CCCAAACAAT
* *
311852 ATATTGCTCTTGCGAGCCAGTCAGA
1 ATATCGCTCTTACGAGCCAGTCAGA
* * *
311877 ATATCACTCTTACGAGCCTAGACAGT
1 ATATCGCTCTTACGAGCC-AGTCAGA
311903 ATATCGCTCTTACGAGCCAGTCAGA
1 ATATCGCTCTTACGAGCCAGTCAGA
*
311928 ATATCGCTCTTACGAGCCTA-TACAGT
1 ATATCGCTCTTACGAGCC-AGT-CAGA
* **
311954 ATATCGCTCTTATGAGCCCAAACA-A
1 ATATCGCTCTTACGAG-CCAGTCAGA
* * * *
311979 TATATCACTATTACGAGCCAGTTAAA
1 -ATATCGCTCTTACGAGCCAGTCAGA
* * *
312005 ATATCGCTCTTACAAGCCACTCATA
1 ATATCGCTCTTACGAGCCAGTCAGA
312030 ATAT
1 ATAT
312034 TACTTCTCTT
Statistics
Matches: 126, Mismatches: 24, Indels: 14
0.77 0.15 0.09
Matches are distributed among these distances:
25 66 0.52
26 58 0.46
27 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (25 bp):
ATATCGCTCTTACGAGCCAGTCAGA
Found at i:311906 original size:51 final size:51
Alignment explanation
Indices: 311826--311997 Score: 211
Period size: 51 Copynumber: 3.4 Consensus size: 51
311816 CCCAAATAGT
* * * * *
311826 ATATCACTCTTACAAGCCCAAACAATATATTGCTCTTGCGAGCCAGTCAGA
1 ATATCACTCTTACGAGCCTAAACAGTATATCGCTCTTACGAGCCAGTCAGA
*
311877 ATATCACTCTTACGAGCCTAGACAGTATATCGCTCTTACGAGCCAGTCAGA
1 ATATCACTCTTACGAGCCTAAACAGTATATCGCTCTTACGAGCCAGTCAGA
* * * **
311928 ATATCGCTCTTACGAGCCTATACAGTATATCGCTCTTATGAGCCCAAACA-A
1 ATATCACTCTTACGAGCCTAAACAGTATATCGCTCTTACGAG-CCAGTCAGA
*
311979 TATATCACTATTACGAGCC
1 -ATATCACTCTTACGAGCC
311998 AGTTAAAATA
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
51 85 0.80
52 21 0.20
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (51 bp):
ATATCACTCTTACGAGCCTAAACAGTATATCGCTCTTACGAGCCAGTCAGA
Found at i:311958 original size:77 final size:76
Alignment explanation
Indices: 311765--312033 Score: 216
Period size: 77 Copynumber: 3.5 Consensus size: 76
311755 TCATACAAGC
* * * * * * * * * * *
311765 CCAGTCAAAGTTTAGCTCTTACGTACCCAGACAGTATATCTCTTTTATGAGCCCAAATAGTATAT
1 CCAGTCAAAATATCGCTCTTACG-AGCCAGTCAGAATATCACTCTTACGAGCCCAAACAATATAT
* *
311830 CACTCTTACAAG
65 CACTATTACGAG
** * * * * * *
311842 CCCAAACAATATATTGCTCTTGCGAGCCAGTCAGAATATCACTCTTACGAGCCTAGACAGTATAT
1 -CCAGTCAAAATATCGCTCTTACGAGCCAGTCAGAATATCACTCTTACGAGCCCAAACAATATAT
* *
311907 CGCTCTTACGAG
65 CACTATTACGAG
* * * *
311919 CCAGTCAGAATATCGCTCTTACGAGCCTA-TACAGTATATCGCTCTTATGAGCCCAAACAATATA
1 CCAGTCAAAATATCGCTCTTACGAGCC-AGT-CAGAATATCACTCTTACGAGCCCAAACAATATA
311983 TCACTATTACGAG
64 TCACTATTACGAG
* * * *
311996 CCAGTTAAAATATCGCTCTTACAAGCCACTCATAATAT
1 CCAGTCAAAATATCGCTCTTACGAGCCAGTCAGAATAT
312034 TACTTCTCTT
Statistics
Matches: 151, Mismatches: 37, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
76 29 0.19
77 106 0.70
78 16 0.11
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (76 bp):
CCAGTCAAAATATCGCTCTTACGAGCCAGTCAGAATATCACTCTTACGAGCCCAAACAATATATC
ACTATTACGAG
Found at i:315234 original size:32 final size:32
Alignment explanation
Indices: 315189--315275 Score: 122
Period size: 32 Copynumber: 2.7 Consensus size: 32
315179 AGACTAGCTG
315189 ACACACTTGCGAACATAGTTCGCACATAGA-AA
1 ACACACTTGCGAACATAGTTCGCACATA-ACAA
* * * *
315221 ACACACTTACGAACACAGTTCGGACATAACAG
1 ACACACTTGCGAACATAGTTCGCACATAACAA
315253 ACACACTTGCGAACATAGTTCGC
1 ACACACTTGCGAACATAGTTCGC
315276 CAAAACACAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 1 0.02
32 46 0.98
ACGTcount: A:0.38, C:0.28, G:0.16, T:0.18
Consensus pattern (32 bp):
ACACACTTGCGAACATAGTTCGCACATAACAA
Found at i:315550 original size:24 final size:24
Alignment explanation
Indices: 315502--315550 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
315492 AGTTAAAATT
* * *
315502 TGTTTATTTGTTTTAATTAACCTC
1 TGTTTATTTGTTTGAATCAAACTC
*
315526 TGTTTATTTGTTTGAGTCAAACTC
1 TGTTTATTTGTTTGAATCAAACTC
315550 T
1 T
315551 TATTACTCTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TGTTTATTTGTTTGAATCAAACTC
Found at i:316292 original size:36 final size:36
Alignment explanation
Indices: 316245--316319 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
316235 CTATCCTAAG
*
316245 TATGATCTAAATTCGAACCGTACTAATCGTATTTAT
1 TATGATCTAAATTCGAACCGTACTAATCATATTTAT
* * * *
316281 TATGATTTAAATTTGAATCGTACTAATCATATTTGT
1 TATGATCTAAATTCGAACCGTACTAATCATATTTAT
316317 TAT
1 TAT
316320 TTAAACTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (36 bp):
TATGATCTAAATTCGAACCGTACTAATCATATTTAT
Found at i:321958 original size:96 final size:96
Alignment explanation
Indices: 321794--321986 Score: 386
Period size: 96 Copynumber: 2.0 Consensus size: 96
321784 TGCCAGCACC
321794 TTGAAAGTTACACATTTATATTGACATAAACTCAGAGACCAGTTAATATTTATCTATCTGTAAAA
1 TTGAAAGTTACACATTTATATTGACATAAACTCAGAGACCAGTTAATATTTATCTATCTGTAAAA
321859 TTCATCTTCTAGATGAAAAGTAAACTACATT
66 TTCATCTTCTAGATGAAAAGTAAACTACATT
321890 TTGAAAGTTACACATTTATATTGACATAAACTCAGAGACCAGTTAATATTTATCTATCTGTAAAA
1 TTGAAAGTTACACATTTATATTGACATAAACTCAGAGACCAGTTAATATTTATCTATCTGTAAAA
321955 TTCATCTTCTAGATGAAAAGTAAACTACATT
66 TTCATCTTCTAGATGAAAAGTAAACTACATT
321986 T
1 T
321987 AATCGCCTTT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
96 97 1.00
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (96 bp):
TTGAAAGTTACACATTTATATTGACATAAACTCAGAGACCAGTTAATATTTATCTATCTGTAAAA
TTCATCTTCTAGATGAAAAGTAAACTACATT
Found at i:331085 original size:38 final size:38
Alignment explanation
Indices: 331002--331086 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 38
330992 TGAGTCTATT
* * * *
331002 CAAAATTGCGCCTAAAATTGGCACTACATGACGATGTC
1 CAAAATTGTGCCCAAAATTAGCACTACATGACGATGCC
* * *
331040 CAGAATTGTGCCCAAAATTATCACTGCATGA-GCATGCC
1 CAAAATTGTGCCCAAAATTAGCACTACATGACG-ATGCC
331078 CAAAATTGT
1 CAAAATTGT
331087 CACTGTACGA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
37 1 0.03
38 37 0.97
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (38 bp):
CAAAATTGTGCCCAAAATTAGCACTACATGACGATGCC
Found at i:334338 original size:24 final size:24
Alignment explanation
Indices: 334295--334576 Score: 222
Period size: 24 Copynumber: 11.8 Consensus size: 24
334285 ATTTCTATAC
* * *
334295 GTTTACACTCGTTAGATTGCACAT
1 GTTTACGCTCGTCAGCTTGCACAT
*
334319 GTTTACGCTCATCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTGCACAT
* * ** * *
334343 GTTTACACTTGTCAGCTTATATAC
1 GTTTACGCTCGTCAGCTTGCACAT
334367 GTTTACGCTCGTCAGCTTGCACAT
1 GTTTACGCTCGTCAGCTTGCACAT
* ** *
334391 GTTTACGCTCTTCAGCTTATATAT
1 GTTTACGCTCGTCAGCTTGCACAT
* ** *
334415 GTTCACGCTCACCAGCTTGCACAC
1 GTTTACGCTCGTCAGCTTGCACAT
* ** **
334439 ATTTACGCTCGTCAGCTTATATGT
1 GTTTACGCTCGTCAGCTTGCACAT
* *
334463 GTTTACACTCGTCAGCTTGCAAAT
1 GTTTACGCTCGTCAGCTTGCACAT
* * *
334487 GTTTATGCTCGTCAGCTTTCACAC
1 GTTTACGCTCGTCAGCTTGCACAT
* * * *
334511 ATTTACGCTCGTTAGCTTGCGCAC
1 GTTTACGCTCGTCAGCTTGCACAT
* * * *
334535 ATTTACGCTCGTTAGCTTGCGCAC
1 GTTTACGCTCGTCAGCTTGCACAT
* *
334559 ATTTATGCTCGTCAGCTT
1 GTTTACGCTCGTCAGCTT
334577 ATATACGTTT
Statistics
Matches: 203, Mismatches: 55, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 203 1.00
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.36
Consensus pattern (24 bp):
GTTTACGCTCGTCAGCTTGCACAT
Found at i:334396 original size:72 final size:72
Alignment explanation
Indices: 334290--334588 Score: 267
Period size: 72 Copynumber: 4.2 Consensus size: 72
334280 TGTCAATTTC
* * * * * *
334290 TATACGTTTACACTCGTTAGATTGCACATGTTTACGCTCATCAGCTTGCACATGTTTACACTTGT
1 TATACGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGT
334355 CAGCTTA
66 CAGCTTA
* ** * * **
334362 TATACGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCTTCAGCTTATATATGTTCACGCTCAC
1 TATACGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGT
*
334427 CAGCTTG
66 CAGCTTA
* * * ** ** * * *
334434 CACACATTTACGCTCGTCAGCTTATATGTGTTTACACTCGTCAGCTTGCAAATGTTTATGCTCGT
1 TATACGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGT
334499 CAGCTT-
66 CAGCTTA
* * * * ** * * ** *
334505 TCACACATTTACGCTCGTTAGCTTGCGCACATTTACGCTCGTTAGCTTGCGCACATTTATGCTCG
1 T-ATACGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCG
334570 TCAGCTTA
65 TCAGCTTA
334578 TATACGTTTAC
1 TATACGTTTAC
334589 TTGATTCAAC
Statistics
Matches: 179, Mismatches: 46, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
72 178 0.99
73 1 0.01
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.36
Consensus pattern (72 bp):
TATACGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGTCAGCTTGCACATGTTTACGCTCGT
CAGCTTA
Found at i:335281 original size:13 final size:14
Alignment explanation
Indices: 335263--335291 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
335253 TAGCCAATTC
335263 TTCTTCTT-TTCTT
1 TTCTTCTTATTCTT
335276 TTCTTCTTATTCTT
1 TTCTTCTTATTCTT
335290 TT
1 TT
335292 AATTTCATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (14 bp):
TTCTTCTTATTCTT
Found at i:335288 original size:19 final size:20
Alignment explanation
Indices: 335259--335306 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
335249 AAAGTAGCCA
* **
335259 ATTCTTCTTCTTTTCTTTTC
1 ATTCTTATTCTTTTAATTTC
335279 -TTCTTATTCTTTTAATTTC
1 ATTCTTATTCTTTTAATTTC
335298 ATTCTTATT
1 ATTCTTATT
335307 ATTATTCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (20 bp):
ATTCTTATTCTTTTAATTTC
Found at i:340749 original size:3 final size:3
Alignment explanation
Indices: 340741--340784 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
340731 AATATTTAGG
*
340741 ATT ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
340785 TATATTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:340787 original size:9 final size:8
Alignment explanation
Indices: 340752--340790 Score: 51
Period size: 9 Copynumber: 4.5 Consensus size: 8
340742 TTATTATTGT
340752 TATTATTA
1 TATTATTA
340760 TTATTATTA
1 -TATTATTA
340769 TTATTATTA
1 -TATTATTA
340778 TATTATTTA
1 TATTA-TTA
340787 TATT
1 TATT
340791 TAATTTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 5 0.17
9 24 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TATTATTA
Found at i:342520 original size:18 final size:18
Alignment explanation
Indices: 342495--342558 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
342485 TAGCTCGTTA
342495 GAGCATATTGGCTCATTT
1 GAGCATATTGGCTCATTT
* *
342513 GAGTATATTGGCTCGTTT
1 GAGCATATTGGCTCATTT
* *
342531 GAGCATACTGGCTCGA-TA
1 GAGCATATTGGCTC-ATTT
342549 GAGCATATTG
1 GAGCATATTG
342559 ACTTATTAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.34
Consensus pattern (18 bp):
GAGCATATTGGCTCATTT
Done.