Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 93 of 136
Found at i:30976629 original size:222 final size:225
Alignment explanation
Indices: 30976170--30976657 Score: 565
Period size: 222 Copynumber: 2.2 Consensus size: 225
30976160 TTAAATATCT
* * * * * *
30976170 TTTGTTTCTTTCTTATAATA-CTCTTTTTTGATGCCATAAGTGATCTTTAAAAAATATTATCAAC
1 TTTGTTTCTTTCTTATAA-AGCTCTTCTTTGATGCC-T---T-AGCATTAATAAATCTCATCAAC
* *
30976234 CAAGCAAATATTTCTCAAAATCAACAATTACCAAGTACACAACAATACTCGTTTCTCAAGAAAAA
60 CAAGCAAATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCT-AAGAAAAA
* * * *
30976299 GAAATGCAAGAATATTACCAATGGAGCAAATAGCCATAATATTCTTTCACCAACAAGGGTAATTC
124 GAAATGCAAGAATATTACCAATGGAACAAATAACCATAATATTCTTGCACCAACAAAGGTAATTC
** ***
30976364 TGATCAAATGATAATCAAGTATTGCACTCAATTGTCA
189 TGATCAAATGATAATCAAGTATCACACTCAACCCTCA
* * * *
30976401 TTTGTTTCTTTTTTATAATGC-CTTTCTTTGATGCCTTAGCATTAATAAATCTCATCAATCAAGT
1 TTTGTTTCTTTCTTATAAAGCTC-TTCTTTGATGCCTTAGCATTAATAAATCTCATCAACCAAGC
* **
30976465 AAATATTTCCCAAAATCAACAATTA-CAAGTACACAACAATATTCATTTCT-TTAAAAA-AAATG
65 AAATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCTAAGAAAAAGAAATG
* * * *
30976527 -AAGAATCTTACCAATGGAAACAAATAATCATAATCTTCTTGCACCAACAAAGGTAATTTTGATC
130 CAAGAATATTACCAATGG-AACAAATAACCATAATATTCTTGCACCAACAAAGGTAATTCTGATC
* * * *
30976591 AAATGGTAATTAAGTATCACACTCAGCCCTCT
194 AAATGATAATCAAGTATCACACTCAACCCTCA
30976623 TTTGTTTCTTTCTTATAAAGCTCTTCTTTGATGCC
1 TTTGTTTCTTTCTTATAAAGCTCTTCTTTGATGCC
30976658 ATAAGTAATA
Statistics
Matches: 219, Mismatches: 34, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
221 16 0.07
222 98 0.45
223 6 0.03
225 23 0.11
226 44 0.20
227 1 0.00
230 2 0.01
231 29 0.13
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (225 bp):
TTTGTTTCTTTCTTATAAAGCTCTTCTTTGATGCCTTAGCATTAATAAATCTCATCAACCAAGCA
AATATTTCCCAAAATCAACAATTACCAAGTACACAACAATACTCATTTCTAAGAAAAAGAAATGC
AAGAATATTACCAATGGAACAAATAACCATAATATTCTTGCACCAACAAAGGTAATTCTGATCAA
ATGATAATCAAGTATCACACTCAACCCTCA
Found at i:30981950 original size:326 final size:329
Alignment explanation
Indices: 30981352--30981982 Score: 858
Period size: 326 Copynumber: 1.9 Consensus size: 329
30981342 TCTTTTGAGC
* * * **
30981352 TAAAAATATTTATTTTATTGTTGTTTATTTATATACACATTGCTAATGATCACTTCTCCATTTAT
1 TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
* * * * * *
30981417 AAATACCTTATCCTCCAAGAAAAATAGGATAAGCAAGAACAAATGACGAAAACTTAGCTCGAGTG
66 AAATACCTCATCCTCCAAAAAAAATAGGATAAGCAAGAACAAATGACAAAAACGTAGCTCAAGTA
* * * * * * *
30981482 TAACCTTGACCTTCTAAAACCATCGAGTCTAGTAACTCTCCAAACCATCTATAGTGTGAACTGTT
131 TAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGCT
* ** * *
30981547 CTCATTTTAGTGGCTATCCATACCTCATACGATGTGAACTACCCTCATTGTATTATTCGGCATAT
196 CCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTACCCTCATTGTATTATTCGACATAT
* *
30981612 TGTGTTACTTAATTGTTAT-AT-TAAA-AATAAGATGAATATTTATTTTATTGTTATTTATCGTT
261 TGTGTAACTTAATTGTTATCATATAAATAAAAAGATGAATATTTATTTTATTGTTATTTATCGTT
30981674 ATAA
326 ATAA
* **
30981678 TAAAAATATTTATTTTATTGATATTTATTTATATACACTTTGCTCGCGATCACTTCTCCACCTAT
1 TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
* * * *
30981743 AAATACCTCATCCTCCAAAAAAAATGGGCTAAGCAATAAGAAA-GTACAAAAACGTAGCTCAAGT
66 AAATACCTCATCCTCCAAAAAAAATAGGATAAGCAAGAACAAATG-ACAAAAACGTAGCTCAAGT
* * *
30981807 ATAACCTCGTCCTTCTAAAACCACCAAATCTAGCGACTCTCCACACCATCTATAGTGTGAACCGC
130 ATAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGC
* *
30981872 TCCCATTTTAGCAGCTCTCCACACCTCATATGATGTGAACTACTCC-CATTGTATTATTCGACAT
195 TCCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTAC-CCTCATTGTATTATTCGACAT
*
30981936 CTTGTGTAACTTAATTGTTATCATAATAAATAAAAAGATGAATATTT
259 ATTGTGTAACTTAATTGTTATCAT-ATAAATAAAAAGATGAATATTT
30981983 GATACATTGT
Statistics
Matches: 261, Mismatches: 38, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
325 1 0.00
326 237 0.91
327 4 0.02
329 4 0.02
330 15 0.06
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.35
Consensus pattern (329 bp):
TAAAAATATTTATTTTATTGATATTTATTTATATACACATTGCTAACGATCACTTCTCCACCTAT
AAATACCTCATCCTCCAAAAAAAATAGGATAAGCAAGAACAAATGACAAAAACGTAGCTCAAGTA
TAACCTCGACCTTCTAAAACCACCAAATCTAGCAACTCTCCAAACCATCTATAGTGTGAACCGCT
CCCATTTTAGCAGCTATCCACACCTCATACGATGTGAACTACCCTCATTGTATTATTCGACATAT
TGTGTAACTTAATTGTTATCATATAAATAAAAAGATGAATATTTATTTTATTGTTATTTATCGTT
ATAA
Found at i:30982205 original size:14 final size:13
Alignment explanation
Indices: 30982183--30982239 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
30982173 CAACATCAAA
30982183 AAACT-AAAACCTT
1 AAACTCAAAA-CTT
*
30982196 AAAC-CTAAAATCTG
1 AAACTC-AAAA-CTT
30982210 AAACTCAAAACTT
1 AAACTCAAAACTT
30982223 AAAACTCAAAACTT
1 -AAACTCAAAACTT
30982237 AAA
1 AAA
30982240 AAAGAGGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
13 9 0.24
14 27 0.73
15 1 0.03
ACGTcount: A:0.56, C:0.21, G:0.02, T:0.21
Consensus pattern (13 bp):
AAACTCAAAACTT
Found at i:30982205 original size:21 final size:20
Alignment explanation
Indices: 30982181--30982240 Score: 57
Period size: 21 Copynumber: 2.9 Consensus size: 20
30982171 CCCAACATCA
*
30982181 AAAAACTAAAACCTTAAACCT
1 AAAAACTAAAA-CTTAAAACT
* * *
30982202 AAAATCTGAAACTCAAAACT
1 AAAAACTAAAACTTAAAACT
*
30982222 TAAAACTCAAAACTTAAAA
1 AAAAACT-AAAACTTAAAA
30982241 AAGAGGCAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAAACTAAAACTTAAAACT
Found at i:30982240 original size:14 final size:14
Alignment explanation
Indices: 30982210--30982240 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
30982200 CTAAAATCTG
30982210 AAACTCAAAACTTA
1 AAACTCAAAACTTA
30982224 AAACTCAAAACTTA
1 AAACTCAAAACTTA
30982238 AAA
1 AAA
30982241 AAGAGGCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.61, C:0.19, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACTCAAAACTTA
Found at i:30982500 original size:17 final size:17
Alignment explanation
Indices: 30982474--30982515 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
30982464 GTCTAACAAA
*
30982474 ATTTTGTAAAAAAAATT
1 ATTTTATAAAAAAAATT
30982491 ATTTTATAAAAAAAATT
1 ATTTTATAAAAAAAATT
30982508 ATTTTATA
1 ATTTTATA
30982516 TGAAAGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTTATAAAAAAAATT
Found at i:30984548 original size:26 final size:24
Alignment explanation
Indices: 30984504--30984556 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
30984494 AAGTTCAAGC
*
30984504 GAGCCATAACGGGTAGCTCATGAA
1 GAGCCATAACGGGTAGCTCATAAA
30984528 GAGCCATATATCGGG-ACGCTCATAAA
1 GAGCCATA-A-CGGGTA-GCTCATAAA
30984554 GAG
1 GAG
30984557 ATGTGGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 8 0.32
25 2 0.08
26 15 0.60
ACGTcount: A:0.34, C:0.21, G:0.28, T:0.17
Consensus pattern (24 bp):
GAGCCATAACGGGTAGCTCATAAA
Found at i:30987114 original size:14 final size:15
Alignment explanation
Indices: 30987085--30987121 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
30987075 CTCACTTTCG
30987085 AAATTAATAGAAATT
1 AAATTAATAGAAATT
*
30987100 AAATTAGTA-AAATT
1 AAATTAATAGAAATT
30987114 AAA-TAATA
1 AAATTAATA
30987122 TAGGTTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 4 0.20
14 8 0.40
15 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.32
Consensus pattern (15 bp):
AAATTAATAGAAATT
Found at i:30990923 original size:91 final size:92
Alignment explanation
Indices: 30990752--30990938 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 92
30990742 CAAAACTCAA
*
30990752 AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTCG
1 AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTAG
*
30990817 ACAAGATTTATTAAGTAGTGAAATCGC
66 ACAAGATTTATTAAGTAGTGAAATCAC
* * * * *
30990844 AACAAGTTTCCAAA-GTCAAAATAACTTAAAATAGTGCAATGCTAAAAATAAGTGCTACTTCTAG
1 AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTAG
30990908 ACAAGATTTATTAAGTAGTGAAATCAC
66 ACAAGATTTATTAAGTAGTGAAATCAC
30990935 AACA
1 AACA
30990939 TAAATTATGC
Statistics
Matches: 88, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
91 75 0.85
92 13 0.15
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (92 bp):
AACAAGTTTCAAAATATCAAAACAACTTAAAATAGTGCAATGCTAAAAATAAGTGCCACTACTAG
ACAAGATTTATTAAGTAGTGAAATCAC
Found at i:30993680 original size:16 final size:17
Alignment explanation
Indices: 30993659--30993695 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
30993649 TAGTTTTTTT
*
30993659 TAAAAATAAAA-AAAAG
1 TAAAAATAAAATAAAAA
30993675 TAAAAATAAAATAAAAA
1 TAAAAATAAAATAAAAA
30993692 TAAA
1 TAAA
30993696 GAAAGCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
TAAAAATAAAATAAAAA
Found at i:30993689 original size:11 final size:11
Alignment explanation
Indices: 30993661--30993695 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
30993651 GTTTTTTTTA
30993661 AAAATAAAAA-
1 AAAATAAAAAT
*
30993671 AAAGTAAAAAT
1 AAAATAAAAAT
30993682 AAAATAAAAAT
1 AAAATAAAAAT
30993693 AAA
1 AAA
30993696 GAAAGCAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:30994960 original size:43 final size:42
Alignment explanation
Indices: 30994913--30995405 Score: 97
Period size: 44 Copynumber: 11.2 Consensus size: 42
30994903 TGCAACCGAG
30994913 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCGATGCA
1 GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTC-ATGCA
* * * * * **
30994956 GGAGGGCAA-GATCTGCTATCTTTGATCTGCTCCACT-ACAACCGA
1 GGA-GGCAAGGCT-TG-TGTCTTCGATCTGCTTCACTGTCATGC-A
* * * *
30995000 GGGCGGTAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGTA
1 -GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTC-ATGCA
* * * * * * * ** **
30995044 GGAAGGCAA-GATCTGTTATCCTCAACCAGCTCCA-TCACAACCGA
1 GG-AGGCAAGGCT-TG-TGTCTTCGATCTGCTTCACTGTCATGC-A
* * *
30995088 GAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
1 G-GAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTC-ATGCA
* * * * * * * **
30995132 GGAAGGCAAGATCTTTTGTCCTCAACCAGCTCCA-TCACAACTG-A
1 GG-AGGCAAG-GCTTGTGTCTTCGATCTGCTTCACTGTC-A-TGCA
* *
30995176 GAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 G-GAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTC-ATGCA
* * * * * ** **
30995220 GGAAGGCAAGATCTAT-TGTCTTCAACCAGCTCCA-TCACAACCGA
1 GG-AGGCAAG-GCT-TGTGTCTTCGATCTGCTTCACTGTCATGC-A
* * *
30995264 GAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCA
1 G-GAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTC-ATGCA
* * * * * * * **
30995308 GGAAGGCAAGATCTTTTGTCCTCAACCAGCTCCA-TCACAACTG-A
1 GG-AGGCAAG-GCTTGTGTCTTCGATCTGCTTCACTGTC-A-TGCA
* *
30995352 GAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCA
1 G-GAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTC-ATGCA
30995396 GGAAGGCAAG
1 GG-AGGCAAG
30995406 ATCTATTGTC
Statistics
Matches: 306, Mismatches: 107, Indels: 73
0.63 0.22 0.15
Matches are distributed among these distances:
42 1 0.00
43 93 0.30
44 120 0.39
45 91 0.30
46 1 0.00
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (42 bp):
GGAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCATGCA
Found at i:30994999 original size:88 final size:88
Alignment explanation
Indices: 30994905--30995656 Score: 1164
Period size: 88 Copynumber: 8.5 Consensus size: 88
30994895 TGCTTCATTG
* * * * * *
30994905 CAACCGAGGGAGGCAAGGCTTGTGTCTTCGATCTGCTTCACTGTCGATGCAGGAGGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
** * ** * *
30994970 GCTATCTTTGATCTGCTCCA-CTA
66 TTTGTCTTCAACCAGCTCCATC-A
* * * * * *
30994993 CAACCGAGGGCGGTAAGGCTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
* * *
30995058 GTTATCCTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
30995081 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
30995146 TTTGTCCTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
* *
30995169 CAACTGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
30995234 ATTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
30995257 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
30995322 TTTGTCCTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
* *
30995345 CAACTGAGAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
*
30995410 ATTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
* **
30995433 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAAAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
30995498 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
* **
30995521 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATACAAAAAGGCAAGATCT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
30995586 TTTGTCTTCAACCAGCTCCATCA
66 TTTGTCTTCAACCAGCTCCATCA
30995609 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAAT
1 CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAAT
30995657 NNNNNNNNNN
Statistics
Matches: 625, Mismatches: 38, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
88 624 1.00
89 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (88 bp):
CAACCGAGAGAGGCAAGGTTTGTGTCTTCGACCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCT
TTTGTCTTCAACCAGCTCCATCA
Found at i:30998871 original size:6 final size:6
Alignment explanation
Indices: 30998855--30998893 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
30998845 TTGACCTCTC
* *
30998855 CTTTTT ATTTTT CTTTTT ATTTTT CTTTTTT CTTTTT CT
1 CTTTTT CTTTTT CTTTTT CTTTTT C-TTTTT CTTTTT CT
30998894 CCTATTTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (6 bp):
CTTTTT
Found at i:30998890 original size:12 final size:12
Alignment explanation
Indices: 30998855--30998884 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
30998845 TTGACCTCTC
30998855 CTTTTTATTTTT
1 CTTTTTATTTTT
30998867 CTTTTTATTTTT
1 CTTTTTATTTTT
30998879 CTTTTT
1 CTTTTT
30998885 TCTTTTTCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTTATTTTT
Found at i:30998919 original size:18 final size:16
Alignment explanation
Indices: 30998898--30998986 Score: 106
Period size: 16 Copynumber: 5.3 Consensus size: 16
30998888 TTTTCTCCTA
*
30998898 TTTTCTTTGATTTTTT
1 TTTTTTTTGATTTTTT
*
30998914 ATTTTTTTGATTTTTT
1 TTTTTTTTGATTTTTT
*
30998930 TTGATTTTTTAATTTTTT
1 TT--TTTTTTGATTTTTT
*
30998948 TTATTTTTGATTTTTTT
1 TTTTTTTTGA-TTTTTT
30998965 TATTTTTTTGATTTTTT
1 T-TTTTTTTGATTTTTT
30998982 TTTTT
1 TTTTT
30998987 AGTCTGAACT
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
16 25 0.40
17 14 0.23
18 23 0.37
ACGTcount: A:0.11, C:0.01, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTTTTTGATTTTTT
Found at i:30998926 original size:9 final size:9
Alignment explanation
Indices: 30998897--30998982 Score: 92
Period size: 9 Copynumber: 9.9 Consensus size: 9
30998887 TTTTTCTCCT
30998897 ATTTTCTTTG
1 ATTTT-TTTG
30998907 A-TTTTTT-
1 ATTTTTTTG
30998914 ATTTTTTTG
1 ATTTTTTTG
30998923 ATTTTTTTTG
1 A-TTTTTTTG
*
30998933 A-TTTTTTA
1 ATTTTTTTG
30998941 ATTTTTTT-
1 ATTTTTTTG
*
30998949 -TATTTTTG
1 ATTTTTTTG
*
30998957 ATTTTTTTT
1 ATTTTTTTG
30998966 ATTTTTTTG
1 ATTTTTTTG
30998975 ATTTTTTT
1 ATTTTTTT
30998983 TTTTAGTCTG
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
7 7 0.11
8 16 0.25
9 32 0.49
10 10 0.15
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (9 bp):
ATTTTTTTG
Found at i:30998926 original size:26 final size:25
Alignment explanation
Indices: 30998897--30998982 Score: 104
Period size: 26 Copynumber: 3.3 Consensus size: 25
30998887 TTTTTCTCCT
30998897 ATTTTCTTTGATTTTTTATTTTTTTG
1 ATTTT-TTTGATTTTTTATTTTTTTG
30998923 ATTTTTTTTGATTTTTTAATTTTTTT-
1 A-TTTTTTTGATTTTTT-ATTTTTTTG
*
30998949 -TATTTTTGATTTTTTTTATTTTTTTG
1 ATTTTTTTGA--TTTTTTATTTTTTTG
30998975 ATTTTTTT
1 ATTTTTTT
30998983 TTTTAGTCTG
Statistics
Matches: 52, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
24 8 0.15
25 8 0.15
26 18 0.35
27 18 0.35
ACGTcount: A:0.13, C:0.01, G:0.06, T:0.80
Consensus pattern (25 bp):
ATTTTTTTGATTTTTTATTTTTTTG
Found at i:30998945 original size:34 final size:33
Alignment explanation
Indices: 30998896--30998986 Score: 121
Period size: 34 Copynumber: 2.7 Consensus size: 33
30998886 CTTTTTCTCC
*
30998896 TATTTTCTTTGATTTTTTATTTTTTTGATTTTTTT
1 TATTTT-TTTAATTTTTT-TTTTTTTGATTTTTTT
30998931 TGA-TTTTTTAATTTTTTTTATTTTTGATTTTTTT
1 T-ATTTTTTTAATTTTTTTT-TTTTTGATTTTTTT
*
30998965 TATTTTTTTGATTTTTTTTTTT
1 TATTTTTTTAATTTTTTTTTTT
30998987 AGTCTGAACT
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
33 6 0.12
34 40 0.78
35 4 0.08
36 1 0.02
ACGTcount: A:0.12, C:0.01, G:0.05, T:0.81
Consensus pattern (33 bp):
TATTTTTTTAATTTTTTTTTTTTTGATTTTTTT
Found at i:30998980 original size:10 final size:10
Alignment explanation
Indices: 30998915--30998983 Score: 73
Period size: 10 Copynumber: 7.7 Consensus size: 10
30998905 TGATTTTTTA
30998915 TTTTTTTGAT
1 TTTTTTTGAT
30998925 TTTTTTTGA-
1 TTTTTTTGAT
*
30998934 -TTTTTTAAT
1 TTTTTTTGAT
30998943 TTTTTTT-A-
1 TTTTTTTGAT
30998951 --TTTTTGAT
1 TTTTTTTGAT
30998959 TTTTTTT-A-
1 TTTTTTTGAT
30998967 TTTTTTTGAT
1 TTTTTTTGAT
30998977 TTTTTTT
1 TTTTTTT
30998984 TTTAGTCTGA
Statistics
Matches: 50, Mismatches: 1, Indels: 16
0.75 0.01 0.24
Matches are distributed among these distances:
6 5 0.10
7 1 0.02
8 14 0.28
9 3 0.06
10 27 0.54
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.83
Consensus pattern (10 bp):
TTTTTTTGAT
Found at i:31009904 original size:9 final size:9
Alignment explanation
Indices: 31009890--31009992 Score: 138
Period size: 9 Copynumber: 11.4 Consensus size: 9
31009880 GTAGTGATTC
*
31009890 AATTCGGAT
1 AATTCGGTT
31009899 AATTC-GTGT
1 AATTCGGT-T
*
31009908 AATTCGGGT
1 AATTCGGTT
31009917 AATTCGGTT
1 AATTCGGTT
*
31009926 AATTCGGGT
1 AATTCGGTT
*
31009935 AATTTGGTT
1 AATTCGGTT
31009944 AATTCGGTT
1 AATTCGGTT
31009953 AATTCGGTT
1 AATTCGGTT
31009962 AATTCAGG-T
1 AATTC-GGTT
31009971 AATTCGGTT
1 AATTCGGTT
31009980 AATTCGGTT
1 AATTCGGTT
31009989 AATT
1 AATT
31009993 TTTAACCAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
8 3 0.04
9 77 0.93
10 3 0.04
ACGTcount: A:0.25, C:0.10, G:0.23, T:0.42
Consensus pattern (9 bp):
AATTCGGTT
Found at i:31023879 original size:9 final size:9
Alignment explanation
Indices: 31023848--31023890 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
31023838 GTTCAAGGTG
31023848 TAATTAATT
1 TAATTAATT
31023857 TAA-TAATTT
1 TAATTAA-TT
31023866 TAATTAATT
1 TAATTAATT
* *
31023875 AAATTTATT
1 TAATTAATT
31023884 TAATTAA
1 TAATTAA
31023891 AAATCTATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 3 0.11
9 22 0.79
10 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TAATTAATT
Found at i:31023888 original size:14 final size:14
Alignment explanation
Indices: 31023849--31023891 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31023839 TTCAAGGTGT
*
31023849 AATTAATTTAA-TA
1 AATTTATTTAATTA
* *
31023862 ATTTTAATTAATTA
1 AATTTATTTAATTA
31023876 AATTTATTTAATTA
1 AATTTATTTAATTA
31023890 AA
1 AA
31023892 AATCTATTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AATTTATTTAATTA
Found at i:31029600 original size:13 final size:13
Alignment explanation
Indices: 31029584--31029636 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
31029574 TTTAAACCAA
31029584 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
31029597 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* * *
31029610 ACTTTTCCACAGT
1 ACTTTTCAAAAGC
*
31029623 AATTTTCAAAAGC
1 ACTTTTCAAAAGC
31029636 A
1 A
31029637 TTGCCAAACT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.38, C:0.25, G:0.08, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:31035639 original size:16 final size:16
Alignment explanation
Indices: 31035618--31035649 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31035608 GTTTTGTTGC
*
31035618 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
31035634 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
31035650 CTTTTAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:31041979 original size:22 final size:22
Alignment explanation
Indices: 31041954--31042001 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
31041944 TGGTAGTTAC
31041954 CATATTTTTCATCACAAAAGTT
1 CATATTTTTCATCACAAAAGTT
31041976 CATATTTTTCATCACAAAAGTT
1 CATATTTTTCATCACAAAAGTT
31041998 CATA
1 CATA
31042002 GAACTCTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.40
Consensus pattern (22 bp):
CATATTTTTCATCACAAAAGTT
Found at i:31047659 original size:18 final size:18
Alignment explanation
Indices: 31047636--31047677 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31047626 ATTCTCAAGT
31047636 TTTTAAGAA-AAATAACAA
1 TTTTAAGAAGAAATAA-AA
*
31047654 TTTTAA-AAGAAATCAAA
1 TTTTAAGAAGAAATAAAA
31047671 TTTTAAG
1 TTTTAAG
31047678 GAAACACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (18 bp):
TTTTAAGAAGAAATAAAA
Found at i:31054601 original size:37 final size:38
Alignment explanation
Indices: 31054550--31054655 Score: 115
Period size: 37 Copynumber: 2.7 Consensus size: 38
31054540 AATTCGAAGC
* *
31054550 AATAAGTTGACACCCAGTGTCTCATCG-GCTAAACCGA
1 AATAATTTGACACCCAGTGTCTCATCGAACTAAACCGA
* * * *
31054587 AATAATTTGGCACCCAGTGCCTCATCGAATTAATCCGA
1 AATAATTTGACACCCAGTGTCTCATCGAACTAAACCGA
*
31054625 AGTAAATAATTGACACCCAGTGTCTCATCGA
1 AAT-AAT--TTGACACCCAGTGTCTCATCGA
31054656 CTCGAAGTCG
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 24 0.43
38 9 0.16
39 3 0.05
41 20 0.36
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (38 bp):
AATAATTTGACACCCAGTGTCTCATCGAACTAAACCGA
Found at i:31055492 original size:11 final size:11
Alignment explanation
Indices: 31055476--31055512 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31055466 ATCCTAACTT
31055476 TTTCTCTTTTC
1 TTTCTCTTTTC
31055487 TTTCTCTTTTCC
1 TTTCTCTTTT-C
31055499 TTT-TC-TTTC
1 TTTCTCTTTTC
31055508 TTTCT
1 TTTCT
31055513 TTCTCTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
9 4 0.17
10 4 0.17
11 12 0.50
12 4 0.17
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTCTTTTC
Found at i:31055503 original size:17 final size:18
Alignment explanation
Indices: 31055475--31055518 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
31055465 AATCCTAACT
31055475 TTTTCTCTTTTCTTTCTC
1 TTTTCTCTTTTCTTTCTC
*
31055493 TTTTC-CTTTTCTTTCTT
1 TTTTCTCTTTTCTTTCTC
31055510 TCTTTCTCT
1 T-TTTCTCT
31055519 GTTTTCGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 9 0.39
19 2 0.09
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTTCTCTTTTCTTTCTC
Found at i:31056446 original size:421 final size:421
Alignment explanation
Indices: 31055662--31056504 Score: 1686
Period size: 421 Copynumber: 2.0 Consensus size: 421
31055652 CATTTATTAG
31055662 TATAGTTTATTTGACTTACTAATTTAACCTATAAATAGGCTCTTTTATAATCTTAGAAAAAAACA
1 TATAGTTTATTTGACTTACTAATTTAACCTATAAATAGGCTCTTTTATAATCTTAGAAAAAAACA
31055727 CTCATTAGATTAGAACTCTTAACACATTCAGAGAATTTTGTGTTTACGTTTTAAGGGTTCTTTGT
66 CTCATTAGATTAGAACTCTTAACACATTCAGAGAATTTTGTGTTTACGTTTTAAGGGTTCTTTGT
31055792 TTTTTGAGTTTTCGGGGTTTAGTTTTATCTCCATCTTTTGTACTCTTCATTCTTTTGCCATTATA
131 TTTTTGAGTTTTCGGGGTTTAGTTTTATCTCCATCTTTTGTACTCTTCATTCTTTTGCCATTATA
31055857 GTAAAATTATCTTTGCCCGTGATTTTTTTTATCCTCTTTGGAGCGGTTTTTCCACGTTAAATTTG
196 GTAAAATTATCTTTGCCCGTGATTTTTTTTATCCTCTTTGGAGCGGTTTTTCCACGTTAAATTTG
31055922 TGTGTTCATCTTCTCAATTTCTTTTGCTATTTTTACTTGTTTGTTGCTTAATCGGGACGATCCTA
261 TGTGTTCATCTTCTCAATTTCTTTTGCTATTTTTACTTGTTTGTTGCTTAATCGGGACGATCCTA
31055987 ACACTTTTTCTATTTCTTTTTCATCTTATTTTTTTTTGTTTTATTATTATTATTATATAATATAT
326 ACACTTTTTCTATTTCTTTTTCATCTTATTTTTTTTTGTTTTATTATTATTATTATATAATATAT
31056052 ATATACTTAAATATTAAGTAAGTATAATTTA
391 ATATACTTAAATATTAAGTAAGTATAATTTA
31056083 TATAGTTTATTTGACTTACTAATTTAACCTATAAATAGGCTCTTTTATAATCTTAGAAAAAAACA
1 TATAGTTTATTTGACTTACTAATTTAACCTATAAATAGGCTCTTTTATAATCTTAGAAAAAAACA
31056148 CTCATTAGATTAGAACTCTTAACACATTCAGAGAATTTTGTGTTTACGTTTTAAGGGTTCTTTGT
66 CTCATTAGATTAGAACTCTTAACACATTCAGAGAATTTTGTGTTTACGTTTTAAGGGTTCTTTGT
31056213 TTTTTGAGTTTTCGGGGTTTAGTTTTATCTCCATCTTTTGTACTCTTCATTCTTTTGCCATTATA
131 TTTTTGAGTTTTCGGGGTTTAGTTTTATCTCCATCTTTTGTACTCTTCATTCTTTTGCCATTATA
31056278 GTAAAATTATCTTTGCCCGTGATTTTTTTTATCCTCTTTGGAGCGGTTTTTCCACGTTAAATTTG
196 GTAAAATTATCTTTGCCCGTGATTTTTTTTATCCTCTTTGGAGCGGTTTTTCCACGTTAAATTTG
31056343 TGTGTTCATCTTCTCAATTTCTTTTGCTATTTTTACTTGTTTGTTGCTTAATCGGGACGATCCTA
261 TGTGTTCATCTTCTCAATTTCTTTTGCTATTTTTACTTGTTTGTTGCTTAATCGGGACGATCCTA
31056408 ACACTTTTTCTATTTCTTTTTCATCTTATTTTTTTTTGTTTTATTATTATTATTATATAATATAT
326 ACACTTTTTCTATTTCTTTTTCATCTTATTTTTTTTTGTTTTATTATTATTATTATATAATATAT
31056473 ATATACTTAAATATTAAGTAAGTATAATTTA
391 ATATACTTAAATATTAAGTAAGTATAATTTA
31056504 T
1 T
31056505 TAATAAATAT
Statistics
Matches: 422, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
421 422 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.50
Consensus pattern (421 bp):
TATAGTTTATTTGACTTACTAATTTAACCTATAAATAGGCTCTTTTATAATCTTAGAAAAAAACA
CTCATTAGATTAGAACTCTTAACACATTCAGAGAATTTTGTGTTTACGTTTTAAGGGTTCTTTGT
TTTTTGAGTTTTCGGGGTTTAGTTTTATCTCCATCTTTTGTACTCTTCATTCTTTTGCCATTATA
GTAAAATTATCTTTGCCCGTGATTTTTTTTATCCTCTTTGGAGCGGTTTTTCCACGTTAAATTTG
TGTGTTCATCTTCTCAATTTCTTTTGCTATTTTTACTTGTTTGTTGCTTAATCGGGACGATCCTA
ACACTTTTTCTATTTCTTTTTCATCTTATTTTTTTTTGTTTTATTATTATTATTATATAATATAT
ATATACTTAAATATTAAGTAAGTATAATTTA
Found at i:31062369 original size:74 final size:74
Alignment explanation
Indices: 31062198--31062360 Score: 326
Period size: 74 Copynumber: 2.2 Consensus size: 74
31062188 AGTTTATATC
31062198 TTTAAAATTTTTAAAAGATTAAATCAATTTTTATCATTTTTAAGGAAGCCAAAGTGCAGTTTTAT
1 TTTAAAATTTTTAAAAGATTAAATCAATTTTTATCATTTTTAAGGAAGCCAAAGTGCAGTTTTAT
31062263 ATTTACTAA
66 ATTTACTAA
31062272 TTTAAAATTTTTAAAAGATTAAATCAATTTTTATCATTTTTAAGGAAGCCAAAGTGCAGTTTTAT
1 TTTAAAATTTTTAAAAGATTAAATCAATTTTTATCATTTTTAAGGAAGCCAAAGTGCAGTTTTAT
31062337 ATTTACTAA
66 ATTTACTAA
31062346 TTTAAAATTTTTAAA
1 TTTAAAATTTTTAAA
31062361 TTTTTAAATA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 89 1.00
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (74 bp):
TTTAAAATTTTTAAAAGATTAAATCAATTTTTATCATTTTTAAGGAAGCCAAAGTGCAGTTTTAT
ATTTACTAA
Found at i:31063330 original size:26 final size:28
Alignment explanation
Indices: 31063271--31063330 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 28
31063261 ATTAATTAAT
* *
31063271 TTTTTTCACTTTTTACTAGATAATATCA
1 TTTTTTCACTTTTTACAACATAATATCA
* *
31063299 TATTTTCA-TTTTT-CAACATAATATTA
1 TTTTTTCACTTTTTACAACATAATATCA
31063325 TTTTTT
1 TTTTTT
31063331 TAAAAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 15 0.56
27 5 0.19
28 7 0.26
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTTTTCACTTTTTACAACATAATATCA
Found at i:31070332 original size:9 final size:9
Alignment explanation
Indices: 31070307--31070348 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
31070297 ATAGAAACTA
31070307 TAAAATATTG
1 TAAAA-ATTG
*
31070317 T-AAAATTT
1 TAAAAATTG
31070325 TAAAAATTG
1 TAAAAATTG
*
31070334 TAAAAATAG
1 TAAAAATTG
31070343 TAAAAA
1 TAAAAA
31070349 AATTTGTATC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
8 4 0.14
9 23 0.82
10 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (9 bp):
TAAAAATTG
Found at i:31073677 original size:16 final size:16
Alignment explanation
Indices: 31073656--31073691 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
31073646 TATATATGGA
31073656 TCAAGATAGAATGATC
1 TCAAGATAGAATGATC
*
31073672 TCAAGATAGGATGATC
1 TCAAGATAGAATGATC
31073688 TCAA
1 TCAA
31073692 AAAGAGTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (16 bp):
TCAAGATAGAATGATC
Found at i:31081609 original size:7 final size:7
Alignment explanation
Indices: 31081599--31081631 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
31081589 TATTATATAC
31081599 TCAATTT
1 TCAATTT
31081606 TCAATTT
1 TCAATTT
31081613 TCAATTT
1 TCAATTT
31081620 TCAATTT
1 TCAATTT
31081627 TCAAT
1 TCAAT
31081632 CTAAACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.55
Consensus pattern (7 bp):
TCAATTT
Found at i:31083847 original size:20 final size:20
Alignment explanation
Indices: 31083824--31083876 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
31083814 AAGCTCTTTT
*
31083824 AAAATTTTAAAATTATTAAA-
1 AAAATTATAAAATTA-TAAAC
**
31083844 AAAACCATAAAATTATAAAC
1 AAAATTATAAAATTATAAAC
31083864 AAAATTCATAAAA
1 AAAATT-ATAAAA
31083877 AAGCTTCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 4 0.15
20 16 0.62
21 6 0.23
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATTATAAAATTATAAAC
Found at i:31087524 original size:30 final size:29
Alignment explanation
Indices: 31087468--31087524 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
31087458 TATTATAAAC
* *
31087468 TGAAAAATTAACTACTAAAACATAAGTGT
1 TGAAAAAATAACTACTAAAAAATAAGTGT
*
31087497 TGAAAAAATAAGTACTAAAAAATTAAGT
1 TGAAAAAATAACTACTAAAAAA-TAAGT
31087525 ATTTAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (29 bp):
TGAAAAAATAACTACTAAAAAATAAGTGT
Found at i:31088254 original size:9 final size:9
Alignment explanation
Indices: 31088240--31088273 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
31088230 GTAGTGATTC
31088240 AATTCGGTT
1 AATTCGGTT
31088249 AATTCGGTT
1 AATTCGGTT
*
31088258 AATTCGGGT
1 AATTCGGTT
31088267 AATTCGG
1 AATTCGG
31088274 GGTAATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (9 bp):
AATTCGGTT
Found at i:31088278 original size:10 final size:9
Alignment explanation
Indices: 31088240--31088280 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
31088230 GTAGTGATTC
*
31088240 AATTCGGTT
1 AATTCGGGT
*
31088249 AATTCGGTT
1 AATTCGGGT
31088258 AATTCGGGT
1 AATTCGGGT
31088267 AATTCGGGGT
1 AATTC-GGGT
31088277 AATT
1 AATT
31088281 TTTACCAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
9 22 0.73
10 8 0.27
ACGTcount: A:0.24, C:0.10, G:0.27, T:0.39
Consensus pattern (9 bp):
AATTCGGGT
Found at i:31091386 original size:2 final size:2
Alignment explanation
Indices: 31091379--31091407 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31091369 AATTGGAATG
31091379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31091408 TACATATTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31095051 original size:62 final size:62
Alignment explanation
Indices: 31094937--31095056 Score: 152
Period size: 62 Copynumber: 1.9 Consensus size: 62
31094927 TCTTAAATAT
* ** * ** *
31094937 AAAAAATTTAACAAATTTAACCCTTAATATTTACAAATTTTTGTCATTTTAGTTCTAATTCC
1 AAAAAATTTAACAAATTTAACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAATTCC
*
31094999 AAAAAATTTAATAAA-TTAGACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAA
1 AAAAAATTTAACAAATTTA-ACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAA
31095057 CTCTAAAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 3 0.06
62 46 0.94
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.38
Consensus pattern (62 bp):
AAAAAATTTAACAAATTTAACCCTCAATATTTACAAAAATCTGTCAAATTAGTCCTAATTCC
Found at i:31097529 original size:26 final size:26
Alignment explanation
Indices: 31097474--31097530 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
31097464 GGGCTGGCCC
* * *
31097474 ATTTTAAAAATAAACATTAAAAAATT
1 ATTTTAAAAATAAAAAATAAAAAATG
31097500 ATTTTAAAAATAAAAAAT-AAAAATAG
1 ATTTTAAAAATAAAAAATAAAAAAT-G
31097526 ATTTT
1 ATTTT
31097531 GATTTAACGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (26 bp):
ATTTTAAAAATAAAAAATAAAAAATG
Found at i:31107954 original size:33 final size:34
Alignment explanation
Indices: 31107915--31107991 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
31107905 TAACTTGAAA
31107915 GTGTCTTCAACAGAGT-ACTC-TAATACTTCATTG
1 GTGTCTTCAACAGA-TAACTCTTAATACTTCATTG
* * *
31107948 GTGTCTTCAACATATAAGTCTTATTACTTCATTG
1 GTGTCTTCAACAGATAACTCTTAATACTTCATTG
31107982 GTGTCTTCAA
1 GTGTCTTCAA
31107992 AACTTTCAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 16 0.41
34 22 0.56
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.40
Consensus pattern (34 bp):
GTGTCTTCAACAGATAACTCTTAATACTTCATTG
Found at i:31113105 original size:16 final size:17
Alignment explanation
Indices: 31113079--31113111 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31113069 GCACGCTGAT
*
31113079 TTTTCCATGTTTTTGCA
1 TTTTCCATGTTTCTGCA
31113096 TTTT-CATGTTTCTGCA
1 TTTTCCATGTTTCTGCA
31113112 ATTGCAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.12, C:0.18, G:0.12, T:0.58
Consensus pattern (17 bp):
TTTTCCATGTTTCTGCA
Found at i:31131135 original size:8 final size:8
Alignment explanation
Indices: 31131122--31131148 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
31131112 AGGAGGATTG
31131122 AATTTTAA
1 AATTTTAA
31131130 AATTTTAA
1 AATTTTAA
31131138 AATTTTAA
1 AATTTTAA
31131146 AAT
1 AAT
31131149 ATAACAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AATTTTAA
Found at i:31131627 original size:38 final size:39
Alignment explanation
Indices: 31131571--31131649 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 39
31131561 ACCCTTCAAT
* *
31131571 ATTTATAGATTCTATCAATTTGGTCCTAATTC-TAAAAA
1 ATTTATAGATTATATCAATTTAGTCCTAATTCTTAAAAA
* * * *
31131609 ATTTATATATTATGTCAATTTAGTCTTGATTCTTAAAAA
1 ATTTATAGATTATATCAATTTAGTCCTAATTCTTAAAAA
31131648 AT
1 AT
31131650 CAAAATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (39 bp):
ATTTATAGATTATATCAATTTAGTCCTAATTCTTAAAAA
Found at i:31133523 original size:2 final size:2
Alignment explanation
Indices: 31133518--31133542 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31133508 AATCTGGTTG
31133518 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
31133543 CAGTGTGTGT
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:31135544 original size:3 final size:3
Alignment explanation
Indices: 31135536--31135567 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
31135526 CTTTTTAAAA
31135536 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
31135568 ACAAGAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:31138318 original size:128 final size:128
Alignment explanation
Indices: 31137937--31138320 Score: 612
Period size: 128 Copynumber: 3.0 Consensus size: 128
31137927 TTATATTGAT
31137937 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGA---TTATTTGACCTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* * *
31137999 GCTAGCATGATCTCATAAAACCTAAGGCACATTACAATATCATTGATAATGATGAACTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
* * * * *
31138062 AATACTAAATAGAATGATGCTGATAATATCACCAAGGCTAATGATCTCTATTTGACTTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* *
31138127 GCTAGCATGATCTCATAAAAACCAAGGCACATTACAATATCACTGATAATCATGAGCTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
* *
31138190 GATACTAAATAGAAAAATGTTGATAATATCACCAAGGCCAATGATCTTTATTTGACCTTCAATTG
1 GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
* * *
31138255 GCTAGCCTGATCTCATAAAACCCAAGGCACATTATAATATCACCGATAATGATGAGCTGCAAC
66 GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
31138318 GAT
1 GAT
31138321 TTACCTTCTT
Statistics
Matches: 234, Mismatches: 22, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
125 41 0.18
128 193 0.82
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (128 bp):
GATACTAAATAGAATAATGTTGATAATATCACCAAGGCTAATGATCTTTATTTGACCTTCAATTG
GCTAGCATGATCTCATAAAACCCAAGGCACATTACAATATCACTGATAATGATGAGCTGCAAC
Found at i:31140745 original size:181 final size:181
Alignment explanation
Indices: 31140441--31140803 Score: 708
Period size: 181 Copynumber: 2.0 Consensus size: 181
31140431 AATAGGTAAA
*
31140441 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATTACCCCAAAAGTCATGGTGATCTA
1 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
31140506 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
66 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
*
31140571 CTCAGAAGGTGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
131 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
31140622 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
1 AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
31140687 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
66 CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
31140752 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
131 CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
31140803 A
1 A
31140804 AAATTAACTA
Statistics
Matches: 180, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
181 180 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (181 bp):
AGAACAATTGGTTACACCATGACAGTGTCTTATGGAGCGATCACCCCAAAAGTCATGGTGATCTA
CACATGGAGACTAGATCACCATGTAGGTAAGTAAGAAACTCACGGTCTTCTGGTGGCACTGATCT
CTCAGAAGATGATTTATTTACGATGCTTATTACCAATGAGAAATAATATAT
Found at i:31149083 original size:6 final size:6
Alignment explanation
Indices: 31149072--31149106 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
31149062 GAGTCTGCAA
31149072 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
31149107 TCTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:31159489 original size:3 final size:3
Alignment explanation
Indices: 31159483--31159526 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
31159473 CTCCCTAAAC
* *
31159483 TAT TAT TAT TAT TAT TAC TAT CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
31159527 ACACCAACCG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:31161682 original size:70 final size:71
Alignment explanation
Indices: 31161557--31161700 Score: 263
Period size: 70 Copynumber: 2.0 Consensus size: 71
31161547 TTCTCATTGC
31161557 TCATAGGCTTAATGATTTTAAGTCTACTACTCTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
1 TCATAGGCTTAATGATTTTAAGTCTACTA--CTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCA
31161622 GGTAATGA
64 GGTAATGA
31161630 TCATAGGCTTAATGATTTTAAGTCTACTA-TTTTTGGTTGTCAGGGTAGTTTTTATCAAACCAGG
1 TCATAGGCTTAATGATTTTAAGTCTACTACTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCAGG
31161694 TAATGA
66 TAATGA
31161700 T
1 T
31161701 GTGTTGTAGG
Statistics
Matches: 71, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
70 42 0.59
73 29 0.41
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (71 bp):
TCATAGGCTTAATGATTTTAAGTCTACTACTTTTTGGTTGTCAGGGTAGTTTTTATCAAACCAGG
TAATGA
Found at i:31166009 original size:120 final size:120
Alignment explanation
Indices: 31165869--31169612 Score: 7391
Period size: 120 Copynumber: 31.2 Consensus size: 120
31165859 TCTTTTTGGG
31165869 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31165934 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31165989 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166054 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166109 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166174 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166229 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166294 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166349 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166414 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166469 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166534 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166589 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166654 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166709 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166774 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166829 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31166894 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31166949 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167014 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167069 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167134 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167189 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167254 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167309 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167374 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167429 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167494 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167549 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167614 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167669 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167734 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167789 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167854 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31167909 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31167974 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168029 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168094 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168149 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168214 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168269 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168334 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168389 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168454 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168509 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168574 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168629 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168694 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168749 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168814 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168869 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31168934 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31168989 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31169054 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31169109 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31169174 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31169229 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
31169294 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31169349 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
**
31169414 ATAAGAATATTGATTATTAAGAATTTTATTAAATTAG-ATATTTTAATTAAAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCT-GTATATTTTAATTAAAATAT
31169469 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
1 ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
* * ** * *
31169534 ATAGGAATACTGATTATTAAGAATTTTATTAAATTATATATTTTAATTATAATAT
66 ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
31169589 ATTTAATAATAATTATGTTTAAAT
1 ATTTAATAATAATTATG-TTAAAT
31169613 ATGATTAAAT
Statistics
Matches: 3615, Mismatches: 6, Indels: 5
1.00 0.00 0.00
Matches are distributed among these distances:
120 3608 1.00
121 7 0.00
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (120 bp):
ATTTAATAATAATTATGTTAAATTATATTTTATAGTATCATATATTATGATTTGAGTAAATTCAT
ATAAGAATATTGATTATTAAGAATTTTATTAAGCTGTATATTTTAATTAAAATAT
Found at i:31169590 original size:16 final size:16
Alignment explanation
Indices: 31169569--31169610 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
31169559 TTATTAAATT
*
31169569 ATATATTTTAATTATA
1 ATATATTTTAATAATA
31169585 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
31169600 AT-TATGTTTAA
1 ATATAT-TTTAA
31169611 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:31169595 original size:15 final size:15
Alignment explanation
Indices: 31169560--31169601 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
31169550 TTAAGAATTT
*
31169560 TATTAAATTAT-ATA
1 TATTTAATTATAATA
31169574 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
31169588 TATTTAATAATAAT
1 TATTTAATTATAAT
31169602 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:31173672 original size:12 final size:12
Alignment explanation
Indices: 31173655--31173687 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31173645 AGAGCCAGAT
31173655 TCATCTTCATCC
1 TCATCTTCATCC
*
31173667 TCATCTTCGTCC
1 TCATCTTCATCC
31173679 TCATCTTCA
1 TCATCTTCA
31173688 AACTTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCC
Found at i:31177873 original size:40 final size:40
Alignment explanation
Indices: 31177815--31177905 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
31177805 CAACCTTTTT
** *
31177815 CAACCTTTTCATTGGATATCTGTTTCGGATATATCCTTTA
1 CAACCTTTTCATTGGATATCCATTTCGGATATACCCTTTA
* *
31177855 CAACCATTTT-ATTTGATATCCATTTCGGATATACCCTTTT
1 CAACC-TTTTCATTGGATATCCATTTCGGATATACCCTTTA
31177895 CAACCTTTTCA
1 CAACCTTTTCA
31177906 AGAATTCAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.09
40 36 0.82
41 4 0.09
ACGTcount: A:0.24, C:0.23, G:0.09, T:0.44
Consensus pattern (40 bp):
CAACCTTTTCATTGGATATCCATTTCGGATATACCCTTTA
Found at i:31179295 original size:8 final size:8
Alignment explanation
Indices: 31179282--31179306 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
31179272 CCACAATTAT
31179282 TCACATAA
1 TCACATAA
31179290 TCACATAA
1 TCACATAA
31179298 TCACATAA
1 TCACATAA
31179306 T
1 T
31179307 TTGCCAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (8 bp):
TCACATAA
Found at i:31180742 original size:35 final size:35
Alignment explanation
Indices: 31180700--31180819 Score: 116
Period size: 35 Copynumber: 3.3 Consensus size: 35
31180690 GTATTGAATG
*
31180700 TGAGCCCAGCTTTAGTTGGATGAACCAACAATGTT
1 TGAGCCCAGCTCTAGTTGGATGAACCAACAATGTT
* * * *
31180735 TGCGCCCAGCACTAGTTGGAT-ATACCGACAATAATAAAT
1 TGAGCCCAGCTCTAGTTGGATGA-ACCAACAAT-GT---T
* *
31180774 GTGAGCCCAGCTCTAGTTGGATGAACCAATAGTGTT
1 -TGAGCCCAGCTCTAGTTGGATGAACCAACAATGTT
31180810 TGAGCCCAGC
1 TGAGCCCAGC
31180820 GTTAGTCGGA
Statistics
Matches: 67, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
34 1 0.01
35 36 0.54
36 2 0.03
39 2 0.03
40 25 0.37
41 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (35 bp):
TGAGCCCAGCTCTAGTTGGATGAACCAACAATGTT
Found at i:31180794 original size:75 final size:75
Alignment explanation
Indices: 31180666--31180838 Score: 222
Period size: 75 Copynumber: 2.3 Consensus size: 75
31180656 AGATTACGGT
* * * * *
31180666 CAGCGCTAGTCGGATTA-ACCGACAGTATTGAATGTGAGCCCAGCTTTAGTTGGATGAACCAACA
1 CAGCACTAGTCGGA-TAGACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACA
*
31180730 ATGTTTGCGCC
65 ATGTTTGAGCC
* * * *
31180741 CAGCACTAGTTGGATATACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAATAG
1 CAGCACTAGTCGGATAGACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACAA
31180806 TGTTTGAGCC
66 TGTTTGAGCC
**
31180816 CAGCGTTAGTCGGATAGACCGAC
1 CAGCACTAGTCGGATAGACCGAC
31180839 GATTGTGTGC
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
74 2 0.02
75 82 0.98
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (75 bp):
CAGCACTAGTCGGATAGACCGACAATAATAAATGTGAGCCCAGCTCTAGTTGGATGAACCAACAA
TGTTTGAGCC
Found at i:31189376 original size:12 final size:12
Alignment explanation
Indices: 31189359--31189391 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31189349 AGAGCCAGAT
31189359 TCATCTTCATCC
1 TCATCTTCATCC
*
31189371 TCATCTTCGTCC
1 TCATCTTCATCC
31189383 TCATCTTCA
1 TCATCTTCA
31189392 AACTTCTCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.39, G:0.03, T:0.42
Consensus pattern (12 bp):
TCATCTTCATCC
Found at i:31190705 original size:24 final size:24
Alignment explanation
Indices: 31190652--31190705 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
31190642 ACTCACATAT
* *
31190652 TAATTAAATAGTTAAAAATATTAT
1 TAATTAAATAGTTAAAAATATGAA
*
31190676 TAAATT-AATATTTAAAAAATATGAA
1 T-AATTAAATAGTT-AAAAATATGAA
31190701 TAATT
1 TAATT
31190706 TTTAAATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 11 0.44
25 14 0.56
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.41
Consensus pattern (24 bp):
TAATTAAATAGTTAAAAATATGAA
Found at i:31192871 original size:80 final size:80
Alignment explanation
Indices: 31192736--31192898 Score: 238
Period size: 80 Copynumber: 2.0 Consensus size: 80
31192726 AAAACTAAAA
* * * * *
31192736 AAAAGTTTAAATTTGACAAATAGACGATCACGTCACAACTTACCTTATCTTTGCGTTACAATGTG
1 AAAAGTTCAAAATTGACAAATAAACGATCACATCACAACTTACCTTATCTCTGCGTTACAATGTG
*
31192801 CATATATGTAAAGCC
66 CATATATGCAAAGCC
* *
31192816 AAAAGTTCAAAATTGACAAATAAAC-AGTCATATCACAACTTACCTTATCTCTGCGTTGCAATGT
1 AAAAGTTCAAAATTGACAAATAAACGA-TCACATCACAACTTACCTTATCTCTGCGTTACAATGT
31192880 GCATATATGCAAAGCC
65 GCATATATGCAAAGCC
31192896 AAA
1 AAA
31192899 GGTGTTCCAA
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.29
Consensus pattern (80 bp):
AAAAGTTCAAAATTGACAAATAAACGATCACATCACAACTTACCTTATCTCTGCGTTACAATGTG
CATATATGCAAAGCC
Found at i:31198681 original size:4 final size:4
Alignment explanation
Indices: 31198672--31198698 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
31198662 TTTGAAACAA
31198672 AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAA
31198699 GCATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:31201157 original size:20 final size:20
Alignment explanation
Indices: 31201132--31201171 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
31201122 CGTAAAATGA
*
31201132 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
31201152 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
31201172 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:31201161 original size:34 final size:35
Alignment explanation
Indices: 31201117--31201183 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
31201107 CAGTAAAATA
*
31201117 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
31201151 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
31201184 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:31201187 original size:14 final size:15
Alignment explanation
Indices: 31201111--31201187 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
31201101 GATAGCCAGT
* *
31201111 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
31201125 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
31201139 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
31201159 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
31201174 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
31201188 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:31202857 original size:23 final size:23
Alignment explanation
Indices: 31202827--31202871 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
31202817 GCATCCTAAT
31202827 TTTTCCACTTTTGTCAAAGATAG
1 TTTTCCACTTTTGTCAAAGATAG
*
31202850 TTTTCCACTTTTGTTAAAGATA
1 TTTTCCACTTTTGTCAAAGATA
31202872 AGTGGAGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (23 bp):
TTTTCCACTTTTGTCAAAGATAG
Found at i:31203910 original size:18 final size:18
Alignment explanation
Indices: 31203865--31203910 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31203855 CTAAAGGAGT
31203865 TGAGAGTTAGTGGGTTAG
1 TGAGAGTTAGTGGGTTAG
* *
31203883 TGGGATTTAGT-GGTTAG
1 TGAGAGTTAGTGGGTTAG
31203900 TGAGAGGTTAG
1 TGAGA-GTTAG
31203911 GATATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (18 bp):
TGAGAGTTAGTGGGTTAG
Found at i:31204502 original size:33 final size:32
Alignment explanation
Indices: 31204446--31204538 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
31204436 ATGATAGTGT
*
31204446 AAGTGTGGCCGTGTGGGCCACACGGGCTAGGCC
1 AAGT-TGGCCGTGTGGGCCACACGGGCAAGGCC
* *
31204479 AAGTTGGGCGTGTTGGCCTACACGGGCAAGGCC
1 AAGTTGGCCGTGTGGGCC-ACACGGGCAAGGCC
* ** *
31204512 AATTTGGATGTGTGGGCCGCACGGGCA
1 AAGTTGGCCGTGTGGGCCACACGGGCA
31204539 TGTGGGCCCA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
32 20 0.39
33 31 0.61
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.18
Consensus pattern (32 bp):
AAGTTGGCCGTGTGGGCCACACGGGCAAGGCC
Found at i:31210078 original size:11 final size:11
Alignment explanation
Indices: 31210062--31210086 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31210052 TTTTGTCTCA
31210062 CGCTACAGTAT
1 CGCTACAGTAT
31210073 CGCTACAGTAT
1 CGCTACAGTAT
31210084 CGC
1 CGC
31210087 ATCTCACCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (11 bp):
CGCTACAGTAT
Found at i:31221120 original size:13 final size:13
Alignment explanation
Indices: 31221102--31221160 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
31221092 CTCAAAATTT
31221102 TCAAAAGCACTTC
1 TCAAAAGCACTTC
* *
31221115 TCAAAAACACTTT
1 TCAAAAGCACTTC
* *
31221128 TCCACAGCACTTC
1 TCAAAAGCACTTC
* *
31221141 TGAAAAGCACTTT
1 TCAAAAGCACTTC
31221154 TCAAAAG
1 TCAAAAG
31221161 TAATGAAGAA
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.39, C:0.27, G:0.08, T:0.25
Consensus pattern (13 bp):
TCAAAAGCACTTC
Found at i:31221128 original size:26 final size:26
Alignment explanation
Indices: 31221099--31221160 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
31221089 ACACTCAAAA
31221099 TTTTCAAAAGCACTTCTCAAAAACAC
1 TTTTCAAAAGCACTTCTCAAAAACAC
* * * *
31221125 TTTTCCACAGCACTTCTGAAAAGCAC
1 TTTTCAAAAGCACTTCTCAAAAACAC
31221151 TTTTCAAAAG
1 TTTTCAAAAG
31221161 TAATGAAGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (26 bp):
TTTTCAAAAGCACTTCTCAAAAACAC
Found at i:31227454 original size:21 final size:22
Alignment explanation
Indices: 31227412--31227456 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
31227402 AAGAAGGCAA
* **
31227412 TAGATGACTTAAATTATTTAAT
1 TAGATGACATAAATTAAATAAT
31227434 TAGATGA-ATAAATTAAATAAT
1 TAGATGACATAAATTAAATAAT
31227455 TA
1 TA
31227457 AGTCTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.49, C:0.02, G:0.09, T:0.40
Consensus pattern (22 bp):
TAGATGACATAAATTAAATAAT
Found at i:31237817 original size:17 final size:17
Alignment explanation
Indices: 31237795--31237832 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
31237785 AATTATAGTA
31237795 CACATGACGACAATAAT
1 CACATGACGACAATAAT
31237812 CACATGACGACAATAAT
1 CACATGACGACAATAAT
31237829 CACA
1 CACA
31237833 CAATGTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (17 bp):
CACATGACGACAATAAT
Found at i:31237915 original size:17 final size:17
Alignment explanation
Indices: 31237895--31237929 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
31237885 AATAATATGC
31237895 AAAACAATTTAAAGTAA
1 AAAACAATTTAAAGTAA
*
31237912 AAAATAATTTAAAGTAA
1 AAAACAATTTAAAGTAA
31237929 A
1 A
31237930 TAATTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.66, C:0.03, G:0.06, T:0.26
Consensus pattern (17 bp):
AAAACAATTTAAAGTAA
Found at i:31239837 original size:28 final size:28
Alignment explanation
Indices: 31239797--31239922 Score: 182
Period size: 28 Copynumber: 4.5 Consensus size: 28
31239787 TGACTTTCGA
*
31239797 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
31239825 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
31239853 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* * *
31239881 CACTAAATGTGCGAGTTTGATTAGTGAA-
1 CACTAAGTGTGCGAGTTTAATT-GTAAAG
31239909 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
31239923 ACTTATTAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
28 85 0.97
29 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:31244706 original size:19 final size:20
Alignment explanation
Indices: 31244665--31244706 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
31244655 GTTTCTATGT
* *
31244665 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
31244685 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
31244704 CAT
1 CAT
31244707 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:31247500 original size:27 final size:27
Alignment explanation
Indices: 31247462--31247521 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
31247452 CGCGCCACAC
* *
31247462 CCCAAAATTTCCAGTGCTCCATTTATG
1 CCCAATATTTCCACTGCTCCATTTATG
31247489 CCCAATATTTCCACTGCTCCATTTATG
1 CCCAATATTTCCACTGCTCCATTTATG
*
31247516 TCCAAT
1 CCCAAT
31247522 TGAAAATTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.25, C:0.32, G:0.08, T:0.35
Consensus pattern (27 bp):
CCCAATATTTCCACTGCTCCATTTATG
Found at i:31258373 original size:79 final size:80
Alignment explanation
Indices: 31258279--31258437 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 80
31258269 ATATTAATTT
31258279 TTGTATTCTTTTTATTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTA
1 TTGTATTCTTTTTATTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTA
31258344 AAAATTAAAAATTAA
66 AAAATTAAAAATTAA
31258359 TTGTATTC-TTTTATTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTA
1 TTGTATTCTTTTTATTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTA
31258423 AAAATTAAAAATTAA
66 AAAATTAAAAATTAA
31258438 CTCTTTTTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 71 0.90
80 8 0.10
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (80 bp):
TTGTATTCTTTTTATTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTA
AAAATTAAAAATTAA
Found at i:31258486 original size:79 final size:76
Alignment explanation
Indices: 31258285--31258460 Score: 282
Period size: 79 Copynumber: 2.3 Consensus size: 76
31258275 ATTTTTGTAT
31258285 TCTTTTTA-TTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTAAAAAT
1 TCTTTTTATTTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTAAAAAT
*
31258349 TAAAAATTAAT
66 TAAAAATTAAC
* *
31258360 TGTATTCTTTTATTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTAAA
1 TCT-TT-TTAT-TTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTAAA
31258425 AATTAAAAATTAAC
63 AATTAAAAATTAAC
31258439 TCTTTTTATTTTAAATAATTTT
1 TCTTTTTATTTTAAA-AATTTT
31258461 TTCAAATTTG
Statistics
Matches: 91, Mismatches: 5, Indels: 8
0.88 0.05 0.08
Matches are distributed among these distances:
75 2 0.02
76 8 0.09
77 11 0.12
78 2 0.02
79 68 0.75
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (76 bp):
TCTTTTTATTTTAAAAATTTTATTAATTTAATTTTTATTCTTTAAAATTATATATTTTTAAAAAT
TAAAAATTAAC
Found at i:31261067 original size:13 final size:13
Alignment explanation
Indices: 31261049--31261073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31261039 TTTTTTTATA
31261049 TTTTTAATTAATC
1 TTTTTAATTAATC
31261062 TTTTTAATTAAT
1 TTTTTAATTAAT
31261074 AACTCTTTTA
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:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTAATTAATC
Found at i:31261142 original size:17 final size:18
Alignment explanation
Indices: 31261109--31261143 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31261099 AGTTATTTCC
31261109 AAATATAATTATTTATGT
1 AAATATAATTATTTATGT
31261127 AAATATAATT-TTTATGT
1 AAATATAATTATTTATGT
31261144 CTGTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
AAATATAATTATTTATGT
Found at i:31264179 original size:18 final size:18
Alignment explanation
Indices: 31264157--31264209 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
31264147 AAAAAACAAA
31264157 GATATTTGAAATATATTAT
1 GATATTTGAAATA-ATTAT
** *
31264176 -ATA-TAAAAATAATAAT
1 GATATTTGAAATAATTAT
31264192 GATATTTGAAATAATTAT
1 GATATTTGAAATAATTAT
31264210 TTGATTTTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
16 4 0.15
17 9 0.35
18 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.42
Consensus pattern (18 bp):
GATATTTGAAATAATTAT
Found at i:31269743 original size:15 final size:16
Alignment explanation
Indices: 31269725--31269762 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
31269715 AATTTATTAT
*
31269725 TTTTTAATTTT-CATA
1 TTTTTAATTTTAAATA
*
31269740 TTTTTATTTTTAAATA
1 TTTTTAATTTTAAATA
31269756 TTTTTAA
1 TTTTTAA
31269763 AACAGAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTAATTTTAAATA
Found at i:31270264 original size:22 final size:22
Alignment explanation
Indices: 31270225--31270270 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
31270215 TATAAAGGGC
31270225 AATTATTTTAAAACAATT-ATA
1 AATTATTTTAAAACAATTAATA
* *
31270246 AATTTTTTTAAAAATAATTAATA
1 AATTATTTT-AAAACAATTAATA
31270269 AA
1 AA
31270271 AATTNNNNNN
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 8 0.38
23 5 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AATTATTTTAAAACAATTAATA
Found at i:31273147 original size:25 final size:24
Alignment explanation
Indices: 31273105--31273153 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
31273095 ATATCTATAA
* *
31273105 ATATTTTTATATACATTAATTAAAT
1 ATATTTTTAAAAACATTAA-TAAAT
*
31273130 ATATTTTTAAAAATATTAATAAAT
1 ATATTTTTAAAAACATTAATAAAT
31273154 CCAAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 5 0.24
25 16 0.76
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (24 bp):
ATATTTTTAAAAACATTAATAAAT
Found at i:31280858 original size:12 final size:12
Alignment explanation
Indices: 31280837--31280872 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
31280827 ACTCAAGCCA
31280837 ATAA-ATAATAT
1 ATAATATAATAT
31280848 ATAATATAATAT
1 ATAATATAATAT
31280860 AT-ATAT-ATAT
1 ATAATATAATAT
31280870 ATA
1 ATA
31280873 TGGTGCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 6 0.26
11 8 0.35
12 9 0.39
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATAATATAATAT
Found at i:31284142 original size:22 final size:22
Alignment explanation
Indices: 31284117--31284169 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
31284107 GTTGTTTTGT
* *
31284117 TACTATTTTACTATTATGTTGC
1 TACTATTTTACTATTATATTAC
* *
31284139 TACTATTTCACTATTATATTAT
1 TACTATTTTACTATTATATTAC
31284161 TACTATTTT
1 TACTATTTT
31284170 GTTATTTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.57
Consensus pattern (22 bp):
TACTATTTTACTATTATATTAC
Found at i:31284967 original size:21 final size:22
Alignment explanation
Indices: 31284934--31284975 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
31284924 AAAAACATGG
*
31284934 AAAATAAATGAACTAAATTCTT
1 AAAAGAAATGAACTAAATTCTT
31284956 AAAAGAAA-GAACTAAATTCT
1 AAAAGAAATGAACTAAATTCT
31284976 AAATATACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.26
Consensus pattern (22 bp):
AAAAGAAATGAACTAAATTCTT
Found at i:31290204 original size:15 final size:15
Alignment explanation
Indices: 31290171--31290220 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
31290161 AGTGTACCAA
31290171 ATATTAT-TCCATCAAT
1 ATATTATAT-CAT-AAT
31290187 ATATTATATCATAAT
1 ATATTATATCATAAT
*
31290202 ATATTTTAT-ATAAT
1 ATATTATATCATAAT
31290216 -TATTA
1 ATATTA
31290221 AATTTAAGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 4 0.13
14 5 0.16
15 11 0.35
16 10 0.32
17 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (15 bp):
ATATTATATCATAAT
Found at i:31293004 original size:2 final size:2
Alignment explanation
Indices: 31292997--31293026 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
31292987 TCAAATAATC
31292997 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31293027 CTAGAAGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31293124 original size:20 final size:20
Alignment explanation
Indices: 31293099--31293139 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31293089 TTGGTGAAAT
* *
31293099 ATCCTAGAATTTAAATTTGC
1 ATCCTAAAAATTAAATTTGC
*
31293119 ATCCTAAAAATTATATTTGC
1 ATCCTAAAAATTAAATTTGC
31293139 A
1 A
31293140 ATGTGGATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (20 bp):
ATCCTAAAAATTAAATTTGC
Found at i:31294323 original size:38 final size:38
Alignment explanation
Indices: 31294281--31294359 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
31294271 TGTCTCAATC
31294281 TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
1 TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
*
31294319 TAAATAACCTAAATTGTTATATTAATTAATGAAAGGTA
1 TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
31294357 TAA
1 TAA
31294360 TAATTTATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.35
Consensus pattern (38 bp):
TAAATAACCTAAACTGTTATATTAATTAATGAAAGGTA
Found at i:31294358 original size:19 final size:19
Alignment explanation
Indices: 31294298--31294364 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
31294288 CCTAAACTGT
31294298 TATATTAATTAATGAAAGG
1 TATATTAATTAATGAAAGG
*
31294317 TATA--AA-TAACCT-AAATTGT
1 TATATTAATTAA--TGAAA--GG
31294336 TATATTAATTAATGAAAGG
1 TATATTAATTAATGAAAGG
*
31294355 TATAATAATT
1 TATATTAATT
31294365 TATTTGACCC
Statistics
Matches: 37, Mismatches: 3, Indels: 16
0.66 0.05 0.29
Matches are distributed among these distances:
16 3 0.08
17 5 0.14
18 1 0.03
19 19 0.51
20 1 0.03
21 5 0.14
22 3 0.08
ACGTcount: A:0.48, C:0.03, G:0.10, T:0.39
Consensus pattern (19 bp):
TATATTAATTAATGAAAGG
Found at i:31300965 original size:161 final size:162
Alignment explanation
Indices: 31300786--31301108 Score: 639
Period size: 161 Copynumber: 2.0 Consensus size: 162
31300776 TATATTTAAA
31300786 ATTTAAATAAATTTGTATTATTTAAAATGATTGGATCATGTCGGTTAACATTTATAAAAAAATTT
1 ATTTAAATAAATTTGTATTATTTAAAATGATTGGATCATGTCGGTTAACATTTATAAAAAAATTT
31300851 ATAGGCTCTGTAATAGATGTAGGAGCAGTCCTACCACTCAAATAATAATAAAATAATTAATTAAG
66 ATAGGCTCTGTAATAGATGTAGGAGCAGTCCTACCACTCAAATAATAATAAAATAATTAATTAAG
31300916 GTTTAACTCCGTTACATTTCAAAACTTAAATT
131 GTTTAACTCCGTTACATTTCAAAACTTAAATT
31300948 ATTTAAAT-AATTTGTATTATTTAAAATGATTGGATCATGTCGGTTAACATTTATAAAAAAATTT
1 ATTTAAATAAATTTGTATTATTTAAAATGATTGGATCATGTCGGTTAACATTTATAAAAAAATTT
31301012 ATAGGCTCTGTAATAGATGTAGGAGCAGTCCTACCACTCAAATAATAATAAAATAATTAATTAAG
66 ATAGGCTCTGTAATAGATGTAGGAGCAGTCCTACCACTCAAATAATAATAAAATAATTAATTAAG
31301077 GTTTAACTCCGTTACATTTCAAAACTTAAATT
131 GTTTAACTCCGTTACATTTCAAAACTTAAATT
31301109 TGTTACTTAA
Statistics
Matches: 161, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
161 153 0.95
162 8 0.05
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.37
Consensus pattern (162 bp):
ATTTAAATAAATTTGTATTATTTAAAATGATTGGATCATGTCGGTTAACATTTATAAAAAAATTT
ATAGGCTCTGTAATAGATGTAGGAGCAGTCCTACCACTCAAATAATAATAAAATAATTAATTAAG
GTTTAACTCCGTTACATTTCAAAACTTAAATT
Found at i:31302413 original size:20 final size:20
Alignment explanation
Indices: 31302388--31302450 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
31302378 AGTTATTAAA
31302388 GTAAACAAAAACTACAATTT
1 GTAAACAAAAACTACAATTT
* ***
31302408 GTAAACTAAAAATTGA-AAAAA
1 GTAAAC-AAAAACT-ACAATTT
*
31302429 GTAAGCAAAAACTACAATTT
1 GTAAACAAAAACTACAATTT
31302449 GT
1 GT
31302451 TTTCTCCATG
Statistics
Matches: 31, Mismatches: 9, Indels: 6
0.67 0.20 0.13
Matches are distributed among these distances:
19 1 0.03
20 16 0.52
21 13 0.42
22 1 0.03
ACGTcount: A:0.56, C:0.11, G:0.10, T:0.24
Consensus pattern (20 bp):
GTAAACAAAAACTACAATTT
Found at i:31314531 original size:22 final size:20
Alignment explanation
Indices: 31314504--31314544 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
31314494 AATAACTTCC
31314504 AAAAAATAGATTGATTTTCTAA
1 AAAAAATAGA-T-ATTTTCTAA
*
31314526 AAAAAATTGATATTTTCTA
1 AAAAAATAGATATTTTCTA
31314545 GTGTTTGGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (20 bp):
AAAAAATAGATATTTTCTAA
Found at i:31314883 original size:23 final size:23
Alignment explanation
Indices: 31314836--31314884 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
31314826 TGATCTAAAC
*
31314836 AAATACTCATATTTATATAATTA
1 AAATACTCATATTTATATAAGTA
*
31314859 AAATATTCATATTT-TATACAGTA
1 AAATACTCATATTTATATA-AGTA
31314882 AAA
1 AAA
31314885 CATTTAGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 4 0.17
23 19 0.83
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (23 bp):
AAATACTCATATTTATATAAGTA
Found at i:31314963 original size:27 final size:25
Alignment explanation
Indices: 31314912--31314964 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
31314902 TTATAAATTG
* *
31314912 TAATATATATTTATTATTAAAATAT
1 TAATATAAATTTATTAATAAAATAT
*
31314937 TAATATAAATATTATTAAATAATATAT
1 TAATATAAAT-TTATT-AATAAAATAT
31314964 T
1 T
31314965 TAAAATATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 5 0.22
27 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATATAAATTTATTAATAAAATAT
Found at i:31314968 original size:23 final size:24
Alignment explanation
Indices: 31314923--31314977 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
31314913 AATATATATT
*
31314923 TATTATTAAAATATTAATAT-AAA
1 TATTATTAAAATAATAATATAAAA
*
31314946 TATTATT-AAATAATATATTTAAAA
1 TATTATTAAAATAATA-ATATAAAA
31314970 TATATATT
1 TAT-TATT
31314978 TGATTCAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 7 0.26
23 10 0.37
24 6 0.22
25 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TATTATTAAAATAATAATATAAAA
Found at i:31318811 original size:23 final size:23
Alignment explanation
Indices: 31318785--31318839 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
31318775 AGCCCATTTA
*
31318785 AGCTTCCTGATAGGCTCTTTGTG
1 AGCTTCCTGATAGGCTCTTTATG
*
31318808 AGCTT-CTCGATATGCTCTTTATG
1 AGCTTCCT-GATAGGCTCTTTATG
*
31318831 AGTTTCCTG
1 AGCTTCCTG
31318840 TTATATGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (23 bp):
AGCTTCCTGATAGGCTCTTTATG
Found at i:31320967 original size:11 final size:11
Alignment explanation
Indices: 31320953--31320996 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
31320943 AGATAAATAT
31320953 TATTTTATTAA
1 TATTTTATTAA
*
31320964 TATTTTAAATATA
1 TATTTT-ATTA-A
*
31320977 TATTTTATTAT
1 TATTTTATTAA
31320988 TATTTTATT
1 TATTTTATT
31320997 TAGTATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
11 15 0.54
12 6 0.21
13 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:31320980 original size:24 final size:23
Alignment explanation
Indices: 31320946--31320994 Score: 80
Period size: 24 Copynumber: 2.1 Consensus size: 23
31320936 TTTAATTAGA
31320946 TAAATATTATTTTATTAATATTT
1 TAAATATTATTTTATTAATATTT
*
31320969 TAAATATATATTTTATTATTATTT
1 TAAATAT-TATTTTATTAATATTT
31320993 TA
1 TA
31320995 TTTAGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TAAATATTATTTTATTAATATTT
Found at i:31322372 original size:207 final size:207
Alignment explanation
Indices: 31322017--31322433 Score: 798
Period size: 207 Copynumber: 2.0 Consensus size: 207
31322007 GTAATAGTGG
31322017 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
1 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
31322082 GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
66 GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
*
31322147 GGCTCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
131 GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
*
31322212 CAAATTGTAGGA
196 CAAATTGCAGGA
*
31322224 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGCCAGGAGGAG
1 AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
*
31322289 GAAAATATATATGAATATTCAGCTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
66 GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
31322354 GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
131 GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
31322419 CAAATTGCAGGA
196 CAAATTGCAGGA
31322431 AAT
1 AAT
31322434 GAATTTTTTT
Statistics
Matches: 206, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
207 206 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (207 bp):
AATTATAGATAATGTTACATATAAGCATGTTATATACATTAAGGATGTGGAATGGACAGGAGGAG
GAAAATATATATGAATATTCAACTAGCATGGGTTTACATTAAAAATGGCTAATTTGCATGTTTTA
GGCCCAGGGACTAAATTGAATAAAAGTAAAACTTTAGGGGTAATTTTGTAAAAATGTCAAAAAAC
CAAATTGCAGGA
Found at i:31324714 original size:105 final size:105
Alignment explanation
Indices: 31324532--31324741 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
31324522 TGGGTTATTC
31324532 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
1 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
31324597 GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
66 GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
31324637 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
1 TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
**
31324702 GCATTTGTTGCTTACGTAGTTGTTTTCCTTTACTTTTCAG
66 GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
31324742 ATTATCGAAA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (105 bp):
TTGATACGTATAGATTTCATATTTGAAATGAATTAATATGATTAAAGTTTATATGAGCTTACTAA
GCATTTGTTGCTTACGTAGTTGTTTTCCAGTACTTTTCAG
Found at i:31327118 original size:35 final size:35
Alignment explanation
Indices: 31327062--31327131 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
31327052 TATATATACT
*
31327062 AAATAAAATTAATAAAATAATAAAATATTATTTAA
1 AAATAAAATTAATAAAATAATAAAATAATATTTAA
* * *
31327097 AAATCAAATTAA-AATATTAATAAACTAATATTTAA
1 AAATAAAATTAATAA-AATAATAAAATAATATTTAA
31327132 TTAATTAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 2 0.07
35 28 0.93
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (35 bp):
AAATAAAATTAATAAAATAATAAAATAATATTTAA
Found at i:31330225 original size:2 final size:2
Alignment explanation
Indices: 31330212--31330264 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
31330202 CAAGCCTTAA
*
31330212 AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
31330254 AC AC AC AC AC A
1 AC AC AC AC AC A
31330265 TATATGAGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.47, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:31332515 original size:31 final size:30
Alignment explanation
Indices: 31332474--31332548 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
31332464 TTTTAATTTG
* *
31332474 ATCAAATTTAATCTTAGTATTTTTTGAATTA
1 ATCAATTTTAATCTTA-TACTTTTTGAATTA
*
31332505 ATCAATTTTAATTCTTATACTTTTTGAATTT
1 ATCAATTTTAA-TCTTATACTTTTTGAATTA
* *
31332536 TTAAATTTTAATC
1 ATCAATTTTAATC
31332549 CTAATCTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
30 2 0.05
31 31 0.82
32 5 0.13
ACGTcount: A:0.33, C:0.08, G:0.04, T:0.55
Consensus pattern (30 bp):
ATCAATTTTAATCTTATACTTTTTGAATTA
Found at i:31339854 original size:3 final size:3
Alignment explanation
Indices: 31339846--31339870 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31339836 TTTTATATTT
31339846 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
31339871 CTTAAGCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:31343495 original size:42 final size:42
Alignment explanation
Indices: 31343409--31343509 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
31343399 GATTTATTCA
* * * * * *
31343409 ATGATGCACTTATGTGTCAGTATAATTGCTTTGGTATATTCG
1 ATGATGCACTTGTGTGCCAATATAATTGCTTTGATACATCCG
*
31343451 ATGATGCACTTGTGTGCCAATATATTTG-TTTCGATACATCCG
1 ATGATGCACTTGTGTGCCAATATAATTGCTTT-GATACATCCG
*
31343493 ATGATGTACTATGTGTG
1 ATGATGCACT-TGTGTG
31343510 TTAGTATAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 3 0.06
42 40 0.82
43 6 0.12
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.41
Consensus pattern (42 bp):
ATGATGCACTTGTGTGCCAATATAATTGCTTTGATACATCCG
Found at i:31348795 original size:15 final size:15
Alignment explanation
Indices: 31348775--31348804 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
31348765 GCATTCGATC
31348775 GAATCAAATCGAATT
1 GAATCAAATCGAATT
31348790 GAATCAAATCGAATT
1 GAATCAAATCGAATT
31348805 AAAATTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
GAATCAAATCGAATT
Found at i:31349633 original size:9 final size:9
Alignment explanation
Indices: 31349619--31349655 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31349609 CATAGTTTGA
31349619 TATTCGAAT
1 TATTCGAAT
31349628 TATTCGAAT
1 TATTCGAAT
*
31349637 TATTCGAGT
1 TATTCGAAT
31349646 TATTCGAAT
1 TATTCGAAT
31349655 T
1 T
31349656 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31350860 original size:17 final size:18
Alignment explanation
Indices: 31350833--31350885 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 18
31350823 GTCAGTGAGC
*
31350833 AATTTTGGTATCAATAAA
1 AATTATGGTATCAATAAA
*
31350851 AA-TATGGTATCGATAAA
1 AATTATGGTATCAATAAA
31350868 AATTGTATGGTATCAATA
1 AA-T-TATGGTATCAATA
31350886 CGTTTTGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 15 0.52
18 2 0.07
20 12 0.41
ACGTcount: A:0.43, C:0.06, G:0.15, T:0.36
Consensus pattern (18 bp):
AATTATGGTATCAATAAA
Found at i:31351107 original size:15 final size:16
Alignment explanation
Indices: 31351076--31351109 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
31351066 AATTTCTTTG
31351076 TTCAAAAACAAATTTTA
1 TTCAAAAAC-AATTTTA
31351093 TTCAAAAAC-ATTTTA
1 TTCAAAAACAATTTTA
31351108 TT
1 TT
31351110 TGTTATATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (16 bp):
TTCAAAAACAATTTTA
Found at i:31351120 original size:23 final size:21
Alignment explanation
Indices: 31351090--31351131 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
31351080 AAAACAAATT
*
31351090 TTATTCAAAAACATTTTATTTG
1 TTATTC-AAAACAATTTATTTG
31351112 TTATATCAAAACAATTTATT
1 TTAT-TCAAAACAATTTATT
31351132 AAATAAAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (21 bp):
TTATTCAAAACAATTTATTTG
Found at i:31354009 original size:25 final size:25
Alignment explanation
Indices: 31353948--31353998 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
31353938 AATAACTTCC
31353948 TTATTTTTAAATATTGTTTAATTAT
1 TTATTTTTAAATATTGTTTAATTAT
31353973 TTATTTTTAAATA-T-TTTAA-TAT
1 TTATTTTTAAATATTGTTTAATTAT
31353995 TTAT
1 TTAT
31353999 GATTCTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 7 0.27
23 5 0.19
24 1 0.04
25 13 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (25 bp):
TTATTTTTAAATATTGTTTAATTAT
Found at i:31385826 original size:21 final size:21
Alignment explanation
Indices: 31385800--31385842 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31385790 TTGTATGTCT
*
31385800 ACAATTACATTCTCGTTAGGC
1 ACAATTACATTCTCCTTAGGC
*
31385821 ACAATTTCATTCTCCTTAGGC
1 ACAATTACATTCTCCTTAGGC
31385842 A
1 A
31385843 AAATATCAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (21 bp):
ACAATTACATTCTCCTTAGGC
Done.