Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008523.1 Hibiscus syriacus cultivar Beakdansim tig00111392_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4657139
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 18
Found at i:257560 original size:18 final size:18
Alignment explanation
Indices: 257519--257562 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
257509 AATGATGATT
*
257519 TACTAATTTAAATAAAAA
1 TACTAAATTAAATAAAAA
* *
257537 -AATAAATTACATAAAAA
1 TACTAAATTAAATAAAAA
257554 TACTAAATT
1 TACTAAATT
257563 CTGTCTATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (18 bp):
TACTAAATTAAATAAAAA
Found at i:258349 original size:111 final size:112
Alignment explanation
Indices: 258138--258487 Score: 621
Period size: 112 Copynumber: 3.1 Consensus size: 112
258128 TTGTCGGTTT
*
258138 GTGTCGATACTTTATAAAAATATATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
258203 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
258250 GTGTCGATACTTTATAAAAATGTATTGATCTATAACAATATAACATGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
258314 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
258361 GTGTCGATACTTTATAAAAATGAATCGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
* * *
258426 GGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
258473 GTGTCGATATTTTAT
1 GTGTCGATACTTTAT
258488 TATAAGTATC
Statistics
Matches: 228, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
111 108 0.47
112 120 0.53
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATTGATCCATAACAATATAACATGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:258669 original size:184 final size:182
Alignment explanation
Indices: 258358--258991 Score: 1000
Period size: 182 Copynumber: 3.5 Consensus size: 182
258348 GGATATATTG
* * *
258358 AAAGTGTCGATACTTTATAAAAATGAATCGATCCATAACAATATAACATGTAAAAAAATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
** ** * *
258423 ACCGGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATGTTGATAGTGTCGATATTTTAT
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATATTTTAT
* *
258488 TATAAGTATCAACACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGTTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGTCAAT
* *
258540 AAAGAGTGTCGATACTTTATAAAAATTTATCGATCCATAACAATATAACAGGTAAAAATATGTCA
1 -AA-AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACA
258605 AAACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATATTTT
64 AAACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATATTTT
* *
258670 ATTATAAGTATCGACAATTTTGGAATTTAAAAGAGAAGAAGTTATAGCGTCAAT
129 ATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGTCAAT
* * *
258724 AAAGTGTCGATACTTTATAAAAATATATCGATCCATAAAAATATAACAGGTACAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* * *
258789 ACCGGTTTCGAAATGACAAAACCGGTAAAGAG-TGACCAGATATGTTGAAAGTGTCGATACTTTA
66 ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCT-ACCGGATATGTTGAAAGTGTCGATATTTTA
* *
258853 TTATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAATTATAGCGCCAAT
130 TTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGTCAAT
*
258906 AAAGTGTCGATACATTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
* *
258971 ATCGGTCTCAAAATGACAAAA
66 ACCGGTCTCGAAATGACAAAA
258992 TCAGTAGTAA
Statistics
Matches: 416, Mismatches: 33, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
181 1 0.00
182 246 0.59
183 4 0.01
184 165 0.40
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAA
ACCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGAAAGTGTCGATATTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAATTATAGCGTCAAT
Found at i:260572 original size:38 final size:38
Alignment explanation
Indices: 260521--260646 Score: 243
Period size: 38 Copynumber: 3.3 Consensus size: 38
260511 AAAAACAACA
260521 ATAAAATTATATTATTAATGTTATATCATCATTCATAT
1 ATAAAATTATATTATTAATGTTATATCATCATTCATAT
260559 ATAAAATTATATTATTAATGTTATATCATCATTCATAT
1 ATAAAATTATATTATTAATGTTATATCATCATTCATAT
*
260597 ATAAAATTATATTATTAATGTAATATCATCATTCATAT
1 ATAAAATTATATTATTAATGTTATATCATCATTCATAT
260635 ATAAAATTATAT
1 ATAAAATTATAT
260647 AAATTATCAT
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
38 87 1.00
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (38 bp):
ATAAAATTATATTATTAATGTTATATCATCATTCATAT
Found at i:261126 original size:24 final size:24
Alignment explanation
Indices: 261094--261145 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
261084 GAACAATTTT
* *
261094 GAAACCTAAGTGAGCGATAAATCC
1 GAAACCTAAGTGACCAATAAATCC
*
261118 GAAAGCTAAGTGACCAATAAATCC
1 GAAACCTAAGTGACCAATAAATCC
261142 GAAA
1 GAAA
261146 AGTATATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.46, C:0.19, G:0.19, T:0.15
Consensus pattern (24 bp):
GAAACCTAAGTGACCAATAAATCC
Found at i:262582 original size:5 final size:5
Alignment explanation
Indices: 262572--262609 Score: 67
Period size: 5 Copynumber: 7.4 Consensus size: 5
262562 GGATCGAATG
262572 GACTC GACTC GACTC GACTC GAGCTC GACTC GACTC GA
1 GACTC GACTC GACTC GACTC GA-CTC GACTC GACTC GA
262610 GTTCTTAACG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 27 0.84
6 5 0.16
ACGTcount: A:0.21, C:0.37, G:0.24, T:0.18
Consensus pattern (5 bp):
GACTC
Found at i:262600 original size:16 final size:16
Alignment explanation
Indices: 262572--262610 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
262562 GGATCGAATG
262572 GACTCGA-CTCGACTC
1 GACTCGAGCTCGACTC
262587 GACTCGAGCTCGACTC
1 GACTCGAGCTCGACTC
262603 GACTCGAG
1 GACTCGAG
262611 TTCTTAACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.18
Consensus pattern (16 bp):
GACTCGAGCTCGACTC
Found at i:265994 original size:18 final size:20
Alignment explanation
Indices: 265971--266055 Score: 75
Period size: 21 Copynumber: 4.2 Consensus size: 20
265961 GGTCCAAATC
265971 AGGAATT-A-CAATGGCTGT
1 AGGAATTCAGCAATGGCTGT
*
265989 AGGAATTTCAGCAGTGGCTGT
1 AGGAA-TTCAGCAATGGCTGT
* *
266010 AGGAATTTCAACAGTGGCTGT
1 AGGAA-TTCAGCAATGGCTGT
* * *
266031 AGGATTTTCAGTAGTGGCTGT
1 AGGA-ATTCAGCAATGGCTGT
266052 AGGA
1 AGGA
266056 TTTTCAGCAG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.09
19 2 0.03
20 1 0.02
21 50 0.86
ACGTcount: A:0.27, C:0.12, G:0.32, T:0.29
Consensus pattern (20 bp):
AGGAATTCAGCAATGGCTGT
Found at i:266008 original size:21 final size:21
Alignment explanation
Indices: 265982--266065 Score: 132
Period size: 21 Copynumber: 4.0 Consensus size: 21
265972 GGAATTACAA
265982 TGGCTGTAGGAATTTCAGCAG
1 TGGCTGTAGGAATTTCAGCAG
*
266003 TGGCTGTAGGAATTTCAACAG
1 TGGCTGTAGGAATTTCAGCAG
* *
266024 TGGCTGTAGGATTTTCAGTAG
1 TGGCTGTAGGAATTTCAGCAG
*
266045 TGGCTGTAGGATTTTCAGCAG
1 TGGCTGTAGGAATTTCAGCAG
266066 GTTTTGTAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.23, C:0.13, G:0.32, T:0.32
Consensus pattern (21 bp):
TGGCTGTAGGAATTTCAGCAG
Found at i:267942 original size:20 final size:20
Alignment explanation
Indices: 267914--267974 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
267904 TTTGTCCGGG
*
267914 TTATAAATATTATATTATAA
1 TTATTAATATTATATTATAA
267934 TTATTAATATTATATTATAA
1 TTATTAATATTATATTATAA
* * *
267954 CTATTATTGTTATTATTATAA
1 TTATTAATATTA-TATTATAA
267975 CAATTATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 28 0.78
21 8 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
TTATTAATATTATATTATAA
Found at i:267950 original size:14 final size:15
Alignment explanation
Indices: 267914--267960 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
267904 TTTGTCCGGG
*
267914 TTATAAATATT-ATA
1 TTATAATTATTAATA
267928 TTATAATTATTAATA
1 TTATAATTATTAATA
267943 TTAT-ATTA-TAACTA
1 TTATAATTATTAA-TA
267957 TTAT
1 TTAT
267961 TGTTATTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 3 0.10
14 20 0.67
15 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAATTATTAATA
Found at i:267969 original size:3 final size:3
Alignment explanation
Indices: 267921--268009 Score: 65
Period size: 3 Copynumber: 30.3 Consensus size: 3
267911 GGGTTATAAA
* * * * *
267921 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT AAC TAT TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
267967 TAT TAT AAC AAT TAT AAT TAT TAT TAG TAT TAT TAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
268010 GCTTATGTTT
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
2 4 0.06
3 60 0.94
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:270728 original size:51 final size:51
Alignment explanation
Indices: 270643--270740 Score: 169
Period size: 51 Copynumber: 1.9 Consensus size: 51
270633 GGAAATGATC
* *
270643 GGCTATAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTAATA
1 GGCTATAAAGAAATATCGGTTTAAACAGGCTGAAATTCCTTGTAACTAATA
*
270694 GGCTGTAAAGAAATATCGGTTTAAACAGGCTGAAATTCCTTGTAACT
1 GGCTATAAAGAAATATCGGTTTAAACAGGCTGAAATTCCTTGTAACT
270741 CTCCCCCTGA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 44 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (51 bp):
GGCTATAAAGAAATATCGGTTTAAACAGGCTGAAATTCCTTGTAACTAATA
Found at i:276903 original size:21 final size:22
Alignment explanation
Indices: 276879--276923 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
276869 ATTGCGGTTG
*
276879 AATTGTTT-ATTA-TTTTTAATT
1 AATT-TTTCATTAGTTTCTAATT
276900 AATTTTTCATTAGTTTCTAATT
1 AATTTTTCATTAGTTTCTAATT
276922 AA
1 AA
276924 CTAGTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 8 0.38
22 10 0.48
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (22 bp):
AATTTTTCATTAGTTTCTAATT
Found at i:280371 original size:18 final size:18
Alignment explanation
Indices: 280348--280385 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
280338 ATTTTTACAA
*
280348 TATTAACATAATTT-TTTT
1 TATTAAAAT-ATTTATTTT
280366 TATTAAAATATTTATTTT
1 TATTAAAATATTTATTTT
280384 TA
1 TA
280386 AAAAAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
TATTAAAATATTTATTTT
Found at i:280614 original size:24 final size:26
Alignment explanation
Indices: 280569--280618 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 26
280559 CGTTCGTGAA
*
280569 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
280595 CGTTC-ATTA-ATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
280619 GAAACAGAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.61
25 4 0.17
26 5 0.22
ACGTcount: A:0.18, C:0.12, G:0.16, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:285137 original size:24 final size:24
Alignment explanation
Indices: 285101--285155 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
285091 ATGGTTAATT
*
285101 TGACACTATCACGACTGATCAATA
1 TGACACTACCACGACTGATCAATA
285125 TGACACTACCACGACTGATCAATA
1 TGACACTACCACGACTGATCAATA
*
285149 TGTCACT
1 TGACACT
285156 TATATATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (24 bp):
TGACACTACCACGACTGATCAATA
Found at i:290417 original size:258 final size:258
Alignment explanation
Indices: 289960--290478 Score: 1020
Period size: 258 Copynumber: 2.0 Consensus size: 258
289950 TAGAGTTATC
289960 TTCGTAGGACCACAAAGAGGCCATCTGGTTGAGAAGACGGCAACCCCTTCCGAACTCACAATCAA
1 TTCGTAGGACCACAAAGAGGCCATCTGGTTGAGAAGACGGCAACCCCTTCCGAACTCACAATCAA
*
290025 ATTGTTATAATACCTTACATCATTTATGTGTATGTCAAATGCCCTGGAGCTTGACGGCGAATCAC
66 ATTGTTATAATACCTTACATCATTTATGAGTATGTCAAATGCCCTGGAGCTTGACGGCGAATCAC
290090 TATTATCCGCAAAATACAGAGCAATGTAATAAGTAGAGTTCGGGAGGGAGAAACGTGGCCATCTC
131 TATTATCCGCAAAATACAGAGCAATGTAATAAGTAGAGTTCGGGAGGGAGAAACGTGGCCATCTC
290155 AACTCCAGGGATTCCGATCGAGTCGTTGAAAGTGCTCTTTCAAATACTTTTGAAGGGGGGATA
196 AACTCCAGGGATTCCGATCGAGTCGTTGAAAGTGCTCTTTCAAATACTTTTGAAGGGGGGATA
290218 TTCGTAGGACCACAAAGAGGCCATCTGGTTGAGAAGACGGCAACCCCTTCCGAACTCACAATCAA
1 TTCGTAGGACCACAAAGAGGCCATCTGGTTGAGAAGACGGCAACCCCTTCCGAACTCACAATCAA
290283 ATTGTTATAATACCTTACATCATTTATGAGTATGTCAAATGCCCTGGAGCTTGACGGCGAATCAC
66 ATTGTTATAATACCTTACATCATTTATGAGTATGTCAAATGCCCTGGAGCTTGACGGCGAATCAC
*
290348 TATTATCCGCAAAATACAGAGCAATTTAATAAGTAGAGTTCGGGAGGGAGAAACGTGGCCATCTC
131 TATTATCCGCAAAATACAGAGCAATGTAATAAGTAGAGTTCGGGAGGGAGAAACGTGGCCATCTC
290413 AACTCCAGGGATTCCGATCGAGTCGTTGAAAGTGCTCTTTCAAATACTTTTGAAGGGGGGATA
196 AACTCCAGGGATTCCGATCGAGTCGTTGAAAGTGCTCTTTCAAATACTTTTGAAGGGGGGATA
290476 TTC
1 TTC
290479 CAGAACCCAG
Statistics
Matches: 259, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
258 259 1.00
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (258 bp):
TTCGTAGGACCACAAAGAGGCCATCTGGTTGAGAAGACGGCAACCCCTTCCGAACTCACAATCAA
ATTGTTATAATACCTTACATCATTTATGAGTATGTCAAATGCCCTGGAGCTTGACGGCGAATCAC
TATTATCCGCAAAATACAGAGCAATGTAATAAGTAGAGTTCGGGAGGGAGAAACGTGGCCATCTC
AACTCCAGGGATTCCGATCGAGTCGTTGAAAGTGCTCTTTCAAATACTTTTGAAGGGGGGATA
Found at i:291680 original size:21 final size:21
Alignment explanation
Indices: 291655--291696 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
291645 TGGGATAGGG
* * *
291655 AAAGGGCGGGAAAGGAGAGGA
1 AAAGGGAGGAAAAGAAGAGGA
291676 AAAGGGAGGAAAAGAAGAGGA
1 AAAGGGAGGAAAAGAAGAGGA
291697 GGAAGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (21 bp):
AAAGGGAGGAAAAGAAGAGGA
Found at i:292848 original size:20 final size:20
Alignment explanation
Indices: 292825--292876 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
292815 AACGCGATCC
292825 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
292845 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
292865 CCAAAATCGCAA
1 CCAGAATCGCAA
292877 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:292893 original size:21 final size:20
Alignment explanation
Indices: 292866--292964 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
292856 AATCAGTTTC
292866 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
292887 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
292908 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
292928 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
292949 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
292965 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:292993 original size:20 final size:20
Alignment explanation
Indices: 292931--293124 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
292921 CGATTTTCCA
* ** *
292931 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
292951 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
292971 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
292991 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
293011 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
293031 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
293051 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
293071 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
293091 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
293112 AAATCGCAACGCG
1 AAATCGCAACGCG
293125 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:293015 original size:60 final size:60
Alignment explanation
Indices: 292931--293124 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
292921 CGATTTTCCA
* ** * *
292931 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
292991 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
293051 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
293112 AAATCGCAACGCG
1 AAATCGCAACGCG
293125 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:293543 original size:33 final size:33
Alignment explanation
Indices: 293504--293574 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
293494 TTCACTTAGA
*
293504 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
293537 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
293570 TTTCA
1 TTTCA
293575 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:293712 original size:14 final size:14
Alignment explanation
Indices: 293693--293747 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
293683 GGAATGACTG
293693 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
293707 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
293726 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
293740 TCGCAACG
1 TCGCAACG
293748 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:293785 original size:19 final size:17
Alignment explanation
Indices: 293758--293874 Score: 72
Period size: 14 Copynumber: 7.1 Consensus size: 17
293748 CGAAACCAAA
*
293758 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCA-T
293777 TCGCGTTGCGA-TTC--
1 TCGCGTTGCGATTTCAT
*
293791 TCTCGTTGCGATTTCATT
1 TCGCGTTGCGATTTCA-T
*
293809 TCGCGTTACGA-TTC--
1 TCGCGTTGCGATTTCAT
*
293823 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATT-TCAT
293841 CTCGCGTTGCGA-TTC--
1 -TCGCGTTGCGATTTCAT
*
293856 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGA-TTTCAT
293874 T
1 T
293875 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
14 29 0.38
15 4 0.05
16 5 0.06
17 8 0.10
18 11 0.14
19 20 0.26
ACGTcount: A:0.11, C:0.25, G:0.21, T:0.44
Consensus pattern (17 bp):
TCGCGTTGCGATTTCAT
Found at i:293799 original size:14 final size:14
Alignment explanation
Indices: 293780--293868 Score: 79
Period size: 14 Copynumber: 5.7 Consensus size: 14
293770 TTTCATTTCG
293780 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
293794 CGTTGCGATTTCATTTCG
1 CGTTGCGA-TTC---TCT
*
293812 CGTTACGATTCTCT
1 CGTTGCGATTCTCT
293826 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
293843 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
293859 CGTTGCGATT
1 CGTTGCGATT
293869 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
14 27 0.44
15 4 0.06
16 5 0.08
17 8 0.13
18 10 0.16
19 8 0.13
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:293854 original size:33 final size:33
Alignment explanation
Indices: 293763--293876 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
293753 CCAAATCGCA
293763 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
293796 TTGCGA-TTTCATTTCGCGTTACGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
293828 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
293861 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
293877 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
32 31 0.42
33 43 0.58
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:293991 original size:24 final size:25
Alignment explanation
Indices: 293943--293996 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
293933 TTATGTTTAT
*
293943 TGTTTTTGGTATATCTTCACAGGTA
1 TGTTTTTGGTATATCTTAACAGGTA
*
293968 -GTTTTTGGTATATC-TAACTTGGTA
1 TGTTTTTGGTATATCTTAAC-AGGTA
293992 TGTTT
1 TGTTT
293997 ATTGTTTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
23 3 0.12
24 18 0.72
25 4 0.16
ACGTcount: A:0.19, C:0.09, G:0.20, T:0.52
Consensus pattern (25 bp):
TGTTTTTGGTATATCTTAACAGGTA
Found at i:295730 original size:90 final size:91
Alignment explanation
Indices: 295548--296006 Score: 803
Period size: 90 Copynumber: 5.1 Consensus size: 91
295538 TAGATTGCTT
295548 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATT-TTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295612 TT-TCTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTGTTTTGTCTTTTGGTTGAA
295637 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295701 TTGTCTTGTTTTGTCTTTTGGTTGAA
66 TTGTCTTGTTTTGTCTTTTGGTTGAA
295727 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
295792 TTTGTCTT-TGTTTGTC-TTTGGTTGAA
66 -TTGTCTTGT-TTTGTCTTTTGGTTGAA
295818 AGTAAATTTG-TCGGTTTGCTGCC-ATTCTGCTAAAC--TGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
295879 ATTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTGTC-TTGTTTTGTCTTTTGGTTGAA
295907 AGTAAATTTGTTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
295972 ATTGTCTTGTTTTGTC-TTTGGTTGAA
65 ATTGTCTTGTTTTGTCTTTTGGTTGAA
295998 AGTAAATTT
1 AGTAAATTT
296007 ATCCATTCAA
Statistics
Matches: 357, Mismatches: 0, Indels: 24
0.94 0.00 0.06
Matches are distributed among these distances:
87 5 0.01
88 35 0.10
89 69 0.19
90 131 0.37
91 62 0.17
92 23 0.06
93 32 0.09
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (91 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTGTCTTGTTTTGTCTTTTGGTTGAA
Found at i:296072 original size:20 final size:19
Alignment explanation
Indices: 296047--296173 Score: 82
Period size: 18 Copynumber: 7.3 Consensus size: 19
296037 AAGTTTACTT
*
296047 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-TAAAA
*
296067 TCGCAACGCGAAAC-CAAA
1 TCGCAACGCGAAACTAAAA
*
296085 TCGCAACGCGAAA-TGAAA
1 TCGCAACGCGAAACTAAAA
*
296103 TCGCAA--CG--AC-AGAA
1 TCGCAACGCGAAACTAAAA
*
296117 TCGCAATGCGAAA-TGAAAA
1 TCGCAACGCGAAACT-AAAA
*
296136 TCGCAA--CG--AC-AAGA
1 TCGCAACGCGAAACTAAAA
*
296150 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACTAAAA
296169 TCGCA
1 TCGCA
296174 TTGCGATTTT
Statistics
Matches: 85, Mismatches: 8, Indels: 29
0.70 0.07 0.24
Matches are distributed among these distances:
14 18 0.21
15 1 0.01
16 6 0.07
17 2 0.02
18 28 0.33
19 17 0.20
20 13 0.15
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAACTAAAA
Found at i:296142 original size:33 final size:32
Alignment explanation
Indices: 296081--296173 Score: 134
Period size: 33 Copynumber: 2.9 Consensus size: 32
296071 AACGCGAAAC
296081 CAAATCGCAACGCGAAATG-AAATCGCAACGA
1 CAAATCGCAACGCGAAATGAAAATCGCAACGA
*
296112 CAGAATCGCAATGCGAAATGAAAATCGCAACGA
1 CA-AATCGCAACGCGAAATGAAAATCGCAACGA
**
296145 CAAGATCGCAACGCGAAACCAAAATCGCA
1 CAA-ATCGCAACGCGAAATGAAAATCGCA
296174 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
31 2 0.04
32 17 0.31
33 36 0.65
ACGTcount: A:0.45, C:0.26, G:0.19, T:0.10
Consensus pattern (32 bp):
CAAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:296191 original size:19 final size:19
Alignment explanation
Indices: 296169--296302 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
296159 GAAACCAAAA
*
296169 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
296188 TCGCGTTGCGA--TTC--T
1 TCGCGTTGCGATTTTCATT
296203 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
296220 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
296236 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
296253 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
296272 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
296292 TCGTGTTGCGA
1 TCGCGTTGCGA
296303 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.09
14 7 0.08
15 5 0.05
16 5 0.05
17 10 0.11
19 46 0.49
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:296215 original size:32 final size:33
Alignment explanation
Indices: 296174--296265 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
296164 CAAAATCGCA
296174 TTGCGATTTTCATTTCGCGTTGCGATTCT-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
296206 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
296239 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
296266 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 28 0.49
33 29 0.51
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:298148 original size:38 final size:37
Alignment explanation
Indices: 298077--298148 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
298067 AATTGATTGT
*
298077 TTTTTGATTGTTTAATTGATTTGTAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAGATGATTCAA
298114 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGT-AAAGATGATT
298149 TGTAAAAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.54
Consensus pattern (37 bp):
TTTTTGATTGTTTAATTGATTTGTAAAGATGATTCAA
Found at i:298149 original size:14 final size:14
Alignment explanation
Indices: 298130--298165 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
298120 ATTGTTTAAT
298130 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
298144 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
298158 TGATTTGT
1 TGATTTGT
298166 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:298361 original size:20 final size:19
Alignment explanation
Indices: 298275--298375 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
298265 CAAAATGACT
298275 ATCGCAATGCG-AATGAAA
1 ATCGCAATGCGAAATGAAA
298293 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
298312 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
298326 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
298345 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
298365 ATCGCAATGCG
1 ATCGCAATGCG
298376 TTTTAATTTC
Statistics
Matches: 74, Mismatches: 2, Indels: 13
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 28 0.38
20 19 0.26
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:298423 original size:33 final size:33
Alignment explanation
Indices: 298372--298707 Score: 201
Period size: 33 Copynumber: 9.8 Consensus size: 33
298362 AAAATCGCAA
*
298372 TGCG-TTTTAATTTCGCATTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
298404 TGCGATTTTCATTTCGCATTGCGATT-T-TCAT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
* *
298435 TTCGCATTCGATTC-TTTCG--TTGCGATTTTCATTTCGCAT
1 TGCG-ATT---TTCATTTCGCATTGCGA--TT-ATCTCG--T
*
298474 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTAT
1 TGCGATTTTCATTTCGCATTGCGA--TT-ATCTCG--T
* *
298512 TGCGA-TTTAATTTCGCATTGCGATTATGTCTGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTC-GT
*
298545 T-CGATTTTCATTTCGCATTGCGATT-T-TCAT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
* * * * *
298575 TTCGCA-TTGCGATTCTCTCGTTGCGATTTTTATTTCGCAT
1 TGCG-ATTTTC-ATT-TCGCATTGCGA---TTATCTCG--T
* *
298615 TGCGATTTTCATTTCGCATTGCGATTCTCACGT
1 TGCGATTTTCATTTCGCATTGCGATTATCTCGT
*
298648 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTATC-TCGT
* *
298682 TGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATT
298708 GTATTTCCGT
Statistics
Matches: 248, Mismatches: 25, Indels: 61
0.74 0.07 0.18
Matches are distributed among these distances:
30 2 0.01
31 13 0.05
32 22 0.09
33 76 0.31
34 40 0.16
35 14 0.06
36 8 0.03
37 20 0.08
38 38 0.15
39 8 0.03
40 7 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTATCTCGT
Found at i:298427 original size:19 final size:19
Alignment explanation
Indices: 298366--298707 Score: 329
Period size: 19 Copynumber: 19.7 Consensus size: 19
298356 GAAATGAAAA
* *
298366 TCGCAATGCG-TTTTAATT
1 TCGCATTGCGATTTTCATT
*
298384 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
298400 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298417 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298436 TCGCATT-CGA--TTC-TT
1 TCGCATTGCGATTTTCATT
298451 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298468 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298487 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
298506 TCGTATTGCGA-TTTAATT
1 TCGCATTGCGATTTTCATT
*
298524 TCGCATTGCGA--TT-ATG
1 TCGCATTGCGATTTTCATT
298540 TCTG--TT-CGATTTTCATT
1 TC-GCATTGCGATTTTCATT
298557 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298576 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
*
298592 TCG--TTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
298609 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298628 TCGCATTGCGATTCTCA--
1 TCGCATTGCGATTTTCATT
298645 -CG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
298661 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
298679 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
298695 TCGCGTTGCGATT
1 TCGCATTGCGATT
298708 GTATTTCCGT
Statistics
Matches: 273, Mismatches: 16, Indels: 69
0.76 0.04 0.19
Matches are distributed among these distances:
13 2 0.01
14 40 0.15
15 7 0.03
16 30 0.11
17 27 0.10
18 33 0.12
19 122 0.45
20 12 0.04
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:298447 original size:51 final size:51
Alignment explanation
Indices: 298366--298640 Score: 255
Period size: 52 Copynumber: 5.3 Consensus size: 51
298356 GAAATGAAAA
* * *
298366 TCGCAATGCG-TTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATT-CGATTATTTCGTTGCGATTTTCATT
*
298417 TCGCATTGCGATTTTCATTTCGCATTCGATTCTTTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTCGATTATTTCGTTGCGATTTTCATT
*
298468 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGA-TTTAATT
1 TCGCATTGCGATTTTCATTTCGCATT-CGA--TT-ATTTCG--TTGCGATTTTCATT
298524 TCGCATTGCGATTATGTC-TGTTCG-ATT---TTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATT-T-TCAT-TTCGCATTCGATT-ATTTCG--TTGCGATTTTCATT
* * *
298576 TCGCATTGCGATTCTCTCGTTGCG-ATT--TTTATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATT-T-TCATTTCGCATTCGATTATTTCG--TTGCGATTTTCATT
298628 TCGCATTGCGATT
1 TCGCATTGCGATT
298641 CTCACGTTGC
Statistics
Matches: 200, Mismatches: 11, Indels: 25
0.85 0.05 0.11
Matches are distributed among these distances:
51 74 0.37
52 80 0.40
53 3 0.01
54 2 0.01
55 5 0.03
56 19 0.09
57 11 0.05
58 6 0.03
ACGTcount: A:0.16, C:0.20, G:0.17, T:0.47
Consensus pattern (51 bp):
TCGCATTGCGATTTTCATTTCGCATTCGATTATTTCGTTGCGATTTTCATT
Found at i:298477 original size:70 final size:70
Alignment explanation
Indices: 298403--298640 Score: 335
Period size: 70 Copynumber: 3.4 Consensus size: 70
298393 GATTATCTCG
298403 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT-CGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTT-AT
298467 TTCGCA
65 TTCGCA
* *
298473 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTATTGCGATTTAATTTCGCATTGCGA--T
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TT-CTTTCG--TTGCGATTT
*
298536 TATGTCTG--
62 TATTTC-GCA
*
298544 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGA-TTTTAT
298608 TTCGCA
65 TTCGCA
298614 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
298641 CTCACGTTGC
Statistics
Matches: 149, Mismatches: 7, Indels: 23
0.83 0.04 0.13
Matches are distributed among these distances:
66 6 0.04
68 5 0.03
69 8 0.05
70 81 0.54
71 29 0.19
72 6 0.04
73 8 0.05
75 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (70 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTATT
TCGCA
Found at i:298641 original size:52 final size:52
Alignment explanation
Indices: 298403--298679 Score: 325
Period size: 52 Copynumber: 5.2 Consensus size: 52
298393 GATTATCTCG
* *
298403 TTGCGATTTTCATTTCGCATTGCGATT-T-TCATTTCGCATTCGATTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCG-ATT---TTCATTTCGCA
* *
298454 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
298511 TTGCGA-TTTAATTTCGCATTGCGATTATGTCTGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
*
298562 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTTATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
298614 TTGCGATTTTCATTTCGCATTGCGATTCTCACGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
298667 TTGCGATTTTCAT
1 TTGCGATTTTCAT
298680 GTTGGGATTT
Statistics
Matches: 200, Mismatches: 12, Indels: 26
0.84 0.05 0.11
Matches are distributed among these distances:
51 49 0.25
52 85 0.43
53 22 0.11
54 6 0.03
55 6 0.03
56 19 0.09
57 9 0.05
58 4 0.02
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:299960 original size:32 final size:33
Alignment explanation
Indices: 299923--299985 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
299913 CAAGTCCATG
299923 AAGCATCT-GGAAACACCTTCTAACAGCGTTAA
1 AAGCATCTGGGAAACACCTTCTAACAGCGTTAA
299955 AAGCATCTGGGAAACACCTTCTAACAGCGTT
1 AAGCATCTGGGAAACACCTTCTAACAGCGTT
299986 GTCAATTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.27
33 22 0.73
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.22
Consensus pattern (33 bp):
AAGCATCTGGGAAACACCTTCTAACAGCGTTAA
Found at i:301206 original size:22 final size:24
Alignment explanation
Indices: 301174--301218 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
301164 CTGAAACATC
301174 ATCAAAATCC-G-TATTGACCAAT
1 ATCAAAATCCGGATATTGACCAAT
*
301196 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
301219 GACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 10 0.50
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:301918 original size:20 final size:20
Alignment explanation
Indices: 301878--302245 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
301868 AAATTTCAGT
* * *
301878 GTTGTGATTTAC-GATTCTC
1 GTTGCGATTTACGGATACGC
*
301897 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
301917 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
301937 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
301957 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
301977 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
301997 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
302017 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
302037 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
302057 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
302077 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
302097 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
302117 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
302137 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
302157 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
302177 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
302197 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
302217 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
302237 GTTGCGATT
1 GTTGCGATT
302246 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 31, Indels: 17
0.87 0.09 0.05
Matches are distributed among these distances:
19 16 0.05
20 288 0.93
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:308713 original size:31 final size:31
Alignment explanation
Indices: 308659--308726 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
308649 AGGGGAAATT
* *
308659 GTCCGTAACGTTATTGATCCGTTCGATTTTA
1 GTCCCTAACGTTATCGATCCGTTCGATTTTA
* *
308690 GTCCCTAATGTTATCGATTCGTTCGATTTTA
1 GTCCCTAACGTTATCGATCCGTTCGATTTTA
308721 GTCCCT
1 GTCCCT
308727 CATCCGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.18, C:0.22, G:0.18, T:0.43
Consensus pattern (31 bp):
GTCCCTAACGTTATCGATCCGTTCGATTTTA
Found at i:315461 original size:208 final size:210
Alignment explanation
Indices: 315076--315793 Score: 1237
Period size: 208 Copynumber: 3.4 Consensus size: 210
315066 GTCCCCCTTG
* * * * * * *
315076 TTTTGAATGCACGAAAAAGTCTGGGAAATCTGCATTTTTTTCTGTTTGGGATGGTGGAATAGTCT
1 TTTTGAATGCATGCAAAATTCTGGGAAATCTGCA--TTTTTCTGTTTGGGTTCGAGGAAAAGTCT
* * **
315141 TAACTTGACTATCAATTTGCTTGAATCACAATATATTTATGATTTAGTTGTG-T-TTTTCTATTA
64 TAACTTGAATATCAATTAGCTTGAATCACAATATATTGCTGATTTAGTTGTGTTGTTTTCTATTA
315204 CATGAGCAAAGTTGTTAACTTATAAGTTTAAGTCCCATGCTTGTGTGTGTTGCTGATTTTCAATT
129 CATGAGCAAAGTTGTTAACTTATAAGTTTAAGTCCCATGCTTGTGTGTGTTGCTGATTTTCAATT
315269 TGTTAGTTGTTTTCTTC
194 TGTTAGTTGTTTTCTTC
*
315286 TTTTGAATGCATGCAAAATTCTGGGAAATCTGCATTTTTCTGGTTGGGTTCGAGGAAAAGTCTTA
1 TTTTGAATGCATGCAAAATTCTGGGAAATCTGCATTTTTCTGTTTGGGTTCGAGGAAAAGTCTTA
315351 ACTTGAATATCAATTAGCTTGAATCACAATATATTGCTGATTTAGTTGTGTTGTTTTCTATTACA
66 ACTTGAATATCAATTAGCTTGAATCACAATATATTGCTGATTTAGTTGTGTTGTTTTCTATTACA
*
315416 TGAGCAAAGTTGTTAACTTATAAGTTTAAGTCCCATGCTTGTGTGTGTTGCTGATTTTCAATTTA
131 TGAGCAAAGTTGTTAACTTATAAGTTTAAGTCCCATGCTTGTGTGTGTTGCTGATTTTCAATTTG
315481 TTAGTTGTTTTC-T-
196 TTAGTTGTTTTCTTC
*
315494 TTTTGGATGCATGCAAAATTCTGGGAAATCTGCATTTTTCTGTTTGGGTTCGAGGAAAAGTCTTA
1 TTTTGAATGCATGCAAAATTCTGGGAAATCTGCATTTTTCTGTTTGGGTTCGAGGAAAAGTCTTA
315559 ACTTGAATATCAATTAGCTTGAATCACAATATATTGCTGATTTAGTTGTGTTGTTTTCTATTACA
66 ACTTGAATATCAATTAGCTTGAATCACAATATATTGCTGATTTAGTTGTGTTGTTTTCTATTACA
*
315624 TGAGCAAAGTTGTTAACTTATAAGTTTAAGTCCCATGCTTGTGTGTGTTGCAGATTTTCAATTTG
131 TGAGCAAAGTTGTTAACTTATAAGTTTAAGTCCCATGCTTGTGTGTGTTGCTGATTTTCAATTTG
315689 TTAGTTGTTTTCTTC
196 TTAGTTGTTTTCTTC
* *
315704 TTTTGAATGCATGCAAAATTCTGGGAAATCTGTATTTTTCTGTTTGGGTTTGAGGAAAAGTCTTA
1 TTTTGAATGCATGCAAAATTCTGGGAAATCTGCATTTTTCTGTTTGGGTTCGAGGAAAAGTCTTA
315769 ACTTGAATATCAATTAGCTTGAATC
66 ACTTGAATATCAATTAGCTTGAATC
315794 CAACTGATTT
Statistics
Matches: 484, Mismatches: 20, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
208 275 0.57
209 3 0.01
210 206 0.43
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.43
Consensus pattern (210 bp):
TTTTGAATGCATGCAAAATTCTGGGAAATCTGCATTTTTCTGTTTGGGTTCGAGGAAAAGTCTTA
ACTTGAATATCAATTAGCTTGAATCACAATATATTGCTGATTTAGTTGTGTTGTTTTCTATTACA
TGAGCAAAGTTGTTAACTTATAAGTTTAAGTCCCATGCTTGTGTGTGTTGCTGATTTTCAATTTG
TTAGTTGTTTTCTTC
Found at i:315965 original size:8 final size:8
Alignment explanation
Indices: 315954--316028 Score: 109
Period size: 8 Copynumber: 9.6 Consensus size: 8
315944 CGCGTGTGCG
315954 TGTGTCTC
1 TGTGTCTC
315962 TGTGTCTC
1 TGTGTCTC
315970 TGTGTCTC
1 TGTGTCTC
315978 TGTGTCTC
1 TGTGTCTC
315986 TGTGTCTC
1 TGTGTCTC
*
315994 TGTGTGTC
1 TGTGTCTC
316002 TGTG--TC
1 TGTGTCTC
*
316008 TGTGTCTG
1 TGTGTCTC
*
316016 TGTGTCTG
1 TGTGTCTC
316024 TGTGT
1 TGTGT
316029 GTGTGCGTGT
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
6 6 0.10
8 57 0.90
ACGTcount: A:0.00, C:0.19, G:0.31, T:0.51
Consensus pattern (8 bp):
TGTGTCTC
Found at i:316029 original size:24 final size:24
Alignment explanation
Indices: 315953--316331 Score: 210
Period size: 24 Copynumber: 15.8 Consensus size: 24
315943 GCGCGTGTGC
* *
315953 GTGTGTCTCTGTGTCTCTGTGTCT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* * *
315977 CTGTGTCTCTGTGTCTCTGTG--T
1 GTGTGTGTCTGTGTCTGTGTGTCT
*
315999 GTCTGTGTCTGTGTCTGTGTGTCT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* * *
316023 GTGTGTGTGTGCGTGTGTGTGTGCGT
1 GTGTGTGTCTGTGTCTGTGTGT-C-T
*
316049 GTGCGTGTGC-GTGTGC-GTGTG-CGT
1 GTGTGTGT-CTGTGT-CTGTGTGTC-T
* * *
316073 GTGCGTGTGC-GTGTGTGTGTGTGT
1 GTGTGTGT-CTGTGTCTGTGTGTCT
* * *
316097 GTGTGTG-C-GTG-C-GTGCGCGCGC
1 GTGTGTGTCTGTGTCTGTGTG-TC-T
* *
316119 GTGTGTGTGTGTGTGCGTGTGCGTGCGT
1 GTGTGTGTCTGTGT-C-TGTGTGT-C-T
*
316147 GTGTGTGTGTGTGTGTCTGTGTGTC-
1 GT--GTGTGTCTGTGTCTGTGTGTCT
316172 -TGTGTGTCTGTGTC--TGTGTCT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* * *
316193 GTGTGTCTGTGTGTCTGTGTGTGT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* *
316217 GTGTGTGTGTGTGTCTCTGTGTCT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* * * *
316241 CTGTGTGTGTGTGTGTGTGTGTGT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* * *
316265 CTGTGTGTCTGTGTGTGTGTGTGT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* * *
316289 GTGTGTGTGTGTGTGTGTGTGTGT
1 GTGTGTGTCTGTGTCTGTGTGTCT
* *
316313 GTGTGTGTGTGTGTGTGTG
1 GTGTGTGTCTGTGTCTGTG
316332 ATATTGTTTT
Statistics
Matches: 293, Mismatches: 39, Indels: 46
0.78 0.10 0.12
Matches are distributed among these distances:
20 10 0.03
22 53 0.18
24 183 0.62
25 1 0.00
26 17 0.06
27 1 0.00
28 15 0.05
29 1 0.00
30 12 0.04
ACGTcount: A:0.00, C:0.12, G:0.43, T:0.45
Consensus pattern (24 bp):
GTGTGTGTCTGTGTCTGTGTGTCT
Found at i:316033 original size:6 final size:6
Alignment explanation
Indices: 315994--316331 Score: 370
Period size: 6 Copynumber: 56.3 Consensus size: 6
315984 TCTGTGTCTC
* * * * *
315994 TGTGTG TCTGTG TCTGTG TCTGTG TGTCTG TGTGTG TGTGCG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * *
316042 TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGCG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * * *
316090 TGTGTG TGTGTG TGCGTG CGTGCG CGCGCG TGTGTG TGTGTG TGCGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * * *
316138 TGCGTG CGTGTG TGTGTG TGTGTG TCTGTG TGTCTG TGTGTC TGTGTC
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * * *
316186 TGTGTC TGTGTG TCTGTG TGTCTG TGTGTG TGTGTG TGTGTG TGTCTC
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
* * * *
316234 TGTGTC TCTGTG TGTGTG TGTGTG TGTGTG TCTGTG TGTCTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
316282 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
1 TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG TGTGTG
316330 TG
1 TG
316332 ATATTGTTTT
Statistics
Matches: 292, Mismatches: 40, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 292 1.00
ACGTcount: A:0.00, C:0.10, G:0.45, T:0.45
Consensus pattern (6 bp):
TGTGTG
Found at i:316033 original size:8 final size:8
Alignment explanation
Indices: 315994--316331 Score: 370
Period size: 8 Copynumber: 42.2 Consensus size: 8
315984 TCTGTGTCTC
*
315994 TGTGTGTC
1 TGTGTGTG
*
316002 TGTGTCTG
1 TGTGTGTG
*
316010 TGTCTGTG
1 TGTGTGTG
*
316018 TGTCTGTG
1 TGTGTGTG
316026 TGTGTGTG
1 TGTGTGTG
*
316034 CGTGTGTG
1 TGTGTGTG
*
316042 TGTGCGTG
1 TGTGTGTG
*
316050 TGCGTGTG
1 TGTGTGTG
* *
316058 CGTGTGCG
1 TGTGTGTG
*
316066 TGTGCGTG
1 TGTGTGTG
*
316074 TGCGTGTG
1 TGTGTGTG
*
316082 CGTGTGTG
1 TGTGTGTG
316090 TGTGTGTG
1 TGTGTGTG
*
316098 TGTGTGCG
1 TGTGTGTG
* *
316106 TGCGTGCG
1 TGTGTGTG
* * *
316114 CGCGCGTG
1 TGTGTGTG
316122 TGTGTGTG
1 TGTGTGTG
*
316130 TGTGCGTG
1 TGTGTGTG
* *
316138 TGCGTGCG
1 TGTGTGTG
316146 TGTGTGTG
1 TGTGTGTG
316154 TGTGTGTG
1 TGTGTGTG
*
316162 TCTGTGTG
1 TGTGTGTG
*
316170 TCTGTGTG
1 TGTGTGTG
* *
316178 TCTGTGTC
1 TGTGTGTG
*
316186 TGTGTCTG
1 TGTGTGTG
*
316194 TGTGTCTG
1 TGTGTGTG
*
316202 TGTGTCTG
1 TGTGTGTG
316210 TGTGTGTG
1 TGTGTGTG
316218 TGTGTGTG
1 TGTGTGTG
* *
316226 TGTGTCTC
1 TGTGTGTG
* *
316234 TGTGTCTC
1 TGTGTGTG
316242 TGTGTGTG
1 TGTGTGTG
316250 TGTGTGTG
1 TGTGTGTG
*
316258 TGTGTGTC
1 TGTGTGTG
*
316266 TGTGTGTC
1 TGTGTGTG
316274 TGTGTGTG
1 TGTGTGTG
316282 TGTGTGTG
1 TGTGTGTG
316290 TGTGTGTG
1 TGTGTGTG
316298 TGTGTGTG
1 TGTGTGTG
316306 TGTGTGTG
1 TGTGTGTG
316314 TGTGTGTG
1 TGTGTGTG
316322 TGTGTGTG
1 TGTGTGTG
316330 TG
1 TG
316332 ATATTGTTTT
Statistics
Matches: 283, Mismatches: 47, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 283 1.00
ACGTcount: A:0.00, C:0.10, G:0.45, T:0.45
Consensus pattern (8 bp):
TGTGTGTG
Found at i:320536 original size:60 final size:60
Alignment explanation
Indices: 320470--320602 Score: 178
Period size: 60 Copynumber: 2.2 Consensus size: 60
320460 GTTTGGGGAT
* * *
320470 CAATTTAAAATGAAAGTCATAGTTTGGGGATGAAAGTGAAATGTTCAAAAGTTCAAGGAC
1 CAATTTAAAATGAAAGTCATAGTTTAGAGATGAAAGTGAAATATTCAAAAGTTCAAGGAC
* * * * *
320530 TC-ATTTAGAATGATAGTCATAGTTTAGAGATGAAATTGAAATATTTAAAAGTTTAAGGAC
1 -CAATTTAAAATGAAAGTCATAGTTTAGAGATGAAAGTGAAATATTCAAAAGTTCAAGGAC
320590 CAATTTAAAATGA
1 CAATTTAAAATGA
320603 GAGTTATACT
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.02
60 60 0.97
61 1 0.02
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (60 bp):
CAATTTAAAATGAAAGTCATAGTTTAGAGATGAAAGTGAAATATTCAAAAGTTCAAGGAC
Found at i:323260 original size:14 final size:14
Alignment explanation
Indices: 323243--323290 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
323233 AAATTTGAGA
*
323243 TTTAATATATTTGC
1 TTTAATATATTTAC
* * *
323257 TTTAAATTTATTAAA
1 TTT-AATATATTTAC
323272 TTTAATATATTTAC
1 TTTAATATATTTAC
323286 TTTAA
1 TTTAA
323291 ATTTATATTT
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (14 bp):
TTTAATATATTTAC
Found at i:323302 original size:18 final size:20
Alignment explanation
Indices: 323267--323311 Score: 76
Period size: 18 Copynumber: 2.4 Consensus size: 20
323257 TTTAAATTTA
323267 TTAAATTTAATATATTTACT
1 TTAAATTTAATATATTTACT
323287 TTAAATTT-ATAT-TTTACT
1 TTAAATTTAATATATTTACT
323305 TTAAATT
1 TTAAATT
323312 GAGATTTGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 13 0.52
19 4 0.16
20 8 0.32
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTAAATTTAATATATTTACT
Found at i:323318 original size:18 final size:18
Alignment explanation
Indices: 323281--323318 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
323271 ATTTAATATA
* *
323281 TTTACTTTAAATTTATAT
1 TTTACTTTAAATTGAGAT
323299 TTTACTTTAAATTGAGAT
1 TTTACTTTAAATTGAGAT
323317 TT
1 TT
323319 GCTATATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
TTTACTTTAAATTGAGAT
Found at i:325831 original size:19 final size:18
Alignment explanation
Indices: 325792--325833 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
325782 TTAGTTCATG
325792 TAAAAATAAATATTTAAAT
1 TAAAAATAAATATTT-AAT
325811 TAAAAATATAATAATTT-AT
1 TAAAAATA-AAT-ATTTAAT
325830 TAAA
1 TAAA
325834 TATTTAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 14 0.67
20 3 0.14
21 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAAATAAATATTTAAT
Found at i:330360 original size:40 final size:40
Alignment explanation
Indices: 330305--330386 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
330295 ACTGAGAAAA
*
330305 AACTGTTAGAATGGATCTAAGGACTAGTCTCGATGTCTTT
1 AACTGTTAGAATGGATCTAAGGACCAGTCTCGATGTCTTT
330345 AACTGTTAGAATGGATCTAAGGACCAGTCTCGATGTCTTT
1 AACTGTTAGAATGGATCTAAGGACCAGTCTCGATGTCTTT
330385 AA
1 AA
330387 ATAATTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (40 bp):
AACTGTTAGAATGGATCTAAGGACCAGTCTCGATGTCTTT
Found at i:331088 original size:172 final size:173
Alignment explanation
Indices: 330792--331139 Score: 603
Period size: 172 Copynumber: 2.0 Consensus size: 173
330782 CCTTTCTAAC
*
330792 ATTAAACATTTAATTTAAACCTCTGAACTCTTTAGCTAAGTGGGGAATTTATATTTTTGGTCCCT
1 ATTAAACATTTAATTTAAACCTCTGAACTCTTTAGCTAAGTGGGGAATTTAAATTTTTGGTCCCT
330857 CCTACTATACCATTTTTAAATAACTGTTTTAGTATTGACCCACCAAAATTGTATCATTTAATTTC
66 CCTACTATACCATTTTTAAATAACTGTTTTAGTATTGACCCACCAAAATTGTATCATTTAATTTC
330922 GATCCCCTTCTAAGTTATTAACTTTGTTCATA-TTCTTAAA-AA
131 GATCCCCTTCTAAGTTATTAACTTTGTTCATACTT-TTAAATAA
*
330964 ATTAAATATTTAATTTAAACCTCTGAACTCTTTAGCTAAGTGGGGAATTTGAAATTTTT-GTCCC
1 ATTAAACATTTAATTTAAACCTCTGAACTCTTTAGCTAAGTGGGGAATTT-AAATTTTTGGTCCC
* * * *
331028 TCCTGCTATACCATTTTTAAATAACTTTTTTAGTATTGACCCATCAAAATTGTGTCATTTAATTT
65 TCCTACTATACCATTTTTAAATAACTGTTTTAGTATTGACCCACCAAAATTGTATCATTTAATTT
331093 CGATCCCCTTCTAAGTTATTAACTTTGTTCATACTTTTAAATAA
130 CGATCCCCTTCTAAGTTATTAACTTTGTTCATACTTTTAAATAA
331137 ATT
1 ATT
331140 TAGAGTTTGA
Statistics
Matches: 167, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
172 153 0.92
173 14 0.08
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (173 bp):
ATTAAACATTTAATTTAAACCTCTGAACTCTTTAGCTAAGTGGGGAATTTAAATTTTTGGTCCCT
CCTACTATACCATTTTTAAATAACTGTTTTAGTATTGACCCACCAAAATTGTATCATTTAATTTC
GATCCCCTTCTAAGTTATTAACTTTGTTCATACTTTTAAATAA
Found at i:337719 original size:90 final size:88
Alignment explanation
Indices: 337567--337740 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 88
337557 CCTAACACAC
* * * *
337567 CCTTTTATAGCCAAGTTAACCTAGTATATTAGGGTTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTAACCTAATATATCAGGGATTTTATTATTTAAAATTAATTAAATCTATA
*
337632 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATT-GAAATTAATAAT
** *
337656 CCTTTTATATTCAAGTTACCCTAATCATATCAGGGATTTTATTATTTAAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTAACCTAAT-ATATCAGGGATTTTATTATTTAAAATTAATTAAATCTAT
337721 ATTTAATTAATTGAAATTAA
65 ATTTAATTAATTGAAATTAA
337741 ATATTTAGGA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 28 0.37
90 48 0.63
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (88 bp):
CCTTTTATAGCCAAGTTAACCTAATATATCAGGGATTTTATTATTTAAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAATAAT
Found at i:347125 original size:19 final size:21
Alignment explanation
Indices: 347101--347140 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
347091 TATAAGATAT
347101 TATATTTT-AATT-TTAATAA
1 TATATTTTAAATTATTAATAA
347120 TATATTTTAAATTATTAATAA
1 TATATTTTAAATTATTAATAA
347141 AATTTATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 4 0.21
21 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TATATTTTAAATTATTAATAA
Found at i:347155 original size:27 final size:26
Alignment explanation
Indices: 347115--347209 Score: 81
Period size: 27 Copynumber: 3.5 Consensus size: 26
347105 TTTTAATTTT
347115 AATAATA-TATTTTAAATTATTAATAA
1 AATAATATTA-TTTAAATTATTAATAA
* *
347141 AATTTATATTATTT--ATTAATTTCATAGA
1 AA-TAATATTATTTAAATT-A-TTAATA-A
347169 AATAATATTA-TTAAATTATTAATAA
1 AATAATATTATTTAAATTATTAATAA
347194 TGAATAATATTATTTA
1 --AATAATATTATTTA
347210 TATATTTAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 18
0.71 0.05 0.23
Matches are distributed among these distances:
25 4 0.07
26 10 0.18
27 30 0.55
28 11 0.20
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.48
Consensus pattern (26 bp):
AATAATATTATTTAAATTATTAATAA
Found at i:347207 original size:19 final size:19
Alignment explanation
Indices: 347183--347254 Score: 60
Period size: 19 Copynumber: 3.7 Consensus size: 19
347173 ATATTATTAA
347183 ATTATTAATAATGAATAAT
1 ATTATTAATAATGAATAAT
* *
347202 ATTATTTAT-AT-ATTTAAT
1 ATTATTAATAATGA-ATAAT
*
347220 ATTAATATAATAATCTAATAAT
1 ATT-AT-TAATAAT-GAATAAT
347242 ATT-TTAATAATGA
1 ATTATTAATAATGA
347255 TATTTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 13
0.70 0.08 0.22
Matches are distributed among these distances:
17 1 0.02
18 10 0.24
19 17 0.40
20 4 0.10
21 2 0.05
22 7 0.17
23 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTATTAATAATGAATAAT
Found at i:347226 original size:27 final size:27
Alignment explanation
Indices: 347100--347231 Score: 71
Period size: 27 Copynumber: 4.9 Consensus size: 27
347090 ATATAAGATA
* *
347100 TTATAT-TTTAATTTTAATAATA-TAT
1 TTATATATTTAATATAAATAATATTAT
* *
347125 TT-TAAATTATTAATA-AAATTTATATTAT
1 TTATATA-T-TTAATATAAA-TAATATTAT
* *
347153 TTAT-TAATTTCATAGAAATAATATTA-
1 TTATAT-ATTTAATATAAATAATATTAT
* *
347179 TTAAAT-TATTAATAATGAATAATATTAT
1 TTATATAT-TTAAT-ATAAATAATATTAT
347207 TTATATATTTAATATTAATATAATA
1 TTATATATTTAATA-TAA-ATAATA
347232 ATCTAATAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 26
0.67 0.11 0.22
Matches are distributed among these distances:
24 2 0.03
25 3 0.04
26 10 0.13
27 34 0.43
28 21 0.27
29 9 0.11
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.52
Consensus pattern (27 bp):
TTATATATTTAATATAAATAATATTAT
Found at i:347704 original size:20 final size:20
Alignment explanation
Indices: 347653--347705 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
347643 ACCTTAATTC
*
347653 AAGTTTATATAATAAATTCAA
1 AAGTTTA-ATATTAAATTCAA
* *
347674 TAGTTTGATATTAAATTCAA
1 AAGTTTAATATTAAATTCAA
*
347694 AATTTTAATATT
1 AAGTTTAATATT
347706 TTTTTAATCG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (20 bp):
AAGTTTAATATTAAATTCAA
Found at i:350092 original size:19 final size:21
Alignment explanation
Indices: 350061--350113 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 21
350051 AATTAATATT
* *
350061 TATAATAGTATTACAATAATA
1 TATAATCGAATTACAATAATA
**
350082 TA-AATC-AATTATTATAATA
1 TATAATCGAATTACAATAATA
350101 TATAATCGAATTA
1 TATAATCGAATTA
350114 ATAATTAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 12 0.46
20 7 0.27
21 7 0.27
ACGTcount: A:0.51, C:0.06, G:0.04, T:0.40
Consensus pattern (21 bp):
TATAATCGAATTACAATAATA
Found at i:350105 original size:21 final size:22
Alignment explanation
Indices: 350069--350113 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
350059 TTTATAATAG
350069 TATTACAATAATATAAATC-AAT
1 TATTACAATAATAT-AATCGAAT
*
350091 TATTATAAT-ATATAATCGAAT
1 TATTACAATAATATAATCGAAT
350112 TA
1 TA
350114 ATAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 8 0.38
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (22 bp):
TATTACAATAATATAATCGAAT
Found at i:350117 original size:19 final size:17
Alignment explanation
Indices: 350075--350122 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 17
350065 ATAGTATTAC
350075 AATAATATAAATCAATT
1 AATAATATAAATCAATT
350092 ATTATAATATATAATCGAATT
1 A--ATAATATA-AATC-AATT
350113 AATAAT-TAAA
1 AATAATATAAA
350123 ATATATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 3 0.11
18 2 0.07
19 13 0.48
20 4 0.15
21 5 0.19
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (17 bp):
AATAATATAAATCAATT
Found at i:356024 original size:15 final size:17
Alignment explanation
Indices: 356004--356036 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
355994 TTTGATTTAT
356004 TTAAATT-CAA-ATAGA
1 TTAAATTACAAGATAGA
356019 TTAAATTACAAGATAGA
1 TTAAATTACAAGATAGA
356036 T
1 T
356037 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (17 bp):
TTAAATTACAAGATAGA
Found at i:356100 original size:18 final size:19
Alignment explanation
Indices: 356077--356119 Score: 79
Period size: 18 Copynumber: 2.3 Consensus size: 19
356067 TACTATTTTT
356077 TTTTTTGTAATTTTTCT-A
1 TTTTTTGTAATTTTTCTGA
356095 TTTTTTGTAATTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
356114 TTTTTT
1 TTTTTT
356120 TTCAAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 17 0.71
19 7 0.29
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (19 bp):
TTTTTTGTAATTTTTCTGA
Found at i:356594 original size:13 final size:12
Alignment explanation
Indices: 356568--356593 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
356558 GACTTATCTC
356568 TTAAAATGTTTT
1 TTAAAATGTTTT
356580 TTAAAATGTTTT
1 TTAAAATGTTTT
356592 TT
1 TT
356594 TTTAGTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (12 bp):
TTAAAATGTTTT
Found at i:358590 original size:12 final size:13
Alignment explanation
Indices: 358558--358601 Score: 54
Period size: 12 Copynumber: 3.4 Consensus size: 13
358548 TTTCATTGCT
*
358558 TATTTCAAACATAA
1 TATTT-AAACTTAA
*
358572 TATTTAAATTTAA
1 TATTTAAACTTAA
358585 -ATTTAAACTTAA
1 TATTTAAACTTAA
358597 TATTT
1 TATTT
358602 TTTTAAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 11 0.42
13 10 0.38
14 5 0.19
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTAAACTTAA
Found at i:359707 original size:21 final size:21
Alignment explanation
Indices: 359667--359709 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
359657 TTCTGCCATC
**
359667 AAATATTTCCAAAATTTTTAA
1 AAATATTTCCAAAAAATTTAA
359688 AAATATTTCCAAAAAATTTAA
1 AAATATTTCCAAAAAATTTAA
359709 A
1 A
359710 TTTTCATAAA
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:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATATTTCCAAAAAATTTAA
Found at i:361001 original size:13 final size:14
Alignment explanation
Indices: 360979--361013 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
360969 ACACAATCAT
360979 TCACT-AAAAAAAA
1 TCACTGAAAAAAAA
*
360992 ACACTGAAAAAAAA
1 TCACTGAAAAAAAA
361006 TCACTGAA
1 TCACTGAA
361014 TCACACCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.63, C:0.17, G:0.06, T:0.14
Consensus pattern (14 bp):
TCACTGAAAAAAAA
Found at i:361528 original size:2 final size:2
Alignment explanation
Indices: 361521--361546 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
361511 TAAACCCCAA
361521 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
361547 TTTTGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:362897 original size:2 final size:2
Alignment explanation
Indices: 362890--362919 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
362880 CAAATTTGAC
362890 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
362920 AAATTCAAAG
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:363431 original size:60 final size:59
Alignment explanation
Indices: 363285--363467 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 59
363275 TTTGGATGAA
* **
363285 TTTGGGGATGAAATTGAAATATTCAAAAGTTTGGGGACTAATTTAGAAAGAGATTCATAG
1 TTTGAGGATGAAATTGAAA-ATTCAAAAGTTTAAGGACTAATTTAGAAAGAGATTCATAG
* *
363345 TTT-AGGGATGCAATT-AGAATGCTCAAAAGTTTAAGGACTAATTTAGAAAGAGATTCATAG
1 TTTGA-GGATGAAATTGAAAAT--TCAAAAGTTTAAGGACTAATTTAGAAAGAGATTCATAG
* * * * *
363405 TTTGAGGATTAAATTGAAACATTCAAAAATTTATGGACCAATTTA-AAATGAGAGTCATAG
1 TTTGAGGATGAAATTGAAA-ATTCAAAAGTTTAAGGACTAATTTAGAAA-GAGATTCATAG
363465 TTT
1 TTT
363468 AGAGACATAT
Statistics
Matches: 104, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
58 2 0.02
59 5 0.05
60 92 0.88
61 3 0.03
62 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (59 bp):
TTTGAGGATGAAATTGAAAATTCAAAAGTTTAAGGACTAATTTAGAAAGAGATTCATAG
Found at i:367610 original size:40 final size:41
Alignment explanation
Indices: 367554--367635 Score: 139
Period size: 40 Copynumber: 2.0 Consensus size: 41
367544 TTCAAATTTC
* *
367554 TTTATTGTTTTTAAATGTAAGATTAAGGCTCTAAAACTTTG
1 TTTATTGTTTTTAAATGTAAGATTAAAGCTCTAAAACATTG
367595 TTTATT-TTTTTAAATGTAAGATTAAAGCTCTAAAACATTG
1 TTTATTGTTTTTAAATGTAAGATTAAAGCTCTAAAACATTG
367635 T
1 T
367636 GTGTGGCGTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 33 0.85
41 6 0.15
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (41 bp):
TTTATTGTTTTTAAATGTAAGATTAAAGCTCTAAAACATTG
Found at i:368234 original size:21 final size:22
Alignment explanation
Indices: 368204--368250 Score: 87
Period size: 21 Copynumber: 2.2 Consensus size: 22
368194 GATTTTTATG
368204 GTTTGATGTTGCAGATTGTTTT
1 GTTTGATGTTGCAGATTGTTTT
368226 GTTT-ATGTTGCAGATTGTTTT
1 GTTTGATGTTGCAGATTGTTTT
368247 GTTT
1 GTTT
368251 TTGTGTCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.13, C:0.04, G:0.26, T:0.57
Consensus pattern (22 bp):
GTTTGATGTTGCAGATTGTTTT
Found at i:369455 original size:2 final size:2
Alignment explanation
Indices: 369448--369487 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
369438 AATCTAACAA
369448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
369488 TCGATAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:371403 original size:139 final size:139
Alignment explanation
Indices: 371153--371430 Score: 547
Period size: 139 Copynumber: 2.0 Consensus size: 139
371143 ACATATAAAG
*
371153 ACAATCTCGATTATAGTGATTTTTTTACAAGACAAAATGTGCAAGATAAACATAATTTAGATTGA
1 ACAATCTCGATTATAGTGATTTTTTTACAAGACAAAATGTGCAAGATAAACATAATTTAGATCGA
371218 ATTAGAGGTGATTACCAAGCGAGTCGATCATGAGTTGGGTAATGTTCAACTCATGCTCGTTAAAA
66 ATTAGAGGTGATTACCAAGCGAGTCGATCATGAGTTGGGTAATGTTCAACTCATGCTCGTTAAAA
371283 AATATTGTT
131 AATATTGTT
371292 ACAATCTCGATTATAGTGATTTTTTTACAAGACAAAATGTGCAAGATAAACATAATTTAGATCGA
1 ACAATCTCGATTATAGTGATTTTTTTACAAGACAAAATGTGCAAGATAAACATAATTTAGATCGA
371357 ATTAGAGGTGATTACCAAGCGAGTCGATCATGAGTTGGGTAATGTTCAACTCATGCTCGTTAAAA
66 ATTAGAGGTGATTACCAAGCGAGTCGATCATGAGTTGGGTAATGTTCAACTCATGCTCGTTAAAA
371422 AATATTGTT
131 AATATTGTT
371431 GCTCGTTAAA
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (139 bp):
ACAATCTCGATTATAGTGATTTTTTTACAAGACAAAATGTGCAAGATAAACATAATTTAGATCGA
ATTAGAGGTGATTACCAAGCGAGTCGATCATGAGTTGGGTAATGTTCAACTCATGCTCGTTAAAA
AATATTGTT
Found at i:381953 original size:17 final size:17
Alignment explanation
Indices: 381931--381978 Score: 96
Period size: 17 Copynumber: 2.8 Consensus size: 17
381921 ACATAATCTT
381931 CATTCAGCGCTGAACAA
1 CATTCAGCGCTGAACAA
381948 CATTCAGCGCTGAACAA
1 CATTCAGCGCTGAACAA
381965 CATTCAGCGCTGAA
1 CATTCAGCGCTGAA
381979 TGGTTCTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (17 bp):
CATTCAGCGCTGAACAA
Found at i:382066 original size:89 final size:89
Alignment explanation
Indices: 381965--382127 Score: 290
Period size: 89 Copynumber: 1.8 Consensus size: 89
381955 CGCTGAACAA
* *
381965 CATTCAGCGCTGAATGGTTCTATTCAACAGTAAACAAGCGATTCCTTAATCTCTTAAGCTCGTTA
1 CATTCAACGCTGAATGATTCTATTCAACAGTAAACAAGCGATTCCTTAATCTCTTAAGCTCGTTA
382030 TTCAGCTCCAACAGAGATGAGTAG
66 TTCAGCTCCAACAGAGATGAGTAG
*
382054 CATTCAACGCTGAATGATTCTATTCAGCAGTAAACAAGCGATTCCTTAATCTCTTAAGCTCGTTA
1 CATTCAACGCTGAATGATTCTATTCAACAGTAAACAAGCGATTCCTTAATCTCTTAAGCTCGTTA
*
382119 TTTAGCTCC
66 TTCAGCTCC
382128 GAAACCGACA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
89 70 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (89 bp):
CATTCAACGCTGAATGATTCTATTCAACAGTAAACAAGCGATTCCTTAATCTCTTAAGCTCGTTA
TTCAGCTCCAACAGAGATGAGTAG
Found at i:383702 original size:34 final size:34
Alignment explanation
Indices: 383660--383727 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
383650 GACCAATACC
**
383660 GGTACGGTATG-ACTATGTTGATCATACAAGAAA
1 GGTACGGTATGCACTAAATTGATCATACAAGAAA
* *
383693 GGTACCGGTATGCACTAAATTGATTATACATGAAA
1 GGTA-CGGTATGCACTAAATTGATCATACAAGAAA
383728 ACAAAGATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 4 0.14
34 7 0.24
35 18 0.62
ACGTcount: A:0.37, C:0.13, G:0.22, T:0.28
Consensus pattern (34 bp):
GGTACGGTATGCACTAAATTGATCATACAAGAAA
Found at i:386436 original size:20 final size:20
Alignment explanation
Indices: 386397--386436 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
386387 GTTTGAATCA
*
386397 AATTAATTATATATTATTTT
1 AATTAATTATAAATTATTTT
* *
386417 AATTAATTGTAAATTGTTTT
1 AATTAATTATAAATTATTTT
386437 TTTTAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (20 bp):
AATTAATTATAAATTATTTT
Found at i:386775 original size:27 final size:28
Alignment explanation
Indices: 386727--386796 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 28
386717 TTAATTATTT
* * *
386727 ATTAAAATTTAATTTTAGTTTTAATAAA
1 ATTATAATTAAATTATAGTTTTAATAAA
* *
386755 ATTATAATTAAATTATA-TTTTTATTAA
1 ATTATAATTAAATTATAGTTTTAATAAA
*
386782 ATTATATTTAAATTA
1 ATTATAATTAAATTA
386797 ATTACATCTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
ATTATAATTAAATTATAGTTTTAATAAA
Found at i:386796 original size:16 final size:16
Alignment explanation
Indices: 386760--386797 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
386750 ATAAAATTAT
*
386760 AATTAAATTATATTTT
1 AATTAAATTATATTTA
*
386776 TATTAAATTATATTTA
1 AATTAAATTATATTTA
386792 AATTAA
1 AATTAA
386798 TTACATCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTAAATTATATTTA
Found at i:387340 original size:10 final size:10
Alignment explanation
Indices: 387313--387389 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 10
387303 TTATAATAAA
*
387313 TATAAAATTT
1 TATAATATTT
*
387323 AATAAATATTT
1 TAT-AATATTT
387334 TATAATAATTT
1 TATAAT-ATTT
*
387345 AATAA-ATTT
1 TATAATATTT
387354 TAATAAT-TATT
1 T-ATAATAT-TT
*
387365 TATAAAATTT
1 TATAATATTT
387375 TAATAATTATTT
1 T-ATAA-TATTT
387387 TAT
1 TAT
387390 TTGAATTTAT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
9 4 0.08
10 17 0.33
11 26 0.50
12 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TATAATATTT
Found at i:387365 original size:21 final size:21
Alignment explanation
Indices: 387319--387386 Score: 93
Period size: 21 Copynumber: 3.2 Consensus size: 21
387309 TAAATATAAA
* *
387319 ATTTAATAAATATTTTATAATA
1 ATTTAATAAAT-TTTAATAATT
387341 ATTTAATAAATTTTAATAATT
1 ATTTAATAAATTTTAATAATT
387362 ATTT-ATAAAATTTTAATAATT
1 ATTTAAT-AAATTTTAATAATT
387383 ATTT
1 ATTT
387387 TATTTGAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 2 0.05
21 30 0.70
22 11 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATAAATTTTAATAATT
Found at i:387367 original size:31 final size:32
Alignment explanation
Indices: 387314--387380 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
387304 TATAATAAAT
387314 ATAAAATTTAATAAATATTTTATAATAA-TTTA
1 ATAAAATTTAATAAATATTTTATAA-AATTTTA
* *
387346 ATAAATTTTAATAATTA-TTTATAAAATTTTA
1 ATAAAATTTAATAAATATTTTATAAAATTTTA
387377 ATAA
1 ATAA
387381 TTATTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 2 0.06
31 15 0.47
32 15 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (32 bp):
ATAAAATTTAATAAATATTTTATAAAATTTTA
Found at i:388267 original size:31 final size:31
Alignment explanation
Indices: 388199--388268 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
388189 TGATTGATGA
* ** *
388199 ACTAAAATCGAACAGATCAATAATGTTAGAG
1 ACTAAAATCGAACAAATCAATAAAATTAAAG
* **
388230 ATTAAAATCGAACAAATTGATAAAATTAAAG
1 ACTAAAATCGAACAAATCAATAAAATTAAAG
388261 ACTAAAAT
1 ACTAAAAT
388269 TAAACAGATC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.54, C:0.10, G:0.11, T:0.24
Consensus pattern (31 bp):
ACTAAAATCGAACAAATCAATAAAATTAAAG
Found at i:388340 original size:28 final size:29
Alignment explanation
Indices: 388292--388350 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 29
388282 AACGTATTGC
388292 ATTACTCTTTTTTTTTTATTGAAATTCAA
1 ATTACTCTTTTTTTTTTATTGAAATTCAA
388321 ATTACTC-TTTTTTTTTATTGAAATTCAA
1 ATTACTCTTTTTTTTTTATTGAAATTCAA
388349 AT
1 AT
388351 ATATCTAATC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 23 0.77
29 7 0.23
ACGTcount: A:0.29, C:0.10, G:0.03, T:0.58
Consensus pattern (29 bp):
ATTACTCTTTTTTTTTTATTGAAATTCAA
Found at i:391513 original size:18 final size:18
Alignment explanation
Indices: 391490--391526 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
391480 CGTTGGAATG
391490 TTTATGATA-GAATTAGAA
1 TTTATGA-AGGAATTAGAA
391508 TTTATGAAGGAATTAGAA
1 TTTATGAAGGAATTAGAA
391526 T
1 T
391527 CTGTCAGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 1 0.06
18 17 0.94
ACGTcount: A:0.43, C:0.00, G:0.19, T:0.38
Consensus pattern (18 bp):
TTTATGAAGGAATTAGAA
Found at i:392144 original size:37 final size:38
Alignment explanation
Indices: 392075--392147 Score: 130
Period size: 38 Copynumber: 1.9 Consensus size: 38
392065 AATCCGACCC
*
392075 GACCCGAATATCACACTTAAAAAAATCCGACCCGACTT
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGACTT
392113 GACCCGAATATCACACTT-AAAAAACCCGACCCGAC
1 GACCCGAATATCACACTTAAAAAAACCCGACCCGAC
392148 CCGAACAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
37 16 0.47
38 18 0.53
ACGTcount: A:0.40, C:0.34, G:0.11, T:0.15
Consensus pattern (38 bp):
GACCCGAATATCACACTTAAAAAAACCCGACCCGACTT
Found at i:400779 original size:71 final size:72
Alignment explanation
Indices: 400656--400793 Score: 217
Period size: 71 Copynumber: 1.9 Consensus size: 72
400646 TTTTAAGTTT
* * * *
400656 AATAATTAAAAAATATTTTTAAACATATTTTTTTATTTTAAATACTCGAAAATATAGTAATTTAG
1 AATAATTAAAAAATATATTTAAACATATTTTTTTATTTAAAAAACTCAAAAATATAGTAATTTAG
400721 TGAGCCC
66 TGAGCCC
400728 AATAATTAAAAAA-A-ATTTAAACATAATTTTTTTATTTAAAAAACTCAAAAATATAGTAATTTA
1 AATAATTAAAAAATATATTTAAACAT-ATTTTTTTATTTAAAAAACTCAAAAATATAGTAATTTA
400791 GTG
65 GTG
400794 GGCTCCATTT
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
70 9 0.15
71 39 0.64
72 13 0.21
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.40
Consensus pattern (72 bp):
AATAATTAAAAAATATATTTAAACATATTTTTTTATTTAAAAAACTCAAAAATATAGTAATTTAG
TGAGCCC
Found at i:411457 original size:31 final size:31
Alignment explanation
Indices: 411419--411487 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
411409 GTTTCAGAAT
* *
411419 TAACAAATTGGTCACTAGTATTATCGATTTG
1 TAACAAATTGGTCACCAATATTATCGATTTG
* * **
411450 TAACAAATTGTTCACCAATGTTATTTATTTG
1 TAACAAATTGGTCACCAATATTATCGATTTG
411481 TAACAAA
1 TAACAAA
411488 ATGATCATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (31 bp):
TAACAAATTGGTCACCAATATTATCGATTTG
Found at i:423085 original size:14 final size:14
Alignment explanation
Indices: 423063--423114 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
423053 GTATTAAAAA
423063 TAATAATTTTTAAAT
1 TAAT-ATTTTTAAAT
423078 TAATATTTTTAAAAT
1 TAATATTTTT-AAAT
* *
423093 TTA-ATTTTTAAAA
1 TAATATTTTTAAAT
423106 TAATATTTT
1 TAATATTTT
423115 CTTTAACCTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 5 0.16
14 17 0.53
15 10 0.31
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATATTTTTAAAT
Found at i:423242 original size:12 final size:12
Alignment explanation
Indices: 423225--423276 Score: 50
Period size: 12 Copynumber: 4.0 Consensus size: 12
423215 TCATCATTAA
423225 AAAATAATTTTT
1 AAAATAATTTTT
*
423237 AAAATATTACTTTCT
1 AAAATA--A-TTTTT
*
423252 AAATTTAATTTTT
1 AAA-ATAATTTTT
423265 AAAATAATTTTT
1 AAAATAATTTTT
423277 TCTTTAACAC
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 14 0.44
13 7 0.22
14 2 0.06
15 7 0.22
16 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (12 bp):
AAAATAATTTTT
Found at i:423269 original size:14 final size:15
Alignment explanation
Indices: 423229--423270 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
423219 CATTAAAAAA
423229 TAATTTTTAAAATAT
1 TAATTTTTAAAATAT
* *
423244 TACTTTCT-AAAT-T
1 TAATTTTTAAAATAT
423257 TAATTTTTAAAATA
1 TAATTTTTAAAATA
423271 ATTTTTTCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 4
0.72 0.14 0.14
Matches are distributed among these distances:
13 7 0.33
14 8 0.38
15 6 0.29
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (15 bp):
TAATTTTTAAAATAT
Found at i:423296 original size:163 final size:166
Alignment explanation
Indices: 422989--423296 Score: 430
Period size: 163 Copynumber: 1.9 Consensus size: 166
422979 TAAGGGGTAG
* * * *
422989 AGTGACTATTTAATCAAATGTTAAGAGTATTTTTTGAGATTATATATTATTTATCGAAATTTAAG
1 AGTGACTATATAATCAAATGTTAAGAGTATTTTATGAGATTATATATTATTTATAGAAATATAAG
* *
423054 TATTAAAAATAATAATTTTTAAATTAATATTTTTAAAATTTAATTTTTAAAATAATATTTTCTTT
66 TATTAAAAATAATAATTTTTAAAATAATATTTCTAAAATTTAATTTTTAAAATAATATTTTCTTT
*
423119 AACCTATGAAAATAGTGTATTTGTGTTTTGGGACAA
131 AACCTATAAAAATAGTGTATTTGTGTTTTGGGACAA
* * * *
423155 AGTGATTATATAATCAAATGTTAAGAGTATTTTATGAGATTATATCTT-TTTATATAAATATCA-
1 AGTGACTATATAATCAAATGTTAAGAGTATTTTATGAGATTATATATTATTTATAGAAATATAAG
* *
423218 TCATT-AAAA-AATAATTTTTAAAATATTACTTTCT-AAATTTAATTTTTAAAATAATTTTTTCT
66 T-ATTAAAAATAATAATTTTTAAAATAATA-TTTCTAAAATTTAATTTTTAAAATAATATTTTCT
423280 TTAACAC-ATAAAAATAG
129 TTAAC-CTATAAAAATAG
423297 AGCTTAATAC
Statistics
Matches: 126, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
163 58 0.46
164 10 0.08
165 14 0.11
166 44 0.35
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (166 bp):
AGTGACTATATAATCAAATGTTAAGAGTATTTTATGAGATTATATATTATTTATAGAAATATAAG
TATTAAAAATAATAATTTTTAAAATAATATTTCTAAAATTTAATTTTTAAAATAATATTTTCTTT
AACCTATAAAAATAGTGTATTTGTGTTTTGGGACAA
Found at i:427981 original size:2 final size:2
Alignment explanation
Indices: 427974--428001 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
427964 TTGATTTTTA
427974 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
428002 GTTTAATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:428373 original size:14 final size:14
Alignment explanation
Indices: 428350--428380 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
428340 GAGAGTTTGA
*
428350 TAAATTTATTTTTT
1 TAAATATATTTTTT
428364 TAAATATATTTTTT
1 TAAATATATTTTTT
428378 TAA
1 TAA
428381 TATTAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TAAATATATTTTTT
Found at i:434988 original size:22 final size:20
Alignment explanation
Indices: 434941--434989 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
434931 AATAATTAAA
* *
434941 AATAAAAAACAAGAAAAAAG
1 AATAAAAAACAAAAAAAAAC
434961 ATATAATAAAACAAAAGAAAAAC
1 A-ATAA-AAAACAAAA-AAAAAC
434984 AATAAA
1 AATAAA
434990 TATCGACGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
20 1 0.04
21 5 0.21
22 12 0.50
23 6 0.25
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (20 bp):
AATAAAAAACAAAAAAAAAC
Found at i:439864 original size:27 final size:26
Alignment explanation
Indices: 439804--439869 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
439794 CCCTTAAAAT
*
439804 TTAAATCCAAACTCTAAATTTTCAAA
1 TTAAATCCAAACTCTAAATTTCCAAA
*
439830 TTATATCCAAAACTCTAAA-TTCCAAA
1 TTAAATCC-AAACTCTAAATTTCCAAA
439856 TTACAATCCCAAAC
1 TTA-AAT-CCAAAC
439870 ACCCTCACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
26 16 0.47
27 16 0.47
28 2 0.06
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (26 bp):
TTAAATCCAAACTCTAAATTTCCAAA
Found at i:440057 original size:30 final size:30
Alignment explanation
Indices: 440018--440118 Score: 132
Period size: 30 Copynumber: 3.4 Consensus size: 30
440008 AAAGAATATT
* * *
440018 AAAATGTGTTGTCGTGCTGCCATTAAGAGA
1 AAAAGGTGTTGTCGTGCTGTCATTGAGAGA
440048 AAAAGGTGTTGTCGTGCTGTCATTGAGAGA
1 AAAAGGTGTTGTCGTGCTGTCATTGAGAGA
* * *
440078 ATAAGATGTTGTCGTGTTGTCATTGAGAGA
1 AAAAGGTGTTGTCGTGCTGTCATTGAGAGA
440108 AGAAA-GTGTTG
1 A-AAAGGTGTTG
440119 CCGTTGCGTG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 60 0.97
31 2 0.03
ACGTcount: A:0.29, C:0.09, G:0.31, T:0.32
Consensus pattern (30 bp):
AAAAGGTGTTGTCGTGCTGTCATTGAGAGA
Found at i:441174 original size:16 final size:16
Alignment explanation
Indices: 441119--441176 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
441109 TAAGATGCGA
441119 TCATTTGATCATTAGG
1 TCATTTGATCATTAGG
* *
441135 TAAATTGAT--TT-GG
1 TCATTTGATCATTAGG
**
441148 TCATTAAATCATTAGG
1 TCATTTGATCATTAGG
441164 TCATTTGATCATT
1 TCATTTGATCATT
441177 CAATTATTAA
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
13 7 0.23
14 2 0.06
15 2 0.06
16 20 0.65
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (16 bp):
TCATTTGATCATTAGG
Found at i:441175 original size:24 final size:24
Alignment explanation
Indices: 441142--441201 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
441132 AGGTAAATTG
*
441142 ATTTGGTCATTAAATCATTAGGTC
1 ATTTGGTCATTAAATCATTAAGTC
* * *
441166 ATTTGATCATTCAATTATTAAGTC
1 ATTTGGTCATTAAATCATTAAGTC
*
441190 ATTCGGTCATTA
1 ATTTGGTCATTA
441202 GGTCATCCGA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.43
Consensus pattern (24 bp):
ATTTGGTCATTAAATCATTAAGTC
Found at i:441218 original size:24 final size:24
Alignment explanation
Indices: 441188--441278 Score: 87
Period size: 24 Copynumber: 3.8 Consensus size: 24
441178 AATTATTAAG
*
441188 TCATTCGGTCATTAGGTCATCCGA
1 TCATTCGATCATTAGGTCATCCGA
* * * *
441212 TCGTTCGATCGTTCGGTCATTCGA
1 TCATTCGATCATTAGGTCATCCGA
* *
441236 TCATTC-AGTCATTAGATCATGCGA
1 TCATTCGA-TCATTAGGTCATCCGA
*
441260 TTATT-GATCATTAGGTCAT
1 TCATTCGATCATTAGGTCAT
441279 TACATCACTA
Statistics
Matches: 53, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
23 12 0.23
24 41 0.77
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (24 bp):
TCATTCGATCATTAGGTCATCCGA
Found at i:441239 original size:8 final size:8
Alignment explanation
Indices: 441188--441271 Score: 55
Period size: 8 Copynumber: 10.6 Consensus size: 8
441178 AATTATTAAG
*
441188 TCATTCGG
1 TCATTCGA
* *
441196 TCATTAGG
1 TCATTCGA
*
441204 TCATCCGA
1 TCATTCGA
*
441212 TCGTTCGA
1 TCATTCGA
* *
441220 TCGTTCGG
1 TCATTCGA
441228 TCATTCGA
1 TCATTCGA
441236 TCATTC-A
1 TCATTCGA
*
441243 GTCATTAGA
1 -TCATTCGA
*
441252 TCATGCGA
1 TCATTCGA
*
441260 TTATT-GA
1 TCATTCGA
441267 TCATT
1 TCATT
441272 AGGTCATTAC
Statistics
Matches: 59, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
7 7 0.12
8 51 0.86
9 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (8 bp):
TCATTCGA
Found at i:442891 original size:29 final size:29
Alignment explanation
Indices: 442849--442937 Score: 124
Period size: 29 Copynumber: 3.1 Consensus size: 29
442839 TACCGGGGGT
*
442849 AGGTCGCCATGCACGCCCGGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
***
442878 AGGTCGCCATGCACGCCCAGCGACCTGGT
1 AGGTCGCCATGCACGCCCAGCGACCTACC
* *
442907 AGGTCGCCATGCATGCCCTGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
442936 AG
1 AG
442938 CCAACGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.18, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:443249 original size:28 final size:27
Alignment explanation
Indices: 443216--443271 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
443206 CATGCATGAA
443216 TCCTTGGTCGCCCCGAGTGCAT-GCGACC
1 TCCTTGGTCG--CCGAGTGCATGGCGACC
*
443244 TCCTTGGTCGCCGGGTGCATGGCGACC
1 TCCTTGGTCGCCGAGTGCATGGCGACC
443271 T
1 T
443272 AGGAGGTCGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 9 0.35
27 7 0.27
28 10 0.38
ACGTcount: A:0.09, C:0.36, G:0.32, T:0.23
Consensus pattern (27 bp):
TCCTTGGTCGCCGAGTGCATGGCGACC
Found at i:450729 original size:20 final size:20
Alignment explanation
Indices: 450701--450742 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
450691 AGGTTGTTGT
*
450701 CAGAAGGGTATAAGCGGTTA
1 CAGAAGGGTATAAGCGGGTA
* *
450721 CAGACGGGTATGAGCGGGTA
1 CAGAAGGGTATAAGCGGGTA
450741 CA
1 CA
450743 TGCATATATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.14, G:0.38, T:0.17
Consensus pattern (20 bp):
CAGAAGGGTATAAGCGGGTA
Found at i:464738 original size:53 final size:53
Alignment explanation
Indices: 464658--464770 Score: 217
Period size: 53 Copynumber: 2.1 Consensus size: 53
464648 GAAAAAAAAT
464658 GCTTTGGGATGTTTGTATAAACTGCGTTTGTGTTCATGTCCTGATGGTGTATG
1 GCTTTGGGATGTTTGTATAAACTGCGTTTGTGTTCATGTCCTGATGGTGTATG
464711 GCTTTGGGATGTTTGTATAAACTGCGTTTGTGTTCATGTCCTGATGGTGTATG
1 GCTTTGGGATGTTTGTATAAACTGCGTTTGTGTTCATGTCCTGATGGTGTATG
*
464764 GATTTGG
1 GCTTTGG
464771 TCAGGTCTTC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 59 1.00
ACGTcount: A:0.15, C:0.11, G:0.31, T:0.43
Consensus pattern (53 bp):
GCTTTGGGATGTTTGTATAAACTGCGTTTGTGTTCATGTCCTGATGGTGTATG
Found at i:469699 original size:15 final size:15
Alignment explanation
Indices: 469669--469706 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
469659 GACGTAAATA
469669 TAATT-CTAATTTAT
1 TAATTACTAATTTAT
469683 TAATCTACTAA-TTAT
1 TAAT-TACTAATTTAT
469698 TAATTACTA
1 TAATTACTA
469707 TAAAATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 9 0.41
16 4 0.18
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTACTAATTTAT
Found at i:470153 original size:29 final size:29
Alignment explanation
Indices: 470120--470175 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
470110 ACGACCTCAT
**
470120 TCTATATTGGTCCATAAACTTTTGAATTC
1 TCTATATTCATCCATAAACTTTTGAATTC
* *
470149 TCTATTTTCATCCCTAAACTTTTGAAT
1 TCTATATTCATCCATAAACTTTTGAAT
470176 GATTAAGGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (29 bp):
TCTATATTCATCCATAAACTTTTGAATTC
Found at i:470159 original size:59 final size:60
Alignment explanation
Indices: 469982--470168 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 60
469972 CATCATACAT
* * ** * * **
469982 CCCAAACTAAGATCATCATTCTAAA-TTACTCTTTAAACGTTTGAACATTTTAATTTCATC
1 CCCAAACTACGATCATCATTCTAAACTT-GTCCATAAACTTTTGAATATTCCAATTTCATC
* * * * *
470042 CCCAAATTATGATCATCATTCTAAACTTGTCCTTAAAGTTTTGAATATTCCAAATTCATC
1 CCCAAACTACGATCATCATTCTAAACTTGTCCATAAACTTTTGAATATTCCAATTTCATC
* * * *
470102 CCCAAACTACGA-CCTCATTCTATA-TTGGTCCATAAACTTTTGAAT-TCTCTATTTTCATC
1 CCCAAACTACGATCATCATTCTAAACTT-GTCCATAAACTTTTGAATAT-TCCAATTTCATC
*
470161 CCTAAACT
1 CCCAAACT
470169 TTTGAATGAT
Statistics
Matches: 104, Mismatches: 20, Indels: 7
0.79 0.15 0.05
Matches are distributed among these distances:
58 3 0.03
59 42 0.40
60 57 0.55
61 2 0.02
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (60 bp):
CCCAAACTACGATCATCATTCTAAACTTGTCCATAAACTTTTGAATATTCCAATTTCATC
Found at i:470295 original size:60 final size:60
Alignment explanation
Indices: 470192--470344 Score: 209
Period size: 60 Copynumber: 2.5 Consensus size: 60
470182 GGGGGATGTT
* * *
470192 ATTGGAATGCTCAAAAGTTTAGGGACCAATTTAGAACGAGAGTCATAGTTTGAGTATGAA
1 ATTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAACGAGAGTCATAATTTGAGGATGAA
* * * *
470252 ATTGAAATGTTCAAAAGTTTAGGGACCAATTTAGAATGTGAGTCATAATTTGAGGATGAT
1 ATTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAACGAGAGTCATAATTTGAGGATGAA
* *
470312 ATTGGAATGTTTAGAAA-TTTAGGGATCAATTTA
1 ATTGGAATGTTCA-AAAGTTTAGGGACCAATTTA
470345 TAGTAGGAGT
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
60 79 0.96
61 3 0.04
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.33
Consensus pattern (60 bp):
ATTGGAATGTTCAAAAGTTTAGGGACCAATTTAGAACGAGAGTCATAATTTGAGGATGAA
Found at i:470364 original size:60 final size:60
Alignment explanation
Indices: 470192--470369 Score: 207
Period size: 60 Copynumber: 3.0 Consensus size: 60
470182 GGGGGATGTT
* * * * *
470192 ATTGGAATGCTCAAAAGTTTAGGGACCAATTTAGAACGAGAGTCATAGTTTGAGTATGAA
1 ATTGAAATGTTCAAAAGTTTAGGGACCAATTTAGAATGTGAGTCATAGTTTGAGGATGAA
* *
470252 ATTGAAATGTTCAAAAGTTTAGGGACCAATTTAGAATGTGAGTCATAATTTGAGGATGAT
1 ATTGAAATGTTCAAAAGTTTAGGGACCAATTTAGAATGTGAGTCATAGTTTGAGGATGAA
* * * * * *
470312 ATTGGAATGTTTAGAAA-TTTAGGGATCAATTTATAGTAG-GAGTTATAGTTTGAGGATG
1 ATTGAAATGTTCA-AAAGTTTAGGGACCAATTTAGAAT-GTGAGTCATAGTTTGAGGATG
470370 TATGATACAA
Statistics
Matches: 102, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
60 98 0.96
61 4 0.04
ACGTcount: A:0.35, C:0.06, G:0.25, T:0.33
Consensus pattern (60 bp):
ATTGAAATGTTCAAAAGTTTAGGGACCAATTTAGAATGTGAGTCATAGTTTGAGGATGAA
Found at i:475602 original size:9 final size:9
Alignment explanation
Indices: 475588--475617 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
475578 TAAAAGGGAA
475588 AAATAAAAT
1 AAATAAAAT
475597 AAATAAAAT
1 AAATAAAAT
*
475606 AAATAAGAT
1 AAATAAAAT
475615 AAA
1 AAA
475618 GGAAAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (9 bp):
AAATAAAAT
Found at i:475627 original size:18 final size:17
Alignment explanation
Indices: 475586--475628 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
475576 GGTAAAAGGG
*
475586 AAAAATAAAATAAATAA
1 AAAAATAAAATAAAGAA
*
475603 AATAAATAAGATAAAGGAA
1 AA-AAATAAAATAAA-GAA
475622 AAAAATA
1 AAAAATA
475629 GTAAAGTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 2 0.09
18 16 0.73
19 4 0.18
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (17 bp):
AAAAATAAAATAAAGAA
Found at i:476127 original size:18 final size:17
Alignment explanation
Indices: 476106--476148 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
476096 ATATATACAT
476106 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
476124 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
476141 ATAA-AATA
1 ATAATAATA
476149 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Done.