Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007853.1 Hibiscus syriacus cultivar Beakdansim tig00110213_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: 2309479
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:300815 original size:16 final size:16
Alignment explanation
Indices: 300794--300825 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
300784 GATACACTTG
300794 GTCTCCTAGCAGATTA
1 GTCTCCTAGCAGATTA
300810 GTCTCCTAGCAGATTA
1 GTCTCCTAGCAGATTA
300826 AGTGCATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (16 bp):
GTCTCCTAGCAGATTA
Found at i:305054 original size:13 final size:13
Alignment explanation
Indices: 305036--305061 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
305026 CGTACTCCGC
305036 CGCCGGCCACCGT
1 CGCCGGCCACCGT
305049 CGCCGGCCACCGT
1 CGCCGGCCACCGT
305062 AAACGGTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:305775 original size:3 final size:3
Alignment explanation
Indices: 305769--305811 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
305759 AATAATTATT
* *
305769 TAA TAA TAA T-A TAA TAA TAA TATA TAA TAA TAT TTA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA T
305812 TTTAATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:305786 original size:22 final size:23
Alignment explanation
Indices: 305758--305812 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
305748 TTTGGGTTTG
*
305758 TAATAATTATTTAATAATA-ATA
1 TAATAATTATATAATAATATATA
*
305780 TAATAATAATATATAATAATATTTA
1 TAATAAT--TATATAATAATATATA
305805 TAATAATT
1 TAATAATT
305813 TTAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 7 0.25
23 1 0.04
24 11 0.39
25 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TAATAATTATATAATAATATATA
Found at i:305817 original size:21 final size:21
Alignment explanation
Indices: 305760--305811 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
305750 TGGGTTTGTA
* *
305760 ATAATTATTTAATAATAATAT
1 ATAATAATATAATAATAATAT
305781 AATAATAATAT-ATAATAATATTT
1 -ATAATAATATAATAATAATA--T
305804 ATAATAAT
1 ATAATAAT
305812 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 9 0.35
22 16 0.62
23 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATAATATAATAATAATAT
Found at i:306118 original size:76 final size:76
Alignment explanation
Indices: 305992--307010 Score: 1869
Period size: 76 Copynumber: 13.4 Consensus size: 76
305982 GAGGTCTTAA
* * *
305992 AAACATCATGCACTGCAGGATTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306057 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
306068 AAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306133 AGGCTTTTTGG
66 AGGCTTTTTGG
306144 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306209 AGGCTTTTTGG
66 AGGCTTTTTGG
*
306220 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306285 AGGCTTTTTGG
66 AGGCTTTTTGG
306296 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306360 AGGCTTTTTGG
66 AGGCTTTTTGG
*
306371 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306436 AGGCTTTTTGG
66 AGGCTTTTTGG
306447 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306512 AGGCTTTTTGG
66 AGGCTTTTTGG
306523 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
306588 AGGTTTTTTGG
66 AGGCTTTTTGG
*
306599 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306664 AGGCTTTTTGG
66 AGGCTTTTTGG
*
306675 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCC
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC--TTTGAAAACATCAAAAAGCTCCC
306740 GAAGGCTTTTTGG
64 GAAGGCTTTTTGG
*
306753 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306818 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
306829 AAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306894 AGGCTTTTTGG
66 AGGCTTTTTGG
*
306905 AAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
306970 AGGCTTTTTGG
66 AGGCTTTTTGG
*
306981 AAACATCATGCACTGAAGGGCTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
307011 TGAGAAATAG
Statistics
Matches: 916, Mismatches: 24, Indels: 6
0.97 0.03 0.01
Matches are distributed among these distances:
75 74 0.08
76 768 0.84
78 74 0.08
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:306691 original size:379 final size:381
Alignment explanation
Indices: 305992--307010 Score: 1889
Period size: 379 Copynumber: 2.7 Consensus size: 381
305982 GAGGTCTTAA
* * * *
305992 AAACATCATGCACTGCAGGATTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
*
306057 AGGCTTTTTGGAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
306122 AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
306187 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
306252 CCGAAGGCTTTGAAAACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
261 CCGAAGGCTTTGAAAACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
306317 TTACAGATGACCCGAAGGC-TTTGAAAACATC-AAAAGCTCCCGAAGGCTTTTTGG
326 TTACAGATGACCCGAAGGCTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
306371 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
*
306436 AGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
*
306501 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
131 AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
*
306566 GAAAACATCAAAAAGCTCCCGAAGGTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
*
306631 CCGAAGGCTTTGAAAACATCAAAAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
261 CCGAAGGCTTTGAAAACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
*
306696 TTACAGATGACCCGAAGGCTTTTTGGAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
326 TTACAGATGACCCGAAGGC-TTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
306753 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTTCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
306818 AGGCTTTTTGGAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
* *
306883 AAAGCTTCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTT
131 AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
*
306948 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATG
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
307011 TGAGAAATAG
Statistics
Matches: 621, Mismatches: 16, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
379 335 0.54
381 11 0.02
382 275 0.44
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (381 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTACCGA
AGGCTTTTTGGAAACATCATGCACTAAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAA
AAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGAC
CCGAAGGCTTTGAAAACATCAAAAAGCTACCGAAGGCTTTTTGGAAACATCATGCACTGAAGGAC
TTACAGATGACCCGAAGGCTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:307695 original size:22 final size:22
Alignment explanation
Indices: 307670--307724 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
307660 CATAAAGCTT
*
307670 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
307692 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
307714 TCATCTTTGAA
1 TCATCTTTGAA
307725 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:310536 original size:83 final size:83
Alignment explanation
Indices: 310397--310742 Score: 647
Period size: 83 Copynumber: 4.2 Consensus size: 83
310387 TTTATTTCTC
*
310397 CTATGAGCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
310462 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
310480 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
310545 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
310563 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATGACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
310628 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
310646 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTCTAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
310711 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
310729 CTATTGAGCACATT
1 CTA-TGAGCACATT
310743 ACATTTGTTC
Statistics
Matches: 258, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 248 0.96
84 10 0.04
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCTAAATTCAATGATTGGTTCTGTATAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:316824 original size:14 final size:16
Alignment explanation
Indices: 316796--316832 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
316786 CTGAATAAAA
316796 AAAAATATATTAAT-AT
1 AAAAATATA-TAATAAT
316812 AAAAATATA-AATAAT
1 AAAAATATATAATAAT
316827 AAAAAT
1 AAAAAT
316833 TTGAAAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 8 0.40
16 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAAATATATAATAAT
Found at i:318291 original size:13 final size:13
Alignment explanation
Indices: 318273--318298 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
318263 CGTACTCCGC
318273 CGCCGGCCACCGT
1 CGCCGGCCACCGT
318286 CGCCGGCCACCGT
1 CGCCGGCCACCGT
318299 AAACGGTGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.54, G:0.31, T:0.08
Consensus pattern (13 bp):
CGCCGGCCACCGT
Found at i:319013 original size:11 final size:11
Alignment explanation
Indices: 319010--319054 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
319000 TAATTATTTA
319010 ATAATAAT-AT
1 ATAATAATAAT
319020 AATAATAATAAT
1 -ATAATAATAAT
319032 ATAATAATAAT
1 ATAATAATAAT
*
319043 ATTTATAATAAT
1 A-TAATAATAAT
319055 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 20 0.65
12 11 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:319014 original size:3 final size:3
Alignment explanation
Indices: 319008--319054 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
318998 AATAATTATT
* *
319008 TAA TAA TAA T-A TAA TAA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
319054 T
1 T
319055 TTTAATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:319081 original size:21 final size:22
Alignment explanation
Indices: 319027--319083 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
319017 TATAATAATA
**
319027 ATAAT-ATAATAATAAT-ATTT
1 ATAATAATAATAATTTTAATTT
**
319047 ATAATAATTTTAATTTTAATTT
1 ATAATAATAATAATTTTAATTT
319069 -TAATAATAATAATTT
1 ATAATAATAATAATTT
319084 AAGTAAAATG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 5 0.17
21 20 0.69
22 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATAATAATAATTTTAATTT
Found at i:327942 original size:106 final size:106
Alignment explanation
Indices: 327754--328125 Score: 602
Period size: 106 Copynumber: 3.5 Consensus size: 106
327744 ACTAATTCAA
* *
327754 TAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATCAGCATAT
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
*
327819 AATATTCCAATCGGTAAACAGCAGCTAATTTTAAATATTAT
66 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
* *
327860 TAGAAACTCAAAATTTACTATCGGAAAGCCAGATAATCAATGAAAATTAACAATCATCAGCTTAT
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
327925 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
66 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
* * *
327966 TAGAAATTCAGAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACATTCATCAGCTTAT
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
328031 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
66 AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
* ** * * * *
328072 TAGAAACTCATAATTTAAAAT-AGAAAACTAAATAATCAATTAAATTTAACAATC
1 TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATC
328126 CTAAGACCAA
Statistics
Matches: 247, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
105 28 0.11
106 219 0.89
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.29
Consensus pattern (106 bp):
TAGAAACTCAAAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACAATCATCAGCTTAT
AATATTCCAATCAGTAAACAGCAGCTAATTTTAAATATTAT
Found at i:328146 original size:212 final size:218
Alignment explanation
Indices: 327619--328154 Score: 622
Period size: 212 Copynumber: 2.5 Consensus size: 218
327609 TTAAAAACTA
* * * * * * * * *
327619 CAGCTAACTTTAAACATTACTAGAAACTCGACA-TTAACAATTAAAAAACCAACTAATCTATGAA
1 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAA-AATCAGAAAACCAAATAATCAATGAA
* * ** *
327683 AATTAACACTCCTCGGAACAA-AAATATTCCAATCAGTAAACAACAGCTAATATTTAGCATTACT
65 AATTAACAATCATAAG-CCAATAAA-ATTCCAATCAGTAAACAACAGCTAATATTTA-CA-TACT
327747 AATTCAATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATC
126 AATTCAATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATC
*
327812 AGCATATAATATTCCAATCGGTAAACAG
191 AGCATATAATATTCCAATCAGTAAACAG
** * * *
327840 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTACTATCGGAAAGCCAGATAATCAATGAAA
1 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAAAATCAGAAAACCAAATAATCAATGAAA
* ** * *
327905 ATTAACAATCATCAGCTTATAATATTCCAATCAGTAAACAGCAGCTAAT-TTTA-A-A-T-ATT-
66 ATTAACAATCATAAGCCAATAAAATTCCAATCAGTAAACAACAGCTAATATTTACATACTAATTC
* * * * * *
327964 ATTAGAAATTCAGAATTTACTATCAGAAAGCCAAATAATCAATGAAAATTAACATTCATCAGCTT
131 AATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATCAGCAT
328029 ATAATATTCCAATCAGTAAACAG
196 ATAATATTCCAATCAGTAAACAG
* * *
328052 CAGCTAATTTTAAATATTATTAGAAACTCATAATTTAAAAT-AGAAAACTAAATAATCAATTAAA
1 CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAAAATCAGAAAACCAAATAATCAATGAAA
* * *
328116 TTTAACAATCCTAAGACCAATAAAATTCCAACCAGTAAA
66 ATTAACAATCATAAG-CCAATAAAATTCCAATCAGTAAA
328155 TTAAAAATAA
Statistics
Matches: 268, Mismatches: 44, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
211 30 0.11
212 138 0.51
213 3 0.01
214 1 0.00
215 1 0.00
217 1 0.00
219 4 0.01
220 26 0.10
221 61 0.23
222 3 0.01
ACGTcount: A:0.47, C:0.17, G:0.08, T:0.28
Consensus pattern (218 bp):
CAGCTAATTTTAAATATTATTAGAAACTCAAAATTTAAAATCAGAAAACCAAATAATCAATGAAA
ATTAACAATCATAAGCCAATAAAATTCCAATCAGTAAACAACAGCTAATATTTACATACTAATTC
AATAGAAACTCAAAATTTACTATCAGAAAGCCAAAGAATCAATGAAAATTAACAATCATCAGCAT
ATAATATTCCAATCAGTAAACAG
Found at i:328743 original size:14 final size:15
Alignment explanation
Indices: 328706--328743 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
328696 AAAGATTTTA
*
328706 TAAATTAATACTTAC
1 TAAATTAATACCTAC
328721 TAAATTAATACCT-C
1 TAAATTAATACCTAC
*
328735 TAAAATAAT
1 TAAATTAAT
328744 GATTTTTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.50, C:0.13, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAATTAATACCTAC
Found at i:335661 original size:2 final size:2
Alignment explanation
Indices: 335654--335678 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
335644 AGTATTTTAA
335654 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
335679 AAGTAAAACT
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:341301 original size:2 final size:2
Alignment explanation
Indices: 341294--341329 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
341284 CCGATTAGTT
341294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
341330 ATAGATTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:346314 original size:7 final size:7
Alignment explanation
Indices: 346302--346335 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
346292 ATACTACATC
346302 ACTTGGG
1 ACTTGGG
346309 ACTTGGG
1 ACTTGGG
*
346316 ATTTGGG
1 ACTTGGG
*
346323 ATTTGGG
1 ACTTGGG
346330 ACTTGG
1 ACTTGG
346336 TCAGTGAAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.09, G:0.41, T:0.35
Consensus pattern (7 bp):
ACTTGGG
Found at i:351898 original size:51 final size:51
Alignment explanation
Indices: 351809--351944 Score: 182
Period size: 51 Copynumber: 2.7 Consensus size: 51
351799 CTGCACCGTT
* * * * *
351809 CTCACCATTACTACTTGAACCAGCACTCAAGGAGGGACCAACAGCAGCATG
1 CTCATCATTACTACTCGAACTAGCACTCGAGGAAGGACCAACAGCAGCATG
**
351860 CTCATCATTACTACTCGAACTAGCACTCGAGGAAGGACCAGTAGCAGCATG
1 CTCATCATTACTACTCGAACTAGCACTCGAGGAAGGACCAACAGCAGCATG
* * *
351911 CTCATCATTACTACTCTAACTAGGACTTGAGGAA
1 CTCATCATTACTACTCGAACTAGCACTCGAGGAA
351945 TTATTCCTGT
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (51 bp):
CTCATCATTACTACTCGAACTAGCACTCGAGGAAGGACCAACAGCAGCATG
Found at i:365072 original size:28 final size:28
Alignment explanation
Indices: 365038--365123 Score: 82
Period size: 31 Copynumber: 2.9 Consensus size: 28
365028 TTTAGGGATA
*
365038 AAATTAGAATGTTCAAAGTTTGATGACT
1 AAATTAGAATGTTCAAAGTTTGAGGACT
* *
365066 AATTTAGAATGAGATTCATAGTTTGAGGACT
1 AAATTAGAAT--G-TTCAAAGTTTGAGGACT
* * *
365097 AAATTAAAATCTTCAAGAGTTTAAGGA
1 AAATTAGAATGTTCAA-AGTTTGAGGA
365124 TCAATTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
28 13 0.28
29 9 0.20
30 1 0.02
31 23 0.50
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (28 bp):
AAATTAGAATGTTCAAAGTTTGAGGACT
Found at i:370269 original size:16 final size:16
Alignment explanation
Indices: 370248--370284 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
370238 GTCTCCAACG
370248 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
370264 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
370280 TTTAT
1 TTTAT
370285 TTATTAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.59
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:372277 original size:22 final size:22
Alignment explanation
Indices: 372252--372293 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
372242 TTGTGTCAAT
372252 GAAGAAAAGCCCATTGTTCTGA
1 GAAGAAAAGCCCATTGTTCTGA
372274 GAAGAAAAGCCCATTGTTCT
1 GAAGAAAAGCCCATTGTTCT
372294 CCACCACAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (22 bp):
GAAGAAAAGCCCATTGTTCTGA
Found at i:400526 original size:45 final size:45
Alignment explanation
Indices: 400469--400555 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
400459 TTTGATAGAG
*
400469 TGTTACTGAAAATATTAT-TTTTTAACTGAAAATATTAATATCCGA
1 TGTTACTGAAAATATTATATTTTTAACAG-AAATATTAATATCCGA
* * *
400514 TGTTATCT-AAAATGTTATATTTTTATCAGAAATGTTAATATC
1 TGTTA-CTGAAAATATTATATTTTTAACAGAAATATTAATATC
400556 GAAAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 26 0.72
46 10 0.28
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (45 bp):
TGTTACTGAAAATATTATATTTTTAACAGAAATATTAATATCCGA
Found at i:400603 original size:21 final size:20
Alignment explanation
Indices: 400565--400612 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
400555 CGAAAATATT
* *
400565 TATTTTAGGTAATGAAATTAA
1 TATTTTAGGTAA-AAAAATAA
*
400586 TATTTTCGGTAAAAAAATAA
1 TATTTTAGGTAAAAAAATAA
*
400606 CATTTTA
1 TATTTTA
400613 ATAACATTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.44, C:0.04, G:0.10, T:0.42
Consensus pattern (20 bp):
TATTTTAGGTAAAAAAATAA
Found at i:402895 original size:15 final size:15
Alignment explanation
Indices: 402864--402913 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
402854 AGTTTTCATC
* *
402864 TAATAAAAAATATAT
1 TAATAAAAATTAAAT
402879 TAATAAAAATTAAAT
1 TAATAAAAATTAAAT
* *
402894 TATTATAAAATTAAAA
1 TAATA-AAAATTAAAT
402910 TAAT
1 TAAT
402914 TATTCAATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATAAAAATTAAAT
Found at i:402910 original size:17 final size:18
Alignment explanation
Indices: 402870--402916 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
402860 CATCTAATAA
402870 AAAATATATTAATAAAAATT
1 AAAAT-TATT-ATAAAAATT
402890 -AAATTATTAT-AAAATT
1 AAAATTATTATAAAAATT
*
402906 AAAATAATTAT
1 AAAATTATTAT
402917 TCAATTAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 6 0.24
17 11 0.44
18 4 0.16
19 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAATTATTATAAAAATT
Found at i:403678 original size:36 final size:35
Alignment explanation
Indices: 403637--403761 Score: 162
Period size: 36 Copynumber: 3.5 Consensus size: 35
403627 GATTATATGT
*
403637 TTAATAAATTATTTATTGATTTGAAAATTTTATATA
1 TTAATAAA-AATTTATTGATTTGAAAATTTTATATA
403673 TTAATAAACAATTTATTGATTTGAAAATTTTATATA
1 TTAATAAA-AATTTATTGATTTGAAAATTTTATATA
*
403709 TTATTAAACAGA-TTATTGATTTGAAAATTTTATATA
1 TTAATAAA-A-ATTTATTGATTTGAAAATTTTATATA
* *
403745 TTATTAAACAATGTATT
1 TTAATAAA-AATTTATT
403762 TTATCAATTT
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
35 1 0.01
36 81 0.98
37 1 0.01
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (35 bp):
TTAATAAAAATTTATTGATTTGAAAATTTTATATA
Found at i:403910 original size:32 final size:33
Alignment explanation
Indices: 403846--403952 Score: 92
Period size: 35 Copynumber: 3.1 Consensus size: 33
403836 TTATTTATTG
**
403846 ATAATTTCTTATATTTATATCAAATTTTAAAATAAT
1 ATAATTTCTTATA-TTATA--AAATTAAAAAATAAT
403882 AT-ATTTCTTATATTATAAAATTAAAAAATTAAAT
1 ATAATTTCTTATATTATAAAATTAAAAAA-T-AAT
* *
403916 ATAACTTTACTGTATATTTTAACA-TAAAAAATAAT
1 ATAA-TTT-CT-TATATTATAAAATTAAAAAATAAT
403951 AT
1 AT
403953 CTAAAATGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
32 9 0.15
33 1 0.02
34 10 0.16
35 16 0.26
36 6 0.10
37 9 0.15
38 10 0.16
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.45
Consensus pattern (33 bp):
ATAATTTCTTATATTATAAAATTAAAAAATAAT
Found at i:406220 original size:2 final size:2
Alignment explanation
Indices: 406213--406246 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
406203 TAACTTATTC
406213 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
406247 GTAGTATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:406312 original size:15 final size:15
Alignment explanation
Indices: 406294--406324 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
406284 GAATTGAGTA
*
406294 CTGCATAAGTGAGAG
1 CTGCAGAAGTGAGAG
406309 CTGCAGAAGTGAGAG
1 CTGCAGAAGTGAGAG
406324 C
1 C
406325 GACCCTCCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.16
Consensus pattern (15 bp):
CTGCAGAAGTGAGAG
Found at i:407543 original size:3 final size:3
Alignment explanation
Indices: 407535--407594 Score: 77
Period size: 3 Copynumber: 20.3 Consensus size: 3
407525 TGTTGAGATG
* * * *
407535 ATA ATA ATA ATA ATA ATA ATA ACA ACA A-A ATT ATA ATA ATA ATG ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
407582 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
407595 AGAATAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
2 2 0.04
3 49 0.96
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:419767 original size:11 final size:11
Alignment explanation
Indices: 419751--419795 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
419741 AAACCCAAAG
*
419751 TATTATTTTAT
1 TATTATTATAT
419762 TATTATTATAT
1 TATTATTATAT
419773 TATTA-TATAT
1 TATTATTATAT
419783 TA-TATATATAT
1 TATTAT-TATAT
419794 TA
1 TA
419796 GATATATATA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 2 0.06
10 7 0.23
11 22 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTATAT
Found at i:419788 original size:2 final size:2
Alignment explanation
Indices: 419768--419841 Score: 97
Period size: 2 Copynumber: 40.0 Consensus size: 2
419758 TTATTATTAT
*
419768 TA TA T- TA T- TA TA TA T- TA TA TA TA TA T- TA GA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
419806 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
419842 GATCCTGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
1 6 0.09
2 58 0.91
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:419839 original size:11 final size:11
Alignment explanation
Indices: 419759--419841 Score: 104
Period size: 11 Copynumber: 7.8 Consensus size: 11
419749 AGTATTATTT
419759 TATTAT-TATTA
1 TATTATATA-TA
419770 TATTAT-TATA
1 TATTATATATA
419780 TATTATATATA
1 TATTATATATA
*
419791 TATTAGATATA
1 TATTATATATA
419802 TA-TATATA-A
1 TATTATATATA
419811 TA-TATATATA
1 TATTATATATA
419821 TATATATATATA
1 TAT-TATATATA
419833 TATTATATA
1 TATTATATA
419842 GATCCTGAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
9 9 0.14
10 16 0.24
11 30 0.45
12 11 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (11 bp):
TATTATATATA
Found at i:419841 original size:15 final size:14
Alignment explanation
Indices: 419768--419841 Score: 97
Period size: 13 Copynumber: 5.7 Consensus size: 14
419758 TTATTATTAT
419768 TATAT-TAT-TATA
1 TATATATATATATA
419780 TAT-TATATATATA
1 TATATATATATATA
*
419793 T-TAGATATATATA
1 TATATATATATATA
419806 TATA-ATATATATA
1 TATATATATATATA
419819 TATATATATATATA
1 TATATATATATATA
419833 TAT-TATATA
1 TATATATATA
419842 GATCCTGAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 9
0.85 0.02 0.14
Matches are distributed among these distances:
11 1 0.02
12 7 0.12
13 34 0.61
14 14 0.25
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (14 bp):
TATATATATATATA
Found at i:420405 original size:16 final size:17
Alignment explanation
Indices: 420374--420406 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
420364 AAGAAAATTC
420374 TTAATATATATTATTTT
1 TTAATATATATTATTTT
*
420391 TTAAT-TATCTTATTTT
1 TTAATATATATTATTTT
420407 ATTAGATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (17 bp):
TTAATATATATTATTTT
Found at i:421746 original size:13 final size:13
Alignment explanation
Indices: 421728--421753 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
421718 ATAGAAAAAA
421728 ATATATATATTAT
1 ATATATATATTAT
421741 ATATATATATTAT
1 ATATATATATTAT
421754 CGAAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATATATATATTAT
Found at i:424096 original size:29 final size:29
Alignment explanation
Indices: 424023--424096 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 29
424013 TAAATGGTAA
424023 AAAACAGAAACTTTAAAAGGCTAAAAGAGCT
1 AAAACAGAAAC-TT-AAAGGCTAAAAGAGCT
* *
424054 AAAACAG-AATTTAAAGGAC-ATAAATAGC-
1 AAAACAGAAACTTAAAGG-CTA-AAAGAGCT
424082 AAAACAGAAACTTAA
1 AAAACAGAAACTTAA
424097 GTGACTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 13 0.35
29 15 0.41
30 2 0.05
31 7 0.19
ACGTcount: A:0.58, C:0.12, G:0.14, T:0.16
Consensus pattern (29 bp):
AAAACAGAAACTTAAAGGCTAAAAGAGCT
Found at i:425867 original size:2 final size:2
Alignment explanation
Indices: 425860--425905 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
425850 ATTTGACTTT
425860 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
425900 TA TA TA
1 TA TA TA
425906 ATCTAATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:427389 original size:129 final size:129
Alignment explanation
Indices: 427236--427493 Score: 482
Period size: 129 Copynumber: 2.0 Consensus size: 129
427226 ATACAGTTGC
*
427236 TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAGTCGAATAAGTTTG
1 TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTTG
*
427301 AATTCATCTTACGTTATATTTGTTTTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
66 AATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
427365 TCAAATTCAAAAATTTT-AGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTT
1 TCAAATTC-AAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTT
427429 GAATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
65 GAATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
427494 AAACAAAAGA
Statistics
Matches: 126, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
129 118 0.94
130 8 0.06
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (129 bp):
TCAAATTCAAAATTTTCAGAAAGAATAACATTTACTTTTACTATTAAATTAATCGAATAAGTTTG
AATTCATCTTACGTTATATTTGTATTAAATGTCGGTACATATGATTCAACAAAGTAAAAGATGA
Found at i:437373 original size:20 final size:20
Alignment explanation
Indices: 437348--437387 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
437338 GCAACTCTCA
437348 TGTGTTCTTTCAAGTGTTTG
1 TGTGTTCTTTCAAGTGTTTG
*
437368 TGTGTTCTTTTAAGTGTTTG
1 TGTGTTCTTTCAAGTGTTTG
437388 GAAGCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.25, T:0.57
Consensus pattern (20 bp):
TGTGTTCTTTCAAGTGTTTG
Found at i:438784 original size:22 final size:21
Alignment explanation
Indices: 438731--438785 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
438721 ACAAGAATAA
438731 TAATATTAATAAAATTAAAATT
1 TAATATTAAT-AAATTAAAATT
*
438753 TAATAATAATAAA-TAAAATTT
1 TAATATTAATAAATTAAAA-TT
438774 TAATTATTAATA
1 TAA-TATTAATA
438786 TGATTTTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 8 0.28
22 16 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATATTAATAAATTAAAATT
Found at i:441661 original size:12 final size:13
Alignment explanation
Indices: 441644--441676 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
441634 TGTATTTTAT
441644 ATTATTAAT-AAA
1 ATTATTAATAAAA
*
441656 ATTATTATTAAAA
1 ATTATTAATAAAA
441669 ATTATTAA
1 ATTATTAA
441677 AACAATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTATTAATAAAA
Found at i:441683 original size:25 final size:24
Alignment explanation
Indices: 441644--441691 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
441634 TGTATTTTAT
441644 ATTATTAATAAAATTATTATTAAAA
1 ATTATTAATAAAATT-TTATTAAAA
*
441669 ATTATTAA-AACAATTTTTTTAAA
1 ATTATTAATAA-AATTTTATTAAA
441692 TTTTATTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTATTAATAAAATTTTATTAAAA
Found at i:443875 original size:98 final size:94
Alignment explanation
Indices: 443698--443894 Score: 304
Period size: 98 Copynumber: 2.1 Consensus size: 94
443688 AAATTATACT
* *
443698 TGATTCATTCATGTCAAATGTATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTTG
1 TGATTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTTA
* *
443763 ACAGCTTTACTCATTTGTGTGTGATTATTTTA
66 ACAACTTTACTCA--T-TGTGTGATTACTTTA
443795 TGATCTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTT
1 TGAT-TCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTT
* *
443860 AATAACTTTATTCATTGTGTGATTACTTTA
65 AACAACTTTACTCATTGTGTGATTACTTTA
443890 TGATT
1 TGATT
443895 AATTGATAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
94 1 0.01
95 18 0.19
96 1 0.01
97 4 0.04
98 69 0.74
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (94 bp):
TGATTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTTA
ACAACTTTACTCATTGTGTGATTACTTTA
Found at i:445676 original size:64 final size:64
Alignment explanation
Indices: 445575--445702 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
445565 CCTTTCATGA
* * *
445575 ACGAGTTGGCAAAAGTGGCAGGGGTAGATGAGAAATGGGTAACTGTTCGGATTCAACATAAAGG
1 ACGAGTTGGCAAAAGAGGCAGGGGTAGATGAGAAATGGGTAACTCTCCGGATTCAACATAAAGG
445639 ACGAGTTGGCAAAAGAGGCAGGGGTAGATGAGAAATGGGTAACTCTCCGGATTCAACATAAAGG
1 ACGAGTTGGCAAAAGAGGCAGGGGTAGATGAGAAATGGGTAACTCTCCGGATTCAACATAAAGG
445703 TGGTGGGGAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.35, C:0.12, G:0.34, T:0.19
Consensus pattern (64 bp):
ACGAGTTGGCAAAAGAGGCAGGGGTAGATGAGAAATGGGTAACTCTCCGGATTCAACATAAAGG
Found at i:448942 original size:5 final size:5
Alignment explanation
Indices: 448549--448955 Score: 735
Period size: 5 Copynumber: 81.6 Consensus size: 5
448539 TATAATATAA
* * * * * *
448549 TATGA TATGA TATGA TATGA TATGA TATGA TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
448599 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
448649 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
448699 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
448749 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
448799 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
448849 TATGG TATGG TATGG TATGG TAT-G TATGG TATGG TATGG TATGG TATGG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
*
448898 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATAG
1 TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG TATGG
*
448948 TATAG TAT
1 TATGG TAT
448956 AATATAGTAT
Statistics
Matches: 399, Mismatches: 2, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
4 4 0.01
5 395 0.99
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (5 bp):
TATGG
Found at i:448956 original size:5 final size:5
Alignment explanation
Indices: 448943--449557 Score: 982
Period size: 5 Copynumber: 122.8 Consensus size: 5
448933 TATGGTATGG
* * *
448943 TATAG TATAG TATAA TATAG TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
448993 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
449043 TATAA TATAA TATAAA TATAAA TATAA TAT-A -ATAA TATAA TATAA TATAA
1 TATAA TATAA TAT-AA TAT-AA TATAA TATAA TATAA TATAA TATAA TATAA
* * * *
449093 TATAA TATAA TAT-A TATAA TATAG TATAG TATAG TATAA TATAA TATAG
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
449142 TATAA TAATATA TATAA TATAA TATAA TATAA TATAA TAATATA TATAA
1 TATAA T-ATA-A TATAA TATAA TATAA TATAA TATAA T-ATA-A TATAA
449191 -ATAA TATAA TATATA TAATAA TATAA TATAA TAT-A TATAAA TATAA
1 TATAA TATAA TATA-A T-ATAA TATAA TATAA TATAA TAT-AA TATAA
449237 TATAA TATAA TATAA TA-AA TATAA TATAA TATAA TAT-A TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
449285 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TAT-A TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
449334 TATAA TATAA TATAA TATAA TATAA TATATA TATAA TAT-A -ATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATA-A TATAA TATAA TATAA TATAA
449383 TAT-A TATATA TAATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATA-A T-ATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
449434 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
449484 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
449534 TATAA TATAA TATAA TATAA TATA
1 TATAA TATAA TATAA TATAA TATA
449558 TAATTTTGAA
Statistics
Matches: 581, Mismatches: 7, Indels: 44
0.92 0.01 0.07
Matches are distributed among these distances:
3 4 0.01
4 32 0.06
5 495 0.85
6 40 0.07
7 10 0.02
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:449615 original size:39 final size:39
Alignment explanation
Indices: 449542--449681 Score: 175
Period size: 39 Copynumber: 3.7 Consensus size: 39
449532 AATATAATAT
* *
449542 AATATA-ATATAATATATA-ATTTTGAAAAATATTTTGAA
1 AATATATATATAATATATAGTTTTTG-AAAACATTTTGAA
449580 AATATATATATAATATATAGTTTTTGAAAACATTTTG--
1 AATATATATATAATATATAGTTTTTGAAAACATTTTGAA
* *
449617 AATATATATAT-A-ATATAGTTTTTTATAACATTTTGAA
1 AATATATATATAATATATAGTTTTTGAAAACATTTTGAA
* *
449654 AAAATATATATAATATATAATTTTTGAA
1 AATATATATATAATATATAGTTTTTGAA
449682 TTTTTAAAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
35 21 0.24
36 1 0.01
37 21 0.24
38 7 0.08
39 33 0.38
40 5 0.06
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (39 bp):
AATATATATATAATATATAGTTTTTGAAAACATTTTGAA
Found at i:449661 original size:37 final size:37
Alignment explanation
Indices: 449572--449705 Score: 134
Period size: 35 Copynumber: 3.7 Consensus size: 37
449562 TTTGAAAAAT
* * *
449572 ATTTTGAAAATATATATATAATATATAGTTTTTGAAAAC
1 ATTTTGAAAAAATATATAT-A-ATATAGTTTTTTATAAC
*
449611 ATTTTG--AATATATATATAATATAGTTTTTTATAAC
1 ATTTTGAAAAAATATATATAATATAGTTTTTTATAAC
* *
449646 ATTTTGAAAAAATATATATAATATA-TAATTTT-TGA-
1 ATTTTGAAAAAATATATATAATATAGT-TTTTTATAAC
* *
449681 ATTTTTAAAAAATATATATTATATA
1 ATTTTGAAAAAATATATATAATATA
449706 AAACATTTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
35 44 0.52
36 4 0.05
37 31 0.36
39 6 0.07
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (37 bp):
ATTTTGAAAAAATATATATAATATAGTTTTTTATAAC
Found at i:449685 original size:35 final size:36
Alignment explanation
Indices: 449572--449705 Score: 132
Period size: 37 Copynumber: 3.7 Consensus size: 36
449562 TTTGAAAAAT
* *
449572 ATTTTGAAAATATATATATAATATATAGTTTTTGAAAAC
1 ATTTTGAAAAAATATATATAATATATAATTTTTG---AC
* * *
449611 ATTTTG--AATATATATATAATATAGT-TTTTTATAAC
1 ATTTTGAAAAAATATATATAATATA-TAATTTT-TGAC
449646 ATTTTGAAAAAATATATATAATATATAATTTTTGA-
1 ATTTTGAAAAAATATATATAATATATAATTTTTGAC
* *
449681 ATTTTTAAAAAATATATATTATATA
1 ATTTTGAAAAAATATATATAATATA
449706 AAACATTTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
35 31 0.37
36 3 0.04
37 41 0.49
38 2 0.02
39 6 0.07
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.47
Consensus pattern (36 bp):
ATTTTGAAAAAATATATATAATATATAATTTTTGAC
Found at i:449737 original size:17 final size:18
Alignment explanation
Indices: 449710--449752 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
449700 TATATAAAAC
*
449710 ATTTATGTATTATATTTT
1 ATTTATTTATTATATTTT
* *
449728 A-TTATTTATTTTCTTTT
1 ATTTATTTATTATATTTT
449745 ATTTATTT
1 ATTTATTT
449753 TGGTCCGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (18 bp):
ATTTATTTATTATATTTT
Found at i:449831 original size:26 final size:26
Alignment explanation
Indices: 449795--449847 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
449785 GTAATAGTCC
*
449795 AACCGAGTGGCAGGC-TAGACCTAGCA
1 AACCGAGTGGCAAGCAT-GACCTAGCA
*
449821 AACCGGGTGGCAAGCATGACCTAGCA
1 AACCGAGTGGCAAGCATGACCTAGCA
449847 A
1 A
449848 TCCAACCCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.32, C:0.26, G:0.30, T:0.11
Consensus pattern (26 bp):
AACCGAGTGGCAAGCATGACCTAGCA
Found at i:453974 original size:20 final size:21
Alignment explanation
Indices: 453929--453988 Score: 77
Period size: 20 Copynumber: 2.8 Consensus size: 21
453919 GGGGGAACCA
453929 GGGGAATCGGTTCCCCTTCAAAG
1 GGGGAATCGGTT-CCC-TCAAAG
453952 GGGGAATCGGTTCCCTC-AAG
1 GGGGAATCGGTTCCCTCAAAG
* *
453972 GGGGGATCGATTCCCTC
1 GGGGAATCGGTTCCCTC
453989 TGTACCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.22
Consensus pattern (21 bp):
GGGGAATCGGTTCCCTCAAAG
Found at i:457823 original size:23 final size:22
Alignment explanation
Indices: 457779--457820 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
457769 GAGTTTATTT
*
457779 TCATTTTTTCAATTTTGAAACA
1 TCATTTTTTCAATTTTAAAACA
457801 TCATTTTTT-ATATTTTAAAA
1 TCATTTTTTCA-ATTTTAAAA
457821 ACAATTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (22 bp):
TCATTTTTTCAATTTTAAAACA
Found at i:460754 original size:12 final size:13
Alignment explanation
Indices: 460723--460754 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
460713 ATTTAGATCG
460723 AAATTTTATTTAT
1 AAATTTTATTTAT
460736 AAATTTTATTTAT
1 AAATTTTATTTAT
460749 -AATTTT
1 AAATTTT
460755 CTTAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
AAATTTTATTTAT
Found at i:464704 original size:17 final size:17
Alignment explanation
Indices: 464665--464717 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
464655 TTATTTTATG
* *
464665 ATTGTTTTTGTTTGTTT
1 ATTGTTTTTATTTATTT
*
464682 GTTTGTTTTTATTTATTT
1 -ATTGTTTTTATTTATTT
* *
464700 ATTGTTTTAATTTTTTT
1 ATTGTTTTTATTTATTT
464717 A
1 A
464718 AATTAAGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.75
Consensus pattern (17 bp):
ATTGTTTTTATTTATTT
Found at i:465446 original size:29 final size:32
Alignment explanation
Indices: 465377--465458 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 32
465367 TGGAAAATGA
** *
465377 ATTACTGGAATTTAAATTACTGAAATTTGAATT
1 ATTACTGGAAAATGAATTACTGAAATTTGAA-T
*
465410 ATTACTGGAAAATGAATTACTGGAATTTG-A-
1 ATTACTGGAAAATGAATTACTGAAATTTGAAT
465440 ATT-CTGGAAAATGAATTAC
1 ATTACTGGAAAATGAATTAC
465459 ATTTCTGGAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
29 16 0.36
30 3 0.07
32 1 0.02
33 25 0.56
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (32 bp):
ATTACTGGAAAATGAATTACTGAAATTTGAAT
Found at i:465454 original size:14 final size:15
Alignment explanation
Indices: 465366--465458 Score: 82
Period size: 15 Copynumber: 6.1 Consensus size: 15
465356 AATTGGTTTT
465366 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
** *
465381 CTGGAATTTAAATTA
1 CTGGAAAATGAATTA
*
465396 CT-GAAATTTGAATTATTA
1 CTGGAAA-ATG-A--ATTA
465414 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
**
465429 CTGGAATTTGAATT-
1 CTGGAAAATGAATTA
465443 CTGGAAAATGAATTA
1 CTGGAAAATGAATTA
465458 C
1 C
465459 ATTTCTGGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
14 15 0.24
15 33 0.53
16 1 0.02
17 1 0.02
18 8 0.13
19 4 0.06
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (15 bp):
CTGGAAAATGAATTA
Found at i:465725 original size:33 final size:32
Alignment explanation
Indices: 465662--465728 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 32
465652 TATTATTAAA
*
465662 TAATGTTTTTATAATTTTATTAATAAAAATAT
1 TAATGTTTTTATAATTTTATAAATAAAAATAT
*
465694 TAATTTTTTTAT-ATTTTAGTGAAATAAAAATAT
1 TAATGTTTTTATAATTTTA-T-AAATAAAAATAT
465727 TA
1 TA
465729 TAAATTATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
31 6 0.19
32 12 0.39
33 13 0.42
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (32 bp):
TAATGTTTTTATAATTTTATAAATAAAAATAT
Found at i:465819 original size:23 final size:23
Alignment explanation
Indices: 465770--465832 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
465760 GTGTTATATT
* **
465770 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
465793 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
465816 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
465833 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:465856 original size:28 final size:29
Alignment explanation
Indices: 465816--466007 Score: 112
Period size: 29 Copynumber: 6.9 Consensus size: 29
465806 CTTTATTAAA
465816 ATATTATTTAAATATATAAATAA-TATTAT
1 ATATTA-TTAAATATATAAATAATTATTAT
*
465845 -TCATTATTAAATATATAAAAAATTTATTAT
1 AT-ATTATTAAATATATAAATAA-TTATTAT
* *
465875 ATATTATTAAA-ATAAAAATATAATATCT-T
1 ATATTATTAAATATATAAATA-ATTAT-TAT
** *
465904 ATATTATTATAATATATTTATTATT-TTAT
1 ATATTATTA-AATATATAAATAATTATTAT
* *
465933 ATAATATTAAA-ATAT-AAT-ATT-GTAT
1 ATATTATTAAATATATAAATAATTATTAT
*
465958 -TATTA-TAAATAT-TAATATTAA-TATTAA
1 ATATTATTAAATATATAA-A-TAATTATTAT
465985 AT-TTATTAAA-ATA-AAAT-ATTATT
1 ATATTATTAAATATATAAATAATTATT
466008 TTGAGTATTT
Statistics
Matches: 129, Mismatches: 15, Indels: 42
0.69 0.08 0.23
Matches are distributed among these distances:
23 5 0.04
24 8 0.06
25 12 0.09
26 5 0.04
27 14 0.11
28 24 0.19
29 34 0.26
30 21 0.16
31 6 0.05
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (29 bp):
ATATTATTAAATATATAAATAATTATTAT
Found at i:465860 original size:19 final size:20
Alignment explanation
Indices: 465808--465860 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
465798 TTAAATATCT
465808 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
465827 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
465848 TTATTAAATATAT
1 TTATTAAATATAT
465861 AAAAAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 7 0.25
20 9 0.32
21 6 0.21
22 6 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:465861 original size:30 final size:25
Alignment explanation
Indices: 465817--465880 Score: 65
Period size: 28 Copynumber: 2.3 Consensus size: 25
465807 TTTATTAAAA
*
465817 TATTATTTAAATATATAAATAATATTAT
1 TATTA-TTAAA-ATATAAAAAAT-TTAT
465845 TCATTATTAAATATATAAAAAATTTAT
1 T-ATTATTAAA-ATATAAAAAATTTAT
465872 TATATATTA
1 TAT-TATTA
465881 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 2 0.06
27 10 0.30
28 17 0.52
29 4 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTATTAAAATATAAAAAATTTAT
Found at i:465916 original size:18 final size:17
Alignment explanation
Indices: 465893--465992 Score: 57
Period size: 18 Copynumber: 5.9 Consensus size: 17
465883 AAAATAAAAA
*
465893 TATAATATCTTATATTAT
1 TATAATATATT-TATTAT
465911 TATAATATATTTATTAT
1 TATAATATATTTATTAT
* * *
465928 T-TTATATAATATTA-AAA
1 TATAATAT-AT-TTATTAT
*
465945 TATAATAT-TGTATTAT
1 TATAATATATTTATTAT
*
465961 TATAA-ATA-TTAATAT
1 TATAATATATTTATTAT
* *
465976 TAATATTAAATTTATTA
1 T-ATAATATATTTATTA
465993 AAATAAAATA
Statistics
Matches: 61, Mismatches: 13, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
15 10 0.16
16 15 0.25
17 13 0.21
18 23 0.38
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
TATAATATATTTATTAT
Found at i:465976 original size:6 final size:6
Alignment explanation
Indices: 465934--465984 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
465924 TTATTTTATA
* * * *
465934 TAATAT TAAAAT ATAATAT T-GTAT TATTAT AAATAT TAATAT TAATAT
1 TAATAT TAATAT -TAATAT TAATAT TAATAT TAATAT TAATAT TAATAT
465982 TAA
1 TAA
465985 ATTTATTAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
5 4 0.11
6 27 0.75
7 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (6 bp):
TAATAT
Found at i:465982 original size:21 final size:21
Alignment explanation
Indices: 465934--465985 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
465924 TTATTTTATA
465934 TAATATTAAAATATAATATTG
1 TAATATTAAAATATAATATTG
*
465955 TATTATTATAAATATTAATA-T-
1 TAATATTA-AAATA-TAATATTG
465976 TAATATTAAA
1 TAATATTAAA
465986 TTTATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 2 0.07
21 14 0.52
22 6 0.22
23 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATATTAAAATATAATATTG
Found at i:466173 original size:42 final size:42
Alignment explanation
Indices: 466126--466242 Score: 171
Period size: 42 Copynumber: 2.8 Consensus size: 42
466116 AATTACGTTT
* *
466126 CGGAAAACCAATTACGTGAAACAAACACTGAAAAATATTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGAAAAATATTTTC
* *
466168 CGGAAAATGAATTACGTGAAACAAACACGGGAAAATATTTTC
1 CGGAAAACGAATTACGTGAAACAAACACGGAAAAATATTTTC
* *
466210 CAGAAGACGAATTACGTGAAACAAACACAGGAA
1 CGGAAAACGAATTACGTGAAACAAACAC-GGAA
466243 TTCGGGGAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 63 0.95
43 3 0.05
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.18
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGGAAAAATATTTTC
Found at i:468652 original size:98 final size:94
Alignment explanation
Indices: 468475--468671 Score: 304
Period size: 98 Copynumber: 2.1 Consensus size: 94
468465 AAATTATACT
* *
468475 TGATTCATTCATGTCAAATGTATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTTG
1 TGATTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTTA
* *
468540 ACAGCTTTACTCATTTGTGTGTGATTATTTTA
66 ACAACTTTACTCA--T-TGTGTGATTACTTTA
468572 TGATCTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTT
1 TGAT-TCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTT
* *
468637 AATAACTTTATTCATTGTGTGATTACTTTA
65 AACAACTTTACTCATTGTGTGATTACTTTA
468667 TGATT
1 TGATT
468672 AATTGATAAT
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
94 1 0.01
95 18 0.19
96 1 0.01
97 4 0.04
98 69 0.74
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (94 bp):
TGATTCATTCATGTCAAATATATGGTTCTTTGTCTCAATTTCATATATAAGATTCTATATCGTTA
ACAACTTTACTCATTGTGTGATTACTTTA
Found at i:482798 original size:32 final size:32
Alignment explanation
Indices: 482757--482822 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
482747 GTTTTTTTTC
482757 TTCTTCTTAAACTCCATTAATATCTTGATTTG
1 TTCTTCTTAAACTCCATTAATATCTTGATTTG
482789 TTCTTCTTAAACTCCATTAATATCTTGATTTG
1 TTCTTCTTAAACTCCATTAATATCTTGATTTG
482821 TT
1 TT
482823 TCAACAATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (32 bp):
TTCTTCTTAAACTCCATTAATATCTTGATTTG
Found at i:486057 original size:14 final size:14
Alignment explanation
Indices: 486038--486064 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
486028 AGCCATTTCA
486038 TTTTTTTCTTTCTT
1 TTTTTTTCTTTCTT
486052 TTTTTTTCTTTCT
1 TTTTTTTCTTTCT
486065 CTCAAACAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTTTCTT
Found at i:486923 original size:3 final size:3
Alignment explanation
Indices: 486915--487006 Score: 121
Period size: 3 Copynumber: 30.7 Consensus size: 3
486905 TTAATATATT
* * * *
486915 TAA TAA TAA AAA AAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
486963 TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
487007 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:487474 original size:113 final size:113
Alignment explanation
Indices: 487255--488107 Score: 1230
Period size: 113 Copynumber: 7.5 Consensus size: 113
487245 TCTTGATGAG
487255 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTTC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TT-
* * ** * *
487320 CTCTGGAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
61 CTCTGGAAATGATGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
487373 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * ** * *
487438 GTAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAATGATGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
*
487486 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
487551 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
*
487599 TTCTTTTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TT-TCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
487662 GAAATGCTGATCCATCAATTAATGAATTCATGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
*
487710 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
487775 GAAAAGATAATCCATCAATTTGATGAATTC-AGAAAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAA-ATGATGAATTCAAG-TAAAAGGTTGAACAAA
*
487824 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
** * *
487889 TCAATGATAATCCATCAAGA-GATGAATTCAGGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAA-ATGATGAATTCAAGTAAAAGGTTGAACAAA
* *
487937 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
488002 GCAATGATAATCCATCAAGA-GATGAATTCAGGTAAAAGGTTGAACAAA
66 GAAATGATGATCCATCAA-ATGATGAATTCAAGTAAAAGGTTGAACAAA
* *
488050 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
488108 CTACCTTGCA
Statistics
Matches: 690, Mismatches: 40, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
111 101 0.15
112 4 0.01
113 419 0.61
114 108 0.16
115 21 0.03
118 37 0.05
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAATGATGATCCATCAAATGATGAATTCAAGTAAAAGGTTGAACAAA
Found at i:488866 original size:50 final size:50
Alignment explanation
Indices: 488793--488933 Score: 273
Period size: 50 Copynumber: 2.8 Consensus size: 50
488783 CTTACCAAAA
*
488793 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
488843 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
488893 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
488934 GGCAAATTCA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.39, C:0.21, G:0.14, T:0.26
Consensus pattern (50 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAAT
Found at i:489081 original size:133 final size:133
Alignment explanation
Indices: 488843--489213 Score: 733
Period size: 133 Copynumber: 2.8 Consensus size: 133
488833 TTTGTCTAAT
488843 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
488908 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
488973 AAC
131 AAC
488976 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
489041 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCATTGATTGGTTCTGTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
489106 AAC
131 AAC
489109 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
489174 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
66 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTT
489214 TCATTTAATG
Statistics
Matches: 237, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 237 1.00
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (133 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
AAC
Found at i:503100 original size:3 final size:3
Alignment explanation
Indices: 503092--503184 Score: 127
Period size: 3 Copynumber: 31.7 Consensus size: 3
503082 TTAATATATT
*
503092 TAA TAA TAA -AA -AA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
503138 TGA TAA TAA TAT TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
503185 TGGATAAAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
2 4 0.05
3 75 0.95
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:506394 original size:14 final size:14
Alignment explanation
Indices: 506372--506403 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
506362 TTAAGAATAA
*
506372 ATTTGTAATTTAAC
1 ATTTATAATTTAAC
506386 ATTTATAATTTAAC
1 ATTTATAATTTAAC
506400 ATTT
1 ATTT
506404 GTAGAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTATAATTTAAC
Found at i:518976 original size:22 final size:23
Alignment explanation
Indices: 518946--519006 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
518936 TCAAACTGAA
*
518946 AAATATGTC-TAAAGACAAAGAG
1 AAATGTGTCATAAAGACAAAGAG
* * *
518968 AAATGTGTCATAAATACAGAGAT
1 AAATGTGTCATAAAGACAAAGAG
*
518991 AATTGTGTCATAAAGA
1 AAATGTGTCATAAAGA
519007 TAGAGTTATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 8 0.25
23 24 0.75
ACGTcount: A:0.49, C:0.08, G:0.18, T:0.25
Consensus pattern (23 bp):
AAATGTGTCATAAAGACAAAGAG
Found at i:526839 original size:170 final size:173
Alignment explanation
Indices: 526630--526972 Score: 649
Period size: 171 Copynumber: 2.0 Consensus size: 173
526620 ACCCATGGTA
526630 TTTTGTGATGGAAGCTAATAAAAAAAACTGGAATATATATTGATAGAAGTGGAACTGAATGAAGA
1 TTTTGTGATGGAAGCTAATAAAAAAAACTGGAATATATATTGATAGAAGTGGAACTGAATGAAGA
526695 A-ATTTATTGTCTTTTCCATGTTCATGCAAAATGAAGCATGCCCTTTAGGTTCTTATTGTCCGCT
66 ACATTTATTGTCTTTTCCATGTTCATGCAAAATGAAGCATGCCCTTTAGGTTCTTATTGTCCGCT
526759 TGCATCGCTGAATAAATCTACCGGAG-TTGTGATCCGTAAGTT
131 TGCATCGCTGAATAAATCTACCGGAGTTTGTGATCCGTAAGTT
526801 TTTTGTGAT-GAAGCTAAT-AAAAAAACTGGAATTATATATTGATAGAAGTGGAACTGAATGAAG
1 TTTTGTGATGGAAGCTAATAAAAAAAACTGGAA-TATATATTGATAGAAGTGGAACTGAATGAAG
526864 AACATTTATTGTCTTTTCCATGTTCATGCAAAATGAAGCATGCCCTTTAGGTTCTTATTGTCCGC
65 AACATTTATTGTCTTTTCCATGTTCATGCAAAATGAAGCATGCCCTTTAGGTTCTTATTGTCCGC
526929 TTGCATCGCTGAATAAATCTACCGGAGTTTGTGATCCGTAAGTT
130 TTGCATCGCTGAATAAATCTACCGGAGTTTGTGATCCGTAAGTT
526973 CATCTCTTTT
Statistics
Matches: 169, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
169 13 0.08
170 42 0.25
171 98 0.58
172 16 0.09
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.34
Consensus pattern (173 bp):
TTTTGTGATGGAAGCTAATAAAAAAAACTGGAATATATATTGATAGAAGTGGAACTGAATGAAGA
ACATTTATTGTCTTTTCCATGTTCATGCAAAATGAAGCATGCCCTTTAGGTTCTTATTGTCCGCT
TGCATCGCTGAATAAATCTACCGGAGTTTGTGATCCGTAAGTT
Found at i:532384 original size:7 final size:7
Alignment explanation
Indices: 532354--532383 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
532344 TCTAAAGTTC
532354 AAATTTA
1 AAATTTA
532361 AAATTTA
1 AAATTTA
532368 AAATTTA
1 AAATTTA
532375 AAA-TTA
1 AAATTTA
532381 AAA
1 AAA
532384 AAATGTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (7 bp):
AAATTTA
Found at i:544455 original size:18 final size:19
Alignment explanation
Indices: 544432--544467 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
544422 ACAGTAATCC
*
544432 TATTCC-CTGGTAATCTTT
1 TATTCCACTGATAATCTTT
544450 TATTCCACTGATAATCTT
1 TATTCCACTGATAATCTT
544468 ACATTCCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (19 bp):
TATTCCACTGATAATCTTT
Found at i:549664 original size:64 final size:65
Alignment explanation
Indices: 549592--549719 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 65
549582 CGTGCACCAA
* *
549592 GTGTGCATCAATGCATGAAATGCATTCGATG-TTTGAAAATAGCCTGAGTGCATCGATGCATGGC
1 GTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGC
* **
549656 GTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 GTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGG
549720 AGAATGCATC
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
64 29 0.50
65 29 0.50
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
GTGTGCATCAATGCATCAAATGCATTCGATGTTTTGAAAATAGCCAGAGTGCATCGATGCATGGC
Found at i:549728 original size:65 final size:64
Alignment explanation
Indices: 549595--549745 Score: 203
Period size: 65 Copynumber: 2.3 Consensus size: 64
549585 GCACCAAGTG
* * * **
549595 TGCATCAATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGATGCATGGCGTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* **
549659 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGAGAA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
* *
549724 TGCATCGGTGCATGGAATGCAT
1 TGCATCGATGCATGAAATGCAT
549746 CGGTGCATGG
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 26 0.35
65 49 0.65
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGGAGAA
Found at i:549743 original size:17 final size:17
Alignment explanation
Indices: 549705--549762 Score: 89
Period size: 17 Copynumber: 3.3 Consensus size: 17
549695 ATATTCAGAG
*
549705 TGCATCGATGCATGGAGAA
1 TGCATCGGTGCAT-G-GAA
549724 TGCATCGGTGCATGGAA
1 TGCATCGGTGCATGGAA
549741 TGCATCGGTGCATGGAA
1 TGCATCGGTGCATGGAA
549758 TGCAT
1 TGCAT
549763 TCGATGTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
17 25 0.66
18 1 0.03
19 12 0.32
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (17 bp):
TGCATCGGTGCATGGAA
Found at i:549760 original size:82 final size:82
Alignment explanation
Indices: 549659--549818 Score: 209
Period size: 82 Copynumber: 2.0 Consensus size: 82
549649 GCATGGCGTG
*
549659 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAA-ATATTCA-GAGTGCATCGATGCATGG-A
1 TGCATCGATGCATCAAATGCATTCGATGTTTT-AAATA-ATTCACGAATGCATCGATGCATGGTA
549721 GAATGCATCGGTGCATGGAA
64 G-ATGCATCGGTGCATGGAA
* ** * * *
549741 TGCATCGGTGCATGGAATGCATTCGATGTTTTAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATCAAATGCATTCGATGTTTTAAATAATTCACGAATGCATCGATGCATGGTAGA
549806 TGCATCGGTGCAT
66 TGCATCGGTGCAT
549819 CACCTCAAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
81 7 0.10
82 60 0.88
83 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (82 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTTAAATAATTCACGAATGCATCGATGCATGGTAGA
TGCATCGGTGCATGGAA
Found at i:553734 original size:74 final size:75
Alignment explanation
Indices: 553651--553793 Score: 207
Period size: 75 Copynumber: 1.9 Consensus size: 75
553641 TTGCTCATAG
* ** *
553651 GGAACCGATT-CCCCCTGAATGGTTTGGCTCCGAGATTTCCAGAATGCTCGGAGGGAACCGATTC
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAGGGAACCGATTC
553715 CCCCATAGGA
66 CCCCATAGGA
* * **
553725 GGAACCGATTCCCCCCTAAACAGTTTTGTTCCGAGAATTCCATTATGCTCGGAGGGAACCGATTC
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAGGGAACCGATTC
553790 CCCC
66 CCCC
553794 CTTTTTACAA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
74 10 0.17
75 50 0.83
ACGTcount: A:0.23, C:0.30, G:0.24, T:0.23
Consensus pattern (75 bp):
GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAGGGAACCGATTC
CCCCATAGGA
Found at i:559595 original size:21 final size:21
Alignment explanation
Indices: 559569--559608 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
559559 CCCCCTTTGA
*
559569 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
559590 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
559609 TGGGTTCTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:562293 original size:72 final size:71
Alignment explanation
Indices: 562168--562330 Score: 195
Period size: 73 Copynumber: 2.3 Consensus size: 71
562158 CCAGATTGCT
* * ** *
562168 CATAGGGAACCGATTCCTCCTGAATGGTTTGGCTCCGAGATTTCCAGAATGCTCGGAGGGAACCG
1 CATAGGGAACCGATTCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTC-GAGGGAACCG
*
562233 ATTCCCC
65 ATCCCCC
* * *
562240 CATAGAGGAACCGATTCCCCCTAAACAGTTTTGTTCCGA-AATTCCAGTATGCTCGAGGGAACCG
1 CATAG-GGAACCGATTCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGAGGGAACCG
562304 ATCCCCC
65 ATCCCCC
*
562311 CA-AGGGGTACCGATTCCCCC
1 CATA-GGGAACCGATTCCCCC
562331 CCTTTTTACA
Statistics
Matches: 79, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
70 15 0.19
71 19 0.24
72 18 0.23
73 27 0.34
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (71 bp):
CATAGGGAACCGATTCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGAGGGAACCGA
TCCCCC
Found at i:567571 original size:64 final size:64
Alignment explanation
Indices: 567487--567665 Score: 241
Period size: 65 Copynumber: 2.8 Consensus size: 64
567477 GAACACTTGA
*** *
567487 TGCATCGATGCACCAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCTGAG
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAG
* * **
567551 TGCATCGATGCATGGCGTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAG
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAG
** * *
567616 TGCATCGATGCATGGAGAATGCATCGGTGCATGGAATGCATTCGATGTTT
1 TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTT
567666 CAATTAATTC
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 45 0.45
65 55 0.55
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATGGAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAG
Found at i:567654 original size:17 final size:19
Alignment explanation
Indices: 567616--567662 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
567606 ATATTCAGAG
567616 TGCATCGATGCATGGAGAA
1 TGCATCGATGCATGGAGAA
*
567635 TGCATCGGTGCAT-G-GAA
1 TGCATCGATGCATGGAGAA
567652 TGCATTCGATG
1 TGCA-TCGATG
567663 TTTCAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 7 0.28
18 6 0.24
19 12 0.48
ACGTcount: A:0.26, C:0.17, G:0.32, T:0.26
Consensus pattern (19 bp):
TGCATCGATGCATGGAGAA
Found at i:567685 original size:65 final size:62
Alignment explanation
Indices: 567506--567712 Score: 211
Period size: 65 Copynumber: 3.2 Consensus size: 62
567496 GCACCAAGTG
* * *
567506 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGC-CTGAGTGCATCGATGCATGGCGTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAT-TCACT-AGTGCATCGATGCATGGAG-A
* *
567570 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGAGA
1 TGCATCGATGCATGAAATGCATTCGATG-TTTG-AAA-ATTCACTAGTGCATCGATGCATGGAG-
567634 A
62 A
* * * * *
567635 TGCATCGGTGCATGGAATGCATTCGATGTTTCAATTAATTCACTAATGCATCGATGCATGGTTGA
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAA--AATTCACTAGTGCATCGATGCATGG-AGA
*
567700 TGCATCGGTGCAT
1 TGCATCGATGCAT
567713 CACCTCAAAT
Statistics
Matches: 122, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
63 2 0.02
64 35 0.29
65 78 0.64
66 5 0.04
67 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (62 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAATTCACTAGTGCATCGATGCATGGAGA
Found at i:567905 original size:20 final size:21
Alignment explanation
Indices: 567882--567921 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
567872 GAATCGAATA
567882 TAAAAT-TGTAAAA-TCATTTG
1 TAAAATCT-TAAAATTCATTTG
567902 TAAAATCTTAAAATTCATTT
1 TAAAATCTTAAAATTCATTT
567922 AACTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TAAAATCTTAAAATTCATTTG
Found at i:573369 original size:59 final size:59
Alignment explanation
Indices: 573255--573370 Score: 146
Period size: 59 Copynumber: 2.0 Consensus size: 59
573245 AACATAATGA
* * * * *
573255 ATGGTCAGGTGACCATTCTGTAACTTTAATAGTTAAGGGACTTAACAAATCAATATCCT
1 ATGGTCAGGGGACCATTCTATAACTTTAATAGTAAAGAGACTTAAAAAATCAATATCCT
*
573314 ATGGTC-GGGGACCATTTTATAACTTTTAATAGTAAAGAGACTTAATAAAAT-AATATC
1 ATGGTCAGGGGACCATTCTATAAC-TTTAATAGTAAAGAGACTTAA-AAAATCAATATC
573371 TTATAGAAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 14 0.29
59 31 0.63
60 4 0.08
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (59 bp):
ATGGTCAGGGGACCATTCTATAACTTTAATAGTAAAGAGACTTAAAAAATCAATATCCT
Found at i:585201 original size:71 final size:71
Alignment explanation
Indices: 585081--585215 Score: 234
Period size: 71 Copynumber: 1.9 Consensus size: 71
585071 TTTACCGTAG
*
585081 ATTTGAATCTAAAATATTATACAATGATTAATAATTTCAATTACAACTCATTTCAATTACGAGTA
1 ATTTGAATCTAAAATATTATACAATGAGTAATAATTTCAATTACAACTCATTTCAATTACGAGTA
585146 CAGTAT
66 CAGTAT
* **
585152 ATTTGAATTTAAAATATTATACAATGAGTAATAATTTCAATTATGACTCATTTCAATTACGAGT
1 ATTTGAATCTAAAATATTATACAATGAGTAATAATTTCAATTACAACTCATTTCAATTACGAGT
585216 GAGAATGTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 60 1.00
ACGTcount: A:0.41, C:0.11, G:0.08, T:0.39
Consensus pattern (71 bp):
ATTTGAATCTAAAATATTATACAATGAGTAATAATTTCAATTACAACTCATTTCAATTACGAGTA
CAGTAT
Found at i:585319 original size:54 final size:54
Alignment explanation
Indices: 585237--585351 Score: 212
Period size: 54 Copynumber: 2.1 Consensus size: 54
585227 GTTATATTAG
585237 ATTTTAACTTAAAATATTAAATATCTACTTTAAAATTTTATATAATTGATAATA
1 ATTTTAACTTAAAATATTAAATATCTACTTTAAAATTTTATATAATTGATAATA
* *
585291 ATTTTAACTTAAAATATTACATATCTACTTTGAAATTTTATATAATTGATAATA
1 ATTTTAACTTAAAATATTAAATATCTACTTTAAAATTTTATATAATTGATAATA
585345 ATTTTAA
1 ATTTTAA
585352 TTACAATCGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (54 bp):
ATTTTAACTTAAAATATTAAATATCTACTTTAAAATTTTATATAATTGATAATA
Found at i:590371 original size:10 final size:9
Alignment explanation
Indices: 590311--590414 Score: 71
Period size: 9 Copynumber: 12.2 Consensus size: 9
590301 TAAATAAAAA
590311 ATATAATA-
1 ATATAATAT
590319 A-ATAATAT
1 ATATAATAT
*
590327 ATATAACAT
1 ATATAATAT
* *
590336 ACATACTAT
1 ATATAATAT
*
590345 ACCAT-A-AT
1 A-TATAATAT
590353 ATATAATAT
1 ATATAATAT
*
590362 A-ATACTAT
1 ATATAATAT
590370 ATACT-ATA-
1 ATA-TAATAT
590378 ATATAATAT
1 ATATAATAT
*
590387 ATACAATAT
1 ATATAATAT
590396 ATAT-ATAT
1 ATATAATAT
*
590404 ATATATTAT
1 ATATAATAT
590413 AT
1 AT
590415 GTCTTCAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 19
0.71 0.10 0.18
Matches are distributed among these distances:
7 9 0.12
8 27 0.36
9 35 0.47
10 4 0.05
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATAATAT
Found at i:590372 original size:2 final size:2
Alignment explanation
Indices: 590351--590414 Score: 59
Period size: 2 Copynumber: 34.0 Consensus size: 2
590341 CTATACCATA
*
590351 AT AT AT A- AT AT A- AT ACT AT AT ACT AT A- AT AT A- AT AT AT AC
1 AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
590391 A- AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
590415 GTCTTCAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
1 6 0.11
2 43 0.81
3 4 0.08
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:590414 original size:17 final size:17
Alignment explanation
Indices: 590311--590413 Score: 76
Period size: 15 Copynumber: 6.3 Consensus size: 17
590301 TAAATAAAAA
*
590311 ATATAATAAATA-ATAT
1 ATATAATATATATATAT
* *
590327 ATATAACATACATACTAT
1 ATATAATATATATA-TAT
*
590345 ACCATAATATATA-ATAT
1 A-TATAATATATATATAT
*
590362 A-ATACTATATACTATA-
1 ATATAATATATA-TATAT
*
590378 ATATAATATATACA-AT
1 ATATAATATATATATAT
590394 ATAT-ATATATATATAT
1 ATATAATATATATATAT
590410 -TATA
1 ATATA
590414 TGTCTTCAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
15 21 0.31
16 17 0.25
17 17 0.25
18 5 0.07
19 8 0.12
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAATATATATATAT
Found at i:590528 original size:36 final size:36
Alignment explanation
Indices: 590431--590735 Score: 271
Period size: 36 Copynumber: 8.4 Consensus size: 36
590421 AAAAACATTA
590431 TATATGTTTTCAAAAACCGTTTTTAAAAAACTATATAT
1 TATATGTTTTC-AAAACCGTTTTT-AAAAACTATATAT
* *
590469 CATATGTTTTCCAAAACCGTTTTTAAAAACTATATAC
1 TATATGTTTT-CAAAACCGTTTTTAAAAACTATATAT
* * **
590506 TATATGTTTTCAAAATCATTTTTTTAAACTATATAT
1 TATATGTTTTCAAAACCGTTTTTAAAAACTATATAT
* *
590542 TATACGTTTTC-AAACTG-TTTTAAAAACTATAT-T
1 TATATGTTTTCAAAACCGTTTTTAAAAACTATATAT
* *
590575 GTACATGCTTTCAAAACCGTTTTT-AAAACTATATAT
1 -TATATGTTTTCAAAACCGTTTTTAAAAACTATATAT
** * *
590611 TATATGTTTTCAAAACTATTTTAAAAAATTATATAT
1 TATATGTTTTCAAAACCGTTTTTAAAAACTATATAT
* **
590647 TATATGCTTTCAAAATCC-TTTGAAAAAAACTATATTAT
1 TATATGTTTTCAAAA-CCGTTT-TTAAAAACTATA-TAT
* * ** * *
590685 ATCTATG-TTTAAAAAATGTTTTCAAAAACTATGTAT
1 -TATATGTTTTCAAAACCGTTTTTAAAAACTATATAT
* *
590721 TATATATTCTCAAAA
1 TATATGTTTTCAAAA
590736 ACTATATTTA
Statistics
Matches: 216, Mismatches: 39, Indels: 26
0.77 0.14 0.09
Matches are distributed among these distances:
33 1 0.00
34 21 0.10
35 40 0.19
36 73 0.34
37 41 0.19
38 34 0.16
39 6 0.03
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (36 bp):
TATATGTTTTCAAAACCGTTTTTAAAAACTATATAT
Found at i:590681 original size:71 final size:71
Alignment explanation
Indices: 590431--590725 Score: 242
Period size: 70 Copynumber: 4.1 Consensus size: 71
590421 AAAAACATTA
* * * *
590431 TATATGTTTTCAAAAACCGTTTTTAAAAAACTATATATCATATGTTTTCCAAAACCGTTTTTAAA
1 TATATGCTTTCAAAATCCGTTTTAAAAAAACTATAT-T-ATATGTTTT-CAAAACTG-TTTTAAA
*
590496 AACTATATAC
62 AACTATATAT
* ** * ** *
590506 TATATGTTTTCAAAATCATTTTTTTAAACTA-TATATTATACGTTTTC-AAACTGTTTTAAAAAC
1 TATATGCTTTCAAAATC-CGTTTTAAAAAAACTATATTATATGTTTTCAAAACTGTTTTAAAAAC
590569 TATAT-T
65 TATATAT
* ** *
590575 GTACATGCTTTCAAAA-CCGTTTTTAAAACTA-TATATTATATGTTTTCAAAACTATTTTAAAAA
1 -TATATGCTTTCAAAATCCG-TTTTAAAAAAACTATATTATATGTTTTCAAAACTGTTTT-AAAA
*
590638 ATTATATAT
63 ACTATATAT
* * * *
590647 TATATGCTTTCAAAATCC-TTTGAAAAAAACTATATTATATCTATGTTTAAAAAATGTTTTCAAA
1 TATATGCTTTCAAAATCCGTTTTAAAAAAACTATATTATA--TGT-TTTCAAAACTGTTTT-AAA
*
590711 AACTATGTAT
62 AACTATATAT
590721 TATAT
1 TATAT
590726 ATTCTCAAAA
Statistics
Matches: 182, Mismatches: 27, Indels: 23
0.78 0.12 0.10
Matches are distributed among these distances:
69 26 0.14
70 45 0.25
71 38 0.21
72 4 0.02
73 10 0.05
74 29 0.16
75 21 0.12
76 9 0.05
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (71 bp):
TATATGCTTTCAAAATCCGTTTTAAAAAAACTATATTATATGTTTTCAAAACTGTTTTAAAAACT
ATATAT
Found at i:590750 original size:23 final size:24
Alignment explanation
Indices: 590706--590751 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
590696 AAAAATGTTT
* *
590706 TCAAAAACTATGTATTATATATTC
1 TCAAAAACTATATATTACATATTC
590730 TCAAAAACTATAT-TTACATATT
1 TCAAAAACTATATATTACATATT
590752 ATGTTATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.43, C:0.13, G:0.02, T:0.41
Consensus pattern (24 bp):
TCAAAAACTATATATTACATATTC
Found at i:599083 original size:93 final size:94
Alignment explanation
Indices: 598924--599123 Score: 303
Period size: 93 Copynumber: 2.1 Consensus size: 94
598914 CTACAATTTT
* *
598924 ATTTTTTTAATTCAAATAGATTAAATTAAAAGATAGGTAAAAATACATTAAAATTAGATATATAA
1 ATTTTTTTAATTCAAATAGATTAAATTAAAAGATAGATAAAAATACATTAAAATTAGATAAATAA
598989 ACATACTA-ATTTTTTTGTAATTTTTCTG
66 ACATACTATATTTTTTTGTAATTTTTCTG
* * * *
599017 ATTTTTTTAATTCAAGTAGATTAATTTACAAGATAGATAAAAATACATTGAAATTAGATAAATAA
1 ATTTTTTTAATTCAAATAGATTAAATTAAAAGATAGATAAAAATACATTAAAATTAGATAAATAA
* *
599082 ACATACTATTTTTTTTTGTGATTTTTCTG
66 ACATACTATATTTTTTTGTAATTTTTCTG
*
599111 ATATTTTGTAATT
1 AT-TTTTTTAATT
599124 TTCTGATTTT
Statistics
Matches: 96, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
93 67 0.70
94 20 0.21
95 9 0.09
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.45
Consensus pattern (94 bp):
ATTTTTTTAATTCAAATAGATTAAATTAAAAGATAGATAAAAATACATTAAAATTAGATAAATAA
ACATACTATATTTTTTTGTAATTTTTCTG
Found at i:599127 original size:18 final size:18
Alignment explanation
Indices: 599104--599141 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
599094 TTTTTGTGAT
599104 TTTTCTGATATTTTGTAA
1 TTTTCTGATATTTTGTAA
* *
599122 TTTTCTGATTTTTTTTAA
1 TTTTCTGATATTTTGTAA
599140 TT
1 TT
599142 CAAATAAATT
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:0.18, C:0.05, G:0.08, T:0.68
Consensus pattern (18 bp):
TTTTCTGATATTTTGTAA
Found at i:599349 original size:16 final size:16
Alignment explanation
Indices: 599324--599357 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
599314 ATATTTGTAA
599324 AATTAATATTAT-AAT
1 AATTAATATTATGAAT
599339 AATTAAATATTATGAAT
1 AATT-AATATTATGAAT
599356 AA
1 AA
599358 AGTAGAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAATATTATGAAT
Found at i:601292 original size:3 final size:3
Alignment explanation
Indices: 601284--601308 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
601274 ACCAAAAGCA
601284 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
601309 GTAGTAGGAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:626200 original size:36 final size:38
Alignment explanation
Indices: 626159--626260 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 38
626149 ACAAGACCGT
* * * *
626159 AATAGAAATATAAA-TAATCCACAATTTGTTTC-GAAA
1 AATAGAAATCTAAATTAATCCATAATTTGGTTCAAAAA
**
626195 AATAGAAATCTAAATTTCTTCCATAATTTGGTTCAAAAA
1 AATAGAAATCTAAA-TTAATCCATAATTTGGTTCAAAAA
*
626234 AATAGAAATCTAAACTAATCCATAATT
1 AATAGAAATCTAAATTAATCCATAATT
626261 GAAAGAAAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
36 13 0.24
38 24 0.44
39 17 0.31
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.32
Consensus pattern (38 bp):
AATAGAAATCTAAATTAATCCATAATTTGGTTCAAAAA
Found at i:627572 original size:23 final size:23
Alignment explanation
Indices: 627546--627589 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
627536 AGAAAAAACA
*
627546 AATAATTATGCTAAAAAAATTAC
1 AATAATTATACTAAAAAAATTAC
*
627569 AATAATTATACTAAACAAATT
1 AATAATTATACTAAAAAAATT
627590 GATCGATTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (23 bp):
AATAATTATACTAAAAAAATTAC
Found at i:634880 original size:22 final size:23
Alignment explanation
Indices: 634827--634884 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
634817 CTTTAATCAC
*
634827 TCAATATTAAAATATTATATTTAA
1 TCAATATTAAAA-ATAATATTTAA
*
634851 T-TAT-TTAAAAA-AATATTTAA
1 TCAATATTAAAAATAATATTTAA
634871 TCAATATTAAAAAT
1 TCAATATTAAAAAT
634885 CACATATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 13 0.46
23 2 0.07
24 1 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
TCAATATTAAAAATAATATTTAA
Found at i:634961 original size:21 final size:18
Alignment explanation
Indices: 634928--634969 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 18
634918 AAATATAGGA
634928 TAAATTACAATTTTAGTATT
1 TAAATTACAATTTT-GT-TT
634948 TAAATTATCAATTTTGTTT
1 TAAATTA-CAATTTTGTTT
634967 TAA
1 TAA
634970 CACCTAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 5 0.24
20 9 0.43
21 7 0.33
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (18 bp):
TAAATTACAATTTTGTTT
Found at i:635545 original size:14 final size:14
Alignment explanation
Indices: 635528--635579 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
635518 CGTTCGTGAA
635528 CGTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
635542 CGTTCGGTTA---T
1 CGTTCGTTTATGTT
635553 -GTTCGTTTATGTT
1 CGTTCGTTTATGTT
*
635566 CGTTCATTTATGTT
1 CGTTCGTTTATGTT
635580 TAACCCAATC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.26
11 1 0.03
13 1 0.03
14 21 0.68
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (14 bp):
CGTTCGTTTATGTT
Found at i:635545 original size:24 final size:24
Alignment explanation
Indices: 635518--635570 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
635508 AGTTCATTTA
635518 CGTTC-GTGAACGTTCGTTTATGTT
1 CGTTCGGT-AACGTTCGTTTATGTT
* *
635542 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTAACGTTCGTTTATGTT
635566 CGTTC
1 CGTTC
635571 ATTTATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.09, C:0.17, G:0.25, T:0.49
Consensus pattern (24 bp):
CGTTCGGTAACGTTCGTTTATGTT
Found at i:635576 original size:24 final size:24
Alignment explanation
Indices: 635529--635579 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
635519 GTTCGTGAAC
*
635529 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
*
635553 GTTCGTTTATGTTCGTTCATTTAT
1 GTTCGTTTATGTTCGTTCAGTTAT
635577 GTT
1 GTT
635580 TAACCCAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCAGTTAT
Found at i:636611 original size:16 final size:16
Alignment explanation
Indices: 636590--636628 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
636580 GAGTCTCGAA
636590 CGTTTATATTCGTGTT
1 CGTTTATATTCGTGTT
*
636606 CGTTTATGTTCGTGTT
1 CGTTTATATTCGTGTT
636622 CGTTTAT
1 CGTTTAT
636629 TTATTAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.10, C:0.13, G:0.21, T:0.56
Consensus pattern (16 bp):
CGTTTATATTCGTGTT
Found at i:636717 original size:16 final size:16
Alignment explanation
Indices: 636693--636723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
636683 AAAAAAAATT
636693 GTTCATTTATGTTCGA
1 GTTCATTTATGTTCGA
*
636709 GTTCGTTTATGTTCG
1 GTTCATTTATGTTCG
636724 TTTATTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.52
Consensus pattern (16 bp):
GTTCATTTATGTTCGA
Found at i:651160 original size:36 final size:35
Alignment explanation
Indices: 651079--651218 Score: 192
Period size: 36 Copynumber: 3.9 Consensus size: 35
651069 AGATGAACAA
*
651079 TTGAATCGAAAGTGCTGATGCTTCCTTCCGTTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCAC
* *
651114 TTGAATCGAAAGTG-TCGGTGCTTCCTTTCGTTCTTC
1 TTGAATCGAAAGTGCT-GATGCTTCCTTTCGTTC-AC
* *
651150 TTGAATCGAAAGTGCCGATGCTTCCTTTTGTTCAC
1 TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCAC
*
651185 TTTGAATCGAAAGTGCTGATGCTTTCTTTCGTTC
1 -TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTC
651219 TTCTTATTCA
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
34 1 0.01
35 30 0.33
36 60 0.66
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (35 bp):
TTGAATCGAAAGTGCTGATGCTTCCTTTCGTTCAC
Found at i:676329 original size:30 final size:30
Alignment explanation
Indices: 676293--676364 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
676283 CTTTCATTTA
*
676293 GGTCCCCTCAACTTTTAA-AACTTGCAATAT
1 GGTCCCC-CAACATTTAATAACTTGCAATAT
* *
676323 GGTCCCCCAACATTTAATTCATTTGCAATAT
1 GGTCCCCCAACATTTAA-TAACTTGCAATAT
676354 GGT-CCCCAACA
1 GGTCCCCCAACA
676365 GTTACGTCGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 9 0.24
30 15 0.41
31 13 0.35
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (30 bp):
GGTCCCCCAACATTTAATAACTTGCAATAT
Found at i:676333 original size:29 final size:31
Alignment explanation
Indices: 676293--676360 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
676283 CTTTCATTTA
*
676293 GGTCCCCTCAACTTTTAA-AACTTGCAATAT
1 GGTCCCCTCAACATTTAATAACTTGCAATAT
* *
676323 GGTCCCC-CAACATTTAATTCATTTGCAATAT
1 GGTCCCCTCAACATTTAA-TAACTTGCAATAT
676354 GGTCCCC
1 GGTCCCC
676361 AACAGTTACG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 9 0.27
30 7 0.21
31 17 0.52
ACGTcount: A:0.26, C:0.29, G:0.12, T:0.32
Consensus pattern (31 bp):
GGTCCCCTCAACATTTAATAACTTGCAATAT
Found at i:676449 original size:29 final size:29
Alignment explanation
Indices: 676374--676465 Score: 130
Period size: 31 Copynumber: 3.1 Consensus size: 29
676364 AGTTACGTCG
676374 GGGACCATATTACAAACGGACTAAATGTT
1 GGGACCATATTACAAACGGACTAAATGTT
676403 GGAGGACCATATTACAAACGGACTAAATGTT
1 -G-GGACCATATTACAAACGGACTAAATGTT
* * * *
676434 GGGACCATATTGCAAACAGATTAAATGCT
1 GGGACCATATTACAAACGGACTAAATGTT
676463 GGG
1 GGG
676466 GGATTGTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
29 27 0.47
30 2 0.04
31 28 0.49
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (29 bp):
GGGACCATATTACAAACGGACTAAATGTT
Done.