Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002660.1 Hibiscus syriacus cultivar Beakdansim tig00005459_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: 2211860
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 9
Found at i:1987483 original size:11 final size:12
Alignment explanation
Indices: 1987441--1987485 Score: 67
Period size: 12 Copynumber: 3.8 Consensus size: 12
1987431 ATTATTTAAA
1987441 CGGGTATTGGGC-
1 CGGGTATT-GGCT
1987453 CGGGTATTGGCT
1 CGGGTATTGGCT
1987465 CGGGTATTGGCT
1 CGGGTATTGGCT
1987477 C-GGTATTGG
1 CGGGTATTGG
1987486 GCCGGGAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.34
12 21 0.66
ACGTcount: A:0.09, C:0.16, G:0.44, T:0.31
Consensus pattern (12 bp):
CGGGTATTGGCT
Found at i:1987533 original size:19 final size:19
Alignment explanation
Indices: 1987509--1987576 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
1987499 CAAGGTATAT
1987509 ATATATATATTTAAATTAA
1 ATATATATATTTAAATTAA
* * *
1987528 ATATATATTTTTTATTTAA
1 ATATATATATTTAAATTAA
* * *
1987547 A-ATAAATTTATTAATATTAT
1 ATATATATAT-TTAA-ATTAA
1987567 ATATATATAT
1 ATATATATAT
1987577 ATATATATAT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
18 7 0.19
19 20 0.54
20 4 0.11
21 6 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATATATATTTAAATTAA
Found at i:1987571 original size:2 final size:2
Alignment explanation
Indices: 1987560--1987589 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1987550 AAATTTATTA
1987560 AT AT -T 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 AT AT AT A
1987590 AATAATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1987632 original size:12 final size:13
Alignment explanation
Indices: 1987617--1987645 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1987607 TTTATCGGAT
1987617 CGGGT-ATCGGGG
1 CGGGTAATCGGGG
1987629 CGGGTAATCGGGG
1 CGGGTAATCGGGG
1987642 CGGG
1 CGGG
1987646 AATTACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.10, C:0.17, G:0.59, T:0.14
Consensus pattern (13 bp):
CGGGTAATCGGGG
Found at i:1987700 original size:6 final size:6
Alignment explanation
Indices: 1987689--1987713 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1987679 TAAATAAGTT
1987689 TCCCCG TCCCCG TCCCCG TCCCCG T
1 TCCCCG TCCCCG TCCCCG TCCCCG T
1987714 TTATCATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.64, G:0.16, T:0.20
Consensus pattern (6 bp):
TCCCCG
Found at i:1988198 original size:18 final size:18
Alignment explanation
Indices: 1988177--1988219 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1988167 TTTGGCTATT
*
1988177 AATATTTAAATATATAAA
1 AATATCTAAATATATAAA
1988195 AATATCTAAATATATAAA
1 AATATCTAAATATATAAA
1988213 AATATCT
1 AATATCT
1988220 GTAATTGAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (18 bp):
AATATCTAAATATATAAA
Found at i:1991790 original size:29 final size:29
Alignment explanation
Indices: 1991753--1991813 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
1991743 AGTACCGTCC
*
1991753 TTATTAATAGCATACTCTTTTTGATTTGT
1 TTATGAATAGCATACTCTTTTTGATTTGT
*
1991782 TTATGAATAGTATACTCTTTTTGATTTGT
1 TTATGAATAGCATACTCTTTTTGATTTGT
1991811 TTA
1 TTA
1991814 GCTCTCCTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (29 bp):
TTATGAATAGCATACTCTTTTTGATTTGT
Found at i:2000297 original size:6 final size:6
Alignment explanation
Indices: 2000288--2000314 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2000278 TGAGGGTGAT
2000288 GGTGGA GGTGGA GGTGGA GGTGGA GGT
1 GGTGGA GGTGGA GGTGGA GGTGGA GGT
2000315 TAAAATGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.19
Consensus pattern (6 bp):
GGTGGA
Found at i:2000532 original size:19 final size:19
Alignment explanation
Indices: 2000494--2000539 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
2000484 TAATAATGAG
*
2000494 TAATATTAATTTATATATT
1 TAATATTAATGTATATATT
2000513 TAATATTAATGTACTA-ATT
1 TAATATTAATGTA-TATATT
*
2000532 TAGTATTA
1 TAATATTA
2000540 TGTTAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (19 bp):
TAATATTAATGTATATATT
Found at i:2000869 original size:29 final size:29
Alignment explanation
Indices: 2000824--2000907 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 29
2000814 TAAAAATTAT
*
2000824 AATTCATTATACGTAAAACAATTTTAAGC
1 AATTCATTATACATAAAACAATTTTAAGC
* * * * *
2000853 AATTCATTCTACATAAAACAGTTTCCATGT
1 AATTCATTATACATAAAACAATTT-TAAGC
*
2000883 AATTCATTTTA-ATTAAAACAATTTT
1 AATTCATTATACA-TAAAACAATTTT
2000908 CATGTAATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
29 22 0.50
30 22 0.50
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.39
Consensus pattern (29 bp):
AATTCATTATACATAAAACAATTTTAAGC
Found at i:2000938 original size:30 final size:30
Alignment explanation
Indices: 2000853--2000953 Score: 125
Period size: 30 Copynumber: 3.4 Consensus size: 30
2000843 AATTTTAAGC
* *
2000853 AATTCATTCTACA-TAAAACAGTTTCCATGT
1 AATTCATTTTA-ATTAAAACAGTTTTCATGT
*
2000883 AATTCATTTTAATTAAAACAATTTTCATGT
1 AATTCATTTTAATTAAAACAGTTTTCATGT
* *
2000913 AATTCATTTTAATTAAAACCGTTTTCAGGT
1 AATTCATTTTAATTAAAACAGTTTTCATGT
2000943 AA-TCAATTTTA
1 AATTC-ATTTTA
2000954 TTATTTTCTA
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
29 3 0.05
30 60 0.95
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.43
Consensus pattern (30 bp):
AATTCATTTTAATTAAAACAGTTTTCATGT
Found at i:2000952 original size:60 final size:59
Alignment explanation
Indices: 2000823--2000953 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 59
2000813 CTAAAAATTA
* ** *
2000823 TAATTCATTATACGTAAAACAATTTTAAGCAATTCATTCTACATAAAACAGTTTCCATG
1 TAATTCATTTTAATTAAAACAATTTTAAGCAATTCATTCTACATAAAACAGTTTCCAGG
* * * * *
2000882 TAATTCATTTTAATTAAAACAATTTTCATGTAATTCATTTTA-ATTAAAACCGTTTTCAGG
1 TAATTCATTTTAATTAAAACAATTTT-AAGCAATTCATTCTACA-TAAAACAGTTTCCAGG
2000942 TAA-TCAATTTTA
1 TAATTC-ATTTTA
2000954 TTATTTTCTA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
59 26 0.43
60 34 0.57
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.41
Consensus pattern (59 bp):
TAATTCATTTTAATTAAAACAATTTTAAGCAATTCATTCTACATAAAACAGTTTCCAGG
Found at i:2001678 original size:40 final size:40
Alignment explanation
Indices: 2001634--2001743 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 40
2001624 ACGAATCCTC
* *
2001634 TGTTCGTGTTCATTTATTTAATTAAACAAGCACAAAATCT
1 TGTTCGTGTTCGTTTATTTAATTAAACAAACACAAAATCT
* * *
2001674 TGTTCGTATTCGTTCATTTAATTAAACAAATACAAAATCT
1 TGTTCGTGTTCGTTTATTTAATTAAACAAACACAAAATCT
* * * *
2001714 TATTCATGTTCGTTTGTTTAA-TAAATAAAC
1 TGTTCGTGTTCGTTTATTTAATTAAACAAAC
2001744 GAACTTTCAC
Statistics
Matches: 58, Mismatches: 12, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
39 7 0.12
40 51 0.88
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (40 bp):
TGTTCGTGTTCGTTTATTTAATTAAACAAACACAAAATCT
Found at i:2014971 original size:2 final size:2
Alignment explanation
Indices: 2014964--2014993 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2014954 AATATTGGGA
2014964 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2014994 GCAATGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2021273 original size:30 final size:30
Alignment explanation
Indices: 2021239--2021295 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
2021229 TACAATGAGA
2021239 AACGCAAATCATGTCAACCATTACCAATGG
1 AACGCAAATCATGTCAACCATTACCAATGG
2021269 AACGCAAATCATGTCAACCATTACCAA
1 AACGCAAATCATGTCAACCATTACCAA
2021296 AGGGGAAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.28, G:0.11, T:0.19
Consensus pattern (30 bp):
AACGCAAATCATGTCAACCATTACCAATGG
Found at i:2021541 original size:19 final size:19
Alignment explanation
Indices: 2021513--2021553 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
2021503 CCGGAAATGT
*
2021513 TAAAAAATAATATTTTAGG
1 TAAAAAATAATATTTTAAG
*
2021532 TAAAATATAATATTTTAAG
1 TAAAAAATAATATTTTAAG
2021551 TAA
1 TAA
2021554 TTTTTTACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (19 bp):
TAAAAAATAATATTTTAAG
Found at i:2026734 original size:34 final size:32
Alignment explanation
Indices: 2026661--2026736 Score: 80
Period size: 34 Copynumber: 2.3 Consensus size: 32
2026651 TTTTTTTAAT
*
2026661 TTTAATTTTAATTTTATCTTTATAATTAAAGC
1 TTTAATTTTAATTTTATCTTTATAATTAAACC
* ** *
2026693 TCCTAATTTTCGTTTTCATCTTTATAATTGAGACC
1 T-TTAATTTTAATTTT-ATCTTTATAATT-AAACC
2026728 TTTAATTTT
1 TTTAATTTT
2026737 TTAATCCAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
32 1 0.03
33 11 0.31
34 19 0.54
35 4 0.11
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (32 bp):
TTTAATTTTAATTTTATCTTTATAATTAAACC
Found at i:2026797 original size:41 final size:43
Alignment explanation
Indices: 2026713--2026808 Score: 126
Period size: 41 Copynumber: 2.3 Consensus size: 43
2026703 CGTTTTCATC
* * *
2026713 TTTATAATTGAGACCTTTAATTTTTTAATCCAACTTTTTTACA
1 TTTATAATTGAGACCTTTAATTTTTCAATCCAACGTTTGTACA
*
2026756 TTTATAATTGATGACC-TT-ATTTTTCAATCCCA-GTTTGTACA
1 TTTATAATTGA-GACCTTTAATTTTTCAATCCAACGTTTGTACA
2026797 TTTATAATTGAG
1 TTTATAATTGAG
2026809 CTCCTAATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 1 0.02
41 18 0.38
42 12 0.25
43 13 0.27
44 4 0.08
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (43 bp):
TTTATAATTGAGACCTTTAATTTTTCAATCCAACGTTTGTACA
Found at i:2031703 original size:17 final size:17
Alignment explanation
Indices: 2031673--2031711 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
2031663 AAATTATAAA
*
2031673 TAAAA-ATATGAAAAAT
1 TAAAATATATAAAAAAT
2031689 TAAAATATATAAAAAAT
1 TAAAATATATAAAAAAT
*
2031706 TTAAAT
1 TAAAAT
2031712 TTTAAATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (17 bp):
TAAAATATATAAAAAAT
Found at i:2032053 original size:2 final size:2
Alignment explanation
Indices: 2032048--2032076 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2032038 ATAACTGTGT
2032048 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2032077 TTGTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2034109 original size:24 final size:24
Alignment explanation
Indices: 2034082--2034128 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
2034072 AATCTATTCG
*
2034082 TTTATGTTCGTTCATTTATGTTCA
1 TTTATGTCCGTTCATTTATGTTCA
*
2034106 TTTATGTCCGTTCGTTTATGTTC
1 TTTATGTCCGTTCATTTATGTTC
2034129 TCCGAACCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.57
Consensus pattern (24 bp):
TTTATGTCCGTTCATTTATGTTCA
Found at i:2044568 original size:19 final size:19
Alignment explanation
Indices: 2044536--2044579 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
2044526 TGTGTGTGAG
*
2044536 TGAACTGTTAAAGTTTGTTA
1 TGAA-TGTTAAAGTCTGTTA
* *
2044556 TGAATGTTGAAGTCTGTTT
1 TGAATGTTAAAGTCTGTTA
2044575 TGAAT
1 TGAAT
2044580 CTGTTATAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.27, C:0.05, G:0.23, T:0.45
Consensus pattern (19 bp):
TGAATGTTAAAGTCTGTTA
Found at i:2045795 original size:36 final size:36
Alignment explanation
Indices: 2045744--2045885 Score: 241
Period size: 36 Copynumber: 4.0 Consensus size: 36
2045734 GCGTTTCTAG
* *
2045744 TCGAACGGAATGAAGCATCGGCACTTCCGATTTAAA
1 TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAA
*
2045780 TCGAACGGAAGGAAGCATCGGTACTTCCGATTCAAA
1 TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAA
2045816 TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAA
1 TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAA
*
2045852 TCGAACGGAAAGAAGCATC-GCACTTCCGATTCAA
1 TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAA
2045886 CTAGAACGAA
Statistics
Matches: 101, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 15 0.15
36 86 0.85
ACGTcount: A:0.34, C:0.24, G:0.23, T:0.19
Consensus pattern (36 bp):
TCGAACGGAAGGAAGCATCGGCACTTCCGATTCAAA
Found at i:2046589 original size:13 final size:13
Alignment explanation
Indices: 2046573--2046599 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2046563 TGTGTTTAAT
2046573 TCGAGGAAATATA
1 TCGAGGAAATATA
2046586 TCGAGGAAATATA
1 TCGAGGAAATATA
2046599 T
1 T
2046600 TTTAGAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (13 bp):
TCGAGGAAATATA
Found at i:2047497 original size:31 final size:31
Alignment explanation
Indices: 2047461--2047519 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2047451 AACTTAAAAG
* *
2047461 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2047492 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2047520 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2047571 original size:22 final size:22
Alignment explanation
Indices: 2047545--2047589 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
2047535 AATAGTGATA
2047545 ATTTTAAAATAAATCAATCCAT
1 ATTTTAAAATAAATCAATCCAT
*
2047567 ATTTTAAAATAAATCAATTCAT
1 ATTTTAAAATAAATCAATCCAT
2047589 A
1 A
2047590 CTAATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (22 bp):
ATTTTAAAATAAATCAATCCAT
Found at i:2047598 original size:22 final size:22
Alignment explanation
Indices: 2047549--2047597 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2047539 GTGATAATTT
**
2047549 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
2047571 TAAAATAAATCAATTCATACTAA
1 TAAAATAAATCAATCCATA-TAA
2047594 TAAA
1 TAAA
2047598 TTATTTAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:2047685 original size:226 final size:222
Alignment explanation
Indices: 2047184--2047794 Score: 1001
Period size: 226 Copynumber: 2.7 Consensus size: 222
2047174 TTAACGTTTA
* *
2047184 CAGACTGTTAAAATAAACTGAAATATAAATAAACTGATTTTTAAACTTAAAAGAGTTTTGCAATA
1 CAGACTGCTAAAATAAACTGAAATATAAATAAACTGTTTTTTAAACTTAAAAGAGTTTTGCAATA
*
2047249 CTGAGATTTAAATCATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAATAAT
66 CTGAGATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAATAAT
* *
2047314 AAATTTTTTTAAATAAATCAATTCATATTTTAAAATAAATCAATCTATATTGAATAAATTATTTA
131 -AATTTTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATACTGAATAAATTATTTA
*
2047379 ATAAATAACCTTATTAAATTAACGTATG
195 ATAAATAACCTTATTAAATTAACGTAGG
* *
2047407 CAAACTGCTAAAATAAACTAAAATATAAATAAACTGATTTTTTAAACTTAAAAGAGTTTTGCAAT
1 CAGACTGCTAAAATAAACTGAAATATAAATAAACTG-TTTTTTAAACTTAAAAGAGTTTTGCAAT
2047472 ACTGAGATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAATAA
65 ACTGAGATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAATAA
* *
2047537 TAGTGATAATTTTAAAATAAATCAATCCATATTTTAAAATAAATCAAT-TCATACT-AATAAATT
130 TA---AT-TTTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCT-ATACTGAATAAATT
*
2047600 ATTTAATAAATAACCTTATTAAATTAACGTCGG
190 ATTTAATAAATAACCTTATTAAATTAACGTAGG
2047633 CAGACTGCTAAAATAAACTGAAATATAAATAAACTGTTTTTTTAAACTTAAAAGAGTTTTGCAAT
1 CAGACTGCTAAAATAAACTGAAATATAAATAAACTG-TTTTTTAAACTTAAAAGAGTTTTGCAAT
* * *
2047698 ATTGAGATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATCAATTCAACTACAATAA
65 ACTGAGATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAATAA
2047763 TAATTTTTTTAAAATAAATCAATTCATATTTT
130 TAA-TTTTTTAAAATAAATCAATTCATATTTT
2047795 TTAATGTTCT
Statistics
Matches: 362, Mismatches: 19, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
223 60 0.17
224 93 0.26
226 168 0.46
227 41 0.11
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.37
Consensus pattern (222 bp):
CAGACTGCTAAAATAAACTGAAATATAAATAAACTGTTTTTTAAACTTAAAAGAGTTTTGCAATA
CTGAGATTTAAATAATTTTAGTTTTACAATACTGAAATTTAAATAATCCATACAACTACAATAAT
AATTTTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCTATACTGAATAAATTATTTAA
TAAATAACCTTATTAAATTAACGTAGG
Found at i:2047723 original size:31 final size:31
Alignment explanation
Indices: 2047687--2047745 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
2047677 AACTTAAAAG
* * *
2047687 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
2047718 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
2047746 CAATTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:2048448 original size:14 final size:15
Alignment explanation
Indices: 2048424--2048461 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
2048414 ATTATTACTA
2048424 AATATTATTTAT-ATC
1 AATA-TATTTATGATC
2048439 AATATATTTATGATC
1 AATATATTTATGATC
2048454 AA-ATATTT
1 AATATATTT
2048462 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (15 bp):
AATATATTTATGATC
Found at i:2051247 original size:31 final size:28
Alignment explanation
Indices: 2051231--2051290 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
2051221 TTCGGCTCTT
2051231 CTAAAATTATATAAATTCATGTTTGCTC
1 CTAAAATTATATAAATTCATGTTTGCTC
* **
2051259 CTAAAATTTTATAAATTCAAATTTGC-C
1 CTAAAATTATATAAATTCATGTTTGCTC
2051286 CTAAA
1 CTAAA
2051291 CTTAAAATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.21
28 23 0.79
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (28 bp):
CTAAAATTATATAAATTCATGTTTGCTC
Found at i:2051690 original size:17 final size:16
Alignment explanation
Indices: 2051646--2051692 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
2051636 TTGTTTTTAA
2051646 ATTTAATTATCAATATT
1 ATTTAATT-TCAATATT
*
2051663 -TATAATATTCAGATATT
1 ATTTAAT-TTCA-ATATT
2051680 ATTTAATTTCAAT
1 ATTTAATTTCAAT
2051693 TTAAATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
16 10 0.40
17 10 0.40
18 5 0.20
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.51
Consensus pattern (16 bp):
ATTTAATTTCAATATT
Found at i:2054103 original size:7 final size:7
Alignment explanation
Indices: 2054093--2054119 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
2054083 AATCGTTGAA
2054093 GAAGGAT
1 GAAGGAT
2054100 GAAGGAT
1 GAAGGAT
2054107 GAAGGAT
1 GAAGGAT
2054114 GAAGGA
1 GAAGGA
2054120 AAGAGAGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (7 bp):
GAAGGAT
Found at i:2054826 original size:26 final size:27
Alignment explanation
Indices: 2054788--2054840 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
2054778 AGAAAGAAAA
*
2054788 TTTTAAATAATAACCCTCTTAGCTTTT
1 TTTTAAATAATAAACCTCTTAGCTTTT
* *
2054815 TTTTCAAT-ATAAACCTCTTGGCTTTT
1 TTTTAAATAATAAACCTCTTAGCTTTT
2054841 ATAATAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (27 bp):
TTTTAAATAATAAACCTCTTAGCTTTT
Found at i:2056471 original size:25 final size:26
Alignment explanation
Indices: 2056418--2056487 Score: 81
Period size: 25 Copynumber: 2.7 Consensus size: 26
2056408 TGAACAATTC
*
2056418 ACAGATCAATAACTATTTTTTTAACAAT
1 ACAGTTCAATAA--ATTTTTTTAACAAT
*
2056446 ACAGTTCAATAAATTTTTTT-ATAAT
1 ACAGTTCAATAAATTTTTTTAACAAT
*
2056471 ACAGTTTAA-AAATTTTT
1 ACAGTTCAATAAATTTTT
2056488 AAATGTTCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
24 8 0.21
25 12 0.31
26 8 0.21
28 11 0.28
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.44
Consensus pattern (26 bp):
ACAGTTCAATAAATTTTTTTAACAAT
Found at i:2057182 original size:2 final size:2
Alignment explanation
Indices: 2057175--2057210 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2057165 TACCAATAAA
*
2057175 AT AT AT AT AA 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
2057211 TATCTTTTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2058016 original size:29 final size:29
Alignment explanation
Indices: 2057984--2058067 Score: 105
Period size: 30 Copynumber: 2.9 Consensus size: 29
2057974 AAAGGACTTC
* * * *
2057984 ACTTTTCATAAATTATAATAGAGGATAAA
1 ACTTTTCACAAATTAAAATACAAGATAAA
*
2058013 ACTTTTCACAAATTACAAATACAAGTTAAA
1 ACTTTTCACAAATTA-AAATACAAGATAAA
*
2058043 ACTTTTCACAAATTAAAATAAAAGA
1 ACTTTTCACAAATTAAAATACAAGA
2058068 CTGCATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 22 0.47
30 25 0.53
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (29 bp):
ACTTTTCACAAATTAAAATACAAGATAAA
Found at i:2058058 original size:17 final size:17
Alignment explanation
Indices: 2058009--2058060 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
2057999 TAATAGAGGA
2058009 TAAAACTTTTCACAAAT
1 TAAAACTTTTCACAAAT
*
2058026 TACAAA----T-ACAAGT
1 TA-AAACTTTTCACAAAT
2058039 TAAAACTTTTCACAAAT
1 TAAAACTTTTCACAAAT
2058056 TAAAA
1 TAAAA
2058061 TAAAAGACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 3 0.11
13 7 0.26
14 1 0.04
16 1 0.04
17 12 0.44
18 3 0.11
ACGTcount: A:0.52, C:0.15, G:0.02, T:0.31
Consensus pattern (17 bp):
TAAAACTTTTCACAAAT
Found at i:2058104 original size:29 final size:29
Alignment explanation
Indices: 2058072--2058159 Score: 109
Period size: 29 Copynumber: 3.3 Consensus size: 29
2058062 AAAAGACTGC
2058072 ATTTTTCATAAATCACAATAAAGAACAAA
1 ATTTTTCATAAATCACAATAAAGAACAAA
*
2058101 ATTTTTCA-CAAT----A-AAAG-ACAAA
1 ATTTTTCATAAATCACAATAAAGAACAAA
2058123 ATTTTTCATAAATCACAATAAAGAACAAA
1 ATTTTTCATAAATCACAATAAAGAACAAA
*
2058152 ACTTTTCA
1 ATTTTTCA
2058160 CAATAAAAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
22 13 0.27
23 7 0.14
24 1 0.02
27 1 0.02
28 7 0.14
29 20 0.41
ACGTcount: A:0.52, C:0.15, G:0.03, T:0.30
Consensus pattern (29 bp):
ATTTTTCATAAATCACAATAAAGAACAAA
Found at i:2058112 original size:22 final size:22
Alignment explanation
Indices: 2058084--2058179 Score: 86
Period size: 22 Copynumber: 4.0 Consensus size: 22
2058074 TTTTCATAAA
2058084 TCACAAT-AAAGAACAAAATTTT
1 TCACAATAAAAG-ACAAAATTTT
2058106 TCACAATAAAAGACAAAATTTT
1 TCACAATAAAAGACAAAATTTT
* *
2058128 TCATAAATCACAATAAAGAACAAAACTTT
1 TCA-CAAT----A-AAAG-ACAAAATTTT
*
2058157 TCACAATAAAAGACAAATTTTT
1 TCACAATAAAAGACAAAATTTT
2058179 T
1 T
2058180 TTCTAAACGT
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
22 29 0.48
23 11 0.18
24 1 0.02
27 1 0.02
28 7 0.11
29 12 0.20
ACGTcount: A:0.53, C:0.15, G:0.04, T:0.28
Consensus pattern (22 bp):
TCACAATAAAAGACAAAATTTT
Found at i:2058115 original size:51 final size:51
Alignment explanation
Indices: 2058072--2058179 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 51
2058062 AAAAGACTGC
*
2058072 ATTTTTCATAAATCACAATAAAGAACAAAATTTTTCACAATAAAAGACAAA
1 ATTTTTCATAAATCACAATAAAGAACAAAACTTTTCACAATAAAAGACAAA
2058123 ATTTTTCATAAATCACAATAAAGAACAAAACTTTTCACAATAAAAGACAAA
1 ATTTTTCATAAATCACAATAAAGAACAAAACTTTTCACAATAAAAGACAAA
*
2058174 TTTTTT
1 ATTTTT
2058180 TTCTAAACGT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 55 1.00
ACGTcount: A:0.52, C:0.14, G:0.04, T:0.31
Consensus pattern (51 bp):
ATTTTTCATAAATCACAATAAAGAACAAAACTTTTCACAATAAAAGACAAA
Found at i:2059146 original size:23 final size:25
Alignment explanation
Indices: 2059114--2059160 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
2059104 TAAAATATTT
*
2059114 TTTTAGAAAAACAAA-ATTAACATA
1 TTTTAGAAAAAAAAATATTAACATA
2059138 TTTT-GAAAAAAAAATATTAACAT
1 TTTTAGAAAAAAAAATATTAACAT
2059161 CTTTAAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.32
Consensus pattern (25 bp):
TTTTAGAAAAAAAAATATTAACATA
Found at i:2059431 original size:499 final size:499
Alignment explanation
Indices: 2058443--2059947 Score: 3003
Period size: 499 Copynumber: 3.0 Consensus size: 499
2058433 CCCTAAGAAA
2058443 AAAATAAAACGAAAAGAGCAATCAAACGACAAAAAAATGCCATAAAAAAGAAAAATATGTCATAA
1 AAAATAAAACGAAAAGAGCAATCAAACGACAAAAAAATGCCATAAAAAAGAAAAATATGTCATAA
2058508 ATGCATATAAAAGCGAGCAATACACTAACGGAGCCGGTATACAATGAGGACATGACACCCCAAAT
66 ATGCATATAAAAGCGAGCAATACACTAACGGAGCCGGTATACAATGAGGACATGACACCCCAAAT
2058573 TTTTTTGGAAAGAAACCTTTATAAGTTTAATCTAAAAATATTTTTTTAGAAAAACAAAATTAACA
131 TTTTTTGGAAAGAAACCTTTATAAGTTTAATCTAAAAATATTTTTTTAGAAAAACAAAATTAACA
2058638 TATTTTGAAAAAAAAATATTAACATCTTTAAACATAATTTCACACTCATTATTCATTTTTATTCA
196 TATTTTGAAAAAAAAATATTAACATCTTTAAACATAATTTCACACTCATTATTCATTTTTATTCA
2058703 TTTAAAAAATATATTCATATAATTTCTAAATTTGACACTCCAAAATACATTTTAACTAAATTTAA
261 TTTAAAAAATATATTCATATAATTTCTAAATTTGACACTCCAAAATACATTTTAACTAAATTTAA
2058768 CACTCGAAATAAATTTTTTAACTTTGCTCATGATACTATAAAAACATAATTATTAAAAATAAGAA
326 CACTCGAAATAAATTTTTTAACTTTGCTCATGATACTATAAAAACATAATTATTAAAAATAAGAA
2058833 AAAGAAGCAAAGATATTATATAAGTAAATAAACGGAAAATAATAAATACGAATGCTGACAAACAG
391 AAAGAAGCAAAGATATTATATAAGTAAATAAACGGAAAATAATAAATACGAATGCTGACAAACAG
2058898 TACTAGAGCTGGTGCAGCCGTTAGCCAGAAAAAAAATAATTTTG
456 TACTAGAGCTGGTGCAGCCGTTAGCCAGAAAAAAAATAATTTTG
2058942 AAAATAAAACGAAAAGAGCAATCAAACGACAAAAAAATGCCATAAAAAAGAAAAATATGTCATAA
1 AAAATAAAACGAAAAGAGCAATCAAACGACAAAAAAATGCCATAAAAAAGAAAAATATGTCATAA
2059007 ATGCATATAAAAGCGAGCAATACACTAACGGAGCCGGTATACAATGAGGACATGACACCCCAAAT
66 ATGCATATAAAAGCGAGCAATACACTAACGGAGCCGGTATACAATGAGGACATGACACCCCAAAT
2059072 TTTTTTGGAAAGAAACCTTTATAAGTTTAATCT-AAAATATTTTTTTAGAAAAACAAAATTAACA
131 TTTTTTGGAAAGAAACCTTTATAAGTTTAATCTAAAAATATTTTTTTAGAAAAACAAAATTAACA
2059136 TATTTTGAAAAAAAAATATTAACATCTTTAAACATAATTTCACACTCATTATTCATTTTTATTCA
196 TATTTTGAAAAAAAAATATTAACATCTTTAAACATAATTTCACACTCATTATTCATTTTTATTCA
2059201 TTTAAAAAATATATTCATATAATTTCTAAATTTGACACTCCAAAATACATTTTAACTAAATTTAA
261 TTTAAAAAATATATTCATATAATTTCTAAATTTGACACTCCAAAATACATTTTAACTAAATTTAA
2059266 CACTCGAAATAAATTTTTTAACTTTGCTCATGATACTATAAAAACATAATTATTAAAAATAAGAA
326 CACTCGAAATAAATTTTTTAACTTTGCTCATGATACTATAAAAACATAATTATTAAAAATAAGAA
2059331 AAAGAAGCAAAGATATTATATAAGTAAATAAACGGAAAATAATAAATACGAATGCTGACAAACAG
391 AAAGAAGCAAAGATATTATATAAGTAAATAAACGGAAAATAATAAATACGAATGCTGACAAACAG
2059396 TACTAGAGCTGGTGCAGCCGTTAGCCAGAAAAAAAATAATTTTG
456 TACTAGAGCTGGTGCAGCCGTTAGCCAGAAAAAAAATAATTTTG
2059440 AAAATAAAACGAAAAGAGCAATCAAACGACAAAAAAATGCCATAAAAAAGAAAAATATGTCATAA
1 AAAATAAAACGAAAAGAGCAATCAAACGACAAAAAAATGCCATAAAAAAGAAAAATATGTCATAA
2059505 ATGCATATAAAAGCGAGCAATACACTAACGGAGCCGGTATACAATGAGGACATGACACCCCAAAT
66 ATGCATATAAAAGCGAGCAATACACTAACGGAGCCGGTATACAATGAGGACATGACACCCCAAAT
2059570 TTTTTTGGAAAGAAACCTTTATAAGTTTAATCTAAAAATATTTTTTTAGAAAAACAAAATTAACA
131 TTTTTTGGAAAGAAACCTTTATAAGTTTAATCTAAAAATATTTTTTTAGAAAAACAAAATTAACA
2059635 TATTTTGAAAAAAAAATATTAACATCTTTAAACATAATTTCACACTCATTATTCATTTTTATTCA
196 TATTTTGAAAAAAAAATATTAACATCTTTAAACATAATTTCACACTCATTATTCATTTTTATTCA
2059700 TTTAAAAAATATATTCATATAATTTCTAAATTTGACACTCCAAAATACATTTTAACTAAATTTAA
261 TTTAAAAAATATATTCATATAATTTCTAAATTTGACACTCCAAAATACATTTTAACTAAATTTAA
2059765 CACTCGAAATAAATTTTTTAACTTTGCTCATGATACTATAAAAACATAATTATTAAAAATAAGAA
326 CACTCGAAATAAATTTTTTAACTTTGCTCATGATACTATAAAAACATAATTATTAAAAATAAGAA
2059830 AAAGAAGCAAAGATATTATATAAGTAAATAAACGGAAAATAATAAATACGAATGCTGACAAACAG
391 AAAGAAGCAAAGATATTATATAAGTAAATAAACGGAAAATAATAAATACGAATGCTGACAAACAG
2059895 TACTAGAGCTGGTGCAGCCGTTAGCCAGAAAAAAAATAATTTTG
456 TACTAGAGCTGGTGCAGCCGTTAGCCAGAAAAAAAATAATTTTG
2059939 AAAATAAAA
1 AAAATAAAA
2059948 GACGAGTTTT
Statistics
Matches: 1005, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
498 498 0.50
499 507 0.50
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.28
Consensus pattern (499 bp):
AAAATAAAACGAAAAGAGCAATCAAACGACAAAAAAATGCCATAAAAAAGAAAAATATGTCATAA
ATGCATATAAAAGCGAGCAATACACTAACGGAGCCGGTATACAATGAGGACATGACACCCCAAAT
TTTTTTGGAAAGAAACCTTTATAAGTTTAATCTAAAAATATTTTTTTAGAAAAACAAAATTAACA
TATTTTGAAAAAAAAATATTAACATCTTTAAACATAATTTCACACTCATTATTCATTTTTATTCA
TTTAAAAAATATATTCATATAATTTCTAAATTTGACACTCCAAAATACATTTTAACTAAATTTAA
CACTCGAAATAAATTTTTTAACTTTGCTCATGATACTATAAAAACATAATTATTAAAAATAAGAA
AAAGAAGCAAAGATATTATATAAGTAAATAAACGGAAAATAATAAATACGAATGCTGACAAACAG
TACTAGAGCTGGTGCAGCCGTTAGCCAGAAAAAAAATAATTTTG
Found at i:2060628 original size:12 final size:12
Alignment explanation
Indices: 2060611--2060649 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2060601 ATTATTTAAA
2060611 AAAAAATGCATG
1 AAAAAATGCATG
2060623 AAAAAATGCATG
1 AAAAAATGCATG
*
2060635 --AATATGCATG
1 AAAAAATGCATG
2060645 AAAAA
1 AAAAA
2060650 TCAGCCGTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.39
12 14 0.61
ACGTcount: A:0.59, C:0.08, G:0.15, T:0.18
Consensus pattern (12 bp):
AAAAAATGCATG
Found at i:2060666 original size:34 final size:34
Alignment explanation
Indices: 2060626--2060706 Score: 117
Period size: 34 Copynumber: 2.4 Consensus size: 34
2060616 ATGCATGAAA
* * *
2060626 AAATGCATGAATATGCATGAAAAATCAGCCGTCC
1 AAATGCATGAAAATGCATGAAAAACCAGCCATCC
* *
2060660 ACATGCATGAAAATGCATGAAAAACCAGTCATCC
1 AAATGCATGAAAATGCATGAAAAACCAGCCATCC
2060694 AAATGCATGAAAA
1 AAATGCATGAAAA
2060707 AGGTGGGTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 41 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.19
Consensus pattern (34 bp):
AAATGCATGAAAATGCATGAAAAACCAGCCATCC
Found at i:2060725 original size:17 final size:17
Alignment explanation
Indices: 2060703--2060737 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2060693 CAAATGCATG
2060703 AAAAAGGTGGGTGTCGC
1 AAAAAGGTGGGTGTCGC
2060720 AAAAAGGTGGGTGTCGC
1 AAAAAGGTGGGTGTCGC
2060737 A
1 A
2060738 TGGTATTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.40, T:0.17
Consensus pattern (17 bp):
AAAAAGGTGGGTGTCGC
Found at i:2062451 original size:18 final size:19
Alignment explanation
Indices: 2062415--2062452 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
2062405 TTTTCAAAGT
*
2062415 TTATGAGTTATTTTGAAAA
1 TTATGAGTTATTTTAAAAA
*
2062434 TTATGTGTT-TTTTAAAAA
1 TTATGAGTTATTTTAAAAA
2062452 T
1 T
2062453 ATATAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (19 bp):
TTATGAGTTATTTTAAAAA
Found at i:2071320 original size:18 final size:19
Alignment explanation
Indices: 2071294--2071329 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2071284 GTAGTGTCTA
*
2071294 TCCTTAAATTTT-TTTGTG
1 TCCTGAAATTTTATTTGTG
2071312 TCCTGAAATTTTATTTGT
1 TCCTGAAATTTTATTTGT
2071330 ATTTATCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (19 bp):
TCCTGAAATTTTATTTGTG
Found at i:2084350 original size:21 final size:21
Alignment explanation
Indices: 2084326--2084445 Score: 109
Period size: 21 Copynumber: 5.8 Consensus size: 21
2084316 TGCATTTCGT
2084326 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
* ** **
2084347 GTTGCGAT-TTTCCATTTCGC
1 GTTGCGATAGTTGAAAATCGC
2084367 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
** * ** **
2084388 GACGCGAT-TTTCCATTTCGC
1 GTTGCGATAGTTGAAAATCGC
2084408 GTTGCGATAGTTGAAAATCGC
1 GTTGCGATAGTTGAAAATCGC
*
2084429 GTTGCGATAGTTAAAAA
1 GTTGCGATAGTTGAAAA
2084446 AAAGATTTTG
Statistics
Matches: 72, Mismatches: 25, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
20 28 0.39
21 44 0.61
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
GTTGCGATAGTTGAAAATCGC
Found at i:2084363 original size:41 final size:41
Alignment explanation
Indices: 2084318--2084436 Score: 211
Period size: 41 Copynumber: 2.9 Consensus size: 41
2084308 ATTCGCGTTG
*
2084318 CATTTCGTGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
**
2084359 CATTTCGCGTTGCGATAGTTGAAAATCGCGACGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
2084400 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGAT
2084437 AGTTAAAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.34
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:2084368 original size:20 final size:20
Alignment explanation
Indices: 2084343--2084415 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
2084333 TAGTTGAAAA
2084343 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
2084363 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
**
2084384 TCGCGACGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
2084404 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2084416 AGTTGAAAAT
Statistics
Matches: 38, Mismatches: 14, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
20 25 0.66
21 13 0.34
ACGTcount: A:0.16, C:0.23, G:0.25, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2085192 original size:20 final size:20
Alignment explanation
Indices: 2085167--2085239 Score: 92
Period size: 20 Copynumber: 3.6 Consensus size: 20
2085157 ACTGTAGACT
2085167 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
2085187 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
2085208 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
2085228 ATCGCAACGCGA
1 ATCGCAACGCGA
2085240 TTTGCGATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:2085209 original size:41 final size:41
Alignment explanation
Indices: 2085164--2085242 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
2085154 ACAACTGTAG
2085164 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
2085205 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTT
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTT
2085243 GCGATTTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:2085361 original size:41 final size:41
Alignment explanation
Indices: 2085304--2085454 Score: 252
Period size: 41 Copynumber: 3.7 Consensus size: 41
2085294 AGATCGCGTT
*
2085304 GCGA-TTTCAACTATCGCAACGCGAAAT-GAAAAATCGCAAT
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAAA-CGCAAC
2085344 GCGATTTTCAACTATCGCAACGCGAAATGGAAAAACGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAAACGCAAC
2085385 GCGATTTTCAACTATCGCAACGCGAAATGGAAAAACGCAAC
1 GCGATTTTCAACTATCGCAACGCGAAATGGAAAAACGCAAC
* *
2085426 GCGATTTTCAACTATCGCAATGCAAAATG
1 GCGATTTTCAACTATCGCAACGCGAAATG
2085455 CAACGTGAAT
Statistics
Matches: 106, Mismatches: 3, Indels: 3
0.95 0.03 0.03
Matches are distributed among these distances:
40 4 0.04
41 96 0.91
42 6 0.06
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
GCGATTTTCAACTATCGCAACGCGAAATGGAAAAACGCAAC
Found at i:2085362 original size:21 final size:21
Alignment explanation
Indices: 2085304--2085445 Score: 94
Period size: 20 Copynumber: 7.0 Consensus size: 21
2085294 AGATCGCGTT
2085304 GCGA-TTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** * ** *
2085324 GCGA-AATGAAAAATCGCAAT
1 GCGATTTTCAACTATCGCAAC
2085344 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * *
2085365 GCGAAATGGAA-AAACGCAAC
1 GCGATTTTCAACTATCGCAAC
2085385 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** * *
2085406 GCGAAATGGAA-AAACGCAAC
1 GCGATTTTCAACTATCGCAAC
2085426 GCGATTTTCAACTATCGCAA
1 GCGATTTTCAACTATCGCAA
2085446 TGCAAAATGC
Statistics
Matches: 83, Mismatches: 36, Indels: 5
0.67 0.29 0.04
Matches are distributed among these distances:
20 46 0.55
21 37 0.45
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:2086801 original size:16 final size:16
Alignment explanation
Indices: 2086782--2086815 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2086772 AAAATTTAGA
*
2086782 ATTTTAAAATAGATAT
1 ATTTTAAAATAAATAT
*
2086798 ATTTTAGAATAAATAT
1 ATTTTAAAATAAATAT
2086814 AT
1 AT
2086816 AATATTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTTAAAATAAATAT
Found at i:2092741 original size:30 final size:30
Alignment explanation
Indices: 2092701--2092769 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
2092691 CATTTTACAT
*
2092701 AAATAGCACCCCTTTTTAAAATAATAACCA
1 AAATAGCACCCCTTTTCAAAATAATAACCA
* ** *
2092731 AAATATCA-CCCTTTTCAAGTTAATTACCA
1 AAATAGCACCCCTTTTCAAAATAATAACCA
2092760 AAATAGCACC
1 AAATAGCACC
2092770 AAAATCGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.43, C:0.25, G:0.04, T:0.28
Consensus pattern (30 bp):
AAATAGCACCCCTTTTCAAAATAATAACCA
Found at i:2092836 original size:17 final size:17
Alignment explanation
Indices: 2092814--2092849 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2092804 ACGTCAACGA
*
2092814 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGACGGG
2092831 TCAACGGTCGGGACGGG
1 TCAACGGTCGGGACGGG
2092848 TC
1 TC
2092850 GGACCAGTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.25, G:0.44, T:0.17
Consensus pattern (17 bp):
TCAACGGTCGGGACGGG
Found at i:2095461 original size:2 final size:2
Alignment explanation
Indices: 2095454--2095502 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2095444 GAATATTTTA
2095454 AT 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 AT
2095496 AT AT AT A
1 AT AT AT A
2095503 ATCTCACCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2102022 original size:352 final size:352
Alignment explanation
Indices: 2101177--2102233 Score: 1974
Period size: 352 Copynumber: 3.0 Consensus size: 352
2101167 TTGTTTGGCC
2101177 CATTACGACACTCTCGTTTTTATTTTACAATCTATGACAAATGCTATAGTATAGGGGAACTCGTC
1 CATTACGACACTCTCGTTTTTATTTTACAATCTATGACAAATGCTATAGTATAGGGGAACTCGTC
2101242 ACCTCGAAGTGATGAGTTCCGTTGGATATATTATTTTATTGGTCCCAATTTAGTGAGCCCAACGT
66 ACCTCGAAGTGATGAGTTCCGTTGGATATATTATTTTATTGGTCCCAATTTAGTGAGCCCAACGT
2101307 GAACTATTATATTAATTTATTTAATGGGACTCGGCACGTCGAGATGACGAGTCCCTAGAGAAATT
131 GAACTATTATATTAATTTATTTAATGGGACTCGGCACGTCGAGATGACGAGTCCCTAGAGAAATT
2101372 ATTTAAAAATAATAATTTAAAATTTTAATTAAAAGTATAAATTAAT-AAAAAAATGTGAGGTGAC
196 ATTTAAAAATAATAATTTAAAATTTTAATTAAAAGTATAAATTAATAAAAAAAATGTGAGGTGAC
*
2101436 GAGTTCCTTTGAATTCAAATAAACTAATCGTTTAGAGCTGTTGGACAACGGACAATAATGGTTAG
261 GAGTTCCTTTGAATTCAAATAAACTAATCGTTTAGAGCTGTTGGACAACGGACAATAACGGTTAG
2101501 TTGTCAACGATCAACAATGAAACTCGT
326 TTGTCAACGATCAACAATGAAACTCGT
2101528 CATTACGACACTCTCGTTTTTATTTTACAATCTATGACAAATGCTATAGTATAGGGGAACTCGTC
1 CATTACGACACTCTCGTTTTTATTTTACAATCTATGACAAATGCTATAGTATAGGGGAACTCGTC
2101593 ACCTCGAAGTGATGAGTTCCGTTGGATATATTATTTTATTGGTCCCAATTTAGTGAGCCCAACGT
66 ACCTCGAAGTGATGAGTTCCGTTGGATATATTATTTTATTGGTCCCAATTTAGTGAGCCCAACGT
* *
2101658 GAACTATTATATTAATTTATTTAATGAGACTCGGCACGTCGAGATGACGAGTCCCTATAGAAATT
131 GAACTATTATATTAATTTATTTAATGGGACTCGGCACGTCGAGATGACGAGTCCCTAGAGAAATT
2101723 ATTTAAAAATAATAATTTAAAATTTTAATTAAAAGTATAAATTAATAAAAAAAATGTGAGGTGAC
196 ATTTAAAAATAATAATTTAAAATTTTAATTAAAAGTATAAATTAATAAAAAAAATGTGAGGTGAC
*
2101788 GAGTTCCTTTGAATTCAAATAAATTAATCGTTTAGAGCTGTTGGACAACGGACAATAACGGTTAG
261 GAGTTCCTTTGAATTCAAATAAACTAATCGTTTAGAGCTGTTGGACAACGGACAATAACGGTTAG
*
2101853 TTGTTAACGATCAACAATGAAACTCGT
326 TTGTCAACGATCAACAATGAAACTCGT
2101880 CATTACGACACTCTCGTTTTTATTTTACAATCTATGACAAATGCTATAGTATAGGGGAACTCGTC
1 CATTACGACACTCTCGTTTTTATTTTACAATCTATGACAAATGCTATAGTATAGGGGAACTCGTC
* *
2101945 ACCTCGAAGTGATGAGTTCCGTTGGATATATTATTTTATTGGTCCCAATTTAGTGAGCACATCGT
66 ACCTCGAAGTGATGAGTTCCGTTGGATATATTATTTTATTGGTCCCAATTTAGTGAGCCCAACGT
*
2102010 GAACTATTATATTAATTTATTTAATGGGACTCGGCACGTCGAGATGACTAGTCCCTAGAGAAATT
131 GAACTATTATATTAATTTATTTAATGGGACTCGGCACGTCGAGATGACGAGTCCCTAGAGAAATT
2102075 ATTTAAAAATAATAATTTAAAATTTTAATTAAAAGTATAAATTAATAAAAAAAA-GTGAGGTGAC
196 ATTTAAAAATAATAATTTAAAATTTTAATTAAAAGTATAAATTAATAAAAAAAATGTGAGGTGAC
* * * * * *
2102139 GAGTTCTTTTGAATTCAAATAAACTAGTCGTTTATAACTGTTGGACAACGAACAATAACGGTCAG
261 GAGTTCCTTTGAATTCAAATAAACTAATCGTTTAGAGCTGTTGGACAACGGACAATAACGGTTAG
2102204 TTGTCAACGATCAACAATGAAACTCGT
326 TTGTCAACGATCAACAATGAAACTCGT
2102231 CAT
1 CAT
2102234 CTCGATGTAA
Statistics
Matches: 687, Mismatches: 18, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
351 336 0.49
352 351 0.51
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (352 bp):
CATTACGACACTCTCGTTTTTATTTTACAATCTATGACAAATGCTATAGTATAGGGGAACTCGTC
ACCTCGAAGTGATGAGTTCCGTTGGATATATTATTTTATTGGTCCCAATTTAGTGAGCCCAACGT
GAACTATTATATTAATTTATTTAATGGGACTCGGCACGTCGAGATGACGAGTCCCTAGAGAAATT
ATTTAAAAATAATAATTTAAAATTTTAATTAAAAGTATAAATTAATAAAAAAAATGTGAGGTGAC
GAGTTCCTTTGAATTCAAATAAACTAATCGTTTAGAGCTGTTGGACAACGGACAATAACGGTTAG
TTGTCAACGATCAACAATGAAACTCGT
Found at i:2103478 original size:22 final size:22
Alignment explanation
Indices: 2103453--2103496 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2103443 TTAATTTCTC
2103453 ATTCTCTTAAGCTTAACATTTA
1 ATTCTCTTAAGCTTAACATTTA
2103475 ATTCTCTTAAGCTTAACATTTA
1 ATTCTCTTAAGCTTAACATTTA
2103497 TCAATCTCAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (22 bp):
ATTCTCTTAAGCTTAACATTTA
Found at i:2108653 original size:58 final size:57
Alignment explanation
Indices: 2108591--2108764 Score: 153
Period size: 58 Copynumber: 3.2 Consensus size: 57
2108581 TATATATCAT
2108591 ATATTGTATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTA
1 ATATT-TATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTA
* * *
2108649 ATATTCATTCTATATAA-AGA-GAAA-A-AA-G-T-T--A-ACTC-GT--ATT-ACTT-
1 ATATTTATT-TATA-AATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTA
*
2108693 TTATTTGATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTA
1 ATATTT-ATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTA
*
2108751 ATATTCATTCTATA
1 ATATTTATT-TATA
2108765 TAAAGAGAAA
Statistics
Matches: 88, Mismatches: 9, Indels: 38
0.65 0.07 0.28
Matches are distributed among these distances:
43 2 0.02
44 10 0.11
45 11 0.12
46 4 0.05
47 2 0.02
48 2 0.02
49 5 0.06
50 2 0.02
52 2 0.02
53 5 0.06
54 2 0.02
55 2 0.02
56 4 0.05
57 14 0.16
58 19 0.22
59 2 0.02
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (57 bp):
ATATTTATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTA
Found at i:2108774 original size:102 final size:102
Alignment explanation
Indices: 2108598--2108798 Score: 402
Period size: 102 Copynumber: 2.0 Consensus size: 102
2108588 CATATATTGT
2108598 ATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTAATATTCATTCTATA
1 ATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTAATATTCATTCTATA
2108663 TAAAGAGAAAAAAGTTAACTCGTATTACTTTTATTTG
66 TAAAGAGAAAAAAGTTAACTCGTATTACTTTTATTTG
2108700 ATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTAATATTCATTCTATA
1 ATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTAATATTCATTCTATA
2108765 TAAAGAGAAAAAAGTTAACTCGTATTACTTTTAT
66 TAAAGAGAAAAAAGTTAACTCGTATTACTTTTAT
2108799 CCCGTTAGAG
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (102 bp):
ATTTATAAATCGATGAAAGACAACGTTATAAATACTCAATAGATTGACTTAATATTCATTCTATA
TAAAGAGAAAAAAGTTAACTCGTATTACTTTTATTTG
Found at i:2108832 original size:102 final size:102
Alignment explanation
Indices: 2108624--2108927 Score: 335
Period size: 102 Copynumber: 3.0 Consensus size: 102
2108614 AAGACAACGT
2108624 TATAAATACTCAATAGATTGACTTAATATTCATTCTATATAAAGAGAAAAAAGTTAACTCGTATT
1 TATAAATACTCAATAGATTGACTTAATATTCATTCTATATAAAGAGAAAAAAGTTAACTCGTATT
** * ** * *
2108689 ACTTTTAT-TTGATTTATA-AA-T-CGATGA-AAGACAACGT
66 ACTTTTATCCCG--TTAGAGAATTATTATGACGAGA-AA--A
2108726 TATAAATACTCAATAGATTGACTTAATATTCATTCTATATAAAGAGAAAAAAGTTAACTCGTATT
1 TATAAATACTCAATAGATTGACTTAATATTCATTCTATATAAAGAGAAAAAAGTTAACTCGTATT
2108791 ACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAA
66 ACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAA
* * * * * * * * *
2108828 TATAATTTCTTAAAAGA-T--CATAACA-ACA--CAACA-AAAGAGAAAAAAGTTAACTCGTATT
1 TATAAATACTCAATAGATTGACTTAATATTCATTCTATATAAAGAGAAAAAAGTTAACTCGTATT
2108886 ACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAA
66 ACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAA
2108923 TATAA
1 TATAA
2108928 TTTCTTAAAA
Statistics
Matches: 181, Mismatches: 16, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
95 67 0.37
96 3 0.02
98 2 0.01
99 5 0.03
101 5 0.03
102 88 0.49
103 2 0.01
104 6 0.03
105 3 0.02
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (102 bp):
TATAAATACTCAATAGATTGACTTAATATTCATTCTATATAAAGAGAAAAAAGTTAACTCGTATT
ACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAA
Found at i:2108929 original size:95 final size:96
Alignment explanation
Indices: 2108766--2108957 Score: 377
Period size: 95 Copynumber: 2.0 Consensus size: 96
2108756 CATTCTATAT
2108766 AAAGAGAAAAAAGTTAACTCGTATTACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAATAT
1 AAAGAGAAAAAAGTTAACTCGTATTACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAATAT
2108831 AATTTCTTAAAAGATCATAACAAC-ACAACA
66 AATTTCTTAAAAGATCATAACAACAACAACA
2108861 AAAGAGAAAAAAGTTAACTCGTATTACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAATAT
1 AAAGAGAAAAAAGTTAACTCGTATTACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAATAT
2108926 AATTTCTTAAAAGATCATAACAACAACAACA
66 AATTTCTTAAAAGATCATAACAACAACAACA
2108957 A
1 A
2108958 CAAAAATTAA
Statistics
Matches: 96, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 89 0.93
96 7 0.07
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (96 bp):
AAAGAGAAAAAAGTTAACTCGTATTACTTTTATCCCGTTAGAGAATTATTATGACGAGAAAATAT
AATTTCTTAAAAGATCATAACAACAACAACA
Found at i:2114102 original size:34 final size:34
Alignment explanation
Indices: 2114064--2114147 Score: 95
Period size: 34 Copynumber: 2.5 Consensus size: 34
2114054 GTAATAAACA
*
2114064 AAATTAATCAAAATACATTAACAA-AAAGTCCAA-C
1 AAATTAATCAAAATAAATTAA-AATAAA-TCCAACC
2114098 AAATTTAA-CAAAATAAATTAAAATAAATCCAACC
1 AAA-TTAATCAAAATAAATTAAAATAAATCCAACC
*
2114132 AAATTAAT-GAAATAAA
1 AAATTAATCAAAATAAA
2114148 GTAAGTATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
33 18 0.41
34 22 0.50
35 4 0.09
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.23
Consensus pattern (34 bp):
AAATTAATCAAAATAAATTAAAATAAATCCAACC
Found at i:2114685 original size:33 final size:33
Alignment explanation
Indices: 2114625--2114688 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
2114615 TCCTCCAGGA
** * *
2114625 GGGGTCATAAAACTCTGTGACGGTGGCGGCGAC
1 GGGGTCATAAAACTAGGCGACGATGGCGGCGAC
2114658 GGGGTCATAAAACTAGGCGACGATGGCGGCG
1 GGGGTCATAAAACTAGGCGACGATGGCGGCG
2114689 GCGACATCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.23, C:0.20, G:0.41, T:0.16
Consensus pattern (33 bp):
GGGGTCATAAAACTAGGCGACGATGGCGGCGAC
Found at i:2115912 original size:30 final size:30
Alignment explanation
Indices: 2115855--2115957 Score: 172
Period size: 30 Copynumber: 3.5 Consensus size: 30
2115845 AGTTCGAATA
*
2115855 AAGGTCGCCGGGTGGTCTGGG-GACCAATG
1 AAGGTCGCCGGGTGTTCTGGGCGACCAATG
*
2115884 AAGGTCGTCGGGTGTTCTGGGCGACCAATG
1 AAGGTCGCCGGGTGTTCTGGGCGACCAATG
2115914 AAGGTCGCCGGGTGTTCTGGGCGACCAATG
1 AAGGTCGCCGGGTGTTCTGGGCGACCAATG
*
2115944 AAGGTCGCCAGGTG
1 AAGGTCGCCGGGTG
2115958 ATCCATGGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
29 19 0.28
30 50 0.72
ACGTcount: A:0.17, C:0.21, G:0.42, T:0.19
Consensus pattern (30 bp):
AAGGTCGCCGGGTGTTCTGGGCGACCAATG
Found at i:2115974 original size:60 final size:58
Alignment explanation
Indices: 2115855--2115976 Score: 147
Period size: 60 Copynumber: 2.1 Consensus size: 58
2115845 AGTTCGAATA
* * * **
2115855 AAGGTCGCCGGGTGGTCTGGGGACCAATGAAGGTCGTCGGGTGTTCTGGGCGACCAATG
1 AAGGTCGCCGGGTGGTCTGGGGACCAATGAAGGTCGCCAGGTGTCCTGGAAGA-CAATG
*
2115914 AAGGTCGCCGGGTGTTCTGGGCGACCAATGAAGGTCGCCAGGTGATCCATGGAAGA-AATG
1 AAGGTCGCCGGGTGGTCTGGG-GACCAATGAAGGTCGCCAGGTG-TCC-TGGAAGACAATG
2115974 AAG
1 AAG
2115977 AAAAGCAAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
59 20 0.37
60 27 0.50
61 2 0.04
62 5 0.09
ACGTcount: A:0.22, C:0.20, G:0.39, T:0.19
Consensus pattern (58 bp):
AAGGTCGCCGGGTGGTCTGGGGACCAATGAAGGTCGCCAGGTGTCCTGGAAGACAATG
Found at i:2116603 original size:50 final size:50
Alignment explanation
Indices: 2116542--2116693 Score: 304
Period size: 50 Copynumber: 3.0 Consensus size: 50
2116532 AAAATTATTG
2116542 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
2116592 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
2116642 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
1 AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
2116692 AA
1 AA
2116694 ATAGGATAAA
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 102 1.00
ACGTcount: A:0.57, C:0.16, G:0.02, T:0.26
Consensus pattern (50 bp):
AATACAAAACAAGATATCCCAATAATCAATTTTAAAATAAATACATACTA
Found at i:2116873 original size:30 final size:30
Alignment explanation
Indices: 2116834--2116915 Score: 92
Period size: 34 Copynumber: 2.6 Consensus size: 30
2116824 TCCCATGGAT
* *
2116834 CACCTGGCGACCTTCATTGGTCGCCCATAA
1 CACCCGGCGACCTTCATTGGTCGCCCAGAA
* *
2116864 CACCCGGCGACCGACCTTCATTGGTCGCCTAGAC
1 CACCC-G-G--CGACCTTCATTGGTCGCCCAGAA
2116898 CACCCGGCGACCTTCATT
1 CACCCGGCGACCTTCATT
2116916 CGAACTGTAG
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
30 15 0.34
31 1 0.02
32 2 0.05
33 1 0.02
34 25 0.57
ACGTcount: A:0.18, C:0.40, G:0.21, T:0.21
Consensus pattern (30 bp):
CACCCGGCGACCTTCATTGGTCGCCCAGAA
Found at i:2116881 original size:34 final size:34
Alignment explanation
Indices: 2116841--2116909 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
2116831 GATCACCTGG
*
2116841 CGACCTTCATTGGTCGCCCATAACACCCGGCGAC
1 CGACCTTCATTGGTCGCCCAGAACACCCGGCGAC
* *
2116875 CGACCTTCATTGGTCGCCTAGACCACCCGGCGAC
1 CGACCTTCATTGGTCGCCCAGAACACCCGGCGAC
2116909 C
1 C
2116910 TTCATTCGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.19, C:0.42, G:0.22, T:0.17
Consensus pattern (34 bp):
CGACCTTCATTGGTCGCCCAGAACACCCGGCGAC
Found at i:2117219 original size:17 final size:17
Alignment explanation
Indices: 2117197--2117251 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
2117187 TATATCTGCA
*
2117197 AAAATAATTAATTAAAT
1 AAAATAATTAAATAAAT
*
2117214 AAAAT-ATTAAAAAAAT
1 AAAATAATTAAATAAAT
* *
2117230 TAAATACTTAAATAAATT
1 AAAATAATTAAATAAA-T
2117248 AAAA
1 AAAA
2117252 ACAAAATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.43
17 13 0.43
18 4 0.13
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAATTAAATAAAT
Found at i:2117251 original size:24 final size:23
Alignment explanation
Indices: 2117215--2117277 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
2117205 TAATTAAATA
*
2117215 AAATATTAA-AAAAATTAAATACTT
1 AAATA-TAATAAAAATAAAATA-TT
*
2117239 AAATA-AATTAAAAACAAAATATT
1 AAATATAA-TAAAAATAAAATATT
2117262 AAATATAATAAAAATA
1 AAATATAATAAAAATA
2117278 TACATTAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 2 0.06
23 14 0.42
24 17 0.52
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (23 bp):
AAATATAATAAAAATAAAATATT
Found at i:2117263 original size:23 final size:24
Alignment explanation
Indices: 2117231--2117275 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
2117221 TAAAAAAATT
2117231 AAATACTTAAATA-AATTAAAAACA
1 AAATACTTAAATATAA-TAAAAACA
2117255 AAATA-TTAAATATAATAAAAA
1 AAATACTTAAATATAATAAAAA
2117276 TATACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (24 bp):
AAATACTTAAATATAATAAAAACA
Found at i:2119852 original size:28 final size:28
Alignment explanation
Indices: 2119821--2119887 Score: 134
Period size: 28 Copynumber: 2.4 Consensus size: 28
2119811 TCTTTCTAGC
2119821 TTCCATTTTCCAAGTATTTCTTTACTTA
1 TTCCATTTTCCAAGTATTTCTTTACTTA
2119849 TTCCATTTTCCAAGTATTTCTTTACTTA
1 TTCCATTTTCCAAGTATTTCTTTACTTA
2119877 TTCCATTTTCC
1 TTCCATTTTCC
2119888 CACCATCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.54
Consensus pattern (28 bp):
TTCCATTTTCCAAGTATTTCTTTACTTA
Found at i:2129890 original size:14 final size:14
Alignment explanation
Indices: 2129871--2129913 Score: 77
Period size: 14 Copynumber: 3.0 Consensus size: 14
2129861 TGACTATGAC
2129871 TGAAAATTTGAATT
1 TGAAAATTTGAATT
2129885 TGAAAATTTGAATTT
1 TGAAAATTTGAA-TT
2129900 TGAAAATTTGAATT
1 TGAAAATTTGAATT
2129914 AGAGTTCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 14 0.50
15 14 0.50
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (14 bp):
TGAAAATTTGAATT
Found at i:2129892 original size:8 final size:8
Alignment explanation
Indices: 2129871--2129911 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
2129861 TGACTATGAC
2129871 TGAAAATT
1 TGAAAATT
2129879 TG--AATT
1 TGAAAATT
2129885 TGAAAATT
1 TGAAAATT
*
2129893 TG-AATTT
1 TGAAAATT
2129900 TGAAAATT
1 TGAAAATT
2129908 TGAA
1 TGAA
2129912 TTAGAGTTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
6 6 0.21
7 6 0.21
8 16 0.57
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (8 bp):
TGAAAATT
Found at i:2129903 original size:15 final size:15
Alignment explanation
Indices: 2129871--2129913 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
2129861 TGACTATGAC
2129871 TGAAAATTTGAA-TT
1 TGAAAATTTGAATTT
2129885 TGAAAATTTGAATTT
1 TGAAAATTTGAATTT
2129900 TGAAAATTTGAATT
1 TGAAAATTTGAATT
2129914 AGAGTTCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 12 0.43
15 16 0.57
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (15 bp):
TGAAAATTTGAATTT
Found at i:2133089 original size:31 final size:30
Alignment explanation
Indices: 2133032--2133089 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
2133022 GTTATTTTGA
* *
2133032 AAAAATTAATTAAATTAAATATAAAAATAT
1 AAAAATTAATTAAATTAAACAAAAAAATAT
**
2133062 AAAAATTAAATTAAATTACCCAAAAAAA
1 AAAAATT-AATTAAATTAAACAAAAAAA
2133090 CTAAAGGGCA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.30
31 16 0.70
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (30 bp):
AAAAATTAATTAAATTAAACAAAAAAATAT
Found at i:2140467 original size:21 final size:23
Alignment explanation
Indices: 2140443--2140492 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
2140433 CTCTTTTTCA
*
2140443 TTGGTTTTAACC-C-ATATGCTG
1 TTGGTTTGAACCTCAATATGCTG
2140464 TTGGTTTGAACCTCAATATGCTG
1 TTGGTTTGAACCTCAATATGCTG
2140487 TTGGTT
1 TTGGTT
2140493 ACATGAGTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.42
22 1 0.04
23 14 0.54
ACGTcount: A:0.18, C:0.16, G:0.22, T:0.44
Consensus pattern (23 bp):
TTGGTTTGAACCTCAATATGCTG
Found at i:2141716 original size:21 final size:21
Alignment explanation
Indices: 2141657--2141718 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 21
2141647 TGGATGTTTT
*
2141657 TGTTATAGGAATTAGGATTCA
1 TGTTATAGGAATTAGGAATCA
** * *
2141678 TG--ATAGTTACTA-TAATCA
1 TGTTATAGGAATTAGGAATCA
2141696 TGTTATAGGAATTAGGAATCA
1 TGTTATAGGAATTAGGAATCA
2141717 TG
1 TG
2141719 ATAATTACTA
Statistics
Matches: 29, Mismatches: 9, Indels: 6
0.66 0.20 0.14
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 7 0.24
21 9 0.31
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (21 bp):
TGTTATAGGAATTAGGAATCA
Found at i:2142026 original size:23 final size:23
Alignment explanation
Indices: 2142000--2142051 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 23
2141990 ACAATCATAA
2142000 CAAATTGTTAGTTACGACTGTAT
1 CAAATTGTTAGTTACGACTGTAT
2142023 CAAA---TT-GTTACGACTGTAT
1 CAAATTGTTAGTTACGACTGTAT
2142042 CAAATTGTTA
1 CAAATTGTTA
2142052 CGATTGTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 17 0.68
20 2 0.08
22 2 0.08
23 4 0.16
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (23 bp):
CAAATTGTTAGTTACGACTGTAT
Found at i:2142034 original size:19 final size:19
Alignment explanation
Indices: 2142010--2142054 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
2142000 CAAATTGTTA
2142010 GTTACGACTGTATCAAATT
1 GTTACGACTGTATCAAATT
2142029 GTTACGACTGTATCAAATT
1 GTTACGACTGTATCAAATT
2142048 GTTACGA
1 GTTACGA
2142055 TTGTTGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (19 bp):
GTTACGACTGTATCAAATT
Found at i:2149723 original size:16 final size:16
Alignment explanation
Indices: 2149683--2149726 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2149673 TTTAAAAAGC
* *
2149683 ATAAAATATATATTTT
1 ATAAAATTTAAATTTT
2149699 ATAAAATTTAAATTTT
1 ATAAAATTTAAATTTT
2149715 A-AAATATTTAAA
1 ATAAA-ATTTAAA
2149727 ATAACTGTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAAATTTAAATTTT
Found at i:2152385 original size:17 final size:17
Alignment explanation
Indices: 2152363--2152397 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2152353 CAACAACCAT
2152363 TTGTATAAGCTTCCACA
1 TTGTATAAGCTTCCACA
2152380 TTGTATAAGCTTCCACA
1 TTGTATAAGCTTCCACA
2152397 T
1 T
2152398 ATCTTTAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (17 bp):
TTGTATAAGCTTCCACA
Found at i:2157255 original size:16 final size:17
Alignment explanation
Indices: 2157224--2157257 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
2157214 AAATATTATT
*
2157224 TTATTATTTATTTTAAA
1 TTATTATTTATATTAAA
2157241 TTATT-TTTATATTAAA
1 TTATTATTTATATTAAA
2157257 T
1 T
2157258 AATAATAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTATATTAAA
Found at i:2161859 original size:3 final size:3
Alignment explanation
Indices: 2161851--2161890 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2161841 TACTTTACCC
2161851 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2161891 TATTATGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2162651 original size:38 final size:38
Alignment explanation
Indices: 2162602--2162677 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
2162592 ATAGTCAGTT
*
2162602 GTTCATTTTGTAATTTTTAATAGTCGAATGACTCAACA
1 GTTCATCTTGTAATTTTTAATAGTCGAATGACTCAACA
2162640 GTTCATCTTGTAATTTTTAATAGTCGAATGACTCAACA
1 GTTCATCTTGTAATTTTTAATAGTCGAATGACTCAACA
2162678 AAGCAATCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (38 bp):
GTTCATCTTGTAATTTTTAATAGTCGAATGACTCAACA
Found at i:2166944 original size:29 final size:29
Alignment explanation
Indices: 2166901--2166983 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
2166891 CTCACCTAAC
*
2166901 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
2166931 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
2166960 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2166984 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:2171709 original size:29 final size:29
Alignment explanation
Indices: 2171666--2171748 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
2171656 CTCACCTAAC
*
2171666 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
2171696 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
2171725 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
2171749 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:2178617 original size:18 final size:19
Alignment explanation
Indices: 2178581--2178617 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2178571 CACGGAATGT
2178581 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
2178601 AAGATTACCAG-GGAATA
1 AAGATTACCAGAGGAATA
2178618 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.11, G:0.22, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:2194176 original size:29 final size:31
Alignment explanation
Indices: 2194139--2194200 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 31
2194129 TATGCTCGTT
2194139 TTTTCAGTTTAGT-TCCTAACG-TTTATTTCG
1 TTTTCAGTTTAGTGT-CTAACGTTTTATTTCG
* *
2194169 TTTT-AGTTTGGTGTCTAATGTTTTATTTCG
1 TTTTCAGTTTAGTGTCTAACGTTTTATTTCG
2194199 TT
1 TT
2194201 ACTCATTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.15, C:0.11, G:0.16, T:0.58
Consensus pattern (31 bp):
TTTTCAGTTTAGTGTCTAACGTTTTATTTCG
Found at i:2196040 original size:27 final size:26
Alignment explanation
Indices: 2195985--2196040 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
2195975 GTGATAGGAA
* *
2195985 GAGGAAGGATAGGGAAGAAGGGGGCG
1 GAGGAAGGACAGGGAAGAAGGCGGCG
* *
2196011 GAGGAGAGGACAGGGAAGGAGGCGGTG
1 GAGGA-AGGACAGGGAAGAAGGCGGCG
2196038 GAG
1 GAG
2196041 AAGACGAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.32, C:0.05, G:0.59, T:0.04
Consensus pattern (26 bp):
GAGGAAGGACAGGGAAGAAGGCGGCG
Found at i:2200580 original size:23 final size:23
Alignment explanation
Indices: 2200504--2200581 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 23
2200494 TTTTTGATTC
* *
2200504 ATGGTTTTGGGTATGGTTGGGAT
1 ATGGTTTTGGGTATGATTTGGAT
**
2200527 ATGG-TTT-GGTAACACTATT-GATT
1 ATGGTTTTGGGTATGA-T-TTGGA-T
2200550 CATGGTTTTGGGTATGATTTGGAT
1 -ATGGTTTTGGGTATGATTTGGAT
2200574 ATGGTTTT
1 ATGGTTTT
2200582 AGGGGGATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 14
0.68 0.10 0.23
Matches are distributed among these distances:
21 4 0.10
22 6 0.14
23 14 0.33
24 7 0.17
25 6 0.14
26 5 0.12
ACGTcount: A:0.18, C:0.04, G:0.32, T:0.46
Consensus pattern (23 bp):
ATGGTTTTGGGTATGATTTGGAT
Found at i:2201018 original size:31 final size:31
Alignment explanation
Indices: 2200982--2201043 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
2200972 TTAAAAGTAT
2200982 TAATAAAAT-ATGACATGTCATATGAG-AAAAA
1 TAATAAAATAAT-ACATGTCA-ATGAGTAAAAA
*
2201013 TAATAAAATAATCCATGTCAATGAGTAAAAA
1 TAATAAAATAATACATGTCAATGAGTAAAAA
2201044 AATTTAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 5 0.18
31 21 0.75
32 2 0.07
ACGTcount: A:0.55, C:0.08, G:0.11, T:0.26
Consensus pattern (31 bp):
TAATAAAATAATACATGTCAATGAGTAAAAA
Found at i:2205687 original size:34 final size:33
Alignment explanation
Indices: 2205649--2205740 Score: 76
Period size: 41 Copynumber: 2.5 Consensus size: 33
2205639 CCACTATCGT
2205649 AAATTCGCGTTGCATTTCGCGTTGCGATAGTTGG
1 AAATTCGCGTTGCATTTCGCGTTGCGATAGTT-G
*
2205683 AAATTGCATTGCGATTTTCCATTTCGCGTTGCGATAGTTG
1 AAATT-C---GCG---TTGCATTTCGCGTTGCGATAGTTG
* *
2205723 AAAATCGCATTGCGATTT
1 AAATTCGCGTTGC-ATTT
2205741 TTCATTTCGC
Statistics
Matches: 46, Mismatches: 4, Indels: 16
0.70 0.06 0.24
Matches are distributed among these distances:
33 3 0.07
34 9 0.20
35 1 0.02
36 2 0.04
38 3 0.07
39 1 0.02
40 5 0.11
41 22 0.48
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (33 bp):
AAATTCGCGTTGCATTTCGCGTTGCGATAGTTG
Found at i:2205706 original size:41 final size:41
Alignment explanation
Indices: 2205661--2205798 Score: 161
Period size: 41 Copynumber: 3.4 Consensus size: 41
2205651 ATTCGCGTTG
* *
2205661 CATTTCGCGTTGCGATAGTTGGAAATTGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
*
2205702 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
* * ** ** * *
2205743 CATTTCGCGTTACGAT-TTTTCATTTCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
*
2205783 CATTTCGCGTTACGAT
1 CATTTCGCGTTGCGAT
2205799 TTTCCATTTC
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 34 0.39
41 53 0.61
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCATTGCGATTTTC
Found at i:2205716 original size:20 final size:20
Alignment explanation
Indices: 2205691--2205818 Score: 148
Period size: 20 Copynumber: 6.3 Consensus size: 20
2205681 GGAAATTGCA
*
2205691 TTGCGATTTTCCATTTCGCG
1 TTGCGATTTTTCATTTCGCG
* ** ** *
2205711 TTGCGATAGTTGAAAATCGCA
1 TTGCGAT-TTTTCATTTCGCG
2205732 TTGCGATTTTTCATTTCGCG
1 TTGCGATTTTTCATTTCGCG
*
2205752 TTACGATTTTTCATTTCGCG
1 TTGCGATTTTTCATTTCGCG
2205772 TTGCGATTTTTCATTTCGCG
1 TTGCGATTTTTCATTTCGCG
* * *
2205792 TTACGATTTTCCATTTCGCA
1 TTGCGATTTTTCATTTCGCG
2205812 TTGCGAT
1 TTGCGAT
2205819 AGTCTACAAT
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
20 75 0.84
21 14 0.16
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTTCATTTCGCG
Found at i:2205735 original size:21 final size:21
Alignment explanation
Indices: 2205665--2205738 Score: 60
Period size: 21 Copynumber: 3.6 Consensus size: 21
2205655 GCGTTGCATT
* *
2205665 TCGCGTTGCGATAGTTGGAAA
1 TCGCATTGCGATAGTTGAAAA
* * ** **
2205686 TTGCATTGCGAT-TTTCCATT
1 TCGCATTGCGATAGTTGAAAA
*
2205706 TCGCGTTGCGATAGTTGAAAA
1 TCGCATTGCGATAGTTGAAAA
2205727 TCGCATTGCGAT
1 TCGCATTGCGAT
2205739 TTTTCATTTC
Statistics
Matches: 37, Mismatches: 15, Indels: 2
0.69 0.28 0.04
Matches are distributed among these distances:
20 13 0.35
21 24 0.65
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATAGTTGAAAA
Found at i:2205782 original size:40 final size:40
Alignment explanation
Indices: 2205688--2205818 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
2205678 GTTGGAAATT
* * * ** **
2205688 GCATTGCGATTTTCCATTTCGCGTTGCGATAGTTGAAAATC
1 GCATTGCGATTTTTCATTTCGCGTTACGAT-TTTCCATTTC
*
2205729 GCATTGCGATTTTTCATTTCGCGTTACGATTTTTCATTTC
1 GCATTGCGATTTTTCATTTCGCGTTACGATTTTCCATTTC
*
2205769 GCGTTGCGATTTTTCATTTCGCGTTACGATTTTCCATTTC
1 GCATTGCGATTTTTCATTTCGCGTTACGATTTTCCATTTC
2205809 GCATTGCGAT
1 GCATTGCGAT
2205819 AGTCTACAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 52 0.65
41 28 0.35
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.44
Consensus pattern (40 bp):
GCATTGCGATTTTTCATTTCGCGTTACGATTTTCCATTTC
Found at i:2205856 original size:40 final size:41
Alignment explanation
Indices: 2205790--2205902 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 41
2205780 TTTCATTTCG
* *
2205790 CGTTACGATTTTCC-ATTTCGCATTGCGATAGTCTACA-ATGT
1 CGTTGCGATTTTCCAAATTCG--TTGCGATAGTCTACAGATGT
* *
2205831 CGTTGCGATTTTCTAAATTCGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
* **
2205872 TGTTGCGATTTTCCAAATTTTTTGCGATAGT
1 CGTTGCGATTTTCCAAATTCGTTGCGATAGT
2205903 TAAAAAAAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 15 0.24
41 42 0.68
42 5 0.08
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.42
Consensus pattern (41 bp):
CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGATGT
Found at i:2205864 original size:19 final size:21
Alignment explanation
Indices: 2205812--2205880 Score: 79
Period size: 19 Copynumber: 3.3 Consensus size: 21
2205802 CCATTTCGCA
2205812 TTGCGATAGTCTACAATGTCG
1 TTGCGATAGTCTACAATGTCG
**
2205833 TTGCGATTTTCTA-AAT-TCG
1 TTGCGATAGTCTACAATGTCG
* *
2205852 TTGCGATAGTCTACAGTTGTTG
1 TTGCGATAGTCTACA-ATGTCG
2205874 TTGCGAT
1 TTGCGAT
2205881 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
19 14 0.36
20 4 0.10
21 12 0.31
22 9 0.23
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (21 bp):
TTGCGATAGTCTACAATGTCG
Found at i:2205993 original size:6 final size:6
Alignment explanation
Indices: 2205982--2206010 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2205972 ACGTATTACT
2205982 ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC
2206011 CGAGACGGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:2206613 original size:19 final size:19
Alignment explanation
Indices: 2206589--2206654 Score: 69
Period size: 19 Copynumber: 3.3 Consensus size: 19
2206579 TTAACTATCA
2206589 CAACGAATTTAGAAAATCG
1 CAACGAATTTAGAAAATCG
* **
2206608 CAACGATAACTGTAGACTATCG
1 CAACG--AA-TTTAGAAAATCG
*
2206630 CAACGAATTTGGAAAATCG
1 CAACGAATTTAGAAAATCG
2206649 CAACGA
1 CAACGA
2206655 CAACTATACA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 19 0.51
20 2 0.05
21 2 0.05
22 14 0.38
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (19 bp):
CAACGAATTTAGAAAATCG
Found at i:2206627 original size:41 final size:41
Alignment explanation
Indices: 2206582--2206675 Score: 143
Period size: 41 Copynumber: 2.3 Consensus size: 41
2206572 ATTTTTTTTA
* * * *
2206582 ACTATCACAACGAATTTAGAAAATCGCAACGATAACTGTAG
1 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTATAC
*
2206623 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTATAC
1 ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTATAC
2206664 ACTATCGCAACG
1 ACTATCGCAACG
2206676 CGATTTTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGAATTTAGAAAATCGCAACGACAACTATAC
Found at i:2206751 original size:22 final size:22
Alignment explanation
Indices: 2206604--2206752 Score: 60
Period size: 22 Copynumber: 6.7 Consensus size: 22
2206594 AATTTAGAAA
**
2206604 ATCGCAACGATAACTGTAGACT
1 ATCGCAACGCGAACTGTAGACT
* * **
2206626 ATCGCAA--CGAA-TTTGGAAA
1 ATCGCAACGCGAACTGTAGACT
* *
2206645 ATCGCAACGAC-AACTATACACT
1 ATCGCAACG-CGAACTGTAGACT
* *
2206667 ATCGCAACGCG-ATTTTCA-ACT
1 ATCGCAACGCGAACTGT-AGACT
* **
2206688 ATCGCAACGCGAACTGGAAATTGGAAA
1 ATCGCAACGCGAACT-G----TAGACT
2206715 ATCGCAACGAC-AACTGTAGACT
1 ATCGCAACG-CGAACTGTAGACT
2206737 ATCGCAACGCGAACTG
1 ATCGCAACGCGAACTG
2206753 GAAAATCACA
Statistics
Matches: 91, Mismatches: 21, Indels: 30
0.64 0.15 0.21
Matches are distributed among these distances:
19 11 0.12
20 2 0.02
21 21 0.23
22 40 0.44
26 1 0.01
27 15 0.16
28 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGCGAACTGTAGACT
Found at i:2206785 original size:20 final size:20
Alignment explanation
Indices: 2206737--2206788 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2206727 ACTGTAGACT
* *
2206737 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGAAAA
*
2206757 ATCACAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
*
2206777 ATCGTAACGCGA
1 ATCGCAACGCGA
2206789 TTTTCAACTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:2206806 original size:21 final size:21
Alignment explanation
Indices: 2206777--2206830 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2206767 GAAATGAAAA
*
2206777 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
2206798 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
2206819 ATCGCAACGCGA
1 ATCGCAACGCGA
2206831 ATTTGCGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:2207432 original size:50 final size:49
Alignment explanation
Indices: 2207374--2207512 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 49
2207364 TGGACATACG
2207374 TGTTGGAGGGTGAATTTAAAACTGATAAAATCTTGGGGCGAACTTGTTTA
1 TGTTGGAGGGTGAATTTAAAACTGATAAAATCTTGGGG-GAACTTGTTTA
2207424 TGTTGGAGGGTGAATTTAAAACTGATAAAATC-T-GGGGAACTTGTTTA
1 TGTTGGAGGGTGAATTTAAAACTGATAAAATCTTGGGGGAACTTGTTTA
*
2207471 TGTTGGAGGGGTGGGTGAATTT-ATACTGATAAAATCTTGGGG
1 TGTTGGA-----GGGTGAATTTAAAACTGATAAAATCTTGGGG
2207513 TGAATTTGAA
Statistics
Matches: 81, Mismatches: 1, Indels: 11
0.87 0.01 0.12
Matches are distributed among these distances:
47 18 0.22
48 3 0.04
49 1 0.01
50 32 0.40
51 13 0.16
52 11 0.14
53 3 0.04
ACGTcount: A:0.29, C:0.06, G:0.31, T:0.34
Consensus pattern (49 bp):
TGTTGGAGGGTGAATTTAAAACTGATAAAATCTTGGGGGAACTTGTTTA
Found at i:2210295 original size:2 final size:2
Alignment explanation
Indices: 2210290--2210332 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2210280 ATGTTGTGTG
2210290 AT AT AT AT AT AT AT AT -T 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 AT
2210331 AT
1 AT
2210333 GAACATAAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2211079 original size:21 final size:21
Alignment explanation
Indices: 2211053--2211095 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2211043 GTGATATGAA
* *
2211053 ATGTGTTACATGAATTATATG
1 ATGTGTGACATGAACTATATG
*
2211074 ATGTGTGATATGAACTATATG
1 ATGTGTGACATGAACTATATG
2211095 A
1 A
2211096 AATGATATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.05, G:0.21, T:0.40
Consensus pattern (21 bp):
ATGTGTGACATGAACTATATG
Done.