Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 52 of 100
Found at i:9566333 original size:32 final size:30
Alignment explanation
Indices: 9566269--9566352 Score: 89
Period size: 32 Copynumber: 2.7 Consensus size: 30
9566259 TAGGATTCTA
* * * *
9566269 AAACCCCTAAAATCCAAAATCTCTTAACTCC
1 AAACCCCTAAAAT-CAAAACCCCTAAAATCC
9566300 AAACCTCCTAAAATCTAAAACCCCTAAAATCC
1 AAACC-CCTAAAATC-AAAACCCCTAAAATCC
*
9566332 AAA-CCCTTAAATCAAAACCCC
1 AAACCCCTAAAATCAAAACCCC
9566353 AAACCTCAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
29 8 0.17
30 8 0.17
31 7 0.15
32 23 0.50
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (30 bp):
AAACCCCTAAAATCAAAACCCCTAAAATCC
Found at i:9566343 original size:14 final size:14
Alignment explanation
Indices: 9566306--9566412 Score: 74
Period size: 14 Copynumber: 7.4 Consensus size: 14
9566296 CTCCAAACCT
9566306 CCTAAAATCTAAAACC
1 CCTAAAATC-AAAA-C
*
9566322 CCTAAAATCCAAAC
1 CCTAAAATCAAAAC
*
9566336 CCTTAAATCAAAAC
1 CCTAAAATCAAAAC
* *
9566350 CCCAAACCTC-AAA-
1 CCTAAA-ATCAAAAC
* *
9566363 GCTAAAACCAAAAC
1 CCTAAAATCAAAAC
*
9566377 CCTAAAATCTTTAAAC
1 CCTAAAATC--AAAAC
**
9566393 TGTAAAATCAAAAC
1 CCTAAAATCAAAAC
9566407 CCTAAA
1 CCTAAA
9566413 CCTTCCATAC
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
12 1 0.01
13 7 0.10
14 35 0.51
15 5 0.07
16 20 0.29
ACGTcount: A:0.50, C:0.30, G:0.02, T:0.18
Consensus pattern (14 bp):
CCTAAAATCAAAAC
Found at i:9566959 original size:25 final size:25
Alignment explanation
Indices: 9566931--9566978 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
9566921 CTGTTTGATG
* * *
9566931 ATAAAATATTTTATAATAAAAAAGA
1 ATAAAACATTTTAAAAGAAAAAAGA
*
9566956 ATAATACATTTTAAAAGAAAAAA
1 ATAAAACATTTTAAAAGAAAAAA
9566979 AGGATCTGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
ATAAAACATTTTAAAAGAAAAAAGA
Found at i:9579175 original size:38 final size:38
Alignment explanation
Indices: 9579132--9579295 Score: 103
Period size: 38 Copynumber: 4.4 Consensus size: 38
9579122 TGGCTCGTGG
9579132 TTTAATCCC-GATCATTTCATTATTTCCCTGACTTGCGA
1 TTTAATCCCAG-TCATTTCATTATTTCCCTGACTTGCGA
* * * * *
9579170 TTTAATCCCAGTCACTTTTATT-TTT--TTGATTTACGG
1 TTTAATCCCAGTCA-TTTCATTATTTCCCTGACTTGCGA
* * * * ** *
9579206 TTCAATCCCAGTCGTCGTCAATATTTGGCT--CATG-G-
1 TTTAATCCCAGTCAT-TTCATTATTTCCCTGACTTGCGA
*
9579241 TTTAATCCC-GATCATTTCATTATTTCCCTGACTTGCTA
1 TTTAATCCCAG-TCATTTCATTATTTCCCTGACTTGCGA
*
9579279 TTTAATCCCAGTTATTT
1 TTTAATCCCAGTCATTT
9579296 TTATTTTTTT
Statistics
Matches: 91, Mismatches: 23, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
34 11 0.12
35 12 0.13
36 26 0.29
37 4 0.04
38 29 0.32
39 9 0.10
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Consensus pattern (38 bp):
TTTAATCCCAGTCATTTCATTATTTCCCTGACTTGCGA
Found at i:9579363 original size:109 final size:109
Alignment explanation
Indices: 9579061--9579350 Score: 447
Period size: 109 Copynumber: 2.7 Consensus size: 109
9579051 TGATTTATGG
* * * * *
9579061 TTTAATCCCAGCCTCTTTTATCTTTTTAACTTACGGTTCAATCCCAGTCGTCGTCAATATTTGGC
1 TTTAATCCCAGTCACTTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATATTTGGC
9579126 TCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTGCGA
66 TCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTGCGA
9579170 TTTAATCCCAGTCACTTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATATTTGGC
1 TTTAATCCCAGTCACTTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATATTTGGC
* *
9579235 TCATGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTGCTA
66 TCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTGCGA
* * * * * *
9579279 TTTAATCCCAGTTATTTTTATTTTTTTGATTTGA-GGTTTAGTCCCAGTCGTCGTCAATCTTTGA
1 TTTAATCCCAGTCACTTTTATTTTTTTGATTT-ACGGTTCAATCCCAGTCGTCGTCAATATTTGG
9579343 CTCGTGGT
65 CTCGTGGT
9579351 CCAATCTCGA
Statistics
Matches: 166, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
109 165 0.99
110 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (109 bp):
TTTAATCCCAGTCACTTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATATTTGGC
TCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTGCGA
Found at i:9579395 original size:109 final size:109
Alignment explanation
Indices: 9579010--9579397 Score: 403
Period size: 109 Copynumber: 3.6 Consensus size: 109
9579000 ATCTTTAATC
* * * * * * ** *
9579010 TTTGACTTGTGGTATAATCTCGATCATTTC-TATAGTTTTCTTGATTTATGGTTTAATCCCAGCC
1 TTTGACTCGTGGTTTAATCCCGATCATTTCAT-TA-TTTCCCTGACTTACAGTTTAATCCCAG-T
* * *
9579074 T-CTTTTATCTTTTTAACTTACGGTTCAATCCCAGTCGTCGTCAATA
63 TACTTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATA
* * *
9579120 TTTGGCTCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTGC-GATTTAATCCCAGTCA
1 TTTGACTCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTACAG-TTTAATCCCAGTTA
9579184 CTTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATA
65 CTTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATA
* * *
9579229 TTTGGCTCATGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTGCTA-TTTAATCCCAGTTA
1 TTTGACTCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTAC-AGTTTAATCCCAGTTA
* * * *
9579293 TTTTTATTTTTTTGATTTGA-GGTTTAGTCCCAGTCGTCGTCAATC
65 CTTTTATTTTTTTGATTT-ACGGTTCAATCCCAGTCGTCGTCAATA
** * * * *
9579338 TTTGACTCGTGGTCCAATCTCGATCACTTC-TATAGTTT-CCTGAATTACAGTTCAATCCCA
1 TTTGACTCGTGGTTTAATCCCGATCATTTCAT-TA-TTTCCCTGACTTACAGTTTAATCCCA
9579398 ATCATCGTTA
Statistics
Matches: 240, Mismatches: 29, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
108 3 0.01
109 204 0.85
110 32 0.13
111 1 0.00
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (109 bp):
TTTGACTCGTGGTTTAATCCCGATCATTTCATTATTTCCCTGACTTACAGTTTAATCCCAGTTAC
TTTTATTTTTTTGATTTACGGTTCAATCCCAGTCGTCGTCAATA
Found at i:9580341 original size:3 final size:3
Alignment explanation
Indices: 9580327--9580405 Score: 72
Period size: 3 Copynumber: 26.3 Consensus size: 3
9580317 TTTTCAGTAG
* ** * *
9580327 AAT AAC AAT AAT AAT TTT AAT AAT AAT AAT AAT AAA AAT -AT ATTT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
*
9580372 AAA AATT AAT AAT AAT AAT -AT AAT AAT AAT AAT A
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9580406 GGAGACAGAA
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
2 4 0.07
3 52 0.87
4 4 0.07
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:9581702 original size:16 final size:14
Alignment explanation
Indices: 9581683--9581826 Score: 103
Period size: 14 Copynumber: 9.8 Consensus size: 14
9581673 CTAGGATTCT
9581683 AAAACCCCTAAAATTC
1 AAAA-CCCTAAAA-TC
*
9581699 AAAATCCCTTAAATCC
1 AAAA-CCCTAAAAT-C
**
9581715 AATCCCCTAAAATCC
1 AAAACCCTAAAAT-C
9581730 AAAACCCCTAAAATC
1 AAAA-CCCTAAAATC
* *
9581745 CAAACCCTTAAATC
1 AAAACCCTAAAATC
* *
9581759 AAAACCCCAAACCTC
1 AAAACCCTAAA-ATC
*
9581774 AAAA--CTAAAACC
1 AAAACCCTAAAATC
9581786 AAAACCCTAAAATCTC
1 AAAACCCTAAAA--TC
* *
9581802 CAAACTCTAAAATC
1 AAAACCCTAAAATC
9581816 AAAACCCTAAA
1 AAAACCCTAAA
9581827 CCTTCCATAC
Statistics
Matches: 100, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
12 5 0.05
13 4 0.04
14 34 0.34
15 23 0.23
16 34 0.34
ACGTcount: A:0.50, C:0.33, G:0.00, T:0.17
Consensus pattern (14 bp):
AAAACCCTAAAATC
Found at i:9581724 original size:31 final size:31
Alignment explanation
Indices: 9581684--9581826 Score: 110
Period size: 31 Copynumber: 4.9 Consensus size: 31
9581674 TAGGATTCTA
* * *
9581684 AAACCCCTAAAATTCAAAATCCCTTAAATCC
1 AAACCCCTAAAATCCAAAACCCCTAAAATCC
*
9581715 AATCCCCTAAAATCCAAAACCCCTAAAATCC
1 AAACCCCTAAAATCCAAAACCCCTAAAATCC
* *
9581746 AAA-CCCTTAAAT-CAAAACCCC--AAACCTC
1 AAACCCCTAAAATCCAAAACCCCTAAAATC-C
*
9581774 AAA--ACTAAAA-CCAAAA-CCCTAAAATCTCC
1 AAACCCCTAAAATCCAAAACCCCTAAAA--TCC
*
9581803 AAA-CTCTAAAAT-CAAAA-CCCTAAA
1 AAACCCCTAAAATCCAAAACCCCTAAA
9581827 CCTTCCATAC
Statistics
Matches: 93, Mismatches: 11, Indels: 17
0.77 0.09 0.14
Matches are distributed among these distances:
26 3 0.03
27 14 0.15
28 7 0.08
29 13 0.14
30 27 0.29
31 29 0.31
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.17
Consensus pattern (31 bp):
AAACCCCTAAAATCCAAAACCCCTAAAATCC
Found at i:9581727 original size:15 final size:15
Alignment explanation
Indices: 9581684--9581766 Score: 87
Period size: 16 Copynumber: 5.5 Consensus size: 15
9581674 TAGGATTCTA
*
9581684 AAACCCCTAAAATTCA
1 AAACCCCTAAAA-TCC
* *
9581700 AAATCCCTTAAATCC
1 AAACCCCTAAAATCC
*
9581715 AATCCCCTAAAATCC
1 AAACCCCTAAAATCC
9581730 AAAACCCCTAAAATCC
1 -AAACCCCTAAAATCC
* *
9581746 AAA-CCCTTAAATCA
1 AAACCCCTAAAATCC
9581760 AAACCCC
1 AAACCCC
9581767 AAACCTCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.21
15 20 0.36
16 24 0.43
ACGTcount: A:0.46, C:0.36, G:0.00, T:0.18
Consensus pattern (15 bp):
AAACCCCTAAAATCC
Found at i:9581783 original size:57 final size:56
Alignment explanation
Indices: 9581721--9581829 Score: 157
Period size: 57 Copynumber: 1.9 Consensus size: 56
9581711 ATCCAATCCC
*
9581721 CTAAAATCCAAAACCCCTAAAA-TCCAAACCCTTAAATCAAAACCCCAAACCTCAAAA
1 CTAAAA-CCAAAA-CCCTAAAACTCCAAACCCTAAAATCAAAACCCCAAACCTCAAAA
* *
9581778 CTAAAACCAAAACCCTAAAATCTCCAAACTCTAAAATCAAAACCCTAAACCT
1 CTAAAACCAAAACCCTAAAA-CTCCAAACCCTAAAATCAAAACCCCAAACCT
9581830 TCCATACCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
55 8 0.17
56 6 0.13
57 33 0.70
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (56 bp):
CTAAAACCAAAACCCTAAAACTCCAAACCCTAAAATCAAAACCCCAAACCTCAAAA
Found at i:9581843 original size:30 final size:29
Alignment explanation
Indices: 9581720--9581844 Score: 98
Period size: 30 Copynumber: 4.3 Consensus size: 29
9581710 AATCCAATCC
*
9581720 CCTAAAATCCAAAACCCCTAAA--ATCCAAA
1 CCTAAAAT-CAAAA-CCCTAAACCTTCCAAA
* *
9581749 CCCTTAAATCAAAACCCCAAACC-T-CAAA
1 -CCTAAAATCAAAACCCTAAACCTTCCAAA
* * *
9581777 ACTAAAACCAAAACCCTAAA-ATCTCCAAA
1 CCTAAAATCAAAACCCTAAACCT-TCCAAA
*
9581806 CTCTAAAATCAAAACCCTAAACCTTCCATA
1 C-CTAAAATCAAAACCCTAAACCTTCCAAA
9581836 CCATAAAAT
1 CC-TAAAAT
9581845 TCAAGCCTTA
Statistics
Matches: 76, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
27 16 0.21
28 11 0.14
29 11 0.14
30 37 0.49
31 1 0.01
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.17
Consensus pattern (29 bp):
CCTAAAATCAAAACCCTAAACCTTCCAAA
Found at i:9582373 original size:25 final size:25
Alignment explanation
Indices: 9582345--9582392 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
9582335 CTGTTTGATG
* * *
9582345 ATAAAATATTTTATAATAAAAAAGA
1 ATAAAACATTTTAAAAGAAAAAAGA
*
9582370 ATAATACATTTTAAAAGAAAAAA
1 ATAAAACATTTTAAAAGAAAAAA
9582393 AAGATCTGTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
ATAAAACATTTTAAAAGAAAAAAGA
Found at i:9585340 original size:29 final size:29
Alignment explanation
Indices: 9585285--9585362 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
9585275 AAATAGATAT
* * *
9585285 TTAAATATTTAAATGATCAAAAATAAAAAAA
1 TTAAAAATTTAAATGAT-TACAAT-AAAAAA
* *
9585316 TT-AAAATTTAATTGATTACAATAAAATA
1 TTAAAAATTTAAATGATTACAATAAAAAA
9585344 TTAAAAATTTAAATGATTA
1 TTAAAAATTTAAATGATTA
9585363 TTAAATTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.17
29 19 0.47
30 12 0.30
31 2 0.05
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (29 bp):
TTAAAAATTTAAATGATTACAATAAAAAA
Found at i:9586067 original size:24 final size:23
Alignment explanation
Indices: 9586040--9586118 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
9586030 GTTAAATAAA
9586040 TAAATAAGTATATTATTAAAATGT
1 TAAATAA-TATATTATTAAAATGT
* **
9586064 TAAATAA-ATCAGTTATTCATGTGT
1 TAAATAATAT-A-TTATTAAAATGT
* * *
9586088 TAAATAAATATATGATGAAAATAT
1 TAAAT-AATATATTATTAAAATGT
9586112 TAAATAA
1 TAAATAA
9586119 ATTATTTTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
22 2 0.05
23 3 0.07
24 32 0.76
25 3 0.07
26 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (23 bp):
TAAATAATATATTATTAAAATGT
Found at i:9590318 original size:38 final size:38
Alignment explanation
Indices: 9590229--9590329 Score: 100
Period size: 38 Copynumber: 2.7 Consensus size: 38
9590219 AAAAATATTC
* * * *
9590229 ATATTATGAAAATAATAATATTATAATATCATTTATTAT
1 ATATTATCAAAATAAT-ATAATATAATATAATATATTAT
* *
9590268 -TGATTATCAAAATAATATAATATTATTTAATATATTAT
1 AT-ATTATCAAAATAATATAATATAATATAATATATTAT
*
9590306 ATATTATTAAAAT-A-ATAATATAAT
1 ATATTATCAAAATAATATAATATAAT
9590330 GCTATTTATT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
36 9 0.17
37 1 0.02
38 28 0.54
39 14 0.27
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (38 bp):
ATATTATCAAAATAATATAATATAATATAATATATTAT
Found at i:9590327 original size:19 final size:18
Alignment explanation
Indices: 9590270--9590326 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
9590260 TTTATTATTG
*
9590270 ATTATCAAAATAATATAAT
1 ATTATTAAAATAATAT-AT
* *
9590289 ATTATTTAATATATTATAT
1 ATTA-TTAAAATAATATAT
9590308 ATTATTAAAATAATA-AT
1 ATTATTAAAATAATATAT
9590325 AT
1 AT
9590327 AATGCTATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
17 4 0.12
18 9 0.28
19 10 0.31
20 9 0.28
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTATTAAAATAATATAT
Found at i:9594679 original size:16 final size:18
Alignment explanation
Indices: 9594642--9594681 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
9594632 AAAAATTTTT
*
9594642 TATTTAAATATCAATACA
1 TATTTTAATATCAATACA
9594660 -ATTTTAATAT-AATA-A
1 TATTTTAATATCAATACA
9594675 TATTTTA
1 TATTTTA
9594682 TTTTACACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
15 1 0.05
16 10 0.50
17 9 0.45
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTTTAATATCAATACA
Found at i:9596337 original size:20 final size:22
Alignment explanation
Indices: 9596312--9596351 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
9596302 GATTTAAAAT
9596312 TTTAATAAAA-AT-TATATAAA
1 TTTAATAAAATATATATATAAA
9596332 TTTAATAAAATATATATATA
1 TTTAATAAAATATATATATA
9596352 TATATATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 2 0.11
22 6 0.33
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTAATAAAATATATATATAAA
Found at i:9596726 original size:15 final size:16
Alignment explanation
Indices: 9596699--9596728 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
9596689 GGTGTTTAGC
9596699 TATTTTTTGAAAAATT
1 TATTTTTTGAAAAATT
9596715 TATTTTTT-AAAAAT
1 TATTTTTTGAAAAAT
9596729 AATATTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TATTTTTTGAAAAATT
Found at i:9596773 original size:25 final size:25
Alignment explanation
Indices: 9596743--9596808 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
9596733 TTAATATAAC
**
9596743 TATTAAAATATTAAAAATTATTTAT
1 TATTAAAATATTAAAAACAATTTAT
**
9596768 TATTAAAATATATTGAAACAATTTAT
1 TATTAAAATAT-TAAAAACAATTTAT
9596794 TATTAAAATTATTAA
1 TATTAAAA-TATTAA
9596809 TATTAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 11 0.33
26 19 0.58
27 3 0.09
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
TATTAAAATATTAAAAACAATTTAT
Found at i:9596924 original size:29 final size:29
Alignment explanation
Indices: 9596891--9596946 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
9596881 AAATAAAACT
9596891 ATTTATTATTTATATTAATAGTTTAAATC
1 ATTTATTATTTATATTAATAGTTTAAATC
*
9596920 ATTTATTATTTATATTAATATTTTAAA
1 ATTTATTATTTATATTAATAGTTTAAA
9596947 ATATTAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
ATTTATTATTTATATTAATAGTTTAAATC
Found at i:9596962 original size:31 final size:29
Alignment explanation
Indices: 9596895--9596971 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
9596885 AAAACTATTT
* *
9596895 ATTATTTATATTAATAGTTTAAATCATTT
1 ATTATTTATATTAATATTTTAAATCATTA
9596924 ATTATTTATATTAATATTTTAAAAT-ATTAAA
1 ATTATTTATATTAATATTTT-AAATCATT--A
*
9596955 ATTATTTATAATAATAT
1 ATTATTTATATTAATAT
9596972 CTGTAGTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 22 0.52
30 4 0.10
31 16 0.38
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (29 bp):
ATTATTTATATTAATATTTTAAATCATTA
Found at i:9597174 original size:22 final size:22
Alignment explanation
Indices: 9597140--9597185 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
9597130 AAAAAAAGTT
*
9597140 TTATTTTAAATTAATTAATAAA
1 TTATTTTAAATTAATCAATAAA
** *
9597162 TTATTTTTTATTAATCAATTAA
1 TTATTTTAAATTAATCAATAAA
9597184 TT
1 TT
9597186 TTCTATCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTATTTTAAATTAATCAATAAA
Found at i:9606745 original size:27 final size:25
Alignment explanation
Indices: 9606689--9606746 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
9606679 AGACTGGTAG
*
9606689 TTGAGAGAGAGGAACGAGCGACAAA
1 TTGAGGGAGAGGAACGAGCGACAAA
* *
9606714 CTGAGGGAGAGTGAGACGAGCGACAGA
1 TTGAGGGAGAG-GA-ACGAGCGACAAA
9606741 TTGAGG
1 TTGAGG
9606747 CAAAGTTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 9 0.33
26 2 0.07
27 16 0.59
ACGTcount: A:0.36, C:0.12, G:0.41, T:0.10
Consensus pattern (25 bp):
TTGAGGGAGAGGAACGAGCGACAAA
Found at i:9607456 original size:16 final size:17
Alignment explanation
Indices: 9607421--9607457 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
9607411 ATTTATTAAT
9607421 AATTATAGTTTTTGAGA
1 AATTATAGTTTTTGAGA
9607438 AATTATAGTTTTTGA-A
1 AATTATAGTTTTTGAGA
9607454 AATT
1 AATT
9607458 TTATTAGAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.49
Consensus pattern (17 bp):
AATTATAGTTTTTGAGA
Found at i:9608311 original size:21 final size:21
Alignment explanation
Indices: 9608285--9608326 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9608275 CATGAGGTCA
9608285 GGGAAGAATATACTAAAATTC
1 GGGAAGAATATACTAAAATTC
*
9608306 GGGAAGAATATACTAACATTC
1 GGGAAGAATATACTAAAATTC
9608327 AATGTTGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAAGAATATACTAAAATTC
Found at i:9610420 original size:24 final size:24
Alignment explanation
Indices: 9610382--9610428 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9610372 TAATTCATAA
* *
9610382 AAAAAGTATTGAAATACCTTAAGT
1 AAAAAGTAATAAAATACCTTAAGT
*
9610406 AAAAAGTAATAAAATATCTTAAG
1 AAAAAGTAATAAAATACCTTAAG
9610429 AAAGAGTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (24 bp):
AAAAAGTAATAAAATACCTTAAGT
Found at i:9613593 original size:2 final size:2
Alignment explanation
Indices: 9613586--9613614 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9613576 TAGAAATTTG
9613586 AT AT 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 A
9613615 AACAATAACA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9616510 original size:162 final size:161
Alignment explanation
Indices: 9615937--9616834 Score: 808
Period size: 161 Copynumber: 5.5 Consensus size: 161
9615927 ATCATTTATT
* * * * * ** *
9615937 GTCTATTTAGGTCTTTTTGTGCTGTTAAAAGGTAAAATTACAAATTTATTATCATTATTATTCTA
1 GTCTGTTTAGGACTTTTTGTGCCGTTAAAAGGCAAAAATACAAA-TT-TGCT-GTTATTATTCTA
* * * * * * *
9616002 TTTTAACCA-TTTAGGTAGGTTAAATACATGATATTAAAGTTGTTTAAATTATTGAACTTAGTTT
63 TTTTAA-CAGTTTTGATAGCTTAAATACATGATACTAAACTTGTTCAAATAATTGAACTTAGTTT
* *** *
9616066 TCA-CGATTGATATGTGTGAAAAAATTACTGCGTAC
127 TCATAG-TTGATATGTGTGAAAAAATTACTATTTAG
* * * * * * *
9616101 GTTTGTCTAGGACTTTTTGTGCTGTTAAAAGGCAAAAATGCAAATTTGCTATTATTGTCCTATTT
1 GTCTGTTTAGGACTTTTTGTGCCGTTAAAAGGCAAAAATACAAATTTGCTGTTATTATTCTATTT
* * * * * *
9616166 GAACAGTTTTGATAGCTTCATTACATGATATTAAACTTGTTCAAATGATTGAACTTAGTTTTCAC
66 TAACAGTTTTGATAGCTTAAATACATGATACTAAACTTGTTCAAATAATTGAACTTAGTTTTCAT
* * *
9616231 AGTTGGTGTGTGTGAAAATATTA-TCATTTAGG
131 AGTTGATATGTGTGAAAAAATTACT-ATTTA-G
* * ** * * * *
9616263 GTTTGTTTAGGAC-TTTTGTGCCATTAAAAGGCAAAAATGTAAATTTGTTGTTATTGTTTTGTTT
1 GTCTGTTTAGGACTTTTTGTGCCGTTAAAAGGCAAAAATACAAATTTGCTGTTATTATTCTATTT
* * * * * *
9616327 TTATAGTTTTGATAGCTTAAATACATTATACTAAACTTGTTCGAATAATTGAACTTAATTTCCAT
66 TAACAGTTTTGATAGCTTAAATACATGATACTAAACTTGTTCAAATAATTGAACTTAGTTTTCAT
* * * * * *
9616392 GGTTCATATGTATGAAAAAGTTACTGTTTAT
131 AGTTGATATGTGTGAAAAAATTACTATTTAG
* * * *
9616423 GTCTGTTTAGGGCTTTTTTATGCCGTTAAAAGGCAAAAATACCAATTTGCTGTTATTATTTTATT
1 GTCTGTTTAGGAC-TTTTTGTGCCGTTAAAAGGCAAAAATACAAATTTGCTGTTATTATTCTATT
* * * *
9616488 TTAACAATTTTGATACCTTAAATACATGATA-TAAAACTTGTTCAAATAATTGAATTTGGTTTTC
65 TTAACAGTTTTGATAGCTTAAATACATGATACT-AAACTTGTTCAAATAATTGAACTTAGTTTTC
* *
9616552 ACT-GTTGATATGTGTGAAAAAATTACCATTTAT
129 A-TAGTTGATATGTGTGAAAAAATTACTATTTAG
* ** * * * * * *
9616585 GTCTATTTAAGG-CTCCTTGTGCCGTTAAAGGGTAAAAATGTA-AAATTTGCTATTATTGTTTTG
1 GTCTGTTT-AGGACTTTTTGTGCCGTTAAAAGGCAAAAA--TACAAATTTGCTGTTATTATTCTA
* * * * *
9616648 TTTTAACAGTTTTGATAGCTTAAATACATCATACTAAACTTGTCCAAATGATTGAATTTGGTTTT
63 TTTTAACAGTTTTGATAGCTTAAATACATGATACTAAACTTGTTCAAATAATTGAACTTAGTTTT
9616713 CATAGTTGATATGTGTGAAAAAATTA-TCATTTAGG
128 CATAGTTGATATGTGTGAAAAAATTACT-ATTTA-G
* * * **
9616748 GTCTATTTAGGACTTTTTGTTCCATTAAAA-GCAAAAATACAAATTTATTGTTATTATTCTATTT
1 GTCTGTTTAGGACTTTTTGTGCCGTTAAAAGGCAAAAATACAAATTTGCTGTTATTATTCTATTT
* *
9616812 TAACAGTTTGGATAGCTTTAATA
66 TAACAGTTTTGATAGCTTAAATA
9616835 ATATATGTTT
Statistics
Matches: 602, Mismatches: 114, Indels: 39
0.80 0.15 0.05
Matches are distributed among these distances:
160 16 0.03
161 262 0.44
162 257 0.43
163 30 0.05
164 37 0.06
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.43
Consensus pattern (161 bp):
GTCTGTTTAGGACTTTTTGTGCCGTTAAAAGGCAAAAATACAAATTTGCTGTTATTATTCTATTT
TAACAGTTTTGATAGCTTAAATACATGATACTAAACTTGTTCAAATAATTGAACTTAGTTTTCAT
AGTTGATATGTGTGAAAAAATTACTATTTAG
Found at i:9616516 original size:323 final size:323
Alignment explanation
Indices: 9616021--9616834 Score: 938
Period size: 323 Copynumber: 2.5 Consensus size: 323
9616011 TTTAGGTAGG
* * * * * * *
9616021 TTAAATACATGATATTAAAGTTGTTTAAATTATTGAACTTAGTTTTCACGATTGATATGTGTGAA
1 TTAAATACATCATACTAAACTTGTTCAAATAATTGAACTTAGTTTTCATGGTTGATATGTGTGAA
** * * * * *
9616086 AAAATTACTGCGTACGTTTGTCTAGGACTTTTTGTGCTGTTAAAAGGCAAAAATGCAAATTTGCT
66 AAAATTACTGTTTACGTCTGTTTAGGACTTTTTTTGCCGTTAAAAGGCAAAAATACAAATTTGCT
* * * * * * * *
9616151 ATTATTGTCCTATTTGAACAGTTTTGATAGCTTCATTACATGATATTAAACTTGTTCAAATGATT
131 GTTATTATTCTATTTTAACAGTTTTGATAGCTTAAATACATGATATAAAACTTGTTCAAATAATT
* * * * * * *
9616216 GAACTTAGTTTTCACAGTTGGTGTGTGTGAAAATATTATCATTTAGGGTTTGTTT-AGGACT-TT
196 GAACTTAGTTTTCACAGTTGATATGTGTGAAAAAATTACCATTTA-GGTCTATTTAAGG-CTCCT
* * * *
9616279 TGTGCCATTAAAAGGCAAAAATGT-AAATTTGTTGTTATTGTTTTGTTTTTATAGTTTTGATAGC
259 TGTGCCATTAAAAGGCAAAAATGTAAAATTTGCTATTATTGTTTTGTTTTAACAGTTTTGATAGC
* * * * * *
9616343 TTAAATACATTATACTAAACTTGTTCGAATAATTGAACTTAATTTCCATGGTTCATATGTATGAA
1 TTAAATACATCATACTAAACTTGTTCAAATAATTGAACTTAGTTTTCATGGTTGATATGTGTGAA
* * * *
9616408 AAAGTTACTGTTTATGTCTGTTTAGGGCTTTTTTATGCCGTTAAAAGGCAAAAATACCAATTTGC
66 AAAATTACTGTTTACGTCTGTTTAGGACTTTTTT-TGCCGTTAAAAGGCAAAAATACAAATTTGC
* * *
9616473 TGTTATTATTTTATTTTAACAATTTTGATACCTTAAATACATGATATAAAACTTGTTCAAATAAT
130 TGTTATTATTCTATTTTAACAGTTTTGATAGCTTAAATACATGATATAAAACTTGTTCAAATAAT
* * * *
9616538 TGAATTTGGTTTTCACTGTTGATATGTGTGAAAAAATTACCATTTATGTCTATTTAAGGCTCCTT
195 TGAACTTAGTTTTCACAGTTGATATGTGTGAAAAAATTACCATTTAGGTCTATTTAAGGCTCCTT
* * *
9616603 GTGCCGTTAAAGGGTAAAAATGTAAAATTTGCTATTATTGTTTTGTTTTAACAGTTTTGATAGC
260 GTGCCATTAAAAGGCAAAAATGTAAAATTTGCTATTATTGTTTTGTTTTAACAGTTTTGATAGC
* * * * *
9616667 TTAAATACATCATACTAAACTTGTCCAAATGATTGAATTTGGTTTTCATAGTTGATATGTGTGAA
1 TTAAATACATCATACTAAACTTGTTCAAATAATTGAACTTAGTTTTCATGGTTGATATGTGTGAA
* * * *
9616732 AAAATTA-TCATTTAGGGTCTATTTAGGACTTTTTGTT-CCATTAAAA-GCAAAAATACAAATTT
66 AAAATTACT-GTTTA-CGTCTGTTTAGGACTTTTT-TTGCCGTTAAAAGGCAAAAATACAAATTT
** * *
9616794 ATTGTTATTATTCTATTTTAACAGTTTGGATAGCTTTAATA
128 GCTGTTATTATTCTATTTTAACAGTTTTGATAGCTTAAATA
9616835 ATATATGTTT
Statistics
Matches: 408, Mismatches: 77, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
322 87 0.21
323 195 0.48
324 108 0.26
325 17 0.04
326 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (323 bp):
TTAAATACATCATACTAAACTTGTTCAAATAATTGAACTTAGTTTTCATGGTTGATATGTGTGAA
AAAATTACTGTTTACGTCTGTTTAGGACTTTTTTTGCCGTTAAAAGGCAAAAATACAAATTTGCT
GTTATTATTCTATTTTAACAGTTTTGATAGCTTAAATACATGATATAAAACTTGTTCAAATAATT
GAACTTAGTTTTCACAGTTGATATGTGTGAAAAAATTACCATTTAGGTCTATTTAAGGCTCCTTG
TGCCATTAAAAGGCAAAAATGTAAAATTTGCTATTATTGTTTTGTTTTAACAGTTTTGATAGC
Found at i:9624801 original size:10 final size:10
Alignment explanation
Indices: 9624771--9624805 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
9624761 TTTCTCAACT
9624771 TAGATTTTTC
1 TAGATTTTTC
* *
9624781 AAAATTTTTC
1 TAGATTTTTC
9624791 TAGATTTTTC
1 TAGATTTTTC
9624801 TAGAT
1 TAGAT
9624806 CTGATCTACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.54
Consensus pattern (10 bp):
TAGATTTTTC
Found at i:9625698 original size:216 final size:216
Alignment explanation
Indices: 9625324--9625760 Score: 802
Period size: 216 Copynumber: 2.0 Consensus size: 216
9625314 TAAGGAATAC
*
9625324 TATCTATATCTGCTTCAAATTCGTCATGGATAGTAAGTCTCTTATCCGAATCCATTAATGATCCA
1 TATCTATATCTGCTTCAAATCCGTCATGGATAGTAAGTCTCTTATCCGAATCCATTAATGATCCA
* * * *
9625389 TTTATAACTATTCAAATTTGACATAAATAGATCAGATAATGATGGATATTCATTTATTTACTATC
66 TTTATAACCATTCAAATTTGACATAAATAGATCAAATAATGATAGATAGTCATTTATTTACTATC
*
9625454 CATTGCCATCCTTATGCCTTTAACCTTCTTTTTCTTCAAAAATCAAGCTTTAAAAATTAGTATAA
131 CATTGCCATCCTTATGCCTTTAACCTTCTTTTTCTTCAAAAATCAAGCTCTAAAAATTAGTATAA
*
9625519 CAGAAATCATGAAACTCGAAA
196 CAGAAACCATGAAACTCGAAA
*
9625540 TATCTATATCTGCTTCGAATCCGTCATGGATAGTAAGTCTCTTATCCGAATCCATTAATGATCCA
1 TATCTATATCTGCTTCAAATCCGTCATGGATAGTAAGTCTCTTATCCGAATCCATTAATGATCCA
9625605 TTTATAACCATTCAAATTTGACATAAATAGATCAAATAATGATAGATAGTCATTTATTTACTATC
66 TTTATAACCATTCAAATTTGACATAAATAGATCAAATAATGATAGATAGTCATTTATTTACTATC
9625670 CATTGCCATCCTTATGCCTTTAACCTTCTTTTTCTTCAAAAATCAAGCTCTAAAAATTAGTATAA
131 CATTGCCATCCTTATGCCTTTAACCTTCTTTTTCTTCAAAAATCAAGCTCTAAAAATTAGTATAA
9625735 CAGAAACCATGAAACTCGAAA
196 CAGAAACCATGAAACTCGAAA
9625756 TATCT
1 TATCT
9625761 TTACTATTGT
Statistics
Matches: 213, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
216 213 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.36
Consensus pattern (216 bp):
TATCTATATCTGCTTCAAATCCGTCATGGATAGTAAGTCTCTTATCCGAATCCATTAATGATCCA
TTTATAACCATTCAAATTTGACATAAATAGATCAAATAATGATAGATAGTCATTTATTTACTATC
CATTGCCATCCTTATGCCTTTAACCTTCTTTTTCTTCAAAAATCAAGCTCTAAAAATTAGTATAA
CAGAAACCATGAAACTCGAAA
Found at i:9635314 original size:34 final size:34
Alignment explanation
Indices: 9635271--9635338 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
9635261 AAGGTCATGT
9635271 TGATATGACAATGTCATGTCACATGTCAAGCACC
1 TGATATGACAATGTCATGTCACATGTCAAGCACC
9635305 TGATATGACAATGTCATGTCACATGTCAAGCACC
1 TGATATGACAATGTCATGTCACATGTCAAGCACC
9635339 ATGCGATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (34 bp):
TGATATGACAATGTCATGTCACATGTCAAGCACC
Found at i:9636181 original size:63 final size:64
Alignment explanation
Indices: 9636088--9636293 Score: 275
Period size: 57 Copynumber: 3.3 Consensus size: 64
9636078 AATTTCGAGG
* *
9636088 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAAAACC-TTTCTTGAGAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTTAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
* * *
9636151 AAAATTGATACTTTCAATTTTTTCTTAAAAAAAAAAACCTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTCCTTAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
* * * *
9636215 AAAATTGATACTTTCAACTTTTCCTT-------AAAACATTTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCTTAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
9636272 AAAATTGATACTTTCAACTTTT
1 AAAATTGATACTTTCAACTTTT
9636294 TCCCAAAAAT
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
57 50 0.38
63 36 0.27
64 46 0.35
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (64 bp):
AAAATTGATACTTTCAACTTTTCCTTAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
Found at i:9636186 original size:64 final size:64
Alignment explanation
Indices: 9636088--9636295 Score: 238
Period size: 64 Copynumber: 3.4 Consensus size: 64
9636078 AATTTCGAGG
* * *
9636088 AAAATTGATACTTTCAACTTTTCCTAAAAAAAAAAAACC-TTTCTTGAGAATTTATTTTTAAGA
1 AAAATTGATACTTTCAATTTTTCTTAAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
*
9636151 AAAATTGATACTTTCAATTTTTTCTT-AAAAAAAAAAACCTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAA-TTTTTCTTAAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
* * * * *
9636215 AAAATTGATACTTTCAACTTTTCCTT--------AAAACATTTTTTTGGAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAA-TTTTTCTTAAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
9636272 AAAATTGATACTTTCAACTTTTTC
1 AAAATTGATACTTTCAA-TTTTTC
9636296 CCAAAAATAT
Statistics
Matches: 133, Mismatches: 10, Indels: 10
0.87 0.07 0.07
Matches are distributed among these distances:
57 51 0.38
63 30 0.23
64 52 0.39
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (64 bp):
AAAATTGATACTTTCAATTTTTCTTAAAAAAAAAAAACCTTTTCTTGAAAATTTATTTTTAAGA
Found at i:9636276 original size:57 final size:58
Alignment explanation
Indices: 9636024--9636311 Score: 231
Period size: 57 Copynumber: 4.8 Consensus size: 58
9636014 GCTTCTGTAC
** * * *
9636024 AAGAGAAAATTGATACTTTCAAC-TTTTCCCTAAAATATTTTTTTTTGAAATTTTAATTTC
1 AAGA-AAAATTGATACTTTCAACTTTTTCCC-AAAA-ACATTTTTTTGAAAATTTATTTTT
* * * * * * *
9636084 GAGGAAAATTGATACTTTCAAC-TTTTCCTAAAAAAAAAAAACCTTTCTTGAGAATTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCC-----CAAAAACA-TTTTTTTGAAAATTTATTTTT
* ** *
9636147 AAGAAAAATTGATACTTTCAATTTTTTCTTAAAAAAAAAAACCTTTTTTTGAAAATTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTC------CCAAAAACATTTTTTTGAAAATTTATTTTT
** *
9636211 AAGAAAAATTGATACTTTCAAC-TTTTCCTTAAAACATTTTTTTGGAAATTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAACATTTTTTTGAAAATTTATTTTT
* *
9636268 AAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAACATTTTTTT
9636312 TGGATTTTAT
Statistics
Matches: 184, Mismatches: 30, Indels: 30
0.75 0.12 0.12
Matches are distributed among these distances:
57 46 0.25
58 18 0.10
59 24 0.13
60 2 0.01
62 1 0.01
63 43 0.23
64 44 0.24
65 6 0.03
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (58 bp):
AAGAAAAATTGATACTTTCAACTTTTTCCCAAAAACATTTTTTTGAAAATTTATTTTT
Found at i:9636365 original size:6 final size:6
Alignment explanation
Indices: 9636328--9636410 Score: 70
Period size: 6 Copynumber: 14.5 Consensus size: 6
9636318 TTATTTAAAG
*
9636328 AAAAT- AAAATA ATAAA-A CAAAATA AAAGTA AAAATA AAAAT- AAAAT-
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AAAATA
* * *
9636374 AAAGT- AAAATA AAAAT- AAAATA AAGACA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
9636411 GAATATTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
5 23 0.36
6 36 0.56
7 5 0.08
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:9636372 original size:11 final size:11
Alignment explanation
Indices: 9636328--9636476 Score: 81
Period size: 11 Copynumber: 12.8 Consensus size: 11
9636318 TTATTTAAAG
9636328 AAAATAAAATAA
1 AAAATAAAAT-A
*
9636340 TAAAACAAAATA
1 -AAAATAAAATA
*
9636352 AAAGTAAAAATA
1 AAAAT-AAAATA
9636364 AAAATAAAAT-
1 AAAATAAAATA
*
9636374 AAAGTAAAATA
1 AAAATAAAATA
9636385 AAAATAAAATA
1 AAAATAAAATA
9636396 AAGACA-AAAATAA
1 AA-A-ATAAAAT-A
*
9636409 AAGAATATTAAACA
1 AA-AATA--AAATA
** **
9636423 AATCTAATCTA
1 AAAATAAAATA
*
9636434 ATAATAATAATA
1 AAAATAA-AATA
9636446 AAAATATAAA-A
1 AAAATA-AAATA
9636457 AAAATAAAATGA
1 AAAATAAAAT-A
9636469 AAAA-AAAA
1 AAAATAAAA
9636477 CCTGGAACGG
Statistics
Matches: 106, Mismatches: 18, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
10 12 0.11
11 37 0.35
12 32 0.30
13 19 0.18
14 3 0.03
15 3 0.03
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAATAAAATA
Found at i:9636384 original size:21 final size:21
Alignment explanation
Indices: 9636332--9636398 Score: 89
Period size: 21 Copynumber: 3.0 Consensus size: 21
9636322 TTAAAGAAAA
*
9636332 TAAAATAATAAAACAAAATAAAAG
1 TAAAAT-A-AAAATAAAAT-AAAG
9636356 TAAAAATAAAAATAAAATAAAG
1 T-AAAATAAAAATAAAATAAAG
9636378 TAAAATAAAAATAAAATAAAG
1 TAAAATAAAAATAAAATAAAG
9636399 ACAAAAATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
21 20 0.49
22 5 0.12
23 9 0.22
24 2 0.05
25 5 0.12
ACGTcount: A:0.76, C:0.01, G:0.04, T:0.18
Consensus pattern (21 bp):
TAAAATAAAAATAAAATAAAG
Found at i:9636410 original size:5 final size:5
Alignment explanation
Indices: 9636328--9636397 Score: 72
Period size: 5 Copynumber: 13.6 Consensus size: 5
9636318 TTATTTAAAG
*
9636328 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT AAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT -AAAAT AAAAT
*
9636374 AAAGT AAAAT AAAAAT AAAAT AAA
1 AAAAT AAAAT -AAAAT AAAAT AAA
9636398 GACAAAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
3 3 0.05
5 36 0.64
6 13 0.23
7 4 0.07
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:9636945 original size:14 final size:15
Alignment explanation
Indices: 9636926--9636957 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
9636916 AAAATTTTTC
9636926 AAAAATTC-CCAAAA
1 AAAAATTCACCAAAA
9636940 AAAAATTCACCAAAA
1 AAAAATTCACCAAAA
9636955 AAA
1 AAA
9636958 TCTATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.69, C:0.19, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAATTCACCAAAA
Found at i:9637245 original size:8 final size:8
Alignment explanation
Indices: 9637232--9637460 Score: 57
Period size: 8 Copynumber: 26.9 Consensus size: 8
9637222 GAAGAGAAGG
9637232 AAAATAAT
1 AAAATAAT
9637240 AAAATAAT
1 AAAATAAT
9637248 AAAATAA-
1 AAAATAAT
9637255 AAAGATAAT
1 AAA-ATAAT
**
9637264 AATAAGGAT
1 AA-AATAAT
* *
9637273 AATATATT
1 AAAATAAT
9637281 AATTAATAGAT
1 AA--AATA-AT
9637292 -AAATAAT
1 AAAATAAT
*
9637299 AATAT-AT
1 AAAATAAT
9637306 ATAAATAGA-
1 A-AAATA-AT
*
9637315 CAAATAAT
1 AAAATAAT
9637323 AATAAT-AT
1 AA-AATAAT
9637331 ATAAATAGAT
1 A-AAATA-AT
9637341 -AAATAAT
1 AAAATAAT
9637348 AAAACATATAT
1 -AAA-ATA-AT
*
9637359 ATATCAACAGAT
1 A-A--AATA-AT
9637371 -AAATAAT
1 AAAATAAT
9637378 AAAAATAAT
1 -AAAATAAT
*
9637387 AAAATAAA
1 AAAATAAT
9637395 ATAAAT-AT
1 A-AAATAAT
* *
9637403 ATATTAAT
1 AAAATAAT
9637411 AAATAGTAAT
1 AAA-A-TAAT
9637421 AATAAATAA-
1 -A-AAATAAT
*
9637430 ACGAATAAT
1 A-AAATAAT
9637439 -AAATACAT
1 AAAATA-AT
9637447 AAAAT-AT
1 AAAATAAT
9637454 AAAATAA
1 AAAATAA
9637461 AGTAAAAAAA
Statistics
Matches: 163, Mismatches: 24, Indels: 68
0.64 0.09 0.27
Matches are distributed among these distances:
7 26 0.16
8 76 0.47
9 28 0.17
10 20 0.12
11 6 0.04
12 6 0.04
13 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.28
Consensus pattern (8 bp):
AAAATAAT
Found at i:9637327 original size:30 final size:30
Alignment explanation
Indices: 9637233--9637387 Score: 111
Period size: 27 Copynumber: 5.6 Consensus size: 30
9637223 AAGAGAAGGA
* *
9637233 AAATAATAA-AATAATA-AAATAAAAAGAT
1 AAATAATAATAATAATATATATAAATAGAT
** *
9637261 -AATAATAAGGATAATATAT-TAATTA-AT
1 AAATAATAATAATAATATATATAAATAGAT
*
9637288 AGAT-A-AATAATAATATATATAAATAG--
1 AAATAATAATAATAATATATATAAATAGAT
*
9637314 ACA-AATAATAAT-A-ATATATAAATAGAT
1 AAATAATAATAATAATATATATAAATAGAT
* * *
9637341 AAATAATAA-AACATATATATATCAACAGAT
1 AAATAATAATAATA-ATATATATAAATAGAT
*
9637371 AAATAATAAAAATAATA
1 AAATAATAATAATAATA
9637388 AAATAAAATA
Statistics
Matches: 99, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
25 12 0.12
26 15 0.15
27 26 0.26
28 17 0.17
29 2 0.02
30 24 0.24
31 3 0.03
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (30 bp):
AAATAATAATAATAATATATATAAATAGAT
Found at i:9637336 original size:25 final size:25
Alignment explanation
Indices: 9637285--9637429 Score: 116
Period size: 25 Copynumber: 5.5 Consensus size: 25
9637275 TATATTAATT
9637285 AATAGATAAATAATAAT-ATATATA
1 AATAGATAAATAATAATAATATATA
*
9637309 AATAGACAAATAATAATAATATATA
1 AATAGATAAATAATAATAATATATA
*
9637334 AATAGATAAATAATAAAACATATATATATC
1 AATAGATAAATAAT---A-ATA-ATATATA
* *
9637364 AACAGATAAATAATAAAAATA-ATAA
1 AATAGATAAATAATAATAATATAT-A
* * *
9637389 AATAAAATAAATATATATTAATAAATA
1 AAT-AGATAAATA-ATAATAATATATA
9637416 GTAATA-ATAAATAA
1 --AATAGATAAATAA
9637430 ACGAATAATA
Statistics
Matches: 99, Mismatches: 10, Indels: 22
0.76 0.08 0.17
Matches are distributed among these distances:
24 18 0.18
25 25 0.25
26 11 0.11
27 16 0.16
28 4 0.04
29 6 0.06
30 19 0.19
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (25 bp):
AATAGATAAATAATAATAATATATA
Found at i:9637376 original size:49 final size:49
Alignment explanation
Indices: 9637285--9637426 Score: 131
Period size: 49 Copynumber: 3.0 Consensus size: 49
9637275 TATATTAATT
*
9637285 AATAGATAAATAAT--AATATATATAAATAGACAAATAATAATAATATATA
1 AATAGATAAATAATAAAATATATATATATAGACAAATAATAATAATA-A-A
* *
9637334 AATAGATAAATAATAAAACATATATATATCA-ACAGAT-A-AATAATAAA
1 AATAGATAAATAATAAAATATATATATAT-AGACAAATAATAATAATAAA
* * *
9637381 AATA-AT-AA-AATAAAATAAATATATATTA-ATAAATAGTAATAATAAA
1 AATAGATAAATAATAAAATATATATATA-TAGACAAATAATAATAATAAA
9637427 TAAACGAATA
Statistics
Matches: 79, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
44 20 0.25
45 3 0.04
46 11 0.14
47 5 0.06
48 1 0.01
49 21 0.27
50 1 0.01
51 16 0.20
52 1 0.01
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.29
Consensus pattern (49 bp):
AATAGATAAATAATAAAATATATATATATAGACAAATAATAATAATAAA
Found at i:9637427 original size:13 final size:12
Alignment explanation
Indices: 9637235--9637461 Score: 72
Period size: 11 Copynumber: 18.9 Consensus size: 12
9637225 GAGAAGGAAA
*
9637235 ATAATAAAATAAT
1 ATAATAATA-AAT
* *
9637248 AAAATAA-AAAG
1 ATAATAATAAAT
**
9637259 ATAATAATAAGG
1 ATAATAATAAAT
*
9637271 ATAATATATTAAT
1 ATAATA-ATAAAT
9637284 -TAATAGAT-AA-
1 ATAATA-ATAAAT
*
9637294 ATAATAATATAT
1 ATAATAATAAAT
*
9637306 ATAAATAGACAAAT
1 AT-AATA-ATAAAT
*
9637320 AATAATAATATAT
1 -ATAATAATAAAT
9637333 A-AATAGATAAAT
1 ATAATA-ATAAAT
* *
9637345 AATAA-AACATAT
1 -ATAATAATAAAT
* *
9637357 ATATATCAACAGAT
1 ATA-AT-AATAAAT
9637371 A-AATAAT-AA-
1 ATAATAATAAAT
9637380 A-AATAATAAA-
1 ATAATAATAAAT
9637390 ATAA-AATAAAT
1 ATAATAATAAAT
9637401 ATATATTAATAAAT
1 ATA-A-TAATAAAT
9637415 AGTAATAATAAAT
1 A-TAATAATAAAT
*
9637428 A-AACGAAT-AAT
1 ATAA-TAATAAAT
9637439 A-AATACATAAAAT
1 ATAATA-AT-AAAT
9637452 ATAA-AATAAA
1 ATAATAATAAA
9637462 GTAAAAAAAA
Statistics
Matches: 167, Mismatches: 21, Indels: 54
0.69 0.09 0.22
Matches are distributed among these distances:
9 7 0.04
10 13 0.08
11 43 0.26
12 38 0.23
13 34 0.20
14 28 0.17
15 4 0.02
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:9637440 original size:3 final size:3
Alignment explanation
Indices: 9637234--9637425 Score: 58
Period size: 3 Copynumber: 59.7 Consensus size: 3
9637224 AGAGAAGGAA
* *
9637234 AAT AAT AA- AAT AAT AA- AAT AA- AA- AGAT AAT AAT AAG GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT
* *
9637276 -AT ATT AATT AAT AGAT AAAT AAT AAT -AT ATAT AAAT AGACA AAT AAT
1 AAT AAT AA-T AAT A-AT -AAT AAT AAT AAT A-AT -AAT A-A-T AAT AAT
* *
9637323 AAT AAT ATAT AAAT AGAT AAAT AAT AAA ACAT ATAT ATAT CAAC AGAT
1 AAT AAT A-AT -AAT A-AT -AAT AAT AAT A-AT A-AT A-AT -AAT A-AT
* * *
9637371 AAAT AAT AAA AAT AAT AA- AAT AA- AAT AAAT ATAT ATT AAT AAAT AGT
1 -AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AAT AAT -AAT AAT
9637418 AAT AAT AA
1 AAT AAT AA
9637426 ATAAACGAAT
Statistics
Matches: 144, Mismatches: 19, Indels: 52
0.67 0.09 0.24
Matches are distributed among these distances:
2 15 0.10
3 79 0.55
4 43 0.30
5 7 0.05
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:9637825 original size:85 final size:84
Alignment explanation
Indices: 9637696--9637882 Score: 261
Period size: 84 Copynumber: 2.2 Consensus size: 84
9637686 GAGCAGAGGT
*** *
9637696 TCAACGACTTTGAAAAACATAAACATTGCTCCTCTAATCAGAGGCTTAACGACTTTGAAAATGAA
1 TCAACGACTTTG-AAAACATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTG-AAA--AA
9637761 TAAA-GCTCCTCTAATCAAAGAC
62 TAAACGCTCCTCTAATCAAAGAC
9637783 TCAACGACTTTGAAAA-ATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAA
1 TCAACGACTTTGAAAACATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAA
* *
9637847 CGGCTCCTCTAATCAGAGGC
66 C-GCTCCTCTAATCAAAGAC
9637867 TCAACGACTTTGAAAA
1 TCAACGACTTTGAAAA
9637883 GTAAGTTGCT
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
82 6 0.07
84 35 0.38
85 35 0.38
86 4 0.04
87 12 0.13
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.24
Consensus pattern (84 bp):
TCAACGACTTTGAAAACATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAA
CGCTCCTCTAATCAAAGAC
Found at i:9637866 original size:41 final size:41
Alignment explanation
Indices: 9637679--9638019 Score: 305
Period size: 41 Copynumber: 8.1 Consensus size: 41
9637669 TTGATCAAAA
* * *
9637679 CTCCTCTGAGCAGAGGTTCAACGACTTTGAAAAACATAAACATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTG-AAAA-ATAAAC--TG
*
9637724 CTCCTCTAATCAGAGGCTTAACGACTTTGAAAATGAATAAA--G
1 CTCCTCTAATCAGAGGCTCAACGACTTTG-AAA--AATAAACTG
* * **
9637766 CTCCTCTAATCAAAGACTCAACGACTTTGAAAAATAAACAAAA
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAC--TG
*
9637809 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACGG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACTG
* **
9637850 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAGTTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACTG
* * * *
9637891 CTCCTCTAAAT-AGAGGCAACCACGACTTTGAAAAATAAATTA
1 CTCCTCT-AATCAGAGGC-TCAACGACTTTGAAAAATAAACTG
* * * * *
9637933 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
1 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACTG
** * *
9637974 CTTTTCTAAACAGAGG--CAACGAAACTTTGAAAAATAAATTG
1 CTCCTCTAATCAGAGGCTCAACG--ACTTTGAAAAATAAACTG
9638015 CTCCT
1 CTCCT
9638020 TAACAGTCAT
Statistics
Matches: 255, Mismatches: 30, Indels: 26
0.82 0.10 0.08
Matches are distributed among these distances:
39 10 0.04
41 111 0.44
42 62 0.24
43 37 0.15
45 29 0.11
46 5 0.02
47 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (41 bp):
CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACTG
Found at i:9637947 original size:83 final size:83
Alignment explanation
Indices: 9637679--9638019 Score: 280
Period size: 83 Copynumber: 4.1 Consensus size: 83
9637669 TTGATCAAAA
* * ** * * *
9637679 CTCCTCTGAGCAGAGGTTCAACGACTTTGAAAAACATAAACATTGCTCCTCTAATCAGAGGCTTA
1 CTCCTCTAAACAGAGGCACAACGACTTTG-AAAA-GT-AA-ATTGCTCCTCTAAACAGAGGC-AA
9637744 --ACGACTTTGAAAATGAATAAA--G
61 CCACGACTTTG-AAA--AATAAATTG
* * * * * *** * * *
9637766 CTCCTCTAATCAAAGACTCAACGACTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGC-TCAA
1 CTCCTCTAAACAGAGGCACAACGACTTTGAAAAGT-AA-ATTGCTCCTCTAAACAGAGGCAACCA
**
9637830 CGACTTTGAAAAATAAACGG
64 CGACTTTGAAAAATAAATTG
* * * *
9637850 CTCCTCTAATCAGAGGCTCAACGACTTTGAAAAGTAAGTTGCTCCTCTAAATAGAGGCAACCACG
1 CTCCTCTAAACAGAGGCACAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACCACG
*
9637915 ACTTTGAAAAATAAATTA
66 ACTTTGAAAAATAAATTG
* ** * *
9637933 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTTTTCTAAACAGAGGCAACGA-A
1 CTCCTCTAAACAGAGGCACAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACCACG
9637997 ACTTTGAAAAATAAATTG
66 ACTTTGAAAAATAAATTG
9638015 CTCCT
1 CTCCT
9638020 TAACAGTCAT
Statistics
Matches: 216, Mismatches: 33, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
82 43 0.20
83 76 0.35
84 36 0.17
85 33 0.15
86 4 0.02
87 24 0.11
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (83 bp):
CTCCTCTAAACAGAGGCACAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACCACG
ACTTTGAAAAATAAATTG
Found at i:9638001 original size:124 final size:125
Alignment explanation
Indices: 9637674--9638019 Score: 319
Period size: 124 Copynumber: 2.7 Consensus size: 125
9637664 AAGATTTGAT
* * ** * *
9637674 CAAAACTCCTCTGAGCAGAGGTTCAACGACTTTGAAAAACATAAACATTGCTCCTCTAATCAGAG
1 CAAAACTCCTCTAAACAGAGGCACAACGACTTTG-AAAA-ATAAAC--GGCTCCTCTAAACAGAG
* * * * *
9637739 GCTTAACGACTTTGAAAATGAATAAA--GCTCCTCT-AATCAAAGAC-TCAACGACTTTGAAAAA
62 GC-CAACGACTTTG-AAA--AATAAATTGCTCCTCTAAAT-AGAGGCAACCACGACTTTGAAAAA
9637800 TAAA
122 TAAA
* * *
9637804 CAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAACGGCTCCTCTAATCAGAGGCTC
1 CAAAACTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAACGGCTCCTCTAAACAGAGGC-C
* *
9637869 AACGACTTTGAAAAGTAAGTTGCTCCTCTAAATAGAGGCAACCACGACTTTGAAAAAT-AA
65 AACGACTTTGAAAAATAAATTGCTCCTCTAAATAGAGGCAACCACGACTTTGAAAAATAAA
** * * ** **
9637929 -ATTACTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTTTTCTAAACAGAGG-CA
1 CAAAACTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAACGGCTCCTCTAAACAGAGGCCA
9637992 ACGAAACTTTGAAAAATAAATTGCTCCT
66 ACG--ACTTTGAAAAATAAATTGCTCCT
9638020 TAACAGTCAT
Statistics
Matches: 186, Mismatches: 24, Indels: 18
0.82 0.11 0.08
Matches are distributed among these distances:
122 5 0.03
123 4 0.02
124 71 0.38
125 17 0.09
126 48 0.26
128 6 0.03
129 4 0.02
130 31 0.17
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (125 bp):
CAAAACTCCTCTAAACAGAGGCACAACGACTTTGAAAAATAAACGGCTCCTCTAAACAGAGGCCA
ACGACTTTGAAAAATAAATTGCTCCTCTAAATAGAGGCAACCACGACTTTGAAAAATAAA
Found at i:9639738 original size:11 final size:10
Alignment explanation
Indices: 9639715--9639779 Score: 55
Period size: 10 Copynumber: 6.3 Consensus size: 10
9639705 TCTTTTTTCA
9639715 TTTTCTCATT
1 TTTTCTCATT
9639725 TTTTCTCTATTTTT
1 TTTTCTC-A---TT
*
9639739 TTTTTTCATT
1 TTTTCTCATT
9639749 TTTTCATC-TT
1 TTTTC-TCATT
9639759 TTTT-TC-TT
1 TTTTCTCATT
9639767 TTTTCTCATT
1 TTTTCTCATT
9639777 TTT
1 TTT
9639780 CATCCATTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
8 8 0.17
9 2 0.04
10 24 0.52
11 3 0.07
13 1 0.02
14 8 0.17
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTCTCATT
Found at i:9639747 original size:24 final size:26
Alignment explanation
Indices: 9639708--9639771 Score: 87
Period size: 24 Copynumber: 2.5 Consensus size: 26
9639698 AATCTTTTCT
*
9639708 TTTTTCATTTTCTCATTTTTTC-TCTA
1 TTTTTC-TTTTTTCATTTTTTCATCTA
*
9639734 TTTTT-TTTTTTCATTTTTTCATCTT
1 TTTTTCTTTTTTCATTTTTTCATCTA
9639759 TTTTTCTTTTTTC
1 TTTTTCTTTTTTC
9639772 TCATTTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 14 0.41
25 8 0.24
26 12 0.35
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.77
Consensus pattern (26 bp):
TTTTTCTTTTTTCATTTTTTCATCTA
Found at i:9639748 original size:32 final size:32
Alignment explanation
Indices: 9639702--9639770 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
9639692 AATTTGAATC
*
9639702 TTTTCTTTTTTCATTTTCTCAT-TTTTTCTCT
1 TTTTTTTTTTTCATTTTCTCATCTTTTTCTCT
* *
9639733 ATTTTTTTTTTTCATTTTTTCATCTTTTTTTCT
1 -TTTTTTTTTTTCATTTTCTCATCTTTTTCTCT
9639766 TTTTT
1 TTTTT
9639771 CTCATTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 25 0.76
33 8 0.24
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.78
Consensus pattern (32 bp):
TTTTTTTTTTTCATTTTCTCATCTTTTTCTCT
Found at i:9639752 original size:8 final size:8
Alignment explanation
Indices: 9639702--9639761 Score: 54
Period size: 8 Copynumber: 7.5 Consensus size: 8
9639692 AATTTGAATC
9639702 TTTTC-TT
1 TTTTCATT
9639709 TTTTCATT
1 TTTTCATT
*
9639717 TTCTCATT
1 TTTTCATT
9639725 TTTTC-TCT
1 TTTTCAT-T
*
9639733 ATTTT-TTT
1 -TTTTCATT
9639741 TTTTCATT
1 TTTTCATT
9639749 TTTTCATCT
1 TTTTCAT-T
9639758 TTTT
1 TTTT
9639762 TTCTTTTTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
7 10 0.23
8 24 0.55
9 10 0.23
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:9639766 original size:8 final size:8
Alignment explanation
Indices: 9639702--9639770 Score: 52
Period size: 8 Copynumber: 8.4 Consensus size: 8
9639692 AATTTGAATC
9639702 TTTTC-TT
1 TTTTCTTT
*
9639709 TTTTCATT
1 TTTTCTTT
* *
9639717 TTCTCATT
1 TTTTCTTT
*
9639725 TTTTCTCTA
1 TTTTCT-TT
9639734 TTTT-TTT
1 TTTTCTTT
9639741 TTTTCATTT
1 TTTTC-TTT
9639750 TTTCATCTTT
1 TTT--TCTTT
9639760 TTTTCTTT
1 TTTTCTTT
9639768 TTT
1 TTT
9639771 CTCATTTTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
7 10 0.20
8 22 0.43
9 11 0.22
10 6 0.12
11 2 0.04
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTCTTT
Found at i:9639778 original size:27 final size:28
Alignment explanation
Indices: 9639705--9639783 Score: 89
Period size: 27 Copynumber: 3.0 Consensus size: 28
9639695 TTGAATCTTT
*
9639705 TCTTTTTTC-ATTTTCTCATTTTT--TC
1 TCTTTTTTCTTTTTTCTCATTTTTCATC
*
9639730 TCTATTTT-TTTTTT-TCATTTTTTCATC
1 TCTTTTTTCTTTTTTCTCA-TTTTTCATC
9639757 T-TTTTTTCTTTTTTCTCATTTTTCATC
1 TCTTTTTTCTTTTTTCTCATTTTTCATC
9639784 CATTGTTGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 3 0.07
25 16 0.36
26 5 0.11
27 18 0.40
28 3 0.07
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (28 bp):
TCTTTTTTCTTTTTTCTCATTTTTCATC
Found at i:9646079 original size:17 final size:17
Alignment explanation
Indices: 9646057--9646099 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
9646047 TACAAACATA
9646057 AAAAAATACA-AAAAAGT
1 AAAAAATACACAAAAA-T
9646074 AAAAAATGA-ACAAAAAT
1 AAAAAAT-ACACAAAAAT
9646091 AAAAAATAC
1 AAAAAATAC
9646100 CCCTAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 1 0.04
17 16 0.70
18 6 0.26
ACGTcount: A:0.77, C:0.07, G:0.05, T:0.12
Consensus pattern (17 bp):
AAAAAATACACAAAAAT
Found at i:9648039 original size:51 final size:51
Alignment explanation
Indices: 9647963--9648070 Score: 198
Period size: 51 Copynumber: 2.1 Consensus size: 51
9647953 ATGAGAAGAA
*
9647963 ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAATGTATCAC
1 ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATCAC
*
9648014 ACATGTATGTTTTAATTTATAGTATTGCTAATGTTTATTTTAAGGTATCAC
1 ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATCAC
9648065 ACATGT
1 ACATGT
9648071 TTTAATCATA
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:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (51 bp):
ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATCAC
Found at i:9648047 original size:28 final size:28
Alignment explanation
Indices: 9647965--9648056 Score: 72
Period size: 28 Copynumber: 3.5 Consensus size: 28
9647955 GAGAAGAAAC
9647965 ATGTATGTTTTAATTTATAGTATTGCTA
1 ATGTATGTTTTAATTTATAGTATTGCTA
* **
9647993 A---A-G-TTTATTTTA-ATGTATCAC-A
1 ATGTATGTTTTAATTTATA-GTATTGCTA
9648015 CATGTATGTTTTAATTTATAGTATTGCTA
1 -ATGTATGTTTTAATTTATAGTATTGCTA
* *
9648044 ATGTTTATTTTAA
1 ATGTATGTTTTAA
9648057 GGTATCACAC
Statistics
Matches: 47, Mismatches: 8, Indels: 18
0.64 0.11 0.25
Matches are distributed among these distances:
22 2 0.04
23 14 0.30
24 1 0.02
25 1 0.02
26 1 0.02
27 1 0.02
28 25 0.53
29 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.52
Consensus pattern (28 bp):
ATGTATGTTTTAATTTATAGTATTGCTA
Found at i:9650538 original size:24 final size:24
Alignment explanation
Indices: 9650507--9650557 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
9650497 ATGAGTTATC
9650507 ATTTGTGTTAGATTTATTATTTTT
1 ATTTGTGTTAGATTTATTATTTTT
*
9650531 ATTTGTGTTATATTTATTATTTTT
1 ATTTGTGTTAGATTTATTATTTTT
9650555 ATT
1 ATT
9650558 AAATTAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (24 bp):
ATTTGTGTTAGATTTATTATTTTT
Found at i:9651629 original size:27 final size:27
Alignment explanation
Indices: 9651587--9651638 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
9651577 TCTTTTTACA
*
9651587 TGGGTTAAAGCCCAATCCAATTTCATT
1 TGGGTTAAAGCCCAATCCAAGTTCATT
* * *
9651614 TGGGTTAAGGCTCAATTCAAGTTCA
1 TGGGTTAAAGCCCAATCCAAGTTCA
9651639 ATTATGGGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
TGGGTTAAAGCCCAATCCAAGTTCATT
Found at i:9653341 original size:18 final size:18
Alignment explanation
Indices: 9653318--9653354 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9653308 TCATTTTCGA
9653318 CATTCTCTTTAGTAAATT
1 CATTCTCTTTAGTAAATT
9653336 CATTCTCTTTAGTAAATT
1 CATTCTCTTTAGTAAATT
9653354 C
1 C
9653355 CCTTATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (18 bp):
CATTCTCTTTAGTAAATT
Found at i:9654302 original size:2 final size:2
Alignment explanation
Indices: 9654297--9654341 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
9654287 ATATATATCT
9654297 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9654338 AG AG
1 AG AG
9654342 TGCACCTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9655134 original size:29 final size:29
Alignment explanation
Indices: 9655094--9655171 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
9655084 TTAAATTATA
*
9655094 ATAAAATATTTAATATAATATATAAAATT
1 ATAAAATTTTTAATATAATATATAAAATT
* *
9655123 TTAAAATTTTTAATATAATAT-TTAAATT
1 ATAAAATTTTTAATATAATATATAAAATT
*
9655151 ATAAAATTATTAAT-TAATATA
1 ATAAAATTTTTAATATAATATA
9655172 ATATTTATAT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 6 0.14
28 18 0.42
29 19 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
ATAAAATTTTTAATATAATATATAAAATT
Found at i:9655179 original size:27 final size:27
Alignment explanation
Indices: 9655085--9655180 Score: 74
Period size: 28 Copynumber: 3.4 Consensus size: 27
9655075 GAATGATTTT
9655085 TAAATTATAATAAAA-TATTTAATATAATATA
1 TAAATT-T-ATAAAATTA-TTAATAT-A-ATA
*
9655116 TAAAATTT-TAAAATTTTTAATATAATA
1 T-AAATTTATAAAATTATTAATATAATA
9655143 TTTAAA-TTATAAAATTATTAAT-TAATA
1 --TAAATTTATAAAATTATTAATATAATA
9655170 TAATATTTATA
1 TAA-ATTTATA
9655181 TCTAACATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 18
0.74 0.03 0.24
Matches are distributed among these distances:
25 3 0.05
26 1 0.02
27 15 0.27
28 16 0.29
29 13 0.23
30 1 0.02
31 2 0.04
32 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
TAAATTTATAAAATTATTAATATAATA
Found at i:9656020 original size:32 final size:32
Alignment explanation
Indices: 9655984--9656095 Score: 91
Period size: 32 Copynumber: 3.5 Consensus size: 32
9655974 TTAAAATTAC
9655984 ATATCATTTTAAAAAATTAAGTAAAAATATTT
1 ATATCATTTTAAAAAATTAAGTAAAAATATTT
** * * * *
9656016 ATATCGGTTTAATAAATTAAATAAAAA-CTCT
1 ATATCATTTTAAAAAATTAAGTAAAAATATTT
* * * * *
9656047 ATATCATATTAAAATATTATGTAGAAATTTTT
1 ATATCATTTTAAAAAATTAAGTAAAAATATTT
** *
9656079 AGGTCATTTTCAAAAAT
1 ATATCATTTTAAAAAAT
9656096 AGATTTTAAT
Statistics
Matches: 58, Mismatches: 21, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
31 21 0.36
32 37 0.64
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATCATTTTAAAAAATTAAGTAAAAATATTT
Found at i:9657467 original size:18 final size:21
Alignment explanation
Indices: 9657445--9657493 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
9657435 ATAAAAATAA
9657445 AATTTATTA-TTA-TATAATT
1 AATTTATTATTTATTATAATT
*
9657464 -ATTTATTTATTTATTTTAATT
1 AATTTA-TTATTTATTATAATT
9657485 AATTTATTA
1 AATTTATTA
9657494 ATAAAACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.20
19 3 0.12
20 3 0.12
21 9 0.36
22 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATTTATTATTTATTATAATT
Found at i:9657546 original size:26 final size:26
Alignment explanation
Indices: 9657502--9657556 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 26
9657492 TAATAAAACT
*
9657502 ATTATTTGATTTTAAAATAATTTAATA
1 ATTATTTGATTTTAAAAT-ATTAAATA
9657529 ATTATTT-ATTTTAAAATATTAAATA
1 ATTATTTGATTTTAAAATATTAAATA
9657554 ATT
1 ATT
9657557 TAAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 10 0.37
26 10 0.37
27 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTATTTGATTTTAAAATATTAAATA
Found at i:9657558 original size:17 final size:17
Alignment explanation
Indices: 9657516--9657562 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
9657506 TTTGATTTTA
*
9657516 AAATAATTTAATA-ATT
1 AAATAATTTAAAATATT
** *
9657532 ATTTATTTTAAAATATT
1 AAATAATTTAAAATATT
9657549 AAATAATTTAAAAT
1 AAATAATTTAAAAT
9657563 TTTTCATATA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATAATTTAAAATATT
Found at i:9657564 original size:25 final size:26
Alignment explanation
Indices: 9657510--9657565 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
9657500 CTATTATTTG
* **
9657510 ATTTTAAAATAATTTAATAATTATTT
1 ATTTTAAAATAATTAAATAATTATAA
9657536 ATTTTAAAAT-ATTAAATAATT-TAAA
1 ATTTTAAAATAATTAAATAATTAT-AA
9657561 ATTTT
1 ATTTT
9657566 TCATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTTAAAATAATTAAATAATTATAA
Found at i:9657673 original size:21 final size:20
Alignment explanation
Indices: 9657643--9657681 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9657633 AAGATAAATT
9657643 TTAATTTATTATTATAATAA
1 TTAATTTATTATTATAATAA
*
9657663 TTAATTTTATTTTTATAAT
1 TTAA-TTTATTATTATAAT
9657682 TTTATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATTTATTATTATAATAA
Found at i:9670359 original size:3 final size:3
Alignment explanation
Indices: 9670351--9670382 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
9670341 ACTTTTTTAC
9670351 TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9670383 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:9670845 original size:50 final size:50
Alignment explanation
Indices: 9670782--9670896 Score: 135
Period size: 49 Copynumber: 2.3 Consensus size: 50
9670772 CTTTCACTGG
* * * * ** *
9670782 AGGCTCTACAACTTTTAAAGATAAATTGAAATGAAATCT-TCTCTCAACAA
1 AGGCTCCATAACTTTTAAAAATAAATTAAAACAAAAACTCT-TCTCAACAA
*
9670832 AGGCTCCATAAC-TTTAAAAATAAATTAAAACAAAAACTCTTCTCATCAA
1 AGGCTCCATAACTTTTAAAAATAAATTAAAACAAAAACTCTTCTCAACAA
9670881 AGGCTCCATAACTTTT
1 AGGCTCCATAACTTTT
9670897 TGAAAACTTT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
49 41 0.75
50 14 0.25
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (50 bp):
AGGCTCCATAACTTTTAAAAATAAATTAAAACAAAAACTCTTCTCAACAA
Found at i:9670929 original size:15 final size:15
Alignment explanation
Indices: 9670909--9670937 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
9670899 AAAACTTTTT
9670909 GAAAATAAATTAAAC
1 GAAAATAAATTAAAC
9670924 GAAAATAAATTAAA
1 GAAAATAAATTAAA
9670938 ACAAGAACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.03, G:0.07, T:0.21
Consensus pattern (15 bp):
GAAAATAAATTAAAC
Found at i:9671070 original size:48 final size:49
Alignment explanation
Indices: 9671018--9671130 Score: 138
Period size: 49 Copynumber: 2.3 Consensus size: 49
9671008 GAGGTGACAT
* * * * * *
9671018 AACTTTAAAAATCTTATGTT-AAAATCCTCCTTTAATCAAAAGCTCTAC
1 AACTTTAAAAATCTCATCTTGAAAAACCTCCTTTAAACAAAAGCTATAA
* * *
9671066 AACTTTAAAAATCTCATCTTGAAAAAGCTCCTTTAAACAAAGGTTATAA
1 AACTTTAAAAATCTCATCTTGAAAAACCTCCTTTAAACAAAAGCTATAA
9671115 AACTTTAAAAATCTCA
1 AACTTTAAAAATCTCA
9671131 CCTAAAAATA
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
48 18 0.33
49 37 0.67
ACGTcount: A:0.43, C:0.19, G:0.05, T:0.33
Consensus pattern (49 bp):
AACTTTAAAAATCTCATCTTGAAAAACCTCCTTTAAACAAAAGCTATAA
Found at i:9671318 original size:33 final size:32
Alignment explanation
Indices: 9671271--9671381 Score: 84
Period size: 33 Copynumber: 3.4 Consensus size: 32
9671261 ACTAAAGTTG
* *
9671271 AAAAATGAAGTGATCGAGACTAAATCGCAAGT
1 AAAAATAAAATGATCGAGACTAAATCGCAAGT
*
9671303 CAAAAATAAAATGATCG-GAACTAACT-GCAAGT
1 -AAAAATAAAATGATCGAG-ACTAAATCGCAAGT
* * * *
9671335 AGAAAATGAAATGA-CTACGACTTAATCACAAGTT
1 A-AAAATAAAATGATCGA-GACTAAATCGCAAG-T
*
9671369 GAAAATAAAATGA
1 AAAAATAAAATGA
9671382 CTAAGATTGA
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
31 2 0.03
32 23 0.37
33 36 0.58
34 1 0.02
ACGTcount: A:0.50, C:0.13, G:0.17, T:0.20
Consensus pattern (32 bp):
AAAAATAAAATGATCGAGACTAAATCGCAAGT
Found at i:9671406 original size:33 final size:33
Alignment explanation
Indices: 9671330--9671495 Score: 124
Period size: 33 Copynumber: 5.1 Consensus size: 33
9671320 GAACTAACTG
* * *
9671330 CAAGTAGAAAATGAAATGACTACGACTT-AATCA
1 CAAGTCGAAAATGAAATGACTAAGA-TTGAACCA
* *
9671363 CAAGTTGAAAATAAAATGACTAAGATTGAACCA
1 CAAGTCGAAAATGAAATGACTAAGATTGAACCA
* * ** * * *
9671396 TAAGTCGAAAATGAAATAACCGAGACTGAGCTA
1 CAAGTCGAAAATGAAATGACTAAGATTGAACCA
9671429 CAAGTC-ATAAATGAAATGACT-AGATTGAACCA
1 CAAGTCGA-AAATGAAATGACTAAGATTGAACCA
* ** * * *
9671461 TAAGTTAAAAATAAAATGAC-AAGAATAAACCA
1 CAAGTCGAAAATGAAATGACTAAGATTGAACCA
9671493 CAA
1 CAA
9671496 ATCAAATAAA
Statistics
Matches: 104, Mismatches: 25, Indels: 9
0.75 0.18 0.07
Matches are distributed among these distances:
32 37 0.36
33 67 0.64
ACGTcount: A:0.51, C:0.14, G:0.15, T:0.20
Consensus pattern (33 bp):
CAAGTCGAAAATGAAATGACTAAGATTGAACCA
Found at i:9672771 original size:21 final size:23
Alignment explanation
Indices: 9672723--9672771 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
9672713 CAATTTAAGC
*
9672723 CTTTTTTTTCTTATTTTAGATCT
1 CTTTTTTTTATTATTTTAGATCT
* *
9672746 TTTTTTTTTATT-TTTTTG-TCT
1 CTTTTTTTTATTATTTTAGATCT
9672767 CTTTT
1 CTTTT
9672772 CACCTCATTC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 7 0.32
22 5 0.23
23 10 0.45
ACGTcount: A:0.08, C:0.10, G:0.04, T:0.78
Consensus pattern (23 bp):
CTTTTTTTTATTATTTTAGATCT
Found at i:9675428 original size:19 final size:21
Alignment explanation
Indices: 9675377--9675426 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
9675367 GTTGATAATG
* *
9675377 CACATAAAATGAAACAATATT
1 CACACAAAATAAAACAATATT
*
9675398 TACACAACAATAAAAC-ATATT
1 CACACAA-AATAAAACAATATT
9675419 CACACAAA
1 CACACAAA
9675427 TATGTAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.58, C:0.20, G:0.02, T:0.20
Consensus pattern (21 bp):
CACACAAAATAAAACAATATT
Found at i:9676109 original size:24 final size:24
Alignment explanation
Indices: 9676082--9676134 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
9676072 AAAAAAATTC
*
9676082 AAATA-TTGAAAACTAAAAAGAAAA
1 AAATAGTTAAAAACTAAAAA-AAAA
*
9676106 AAATAGTTAAAAACTATAAAAAAA
1 AAATAGTTAAAAACTAAAAAAAAA
9676130 AAATA
1 AAATA
9676135 AAGCTTGGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 14 0.54
25 12 0.46
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.19
Consensus pattern (24 bp):
AAATAGTTAAAAACTAAAAAAAAA
Found at i:9677012 original size:17 final size:17
Alignment explanation
Indices: 9676992--9677083 Score: 69
Period size: 18 Copynumber: 5.1 Consensus size: 17
9676982 TTTAGGAAAA
9676992 TTTAATATTTTAATTTT
1 TTTAATATTTTAATTTT
9677009 TTTAATATTTTCAAATTTT
1 TTTAATATTTT--AATTTT
* ****
9677028 TATT-TTGAAGAAAATTTT
1 T-TTAAT-ATTTTAATTTT
9677046 TTTAAATATTTTAATTTT
1 TTT-AATATTTTAATTTT
*
9677064 TTAAATATTTTCAATTTT
1 TTTAATATTTT-AATTTT
9677082 TT
1 TT
9677084 CCTTGGTTCT
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
17 21 0.37
18 24 0.42
19 9 0.16
20 3 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTAATATTTTAATTTT
Found at i:9677061 original size:18 final size:19
Alignment explanation
Indices: 9677040--9677083 Score: 74
Period size: 17 Copynumber: 2.4 Consensus size: 19
9677030 TTTTGAAGAA
9677040 AATTTTTTTAAATATTTT-
1 AATTTTTTTAAATATTTTC
9677058 AA-TTTTTTAAATATTTTC
1 AATTTTTTTAAATATTTTC
9677076 AATTTTTT
1 AATTTTTT
9677084 CCTTGGTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.62
18 4 0.17
19 5 0.21
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
AATTTTTTTAAATATTTTC
Found at i:9677345 original size:9 final size:9
Alignment explanation
Indices: 9677333--9677372 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
9677323 AAAAAAAAAC
9677333 AAAAAAAGT
1 AAAAAAAGT
9677342 AAAAAAAG-
1 AAAAAAAGT
9677350 AATAAAAA-T
1 AA-AAAAAGT
9677359 -AAAAAAGT
1 AAAAAAAGT
9677367 AAAAAA
1 AAAAAA
9677373 TGCCCCTGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
7 5 0.19
8 4 0.15
9 18 0.67
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.10
Consensus pattern (9 bp):
AAAAAAAGT
Found at i:9677347 original size:17 final size:17
Alignment explanation
Indices: 9677318--9677364 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
9677308 GAATACAAAT
9677318 ATAAAAA-AAAAAAACA
1 ATAAAAATAAAAAAACA
*
9677334 A-AAAAAGTAAAAAAAGA
1 ATAAAAA-TAAAAAAACA
9677351 ATAAAAATAAAAAA
1 ATAAAAATAAAAAA
9677365 GTAAAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.19
16 1 0.04
17 16 0.59
18 5 0.19
ACGTcount: A:0.85, C:0.02, G:0.04, T:0.09
Consensus pattern (17 bp):
ATAAAAATAAAAAAACA
Found at i:9677348 original size:25 final size:25
Alignment explanation
Indices: 9677320--9677372 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
9677310 ATACAAATAT
*
9677320 AAAAA-AAAAAAACAAAAAAAGTAA
1 AAAAAGAAAAAAAAAAAAAAAGTAA
* *
9677344 AAAAAGAATAAAAATAAAAAAGTAA
1 AAAAAGAAAAAAAAAAAAAAAGTAA
9677369 AAAA
1 AAAA
9677373 TGCCCCTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.85, C:0.02, G:0.06, T:0.08
Consensus pattern (25 bp):
AAAAAGAAAAAAAAAAAAAAAGTAA
Found at i:9677427 original size:39 final size:39
Alignment explanation
Indices: 9677384--9677471 Score: 167
Period size: 39 Copynumber: 2.3 Consensus size: 39
9677374 GCCCCTGATC
9677384 AACGACTCAGTCCAAAGTTAGCGGTCCGATTCGGCTTAA
1 AACGACTCAGTCCAAAGTTAGCGGTCCGATTCGGCTTAA
9677423 AACGACTCAGTCCAAAGTTAGCGGTCCGATTCGGCTTAA
1 AACGACTCAGTCCAAAGTTAGCGGTCCGATTCGGCTTAA
*
9677462 AACAACTCAG
1 AACGACTCAG
9677472 ACAAGTTTAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (39 bp):
AACGACTCAGTCCAAAGTTAGCGGTCCGATTCGGCTTAA
Found at i:9678261 original size:3 final size:3
Alignment explanation
Indices: 9678255--9678328 Score: 148
Period size: 3 Copynumber: 24.7 Consensus size: 3
9678245 TTTTTTTTAC
9678255 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
9678303 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
9678329 AAATAAATAC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9678922 original size:30 final size:31
Alignment explanation
Indices: 9678879--9678956 Score: 88
Period size: 30 Copynumber: 2.5 Consensus size: 31
9678869 AAATTTTTTG
* *
9678879 GAAATTTCCAAA-TTTTGGCTGAATTTTTCGAT
1 GAAATTT-CAAATTTTTGGATG-ACTTTTCGAT
9678911 GAAATTT-AAATTTTTGGATGACTTTTCGAT
1 GAAATTTCAAATTTTTGGATGACTTTTCGAT
* *
9678941 GAGATTTCCAATTTTT
1 GAAATTTCAAATTTTT
9678957 TGTGAGATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 18 0.45
31 15 0.38
32 7 0.17
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (31 bp):
GAAATTTCAAATTTTTGGATGACTTTTCGAT
Found at i:9678954 original size:31 final size:32
Alignment explanation
Indices: 9678879--9678956 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 32
9678869 AAATTTTTTG
* * *
9678879 GAAATTTCCAAATTTTGGCTGAATTTTTCGAT
1 GAAATTTCCAATTTTTGGATGAACTTTTCGAT
*
9678911 GAAATTT-AAATTTTTGGATG-ACTTTTCGAT
1 GAAATTTCCAATTTTTGGATGAACTTTTCGAT
*
9678941 GAGATTTCCAATTTTT
1 GAAATTTCCAATTTTT
9678957 TGTGAGATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
30 15 0.38
31 17 0.44
32 7 0.18
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (32 bp):
GAAATTTCCAATTTTTGGATGAACTTTTCGAT
Found at i:9685644 original size:13 final size:13
Alignment explanation
Indices: 9685623--9685668 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
9685613 AGAGGGCTAG
*
9685623 AAAAGAAAAAGCA
1 AAAATAAAAAGCA
9685636 AAAAT-AAAAG-A
1 AAAATAAAAAGCA
* *
9685647 AAAATAGAATGCA
1 AAAATAAAAAGCA
9685660 AAAATAAAA
1 AAAATAAAA
9685669 GAAGAATAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
11 6 0.22
12 8 0.30
13 13 0.48
ACGTcount: A:0.76, C:0.04, G:0.11, T:0.09
Consensus pattern (13 bp):
AAAATAAAAAGCA
Found at i:9685651 original size:11 final size:12
Alignment explanation
Indices: 9685629--9685669 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
9685619 CTAGAAAAGA
9685629 AAAAGCAAAAAT
1 AAAAGCAAAAAT
9685641 AAAAG-AAAAAT
1 AAAAGCAAAAAT
*
9685652 AGAATGCAAAAAT
1 A-AAAGCAAAAAT
9685665 AAAAG
1 AAAAG
9685670 AAGAATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 7 0.28
12 11 0.44
13 7 0.28
ACGTcount: A:0.73, C:0.05, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAAGCAAAAAT
Found at i:9685660 original size:24 final size:24
Alignment explanation
Indices: 9685633--9685681 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
9685623 AAAAGAAAAA
9685633 GCAAAAATAAAAGAAAAATAGAAT
1 GCAAAAATAAAAGAAAAATAGAAT
*
9685657 GCAAAAATAAAAGAAGAATAGAAT
1 GCAAAAATAAAAGAAAAATAGAAT
9685681 G
1 G
9685682 ATCCAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.67, C:0.04, G:0.16, T:0.12
Consensus pattern (24 bp):
GCAAAAATAAAAGAAAAATAGAAT
Found at i:9691735 original size:87 final size:86
Alignment explanation
Indices: 9691584--9691821 Score: 297
Period size: 86 Copynumber: 2.8 Consensus size: 86
9691574 ATTAACAAGG
* * * *
9691584 AGCTTTATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAGAAGA-CCTTTATTTA-TTTTCTAA
1 AGCTTT-TTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAGAGGAGCC-TTATTTATTTTTC-AA
9691646 AGTTGTTAAGCCTCTGTTTAGAGA
63 AGTTGTTAAGCCTCTGTTTAGAGA
9691670 AGCTTTGTTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAGAGGAGCCTTATTTATTTTTCAAAG
1 AGCTTT-TTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAGAGGAGCCTTATTTATTTTTCAAAG
*
9691735 TTGTTGAGCCTCTGTTTAGAGA
65 TTGTTAAGCCTCTGTTTAGAGA
* * * * *
9691757 AGCTTTTTTATTTTCCAAAAGTCT-TTAAGCTT-TTATTTAGAGGAGCTTTGTTTATTTTTTAAA
1 AGCTTTTTTATTTTTCAAAAGT-TGTTAAGCTTCTGA-TTAGAGGAGCCTTATTTATTTTTCAAA
9691820 GT
64 GT
9691822 CATTAAGAGC
Statistics
Matches: 136, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
85 2 0.01
86 65 0.48
87 62 0.46
88 7 0.05
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.47
Consensus pattern (86 bp):
AGCTTTTTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAGAGGAGCCTTATTTATTTTTCAAAGT
TGTTAAGCCTCTGTTTAGAGA
Found at i:9691814 original size:130 final size:130
Alignment explanation
Indices: 9691581--9691815 Score: 359
Period size: 130 Copynumber: 1.8 Consensus size: 130
9691571 ATGATTAACA
* *
9691581 AGGAGCTTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAAGACCTTTATTTATTTTCTAA
1 AGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAAGACCTTTATTTATTTTCAAA
*
9691646 AGTTGTTAAGCCTCTGTTTAGAGAAGCTTTGTTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAG
66 AGTTGTTAAGCCTCTATTTAGAGAAGCTTTGTTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAG
*
9691711 AGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG-AGAAGCTTT-TTTATTTTCCA
1 AGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAAG-ACCTTTATTTATTTT-CA
* * *
9691774 AAAGTCT-TTAAGCTTTTATTTAGAGGAGCTTTGTTTATTTTT
64 AAAGT-TGTTAAGCCTCTATTTAGAGAAGCTTTGTTTATTTTT
9691816 TAAAGTCATT
Statistics
Matches: 95, Mismatches: 7, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
129 10 0.11
130 84 0.88
131 1 0.01
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.47
Consensus pattern (130 bp):
AGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAAGACCTTTATTTATTTTCAAA
AGTTGTTAAGCCTCTATTTAGAGAAGCTTTGTTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAG
Found at i:9691828 original size:43 final size:43
Alignment explanation
Indices: 9691581--9691821 Score: 263
Period size: 43 Copynumber: 5.6 Consensus size: 43
9691571 ATGATTAACA
* *
9691581 AGGAGCTTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG
1 AGGAGCTTTATTTATTTTTAAAAGTTGTTAAGCCTCTGTTTAG
* *
9691624 AAGACCTTTATTTATTTTCT-AAAGTTGTTAAGCCTCTGTTTAG
1 AGGAGCTTTATTTATTTT-TAAAAGTTGTTAAGCCTCTGTTTAG
* * * *
9691667 AGAAGCTTTGTTTATTTTTCAAAAGTTGTTAAGCTTCTGATTAG
1 AGGAGCTTTATTTATTTTT-AAAAGTTGTTAAGCCTCTGTTTAG
* * *
9691711 AGGAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAG
1 AGGAGCTTTATTTATTTTTAAAAGTTGTTAAGCCTCTGTTTAG
* * * * *
9691754 AGAAGCTTT-TTTATTTTCCAAAAGTCT-TTAAGCTTTTATTTAG
1 AGGAGCTTTATTTATTTT-TAAAAGT-TGTTAAGCCTCTGTTTAG
* *
9691797 AGGAGCTTTGTTTATTTTTTAAAGT
1 AGGAGCTTTATTTATTTTTAAAAGT
9691822 CATTAAGAGC
Statistics
Matches: 165, Mismatches: 27, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
42 9 0.05
43 109 0.66
44 47 0.28
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.47
Consensus pattern (43 bp):
AGGAGCTTTATTTATTTTTAAAAGTTGTTAAGCCTCTGTTTAG
Found at i:9691842 original size:73 final size:74
Alignment explanation
Indices: 9691763--9691899 Score: 174
Period size: 73 Copynumber: 1.9 Consensus size: 74
9691753 GAGAAGCTTT
* * *
9691763 TTTA-TTTTCCAAAAGTCT-TTAAGCTTTTATTTAGAGGAGCT-TTGTTTATTTTTT-AAAGTCA
1 TTTATTTTTCC-AAAGT-TGTTAAGCTTCTATTTAAAGGAG-TATTATTTATTTTTTCAAAGTCA
9691824 TTAAGAGCATTG
63 TTAAGAGCATTG
* *
9691836 TTTATTTTTTCAAAGTTGTTGAGCTTCTATTTAAAGGAGTATTATTTATTTTTTCAAAGTCATT
1 TTTATTTTTCCAAAGTTGTTAAGCTTCTATTTAAAGGAGTATTATTTATTTTTTCAAAGTCATT
9691900 GAGCCTCTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
72 2 0.04
73 39 0.71
74 14 0.25
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (74 bp):
TTTATTTTTCCAAAGTTGTTAAGCTTCTATTTAAAGGAGTATTATTTATTTTTTCAAAGTCATTA
AGAGCATTG
Found at i:9691886 original size:44 final size:44
Alignment explanation
Indices: 9691836--9691949 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
9691826 AAGAGCATTG
* * *
9691836 TTTATTTTTTCAAAGTTGTTGAGCTTCTATTTAAAGGAGTA-T-TA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTAGTTAAA--AGAACTCTA
** *
9691880 TTTATTTTTTCAAAGTCATTGAGCCTCTGGTTAAAAGAACTCTA
1 TTTATTTTTTCAAAGTTGTTGAGCCTCTAGTTAAAAGAACTCTA
* *
9691924 TTTACTTTTTCAAAGTTGTAGAGCCT
1 TTTATTTTTTCAAAGTTGTTGAGCCT
9691950 TTGTTTAGAG
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
42 3 0.05
43 1 0.02
44 54 0.93
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (44 bp):
TTTATTTTTTCAAAGTTGTTGAGCCTCTAGTTAAAAGAACTCTA
Found at i:9692674 original size:20 final size:20
Alignment explanation
Indices: 9692637--9692675 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9692627 AAGAGAGAGG
*
9692637 GAGAGAAAAAGGGAAAAACA
1 GAGAGAAAAAAGGAAAAACA
9692657 GAGAGAAAAAAAGGAAAAA
1 GAGAG-AAAAAAGGAAAAA
9692676 TCCAGAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (20 bp):
GAGAGAAAAAAGGAAAAACA
Found at i:9694994 original size:51 final size:50
Alignment explanation
Indices: 9694918--9695024 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 50
9694908 ATGAGAAGAA
*
9694918 ACATGCATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATCAC
1 ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATC-C
9694969 ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATCC
1 ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATCC
9695019 ACATGT
1 ACATGT
9695025 TTTAATCATA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
50 7 0.13
51 48 0.87
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (50 bp):
ACATGTATGTTTTAATTTATAGTATTGCTAAAGTTTATTTTAAGGTATCC
Found at i:9697479 original size:24 final size:24
Alignment explanation
Indices: 9697448--9697498 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
9697438 ATGAGTTATC
9697448 ATTTGTGTTAGATTTATTATTTTT
1 ATTTGTGTTAGATTTATTATTTTT
*
9697472 ATTTGTGTTATATTTATTATTTTT
1 ATTTGTGTTAGATTTATTATTTTT
9697496 ATT
1 ATT
9697499 AAATTAATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.22, C:0.00, G:0.10, T:0.69
Consensus pattern (24 bp):
ATTTGTGTTAGATTTATTATTTTT
Found at i:9700285 original size:18 final size:18
Alignment explanation
Indices: 9700262--9700298 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
9700252 TCATTTTCGA
9700262 CATTCTCTTTAGTAAATT
1 CATTCTCTTTAGTAAATT
9700280 CATTCTCTTTAGTAAATT
1 CATTCTCTTTAGTAAATT
9700298 C
1 C
9700299 CCTTATGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (18 bp):
CATTCTCTTTAGTAAATT
Found at i:9700357 original size:2 final size:2
Alignment explanation
Indices: 9700350--9700380 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9700340 CAAACACCTT
9700350 TA 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 TA T
9700381 CGGACTTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9701258 original size:2 final size:2
Alignment explanation
Indices: 9701253--9701278 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9701243 ATATATATCT
9701253 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
9701279 GAGTGCACCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9702074 original size:28 final size:28
Alignment explanation
Indices: 9702035--9702109 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 28
9702025 TTAAATTATA
*
9702035 ATAAAATATTT-ATATAATATATAAAATT
1 ATAAAATTTTTAATATAATAT-TAAAATT
* *
9702063 TTAAAATTTTTAATATAATATTTAAATT
1 ATAAAATTTTTAATATAATATTAAAATT
*
9702091 ATAAAATTATTAAT-TAATA
1 ATAAAATTTTTAATATAATA
9702110 AATATTTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.12
28 27 0.66
29 9 0.22
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATAAAATTTTTAATATAATATTAAAATT
Found at i:9702960 original size:32 final size:32
Alignment explanation
Indices: 9702924--9703035 Score: 91
Period size: 32 Copynumber: 3.5 Consensus size: 32
9702914 TTAAAATTAC
9702924 ATATCATTTTAAAAAATTAAGTAAAAATATTT
1 ATATCATTTTAAAAAATTAAGTAAAAATATTT
** * * * *
9702956 ATATCGGTTTAATAAATTAAATAAAAA-CTCT
1 ATATCATTTTAAAAAATTAAGTAAAAATATTT
* * * * *
9702987 ATATCATATTAAAATATTATGTAGAAATTTTT
1 ATATCATTTTAAAAAATTAAGTAAAAATATTT
** *
9703019 AGGTCATTTTCAAAAAT
1 ATATCATTTTAAAAAAT
9703036 AGATTTTAAT
Statistics
Matches: 58, Mismatches: 21, Indels: 2
0.72 0.26 0.02
Matches are distributed among these distances:
31 21 0.36
32 37 0.64
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.40
Consensus pattern (32 bp):
ATATCATTTTAAAAAATTAAGTAAAAATATTT
Found at i:9704405 original size:18 final size:21
Alignment explanation
Indices: 9704383--9704431 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
9704373 ATAAAAATAA
9704383 AATTTATTA-TTA-TATAATT
1 AATTTATTATTTATTATAATT
*
9704402 -ATTTATTTATTTATTTTAATT
1 AATTTA-TTATTTATTATAATT
9704423 AATTTATTA
1 AATTTATTA
9704432 ATAAAACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.20
19 3 0.12
20 3 0.12
21 9 0.36
22 5 0.20
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATTTATTATTTATTATAATT
Found at i:9704484 original size:26 final size:26
Alignment explanation
Indices: 9704440--9704494 Score: 85
Period size: 25 Copynumber: 2.1 Consensus size: 26
9704430 TAATAAAACT
*
9704440 ATTATTTGATTTTAAAATAATTTAATA
1 ATTATTTGATTTTAAAAT-ATTAAATA
9704467 ATTATTT-ATTTTAAAATATTAAATA
1 ATTATTTGATTTTAAAATATTAAATA
9704492 ATT
1 ATT
9704495 TAAAATTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 10 0.37
26 10 0.37
27 7 0.26
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTATTTGATTTTAAAATATTAAATA
Found at i:9704496 original size:17 final size:17
Alignment explanation
Indices: 9704454--9704500 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
9704444 TTTGATTTTA
*
9704454 AAATAATTTAATA-ATT
1 AAATAATTTAAAATATT
** *
9704470 ATTTATTTTAAAATATT
1 AAATAATTTAAAATATT
9704487 AAATAATTTAAAAT
1 AAATAATTTAAAAT
9704501 TTTTCATATA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATAATTTAAAATATT
Found at i:9704502 original size:25 final size:26
Alignment explanation
Indices: 9704448--9704503 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
9704438 CTATTATTTG
* **
9704448 ATTTTAAAATAATTTAATAATTATTT
1 ATTTTAAAATAATTAAATAATTATAA
9704474 ATTTTAAAAT-ATTAAATAATT-TAAA
1 ATTTTAAAATAATTAAATAATTAT-AA
9704499 ATTTT
1 ATTTT
9704504 TCATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 15 0.58
26 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
ATTTTAAAATAATTAAATAATTATAA
Found at i:9704611 original size:21 final size:20
Alignment explanation
Indices: 9704581--9704619 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
9704571 AAGATAAATT
9704581 TTAATTTATTATTATAATAA
1 TTAATTTATTATTATAATAA
*
9704601 TTAATTTTATTTTTATAAT
1 TTAA-TTTATTATTATAAT
9704620 TTTATTATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAATTTATTATTATAATAA
Found at i:9706976 original size:2 final size:2
Alignment explanation
Indices: 9706971--9707010 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
9706961 TGTATGTGTG
*
9706971 TA TA TA TA CA 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 TA TA
9707011 CACCCAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:9712827 original size:2 final size:2
Alignment explanation
Indices: 9712820--9712854 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
9712810 TCTCCTTCAT
9712820 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9712855 TGCCATCGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9731104 original size:20 final size:18
Alignment explanation
Indices: 9731079--9731143 Score: 71
Period size: 18 Copynumber: 3.6 Consensus size: 18
9731069 TGCAAGAGTG
9731079 TCATGCAAATATATTAATTA
1 TCATGCAAATATA-TAA-TA
*
9731099 TCATGC-AATA-ATAACAA
1 TCATGCAAATATATAA-TA
*
9731116 TCATGTAAATATATAATA
1 TCATGCAAATATATAATA
9731134 TCATGCAAAT
1 TCATGCAAAT
9731144 CAAATATAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
17 9 0.24
18 15 0.39
19 8 0.21
20 6 0.16
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (18 bp):
TCATGCAAATATATAATA
Found at i:9731453 original size:20 final size:20
Alignment explanation
Indices: 9731386--9731489 Score: 68
Period size: 20 Copynumber: 5.1 Consensus size: 20
9731376 TGCAAATAGA
**
9731386 TATGCAATTAAATATACGAT
1 TATGCAATTAAATATATAAT
* * *
9731406 CATGCAATT-AATAATGTAAAA
1 TATGCAATTAAAT-ATAT-AAT
*
9731427 CATGCAATTAAATATATAAT
1 TATGCAATTAAATATATAAT
*
9731447 TATGCAAAT-AATAATATAAAT
1 TATGCAATTAAAT-ATAT-AAT
* * *
9731468 TATGCAAATAAACATACAAT
1 TATGCAATTAAATATATAAT
9731488 TA
1 TA
9731490 GATCTAATAA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
19 6 0.09
20 28 0.42
21 28 0.42
22 5 0.07
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.32
Consensus pattern (20 bp):
TATGCAATTAAATATATAAT
Found at i:9731470 original size:21 final size:21
Alignment explanation
Indices: 9731407--9731478 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
9731397 ATATACGATC
* * **
9731407 ATGCAATTAATAATGTAAAAC
1 ATGCAAATAATAATATAAATT
*
9731428 ATGC-AATTA-AATATATAATT
1 ATGCAAATAATAATATA-AATT
9731448 ATGCAAATAATAATATAAATT
1 ATGCAAATAATAATATAAATT
9731469 ATGCAAATAA
1 ATGCAAATAA
9731479 ACATACAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.12
20 9 0.21
21 22 0.52
22 6 0.14
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (21 bp):
ATGCAAATAATAATATAAATT
Found at i:9731489 original size:41 final size:41
Alignment explanation
Indices: 9731385--9731489 Score: 129
Period size: 41 Copynumber: 2.6 Consensus size: 41
9731375 ATGCAAATAG
* * * *
9731385 ATATGCAATTAAATATACGATCATGCAATTAATAATGTAAA
1 ATATGCAATTAAATATACAATTATGCAAATAATAATATAAA
* *
9731426 ACATGCAATTAAATATATAATTATGCAAATAATAATATAAA
1 ATATGCAATTAAATATACAATTATGCAAATAATAATATAAA
* * *
9731467 TTATGCAAATAAACATACAATTA
1 ATATGCAATTAAATATACAATTA
9731490 GATCTAATAA
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.31
Consensus pattern (41 bp):
ATATGCAATTAAATATACAATTATGCAAATAATAATATAAA
Found at i:9732209 original size:18 final size:18
Alignment explanation
Indices: 9732168--9732210 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
9732158 TCTAAGATAG
* * *
9732168 AATCCAAGAGTTGAATTG
1 AATCCAAAAGCTGAATTA
*
9732186 AGTCCAAAAGCTGAATTA
1 AATCCAAAAGCTGAATTA
9732204 AATCCAA
1 AATCCAA
9732211 GATTTTCATG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.23
Consensus pattern (18 bp):
AATCCAAAAGCTGAATTA
Found at i:9735051 original size:17 final size:16
Alignment explanation
Indices: 9735029--9735069 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
9735019 GCCAGTGTCT
9735029 TCTTTTTTTTCTTCCTC
1 TCTTTTTTTT-TTCCTC
9735046 TC-TTTTTTTTTCCTC
1 TCTTTTTTTTTTCCTC
*
9735061 TATTTTTTT
1 TCTTTTTTT
9735070 CCTCTATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 7 0.32
16 13 0.59
17 2 0.09
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (16 bp):
TCTTTTTTTTTTCCTC
Done.