Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 147 of 198
Found at i:46757486 original size:37 final size:37
Alignment explanation
Indices: 46757444--46757514 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
46757434 AGTATTACTT
46757444 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
46757481 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
46757515 AAAAAATGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.49, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAGTTATTAAATGAG
Found at i:46757526 original size:19 final size:19
Alignment explanation
Indices: 46757450--46757518 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
46757440 ACTTAATAGT
46757450 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* * *
46757469 TTATTAAATGAGAATAG-T
1 TTATTAAATTAAAATAGAG
46757487 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
46757506 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
46757519 AATGAGTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 20 0.47
19 23 0.53
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:46757625 original size:27 final size:26
Alignment explanation
Indices: 46757588--46757670 Score: 103
Period size: 27 Copynumber: 3.1 Consensus size: 26
46757578 GCCTAATTTT
46757588 AATCCTTTGGCACCATTGGTGCCGCC
1 AATCCTTTGGCACCATTGGTGCCGCC
*
46757614 AATCACTTTGGCACCATTGGTGCCACC
1 AATC-CTTTGGCACCATTGGTGCCGCC
* ** *
46757641 AATCTCTTTGCCACTTTTGGTACCGCC
1 AATC-CTTTGGCACCATTGGTGCCGCC
46757668 AAT
1 AAT
46757671 GTGATTGGCC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 4 0.08
27 45 0.92
ACGTcount: A:0.19, C:0.33, G:0.18, T:0.30
Consensus pattern (26 bp):
AATCCTTTGGCACCATTGGTGCCGCC
Found at i:46757775 original size:24 final size:25
Alignment explanation
Indices: 46757743--46757792 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
46757733 TTTCGTAAAT
46757743 AATAAAAAAAG-TAATATTTTGGTA
1 AATAAAAAAAGTTAATATTTTGGTA
46757767 AATAAAAAAAGTTATAATATTTTGGT
1 AATAAAAAAAG-T-TAATATTTTGGT
46757793 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 11 0.48
27 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (25 bp):
AATAAAAAAAGTTAATATTTTGGTA
Found at i:46758673 original size:18 final size:18
Alignment explanation
Indices: 46758637--46758673 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
46758627 TAAGTTTTCG
* *
46758637 AATTCGAATAACTCGAAT
1 AATTCGAATAAATCAAAT
46758655 AATTCGAATAAATCAAAT
1 AATTCGAATAAATCAAAT
46758673 A
1 A
46758674 TCAAATTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (18 bp):
AATTCGAATAAATCAAAT
Found at i:46758766 original size:30 final size:30
Alignment explanation
Indices: 46758732--46758813 Score: 146
Period size: 30 Copynumber: 2.7 Consensus size: 30
46758722 ATTTTTTCCT
46758732 CAAAACTTTTACTCCTTCCCACTTTCCCCC
1 CAAAACTTTTACTCCTTCCCACTTTCCCCC
*
46758762 CAAAACTTTTACTCCTTCCCACTTTTCCCC
1 CAAAACTTTTACTCCTTCCCACTTTCCCCC
46758792 CAAAACTTTTACTCCCTTCCCA
1 CAAAACTTTTACT-CCTTCCCA
46758814 TCCCAACCCA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 42 0.84
31 8 0.16
ACGTcount: A:0.22, C:0.44, G:0.00, T:0.34
Consensus pattern (30 bp):
CAAAACTTTTACTCCTTCCCACTTTCCCCC
Found at i:46758965 original size:30 final size:30
Alignment explanation
Indices: 46758916--46758974 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
46758906 AACTTTTTAT
*
46758916 TTTCCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTCCCCCAAAACTTTTACTCCCTTCCCAC
46758945 TTTCCCCCTAAAACTTTTACTCCCTTCCCA
1 TTTCCCCC-AAAACTTTTACTCCCTTCCCA
46758975 TCTCACCCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.30
30 14 0.52
31 5 0.19
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (30 bp):
TTTCCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:46760709 original size:34 final size:32
Alignment explanation
Indices: 46760632--46760710 Score: 81
Period size: 34 Copynumber: 2.4 Consensus size: 32
46760622 TTTATTTTAA
46760632 AATAAATTTTTAAAATATAATATATTAAATAT
1 AATAAATTTTTAAAATATAATATATTAAATAT
* *
46760664 ATTAATTTTTTTAAAA-A-AATACTATCATAAATAT
1 AATAA-ATTTTTAAAATATAATA-TAT--TAAATAT
46760698 AATAAACTTTTTA
1 AATAAA-TTTTTA
46760711 TTATATTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
31 4 0.11
32 8 0.21
33 9 0.24
34 17 0.45
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (32 bp):
AATAAATTTTTAAAATATAATATATTAAATAT
Found at i:46771018 original size:64 final size:64
Alignment explanation
Indices: 46770917--46771045 Score: 204
Period size: 64 Copynumber: 2.0 Consensus size: 64
46770907 TGAGCATCCC
* * * *
46770917 GATCGGTAGTGATTCTACATGTGTTGTGGACATACCGCAGCTCTTTGTGAGCGTCCTGTTATAT
1 GATCGGTAGTGATCCTACATGTGTTGCGGACATACCGCAACTCTTTATGAGCGTCCTGTTATAT
* *
46770981 GATCGGTAGTGATCCTGCATGTGTTGCGGACATACCGCAACTCTTTATTAGCGTCCTGTTATAT
1 GATCGGTAGTGATCCTACATGTGTTGCGGACATACCGCAACTCTTTATGAGCGTCCTGTTATAT
46771045 G
1 G
46771046 GCTCTTTAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (64 bp):
GATCGGTAGTGATCCTACATGTGTTGCGGACATACCGCAACTCTTTATGAGCGTCCTGTTATAT
Found at i:46771139 original size:26 final size:25
Alignment explanation
Indices: 46771109--46771184 Score: 82
Period size: 26 Copynumber: 3.0 Consensus size: 25
46771099 CCGGAGCTCT
46771109 TGATTAAAGGCTCTTCGTGAGCTTCC
1 TGATTAAAGGCTCTT-GTGAGCTTCC
* * *
46771135 TGATTAAAAGTTCTTTGTGAACTTCC
1 TGATTAAAGGCTC-TTGTGAGCTTCC
* *
46771161 TGATT-ATGGCTCTTATGAGCTTCC
1 TGATTAAAGGCTCTTGTGAGCTTCC
46771185 CGTTATATAG
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
24 10 0.24
25 4 0.10
26 25 0.61
27 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (25 bp):
TGATTAAAGGCTCTTGTGAGCTTCC
Found at i:46771230 original size:23 final size:22
Alignment explanation
Indices: 46771201--46771254 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
46771191 ATAGCCTGGA
46771201 TAAGCTTCCTGATAGGCTCTTTG
1 TAAGCTTCC-GATAGGCTCTTTG
*
46771224 TAAGCTTTCCGATATGCTCTTTG
1 TAAGC-TTCCGATAGGCTCTTTG
*
46771247 TGAGCTTC
1 TAAGCTTC
46771255 TTAATTAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 3 0.11
23 21 0.75
24 4 0.14
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.41
Consensus pattern (22 bp):
TAAGCTTCCGATAGGCTCTTTG
Found at i:46771291 original size:26 final size:26
Alignment explanation
Indices: 46771215--46771293 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
46771205 CTTCCTGATA
*
46771215 GGCTCTTTGTAAGCTTTCC-G--ATAT
1 GGCTCTTTGTGAG-TTTCCTGTTATAT
* * *
46771239 -GCTCTTTGTGAGCTTCTTAATTA-AT
1 GGCTCTTTGTGAGTTTCCT-GTTATAT
46771264 GGCTCTTTGTGAGTTTCCTGTTATAT
1 GGCTCTTTGTGAGTTTCCTGTTATAT
46771290 GGCT
1 GGCT
46771294 TGAGAGAGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
22 3 0.07
23 11 0.26
25 5 0.12
26 23 0.55
ACGTcount: A:0.15, C:0.18, G:0.22, T:0.46
Consensus pattern (26 bp):
GGCTCTTTGTGAGTTTCCTGTTATAT
Found at i:46772514 original size:79 final size:79
Alignment explanation
Indices: 46772383--46772540 Score: 307
Period size: 79 Copynumber: 2.0 Consensus size: 79
46772373 TGTTTAAGTG
*
46772383 TTGGTATAGGTGGAAGACAAATTGGGTGAGAAATGTGGCTTGGAAAATAGCCTATTATCGTTCAC
1 TTGGTATAGGTGGAAGACAAATTAGGTGAGAAATGTGGCTTGGAAAATAGCCTATTATCGTTCAC
46772448 ACGGGCAAAGACAC
66 ACGGGCAAAGACAC
46772462 TTGGTATAGGTGGAAGACAAATTAGGTGAGAAATGTGGCTTGGAAAATAGCCTATTATCGTTCAC
1 TTGGTATAGGTGGAAGACAAATTAGGTGAGAAATGTGGCTTGGAAAATAGCCTATTATCGTTCAC
46772527 ACGGGCAAAGACAC
66 ACGGGCAAAGACAC
46772541 GGGTGTGTGT
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 78 1.00
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (79 bp):
TTGGTATAGGTGGAAGACAAATTAGGTGAGAAATGTGGCTTGGAAAATAGCCTATTATCGTTCAC
ACGGGCAAAGACAC
Found at i:46777995 original size:13 final size:12
Alignment explanation
Indices: 46777979--46778075 Score: 65
Period size: 12 Copynumber: 7.9 Consensus size: 12
46777969 AGATAAAAGG
46777979 TTAATTGAAAAAC
1 TTAA-TGAAAAAC
*
46777992 TTAATATTAAAAAC
1 TT-A-ATGAAAAAC
* *
46778006 TTGATGGAAAAC
1 TTAATGAAAAAC
*
46778018 TTTATGAAAAGAC
1 TTAATGAAAA-AC
*
46778031 TTGATGAAAAAC
1 TTAATGAAAAAC
46778043 TTAA--AAAGAAC
1 TTAATGAAA-AAC
* *
46778054 TTGATGCAAAAC
1 TTAATGAAAAAC
46778066 TTAAT-AAAAA
1 TTAATGAAAAA
46778076 AAAACCTTGA
Statistics
Matches: 66, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
10 3 0.05
11 10 0.15
12 27 0.41
13 15 0.23
14 10 0.15
15 1 0.02
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.28
Consensus pattern (12 bp):
TTAATGAAAAAC
Found at i:46778035 original size:25 final size:23
Alignment explanation
Indices: 46778000--46778067 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 23
46777990 ACTTAATATT
*
46778000 AAAA-ACTTGATGGAAAACTTTA
1 AAAAGACTTGATGAAAAACTTTA
46778022 TGAAAAGACTTGATGAAAAAC-TTA
1 --AAAAGACTTGATGAAAAACTTTA
*
46778046 AAAAGAACTTGATGCAAAACTT
1 AAAAG-ACTTGATGAAAAACTT
46778068 AATAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
22 5 0.13
23 13 0.33
24 8 0.21
25 13 0.33
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (23 bp):
AAAAGACTTGATGAAAAACTTTA
Found at i:46778074 original size:25 final size:25
Alignment explanation
Indices: 46777984--46778121 Score: 113
Period size: 25 Copynumber: 5.3 Consensus size: 25
46777974 AAAGGTTAAT
46777984 TGAAAAACTTAATATTAAA-AACTTGA
1 TGAAAAACTTAATA--AAAGAACTTGA
* *
46778010 TGGAAAACTTTATGAAAAG-ACTTGA
1 TGAAAAACTTAAT-AAAAGAACTTGA
46778035 TGAAAAACTT-A-AAAAGAACTTGA
1 TGAAAAACTTAATAAAAGAACTTGA
* *
46778058 TGCAAAACTTAATAAAAAAAAACCTTGATAA
1 TGAAAAACTTAAT--AAAAGAA-CTTG---A
* *
46778089 TTAAAAACTTGATAAAAGAACTTGA
1 TGAAAAACTTAATAAAAGAACTTGA
46778114 TGAAAAAC
1 TGAAAAAC
46778122 ACTTGAAGAA
Statistics
Matches: 91, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
22 5 0.05
23 15 0.16
24 2 0.02
25 26 0.29
26 11 0.12
27 7 0.08
28 8 0.09
29 6 0.07
31 11 0.12
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (25 bp):
TGAAAAACTTAATAAAAGAACTTGA
Found at i:46778079 original size:15 final size:15
Alignment explanation
Indices: 46778061--46778105 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
46778051 AACTTGATGC
*
46778061 AAAACTTAATAAAAA
1 AAAACTTGATAAAAA
**
46778076 AAAACCTTGATAATTA
1 AAAA-CTTGATAAAAA
46778092 AAAACTTGATAAAA
1 AAAACTTGATAAAA
46778106 GAACTTGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.62, C:0.09, G:0.04, T:0.24
Consensus pattern (15 bp):
AAAACTTGATAAAAA
Found at i:46778125 original size:14 final size:13
Alignment explanation
Indices: 46778000--46778132 Score: 73
Period size: 12 Copynumber: 10.2 Consensus size: 13
46777990 ACTTAATATT
46778000 AAAAACTTGATG-
1 AAAAACTTGATGA
* *
46778012 GAAAACTTTATGA
1 AAAAACTTGATGA
*
46778025 AAAGACTTGATG-
1 AAAAACTTGATGA
46778037 AAAAACTT-A--A
1 AAAAACTTGATGA
46778047 AAAGAACTTGATG-
1 AAA-AACTTGATGA
* * *
46778060 CAAAACTTAATAAAA
1 AAAAACTTGAT--GA
*
46778075 AAAAACCTTGATAA
1 AAAAA-CTTGATGA
46778089 TTAAAAACTTGAT-A
1 --AAAAACTTGATGA
46778103 AAAGAACTTGATGA
1 AAA-AACTTGATGA
*
46778117 AAAACACTTGAAGA
1 AAAA-ACTTGATGA
46778131 AA
1 AA
46778133 GAAAATACTT
Statistics
Matches: 94, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
10 3 0.03
11 6 0.06
12 28 0.30
13 20 0.21
14 17 0.18
15 10 0.11
16 10 0.11
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (13 bp):
AAAAACTTGATGA
Found at i:46781071 original size:23 final size:24
Alignment explanation
Indices: 46781044--46781091 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
46781034 AGGTCAAAAA
46781044 TAGGATGTGATAGGTG-AAATTTT
1 TAGGATGTGATAGGTGAAAATTTT
* *
46781067 TAGGATTTGATGGGTGAAAATTTT
1 TAGGATGTGATAGGTGAAAATTTT
46781091 T
1 T
46781092 TAGAAGAGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (24 bp):
TAGGATGTGATAGGTGAAAATTTT
Found at i:46781487 original size:6 final size:6
Alignment explanation
Indices: 46781472--46781528 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
46781462 GTTTCTCTGC
46781472 AAAAAT -AAAAT AAAAAT AAAAAT -AAAAT AAAATAGT AAAAAT AAATAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA-A-T AAAAAT AAA-AAT
*
46781521 AATAAT AA
1 AAAAAT AA
46781529 TAGGAAAATT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
5 10 0.22
6 23 0.51
7 7 0.16
8 5 0.11
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (6 bp):
AAAAAT
Found at i:46781488 original size:11 final size:11
Alignment explanation
Indices: 46781472--46781505 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
46781462 GTTTCTCTGC
46781472 AAAAATAAAAT
1 AAAAATAAAAT
46781483 AAAAATAAAA-
1 AAAAATAAAAT
46781493 ATAAAATAAAAT
1 A-AAAATAAAAT
46781505 A
1 A
46781506 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 19 0.90
12 1 0.05
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:46781501 original size:22 final size:25
Alignment explanation
Indices: 46781473--46781549 Score: 74
Period size: 25 Copynumber: 3.2 Consensus size: 25
46781463 TTTCTCTGCA
46781473 AAAATAAA-A-TAAAAATAAA-AAT
1 AAAATAAATAGTAAAAATAAATAAT
46781495 AAAATAAAATAGTAAAAATAAATAAT
1 AAAAT-AAATAGTAAAAATAAATAAT
* * *
46781521 AATAAT-AATAGGAAAATTAAA-ATT
1 AA-AATAAATAGTAAAAATAAATAAT
46781545 AAAAT
1 AAAAT
46781550 GTTTTTTCCA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
22 5 0.11
23 6 0.13
24 5 0.11
25 23 0.49
26 5 0.11
27 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (25 bp):
AAAATAAATAGTAAAAATAAATAAT
Found at i:46781516 original size:25 final size:26
Alignment explanation
Indices: 46781482--46781549 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
46781472 AAAAATAAAA
46781482 TAAAAATAAAAATAAAATAA-AATAG
1 TAAAAATAAAAATAAAATAATAATAG
46781507 TAAAAAT--AAATAATAATAATAATAG
1 TAAAAATAAAAATAA-AATAATAATAG
* * *
46781532 GAAAATTAAAATTAAAAT
1 TAAAAATAAAAATAAAAT
46781550 GTTTTTTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 6 0.17
24 5 0.14
25 17 0.47
26 3 0.08
27 5 0.14
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (26 bp):
TAAAAATAAAAATAAAATAATAATAG
Found at i:46788340 original size:23 final size:23
Alignment explanation
Indices: 46788287--46788352 Score: 73
Period size: 23 Copynumber: 2.8 Consensus size: 23
46788277 AATGATTAAA
*
46788287 AACTTGATGGAAAACTTTATGAAAAG
1 AACTTGATGAAAAAC-TTA--AAAAG
46788313 -A-TTGATGAAAAACTTAAAAAG
1 AACTTGATGAAAAACTTAAAAAG
*
46788334 AACTTGATGCAAAACTTAA
1 AACTTGATGAAAAACTTAA
46788353 TAAAAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 5 0.14
22 1 0.03
23 18 0.50
24 11 0.31
25 1 0.03
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (23 bp):
AACTTGATGAAAAACTTAAAAAG
Found at i:46791262 original size:21 final size:22
Alignment explanation
Indices: 46791238--46791278 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
46791228 TTTCATGTTA
*
46791238 AATTTAT-GTTAATTATTTTTT
1 AATTTATGGATAATTATTTTTT
46791259 AATTTATGGATAATTATTTT
1 AATTTATGGATAATTATTTT
46791279 AATACATACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.32, C:0.00, G:0.07, T:0.61
Consensus pattern (22 bp):
AATTTATGGATAATTATTTTTT
Found at i:46794004 original size:4 final size:4
Alignment explanation
Indices: 46793995--46794032 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
46793985 TTGAAAAAGG
46793995 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TT
46794033 TAAGCATGCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:46795000 original size:40 final size:40
Alignment explanation
Indices: 46794955--46795055 Score: 132
Period size: 40 Copynumber: 2.5 Consensus size: 40
46794945 CAAATGCCAT
*
46794955 TATAGATCGAGCATTAACGGTGCTT-TTGGAAAAACACCGC
1 TATAGATCGAGCATTAACGGCGCTTCTT-GAAAAACACCGC
* *
46794995 TATAGATAGAGCATTAGCGGCGCTTCTTGAAAAACACCGC
1 TATAGATCGAGCATTAACGGCGCTTCTTGAAAAACACCGC
* * *
46795035 TATAGGTCAACCATTAACGGC
1 TATAGATCGAGCATTAACGGC
46795056 ATTTTTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 50 0.96
41 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (40 bp):
TATAGATCGAGCATTAACGGCGCTTCTTGAAAAACACCGC
Found at i:46795244 original size:118 final size:118
Alignment explanation
Indices: 46795076--46795293 Score: 323
Period size: 118 Copynumber: 1.8 Consensus size: 118
46795066 AAACGCCGCG
* * * *
46795076 AAAAAGTTAAGCACAACGCCGTCGTTTTATGTTGAGCTTTAGTGGCATTAGCGGGGCTTTTTGAA
1 AAAAAGTTAAGCAAAACGACGTCGTTTTACGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTT-AA
* * *
46795141 -AAACGCCGCTATAGATCGAGCATTAGCGGCGCTTTTGGATAAACACCGCAAAA
65 TAAACGCCGCAATAGATCGAGAATTAGCAGCGCTTTTGGATAAACACCGCAAAA
*
46795194 AAAAAGTTGAGCAAAACGACGTCGTTTGT-CGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTAA
1 AAAAAGTTAAGCAAAACGACGTCGTTT-TACGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTAA
*
46795258 TAAATGCCGCAATAGATCGAGAATTAGCAGCGCTTT
65 TAAACGCCGCAATAGATCGAGAATTAGCAGCGCTTT
46795294 GTCGAAAACG
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
117 2 0.02
118 86 0.97
119 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (118 bp):
AAAAAGTTAAGCAAAACGACGTCGTTTTACGTTGAGCTTTAGTGGCATTAGCGGCGCTTTTTAAT
AAACGCCGCAATAGATCGAGAATTAGCAGCGCTTTTGGATAAACACCGCAAAA
Found at i:46795669 original size:7 final size:7
Alignment explanation
Indices: 46795659--46795915 Score: 108
Period size: 7 Copynumber: 36.7 Consensus size: 7
46795649 TGTAATAATA
46795659 TTTAGGG
1 TTTAGGG
46795666 TTTAGGG
1 TTTAGGG
* *
46795673 TATA-GA
1 TTTAGGG
*
46795679 TTTATGG
1 TTTAGGG
*
46795686 TTTGGGG
1 TTTAGGG
*
46795693 TTTAAGG
1 TTTAGGG
46795700 TTTAGGG
1 TTTAGGG
****
46795707 TTTCTAA
1 TTTAGGG
*
46795714 TTTAGTG
1 TTTAGGG
* *
46795721 TTAAGAG
1 TTTAGGG
*
46795728 TTTAGTG
1 TTTAGGG
* *
46795735 TTTATGT
1 TTTAGGG
46795742 TTTAGGG
1 TTTAGGG
*
46795749 TGTA-GG
1 TTTAGGG
*
46795755 TTTATGG
1 TTTAGGG
*
46795762 TTTAGTG
1 TTTAGGG
*
46795769 TTTATGG
1 TTTAGGG
46795776 TTTAGGG
1 TTTAGGG
46795783 TTTAGGG
1 TTTAGGG
* *
46795790 GTTATGAG
1 TTTA-GGG
* *
46795798 CTTATGG
1 TTTAGGG
46795805 TTTAAGGG
1 TTT-AGGG
46795813 -TTAGGGG
1 TTTA-GGG
*
46795820 CTTAGGG
1 TTTAGGG
*
46795827 TTTAAGG
1 TTTAGGG
**
46795834 TTTAAAG
1 TTTAGGG
* ***
46795841 TCTATAT
1 TTTAGGG
46795848 TTTAGGG
1 TTTAGGG
*
46795855 TTTAAAGG
1 TTT-AGGG
* *
46795863 CTTAGAG
1 TTTAGGG
46795870 TTTAGGG
1 TTTAGGG
*
46795877 TTTATGG
1 TTTAGGG
*
46795884 TTTA-GT
1 TTTAGGG
46795890 TTTAGGG
1 TTTAGGG
*
46795897 TTTAGTG
1 TTTAGGG
*
46795904 TTTATGG
1 TTTAGGG
46795911 TTTAG
1 TTTAG
46795916 CTAAAAACAT
Statistics
Matches: 179, Mismatches: 63, Indels: 16
0.69 0.24 0.06
Matches are distributed among these distances:
6 15 0.08
7 148 0.83
8 16 0.09
ACGTcount: A:0.20, C:0.02, G:0.32, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:46795808 original size:22 final size:21
Alignment explanation
Indices: 46795760--46795830 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
46795750 GTAGGTTTAT
* * *
46795760 GGTTTAGTGTTTATGGTTTAG
1 GGTTTAGGGGTTATGGCTTAG
*
46795781 GGTTTAGGGGTTATGAGCTTAT
1 GGTTTAGGGGTTATG-GCTTAG
* *
46795803 GGTTTAAGGGTTAGGGGCTTAG
1 GGTTTAGGGGTTA-TGGCTTAG
46795825 GGTTTA
1 GGTTTA
46795831 AGGTTTAAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 13 0.32
22 27 0.66
23 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.38, T:0.42
Consensus pattern (21 bp):
GGTTTAGGGGTTATGGCTTAG
Found at i:46795831 original size:22 final size:22
Alignment explanation
Indices: 46795777--46795833 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
46795767 TGTTTATGGT
* *
46795777 TTAGGGTTTAGGGGTTATGAGC
1 TTAGGGTTTAAGGGTTAGGAGC
* *
46795799 TTATGGTTTAAGGGTTAGGGGC
1 TTAGGGTTTAAGGGTTAGGAGC
46795821 TTAGGGTTTAAGG
1 TTAGGGTTTAAGG
46795834 TTTAAAGTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.04, G:0.40, T:0.37
Consensus pattern (22 bp):
TTAGGGTTTAAGGGTTAGGAGC
Found at i:46795835 original size:29 final size:29
Alignment explanation
Indices: 46795753--46795838 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 29
46795743 TTAGGGTGTA
* * *
46795753 GGTTTATGGTTTAGTGTTTATGGTTT-AG
1 GGTTTAGGGGTTAGAGTTTATGGTTTAAG
*
46795781 GGTTTAGGGGTTATGAGCTTATGGTTTAAG
1 GGTTTAGGGGTTA-GAGTTTATGGTTTAAG
* *
46795811 GG-TTAGGGGCTTAGGGTTTAAGGTTTAA
1 GGTTTAGGGG-TTAGAGTTTATGGTTTAA
46795839 AGTCTATATT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 11 0.23
29 30 0.62
30 7 0.15
ACGTcount: A:0.19, C:0.02, G:0.36, T:0.43
Consensus pattern (29 bp):
GGTTTAGGGGTTAGAGTTTATGGTTTAAG
Found at i:46795901 original size:27 final size:27
Alignment explanation
Indices: 46795864--46795915 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
46795854 GTTTAAAGGC
46795864 TTAGAGTTTAGGGTTTATGGTTTAGTT
1 TTAGAGTTTAGGGTTTATGGTTTAGTT
* *
46795891 TTAGGGTTTAGTGTTTATGGTTTAG
1 TTAGAGTTTAGGGTTTATGGTTTAG
46795916 CTAAAAACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.31, T:0.52
Consensus pattern (27 bp):
TTAGAGTTTAGGGTTTATGGTTTAGTT
Found at i:46796117 original size:43 final size:42
Alignment explanation
Indices: 46796053--46796133 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 42
46796043 AAGGTTAATT
* *
46796053 AAGTTGAGCAATAGTAGCGTTTTTTTGCTCAAAATGCCATGAA
1 AAGTTGAACAATAGTAGCGTTTTTTTG-TCAAAACGCCATGAA
46796096 AAGTTGAACAATAGT-GACGTTTTTTTGTCAAAACGCCA
1 AAGTTGAACAATAGTAG-CGTTTTTTTGTCAAAACGCCA
46796134 CAAATATGTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
42 11 0.31
43 24 0.69
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (42 bp):
AAGTTGAACAATAGTAGCGTTTTTTTGTCAAAACGCCATGAA
Found at i:46796457 original size:16 final size:16
Alignment explanation
Indices: 46796436--46796471 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
46796426 CCGGCGGTCG
46796436 CTCTGTCACCCGCTTC
1 CTCTGTCACCCGCTTC
*
46796452 CTCTGTCGCCCGCTTC
1 CTCTGTCACCCGCTTC
46796468 CTCT
1 CTCT
46796472 ATTCACGGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.50, G:0.14, T:0.33
Consensus pattern (16 bp):
CTCTGTCACCCGCTTC
Found at i:46797283 original size:21 final size:19
Alignment explanation
Indices: 46797269--46797309 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
46797259 AATTACAATT
*
46797269 ATTATATTTTAAATTTTAA
1 ATTAAATTTTAAATTTTAA
46797288 ATTTTAAATTTTAAATTTTAA
1 A--TTAAATTTTAAATTTTAA
46797309 A
1 A
46797310 AATAATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 1 0.05
21 18 0.95
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTAAATTTTAAATTTTAA
Found at i:46797286 original size:7 final size:7
Alignment explanation
Indices: 46797274--46797309 Score: 72
Period size: 7 Copynumber: 5.1 Consensus size: 7
46797264 CAATTATTAT
46797274 ATTTTAA
1 ATTTTAA
46797281 ATTTTAA
1 ATTTTAA
46797288 ATTTTAA
1 ATTTTAA
46797295 ATTTTAA
1 ATTTTAA
46797302 ATTTTAA
1 ATTTTAA
46797309 A
1 A
46797310 AATAATTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTTAA
Found at i:46797341 original size:14 final size:14
Alignment explanation
Indices: 46797268--46797344 Score: 77
Period size: 14 Copynumber: 5.6 Consensus size: 14
46797258 TAATTACAAT
46797268 TATTATATTTTAAA
1 TATTATATTTTAAA
* *
46797282 TTTTAAATTTTAAA
1 TATTATATTTTAAA
* *
46797296 TTTTAAATTTTAAA
1 TATTATATTTTAAA
* * *
46797310 -AATA-ATTATAAT
1 TATTATATTTTAAA
46797322 TATTATATTTTAAA
1 TATTATATTTTAAA
46797336 TATTATATT
1 TATTATATT
46797345 ACTCAATTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
12 6 0.12
13 5 0.10
14 41 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTATATTTTAAA
Found at i:46797461 original size:9 final size:9
Alignment explanation
Indices: 46797449--46797480 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
46797439 ATCATATCAA
46797449 AACTTACAT
1 AACTTACAT
46797458 AACTTACAT
1 AACTTACAT
*
46797467 AATTTACAT
1 AACTTACAT
46797476 AACTT
1 AACTT
46797481 GAAAGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (9 bp):
AACTTACAT
Found at i:46797549 original size:9 final size:9
Alignment explanation
Indices: 46797537--46797718 Score: 131
Period size: 9 Copynumber: 20.0 Consensus size: 9
46797527 TATATCATAT
46797537 CATAACTTA
1 CATAACTTA
*
46797546 CATAACTCA
1 CATAACTTA
*
46797555 CATAACATA
1 CATAACTTA
46797564 CATAACTTA
1 CATAACTTA
46797573 -ATAACTTA
1 CATAACTTA
* *
46797581 TATATATCATA
1 CATA-A-CTTA
46797592 TCATAACTTA
1 -CATAACTTA
*
46797602 CATAACTCA
1 CATAACTTA
46797611 CATAACTTA
1 CATAACTTA
46797620 -ATAACTTA
1 CATAACTTA
* *
46797628 TATATATCATA
1 CATA-A-CTTA
*
46797639 TCATAACTTT
1 -CATAACTTA
* *
46797649 CAAAACTCA
1 CATAACTTA
*
46797658 CATAACTCA
1 CATAACTTA
46797667 CATAACTTA
1 CATAACTTA
46797676 CATAA--TA
1 CATAACTTA
*
46797683 CATAA-ATA
1 CATAACTTA
* * *
46797691 TATATCATA
1 CATAACTTA
46797700 TCATAACTTA
1 -CATAACTTA
46797710 CATAACTTA
1 CATAACTTA
46797719 ATTATACTTA
Statistics
Matches: 139, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
7 7 0.05
8 21 0.15
9 84 0.60
10 13 0.09
11 8 0.06
12 6 0.04
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:46797600 original size:56 final size:57
Alignment explanation
Indices: 46797508--46797716 Score: 233
Period size: 56 Copynumber: 3.8 Consensus size: 57
46797498 CTTTGGATCT
*
46797508 TAACTTAATAACTTATATATATATCATATCATAACTTACATAACTCACATAACATACA
1 TAACTTAATAACATATATATATATCATATCATAACTTACATAACTCACATAAC-TACA
46797566 TAACTTAATAAC-T-TATATATATCATATCATAACTTACATAACTCACATAACTTA-A
1 TAACTTAATAACATATATATATATCATATCATAACTTACATAACTCACATAAC-TACA
* * * * *
46797621 TAACTT-AT-ATATATCATATCATAAC-TTTCAAAACTCACATAACTCACATAACT---
1 TAACTTAATAACATAT-ATAT-ATATCATATCATAACTTACATAACTCACATAACTACA
* *
46797674 T-ACATAAT-ACATAAATATATATCATATCATAACTTACATAACT
1 TAACTTAATAACATATATATATATCATATCATAACTTACATAACT
46797717 TAATTATACT
Statistics
Matches: 132, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
51 4 0.03
52 23 0.17
53 8 0.06
54 3 0.02
55 9 0.07
56 68 0.52
57 5 0.04
58 12 0.09
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (57 bp):
TAACTTAATAACATATATATATATCATATCATAACTTACATAACTCACATAACTACA
Found at i:46797605 original size:47 final size:47
Alignment explanation
Indices: 46797546--46797675 Score: 199
Period size: 47 Copynumber: 2.7 Consensus size: 47
46797536 TCATAACTTA
*
46797546 CATAACTCACATAACAT-ACATAACTTAATAACTTATATATATCATAT
1 CATAACTTACATAAC-TCACATAACTTAATAACTTATATATATCATAT
46797593 CATAACTTACATAACTCACATAACTTAATAACTTATATATATCATAT
1 CATAACTTACATAACTCACATAACTTAATAACTTATATATATCATAT
* * *
46797640 CATAACTTTCAAAACTCACATAACTCACATAACTTA
1 CATAACTTACATAACTCACATAACTTA-ATAACTTA
46797676 CATAATACAT
Statistics
Matches: 77, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
46 1 0.01
47 68 0.88
48 8 0.10
ACGTcount: A:0.45, C:0.22, G:0.00, T:0.33
Consensus pattern (47 bp):
CATAACTTACATAACTCACATAACTTAATAACTTATATATATCATAT
Found at i:46803526 original size:20 final size:21
Alignment explanation
Indices: 46803501--46803540 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46803491 TGACAGGATG
46803501 TTGACTAGA-GTTGACCATCA
1 TTGACTAGATGTTGACCATCA
*
46803521 TTGACTGGATGTTGACCATC
1 TTGACTAGATGTTGACCATC
46803541 CATGTGGCGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
TTGACTAGATGTTGACCATCA
Found at i:46805328 original size:21 final size:21
Alignment explanation
Indices: 46805302--46805341 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
46805292 GCAGCTATAG
46805302 ATCATGACTTATAGCGGCGTT
1 ATCATGACTTATAGCGGCGTT
*
46805323 ATCATGACTTTTAGCGGCG
1 ATCATGACTTATAGCGGCG
46805342 CTTTCCCCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.33
Consensus pattern (21 bp):
ATCATGACTTATAGCGGCGTT
Found at i:46805421 original size:42 final size:42
Alignment explanation
Indices: 46805352--46805447 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
46805342 CTTTCCCCAC
* * * * *
46805352 AAACGCCGCTATAGATCATGACTTTTAGC-GTCCTTTTTTTAT
1 AAACGCCGCTAAAGAACACGACCTTTAGCGGT-CTTTTTTTAA
*
46805394 AAACGCCGCTAAAGAACACGACCTTTAGCGGTGTTTTTTTAA
1 AAACGCCGCTAAAGAACACGACCTTTAGCGGTCTTTTTTTAA
*
46805436 AAACGCCACTAA
1 AAACGCCGCTAA
46805448 TTTTGACAGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
42 44 0.96
43 2 0.04
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACACGACCTTTAGCGGTCTTTTTTTAA
Found at i:46805775 original size:22 final size:21
Alignment explanation
Indices: 46805731--46805802 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
46805721 TTCTACTCTG
* *
46805731 CTCTGCTTCCCTCACTGCAGC
1 CTCTGCTTCCCTCGCTGCTGC
*
46805752 CTCTGCTTCTCCTCGCTGTTGC
1 CTCTGCTTC-CCTCGCTGCTGC
*
46805774 CTCTACTTCCCTCGCTGCTGC
1 CTCTGCTTCCCTCGCTGCTGC
*
46805795 ATCTGCTT
1 CTCTGCTT
46805803 TAAGTTGTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 26 0.60
22 17 0.40
ACGTcount: A:0.06, C:0.43, G:0.15, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCTGC
Found at i:46807060 original size:21 final size:21
Alignment explanation
Indices: 46807034--46807077 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
46807024 TGTCCCAAAT
46807034 TGATTGCGTTTTTTGCACGAA
1 TGATTGCGTTTTTTGCACGAA
*
46807055 TGATTGTGTTTTTTGCACGAA
1 TGATTGCGTTTTTTGCACGAA
46807076 TG
1 TG
46807078 TAGCAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.18, C:0.11, G:0.25, T:0.45
Consensus pattern (21 bp):
TGATTGCGTTTTTTGCACGAA
Found at i:46809130 original size:39 final size:39
Alignment explanation
Indices: 46809060--46809137 Score: 122
Period size: 41 Copynumber: 2.0 Consensus size: 39
46809050 ATTTGATGCA
46809060 TTAATATGACATTATTTTTAATTGTTAAATTTTTAAAATTT
1 TTAATATGACATTA-TTTTAATTGTTAAA-TTTTAAAATTT
*
46809101 TTAATATGACATTA-TTTAATTGTTCAATTTTAAAATT
1 TTAATATGACATTATTTTAATTGTTAAATTTTAAAATT
46809138 GAATAATGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
38 10 0.28
39 12 0.33
41 14 0.39
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (39 bp):
TTAATATGACATTATTTTAATTGTTAAATTTTAAAATTT
Found at i:46809454 original size:7 final size:7
Alignment explanation
Indices: 46809439--46809510 Score: 99
Period size: 7 Copynumber: 10.0 Consensus size: 7
46809429 AGATCATAGG
46809439 CCCTAAA
1 CCCTAAA
*
46809446 CCTTAAA
1 CCCTAAA
46809453 CCCTAAA
1 CCCTAAA
*
46809460 CCTATAAAA
1 CC-CT-AAA
46809469 CCCTAAA
1 CCCTAAA
46809476 CCCTAAA
1 CCCTAAA
46809483 CCCTAAA
1 CCCTAAA
46809490 CCCTAAA
1 CCCTAAA
*
46809497 CCCTAAG
1 CCCTAAA
46809504 CCCTAAA
1 CCCTAAA
46809511 TTAACTACGA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
7 50 0.88
8 2 0.04
9 5 0.09
ACGTcount: A:0.43, C:0.39, G:0.01, T:0.17
Consensus pattern (7 bp):
CCCTAAA
Found at i:46809704 original size:14 final size:13
Alignment explanation
Indices: 46809694--46809744 Score: 57
Period size: 14 Copynumber: 3.7 Consensus size: 13
46809684 ATAAACCTTA
46809694 AACCCTTAACCCTT
1 AACCCTTAACCC-T
*
46809708 AACCCCTAACACCT
1 AACCCTTAAC-CCT
*
46809722 AAACCCTAAACCCT
1 -AACCCTTAACCCT
46809736 AACCCTTAA
1 AACCCTTAA
46809745 ATCATAATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 8 0.26
14 13 0.42
15 10 0.32
ACGTcount: A:0.37, C:0.43, G:0.00, T:0.20
Consensus pattern (13 bp):
AACCCTTAACCCT
Found at i:46809745 original size:14 final size:14
Alignment explanation
Indices: 46809689--46809735 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
46809679 TAACTATAAA
46809689 CCTTAAACCCTTAAC
1 CCTTAAACCC-TAAC
*
46809704 CCTTAACCCCTAAC
1 CCTTAAACCCTAAC
46809718 ACC-TAAACCCTAAAC
1 -CCTTAAACCCT-AAC
46809733 CCT
1 CCT
46809736 AACCCTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 13 0.48
15 14 0.52
ACGTcount: A:0.34, C:0.45, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTTAAACCCTAAC
Found at i:46809822 original size:14 final size:14
Alignment explanation
Indices: 46809803--46809829 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
46809793 AGAACATATA
46809803 TAAACTCTAAACCT
1 TAAACTCTAAACCT
46809817 TAAACTCTAAACC
1 TAAACTCTAAACC
46809830 CTGAATTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.30, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACTCTAAACCT
Found at i:46809885 original size:28 final size:28
Alignment explanation
Indices: 46809853--46809912 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
46809843 TATATATTTA
* ** *
46809853 TAAACTATAAACTCTAAACCCCAACCCT
1 TAAACAATAAACAATAAACCACAACCCT
*
46809881 TAAACAATAAACAATAAACCATAACCCT
1 TAAACAATAAACAATAAACCACAACCCT
46809909 TAAA
1 TAAA
46809913 TCCATAATCC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (28 bp):
TAAACAATAAACAATAAACCACAACCCT
Found at i:46810116 original size:73 final size:73
Alignment explanation
Indices: 46810019--46810180 Score: 209
Period size: 76 Copynumber: 2.2 Consensus size: 73
46810009 TGCTTGACTA
* * **
46810019 TTGCGGCACTTTTTAAAAAACGCCACCAATGTCTCTAAAGCT-AAAGAAAAACGACATCGTTTGC
1 TTGCGGC-GTTTTTAAAAAACGCCACCAATGTCTCTAAAGCTAAAAAAAAAAAAACATCGTTTGC
46810083 TTAAAACTT
65 TTAAAACTT
* * *
46810092 TTGCGGCGTTTTTCAAAAAGCGCCACCAGTGTCTCTAAAGCTAAAAAAAAAAAAAAACGTCGTTT
1 TTGCGGCGTTTTT-AAAAAACGCCACCAATGTCTCTAAAGCT--AAAAAAAAAAAAACATCGTTT
46810157 GCTTAAAACTT
63 GCTTAAAACTT
*
46810168 TTGCGGCGCTTTT
1 TTGCGGCGTTTTT
46810181 GTGAAATCGC
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
72 5 0.06
73 33 0.43
76 39 0.51
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (73 bp):
TTGCGGCGTTTTTAAAAAACGCCACCAATGTCTCTAAAGCTAAAAAAAAAAAAACATCGTTTGCT
TAAAACTT
Found at i:46810233 original size:31 final size:31
Alignment explanation
Indices: 46810195--46810256 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
46810185 AATCGCCGCT
*
46810195 AATGCTTGACTTCTGCGGTGTTTTTCAAAGA
1 AATGCTTGACTTCTGCGATGTTTTTCAAAGA
46810226 AATGCTTGACTTCTGCGATGTTTTTCAAAGA
1 AATGCTTGACTTCTGCGATGTTTTTCAAAGA
46810257 GCGCCACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (31 bp):
AATGCTTGACTTCTGCGATGTTTTTCAAAGA
Found at i:46810418 original size:24 final size:24
Alignment explanation
Indices: 46810391--46810443 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
46810381 GTCTCTAAAT
46810391 CTTAAGAA-AAAATGA-AGACGTTTG
1 CTTAA-AATAAAATGACA-ACGTTTG
*
46810415 CTTAAAATAAAATGACATCGTTTG
1 CTTAAAATAAAATGACAACGTTTG
46810439 CTTAA
1 CTTAA
46810444 CACTTTTGCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 2 0.08
24 23 0.88
25 1 0.04
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (24 bp):
CTTAAAATAAAATGACAACGTTTG
Found at i:46810758 original size:114 final size:113
Alignment explanation
Indices: 46810439--46810768 Score: 430
Period size: 115 Copynumber: 2.9 Consensus size: 113
46810429 ACATCGTTTG
* * *
46810439 CTTAACACTTTTGCGGCGCTTT-TGATAAAGCGCCGCTAATTCTTGAATATTTTGG-CGTTTCTA
1 CTTAACTCTTTTGCGGCGCTTTGTGAT--AGCGCCGCTAATGCTTG--TCTTTTGGACGTTTCTA
* *
46810502 GAAAAGCGCCACCAATGTCGCTAAAGCTCAACAAGAAAACGGCGTCGTTTGA
62 GAAAAGCGCCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
* * *
46810554 CTTAACTTTTTTTGCGGCGCTTTGTGATAGTGCCGCTAATGCTTGTCTTTTGTAGCGTTTCTAGA
1 CTTAAC-TCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTGGA-CGTTTCTAGA
*
46810619 AAAGCACCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
64 AAAGCGCCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
* **
46810669 CTTAACTCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTGCGACGTTTTTTTAA
1 CTTAACTCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTG-GACGTTTCTAGAA
* * ** *
46810734 AAGCGCCACTAATATCTTTGAAGCTCAACAAAAAA
65 AAGCGCCACCAATGTCGCTAAAGCTCAACAAAAAA
46810769 TGACATTGTT
Statistics
Matches: 189, Mismatches: 21, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
113 6 0.03
114 80 0.42
115 85 0.45
116 14 0.07
117 4 0.02
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (113 bp):
CTTAACTCTTTTGCGGCGCTTTGTGATAGCGCCGCTAATGCTTGTCTTTTGGACGTTTCTAGAAA
AGCGCCACCAATGTCGCTAAAGCTCAACAAAAAAACGGCGTCGTTTAA
Found at i:46820707 original size:7 final size:7
Alignment explanation
Indices: 46820697--46820723 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
46820687 AATTTGGTAT
46820697 TTTTAAA
1 TTTTAAA
46820704 TTTTAAA
1 TTTTAAA
46820711 TTTTAAA
1 TTTTAAA
46820718 TTTTAA
1 TTTTAA
46820724 GATTGAAAAA
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:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTTTAAA
Found at i:46824616 original size:2 final size:2
Alignment explanation
Indices: 46824609--46824635 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46824599 NNNNNNNTTA
46824609 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 A
46824636 AAGAGAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46836014 original size:14 final size:12
Alignment explanation
Indices: 46835985--46836148 Score: 98
Period size: 12 Copynumber: 13.0 Consensus size: 12
46835975 GTTCATTTAA
*
46835985 TCATCAAGTCTT
1 TCATCAAGTTTT
46835997 TCATCAAGTGTTTT
1 TCATCAA--GTTTT
46836011 TCATCAAGTTTT
1 TCATCAAGTTTT
* *
46836023 TAATCAAGTCTT
1 TCATCAAGTTTT
**
46836035 TCATCAAGTCAT
1 TCATCAAGTTTT
*
46836047 TAATCAAGTTTT
1 TCATCAAGTTTT
*
46836059 TAATTACCAAGTTTTT
1 TCA-T--CAAG-TTTT
* *
46836075 TTATTAAGTTTT
1 TCATCAAGTTTT
*
46836087 GCATCAAGTTCTT
1 TCATCAAGTT-TT
* *
46836100 T--TTAAGCTTT
1 TCATCAAGTTTT
46836110 TCATCAAGTCTTT
1 TCATCAAGT-TTT
*
46836123 TTATCAAGTGTTTT
1 TCATCAA--GTTTT
*
46836137 TAATCAAGTTTT
1 TCATCAAGTTTT
46836149 CAATCAAGCT
Statistics
Matches: 120, Mismatches: 20, Indels: 24
0.73 0.12 0.15
Matches are distributed among these distances:
10 3 0.03
11 5 0.04
12 64 0.53
13 15 0.12
14 20 0.17
15 7 0.06
16 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.49
Consensus pattern (12 bp):
TCATCAAGTTTT
Found at i:46836101 original size:25 final size:24
Alignment explanation
Indices: 46836066--46836124 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
46836056 TTTTAATTAC
*
46836066 CAAGTTTTTTTATTAAG-TTTTGCAT
1 CAAGTTCTTTT-TTAAGCTTTT-CAT
46836091 CAAGTTC-TTTTTAAGCTTTTCAT
1 CAAGTTCTTTTTTAAGCTTTTCAT
46836114 CAAG-TCTTTTT
1 CAAGTTCTTTTT
46836125 ATCAAGTGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
22 2 0.06
23 16 0.52
24 7 0.23
25 6 0.19
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.54
Consensus pattern (24 bp):
CAAGTTCTTTTTTAAGCTTTTCAT
Found at i:46836124 original size:22 final size:23
Alignment explanation
Indices: 46836078--46836125 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
46836068 AGTTTTTTTA
46836078 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTGCATCAAGTTCTTT
46836101 TTAAGCTTTT-CATCAAG-TCTTT
1 TTAAG-TTTTGCATCAAGTTCTTT
46836123 TTA
1 TTA
46836126 TCAAGTGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 8 0.33
23 12 0.50
24 4 0.17
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (23 bp):
TTAAGTTTTGCATCAAGTTCTTT
Found at i:46838669 original size:11 final size:13
Alignment explanation
Indices: 46838653--46838684 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
46838643 ATTTCACGGA
46838653 AAAATTTCA-T-G
1 AAAATTTCATTCG
46838664 AAAATTTCATTCG
1 AAAATTTCATTCG
46838677 AAAATTTC
1 AAAATTTC
46838685 GAGGTTTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 1 0.05
13 9 0.47
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (13 bp):
AAAATTTCATTCG
Found at i:46839452 original size:33 final size:33
Alignment explanation
Indices: 46839414--46839532 Score: 114
Period size: 33 Copynumber: 3.4 Consensus size: 33
46839404 TCCCCTAAGG
*
46839414 GGTTGCTAAGTGCTGATTCCCCAAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
46839447 GGTTGCTAAGTGCTGATACCTCCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
46839489 GGTTGC-AAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
46839521 GGTTGCTAAGTG
1 GGTTGCTAAGTG
46839533 TTGAATCCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
32 7 0.10
33 24 0.35
34 5 0.07
35 2 0.03
36 2 0.03
38 2 0.03
39 2 0.03
40 6 0.09
41 12 0.17
42 7 0.10
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:46839456 original size:102 final size:103
Alignment explanation
Indices: 46839280--46839509 Score: 315
Period size: 102 Copynumber: 2.3 Consensus size: 103
46839270 ATTGAATATA
* * ****
46839280 AAGGGGGTTGCTAAGTACTGATT-CCCTCAAGGGGTTGCTAAGTGCTGATTTCCTGGTTCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
* *
46839344 TGGTTGCTAAGTGCTGAGT-CCACCGTATTTTAAATTTG
66 TGGTTGCTAAGTGCTGA-TACCACCGTATCTTAAATGTG
* *
46839382 AAGGGGGTTGCTGAGTGCTAATTCCCCT-AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
*
46839446 TGGTTGCTAAGTGCTGATACCTCCGTATCTTAAATGTG
66 TGGTTGCTAAGTGCTGATACCACCGTATCTTAAATGTG
*
46839484 AAAGGGGTTGC-AAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
46839510 GAATCATTGG
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
101 14 0.12
102 94 0.84
103 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (103 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
TGGTTGCTAAGTGCTGATACCACCGTATCTTAAATGTG
Found at i:46846378 original size:50 final size:50
Alignment explanation
Indices: 46846259--46846507 Score: 282
Period size: 50 Copynumber: 4.8 Consensus size: 50
46846249 GATAATAACA
* *** *
46846259 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTCTCATGTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCATCTCGG
* * *
46846310 TGCCCATGCCATGCCCCAGACATGGTCTTACAGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
46846360 TGCCAATGCCATCTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
46846410 TGCCCATGCCATGTCCCAGACATGGTCTTAAAGGGGACACCTCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGG--ACCTC-TCATCTC--GG
* * *
46846465 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
46846508 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
50 89 0.53
51 29 0.17
52 5 0.03
53 6 0.04
54 4 0.02
55 2 0.01
56 32 0.19
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:46846445 original size:100 final size:104
Alignment explanation
Indices: 46846258--46846507 Score: 328
Period size: 100 Copynumber: 2.4 Consensus size: 104
46846248 TGATAATAAC
* *** *
46846258 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGGTGTTCTCATGTCGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATCTCGGTGCCCATGCCATG
* *
46846323 CCCCAGACATGGTCTTACAGGGG-ACCTC-TCATCT-TGG
65 CCCCAGACATGGTCTTAAAGGGGAACCTCATCATCTAAGG
* * *
46846360 -TGCCAATGCCATCTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGC
*
46846424 CCCAGACATGGTCTTAAAGGGGACACCTCATGATCTCAAGG
66 CCCAGACATGGTCTTAAAGGGGA-ACCTCATCATCT-AAGG
* *
46846465 ATGCCAATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
46846508 TTACCCAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
100 46 0.36
101 31 0.24
102 5 0.04
103 5 0.04
105 2 0.02
106 39 0.30
ACGTcount: A:0.21, C:0.30, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATGC
CCCAGACATGGTCTTAAAGGGGAACCTCATCATCTAAGG
Found at i:46846879 original size:30 final size:30
Alignment explanation
Indices: 46846845--46846902 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
46846835 CCTTGACTCT
46846845 AACTTTTACAAAATTACGA-TTTTGCCCCTA
1 AACTTTTACAAAATTAC-ATTTTTGCCCCTA
* *
46846875 AACTTTTGCATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACATTTTTGCCCC
46846903 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 24 0.96
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (30 bp):
AACTTTTACAAAATTACATTTTTGCCCCTA
Found at i:46853958 original size:50 final size:51
Alignment explanation
Indices: 46853843--46854081 Score: 268
Period size: 50 Copynumber: 4.6 Consensus size: 51
46853833 GATAATAACA
* * * ***
46853843 TGCCAAAGCCATGTCCCAGACATGGTCTTCCATGGGGTGTTCTCATGC-CGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCAT-CTCGG
*
46853894 TGCCCATGCCATGTCCCAGACATGGTCTTACA-GGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCATCTCGG
* * *
46853944 TGCCAACGCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCATCTCGG
* * * * *
46853994 TGCCCATGCCATGTCCCAGGCATGGTCTTACAGGGGGTCTCGCATGATCTCAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGAC-CTC-TCATCTC--GG
46854049 ATGCCAATGCCATGTCCCAGACATGGTCTTACA
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACA
46854082 TGAGATCTCT
Statistics
Matches: 161, Mismatches: 20, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
49 1 0.01
50 88 0.55
51 33 0.20
52 2 0.01
53 6 0.04
55 1 0.01
56 30 0.19
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGGACCTCTCATCTCGG
Found at i:46854021 original size:100 final size:105
Alignment explanation
Indices: 46853842--46854083 Score: 316
Period size: 100 Copynumber: 2.3 Consensus size: 105
46853832 TGATAATAAC
* *** *
46853842 ATGCCAAAGCCATGTCCCAGACATGGTCTTCCATGGGGTGTTCTCATGCCGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACAT-GGGACCTCTCATGCCAGTGCCCATGCCATG
*
46853907 TCCCAGACATGGTCTTACA-GGGGAC-CTC-TCATCTC-GG
65 TCCCAGACATGGTCTTACAGGGGGACTCGCATCATCTCAGG
*
46853944 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCAGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGC-CAGTGCCCATGCCATG
* * *
46854007 TCCCAGGCATGGTCTTACAGGGGGTCTCGCATGATCTCAAGG
65 TCCCAGACATGGTCTTACAGGGGGACTCGCATCATCTC-AGG
*
46854049 ATGCCAATGCCATGTCCCAGACATGGTCTTACATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATG
46854084 AGATCTCTTT
Statistics
Matches: 122, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
99 1 0.01
100 42 0.34
101 36 0.30
102 2 0.02
103 6 0.05
105 2 0.02
106 33 0.27
ACGTcount: A:0.20, C:0.31, G:0.24, T:0.24
Consensus pattern (105 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGCCAGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGGACTCGCATCATCTCAGG
Found at i:46854450 original size:30 final size:30
Alignment explanation
Indices: 46854416--46854473 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
46854406 CCTCGACTCT
46854416 AACTTTGACAAAATTACAATTTTGCCCCTA
1 AACTTTGACAAAATTACAATTTTGCCCCTA
* * *
46854446 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
46854474 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:46856809 original size:33 final size:33
Alignment explanation
Indices: 46856771--46856889 Score: 114
Period size: 33 Copynumber: 3.4 Consensus size: 33
46856761 TCCCCTAAGG
*
46856771 GGTTGCTAAGTGCTGATTCCCCAAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
46856804 GGTTGCTAAGTGCTGATACCTCCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCGAATC----AT-TG---GT
46856846 GGTTGC-AAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
46856878 GGTTGCTAAGTG
1 GGTTGCTAAGTG
46856890 TTGAATCCAT
Statistics
Matches: 69, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
32 7 0.10
33 24 0.35
34 5 0.07
35 2 0.03
36 2 0.03
38 2 0.03
39 2 0.03
40 6 0.09
41 12 0.17
42 7 0.10
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
Found at i:46856813 original size:102 final size:103
Alignment explanation
Indices: 46856637--46856866 Score: 315
Period size: 102 Copynumber: 2.3 Consensus size: 103
46856627 ATTGAATATA
* * ****
46856637 AAGGGGGTTGCTAAGTACTGATT-CCCTCAAGGGGTTGCTAAGTGCTGATTTCCTGGTTCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
* *
46856701 TGGTTGCTAAGTGCTGAGT-CCACCGTATTTTAAATTTG
66 TGGTTGCTAAGTGCTGA-TACCACCGTATCTTAAATGTG
* *
46856739 AAGGGGGTTGCTGAGTGCTAATTCCCCT-AAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
1 AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
*
46856803 TGGTTGCTAAGTGCTGATACCTCCGTATCTTAAATGTG
66 TGGTTGCTAAGTGCTGATACCACCGTATCTTAAATGTG
*
46856841 AAAGGGGTTGC-AAGTGCTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
46856867 GAATCATTGG
Statistics
Matches: 112, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
101 14 0.12
102 94 0.84
103 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (103 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCTCAAGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGG
TGGTTGCTAAGTGCTGATACCACCGTATCTTAAATGTG
Found at i:46861987 original size:14 final size:12
Alignment explanation
Indices: 46861958--46862121 Score: 107
Period size: 12 Copynumber: 13.0 Consensus size: 12
46861948 GTTCATTTAA
*
46861958 TCATCAAGTCTT
1 TCATCAAGTTTT
46861970 TCATCAAGTGTTTT
1 TCATCAA--GTTTT
46861984 TCATCAAGTTTT
1 TCATCAAGTTTT
* *
46861996 TAATCAAGTCTT
1 TCATCAAGTTTT
**
46862008 TCATCAAGTCAT
1 TCATCAAGTTTT
*
46862020 TAATCAAGTTTT
1 TCATCAAGTTTT
*
46862032 TAATTACCAAGTTTTT
1 TCA-T--CAAG-TTTT
* *
46862048 TTATTAAGTTTT
1 TCATCAAGTTTT
*
46862060 GCATCAAGTTCTT
1 TCATCAAGTT-TT
* *
46862073 T--TTAAGCTTT
1 TCATCAAGTTTT
46862083 TCATCAAGTCTTT
1 TCATCAAGT-TTT
46862096 TCATCAAGTGTTTT
1 TCATCAA--GTTTT
*
46862110 TAATCAAGTTTT
1 TCATCAAGTTTT
46862122 CAATCAAGCT
Statistics
Matches: 121, Mismatches: 19, Indels: 24
0.74 0.12 0.15
Matches are distributed among these distances:
10 3 0.02
11 5 0.04
12 64 0.53
13 16 0.13
14 20 0.17
15 7 0.06
16 6 0.05
ACGTcount: A:0.27, C:0.15, G:0.10, T:0.48
Consensus pattern (12 bp):
TCATCAAGTTTT
Found at i:46862074 original size:25 final size:24
Alignment explanation
Indices: 46862039--46862096 Score: 68
Period size: 23 Copynumber: 2.5 Consensus size: 24
46862029 TTTTAATTAC
*
46862039 CAAGTTTTTTTATTAAG-TTTTGCAT
1 CAAGTTCTTTT-TTAAGCTTTT-CAT
46862064 CAAGTTC-TTTTTAAGCTTTTCAT
1 CAAGTTCTTTTTTAAGCTTTTCAT
46862087 CAAG-TCTTTT
1 CAAGTTCTTTT
46862097 CATCAAGTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.07
23 15 0.50
24 7 0.23
25 6 0.20
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.53
Consensus pattern (24 bp):
CAAGTTCTTTTTTAAGCTTTTCAT
Found at i:46866453 original size:40 final size:40
Alignment explanation
Indices: 46866396--46866490 Score: 118
Period size: 40 Copynumber: 2.4 Consensus size: 40
46866386 CATTTGGATA
* * * *
46866396 GAAAACACCGCTGAAGATCGAGCATTAGCGGTGTTTTACT
1 GAAAACGCCGCTAAAGATCGAGCATTAACGGCGTTTTACT
* * *
46866436 TAAAACGCCGCTAAAGATCTAGCATTAACGGCGTTTTCCT
1 GAAAACGCCGCTAAAGATCGAGCATTAACGGCGTTTTACT
*
46866476 GAAAGCGCCGCTAAA
1 GAAAACGCCGCTAAA
46866491 AATAAGAATT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (40 bp):
GAAAACGCCGCTAAAGATCGAGCATTAACGGCGTTTTACT
Found at i:46866698 original size:41 final size:41
Alignment explanation
Indices: 46866571--46866708 Score: 168
Period size: 41 Copynumber: 3.4 Consensus size: 41
46866561 CTTTCGTTGA
* *
46866571 TTTAGCGGCGTTTTTGAAGAAGCGTCGCTAAAGCTTAGAGC
1 TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
* * *
46866612 TTTAGCGGCATTTTTGAATAAGCGTCGCTAATGCTCAGAGG
1 TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
* * ** * **
46866653 TTTAGTGGCATTTCTGAAGAAGCGTCGCTAATTATTGGATT
1 TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
46866694 TTTAGCGGCATTTTT
1 TTTAGCGGCATTTTT
46866709 CCAAAAGTGC
Statistics
Matches: 81, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (41 bp):
TTTAGCGGCATTTTTGAAGAAGCGTCGCTAATGCTTAGAGC
Found at i:46866723 original size:82 final size:80
Alignment explanation
Indices: 46866571--46866748 Score: 196
Period size: 82 Copynumber: 2.2 Consensus size: 80
46866561 CTTTCGTTGA
* * * *
46866571 TTTAGCGGCGTTTTTGAAGAAGCGTCGCTAAAGCTTAGAGCTTTAGCGGCATTTTTGAATAAGCG
1 TTTAGCGGCATTTCTGAAGAAGCGTCGCTAAAGATTAGAGCTTTAGCGGCATTTTTCAATAAGCG
*
46866636 TCGCTAATGCTCAGAGG
66 CCGCTAATG-TCAG-GG
* ** * ** *
46866653 TTTAGTGGCATTTCTGAAGAAGCGTCGCTAATTATTGGATTTTTAGCGGCATTTTTCCAA-AAGT
1 TTTAGCGGCATTTCTGAAGAAGCGTCGCTAAAGATTAGAGCTTTAGCGGCATTTTT-CAATAAGC
46866717 GCCGCTAATGTCAGGG
65 GCCGCTAATGTCAGGG
*
46866733 TTTTAGCGGCGTTTCT
1 -TTTAGCGGCATTTCT
46866749 TTAAGAGCGC
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
80 2 0.03
81 17 0.21
82 59 0.74
83 2 0.03
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (80 bp):
TTTAGCGGCATTTCTGAAGAAGCGTCGCTAAAGATTAGAGCTTTAGCGGCATTTTTCAATAAGCG
CCGCTAATGTCAGGG
Found at i:46870321 original size:13 final size:13
Alignment explanation
Indices: 46870299--46870395 Score: 81
Period size: 13 Copynumber: 7.4 Consensus size: 13
46870289 AAGAAAAAGT
*
46870299 TTACTAAAATATA
1 TTACTCAAATATA
46870312 TTACTCAAATATA
1 TTACTCAAATATA
* *
46870325 TTACTTAAATACA
1 TTACTCAAATATA
46870338 TTACTTACTAAA-AT-
1 TTAC-T-C-AAATATA
* * *
46870352 TTACTTAATTACA
1 TTACTCAAATATA
*
46870365 TTACTTAAATATA
1 TTACTCAAATATA
*
46870378 TTACTCAAATACA
1 TTACTCAAATATA
46870391 TTACT
1 TTACT
46870396 TACTAAAATT
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
11 2 0.03
12 1 0.01
13 55 0.82
14 5 0.07
15 1 0.01
16 3 0.04
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.41
Consensus pattern (13 bp):
TTACTCAAATATA
Found at i:46870355 original size:27 final size:27
Alignment explanation
Indices: 46870325--46870407 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
46870315 CTCAAATATA
46870325 TTACTTAAATACATTACTTACTAAAAT
1 TTACTTAAATACATTACTTACTAAAAT
* *
46870352 TTACTTAATTACATTACTTA--AATAT
1 TTACTTAAATACATTACTTACTAAAAT
*
46870377 ATTACTCAAATACATTACTTACTAAAAT
1 -TTACTTAAATACATTACTTACTAAAAT
46870405 TTA
1 TTA
46870408 AGTATATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
25 4 0.08
26 18 0.38
27 22 0.46
28 4 0.08
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.42
Consensus pattern (27 bp):
TTACTTAAATACATTACTTACTAAAAT
Found at i:46870378 original size:53 final size:55
Alignment explanation
Indices: 46870293--46870522 Score: 202
Period size: 53 Copynumber: 4.1 Consensus size: 55
46870283 TTCAAAAAGA
* * * *
46870293 AAAAGTTTACTAAAATATATTACTCAAATATATTACTTAAATACATTAC-TTAC-T
1 AAAA-TTTACTTAATTACATTACTTAAATATATTACTTAAATACATTACATTACTT
*
46870347 AAAATTTACTTAATTACATTACTTAAATATATTACTCAAATACATTAC-TTAC-T
1 AAAATTTACTTAATTACATTACTTAAATATATTACTTAAATACATTACATTACTT
* * * *
46870400 AAAATTTAAGTATATATTACATTACTTACAT-TACTTACTAAAATATATTACATTACTT
1 AAAATTT-ACT-TA-ATTACATTACTTAAATATA-TTACTTAAATACATTACATTACTT
* * * * * * *
46870458 AAATATTTTACTTACTAAAATTTA-TTTAATACATTACTTAAATATATTACATAACTT
1 AAA-A-TTTACTTAATTACA-TTACTTAAATATATTACTTAAATACATTACATTACTT
46870515 AAAATTTA
1 AAAATTTA
46870523 TATATATATA
Statistics
Matches: 148, Mismatches: 18, Indels: 19
0.80 0.10 0.10
Matches are distributed among these distances:
53 51 0.34
54 6 0.04
55 8 0.05
56 31 0.21
57 36 0.24
58 10 0.07
59 3 0.02
60 3 0.02
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (55 bp):
AAAATTTACTTAATTACATTACTTAAATATATTACTTAAATACATTACATTACTT
Found at i:46870455 original size:18 final size:18
Alignment explanation
Indices: 46870429--46870519 Score: 78
Period size: 18 Copynumber: 4.9 Consensus size: 18
46870419 CATTACTTAC
46870429 ATTAC-TTACTAAAATAT
1 ATTACATTACTAAAATAT
*
46870446 ATTACATTACTTAAATAT
1 ATTACATTACTAAAATAT
*
46870464 TTTAC-TTACTAAAATTTATTT
1 ATTACATTACTAAAA--TA--T
* *
46870485 AATACATTACTTAAATAT
1 ATTACATTACTAAAATAT
*
46870503 ATTACATAACTTAAAAT
1 ATTACATTAC-TAAAAT
46870520 TTATATATAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
17 13 0.22
18 24 0.41
19 7 0.12
20 2 0.03
21 4 0.07
22 8 0.14
ACGTcount: A:0.45, C:0.11, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTACATTACTAAAATAT
Found at i:46870472 original size:22 final size:22
Alignment explanation
Indices: 46870421--46870472 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
46870411 ATATATTACA
46870421 TTACTTACATTACTTACTAAAAT
1 TTACTTACATTACTTAC-AAAAT
* *
46870444 ATA-TTACATTACTTA-AATATT
1 TTACTTACATTACTTACAA-AAT
46870465 TTACTTAC
1 TTACTTAC
46870473 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 16 0.67
23 2 0.08
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (22 bp):
TTACTTACATTACTTACAAAAT
Found at i:46870478 original size:17 final size:17
Alignment explanation
Indices: 46870429--46870483 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
46870419 CATTACTTAC
46870429 ATTACTTACTAAAATAT
1 ATTACTTACTAAAATAT
*
46870446 ATTACATTACTTAAATAT
1 ATTAC-TTACTAAAATAT
* *
46870464 TTTACTTACTAAAATTT
1 ATTACTTACTAAAATAT
46870481 ATT
1 ATT
46870484 TAATACATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (17 bp):
ATTACTTACTAAAATAT
Found at i:46870491 original size:39 final size:38
Alignment explanation
Indices: 46870372--46870523 Score: 132
Period size: 39 Copynumber: 4.0 Consensus size: 38
46870362 ACATTACTTA
* * *
46870372 AATATATTACTCAAATACATTACTTACTAAAATTTAAGT
1 AATACATTACTTAAATACATTACTTACTAAAATTT-ATT
* **
46870411 -ATATATTACATTACTTACATTACTTACTAAAA--TA-T
1 AATACATTAC-TTAAATACATTACTTACTAAAATTTATT
* **
46870446 ATTACATTACTTAAATATTTTACTTACTAAAATTTATTT
1 AATACATTACTTAAATACATTACTTACTAAAATTTA-TT
* *
46870485 AATACATTACTTAAATATATTACATAACTTAAAATTTAT
1 AATACATTACTTAAATACATTAC-TTAC-TAAAATTTAT
46870524 ATATATATAT
Statistics
Matches: 93, Mismatches: 12, Indels: 15
0.77 0.10 0.12
Matches are distributed among these distances:
35 19 0.20
36 8 0.09
37 3 0.03
38 9 0.10
39 41 0.44
40 4 0.04
41 9 0.10
ACGTcount: A:0.44, C:0.12, G:0.01, T:0.43
Consensus pattern (38 bp):
AATACATTACTTAAATACATTACTTACTAAAATTTATT
Found at i:46872503 original size:66 final size:66
Alignment explanation
Indices: 46872397--46872541 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 66
46872387 AGCAAATTAC
* * *
46872397 ACAACTTAAAGCGGAGGCAGCATCGAGAGAAGCTGAGGTTCAAA-AAAGATATGAAGAACTCCAG
1 ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAG-TATGAAGAACTCCAC
46872461 CT
65 CT
* * * * *
46872463 ACAACTTAAAGTAGATGTAGCAGCGAGAGAAGCTGAGGTTCAAAGGACGTATGAAGAACTCCACC
1 ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCACC
46872528 T
66 T
* *
46872529 GCAGCTTAAAGCA
1 ACAACTTAAAGCA
46872542 TATGCGACAG
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.26, T:0.17
Consensus pattern (66 bp):
ACAACTTAAAGCAGAGGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCACC
T
Found at i:46872966 original size:43 final size:43
Alignment explanation
Indices: 46872896--46873333 Score: 537
Period size: 43 Copynumber: 10.3 Consensus size: 43
46872886 AAACTGCAGT
* * *
46872896 TAAAAGTCATGGTCTTTAGCGGCGCTTGTGGAAAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * *
46872939 TAAAGGTCGTGGTCTATAGCAGCGCTTGTGGAAAAAGCACCGT
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
*
46872982 TAATGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * *
46873025 TAAAGGTCGTGGCCTATAGCGGCGTTTGTGGGAAAA-CGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * * * **
46873067 TAAAGGTCTTGGTCTATAACGGCATTTGTGGGAAAAGTACCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* *
46873110 TAAAGGTCGTGGTCTATAGCGGCGTTTGTAGG-GAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAAGCGCCGC
**
46873153 TAAAGGTTGTGGTCTATAGCGGCGTTTGTGGAGAAAA-CGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGA-AAAAGCGCCGC
* * * *
46873196 TAAAGGTCATGGCCTATAGTGGCATTTGTGG-AAAAGTGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
* * *
46873238 TAAAAGTCATGGTCTATAGCGGCATTTGTCGG-AAAAGCGACGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAAGCGCCGC
*
46873281 TAAAGGTCATGGTCTATAGCTGCGTTTGT-GAAAAAGCGCCGC
1 TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
46873323 TAAAGGTCATG
1 TAAAGGTCATG
46873334 ACCTTTAGCG
Statistics
Matches: 343, Mismatches: 45, Indels: 15
0.85 0.11 0.04
Matches are distributed among these distances:
41 5 0.01
42 92 0.27
43 241 0.70
44 5 0.01
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (43 bp):
TAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
Found at i:46873147 original size:128 final size:128
Alignment explanation
Indices: 46872896--46873349 Score: 574
Period size: 128 Copynumber: 3.5 Consensus size: 128
46872886 AAACTGCAGT
* * * * * *
46872896 TAAAAGTCATGGTCTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCAG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
** * * * *
46872961 CGCTTGTGGAAAAAGCACCGTTAATGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGC
66 CATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGG-AAAAGCGCCGC
* * * *
46873025 TAAAGGTCGTGGCCTATAGCGGCGTTTGTGGGAAAA-CGCCGCTAAAGGTCTTGGTCTATAACGG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
* *
46873089 CATTTGTGGGAAAAGTACCGCTAAAGGTCGTGGTCTATAGCGGCGTTTGTAGGGAAAGCGCCGC
66 CATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAGCGCCGC
* * *
46873153 TAAAGGTTGTGGTCTATAGCGGCGTTTGTGGAGAAAA-CGCCGCTAAAGGTCATGGCCTATAGTG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGA-AAAAGCGCCGCTAAAGGTCATGGTCTATAGCG
* * * *
46873217 GCATTTGT-GGAAAAGTGCCGCTAAAAGTCATGGTCTATAGCGGCATTTGTCGGAAAAGCGACGC
65 GCATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGT-GGAAAAGCGCCGC
* * ** *
46873281 TAAAGGTCATGGTCTATAGCTGCGTTTGT-GAAAAAGCGCCGCTAAAGGTCATGACCTTTAGCGG
1 TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
46873345 CATTT
66 CATTT
46873350 ATTTATAAAA
Statistics
Matches: 285, Mismatches: 37, Indels: 8
0.86 0.11 0.02
Matches are distributed among these distances:
126 4 0.01
127 32 0.11
128 182 0.64
129 67 0.24
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (128 bp):
TAAAGGTCGTGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGG
CATTTGTGGGAAAAGTACCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAGCGCCGC
Found at i:46873226 original size:171 final size:170
Alignment explanation
Indices: 46872896--46873333 Score: 576
Period size: 171 Copynumber: 2.6 Consensus size: 170
46872886 AAACTGCAGT
* * ** * *
46872896 TAAAAGTCATGGTCTTTAGCGGCGCTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTCTATAGCAG
1 TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTCTATAGCAG
* * * *
46872961 CGCTTGTGGAAAAAGCACCGTTAATGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCT
66 CGTTTGTGG-AAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCT
* *
46873026 AAAGGTCGTGGCCTATAGCGGCGTTTGTGGGAAAA-CGCCGC
130 AAAGGTCATGGCCTATAGCGGCATTTGT-GGAAAAGCGCCGC
* * * *
46873067 TAAAGGTCTTGGTCTATAACGGCATTTGTGGGAAAAGTACCGCTAAAGGTCGTGGTCTATAGCGG
1 TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTCTATAGCAG
* **
46873132 CGTTTGTAGGGAAAGCGCCGCTAAAGGTTGTGGTCTATAGCGGCGTTTGTGGAGAAAA-CGCCGC
66 CGTTTGT-GGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGA-AAAAGCGCCGC
* *
46873196 TAAAGGTCATGGCCTATAGTGGCATTTGTGGAAAAGTGCCGC
129 TAAAGGTCATGGCCTATAGCGGCATTTGTGGAAAAGCGCCGC
* * * *
46873238 TAAAAGTCATGGTCTATAGCGGCATTTGTCGGAAAAGCGA-CGCTAAAGGTCATGGTCTATAGCT
1 TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGC-ACCGCTAAAGGTCGTGGTCTATAGCA
*
46873302 GCGTTTGTGAAAAAGCGCCGCTAAAGGTCATG
65 GCGTTTGTGGAAAAGCGCCGCTAAAGGTCATG
46873334 ACCTTTAGCG
Statistics
Matches: 231, Mismatches: 32, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
170 26 0.11
171 198 0.86
172 7 0.03
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (170 bp):
TAAAAGTCATGGTCTATAACGGCATTTGTGGGAAAAGCACCGCTAAAGGTCGTGGTCTATAGCAG
CGTTTGTGGAAAAGCGCCGCTAAAGGTCATGGTCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTA
AAGGTCATGGCCTATAGCGGCATTTGTGGAAAAGCGCCGC
Found at i:46874771 original size:134 final size:134
Alignment explanation
Indices: 46874522--46874798 Score: 482
Period size: 134 Copynumber: 2.1 Consensus size: 134
46874512 GAGGTAGATT
* *
46874522 TATCAATAATTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
1 TATCGATACTTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
* *
46874587 CAAGTTTGGTATCATTTTTTTATGTGGTGTCGATACCATTTTGGGAAAATATCGATACCCTAAGG
66 CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
46874652 TCAA
131 TCAA
* * * *
46874656 TATCGATACTTTAAGAAAGGTACTGATAATTTTTGACATTTTAAATTTTGGTGAGAAATAGAATG
1 TATCGATACTTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
46874721 CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
66 CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
46874786 TCAA
131 TCAA
46874790 TATCGATAC
1 TATCGATAC
46874799 CTACGTGATT
Statistics
Matches: 135, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
134 135 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (134 bp):
TATCGATACTTTAAGAAAGGTAATGATAATTTTTAACATTTTAAATTTTGGTCAAAAATAGAATG
CAAGTTTGGTATCATTTTTTTATGTGGTATCAATACCATTTTGGGAAAATATCGATACCCTAAGG
TCAA
Found at i:46875172 original size:174 final size:174
Alignment explanation
Indices: 46874881--46875229 Score: 565
Period size: 174 Copynumber: 2.0 Consensus size: 174
46874871 TGTACGCCTA
* *
46874881 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGGAAATGCGAAGAATAACATG
1 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGCAAATGCAAAGAATAACATG
* * * *
46874946 TGTCGACTTTAATAAAATGAACGTTGTAACGTATAAGTAGTGAGACGGTGGTGTGACATCTTTAT
66 TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGACGGTGGTGTGACATCTTTAT
*
46875011 ATTCGGGC-TTGACAACCAGCCCGGGTATAGGGTGTTACAAGGAT
131 ATTCGGGCTTTG-CAACCAGCCCGAGTATAGGGTGTTACAAGGAT
*
46875055 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTGTGCAAATGCAAAGAATAACATG
1 GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGCAAATGCAAAGAATAACATG
*
46875120 TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGATGGTGGTGTGACATCTTTAT
66 TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGACGGTGGTGTGACATCTTTAT
** * *
46875185 ATTCGGGCTTTGTGACCAGGCCGAGTATAGGGTGTTATAAGGAT
131 ATTCGGGCTTTGCAACCAGCCCGAGTATAGGGTGTTACAAGGAT
46875229 G
1 G
46875230 AAAAGTCAAT
Statistics
Matches: 161, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
174 158 0.98
175 3 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (174 bp):
GCATGATTTAATGATGATTAATGCATGTATGTCTTAAAACCTATGCAAATGCAAAGAATAACATG
TGTCAAATTTAATAAAATGAAAGTTGTAACGTACAAGTAGTGAGACGGTGGTGTGACATCTTTAT
ATTCGGGCTTTGCAACCAGCCCGAGTATAGGGTGTTACAAGGAT
Found at i:46876964 original size:44 final size:44
Alignment explanation
Indices: 46876901--46876990 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
46876891 TCTCCAATTT
46876901 ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
1 ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
*
46876945 ACTAAGGGTCCAAATGAGGACTAGTATCAACATTTTAAGGAGTG
1 ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
46876989 AC
1 AC
46876991 CTTTAGGGTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (44 bp):
ACTAAGGGTCCAAATGAGGACTAGTATCAAAATTTTAAGGAGTG
Found at i:46878160 original size:6 final size:6
Alignment explanation
Indices: 46878139--46878211 Score: 58
Period size: 6 Copynumber: 11.7 Consensus size: 6
46878129 ACTAACTTTA
* * * *
46878139 TTTAGT TTTATGT TTTATT TTTATT TGTACT TTTATT TTTATT ATTAGTT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT
*
46878189 GTTTTTAT TTTA-T TTTATT TTTA
1 -TTTAT-T TTTATT TTTATT TTTA
46878212 AGACTTATAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 5 0.09
6 33 0.62
7 12 0.23
8 3 0.06
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:46878202 original size:21 final size:23
Alignment explanation
Indices: 46878144--46878199 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
46878134 CTTTATTTAG
* *
46878144 TTTTATGTTTTATTTTTATTTGTA
1 TTTTAT-TTTTATTATTAGTTGTA
46878168 CTTTTATTTTTATTATTAGTTGT-
1 -TTTTATTTTTATTATTAGTTGTA
46878191 TTTTATTTT
1 TTTTATTTT
46878200 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
22 9 0.31
24 14 0.48
25 6 0.21
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.75
Consensus pattern (23 bp):
TTTTATTTTTATTATTAGTTGTA
Found at i:46879930 original size:5 final size:5
Alignment explanation
Indices: 46879925--46879967 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
46879915 TGCTATAATT
* * * *
46879925 TGATT TGATA TGATA TGATA TGATA TGGTC TGATC TGATA TGA
1 TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGATA TGA
46879968 AATACTACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.42
Consensus pattern (5 bp):
TGATA
Found at i:46882996 original size:21 final size:23
Alignment explanation
Indices: 46882966--46883016 Score: 61
Period size: 21 Copynumber: 2.2 Consensus size: 23
46882956 ACATTAACAC
*
46882966 TTCAACACATTT-CCAAGCC-AA
1 TTCAAAACATTTACCAAGCCAAA
46882987 TTCAAAACATTTAAGCCAAGCCAAA
1 TTCAAAACATTT-A-CCAAGCCAAA
46883012 TTCAA
1 TTCAA
46883017 GTCTTATGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 11 0.44
24 7 0.28
25 7 0.28
ACGTcount: A:0.43, C:0.27, G:0.06, T:0.24
Consensus pattern (23 bp):
TTCAAAACATTTACCAAGCCAAA
Found at i:46885844 original size:98 final size:98
Alignment explanation
Indices: 46885670--46885866 Score: 335
Period size: 98 Copynumber: 2.0 Consensus size: 98
46885660 ATACAATAAA
46885670 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
*
46885735 CCTTTAGAATCCCAAACTCAGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
* *
46885768 ACTTTAAAAGAA-AGTCCGCTTATCCAAGATTTAAGAAATCACACCCAATATGTTAGGGCA-TAA
1 ACTTTAAAAGAACA-TCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACT-A
46885831 TTCCTTTAAAATCCCAAACTCAGAATATTTCCTTT
64 TTCCTTTAAAATCCCAAACTCAGAATATTTCCTTT
46885866 A
1 A
46885867 TGATTTTTAA
Statistics
Matches: 94, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
97 2 0.02
98 92 0.98
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACTATT
CCTTTAAAATCCCAAACTCAGAATATTTCCTTT
Found at i:46886835 original size:3 final size:3
Alignment explanation
Indices: 46886822--46886861 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
46886812 TTGTATGTAC
* *
46886822 ATA AAA ATA ATA ATT AT- ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
46886862 GATGATGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:46888879 original size:132 final size:132
Alignment explanation
Indices: 46888275--46888861 Score: 879
Period size: 132 Copynumber: 4.4 Consensus size: 132
46888265 NNNNNNGTTA
* *
46888275 CCAGAGAAGTAGAATTAGTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCA
* * *
46888340 TCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTAAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCT
46888405 GC
131 GC
* *
46888407 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCTCTATAACCACGGGGAGGTAAAATCTGCCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCA
* * *
46888472 TCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCT
*
46888537 AC
131 GC
* *
46888539 CCAGAGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGTCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCA
* *
46888604 TCTTTGATCTGCTCCACTACTGCTTACGGAGACAAGATCTGAAATCTTCAATCTATTCCGCTGCT
66 TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCT
*
46888669 GT
131 GC
* * *
46888671 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACTGGGAGGTAAAATCTACCA
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCA
* * * * *
46888736 TATTTGATCTGC-CCTACTACTGTTTAGGGAGACAAGATCTGAAATCTTCGATCTATTTCGCTGC
66 TCTTTGATCTGCTCC-ACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGC
*
46888800 TGT
130 TGC
* * * * **
46888803 CCTGGGAAGTATAATTACTGGCTTCAATGTACTCCACTGTGACCACAATGAGGTAAAAT
1 CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAAT
46888862 TTACCGTCTT
Statistics
Matches: 420, Mismatches: 34, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
131 2 0.00
132 418 1.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
CCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCTGCCA
TCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCT
GC
Found at i:46891828 original size:1 final size:1
Alignment explanation
Indices: 46891824--46891898 Score: 51
Period size: 1 Copynumber: 75.0 Consensus size: 1
46891814 CCATTTTTCC
* * * * * * * * * *
46891824 TTTTTTTTTGTTTTGTTTTGTTTTTTGTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
46891889 TTGTTTTTTT
1 TTTTTTTTTT
46891899 GAATCTGAAC
Statistics
Matches: 52, Mismatches: 22, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (1 bp):
T
Found at i:46891837 original size:6 final size:6
Alignment explanation
Indices: 46891824--46891896 Score: 109
Period size: 6 Copynumber: 12.7 Consensus size: 6
46891814 CCATTTTTCC
46891824 TTTT-T TTTTG- TTTTG- TTTTGT TTTT-T GTTTTGT TTTTGT TTTTGT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT -TTTTGT TTTTGT TTTTGT
46891869 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTT
46891897 TTGAATCTGA
Statistics
Matches: 64, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
5 15 0.23
6 48 0.75
7 1 0.02
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (6 bp):
TTTTGT
Found at i:46905976 original size:21 final size:21
Alignment explanation
Indices: 46905952--46905999 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
46905942 GTGTGTGGAG
*
46905952 TAGCCACACAGGTATATGGGA
1 TAGCCACACAGGCATATGGGA
* * *
46905973 TAGCCATACGGGCATGTGGGA
1 TAGCCACACAGGCATATGGGA
46905994 TAGCCA
1 TAGCCA
46906000 AACGGCCATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.21, G:0.31, T:0.19
Consensus pattern (21 bp):
TAGCCACACAGGCATATGGGA
Found at i:46906004 original size:21 final size:21
Alignment explanation
Indices: 46905968--46906010 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
46905958 CACAGGTATA
* *
46905968 TGGGATAGCCATACGGGCATG
1 TGGGATAGCCAAACGGCCATG
46905989 TGGGATAGCCAAACGGCCATG
1 TGGGATAGCCAAACGGCCATG
46906010 T
1 T
46906011 CCTTGAGCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.35, T:0.19
Consensus pattern (21 bp):
TGGGATAGCCAAACGGCCATG
Found at i:46907572 original size:18 final size:18
Alignment explanation
Indices: 46907549--46907595 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
46907539 CACAAAGTTA
46907549 CGAGCTCACTCAAGACTG
1 CGAGCTCACTCAAGACTG
* * *
46907567 CGAGCTCTC-CAATAGTG
1 CGAGCTCACTCAAGACTG
46907584 CGAGCTCA-TCAA
1 CGAGCTCACTCAA
46907596 AGCTACAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.28, C:0.32, G:0.21, T:0.19
Consensus pattern (18 bp):
CGAGCTCACTCAAGACTG
Found at i:46912758 original size:31 final size:31
Alignment explanation
Indices: 46912723--46912784 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
46912713 ACTCCTTTGG
46912723 CCCTCAACTTGCACACATTTACTGTTGCATA
1 CCCTCAACTTGCACACATTTACTGTTGCATA
46912754 CCCTCAACTTGCACACATTTACTGTTGCATA
1 CCCTCAACTTGCACACATTTACTGTTGCATA
46912785 TTCTTTCTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.26, C:0.32, G:0.10, T:0.32
Consensus pattern (31 bp):
CCCTCAACTTGCACACATTTACTGTTGCATA
Found at i:46914226 original size:8 final size:7
Alignment explanation
Indices: 46914199--46914223 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
46914189 AATTTGGTAT
46914199 TTTTAAA
1 TTTTAAA
46914206 TTTTAAA
1 TTTTAAA
46914213 TTTTAAA
1 TTTTAAA
46914220 TTTT
1 TTTT
46914224 TAAGATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:46918267 original size:2 final size:2
Alignment explanation
Indices: 46918260--46918284 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
46918250 GTAAATATTA
46918260 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
46918285 ATAAGNNNNN
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:46921177 original size:108 final size:108
Alignment explanation
Indices: 46920987--46921197 Score: 316
Period size: 108 Copynumber: 1.9 Consensus size: 108
46920977 TGCCGAAATG
*
46920987 AGAAAGGTGCATATTGGCCAATTATTTCTAACCTTCCTCGTGTGAGGATAAATTATGATGACATC
1 AGAAAGCTGCATATTGGCCAATTATTTCTAACCTTCCTC-TGTGAGGATAAATTATGATGACATC
*
46921052 CTCTGAACAAGAACAAGCAGATTGCATTTCTAGATGGATAGCAA
65 CTCTGAACAAGAACAAGCAGATTGCATTCCTAGATGGATAGCAA
* * * *
46921096 AGAAAGCTGCATATTGGCCTATTATTTCTCACCTTCACT-TGTGAGGATAAGTTATGTTGACATC
1 AGAAAGCTGCATATTGGCCAATTATTTCTAACCTTC-CTCTGTGAGGATAAATTATGATGACATC
* * *
46921160 TTCTGAACAAGCACAAGCGGATTGCATTCCTAGATGGA
65 CTCTGAACAAGAACAAGCAGATTGCATTCCTAGATGGA
46921198 CAGCGAAAAC
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
108 57 0.62
109 33 0.36
110 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (108 bp):
AGAAAGCTGCATATTGGCCAATTATTTCTAACCTTCCTCTGTGAGGATAAATTATGATGACATCC
TCTGAACAAGAACAAGCAGATTGCATTCCTAGATGGATAGCAA
Found at i:46924189 original size:19 final size:20
Alignment explanation
Indices: 46924165--46924203 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
46924155 AGAAAAAGAA
46924165 CGAAAAGTAT-AAAAGATGG
1 CGAAAAGTATAAAAAGATGG
46924184 CGAAAAGTATAAAAAGATGG
1 CGAAAAGTATAAAAAGATGG
46924204 AGATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (20 bp):
CGAAAAGTATAAAAAGATGG
Found at i:46924340 original size:13 final size:13
Alignment explanation
Indices: 46924322--46924349 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
46924312 AAAAAAGTCT
46924322 ATTTATAGGTTAA
1 ATTTATAGGTTAA
46924335 ATTTATAGGTTAA
1 ATTTATAGGTTAA
46924348 AT
1 AT
46924350 AATAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.46
Consensus pattern (13 bp):
ATTTATAGGTTAA
Found at i:46925566 original size:23 final size:23
Alignment explanation
Indices: 46925532--46925582 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
46925522 CCATGTGCCA
*
46925532 TGTAATATCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
46925555 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
46925578 AGTAA
1 TGTAA
46925583 GAAAGTAGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.10, T:0.27
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:46925965 original size:2 final size:2
Alignment explanation
Indices: 46925958--46925986 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46925948 ATGGTCAAAT
46925958 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 A
46925987 ATTCTAGAAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:46937107 original size:54 final size:54
Alignment explanation
Indices: 46937025--46937127 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
46937015 AACCTTATTT
* * *
46937025 CAAAAAACACCATTGTTCAAGAGGAAGCTACTGTTCAGGGGGAAACTATAGTTC
1 CAAAAAACACCATTATTCAAGAGGAAGCTACTGCTCAAGGGGAAACTATAGTTC
*
46937079 CAAAAAACACCATTATTCAATG-GGAAGCTACTGCTCAAGGGGAGACTAT
1 CAAAAAACACCATTATTCAA-GAGGAAGCTACTGCTCAAGGGGAAACTAT
46937128 TATTTAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 43 0.98
55 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.21
Consensus pattern (54 bp):
CAAAAAACACCATTATTCAAGAGGAAGCTACTGCTCAAGGGGAAACTATAGTTC
Found at i:46940069 original size:5 final size:5
Alignment explanation
Indices: 46940059--46940156 Score: 187
Period size: 5 Copynumber: 19.6 Consensus size: 5
46940049 ATGTTTTAAA
*
46940059 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TGTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
46940109 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT
46940157 TATGTAAAAA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 91 1.00
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:46940331 original size:19 final size:20
Alignment explanation
Indices: 46940300--46940343 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
46940290 TTATATTATT
*
46940300 AGAAAAAAGCAAATG-AAAA
1 AGAAAAAAGCAAAAGCAAAA
46940319 AGAAAGAAA-CAAAAGCAAAA
1 AGAAA-AAAGCAAAAGCAAAA
46940339 AGAAA
1 AGAAA
46940344 CAGAAAGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (20 bp):
AGAAAAAAGCAAAAGCAAAA
Found at i:46940352 original size:17 final size:17
Alignment explanation
Indices: 46940321--46940366 Score: 76
Period size: 17 Copynumber: 2.8 Consensus size: 17
46940311 AATGAAAAAG
46940321 AAAGAAACA-AAAGCAA
1 AAAGAAACAGAAAGCAA
46940337 AAAGAAACAGAAAGCAA
1 AAAGAAACAGAAAGCAA
*
46940354 AACGAAACAGAAA
1 AAAGAAACAGAAA
46940367 AGGAAGGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
16 9 0.32
17 19 0.68
ACGTcount: A:0.72, C:0.13, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAACAGAAAGCAA
Found at i:46940366 original size:23 final size:22
Alignment explanation
Indices: 46940315--46940355 Score: 59
Period size: 20 Copynumber: 1.9 Consensus size: 22
46940305 AAAGCAAATG
46940315 AAAAAG-AA-AGAAACAAAAGC
1 AAAAAGAAACAGAAACAAAAGC
46940335 AAAAAGAAACAGAAAGCAAAA
1 AAAAAGAAACAGAAA-CAAAA
46940356 CGAAACAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 5 0.28
23 5 0.28
ACGTcount: A:0.76, C:0.10, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAACAGAAACAAAAGC
Found at i:46941521 original size:21 final size:21
Alignment explanation
Indices: 46941448--46941555 Score: 128
Period size: 23 Copynumber: 5.0 Consensus size: 21
46941438 GGCTTTGCCG
*
46941448 ATCAGGCACTTTATGTATCGT
1 ATCAGGCACTTTATGTGTCGT
46941469 ACATCAGGCACTTTATGTGTCGT
1 --ATCAGGCACTTTATGTGTCGT
46941492 ATCTCAGGCACTTTATGTGTCGT
1 A--TCAGGCACTTTATGTGTCGT
* **
46941515 ATCAGGCACCTCGTGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
*
46941536 TTCAGGCAC-TTATGTGTCGT
1 ATCAGGCACTTTATGTGTCGT
46941556 TTACTGATCA
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
20 9 0.12
21 26 0.34
23 41 0.54
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (21 bp):
ATCAGGCACTTTATGTGTCGT
Found at i:46944186 original size:15 final size:15
Alignment explanation
Indices: 46944161--46944208 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
46944151 AAGGTTGTAG
* *
46944161 TAATAATAATAATGA
1 TAATGATAATAATAA
*
46944176 TGATGATAATAATAA
1 TAATGATAATAATAA
*
46944191 TAATGATAATAATTA
1 TAATGATAATAATAA
46944206 TAA
1 TAA
46944209 AAAAAACAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (15 bp):
TAATGATAATAATAA
Found at i:46944228 original size:3 final size:3
Alignment explanation
Indices: 46944161--46944208 Score: 51
Period size: 3 Copynumber: 16.0 Consensus size: 3
46944151 AAGGTTGTAG
* * * * *
46944161 TAA TAA TAA TAA TGA TGA TGA TAA TAA TAA TAA TGA TAA TAA TTA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
46944209 AAAAAACAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.35
Consensus pattern (3 bp):
TAA
Done.