Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009344.1 Hibiscus syriacus cultivar Beakdansim tig00113124_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4287485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 24
Found at i:844654 original size:22 final size:22
Alignment explanation
Indices: 844605--844653 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
844595 ATAAATTATT
**
844605 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
*
844627 TAAAATAAATCAATCCGTACTAA
1 TAAAATAAATCAATCCATA-TAA
844650 TAAA
1 TAAA
844654 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:844683 original size:22 final size:22
Alignment explanation
Indices: 844657--844699 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
844647 TAATAAATTA
844657 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
844679 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
844700 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:844708 original size:22 final size:22
Alignment explanation
Indices: 844659--844707 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
844649 ATAAATTATT
**
844659 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
844681 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
844704 TAAA
1 TAAA
844708 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:844788 original size:22 final size:23
Alignment explanation
Indices: 844713--844787 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 23
844703 ATAAATTATT
844713 TAAAATAAATCAATCCATAC-AA
1 TAAAATAAATCAATCCATACTAA
**
844735 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCCATACTAA
844761 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATACTAA
844784 TAAA
1 TAAA
844788 TTATTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 16 0.37
23 8 0.19
25 3 0.07
26 16 0.37
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (23 bp):
TAAAATAAATCAATCCATACTAA
Found at i:844817 original size:18 final size:18
Alignment explanation
Indices: 844764--844820 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
844754 CATATTTTAA
*
844764 AATAAATCAATCCATACT
1 AATAAATCAATTCATACT
* *
844782 AATAAAT-TATT--TA-A
1 AATAAATCAATTCATACT
844796 AATAAATCAATTCATACT
1 AATAAATCAATTCATACT
844814 AATAAAT
1 AATAAAT
844821 TATTTTAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 7 0.23
15 5 0.17
17 4 0.13
18 14 0.47
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.33
Consensus pattern (18 bp):
AATAAATCAATTCATACT
Found at i:844828 original size:65 final size:62
Alignment explanation
Indices: 844756--844897 Score: 196
Period size: 65 Copynumber: 2.2 Consensus size: 62
844746 AATCAATCCA
844756 TATTTTAAAATAAATCAATCCATA-CTAATAAATTATTTAAAATAAATCAATTCATACTAATAAA
1 TATTTTAAAATAAATCAATCCATATCTAATAAATTATTTAAAATAAAT--ATT-ATA-TAATAAA
844820 T
62 T
* * * * *
844821 TATTTTAAAATAAATCAATCCATATTTTATAATTTATTTAAAGTAAATATTTTATAATAAAT
1 TATTTTAAAATAAATCAATCCATATCTAATAAATTATTTAAAATAAATATTATATAATAAAT
844883 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
844898 TATTTTAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
62 23 0.32
63 2 0.03
64 3 0.04
65 24 0.34
66 19 0.27
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (62 bp):
TATTTTAAAATAAATCAATCCATATCTAATAAATTATTTAAAATAAATATTATATAATAAAT
Found at i:844833 original size:33 final size:33
Alignment explanation
Indices: 844756--844897 Score: 170
Period size: 33 Copynumber: 4.5 Consensus size: 33
844746 AATCAATCCA
844756 TATTTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAAT
*
844789 TA-TTTAAAATAAATCAATTCATACTAATAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAAT
* * *
844821 TATTTTAAAATAAATCAATCCATATTTTATAATT
1 TATTTTAAAATAAATCAATCCATA-CTAATAAAT
* **
844855 TA-TTTAAAGTAAAT--AT-TTTA-TAATAAAT
1 TATTTTAAAATAAATCAATCCATACTAATAAAT
844883 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
844898 TATTTTAAAA
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
28 8 0.08
29 11 0.12
30 2 0.02
31 2 0.02
32 31 0.33
33 33 0.35
34 8 0.08
ACGTcount: A:0.50, C:0.07, G:0.01, T:0.42
Consensus pattern (33 bp):
TATTTTAAAATAAATCAATCCATACTAATAAAT
Found at i:844888 original size:15 final size:15
Alignment explanation
Indices: 844857--844912 Score: 87
Period size: 15 Copynumber: 3.8 Consensus size: 15
844847 TTATAATTTA
*
844857 TTTAAAGTAAA-TAT
1 TTTAAAATAAATTAT
*
844871 TTTATAATAAATTAT
1 TTTAAAATAAATTAT
844886 TTTAAAATAAATTAT
1 TTTAAAATAAATTAT
844901 TTTAAAATAAAT
1 TTTAAAATAAAT
844913 AACCTTATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
14 9 0.24
15 29 0.76
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
TTTAAAATAAATTAT
Found at i:850638 original size:18 final size:18
Alignment explanation
Indices: 850615--850712 Score: 97
Period size: 18 Copynumber: 5.9 Consensus size: 18
850605 GCGTAGAATT
850615 TGTCCCGTAGGACCACTA
1 TGTCCCGTAGGACCACTA
850633 TGTCCCGTAGGACCACTA
1 TGTCCCGTAGGACCACTA
850651 TGTCCCGTAGG------A
1 TGTCCCGTAGGACCACTA
* *
850663 --TCACGTA-GAACACATA
1 TGTCCCGTAGGACCAC-TA
850679 TGTCCCGTAGGACCACTA
1 TGTCCCGTAGGACCACTA
*
850697 TGTCCCATAGGACCAC
1 TGTCCCGTAGGACCAC
850713 GTAGAACCCT
Statistics
Matches: 66, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
9 1 0.02
10 6 0.09
12 1 0.02
16 1 0.02
18 52 0.79
19 5 0.08
ACGTcount: A:0.26, C:0.32, G:0.21, T:0.21
Consensus pattern (18 bp):
TGTCCCGTAGGACCACTA
Found at i:850681 original size:46 final size:46
Alignment explanation
Indices: 850631--850719 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
850621 GTAGGACCAC
* *
850631 TATGTCCCGTAGGACCACTATGTCCCGTAGGATCACGTAGAACACA
1 TATGTCCCGTAGGACCACTATGTCCCATAGGACCACGTAGAACACA
850677 TATGTCCCGTAGGACCACTATGTCCCATAGGACCACGTAGAAC
1 TATGTCCCGTAGGACCACTATGTCCCATAGGACCACGTAGAAC
850720 CCTCGACTCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
TATGTCCCGTAGGACCACTATGTCCCATAGGACCACGTAGAACACA
Found at i:851137 original size:4 final size:4
Alignment explanation
Indices: 851128--851154 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
851118 AACCTATTGT
851128 CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CAT
851155 TTAGCACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (4 bp):
CATA
Found at i:851193 original size:25 final size:25
Alignment explanation
Indices: 851164--851213 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
851154 TTTAGCACCA
*
851164 TATCACTACATGTTTATGCTTCAGT
1 TATCACTACATGTTTACGCTTCAGT
*
851189 TATCACTATATGTTTACGCTTCAGT
1 TATCACTACATGTTTACGCTTCAGT
851214 ACCCTTGATC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (25 bp):
TATCACTACATGTTTACGCTTCAGT
Found at i:853054 original size:28 final size:28
Alignment explanation
Indices: 853022--853078 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
853012 TCATTGTTTC
*** *
853022 TTTCAAGTACTGGTTCGACGATATAATG
1 TTTCAAGTACTAACTCGACGAAATAATG
853050 TTTCAAGTACTAACTCGACGAAATAATG
1 TTTCAAGTACTAACTCGACGAAATAATG
853078 T
1 T
853079 AAATAGAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (28 bp):
TTTCAAGTACTAACTCGACGAAATAATG
Found at i:857249 original size:14 final size:14
Alignment explanation
Indices: 857230--857256 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
857220 GTTCGGTTAT
857230 GTTCATTTATGTTC
1 GTTCATTTATGTTC
857244 GTTCATTTATGTT
1 GTTCATTTATGTT
857257 TAACCTAATC
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:0.15, C:0.11, G:0.15, T:0.59
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:858353 original size:10 final size:10
Alignment explanation
Indices: 858320--858358 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
858310 GGGTCTTCAA
858320 CGTTTATGTT
1 CGTTTATGTT
*
858330 CGTGTTCGTGTT
1 CGT-TT-ATGTT
858342 CGTTTATGTT
1 CGTTTATGTT
858352 CGTTTAT
1 CGTTTAT
858359 TTATTAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 14 0.56
11 4 0.16
12 7 0.28
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:858386 original size:18 final size:18
Alignment explanation
Indices: 858363--858398 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
858353 GTTTATTTAT
858363 TAAATGAACGAACATGAA
1 TAAATGAACGAACATGAA
858381 TAAATGAACGAACATGAA
1 TAAATGAACGAACATGAA
858399 CAAGCTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.17
Consensus pattern (18 bp):
TAAATGAACGAACATGAA
Found at i:861503 original size:62 final size:63
Alignment explanation
Indices: 861388--861516 Score: 179
Period size: 62 Copynumber: 2.1 Consensus size: 63
861378 CAATGCTTAG
* ** * *
861388 AAACTCACCAAAACATGAAAAATCTCAACTTTTTTCAAGCAAGATAGAGCAAACAATTTACAA
1 AAACTCACCAAAACATAAAAAATCTCAACAATTTTCAAGCAAAATAGAGCAAACAAGTTACAA
* * *
861451 AAACTCACCAAAACATAAAAAATCTCAA-AATTTTCAAGCAAAATGGATCAAACAAGTTCCAA
1 AAACTCACCAAAACATAAAAAATCTCAACAATTTTCAAGCAAAATAGAGCAAACAAGTTACAA
861513 AAAC
1 AAAC
861517 CCAAACTTCA
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
62 31 0.53
63 27 0.47
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.20
Consensus pattern (63 bp):
AAACTCACCAAAACATAAAAAATCTCAACAATTTTCAAGCAAAATAGAGCAAACAAGTTACAA
Found at i:862153 original size:15 final size:17
Alignment explanation
Indices: 862116--862151 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
862106 TTATGAGATG
*
862116 AAAATATTATTATTGTA
1 AAAATATAATTATTGTA
862133 AAAATATAATTATT-TA
1 AAAATATAATTATTGTA
862149 AAA
1 AAA
862152 TAATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (17 bp):
AAAATATAATTATTGTA
Found at i:867756 original size:19 final size:18
Alignment explanation
Indices: 867732--867793 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
867722 TGAACATGGC
867732 ATTTTATGACTTAAGTTCA
1 ATTTTATGACTT-AGTTCA
867751 ATTTTAT--C--A--TCA
1 ATTTTATGACTTAGTTCA
*
867763 ATTATATGACTTGAGTTCA
1 ATTTTATGACTT-AGTTCA
867782 ATTTTATGACTT
1 ATTTTATGACTT
867794 CTTCTGCTGA
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
12 9 0.26
14 2 0.06
17 2 0.06
19 21 0.62
ACGTcount: A:0.31, C:0.11, G:0.10, T:0.48
Consensus pattern (18 bp):
ATTTTATGACTTAGTTCA
Found at i:871331 original size:20 final size:20
Alignment explanation
Indices: 871303--871342 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
871293 ATTTAAATGA
* *
871303 TAAAAGAACATAATCGAACG
1 TAAAAGAACACAAACGAACG
*
871323 TAAACGAACACAAACGAACG
1 TAAAAGAACACAAACGAACG
871343 AACATAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
TAAAAGAACACAAACGAACG
Found at i:871366 original size:23 final size:23
Alignment explanation
Indices: 871339--871392 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
871329 AACACAAACG
* * *
871339 AACGAACATAATAAATTAACATA
1 AACGAACACAAAAAACTAACATA
871362 AACGAACACAAAAAACTAACATA
1 AACGAACACAAAAAACTAACATA
871385 AACGAACA
1 AACGAACA
871393 ACACAAATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.63, C:0.19, G:0.06, T:0.13
Consensus pattern (23 bp):
AACGAACACAAAAAACTAACATA
Found at i:871423 original size:32 final size:32
Alignment explanation
Indices: 871369--871432 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
871359 ATAAACGAAC
*
871369 ACAAAAAACTAACATAAACGAACA-ACACAAAT
1 ACAAAAAACAAACATAAACGAACACA-ACAAAT
* **
871401 ACAAAAAACAAACTTATTCGAACACAACAAAT
1 ACAAAAAACAAACATAAACGAACACAACAAAT
871433 GAATGTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 26 0.96
33 1 0.04
ACGTcount: A:0.62, C:0.22, G:0.03, T:0.12
Consensus pattern (32 bp):
ACAAAAAACAAACATAAACGAACACAACAAAT
Found at i:872991 original size:20 final size:20
Alignment explanation
Indices: 872968--873057 Score: 153
Period size: 20 Copynumber: 4.5 Consensus size: 20
872958 GTCTGTGCGG
*
872968 TGCAGACGTGGCCTTATGTC
1 TGCAGACGTCGCCTTATGTC
*
872988 TGCAGACGTCGTCTTATGTC
1 TGCAGACGTCGCCTTATGTC
*
873008 TGCAGACGTCGTCTTATGTC
1 TGCAGACGTCGCCTTATGTC
873028 TGCAGACGTCGCCTTATGTC
1 TGCAGACGTCGCCTTATGTC
873048 TGCAGACGTC
1 TGCAGACGTC
873058 TTCTAACCTC
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 67 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.31
Consensus pattern (20 bp):
TGCAGACGTCGCCTTATGTC
Found at i:873151 original size:25 final size:24
Alignment explanation
Indices: 873116--873207 Score: 114
Period size: 24 Copynumber: 3.7 Consensus size: 24
873106 TTTTAATTTT
873116 AATA-TAATTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
*
873139 AATATTAATTTTTTAATATTATATTATA
1 AATATTAATTTTTTAA-A-TA-AAT-TA
*
873167 AATATTAATTTTTTTAAACAAATTA
1 AATATTAA-TTTTTTAAATAAATTA
873192 AATATTAATTTTTTAA
1 AATATTAATTTTTTAA
873208 TATTATATTA
Statistics
Matches: 60, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
23 4 0.07
24 19 0.32
25 11 0.18
26 4 0.07
27 3 0.05
28 11 0.18
29 8 0.13
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:873158 original size:14 final size:14
Alignment explanation
Indices: 873112--873180 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
873102 TTGATTTTAA
873112 TTTTAATA-TAATT
1 TTTTAATATTAATT
873125 TTTTAA-A-TAA--
1 TTTTAATATTAATT
* *
873135 ATTAAATATTAATT
1 TTTTAATATTAATT
873149 TTTTAATATT-ATAT
1 TTTTAATATTAAT-T
* *
873163 TATAAATATTAATT
1 TTTTAATATTAATT
873177 TTTT
1 TTTT
873181 TAAACAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
10 4 0.10
11 1 0.02
12 7 0.17
13 8 0.19
14 20 0.48
15 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TTTTAATATTAATT
Found at i:873172 original size:28 final size:28
Alignment explanation
Indices: 873137--873232 Score: 119
Period size: 28 Copynumber: 3.5 Consensus size: 28
873127 TTAAATAAAT
873137 TAAATATTAATTTTTTAATATTATATTA
1 TAAATATTAATTTTTTAATATTATATTA
* *
873165 TAAATATTAATTTTTTTAA-A-CA-AAT-
1 TAAATATTAA-TTTTTTAATATTATATTA
873190 TAAATATTAATTTTTTAATATTATATTA
1 TAAATATTAATTTTTTAATATTATATTA
*
873218 TAGATATTTAATTTT
1 TAAATA-TTAATTTT
873233 ATATCATATA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
24 8 0.14
25 11 0.19
26 3 0.05
27 3 0.05
28 16 0.28
29 16 0.28
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
TAAATATTAATTTTTTAATATTATATTA
Found at i:873190 original size:53 final size:53
Alignment explanation
Indices: 873116--873232 Score: 193
Period size: 53 Copynumber: 2.2 Consensus size: 53
873106 TTTTAATTTT
*
873116 AATA-TAA-TTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATA
1 AATATTAATTTTTTTAAACAAATTAAATATTAATTTTTTAATATTATATTATA
873167 AATATTAATTTTTTTAAACAAATTAAATATTAATTTTTTAATATTATATTATA
1 AATATTAATTTTTTTAAACAAATTAAATATTAATTTTTTAATATTATATTATA
*
873220 GATATTTAATTTT
1 AATA-TTAATTTT
873233 ATATCATATA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 4 0.07
52 3 0.05
53 46 0.75
54 8 0.13
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (53 bp):
AATATTAATTTTTTTAAACAAATTAAATATTAATTTTTTAATATTATATTATA
Found at i:873268 original size:16 final size:17
Alignment explanation
Indices: 873227--873272 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 17
873217 ATAGATATTT
*
873227 AATTTTATATCATATAA
1 AATTTTATATTATATAA
873244 ATTATTTTATATTAT-TAA
1 A--ATTTTATATTATATAA
873262 AATTTTATATT
1 AATTTTATATT
873273 TATTTTAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 4 0.15
19 11 0.42
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTTATATTATATAA
Found at i:876579 original size:315 final size:315
Alignment explanation
Indices: 875992--876628 Score: 961
Period size: 315 Copynumber: 2.0 Consensus size: 315
875982 TACTCATGTT
* * *
875992 TTCAGCAGACAATGCTTGTTCCTTTTTGAACAAATCTTCTAACGAAGTAACTTTGGAAATTAAAA
1 TTCAGCAGAAAATGCTTGTTCCTTTCTGAACAAATCCTCTAACGAAGTAACTTTGGAAATTAAAA
* * ** * * * * * * *
876057 TATTTATTTCAGTTTCTGCCTCTGTAAGTCTTGATTCTGCCTCTTGTCTATTCATGTTTGCAATT
66 TATTTATTTCAATTTCAGAATCTCTAAGTCTTGATACCGCCACTTCTCTATTCACGTTTGCAACT
*
876122 TTTACTTCCTCCTCTAAGGCTTTTTTTGAGTTGTCAGCAAGAGCTAATTGAGTTTGCACATCTTT
131 TTTACTTCCTCCTCTAAGGCTTTCTTTGAGTTGTCAGCAAGAGCTAATTGAGTTTGCACATCTTT
*
876187 GAACCTTGTCTCGGCTTCGCTTAGTTGATTCTCCAATGTTTGAAGCTGTTTTTGAGATTCAGTGA
196 GAACCTTGTCTCAGCTTCGCTTAGTTGATTCTCCAATGTTTGAAGCTGTTTTTGAGATTCAGTGA
* * *
876252 AAGCCATCTGCAATTCCGATTTTTCTTCTTCGGTCAGCGCTAGCTTCTCCTCTAG
261 AAGCCATCTGCAATTCCGACTTTTCTTCTTCGGACAGCACTAGCTTCTCCTCTAG
* * * ** * *
876307 TTCAGCTGAAAATGTTTGTTCCTTTCTGATCACTTCCTCTAATGAAGTAACTTTGGAAATTAAAG
1 TTCAGCAGAAAATGCTTGTTCCTTTCTGAACAAATCCTCTAACGAAGTAACTTTGGAAATTAAAA
*
876372 TCTTTATTTCAATTTCAGAATCTCTAAGTCTTGATACCGCCACTTCTCTATTCACGTTTGCAACT
66 TATTTATTTCAATTTCAGAATCTCTAAGTCTTGATACCGCCACTTCTCTATTCACGTTTGCAACT
* *
876437 TTTACTTCCTCCTCTACGGAC-TTCTTTGAGTTGTCATCAAGAGCTAATTGAGTTTGCACATCTT
131 TTTACTTCCTCCTCTAAGG-CTTTCTTTGAGTTGTCAGCAAGAGCTAATTGAGTTTGCACATCTT
* * *
876501 TGAACTTTGTCTCAGCTTCGCTTAGTTGATTCTGCAATGTTTGAAGCTGTTTTTGAGATTCGGTG
195 TGAACCTTGTCTCAGCTTCGCTTAGTTGATTCTCCAATGTTTGAAGCTGTTTTTGAGATTCAGTG
876566 AAAGCCATCTGCAATTCCGACTTTTCTTCTTCGGACAGCACTAGCTTCTCCTCTAG
260 AAAGCCATCTGCAATTCCGACTTTTCTTCTTCGGACAGCACTAGCTTCTCCTCTAG
*
876622 TTGAGCA
1 TTCAGCA
876629 ATCCCGCGTG
Statistics
Matches: 287, Mismatches: 34, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
315 286 1.00
316 1 0.00
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.40
Consensus pattern (315 bp):
TTCAGCAGAAAATGCTTGTTCCTTTCTGAACAAATCCTCTAACGAAGTAACTTTGGAAATTAAAA
TATTTATTTCAATTTCAGAATCTCTAAGTCTTGATACCGCCACTTCTCTATTCACGTTTGCAACT
TTTACTTCCTCCTCTAAGGCTTTCTTTGAGTTGTCAGCAAGAGCTAATTGAGTTTGCACATCTTT
GAACCTTGTCTCAGCTTCGCTTAGTTGATTCTCCAATGTTTGAAGCTGTTTTTGAGATTCAGTGA
AAGCCATCTGCAATTCCGACTTTTCTTCTTCGGACAGCACTAGCTTCTCCTCTAG
Found at i:884545 original size:18 final size:18
Alignment explanation
Indices: 884522--884558 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
884512 ATCTACACCT
884522 GAAGTTGAATACATGACA
1 GAAGTTGAATACATGACA
884540 GAAGTTGAATACATGACA
1 GAAGTTGAATACATGACA
884558 G
1 G
884559 TAGCTGAAGC
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:0.43, C:0.11, G:0.24, T:0.22
Consensus pattern (18 bp):
GAAGTTGAATACATGACA
Found at i:884566 original size:18 final size:18
Alignment explanation
Indices: 884522--884566 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
884512 ATCTACACCT
*
884522 GAAGTTGAATACATGACA
1 GAAGCTGAATACATGACA
*
884540 GAAGTTGAATACATGACA
1 GAAGCTGAATACATGACA
*
884558 GTAGCTGAA
1 GAAGCTGAA
884567 GCTGCAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.42, C:0.11, G:0.24, T:0.22
Consensus pattern (18 bp):
GAAGCTGAATACATGACA
Found at i:885538 original size:20 final size:20
Alignment explanation
Indices: 885515--885566 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
885505 AACGCGATCC
885515 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
885535 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
885555 CCAAAATCGCAA
1 CCAGAATCGCAA
885567 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:885683 original size:20 final size:20
Alignment explanation
Indices: 885622--885812 Score: 201
Period size: 20 Copynumber: 9.6 Consensus size: 20
885612 GATTTTCCAT
* ** *
885622 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
885642 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
885662 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
885682 AATCGTAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
885702 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
885722 AATCGCAATGCGTATCCGT-
1 AATCGCAACGCGTATCCGTA
885741 -ATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
885760 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
885781 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
885801 AATCGCAACGCG
1 AATCGCAACGCG
885813 ATTTTAAAGC
Statistics
Matches: 141, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
18 17 0.12
19 2 0.01
20 104 0.74
21 17 0.12
22 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:885705 original size:60 final size:60
Alignment explanation
Indices: 885622--885812 Score: 233
Period size: 60 Copynumber: 3.2 Consensus size: 60
885612 GATTTTCCAT
* ** * *
885622 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * * *** *
885682 AATCGTAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT-
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
**
885741 -ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
885801 AATCGCAACGCG
1 AATCGCAACGCG
885813 ATTTTAAAGC
Statistics
Matches: 107, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
58 30 0.28
59 19 0.18
60 47 0.44
61 11 0.10
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:885761 original size:78 final size:79
Alignment explanation
Indices: 885663--885808 Score: 215
Period size: 78 Copynumber: 1.9 Consensus size: 79
885653 GAACACATAA
* * * * **
885663 ATCGCAACGCGTATCCGTAAATCGTAACG-TGTATCCGT-AAATCGCAACGCGTATGGGTAAATC
1 ATCGCAACGCGTATCCGTAAATCGCAACGAT-AATACATAAAATCGCAACGCGTATCCGTAAATC
885726 GCAATGCGTATCCGT
65 GCAATGCGTATCCGT
885741 ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCG
1 ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCG
885806 CAA
66 CAA
885809 CGCGATTTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
78 32 0.53
79 28 0.47
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (79 bp):
ATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAATCG
CAATGCGTATCCGT
Found at i:885833 original size:59 final size:59
Alignment explanation
Indices: 885657--885812 Score: 165
Period size: 58 Copynumber: 2.6 Consensus size: 59
885647 CAACGCGAAC
* * * *
885657 ACAT-AAATCGCAACGCGTATCCGTAAATCGTAACGTGTATCCGTAAATCGCAACGCGT-AT
1 ACATAAAATCGCAACGCGTATCCGT--ATCGCAACGCGTATCCGTAAAGCGCAACG-ATAAT
*** * *
885717 GGGT-AAATCGCAATGCGTATCCGTATCGCAACGCGTATCCGTAAATCGCAACGATAAT
1 ACATAAAATCGCAACGCGTATCCGTATCGCAACGCGTATCCGTAAAGCGCAACGATAAT
885775 ACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 ACATAAAATCGCAACGCGTATCCGT--ATCGCAACGCG
885813 ATTTTAAAGC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
57 1 0.01
58 30 0.37
59 19 0.23
60 20 0.25
61 11 0.14
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.21
Consensus pattern (59 bp):
ACATAAAATCGCAACGCGTATCCGTATCGCAACGCGTATCCGTAAAGCGCAACGATAAT
Found at i:886031 original size:23 final size:21
Alignment explanation
Indices: 885996--886037 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
885986 TCCGAGAATA
885996 CATATTATAAATTATAATTAG
1 CATATTATAAATTATAATTAG
*
886017 CATATATATATAATTCTAATT
1 CATAT-TATA-AATTATAATT
886038 TAGTAATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (21 bp):
CATATTATAAATTATAATTAG
Found at i:887066 original size:22 final size:21
Alignment explanation
Indices: 886989--887066 Score: 56
Period size: 22 Copynumber: 3.8 Consensus size: 21
886979 ATTTAAATTC
*
886989 TATATTTATTT-ATTA-TGAA
1 TATATTTATTTAATTATTGTA
* * *
887008 TAT-TTTATTTAGTTATTTTT
1 TATATTTATTTAATTATTGTA
*
887028 TAGTA-TTAGTTATATTATTGTA
1 TA-TATTTATTTA-ATTATTGTA
887050 TACTATTTATTTAATTA
1 TA-TATTTATTTAATTA
887067 GGTGAATGAT
Statistics
Matches: 43, Mismatches: 10, Indels: 9
0.69 0.16 0.15
Matches are distributed among these distances:
18 7 0.16
19 6 0.14
20 3 0.07
21 7 0.16
22 14 0.33
23 6 0.14
ACGTcount: A:0.31, C:0.01, G:0.06, T:0.62
Consensus pattern (21 bp):
TATATTTATTTAATTATTGTA
Found at i:889832 original size:23 final size:23
Alignment explanation
Indices: 889797--889854 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
889787 AATTATCCCG
*
889797 AATGACCATATAGGTTTACACAGA
1 AATG-CCACATAGGTTTACACAGA
* *
889821 AATGCCACATAGGTTTGCACCGA
1 AATGCCACATAGGTTTACACAGA
*
889844 AGTGCCACATA
1 AATGCCACATA
889855 TTTATCCCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (23 bp):
AATGCCACATAGGTTTACACAGA
Found at i:889872 original size:21 final size:21
Alignment explanation
Indices: 889840--889918 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
889830 TAGGTTTGCA
*
889840 CCGAAGTG-CCACATATTTATC
1 CCGAAG-GACCACATAATTATC
* *
889861 CCGAATGACCACATAATTGTC
1 CCGAAGGACCACATAATTATC
* *
889882 CCGAAGGACAATATAATTATC
1 CCGAAGGACCACATAATTATC
889903 CCGAAGGACCACATAA
1 CCGAAGGACCACATAA
889919 GACCCTCGAC
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
20 1 0.02
21 47 0.98
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.22
Consensus pattern (21 bp):
CCGAAGGACCACATAATTATC
Found at i:917118 original size:316 final size:319
Alignment explanation
Indices: 916505--917139 Score: 1069
Period size: 316 Copynumber: 2.0 Consensus size: 319
916495 GTTGAGTGAT
*
916505 TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTGGTCACTGG
1 TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTAGTCACTGG
916570 TATAATTTACCCTTTATTTTAAATAATTTACTTTTAAATTTTTTTAACTAATTTATAATTTTATA
66 TATAATTTACCCTTTATTTTAAATAATTTACTTTTAAATTTTTTTAACTAATTTATAATTTTATA
* *
916635 TGTTGGGCTCTTTAAAATTTAAATTTTTATAAATTGGTGTTCATCGTTAATAGTGTTGGTCGAGT
131 TGTTGGGCTCTTT--AA--TAAATTTTTATAAATTGATGTTCATCGTTAATAGTGTTCGTCGAGT
*
916700 ACCATAGAATTTTCCTAAAGAAAATCATAGTAAGATCTAAATATTACTAAAATTCCATATTAGCC
192 ACCATAGAATTTTCCTAAAGAAAATCACAGTAAGATCTAAATATTACTAAAATTCCATATTAGCC
916765 GACCAACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTATAGAATTGAC
257 GACCAACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTATAGAATTGAC
* * * *
916828 TTGATTGATAAAATTTCAAAAATTATGGTCAAAATGAAAAGAGATAATAGTTAGGTAGTCATTGG
1 TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTAGTCACTGG
* * *
916893 TATAGTTTACCCTTTATTTTAAATAATTTACTTTTTATTTTTTTTAACTAATTTATAATTTTATA
66 TATAATTTACCCTTTATTTTAAATAATTTACTTTTAAATTTTTTTAACTAATTTATAATTTTATA
* *
916958 TGTTGGGCTCTTT-A-AAA-TTTTATAAATTGATGTTCATCGTTAATGGTGTTCGTCGAGTACCG
131 TGTTGGGCTCTTTAATAAATTTTTATAAATTGATGTTCATCGTTAATAGTGTTCGTCGAGTACCA
*
917020 TAGAATTTTCCTAAAGAAAATCACAGTAAGATCTTAATATTACTAAAATTCCATATTAGCCGACC
196 TAGAATTTTCCTAAAGAAAATCACAGTAAGATCTAAATATTACTAAAATTCCATATTAGCCGACC
* *
917085 AACTGTAGTAAAAAAGGTATTCGTTATCCAAATGTAAAAGAAATCATTATAGAAT
261 AACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTATAGAAT
917140 AAAAGATATC
Statistics
Matches: 296, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
316 157 0.53
317 3 0.01
320 1 0.00
323 135 0.46
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (319 bp):
TTGATTGATAAAATTTAAAAAATGATGGTCAAAATGAAAAGAGACAATAGTTAGGTAGTCACTGG
TATAATTTACCCTTTATTTTAAATAATTTACTTTTAAATTTTTTTAACTAATTTATAATTTTATA
TGTTGGGCTCTTTAATAAATTTTTATAAATTGATGTTCATCGTTAATAGTGTTCGTCGAGTACCA
TAGAATTTTCCTAAAGAAAATCACAGTAAGATCTAAATATTACTAAAATTCCATATTAGCCGACC
AACTATAGTAAAAAAAGTATTCGTTATCCAAATGTAAAAGAAATCATTATAGAATTGAC
Found at i:920819 original size:5 final size:5
Alignment explanation
Indices: 920804--920839 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
920794 GCAATTTTCG
*
920804 TAAAGA TAAAA TAAAA TAAAA TAAAA CAAAA TAAAA
1 TAAA-A TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
920840 GTGCAAAAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:921435 original size:33 final size:32
Alignment explanation
Indices: 921398--921484 Score: 86
Period size: 36 Copynumber: 2.6 Consensus size: 32
921388 TTAATTTGTG
921398 CAATAAAATAAAATGTTAGTAAATTAGTAAGAA
1 CAATAAAATAAAA-GTTAGTAAATTAGTAAGAA
** *
921431 CAATAAAAATAAAA-AAAGTCAATATGTTAGTATGAA
1 CAAT-AAAATAAAAGTTAGT-AA-A--TTAGTAAGAA
921467 CAATAAAATAAAAGTTAG
1 CAATAAAATAAAAGTTAG
921485 AATGTTAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
32 3 0.07
33 6 0.14
34 10 0.23
35 9 0.21
36 15 0.35
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGTAAATTAGTAAGAA
Found at i:921490 original size:32 final size:32
Alignment explanation
Indices: 921398--921496 Score: 94
Period size: 32 Copynumber: 2.9 Consensus size: 32
921388 TTAATTTGTG
*
921398 CAATAAAATAAAATGTTAGTAA-ATTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTAAGAA
* *
921431 CAATAAAAATAAAAAAAGTCA-ATATGTTAGTATGAA
1 CAAT-AAAAT---AAAAGTTAGA-ATGTTAGTAAGAA
921467 CAATAAAATAAAAGTTAGAATGTTAGTAAG
1 CAATAAAATAAAAGTTAGAATGTTAGTAAG
921497 TTAGAAAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
32 17 0.31
33 5 0.09
34 6 0.11
35 6 0.11
36 16 0.30
37 4 0.07
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTAAGAA
Found at i:923041 original size:198 final size:201
Alignment explanation
Indices: 922627--923130 Score: 646
Period size: 208 Copynumber: 2.5 Consensus size: 201
922617 TGGAGATAAT
* * *
922627 TTGATGTTAAAGACGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTTAGGTGAATTGTT
1 TTGATGTTGAAGA-GACGCTGCTCATCCGTATTGAAGAGATCTGGTCATTTTCAGGTGAATTGTT
* * * *
922692 TGTTGAAGATGGCGATATTCCTTCGCATTGAGGAAAGCGGGTCTATCTGGAGATAATTTGGAGGC
65 TGTTGAAGATGACGTTATTCCTTCGCATTGAGGAAAGCAGGTCAATCTGGAGATAA-TT-GAGGC
* *
922757 AATACGGTTCATTCGTGTTGAGGAAGTCTGATTGTCTTACGATGACGCTACTCCTTCGTGTTGAG
128 -ATAC-G--CATTCGTGTTGAGGAAGTCTGATTGTCTTACGATGACGCTACTCCTTCGTGTTAAA
*
922822 GAGATCGGGTCAA
189 GAGATCAGGTCAA
922835 TTGATGTTGAAGATGACGCTGCTCATCCGTATTGAAGAGATCTGGTCATTTTCAGGTGAATTGTT
1 TTGATGTTGAAGA-GACGCTGCTCATCCGTATTGAAGAGATCTGGTCATTTTCAGGTGAATTGTT
* * * * *
922900 TGTTGAAGATGACGTTGTTCCTTTGCGTTTGGGGAAATCAGGTCAATCTGGAGATAA-T-ACGGC
65 TGTTGAAGATGACGTTATTCCTTCGC-ATTGAGGAAAGCAGGTCAATCTGGAGATAATTGA-GGC
* * *
922963 -T-C-C-TTCGTGTTGAGGAAGTCTGATTGTCTTAGGATGACGCTGCTTCTTCGTGTTAAAGAGA
128 ATACGCATTCGTGTTGAGGAAGTCTGATTGTCTTACGATGACGCTACTCCTTCGTGTTAAAGAGA
923024 TCAGGTCAA
193 TCAGGTCAA
* *
923033 TTGATGTTG-A-AGACGCTGCTCATTCGTATTGAAGAGATCTGGTCATTTTCAGGTAAATTGTTT
1 TTGATGTTGAAGAGACGCTGCTCATCCGTATTGAAGAGATCTGGTCATTTTCAGGTGAATTGTTT
* * * *
923096 GTTGAAGATGACATTATTCCTCCACGTTGAGGAAA
66 GTTGAAGATGACGTTATTCCTTCGCATTGAGGAAA
923131 TCGAGTCCAT
Statistics
Matches: 266, Mismatches: 28, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
194 8 0.03
195 70 0.26
196 1 0.00
197 1 0.00
198 70 0.26
199 1 0.00
203 1 0.00
204 1 0.00
205 1 0.00
206 3 0.01
207 1 0.00
208 83 0.31
209 25 0.09
ACGTcount: A:0.24, C:0.15, G:0.27, T:0.34
Consensus pattern (201 bp):
TTGATGTTGAAGAGACGCTGCTCATCCGTATTGAAGAGATCTGGTCATTTTCAGGTGAATTGTTT
GTTGAAGATGACGTTATTCCTTCGCATTGAGGAAAGCAGGTCAATCTGGAGATAATTGAGGCATA
CGCATTCGTGTTGAGGAAGTCTGATTGTCTTACGATGACGCTACTCCTTCGTGTTAAAGAGATCA
GGTCAA
Found at i:923392 original size:403 final size:399
Alignment explanation
Indices: 922624--923479 Score: 953
Period size: 403 Copynumber: 2.1 Consensus size: 399
922614 ATTTGGAGAT
* * * *
922624 AATTTGATGTTAAAGACGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTTAGGTGAATT
1 AATTTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATT
* * * * * * *
922689 GTTTGTTGAAGATGGCGATATTCCTTCGCATTGAGGAAAGCGGGTCTATCTGGAGATAATTTGGA
66 GTTTGTTGAAGATGACGATATTCCTCCACATTGAGGAAAGCGAGTCCATCAGAAGATAATTTGGA
* * * * *
922754 GGCAATACGGTTCATTCGTGTTGAGGAAGTCTGATTGTCTTACGATGACGCTACTCCTTCGTGTT
131 GCCAATACGATTCATTCGTATTGAAGAAGTCTGATTGTCTTACGATGACACTACTCCTTCGTGTT
*** *
922819 GAGGAGATCGGGTCAATTGATGTTGAAGATGACGCTGCTCATCCGTATTGAAGAGATCTGGTCAT
196 GAGGAGATCCAATCAATTGATGTTGAAGATGACACTGCTCATCCGTATTGAAGAGATCTGGTCAT
*** * * *
922884 TTTCAGGTGAATTGTTTGTTGAAGATGACGTTGTTCCTTTGCGTTTGGGGAAATCAGGTCAATCT
261 TTT---GTGAA-T-TAAATT--A-ATGACGTTGTTCCTTCGCGTTTGAGGAAATCAGGTCAATCA
* * * * *
922949 GGAGATAATACGGCTCCTTCGTGTTGAGGAAGTCTGATTGTCTTAGGATGACGCTGCTTCTTCGT
318 GGAGATAATACGGCTCCTTCATGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTTCTTCGT
923014 GTTAAAGAGATCAGGTC
383 GTTAAAGAGATCAGGTC
* *
923031 AA-TTGATGTTG-A-A-GACGCTGCTCATTCGTATTGAAGAGATCTGGTCATTTTCAGGTAAATT
1 AATTTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATT
* *
923092 GTTTGTTGAAGATGAC-ATTATTCCTCCACGTTGAGGAAATCGAGTCCATCAGAAGATAATTTGG
66 GTTTGTTGAAGATGACGA-TATTCCTCCACATTGAGGAAAGCGAGTCCATCAGAAGATAATTTGG
* * * * * *
923156 AGCCAATATGATTCTTTCGTATTGAAGAAGTTTGATTGT-TTGAGGTTGACAACTGCTCCTTCGC
130 AGCCAATACGATTCATTCGTATTGAAGAAGTCTGATTGTCTT-ACGATGAC-ACTACTCCTTCG-
*
923220 T-TTGAGGAGATCCAATCAATTTGATGTTGAAGATGACACTGCTCATCCGTGTTGAAGAGATCTG
192 TGTTGAGGAGATCCAATCAA-TTGATGTTGAAGATGACACTGCTCATCCGTATTGAAGAGATCTG
* *
923284 GTCGTTTT-T-AA-TAAATT-ATGACGTTGTTCCTTCGCG-TTGAGGAAATCGGGTCAATCAGGA
256 GTCATTTTGTGAATTAAATTAATGACGTTGTTCCTTCGCGTTTGAGGAAATCAGGTCAATCAGGA
* *
923344 GATATTTTGGGGACAATACGGTTCCTTCATGATGAGGAAGTTTGATTGTCTGAAGATGACACTGC
321 G--A---T------AATACGGCTCCTTCATGATGAGGAAGTCTGATTGTCTGAAGATGACACTGC
* * * *
923409 TTCTTCGTGTTGAGGAGATCGGGTT
375 TTCTTCGTGTTAAAGAGATCAGGTC
*
923434 AATTTGATGTTGAAGATGACACTGCTCATCCGTGTTGAAGAGATCT
1 AATTTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCT
923480 TGGCCATCTT
Statistics
Matches: 377, Mismatches: 52, Indels: 40
0.80 0.11 0.09
Matches are distributed among these distances:
392 22 0.06
393 18 0.05
394 1 0.00
397 4 0.01
400 2 0.01
401 1 0.00
402 3 0.01
403 202 0.54
404 35 0.09
405 52 0.14
406 9 0.02
407 28 0.07
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.34
Consensus pattern (399 bp):
AATTTGATGTTGAAGATGACGCTGCTCATCCGTGTTGAAGAGATCTGGTCATTTTCAGGTAAATT
GTTTGTTGAAGATGACGATATTCCTCCACATTGAGGAAAGCGAGTCCATCAGAAGATAATTTGGA
GCCAATACGATTCATTCGTATTGAAGAAGTCTGATTGTCTTACGATGACACTACTCCTTCGTGTT
GAGGAGATCCAATCAATTGATGTTGAAGATGACACTGCTCATCCGTATTGAAGAGATCTGGTCAT
TTTGTGAATTAAATTAATGACGTTGTTCCTTCGCGTTTGAGGAAATCAGGTCAATCAGGAGATAA
TACGGCTCCTTCATGATGAGGAAGTCTGATTGTCTGAAGATGACACTGCTTCTTCGTGTTAAAGA
GATCAGGTC
Found at i:923449 original size:197 final size:198
Alignment explanation
Indices: 923120--923479 Score: 510
Period size: 198 Copynumber: 1.8 Consensus size: 198
923110 TATTCCTCCA
* * * * *
923120 CGTTGAGGAAATCGAGTCCATCAGAAGATAATTTGGAGCCAATATGATTCTTTCGTATTGAAGAA
1 CGTTGAGGAAATCGAGTCAATCAGAAGATAATTTGGAGACAATACGATTCCTTCATATTGAAGAA
* * *
923185 GTTTGATTGTTTGAGGTTGACAACTGCTCCTTCGCTTTGAGGAGATCCAATCAATTTGATGTTGA
66 GTTTGATTGTCTGAAGATGACAACTGCTCCTTCGCTTTGAGGAGATCCAATCAATTTGATGTTGA
923250 AGATGACACTGCTCATCCGTGTTGAAGAGATCTGGTCGTTTTTAATAAATTATGACGTTGTTCCT
131 AGATGACACTGCTCATCCGTGTTGAAGAGATCTGGTCGTTTTTAATAAATTATGACGTTGTTCCT
923315 TCG
196 TCG
* * * * * *
923318 CGTTGAGGAAATCGGGTCAATCAGGAGATATTTTGGGGACAATACGGTTCCTTCATGA-TGAGGA
1 CGTTGAGGAAATCGAGTCAATCAGAAGATAATTTGGAGACAATACGATTCCTTCAT-ATTGAAGA
* *** *
923382 AGTTTGATTGTCTGAAGATGAC-ACTGCTTCTTCG-TGTTGAGGAGATCGGGTTAATTTGATGTT
65 AGTTTGATTGTCTGAAGATGACAACTGCTCCTTCGCT-TTGAGGAGATCCAATCAATTTGATGTT
923445 GAAGATGACACTGCTCATCCGTGTTGAAGAGATCT
129 GAAGATGACACTGCTCATCCGTGTTGAAGAGATCT
923480 TGGCCATCTT
Statistics
Matches: 141, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
196 1 0.01
197 69 0.49
198 70 0.50
199 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (198 bp):
CGTTGAGGAAATCGAGTCAATCAGAAGATAATTTGGAGACAATACGATTCCTTCATATTGAAGAA
GTTTGATTGTCTGAAGATGACAACTGCTCCTTCGCTTTGAGGAGATCCAATCAATTTGATGTTGA
AGATGACACTGCTCATCCGTGTTGAAGAGATCTGGTCGTTTTTAATAAATTATGACGTTGTTCCT
TCG
Found at i:924347 original size:85 final size:83
Alignment explanation
Indices: 924248--924432 Score: 210
Period size: 83 Copynumber: 2.2 Consensus size: 83
924238 GTCATCGAGT
* * * * * *
924248 TGAATGGAATCAAACTTGAAGGCGTTTATTAACATATAACCCTTCTCGCATTGAGTTATGATGTA
1 TGAATGTAATCAAACTCGAA-G-GATGATTAACAGATAACCCTTCTCACATTGAGTTATGATGTA
924313 AATTTGACATGTCC-TTGAGC
64 AATTTGACATG-CCTTTGAGC
* * * *
924333 TGAATGTAATCAAACTCGAAGGATGGTTGACAGATAACCCTTCTCACCTTGAGTTATGTTGTAAA
1 TGAATGTAATCAAACTCGAAGGATGATTAACAGATAACCCTTCTCACATTGAGTTATGATGTAAA
*
924398 TTTGATATGCCTTTGAGC
66 TTTGACATGCCTTTGAGC
* * *
924416 TGAGTGTAGTCGAACTC
1 TGAATGTAATCAAACTC
924433 AAAGATCTTG
Statistics
Matches: 85, Mismatches: 14, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
82 2 0.02
83 64 0.75
84 1 0.01
85 18 0.21
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (83 bp):
TGAATGTAATCAAACTCGAAGGATGATTAACAGATAACCCTTCTCACATTGAGTTATGATGTAAA
TTTGACATGCCTTTGAGC
Found at i:924396 original size:83 final size:83
Alignment explanation
Indices: 924283--924475 Score: 237
Period size: 83 Copynumber: 2.3 Consensus size: 83
924273 TTATTAACAT
*
924283 ATAACCCTTCTCGCATTGAGTTATGATGTAAATTTGACATGTCC-TTGAGCTGAATGTAATCAAA
1 ATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGACATG-CCTTTGAGCTGAATGTAATCAAA
*
924347 CTCGAAGGA-TGGTTGACAG
65 CTC-AAAGATTGGTTGACAG
* * * * * *
924366 ATAACCCTTCTCACCTTGAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAGTGTAGTCGAAC
1 ATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGACATGCCTTTGAGCTGAATGTAATCAAAC
*
924431 TCAAAGATCTTGGTTGATAG
66 TCAAAGA--TTGGTTGACAG
* *
924451 ATAGCCCTTCTCGCCTTGAGCTATG
1 ATAACCCTTCTCGCCTTGAGTTATG
924476 CTGTGAATAG
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
82 6 0.06
83 57 0.61
85 31 0.33
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (83 bp):
ATAACCCTTCTCGCCTTGAGTTATGATGTAAATTTGACATGCCTTTGAGCTGAATGTAATCAAAC
TCAAAGATTGGTTGACAG
Found at i:926426 original size:2 final size:2
Alignment explanation
Indices: 926419--926484 Score: 123
Period size: 2 Copynumber: 33.0 Consensus size: 2
926409 ACAACAAGGG
926419 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
926461 AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT
926485 GGATAAATGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:928449 original size:63 final size:63
Alignment explanation
Indices: 928346--928469 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
928336 TATGATGATC
* *
928346 ATGCAGAATGCGAATATGCAAATACAGATGCAAAAGTGATGATCCTCTGACATGCAATGCATT
1 ATGCAGAATGCGAAGATGCAAATACAGATGCAAAAGTGATGATCCTCTGAAATGCAATGCATT
* * *
928409 ATGCAGAATGCGAAGATGCAAATGCAGATGCAAAATTGATGATCCTCTTAAATGCAATGCA
1 ATGCAGAATGCGAAGATGCAAATACAGATGCAAAAGTGATGATCCTCTGAAATGCAATGCA
928470 ACAAGGGACG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.39, C:0.17, G:0.21, T:0.23
Consensus pattern (63 bp):
ATGCAGAATGCGAAGATGCAAATACAGATGCAAAAGTGATGATCCTCTGAAATGCAATGCATT
Found at i:930601 original size:19 final size:19
Alignment explanation
Indices: 930577--930619 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
930567 ATTTTTTGAA
930577 TTTTATAAATTTAATAAT-T
1 TTTTATAAATTT-ATAATAT
**
930596 TTTTATTTATTTATAATAT
1 TTTTATAAATTTATAATAT
930615 TTTTA
1 TTTTA
930620 AATAATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTATAAATTTATAATAT
Found at i:931921 original size:25 final size:25
Alignment explanation
Indices: 931863--931921 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 25
931853 CACCTCGATT
*
931863 TAATTTTTTTTAAAATTTATAAAAA
1 TAATTTTTATTAAAATTTATAAAAA
* *
931888 T-TTTATTTATT-AAATTTTTAAAAAA
1 TAATT-TTTATTAAAATTTAT-AAAAA
931913 TAATTTTTA
1 TAATTTTTA
931922 AATAAAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
24 9 0.33
25 16 0.59
26 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAATTTTTATTAAAATTTATAAAAA
Found at i:937781 original size:9 final size:9
Alignment explanation
Indices: 937769--937833 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
937759 CTCTTCTTCT
937769 TTCTCTTTC
1 TTCTCTTTC
*
937778 TTCTTTTTC
1 TTCTCTTTC
*
937787 TTCTCCTTC
1 TTCTCTTTC
937796 TTCTCTTTC
1 TTCTCTTTC
* * *
937805 TCCTTTTTA
1 TTCTCTTTC
937814 TTCTCCTTTCC
1 TTCT-CTTT-C
937825 TTCTTCTTT
1 TTC-TCTTT
937834 GCATACTCAC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
9 32 0.74
10 3 0.07
11 7 0.16
12 1 0.02
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (9 bp):
TTCTCTTTC
Found at i:937801 original size:27 final size:28
Alignment explanation
Indices: 937764--937821 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
937754 ACTGACTCTT
* *
937764 CTTCTTTCTCTTTCTTCTTTTTCTTCTC
1 CTTCTTTCTCTTTCTCCTTTTTATTCTC
937792 CTTC-TTCTCTTTCTCCTTTTTATTCTC
1 CTTCTTTCTCTTTCTCCTTTTTATTCTC
937819 CTT
1 CTT
937822 TCCTTCTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (28 bp):
CTTCTTTCTCTTTCTCCTTTTTATTCTC
Found at i:937829 original size:27 final size:27
Alignment explanation
Indices: 937770--937829 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
937760 TCTTCTTCTT
* * *
937770 TCTCTTTCTTCTTTTTCTTCTCCTTCT
1 TCTCTTTCTCCTTTTTATTCTCCTTCC
937797 TCTCTTTCTCCTTTTTATTCTCCTTTCC
1 TCTCTTTCTCCTTTTTATTCTCC-TTCC
937825 T-TCTT
1 TCTCTT
937830 CTTTGCATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (27 bp):
TCTCTTTCTCCTTTTTATTCTCCTTCC
Found at i:943668 original size:64 final size:64
Alignment explanation
Indices: 943567--943691 Score: 223
Period size: 64 Copynumber: 2.0 Consensus size: 64
943557 ATGTTATATT
* * *
943567 ATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGC
1 ATTTAACAGGAAATATTATCAAGTACAATAACATATTAAGTAGCTCTTATATAATATAATAGGC
943631 ATTTAACAGGAAATATTATCAAGTACAATAACATATTAAGTAGCTCTTATATAATATAATA
1 ATTTAACAGGAAATATTATCAAGTACAATAACATATTAAGTAGCTCTTATATAATATAATA
943692 AGTAGCGCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 58 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (64 bp):
ATTTAACAGGAAATATTATCAAGTACAATAACATATTAAGTAGCTCTTATATAATATAATAGGC
Found at i:943693 original size:23 final size:23
Alignment explanation
Indices: 943658--943705 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
943648 ATCAAGTACA
* *
943658 ATAACATATTAAGTAGCTCTTAT
1 ATAACATAATAAGTAGCGCTTAT
*
943681 ATAATATAATAAGTAGCGCTTAT
1 ATAACATAATAAGTAGCGCTTAT
943704 AT
1 AT
943706 TGACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (23 bp):
ATAACATAATAAGTAGCGCTTAT
Found at i:945711 original size:20 final size:20
Alignment explanation
Indices: 945686--945729 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
945676 AGTAGCGCTT
945686 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
945706 TACCGGTTTTATCATTTTGA
1 TACCGGTTTTATCATTTTGA
945726 TACC
1 TACC
945730 AATTTTATCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (20 bp):
TACCGGTTTTATCATTTTGA
Found at i:945735 original size:20 final size:20
Alignment explanation
Indices: 945692--945738 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
945682 GCTTTACCGG
**
945692 TTTTATCATTTTGATACCGG
1 TTTTATCATTTTGATACCAA
945712 TTTTATCATTTTGATACCAA
1 TTTTATCATTTTGATACCAA
945732 TTTTATC
1 TTTTATC
945739 GTTGTGGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTTATCATTTTGATACCAA
Found at i:946116 original size:27 final size:27
Alignment explanation
Indices: 946064--946117 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
946054 CCAAATTTAT
* * *
946064 TAAATATCTTTTAATATATTCGATAAC
1 TAAATATATTTTAATATATCCAATAAC
*
946091 TAAATATATTTTAATGTATCCAATAAC
1 TAAATATATTTTAATATATCCAATAAC
946118 ACCATATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (27 bp):
TAAATATATTTTAATATATCCAATAAC
Found at i:946724 original size:20 final size:20
Alignment explanation
Indices: 946659--946888 Score: 246
Period size: 20 Copynumber: 11.5 Consensus size: 20
946649 CGATTTTCCA
** *
946659 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
946679 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
946699 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
946719 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
946739 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
946759 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
946779 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
946799 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
946819 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
*
946839 AAATCGCAACGAGAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
946859 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
946879 AAATCACAAC
1 AAATCGCAAC
946889 ACTGAAATTT
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 183 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:947610 original size:24 final size:24
Alignment explanation
Indices: 947571--947617 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
947561 AAATTTGGTC
947571 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
947595 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
947618 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:947809 original size:12 final size:12
Alignment explanation
Indices: 947792--947816 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
947782 ATATAATCCT
947792 GAAGAAGAAAAA
1 GAAGAAGAAAAA
947804 GAAGAAGAAAAA
1 GAAGAAGAAAAA
947816 G
1 G
947817 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:950179 original size:53 final size:53
Alignment explanation
Indices: 950135--950304 Score: 324
Period size: 53 Copynumber: 3.2 Consensus size: 53
950125 GAAATGAAAA
950135 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
*
950188 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
950241 TCGCATTGCGATTCTCTCGTTGCGATTTTCA-TTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
950293 TCGCATTGCGAT
1 TCGCATTGCGAT
950305 AGTCAATTTT
Statistics
Matches: 115, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 32 0.28
53 83 0.72
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTCGCATTGCGATTTTCATT
Found at i:950191 original size:19 final size:19
Alignment explanation
Indices: 950154--950304 Score: 196
Period size: 19 Copynumber: 8.4 Consensus size: 19
950144 GATTCTCTCG
950154 TTGCGATTTTCATTTTCGCA
1 TTGCGATTTTCA-TTTCGCA
950174 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
950193 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
950207 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
950227 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
950246 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
950260 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
950279 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
950298 TTGCGAT
1 TTGCGAT
950305 AGTCAATTTT
Statistics
Matches: 116, Mismatches: 4, Indels: 23
0.81 0.03 0.16
Matches are distributed among these distances:
14 12 0.10
16 14 0.12
17 12 0.10
18 2 0.02
19 49 0.42
20 27 0.23
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:950269 original size:33 final size:34
Alignment explanation
Indices: 950135--950286 Score: 145
Period size: 33 Copynumber: 4.4 Consensus size: 34
950125 GAAATGAAAA
950135 TCGCATTGCGATTCTCTCG-TTGCGATTTTCATTT
1 TCGCATTGCGATTCTCTCGATTGCGATTTTCA-TT
* *
950169 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 TCGCATTGCGA--TTC-TCTCG-ATTGCGATT-T-TCATT
* *
950209 GCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATT
1 TCGCA-TTGCGATTCTCTCG-ATTGCGATTTTCATT
950241 TCGCATTGCGATTCTCTCG-TTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
950274 TCGCATTGCGATT
1 TCGCATTGCGATT
950287 TTCATTTCGC
Statistics
Matches: 98, Mismatches: 8, Indels: 25
0.75 0.06 0.19
Matches are distributed among these distances:
32 9 0.09
33 32 0.33
34 25 0.26
35 3 0.03
36 3 0.03
37 6 0.06
39 10 0.10
40 8 0.08
41 2 0.02
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCGATTGCGATTTTCATT
Found at i:950415 original size:33 final size:33
Alignment explanation
Indices: 950363--950524 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
950353 CCATTACATT
950363 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
950397 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
950429 T-GAAAAT-CGCAACGATAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
950468 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
*
950501 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
950525 TTGCGATTCT
Statistics
Matches: 105, Mismatches: 12, Indels: 23
0.75 0.09 0.16
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 54 0.51
34 10 0.10
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:950419 original size:19 final size:19
Alignment explanation
Indices: 950363--950530 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
950353 CCATTACATT
950363 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
950383 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
950397 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
950416 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
950435 TCGCAA--CG--AT-AGAA
1 TCGCAATGCGAAATGAAAA
950449 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
950468 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
950487 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
950501 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
950520 TCGCATTGCGA
1 TCGCAATGCGA
950531 TTCTCCCATT
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 29 0.23
15 4 0.03
16 6 0.05
17 5 0.04
18 5 0.04
19 70 0.56
20 6 0.05
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:950442 original size:52 final size:52
Alignment explanation
Indices: 950363--950530 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
950353 CCATTACATT
950363 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
950416 TCGCAATGCGAAATGAAAATCGCAACGATAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
950468 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
950520 TCGCATTGCGA
1 TCGCAATGCGA
950531 TTCTCCCATT
Statistics
Matches: 111, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
52 102 0.92
53 9 0.08
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:950579 original size:19 final size:19
Alignment explanation
Indices: 950537--950636 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
950527 GCGATTCTCC
950537 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
950557 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
950576 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
950592 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
950609 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
950628 CATTGCGAT
1 CATTGCGAT
950637 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:950633 original size:52 final size:53
Alignment explanation
Indices: 950520--950636 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
950510 GAAATTAAAA
950520 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
950573 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
950625 TCGCATTGCGAT
1 TCGCATTGCGAT
950637 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:950762 original size:14 final size:14
Alignment explanation
Indices: 950743--950779 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
950733 CATCAATTAC
950743 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
950757 ACAAATCATCTTTT
1 ACAAATCAACTTTT
950771 ACAAATCAA
1 ACAAATCAA
950780 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:952744 original size:19 final size:19
Alignment explanation
Indices: 952704--952824 Score: 135
Period size: 19 Copynumber: 6.6 Consensus size: 19
952694 TAGTTTACTT
* *
952704 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
952724 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
952743 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
952762 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
952776 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
952795 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
952814 TCGCAATGCGA
1 TCGCAACGCGA
952825 TTTTGGTTTC
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
14 8 0.09
16 5 0.06
17 5 0.06
19 57 0.66
20 12 0.14
ACGTcount: A:0.45, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:952842 original size:19 final size:19
Alignment explanation
Indices: 952820--952948 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
952810 AAAATCGCAA
952820 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
952839 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
952853 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
952872 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
952886 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
952905 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
952924 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
952944 TGCGA
1 TGCGA
952949 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:952862 original size:33 final size:33
Alignment explanation
Indices: 952820--952911 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
952810 AAAATCGCAA
952820 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
952853 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
952886 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
952912 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:953151 original size:93 final size:93
Alignment explanation
Indices: 952992--953465 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
952982 TTGAATGGAT
952992 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
953057 AGTTTAGCAGAATTGGCAGCAACGGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
953085 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
953150 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
953178 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
953243 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
953271 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
953336 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
953364 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
953429 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
953457 AAATTTACT
1 AAATTTACT
953466 AAGCAATCTA
Statistics
Matches: 377, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 377 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:954699 original size:20 final size:20
Alignment explanation
Indices: 954671--954900 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
954661 AAATTTCAGT
* ** *
954671 GTTGTGATTTACATATTCTC
1 GTTGCGATTTACGGATTCGC
*
954691 GTTGCGATTTACGGATTCTC
1 GTTGCGATTTACGGATTCGC
**
954711 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
954731 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
954751 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
954771 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
954791 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
954811 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
954831 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
954851 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
954871 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
954891 GTTGCGATTT
1 GTTGCGATTT
954901 TGGAAAATCG
Statistics
Matches: 183, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 182 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:956042 original size:23 final size:23
Alignment explanation
Indices: 956016--956064 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
956006 TACACCGTTG
956016 ATGGATTGTAACATAAAATGATA
1 ATGGATTGTAACATAAAATGATA
956039 ATGGATTGTAACATAAAATGATA
1 ATGGATTGTAACATAAAATGATA
956062 ATG
1 ATG
956065 TTTATAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (23 bp):
ATGGATTGTAACATAAAATGATA
Found at i:961784 original size:131 final size:131
Alignment explanation
Indices: 961624--962106 Score: 788
Period size: 131 Copynumber: 3.7 Consensus size: 131
961614 TATCAACATA
* *
961624 TTACCATGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATTG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
* * * *
961689 ATACTTTATATATGAGTATCGATACTAGGATATTTACGCCTATTTTCATTATACAGGTAAGACCG
66 ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAAGAACG
961754 T
131 T
* * *
961755 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAATATCA
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
*
961820 ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGT-AGAAAT
66 ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAAG-AAC
961884 GT
130 GT
*
961886 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTAAAAGTATCG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
* * * *
961951 ATACTTTGTATATAAGTATCAATACTTGGACATTTACGCCTATTTTCATTATACCGGTAGGAACG
66 ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAAGAACG
*
962016 C
131 T
*
962017 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCG
1 TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
*
962082 ATACTTTATATATGTGTATCGATAC
66 ATACTTTATATATGAGTATCGATAC
962107 ATTTTGCGTG
Statistics
Matches: 324, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
130 2 0.01
131 321 0.99
132 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (131 bp):
TTACCGTGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTATAAGTATCG
ATACTTTATATATGAGTATCGATACTTGGACATTTACGCCTATTTTCATTATACCGGTAAGAACG
T
Found at i:962169 original size:20 final size:20
Alignment explanation
Indices: 962144--962196 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
962134 ATACTAGAAT
*
962144 AAAGTATCTATACCTATATA
1 AAAGTATCAATACCTATATA
962164 AAAGTATCAATACCTATATA
1 AAAGTATCAATACCTATATA
962184 AAAGTATCAATAC
1 AAAGTATCAATAC
962197 TTGGTATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.30
Consensus pattern (20 bp):
AAAGTATCAATACCTATATA
Found at i:963752 original size:196 final size:195
Alignment explanation
Indices: 963438--963952 Score: 691
Period size: 196 Copynumber: 2.6 Consensus size: 195
963428 GCTTTTTTAT
* *
963438 TTCTTTTAAATTCCTAAAGTACCGATACTATGGTACATATACTTATAAACGTATCGATAC---TT
1 TTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAACGTATCGATACAAATT
* * *
963500 TCAACAATTCCGGTAACGT-TTTACCGATTTTGTCAAATTGAAATTGGTTTTGTCAAATTTCAAC
66 TCAACAATTCC-GTAAC-TCTTTTCAG-TTTTGTCAAATTGAAATCGGTTTTGTCAAATTTCAAC
* * * *
963564 CTGTTATATTGTTATGTATCGATACATATGTCTAAGGTATCGATACTTTATAGGCGCTATTATTG
128 ATGTTATATTGTCATGTATCGATACATATGTCTAAGGTATCGATACTTTACAAGCGCTATTATTG
963629 CAA
193 CAA
* * * *
963632 TTCTTTTAAATTTCTAAAGTACTGCTACTTTGGTACATATACTTATAAAAGTAGCGATACAAATT
1 TTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAACGTATCGATACAAATT
* * *
963697 TCAACCATTCCGTAACTCTTTGTCAGTTTTGACAAATTGAAATCGGTTTTGTCAAATTTTAACAT
66 TCAACAATTCCGTAACTCTTT-TCAGTTTTGTCAAATTGAAATCGGTTTTGTCAAATTTCAACAT
* *
963762 GTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGATACTTTACAATCGCTATTATTGCA
130 GTTATATTGTCATGTATCGATACATATGTCTAAGGTATCGATACTTTACAAGCGCTATTATTGCA
963827 A
195 A
* *
963828 TTCTTTTAAATTCCTAAAGTA-TCGATACTTTGATACATATACTTATAAACGTATCAATACAAAT
1 TTCTTTTAAATTCCTAAAGTACT-GATACTTTGGTACATATACTTATAAACGTATCGATACAAAT
* * * ** *
963892 TTCAACAATTTCGTTAGCTCTTTATCGGTTTTGTCAAATTTCAACCGGTTTTGTC-AATTTC
65 TTCAACAATTCCG-TAACTCTTT-TCAGTTTTGTCAAATTGAAATCGGTTTTGTCAAATTTC
963953 CAATCGGTTT
Statistics
Matches: 280, Mismatches: 34, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
194 54 0.19
195 2 0.01
196 176 0.63
197 48 0.17
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (195 bp):
TTCTTTTAAATTCCTAAAGTACTGATACTTTGGTACATATACTTATAAACGTATCGATACAAATT
TCAACAATTCCGTAACTCTTTTCAGTTTTGTCAAATTGAAATCGGTTTTGTCAAATTTCAACATG
TTATATTGTCATGTATCGATACATATGTCTAAGGTATCGATACTTTACAAGCGCTATTATTGCAA
Found at i:963942 original size:20 final size:20
Alignment explanation
Indices: 963917--963997 Score: 101
Period size: 20 Copynumber: 4.0 Consensus size: 20
963907 AGCTCTTTAT
963917 CGGTTTTGTCAAATTTCAAC
1 CGGTTTTGTCAAATTTCAAC
*
963937 CGGTTTTGTC-AATTTCCAAT
1 CGGTTTTGTCAAATTT-CAAC
**
963957 CGGTTTTGTCAAATTGAAAC
1 CGGTTTTGTCAAATTTCAAC
* *
963977 TGGTTTTGTCAAATTTTAAC
1 CGGTTTTGTCAAATTTCAAC
963997 C
1 C
963998 TTTTATATTG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
19 5 0.10
20 42 0.82
21 4 0.08
ACGTcount: A:0.25, C:0.17, G:0.16, T:0.42
Consensus pattern (20 bp):
CGGTTTTGTCAAATTTCAAC
Found at i:964024 original size:237 final size:236
Alignment explanation
Indices: 963722--964362 Score: 944
Period size: 237 Copynumber: 2.7 Consensus size: 236
963712 CTCTTTGTCA
*
963722 GTTTTGACAAATTGAAA-TCGGTTTTGTCAAATTTTAACATGTTATATTGTCATGTATCGATACA
1 GTTTTGTCAAATTGAAACT-GGTTTTGTCAAATTTTAACATGTTATATTGTCATGTATCGATACA
* *
963786 TGTGTCTAAGGTATCGATACTTTACAATCGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATC
65 TGTGTGTAAGGTATCGATACTTTATAA-CGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATC
963851 GATACTTTGATACATATACTTATAAACGTATCAATACAAATTTCAACAATTTCGTTAGCTCTTTA
129 GATACTTTGATACATATACTTATAAACGTATCAATACAAATTTCAACAATTTCGTTAGCTCTTTA
* *
963916 TCGGTTTTGTCAAATTTCAACCGGTTTTGTCAATTTCCAATCG
194 TCGGTTTTGTCAAATTTAAACCGATTTTGTCAATTTCCAATCG
* *
963959 GTTTTGTCAAATTGAAACTGGTTTTGTCAAATTTTAACCTTTTATATTGTCATGTATCGATACAT
1 GTTTTGTCAAATTGAAACTGGTTTTGTCAAATTTTAACATGTTATATTGTCATGTATCGATACAT
** ** * * * * *
964024 GTGTGTAAGGTATCGATACTTTATAGACATTATTATTGCGGTTCTTTTAAATTCATACAGCACCA
66 GTGTGTAAGGTATCGATACTTTATA-ACGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATCG
* *
964089 ATACTTTGGTGCATATACTTATAAACGTATCAATACAAATTTCAACAATTTCGTTAGCTCTTTAT
130 ATACTTTGATACATATACTTATAAACGTATCAATACAAATTTCAACAATTTCGTTAGCTCTTTAT
964154 CGGTTTTGTCAAATTTAAACCGATTTTGTCAATTTCCAATCG
195 CGGTTTTGTCAAATTTAAACCGATTTTGTCAATTTCCAATCG
* ** * *
964196 GTTTTTTCAAATTGAAACAAGATTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACAT
1 GTTTTGTCAAATTGAAACTGGTTTTGTCAAATTTTAACATGTTATATTGTCATGTATCGATACAT
* * * *
964261 GTGTGTAAGGTAACGAGACTTTATAGGA-GCTTTTATTGCAATTCTTTTAAATTACTAAAGTATC
66 GTGTGTAAGGTATCGATACTTTATA--ACGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATC
* * * *
964325 GTTACTTTTATACATATACTTATAAAGGTATCGATACA
129 GATACTTTGATACATATACTTATAAACGTATCAATACA
964363 TGTCTACTTT
Statistics
Matches: 357, Mismatches: 44, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
237 353 0.99
238 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (236 bp):
GTTTTGTCAAATTGAAACTGGTTTTGTCAAATTTTAACATGTTATATTGTCATGTATCGATACAT
GTGTGTAAGGTATCGATACTTTATAACGCTATTATTGCAATTCTTTTAAATTCCTAAAGTATCGA
TACTTTGATACATATACTTATAAACGTATCAATACAAATTTCAACAATTTCGTTAGCTCTTTATC
GGTTTTGTCAAATTTAAACCGATTTTGTCAATTTCCAATCG
Found at i:964182 original size:20 final size:20
Alignment explanation
Indices: 964157--964229 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
964147 TCTTTATCGG
964157 TTTTGTCAAATTTAAACCGA
1 TTTTGTCAAATTTAAACCGA
* * *
964177 TTTTGTC-AATTTCCAATCGG
1 TTTTGTCAAATTT-AAACCGA
* * *
964197 TTTTTTCAAATTGAAACAAGA
1 TTTTGTCAAATTTAAAC-CGA
964218 -TTTGTCAAATTT
1 TTTTGTCAAATTT
964230 CAACATGTTA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
19 5 0.13
20 29 0.74
21 5 0.13
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (20 bp):
TTTTGTCAAATTTAAACCGA
Found at i:964198 original size:40 final size:41
Alignment explanation
Indices: 964152--964230 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 41
964142 TTAGCTCTTT
* *
964152 ATCGGTTTTGTCAAATTTAAAC-CGATTTTGTC-AATTTCCA
1 ATCGGTTTTGTCAAATTGAAACAAGA-TTTGTCAAATTTCCA
*
964192 ATCGGTTTTTTCAAATTGAAACAAGATTTGTCAAATTTC
1 ATCGGTTTTGTCAAATTGAAACAAGATTTGTCAAATTTC
964231 AACATGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
40 26 0.76
41 8 0.24
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (41 bp):
ATCGGTTTTGTCAAATTGAAACAAGATTTGTCAAATTTCCA
Found at i:965464 original size:36 final size:36
Alignment explanation
Indices: 965416--965487 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
965406 TATGTGCAGG
965416 GGGAACAAATTCCCCCCT-GGAGGGTATCGATTCCCC
1 GGGAACAAATT-CCCCCTGGGAGGGTATCGATTCCCC
* *
965452 GGGAACAGATTCCCCCTGGGGGGGTATCGATTCCCC
1 GGGAACAAATTCCCCCTGGGAGGGTATCGATTCCCC
965488 CCTAAATGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 6 0.18
36 27 0.82
ACGTcount: A:0.19, C:0.32, G:0.29, T:0.19
Consensus pattern (36 bp):
GGGAACAAATTCCCCCTGGGAGGGTATCGATTCCCC
Found at i:965947 original size:46 final size:46
Alignment explanation
Indices: 965896--966000 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
965886 CTATATGACT
*
965896 ATATGAAATGATATATGAATATGCAATACATGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACATGATACATGTGATATG
* *
965942 ATATGAAATGACATATGAATATGTAATACGTGATACATGTGATATG
1 ATATGAAATGACATATGAATATGCAATACATGATACATGTGATATG
965988 ATATGAAAT-ACAT
1 ATATGAAATGACAT
966001 GGTTACATAT
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 4 0.07
46 52 0.93
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (46 bp):
ATATGAAATGACATATGAATATGCAATACATGATACATGTGATATG
Found at i:966205 original size:38 final size:38
Alignment explanation
Indices: 966162--966244 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
966152 ATAGGTCATA
* *
966162 CGGGACACAGATTACATCCTTCGGGATGACAGGTCCTT
1 CGGGACACAAATGACATCCTTCGGGATGACAGGTCCTT
* *
966200 CGGGACACAAATGACATCCTTTGGGATGATAGGTCCTT
1 CGGGACACAAATGACATCCTTCGGGATGACAGGTCCTT
966238 CGGGACA
1 CGGGACA
966245 TTTATACGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (38 bp):
CGGGACACAAATGACATCCTTCGGGATGACAGGTCCTT
Found at i:971515 original size:14 final size:14
Alignment explanation
Indices: 971498--971529 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
971488 AATGAACATA
971498 AACGAACATAACAG
1 AACGAACATAACAG
*
971512 AACGAACATAACCG
1 AACGAACATAACAG
971526 AACG
1 AACG
971530 TTCACGAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.25, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACAG
Found at i:971518 original size:24 final size:24
Alignment explanation
Indices: 971478--971528 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
971468 GATTGGGTTA
*
971478 AACATAAATGAATGAACATAAACG
1 AACATAAATGAACGAACATAAACG
*
971502 AACATAACA-GAACGAACATAACCG
1 AACATAA-ATGAACGAACATAAACG
971526 AAC
1 AAC
971529 GTTCACGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.57, C:0.20, G:0.12, T:0.12
Consensus pattern (24 bp):
AACATAAATGAACGAACATAAACG
Found at i:973046 original size:2 final size:2
Alignment explanation
Indices: 973039--973080 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
973029 AAATAAAACA
973039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
973081 CAAATAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:976887 original size:24 final size:24
Alignment explanation
Indices: 976855--976901 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
976845 TGCCTATGCT
976855 TCTTCTCAGCATAAACAAGCTGCA
1 TCTTCTCAGCATAAACAAGCTGCA
* *
976879 TCTTCTCAGCATGAGCAAGCTGC
1 TCTTCTCAGCATAAACAAGCTGC
976902 CTCTAGTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (24 bp):
TCTTCTCAGCATAAACAAGCTGCA
Found at i:978801 original size:20 final size:22
Alignment explanation
Indices: 978756--978813 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
978746 GCATGGGTAG
978756 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
978780 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
978800 TGCATCAATGCACT
1 TGCATCGATGCACT
978814 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:985564 original size:32 final size:31
Alignment explanation
Indices: 985522--985625 Score: 129
Period size: 32 Copynumber: 3.2 Consensus size: 31
985512 TTATGTTGAT
985522 TTTA-TTTAGACTTATTAGTGTTATGGTGTTA
1 TTTATTTTAGACTTATT-GTGTTATGGTGTTA
*
985553 TTTATTTTAGACTTAATGGTGTTATGGTGTTA
1 TTTATTTTAGACTT-ATTGTGTTATGGTGTTA
* *
985585 TTTATTTTAGATTTATTGATATTTAATGGTGTTA
1 TTTATTTTAGACTTATTG-T-GTT-ATGGTGTTA
985619 TTTATTT
1 TTTATTT
985626 AATTGTTTAT
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
31 7 0.11
32 37 0.58
33 4 0.06
34 16 0.25
ACGTcount: A:0.23, C:0.02, G:0.17, T:0.58
Consensus pattern (31 bp):
TTTATTTTAGACTTATTGTGTTATGGTGTTA
Found at i:985624 original size:17 final size:17
Alignment explanation
Indices: 985576--985628 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
985566 TAATGGTGTT
*
985576 ATGGTGTTATTTATTTT
1 ATGGTGTTATTTATTTA
*
985593 A-GAT-TTATTGATATTTA
1 ATGGTGTTATT--TATTTA
985610 ATGGTGTTATTTATTTA
1 ATGGTGTTATTTATTTA
985627 AT
1 AT
985629 TGTTTATCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
15 5 0.17
16 2 0.07
17 15 0.52
18 2 0.07
19 5 0.17
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.58
Consensus pattern (17 bp):
ATGGTGTTATTTATTTA
Found at i:985821 original size:73 final size:73
Alignment explanation
Indices: 985687--985822 Score: 211
Period size: 73 Copynumber: 1.9 Consensus size: 73
985677 TTATTTAGCC
* * *
985687 ACTTCAGTTTCAGATTAATAGTTTAATTGACTTTTGTTGTTATGGTGTTATTGTGGATTATTTTT
1 ACTTCAGTTTCAGATTAATAGTGTAATTGACTTTTGGTGTTATGGTGTTATGGTGGATTATTTTT
985752 TGCTACTA
66 TGCTACTA
* *
985760 ACTTCCGTTTCAGATTAATAGTGTAATTGACTTTTGGTGTTATTGGTGTTATGGTTG-TTATTT
1 ACTTCAGTTTCAGATTAATAGTGTAATTGACTTTTGGTGTTA-TGGTGTTATGGTGGATTATTT
985823 AAAATTGTAC
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 45 0.79
74 12 0.21
ACGTcount: A:0.21, C:0.08, G:0.20, T:0.51
Consensus pattern (73 bp):
ACTTCAGTTTCAGATTAATAGTGTAATTGACTTTTGGTGTTATGGTGTTATGGTGGATTATTTTT
TGCTACTA
Found at i:986997 original size:11 final size:11
Alignment explanation
Indices: 986981--987005 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
986971 TTTTTAGAAT
986981 AATTTAATATA
1 AATTTAATATA
986992 AATTTAATATA
1 AATTTAATATA
987003 AAT
1 AAT
987006 ATATAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTTAATATA
Found at i:989341 original size:13 final size:13
Alignment explanation
Indices: 989325--989349 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
989315 GAATTAGATA
989325 TTTAAATTTAAAG
1 TTTAAATTTAAAG
989338 TTTAAATTTAAA
1 TTTAAATTTAAA
989350 AGTGTGAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTAAATTTAAAG
Found at i:998485 original size:28 final size:28
Alignment explanation
Indices: 998444--998498 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
998434 GACCCTTAAA
*
998444 CATTAAATCATAAATCCCAAACATCAAG
1 CATTAAACCATAAATCCCAAACATCAAG
*
998472 CATTAAACCTTAAATCCCAAACATCAA
1 CATTAAACCATAAATCCCAAACATCAA
998499 ACCACAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.49, C:0.27, G:0.02, T:0.22
Consensus pattern (28 bp):
CATTAAACCATAAATCCCAAACATCAAG
Found at i:999127 original size:23 final size:23
Alignment explanation
Indices: 999101--999145 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
999091 AGTGTTATGT
999101 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
999124 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
999146 AAATATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:999151 original size:23 final size:23
Alignment explanation
Indices: 999102--999152 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
999092 GTGTTATGTT
**
999102 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
999125 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
999148 ATATT
1 ATATT
999153 ATTATATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:999169 original size:35 final size:34
Alignment explanation
Indices: 999101--999174 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 34
999091 AGTGTTATGT
*
999101 TATATTTTAAAAATATTAATTAGTATATTTTAAA
1 TATATTTTAAAAATATTAATTAGTATATATTAAA
*
999135 TATATTTATTAAAATATT-ATTA-TATTAATATTAAA
1 TATATTT-TAAAAATATTAATTAGTA-T-ATATTAAA
999170 TATAT
1 TATAT
999175 AAATAATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 2 0.06
34 12 0.34
35 21 0.60
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
TATATTTTAAAAATATTAATTAGTATATATTAAA
Found at i:1001598 original size:187 final size:188
Alignment explanation
Indices: 1001269--1001641 Score: 631
Period size: 187 Copynumber: 2.0 Consensus size: 188
1001259 AATTTTTGGG
* * *
1001269 CGCTTGTGGGGGTGCTAATCCTTCCCCACGCGTAACTGACTCTCGAACCTGATCTCTGGATTTTT
1 CGCTTGTGGGGGTACTAATCCTTCCCCACGCGTAACTGACTCCCGAACCTGATCTCTGGATTTTC
* *
1001334 GTAGACCCCAAAACTCGATATTTTATTAAAATAAAATGTTTTATTAAAATCACCCAATTTTTACG
66 GCAGACCCCAAAACTCGATATTTTATTAAAATAAAATGTTTTATTAAAACCACCCAATTTTTACG
* *
1001399 GTGCTCCAATCTCACCTTAAATGATTGGTGGTGAATCCTCACATTTCGAAACGATTGA
131 GTGCTCCAATCTCACCTTAAATGATTGGTGGAGAATCCTCACACTTCGAAACGATTGA
* *
1001457 CGCTTGT-GGGGTACTAATCCTTCCCCACGCGTAACTGACTCCCGAACCTGATTTTTGGATTTTC
1 CGCTTGTGGGGGTACTAATCCTTCCCCACGCGTAACTGACTCCCGAACCTGATCTCTGGATTTTC
*
1001521 GCAGACCCCAAAACTCGATATTTTATTAAAATAAAATGTTTTATTAAAACCACCCAGTTTTTACG
66 GCAGACCCCAAAACTCGATATTTTATTAAAATAAAATGTTTTATTAAAACCACCCAATTTTTACG
* *
1001586 GTGTTCCAATCTCACCTTAAATGATTGGTGGAGACTCCTCACACTTCGAAACGATT
131 GTGCTCCAATCTCACCTTAAATGATTGGTGGAGAATCCTCACACTTCGAAACGATT
1001642 TTCAAAGAGA
Statistics
Matches: 173, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
187 166 0.96
188 7 0.04
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (188 bp):
CGCTTGTGGGGGTACTAATCCTTCCCCACGCGTAACTGACTCCCGAACCTGATCTCTGGATTTTC
GCAGACCCCAAAACTCGATATTTTATTAAAATAAAATGTTTTATTAAAACCACCCAATTTTTACG
GTGCTCCAATCTCACCTTAAATGATTGGTGGAGAATCCTCACACTTCGAAACGATTGA
Found at i:1002861 original size:27 final size:27
Alignment explanation
Indices: 1002831--1002885 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1002821 AAAAACAATT
1002831 AATATAAACATGAAATAAAAAGGTGTC
1 AATATAAACATGAAATAAAAAGGTGTC
1002858 AATATAAACATGAAATAAAAAGGTGTC
1 AATATAAACATGAAATAAAAAGGTGTC
1002885 A
1 A
1002886 TCAACTACCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (27 bp):
AATATAAACATGAAATAAAAAGGTGTC
Found at i:1003483 original size:17 final size:16
Alignment explanation
Indices: 1003451--1003482 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1003441 CAAGCTCGAC
*
1003451 TCGAACTCGAAAAAAA
1 TCGAACTCAAAAAAAA
1003467 TCGAACTCAAAAAAAA
1 TCGAACTCAAAAAAAA
1003483 AAATCAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.19, G:0.09, T:0.12
Consensus pattern (16 bp):
TCGAACTCAAAAAAAA
Found at i:1006873 original size:29 final size:29
Alignment explanation
Indices: 1006837--1006893 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
1006827 AGTGTTGACC
1006837 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
1006866 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
1006894 ACCCTTGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.35, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:1006928 original size:21 final size:21
Alignment explanation
Indices: 1006902--1006943 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1006892 CTACCCTTGC
1006902 TCAAACAGAGAGAATGAACGT
1 TCAAACAGAGAGAATGAACGT
1006923 TCAAACAGAGAGAATGAACGT
1 TCAAACAGAGAGAATGAACGT
1006944 GTTGCATGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.24, T:0.14
Consensus pattern (21 bp):
TCAAACAGAGAGAATGAACGT
Found at i:1007006 original size:29 final size:29
Alignment explanation
Indices: 1006973--1007028 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
1006963 TCCCAACACA
* *
1006973 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCAACCTTG
1007002 TAGGTCGCCATGCACTCCGGGCAACCT
1 TAGGTCGCCATGCACTCCGGGCAACCT
1007029 ACCTTCGCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.14, C:0.38, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCAACCTTG
Found at i:1007073 original size:33 final size:33
Alignment explanation
Indices: 1007036--1007100 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1007026 CCTACCTTCG
*
1007036 CTCGGCTT-CCCTCGGATTCCCTCGCATAGCTCT
1 CTCGG-TTGCCCTCGGATGCCCTCGCATAGCTCT
1007069 CTCGGTTGCCCTCGGATGCCCTCGCATAGCTC
1 CTCGGTTGCCCTCGGATGCCCTCGCATAGCTC
1007101 GTTCGGATGG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.07
33 28 0.93
ACGTcount: A:0.09, C:0.42, G:0.22, T:0.28
Consensus pattern (33 bp):
CTCGGTTGCCCTCGGATGCCCTCGCATAGCTCT
Found at i:1007088 original size:10 final size:10
Alignment explanation
Indices: 1007044--1007170 Score: 56
Period size: 10 Copynumber: 11.3 Consensus size: 10
1007034 CGCTCGGCTT
*
1007044 CCCTCGGATT
1 CCCTCGGATG
*
1007054 CCCTCGCATAG
1 CCCTCGGAT-G
*
1007065 CTCTCTCGGTTG
1 C-C-CTCGGATG
1007077 CCCTCGGATG
1 CCCTCGGATG
*
1007087 CCCTCGCATAG
1 CCCTCGGAT-G
*
1007098 CTCGTTCGGATGG
1 C-C-CTCGGAT-G
1007111 CCTCGGTCGGATG
1 CC-C--TCGGATG
*
1007124 GCCTCGGATG
1 CCCTCGGATG
*
1007134 CTCTCGGATGG
1 CCCTCGGAT-G
1007145 CCTCGGTCGGATG
1 CC-C--TCGGATG
*
1007158 GCCTCGGATG
1 CCCTCGGATG
1007168 CCC
1 CCC
1007171 AGCGTGTTGG
Statistics
Matches: 88, Mismatches: 17, Indels: 24
0.68 0.13 0.19
Matches are distributed among these distances:
10 46 0.52
11 6 0.07
12 8 0.09
13 16 0.18
14 12 0.14
ACGTcount: A:0.09, C:0.35, G:0.31, T:0.24
Consensus pattern (10 bp):
CCCTCGGATG
Found at i:1007115 original size:33 final size:33
Alignment explanation
Indices: 1007044--1007116 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
1007034 CGCTCGGCTT
* *
1007044 CCCTCGGATTCCCTCGCATAGCTCTCTCGGTTG
1 CCCTCGGATGCCCTCGCATAGCTCTCTCGGATG
1007077 CCCTCGGATGCCCTCGCATAGCTCGT-TCGGATG
1 CCCTCGGATGCCCTCGCATAGCTC-TCTCGGATG
*
1007110 GCCTCGG
1 CCCTCGG
1007117 TCGGATGGCC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.10, C:0.38, G:0.26, T:0.26
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAGCTCTCTCGGATG
Found at i:1007120 original size:14 final size:14
Alignment explanation
Indices: 1007098--1007164 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
1007088 CCTCGCATAG
*
1007098 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
1007112 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1007126 CTCGGATGCTCTCGGATGGC
1 CTC-G--G---TCGGATGGC
1007146 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
1007160 CTCGG
1 CTCGG
1007165 ATGCCCAGCG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 30 0.65
15 1 0.02
17 2 0.04
19 1 0.02
20 12 0.26
ACGTcount: A:0.07, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:1007146 original size:34 final size:35
Alignment explanation
Indices: 1007080--1007168 Score: 135
Period size: 34 Copynumber: 2.5 Consensus size: 35
1007070 TCGGTTGCCC
* *
1007080 TCGGATGCCCTCGCATAGCTCGTTCGGATGGCCTCGG
1 TCGGATGGCCTCGGAT-GCTCG-TCGGATGGCCTCGG
1007117 TCGGATGGCCTCGGATGCTC-TCGGATGGCCTCGG
1 TCGGATGGCCTCGGATGCTCGTCGGATGGCCTCGG
1007151 TCGGATGGCCTCGGATGC
1 TCGGATGGCCTCGGATGC
1007169 CCAGCGTGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
34 32 0.64
36 4 0.08
37 14 0.28
ACGTcount: A:0.10, C:0.30, G:0.36, T:0.24
Consensus pattern (35 bp):
TCGGATGGCCTCGGATGCTCGTCGGATGGCCTCGG
Found at i:1014112 original size:37 final size:36
Alignment explanation
Indices: 1014037--1014112 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1014027 TTTTTATATT
*
1014037 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
1014073 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
1014110 TTT
1 TTT
1014113 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:1015877 original size:19 final size:19
Alignment explanation
Indices: 1015853--1015929 Score: 64
Period size: 19 Copynumber: 3.8 Consensus size: 19
1015843 TTATTAAAAG
*
1015853 TTATAACATAATATTTCAA
1 TTATAAGATAATATTTCAA
* *
1015872 TTATAAGATATTATTTTTTAAA
1 TTATAAGATA--A-TATTTCAA
* *
1015894 GTTATAATATAATCTTTCAA
1 -TTATAAGATAATATTTCAA
*
1015914 TTATAAGATATTATTT
1 TTATAAGATAATATTT
1015930 TATTATTATT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
19 22 0.49
20 6 0.13
21 2 0.04
22 6 0.13
23 9 0.20
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (19 bp):
TTATAAGATAATATTTCAA
Found at i:1015897 original size:42 final size:42
Alignment explanation
Indices: 1015849--1015930 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
1015839 CGTATTATTA
1015849 AAAGTTATAACATAATATTTCAATTATAAGATATTATTTTTT
1 AAAGTTATAACATAATATTTCAATTATAAGATATTATTTTTT
* *
1015891 AAAGTTATAATATAATCTTTCAATTATAAGATATTATTTT
1 AAAGTTATAACATAATATTTCAATTATAAGATATTATTTT
1015931 ATTATTATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (42 bp):
AAAGTTATAACATAATATTTCAATTATAAGATATTATTTTTT
Found at i:1015937 original size:21 final size:21
Alignment explanation
Indices: 1015871--1015938 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 21
1015861 TAATATTTCA
1015871 ATTATAAGATATTATTTT-TT
1 ATTATAAGATATTATTTTATT
* * * *
1015891 AAAGTTATAATATAATCTTTCA--
1 --A-TTATAAGATATTATTTTATT
1015913 ATTATAAGATATTATTTTATT
1 ATTATAAGATATTATTTTATT
1015934 ATTAT
1 ATTAT
1015939 TTTTATTATT
Statistics
Matches: 34, Mismatches: 8, Indels: 9
0.67 0.16 0.18
Matches are distributed among these distances:
19 14 0.41
20 1 0.03
21 5 0.15
22 1 0.03
23 13 0.38
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.53
Consensus pattern (21 bp):
ATTATAAGATATTATTTTATT
Found at i:1019723 original size:22 final size:22
Alignment explanation
Indices: 1019657--1019723 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1019647 GTTTTTGAAT
*
1019657 AAATGATTTGTATTATGTTATA
1 AAATGATTTTTATTATGTTATA
* * *
1019679 AAATATATTTTTAACT-TG-AATA
1 AAAT-GATTTTT-ATTATGTTATA
1019701 AAATGATTTTTATTATGTTATA
1 AAATGATTTTTATTATGTTATA
1019723 A
1 A
1019724 TTTTTGGGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
20 2 0.06
21 8 0.24
22 15 0.44
23 7 0.21
24 2 0.06
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.49
Consensus pattern (22 bp):
AAATGATTTTTATTATGTTATA
Found at i:1021931 original size:21 final size:20
Alignment explanation
Indices: 1021891--1021972 Score: 121
Period size: 20 Copynumber: 4.0 Consensus size: 20
1021881 AATAGAATGT
1021891 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
1021911 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
1021931 CCAGGGGGAACAGATTCCCCC
1 CCAGGGGGTACAGATT-CCCC
1021952 CCAGGGGGTATC-GATTCCCC
1 CCAGGGGGTA-CAGATTCCCC
1021972 C
1 C
1021973 TGTCTAACGG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
20 38 0.68
21 17 0.30
22 1 0.02
ACGTcount: A:0.18, C:0.38, G:0.29, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Done.