Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007999.1 Hibiscus syriacus cultivar Beakdansim tig00110450_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: 11700749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 50
Found at i:1051362 original size:13 final size:13
Alignment explanation
Indices: 1051346--1051375 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1051336 AATGCACCCC
*
1051346 TGCAGTGCATCCT
1 TGCAGTGCATCCA
1051359 TGCAGTGCATCCA
1 TGCAGTGCATCCA
1051372 TGCA
1 TGCA
1051376 CCTGCACTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (13 bp):
TGCAGTGCATCCA
Found at i:1051387 original size:22 final size:23
Alignment explanation
Indices: 1051362--1051404 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1051352 GCATCCTTGC
1051362 AGTGCATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
1051384 AGTGCATCGATGCACCATGCA
1 AGTGCATCCATGCACCATGCA
1051405 GTGCAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:1052641 original size:19 final size:20
Alignment explanation
Indices: 1052617--1052664 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
1052607 AACGATTTTC
*
1052617 TTTTGAAAACAAAAAT-AGA
1 TTTTGAAAACAAAAATGAAA
* *
1052636 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
1052656 TTTTGAAAA
1 TTTTGAAAA
1052665 AGGATTTAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:1053978 original size:29 final size:30
Alignment explanation
Indices: 1053910--1053967 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 30
1053900 ATTTAAGGCA
1053910 AAATGGTTTTTGGACTTGAATTGAATTTAAT
1 AAAT-GTTTTTGGACTTGAATTGAATTTAAT
1053941 AAATGTTTTTGGACTT-AATTGAATTTA
1 AAATGTTTTTGGACTTGAATTGAATTTA
1053968 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.41
30 12 0.44
31 4 0.15
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (30 bp):
AAATGTTTTTGGACTTGAATTGAATTTAAT
Found at i:1054096 original size:22 final size:23
Alignment explanation
Indices: 1054068--1054110 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1054058 GCACCCCTGC
1054068 AGTGCATCCATGCACC-TGCACT
1 AGTGCATCCATGCACCATGCACT
*
1054090 AGTGCATCGATGCACCATGCA
1 AGTGCATCCATGCACCATGCA
1054111 GAGCATCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.26, C:0.33, G:0.21, T:0.21
Consensus pattern (23 bp):
AGTGCATCCATGCACCATGCACT
Found at i:1054603 original size:34 final size:32
Alignment explanation
Indices: 1054563--1054632 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
1054553 TTTTGTAAAG
* *
1054563 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1054597 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1054629 GGGA
1 GGGA
1054633 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1055821 original size:55 final size:55
Alignment explanation
Indices: 1055755--1056002 Score: 368
Period size: 55 Copynumber: 4.6 Consensus size: 55
1055745 GTATGTGTAA
* *
1055755 AAAATTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGACACTTTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTTTGTGTGC
* *
1055810 AAAACTAAGAAATTCATAATAA-TTTATGAATTTCCGTATGGGAC-CCTCGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT-GGACACTTTGTGTGC
**
1055864 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTTTGTGTGC
1055919 AAAACTAAGAAATTC---ATAA--TTATGAATTTCCGTAT-GAGCACTTTGTGTGC
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGA-CACTTTGTGTGC
1055969 AAAACTAAGAAATTCATAATAAGTTTATGAATTT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTT
1056003 TCATATTGGT
Statistics
Matches: 174, Mismatches: 10, Indels: 18
0.86 0.05 0.09
Matches are distributed among these distances:
49 1 0.01
50 42 0.24
52 4 0.02
53 4 0.02
54 48 0.28
55 75 0.43
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.35
Consensus pattern (55 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGACACTTTGTGTGC
Found at i:1056022 original size:105 final size:107
Alignment explanation
Indices: 1055755--1056013 Score: 382
Period size: 105 Copynumber: 2.4 Consensus size: 107
1055745 GTATGTGTAA
* *
1055755 AAAATTAAGAAATTCATAATAAGTTTATGAATTTTCGTA-TGGACACTTTGTGTGCAAAACTAAG
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGG-TACTTTGTGTGCAAAACTAAG
*
1055819 AAATTCATAATAATTTATGAATTTCCGTATGGGACCCTCGTGTGC
65 AAATTC--AATAATTTATGAATTTCCGTATGGCACCCTCGTGTGC
* *
1055864 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTGTGTGCAAAACTAAGA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGTACTTTGTGTGCAAAACTAAGA
* *
1055929 AATTC-ATAA-TTATGAATTTCCGTATGAGCA-CTTTGTGTGC
66 AATTCAATAATTTATGAATTTCCGTATG-GCACCCTCGTGTGC
*
1055969 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGTA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGTA
1056014 GGGGGTGTGA
Statistics
Matches: 138, Mismatches: 10, Indels: 8
0.88 0.06 0.05
Matches are distributed among these distances:
105 67 0.49
106 6 0.04
109 63 0.46
110 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (107 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGTACTTTGTGTGCAAAACTAAGA
AATTCAATAATTTATGAATTTCCGTATGGCACCCTCGTGTGC
Found at i:1056037 original size:105 final size:104
Alignment explanation
Indices: 1055755--1056042 Score: 292
Period size: 105 Copynumber: 2.7 Consensus size: 104
1055745 GTATGTGTAA
* * * ** *** *
1055755 AAAATTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGACACTTTGTGTGCAAAACTAAGA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGTACGGGGTGTGCAAAACCAAGA
*
1055820 AATTCATAATAATTTATGAATTTCCGTATGGGACCCTCGTGTGC
66 AA-T--T-ATAA-TTATGAATTTCCGTATGGCACCCTCGTGTGC
* *** *
1055864 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGTACTTTGTGTGCAAAACTAAGA
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGTACGGGGTGTGCAAAACCAAGA
* *
1055929 AATTCATAATTATGAATTTCCGTATGAGCA-CTTTGTGTGC
66 AATT-ATAATTATGAATTTCCGTATG-GCACCCTCGTGTGC
* * * * *
1055969 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGTAGGGGGTGTG-AAACCCACAT
1 AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGTACGGGGTGTGCAAAACCA-AG
1056033 AAATTATAAT
65 AAATTATAAT
1056043 AAGTTGTGAA
Statistics
Matches: 159, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
104 10 0.06
105 78 0.49
106 7 0.04
108 1 0.01
109 63 0.40
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (104 bp):
AAAACTAAGAAATTCATAATAAGTTTATGAATTTCCATATGGGTACGGGGTGTGCAAAACCAAGA
AATTATAATTATGAATTTCCGTATGGCACCCTCGTGTGC
Found at i:1060569 original size:20 final size:20
Alignment explanation
Indices: 1060546--1060584 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1060536 TAGTATCAAT
* *
1060546 ACCCAGGGGTCGGTATCGAC
1 ACCCAGAGGTCAGTATCGAC
1060566 ACCCAGAGGTCAGTATCGA
1 ACCCAGAGGTCAGTATCGA
1060585 TACTAAAGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.28, G:0.31, T:0.15
Consensus pattern (20 bp):
ACCCAGAGGTCAGTATCGAC
Found at i:1063110 original size:23 final size:23
Alignment explanation
Indices: 1063076--1063145 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
1063066 GAGTCGAGGG
*
1063076 TTCTACGCGGTCATTCGGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
* * *
1063099 TTCTAGGTGGTCCTTCGGG-TCAT
1 TTCTACGCGGTCCTTCGGGAT-AA
1063122 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
1063145 T
1 T
1063146 ACTGTGGTCC
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.95
24 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.27, T:0.34
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGATAA
Found at i:1063128 original size:46 final size:44
Alignment explanation
Indices: 1063076--1063167 Score: 130
Period size: 46 Copynumber: 2.0 Consensus size: 44
1063066 GAGTCGAGGG
* *
1063076 TTCTACGCGGTCATTCGGGATAATTCTAGGTGGTCCTTCGGGTCAT
1 TTCTACGCGGTCATTCGGGATAATACT--GTGGTCCTTCGGGGCAT
* *
1063122 TTCTACGCGGTCCTTCGGGATAATACTGTGGTCCTTTGGGGCAT
1 TTCTACGCGGTCATTCGGGATAATACTGTGGTCCTTCGGGGCAT
1063166 TT
1 TT
1063168 ATATATGGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 17 0.40
46 25 0.60
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.36
Consensus pattern (44 bp):
TTCTACGCGGTCATTCGGGATAATACTGTGGTCCTTCGGGGCAT
Found at i:1072561 original size:45 final size:44
Alignment explanation
Indices: 1072493--1072636 Score: 182
Period size: 44 Copynumber: 3.2 Consensus size: 44
1072483 TGTTGGATTT
** * * *
1072493 CCAACTTATTT-ATCGAACTATGTTGGAGATGTTACCAGCATTA
1 CCAACTTATTTCATAAAACTATGTTAGAGCTATTACCAGCATTA
*
1072536 CCTAACTTATTTCATAAAACTATGTTAGAGCTATAACCAGCATTA
1 CC-AACTTATTTCATAAAACTATGTTAGAGCTATTACCAGCATTA
* * *
1072581 CCAACTTATTTCCTAAAACTATATTAGAGCTATTACCAACATTA
1 CCAACTTATTTCATAAAACTATGTTAGAGCTATTACCAGCATTA
1072625 CCCAACTTATTT
1 -CCAACTTATTT
1072637 TCTACATTTC
Statistics
Matches: 88, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
43 2 0.02
44 47 0.53
45 39 0.44
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (44 bp):
CCAACTTATTTCATAAAACTATGTTAGAGCTATTACCAGCATTA
Found at i:1074396 original size:19 final size:19
Alignment explanation
Indices: 1074350--1074396 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1074340 CCAATCTATT
*
1074350 GATGGTATGAACATTAGTA
1 GATGATATGAACATTAGTA
*
1074369 GATGGTATGAACATTAGTA
1 GATGATATGAACATTAGTA
*
1074388 GTTGATATG
1 GATGATATG
1074397 GTCTACGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (19 bp):
GATGATATGAACATTAGTA
Found at i:1074398 original size:24 final size:19
Alignment explanation
Indices: 1074350--1074388 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1074340 CCAATCTATT
1074350 GATGGTATGAACATTAGTA
1 GATGGTATGAACATTAGTA
1074369 GATGGTATGAACATTAGTA
1 GATGGTATGAACATTAGTA
1074388 G
1 G
1074389 TTGATATGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (19 bp):
GATGGTATGAACATTAGTA
Found at i:1082365 original size:45 final size:45
Alignment explanation
Indices: 1082287--1082390 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 45
1082277 TGTTTGATTT
* *
1082287 CCAACTTATTT-CTCAAACTATGTTGGAGCTATTACCAGCATTAC
1 CCAACTTATTTCCTAAAACTATGTTAGAGCTATTACCAGCATTAC
* *
1082331 CCAACTTATTTCCTAAAACTATGTTAGAGTTATTACCAGGATTAC
1 CCAACTTATTTCCTAAAACTATGTTAGAGCTATTACCAGCATTAC
1082376 CCAACTTATTTCCTA
1 CCAACTTATTTCCTA
1082391 CTTATCTCTC
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
44 11 0.20
45 44 0.80
ACGTcount: A:0.31, C:0.24, G:0.10, T:0.36
Consensus pattern (45 bp):
CCAACTTATTTCCTAAAACTATGTTAGAGCTATTACCAGCATTAC
Found at i:1094410 original size:28 final size:28
Alignment explanation
Indices: 1094359--1094414 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1094349 AATTATCTAG
**
1094359 ATTATTTTACGAATATTTTTAGATATAT
1 ATTATTTTACGAATATTTCAAGATATAT
1094387 ATTATTTTA-GAATATTATCAAGATATAT
1 ATTATTTTACGAATATT-TCAAGATATAT
1094415 CTCATAAATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 7 0.28
28 18 0.72
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (28 bp):
ATTATTTTACGAATATTTCAAGATATAT
Found at i:1094550 original size:20 final size:20
Alignment explanation
Indices: 1094525--1094576 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1094515 ATAAATTTAG
*
1094525 TTAATTTCTACAAATCACTT
1 TTAATTTATACAAATCACTT
*
1094545 TTAATTTATACAAATCCCTT
1 TTAATTTATACAAATCACTT
1094565 TTAATTTGATAC
1 TTAATTT-ATAC
1094577 TTTAATTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 25 0.86
21 4 0.14
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (20 bp):
TTAATTTATACAAATCACTT
Found at i:1106766 original size:18 final size:19
Alignment explanation
Indices: 1106727--1106769 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1106717 GGATATGAAT
1106727 GGTCAATCCGTAGTGTTAA
1 GGTCAATCCGTAGTGTTAA
1106746 GGTCAATCCGTAGTG-TAA
1 GGTCAATCCGTAGTGTTAA
1106764 GGTCAA
1 GGTCAA
1106770 CATTGATGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (19 bp):
GGTCAATCCGTAGTGTTAA
Found at i:1124032 original size:30 final size:30
Alignment explanation
Indices: 1123996--1124068 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
1123986 CCCGAAGGAC
*
1123996 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1124026 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
1124056 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1124069 CGAAGAACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:1124088 original size:30 final size:30
Alignment explanation
Indices: 1124054--1124205 Score: 105
Period size: 30 Copynumber: 5.0 Consensus size: 30
1124044 GATCCTCGGC
*
1124054 AACTGTCCATAGGTCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCGAAGAACATAGGTA
* **
1124084 AACTGTCC-TATGTTCCTTAGAACATAGGTA
1 AACTGTCCATA-GGTCCGAAGAACATAGGTA
* *
1124114 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTC-CGAAGA-ACATAGGTA
** * * **
1124145 TTCTGTCTATA-TTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCGAAGAACATAGGTA
* *
1124174 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTGTCCATAGGTC-CGAAGA-ACATAGGTA
1124205 A
1 A
1124206 TTCTATCCAT
Statistics
Matches: 94, Mismatches: 20, Indels: 15
0.73 0.16 0.12
Matches are distributed among these distances:
29 22 0.23
30 39 0.41
31 33 0.35
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (30 bp):
AACTGTCCATAGGTCCGAAGAACATAGGTA
Found at i:1124123 original size:60 final size:61
Alignment explanation
Indices: 1124055--1124239 Score: 268
Period size: 60 Copynumber: 3.0 Consensus size: 61
1124045 ATCCTCGGCA
* * *
1124055 ACTGTCCATAGGTC-CG-AAGAACCTAGGTAAACTGTCCTATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCTCGAAAG-ACATAGGTAATCTGTCCTATGTTCCTTAGAACATAGGTAT
* *
1124115 ACTGTCCATATGTCTCGAAAGACATAGGTATTCTGT-CTATATTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCTCGAAAGACATAGGTAATCTGTCCTATGTTCCTTAGAACATAGGTAT
*
1124175 ACTGTCCATATGTCTCGAAAGACATAGGTAATTCTATCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCTCGAAAGACATAGGTAA-TCTGTCC-TATGTTCCTTAGAACATAGGTAT
1124238 AC
1 AC
1124240 CCTCAACTCT
Statistics
Matches: 112, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
60 66 0.59
61 18 0.16
62 4 0.04
63 24 0.21
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (61 bp):
ACTGTCCATATGTCTCGAAAGACATAGGTAATCTGTCCTATGTTCCTTAGAACATAGGTAT
Found at i:1124140 original size:31 final size:32
Alignment explanation
Indices: 1124055--1124239 Score: 156
Period size: 31 Copynumber: 6.1 Consensus size: 32
1124045 ATCCTCGGCA
* * *
1124055 ACTGTCCATAGGTC-CG-AAGAACCTAGGTAA
1 ACTGTCCATATGTCTCGAAAGAACATAGGTAT
***
1124085 ACTGTCC-TATGT-TCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCTCGAAAGAACATAGGTAT
1124115 ACTGTCCATATGTCTCGAAAG-ACATAGGTAT
1 ACTGTCCATATGTCTCGAAAGAACATAGGTAT
* * **
1124146 TCTGTCTATAT-TC-C-TTAGAACATAGGTAT
1 ACTGTCCATATGTCTCGAAAGAACATAGGTAT
1124175 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAT
1 ACTGTCCATATGTCTCGAAAGAACATAGGT-AT
* * ***
1124207 TCTATCCATATGT-TCCTTAGAACATAGGTAT
1 ACTGTCCATATGTCTCGAAAGAACATAGGTAT
1124238 AC
1 AC
1124240 CCTCAACTCT
Statistics
Matches: 123, Mismatches: 22, Indels: 19
0.75 0.13 0.12
Matches are distributed among these distances:
28 2 0.02
29 25 0.20
30 29 0.24
31 40 0.33
32 27 0.22
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (32 bp):
ACTGTCCATATGTCTCGAAAGAACATAGGTAT
Found at i:1128673 original size:31 final size:31
Alignment explanation
Indices: 1128605--1128789 Score: 177
Period size: 31 Copynumber: 6.1 Consensus size: 31
1128595 ATCCTCAGCA
* * *
1128605 ACTGTCCATAGGTTCCGAAGAACCTAGGTA-
1 ACTGTCCATATGTTCCTAAGAACATAGGTAT
*
1128635 ACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTTCCTAAGAACATAGGTAT
**
1128666 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAT
1 ACTGTCCATATGT-TCCTAAGAACATAGGT-AT
* *
1128698 TCTGTCCA-ATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATATGTTCCTAAGAACATAGGTAT
**
1128728 ACTGTCCATATGTCTCGAAAG-ACATAGGTAAT
1 ACTGTCCATATGT-TCCTAAGAACATAGGT-AT
* *
1128760 TCTGTCCATAT-TTCCTTAGAAC--AGGTAT
1 ACTGTCCATATGTTCCTAAGAACATAGGTAT
1128788 AC
1 AC
1128790 CCTCACTCTT
Statistics
Matches: 127, Mismatches: 20, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
28 3 0.02
29 4 0.03
30 43 0.34
31 48 0.38
32 29 0.23
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (31 bp):
ACTGTCCATATGTTCCTAAGAACATAGGTAT
Found at i:1128722 original size:62 final size:63
Alignment explanation
Indices: 1128629--1128789 Score: 280
Period size: 62 Copynumber: 2.7 Consensus size: 63
1128619 CCGAAGAACC
1128629 TAGGTAA--CTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1128690 TAGGTAATTCTGTCCA-ATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1128752 TAGGTAATTCTGTCCATAT-TTCCTTAGAAC--AGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATAC
1128790 CCTCACTCTT
Statistics
Matches: 97, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
60 8 0.08
61 7 0.07
62 73 0.75
63 9 0.09
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
Found at i:1144751 original size:12 final size:12
Alignment explanation
Indices: 1144734--1144758 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1144724 AAGTGAAGAT
1144734 GAAAATTATGGG
1 GAAAATTATGGG
1144746 GAAAATTATGGG
1 GAAAATTATGGG
1144758 G
1 G
1144759 GGGGGGGAAA
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:0.40, C:0.00, G:0.36, T:0.24
Consensus pattern (12 bp):
GAAAATTATGGG
Found at i:1148082 original size:10 final size:11
Alignment explanation
Indices: 1148067--1148095 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1148057 TATAGTGAAG
1148067 AAAATTAT-GA
1 AAAATTATGGA
1148077 AAAATTATGGA
1 AAAATTATGGA
1148088 AAAATTAT
1 AAAATTAT
1148096 ATAAGTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (11 bp):
AAAATTATGGA
Found at i:1149277 original size:58 final size:58
Alignment explanation
Indices: 1149207--1149319 Score: 217
Period size: 58 Copynumber: 1.9 Consensus size: 58
1149197 GAATCATTGG
1149207 TACAATTGACATGCTATGAGGTGGAGCGATTATCGATCGATCTTATATGGGTACACGA
1 TACAATTGACATGCTATGAGGTGGAGCGATTATCGATCGATCTTATATGGGTACACGA
*
1149265 TACAATTGACATGCTATGAGGTGGAGTGATTATCGATCGATCTTATATGGGTACA
1 TACAATTGACATGCTATGAGGTGGAGCGATTATCGATCGATCTTATATGGGTACA
1149320 TTCGTGTACG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (58 bp):
TACAATTGACATGCTATGAGGTGGAGCGATTATCGATCGATCTTATATGGGTACACGA
Found at i:1152978 original size:18 final size:18
Alignment explanation
Indices: 1152952--1152986 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1152942 ACCCGATCTG
1152952 ACCCGACCCGACCCATTA
1 ACCCGACCCGACCCATTA
*
1152970 ACCCTACCCGACCCATT
1 ACCCGACCCGACCCATT
1152987 GACCTGACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.51, G:0.09, T:0.14
Consensus pattern (18 bp):
ACCCGACCCGACCCATTA
Found at i:1153003 original size:13 final size:13
Alignment explanation
Indices: 1152985--1153016 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
1152975 ACCCGACCCA
1152985 TTGACCTGACTCG
1 TTGACCTGACTCG
1152998 TTGACCTGACTCG
1 TTGACCTGACTCG
1153011 TTGACC
1 TTGACC
1153017 AACCGTTGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (13 bp):
TTGACCTGACTCG
Found at i:1157188 original size:24 final size:24
Alignment explanation
Indices: 1157154--1157262 Score: 89
Period size: 24 Copynumber: 4.5 Consensus size: 24
1157144 GAATATTTTA
* *
1157154 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATATCTGATCTGAATTCTGT
* * *
1157178 TTTGATATCTGATCTGAAATCTAT
1 TCTGATATCTGATCTGAATTCTGT
* *
1157202 TCTGAT-TCCTAACCT-AGATTCTGT
1 TCTGATAT-CTGATCTGA-ATTCTGT
*
1157226 TCTGATATCTGATCTGAATTATGCT
1 TCTGATATCTGATCTGAATTCTG-T
*
1157251 T-TGATTTCTGAT
1 TCTGATATCTGAT
1157263 ATCTCCATTT
Statistics
Matches: 66, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
23 2 0.03
24 60 0.91
25 4 0.06
ACGTcount: A:0.22, C:0.16, G:0.15, T:0.48
Consensus pattern (24 bp):
TCTGATATCTGATCTGAATTCTGT
Found at i:1160803 original size:15 final size:15
Alignment explanation
Indices: 1160783--1160812 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1160773 AAAGTAATTT
*
1160783 GAGGATTCGTACTTA
1 GAGGATTCATACTTA
1160798 GAGGATTCATACTTA
1 GAGGATTCATACTTA
1160813 ACTCGATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (15 bp):
GAGGATTCATACTTA
Found at i:1162341 original size:24 final size:24
Alignment explanation
Indices: 1162235--1162341 Score: 81
Period size: 24 Copynumber: 4.5 Consensus size: 24
1162225 ATATTTTATC
* * *
1162235 TGATTTCTAATTTGAATTCTGTTT
1 TGATTTCTGATCTGAATTATGTTT
** * * *
1162259 TGACATCTGATATGAAATATGTTC
1 TGATTTCTGATCTGAATTATGTTT
* * * * *
1162283 TGATTCCTAACCTGGATTATGTTA
1 TGATTTCTGATCTGAATTATGTTT
1162307 TGATATT-TGATCTGAATTATGTTT
1 TGAT-TTCTGATCTGAATTATGTTT
1162331 TGATTTCTGAT
1 TGATTTCTGAT
1162342 ATCTCCATTT
Statistics
Matches: 60, Mismatches: 21, Indels: 4
0.71 0.25 0.05
Matches are distributed among these distances:
23 2 0.03
24 57 0.95
25 1 0.02
ACGTcount: A:0.25, C:0.10, G:0.16, T:0.49
Consensus pattern (24 bp):
TGATTTCTGATCTGAATTATGTTT
Found at i:1165283 original size:84 final size:84
Alignment explanation
Indices: 1165138--1165393 Score: 300
Period size: 84 Copynumber: 3.0 Consensus size: 84
1165128 AGACCTAAGG
* * *
1165138 ATACCCTTGGGTAGGCCCATAGGCCCCAAGGCATATCCTTAGGTTTGTTCCCTTTGTTGTGTGCT
1 ATACCCTTGGGTA-GCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
1165203 TAGGGTAACCCTACGGATCT-
65 TAGGGTAA-CCTACGGATCTA
*
1165223 A-ACCCTTGGGTAGTCCCATAGGCCCCAGGGAATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
1 ATACCCTTGGGTAG-CCCATAGGCCCCAAGGAATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCT
*
1165287 TAGGGTAACCTACAGATCTAA
65 TAGGGTAACCTACGGATCT-A
* * * * * *
1165308 GGATACCCTTGGGTAGGCAATAGTCCCCAAGGAATATCCTTAGGTTGGCTCCATTTTTGCTATGT
1 --ATACCCTTGGGTAGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTTCC--CTTTGCTGTGT
*
1165373 GCTTAGGATAAGTCCTACGGA
62 GCTTAGGGTAA--CCTACGGA
1165394 CGCAGTTATG
Statistics
Matches: 147, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
83 11 0.07
84 65 0.44
85 1 0.01
87 32 0.22
88 12 0.08
89 19 0.13
91 7 0.05
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (84 bp):
ATACCCTTGGGTAGCCCATAGGCCCCAAGGAATATCCTTAGGTTGGTTCCCTTTGCTGTGTGCTT
AGGGTAACCTACGGATCTA
Found at i:1173302 original size:16 final size:16
Alignment explanation
Indices: 1173281--1173314 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1173271 ATATATTTTA
1173281 TAAATGACCATTAAAT
1 TAAATGACCATTAAAT
**
1173297 TAAATGAGTATTAAAT
1 TAAATGACCATTAAAT
1173313 TA
1 TA
1173315 TATTGGAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (16 bp):
TAAATGACCATTAAAT
Found at i:1173775 original size:27 final size:27
Alignment explanation
Indices: 1173739--1173797 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1173729 GAAATTAGGT
1173739 AAAC-TAATAATATGGTCAATTAACAA
1 AAACATAATAATATGGTCAATTAACAA
*
1173765 AAACATAATAATATGGTCATTTAACAA
1 AAACATAATAATATGGTCAATTAACAA
1173792 AAACAT
1 AAACAT
1173798 GCACATAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 4 0.13
27 27 0.87
ACGTcount: A:0.54, C:0.12, G:0.07, T:0.27
Consensus pattern (27 bp):
AAACATAATAATATGGTCAATTAACAA
Found at i:1181858 original size:26 final size:26
Alignment explanation
Indices: 1181822--1181874 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1181812 TGATCCAGGC
1181822 AACTTCATTATTCCCTATTCTATAGG
1 AACTTCATTATTCCCTATTCTATAGG
1181848 AACTTCATTATTCCCTATTCTATAGG
1 AACTTCATTATTCCCTATTCTATAGG
1181874 A
1 A
1181875 GTTAATTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.42
Consensus pattern (26 bp):
AACTTCATTATTCCCTATTCTATAGG
Found at i:1189651 original size:13 final size:13
Alignment explanation
Indices: 1189633--1189663 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1189623 TGACTTTTTT
1189633 GTCAAAGTCAACC
1 GTCAAAGTCAACC
*
1189646 GTCAAAGTCAACG
1 GTCAAAGTCAACC
1189659 GTCAA
1 GTCAA
1189664 CACTCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (13 bp):
GTCAAAGTCAACC
Found at i:1197427 original size:15 final size:16
Alignment explanation
Indices: 1197398--1197428 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1197388 CGACAAATAT
1197398 AAAATATGACTTTTTA
1 AAAATATGACTTTTTA
*
1197414 AAAATTTGACTTTTT
1 AAAATATGACTTTTT
1197429 TGTCAAAGTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
AAAATATGACTTTTTA
Found at i:1197448 original size:13 final size:13
Alignment explanation
Indices: 1197430--1197460 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1197420 TGACTTTTTT
1197430 GTCAAAGTCAACC
1 GTCAAAGTCAACC
*
1197443 GTCAAAGTCAACG
1 GTCAAAGTCAACC
1197456 GTCAA
1 GTCAA
1197461 CACTCAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.16
Consensus pattern (13 bp):
GTCAAAGTCAACC
Found at i:1201729 original size:24 final size:24
Alignment explanation
Indices: 1201697--1201745 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1201687 TAAATATAGT
1201697 ACCAATAAATAATAATTTAATTTA
1 ACCAATAAATAATAATTTAATTTA
1201721 ACCAATAAATAATAATTTAATTTA
1 ACCAATAAATAATAATTTAATTTA
1201745 A
1 A
1201746 AACATGTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (24 bp):
ACCAATAAATAATAATTTAATTTA
Found at i:1202934 original size:22 final size:22
Alignment explanation
Indices: 1202907--1202954 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1202897 AACAGTCAAC
*
1202907 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCG
*
1202929 GGTCAATAGTCGGGTCGGGTCG
1 GGTCAACAGTCGGGTCGGGTCG
1202951 GGTC
1 GGTC
1202955 GGTCGGTGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.21, G:0.48, T:0.21
Consensus pattern (22 bp):
GGTCAACAGTCGGGTCGGGTCG
Found at i:1202961 original size:4 final size:5
Alignment explanation
Indices: 1202914--1202960 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
1202904 AACGGTCAAC
* *
1202914 GGTCG GGTCG GGTCG GGTCAAT AGTCG GGTCG GGTCG GGTC- GGTCG G
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG G
1202961 TGGGGTCAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 4 0.11
5 28 0.80
7 3 0.09
ACGTcount: A:0.06, C:0.19, G:0.53, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1202976 original size:9 final size:9
Alignment explanation
Indices: 1202964--1203023 Score: 57
Period size: 9 Copynumber: 6.3 Consensus size: 9
1202954 CGGTCGGTGG
*
1202964 GGTCAGACC
1 GGTCAAACC
1202973 GGTCAAACC
1 GGTCAAACC
*
1202982 GGTCAAACT
1 GGTCAAACC
*
1202991 GGTTCGAACC
1 GG-TCAAACC
1203001 GGTCGAAAACC
1 GGTC--AAACC
*
1203012 GGTTAAACC
1 GGTCAAACC
1203021 GGT
1 GGT
1203024 TTCCAGCAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 28 0.67
10 7 0.17
11 7 0.17
ACGTcount: A:0.28, C:0.27, G:0.28, T:0.17
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1206023 original size:13 final size:13
Alignment explanation
Indices: 1206001--1206045 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
1205991 GTCACAAACC
*
1206001 GACCCTACCCGTT
1 GACCCGACCCGTT
1206014 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1206027 GACTCGACCCGTT
1 GACCCGACCCGTT
1206040 GACCCG
1 GACCCG
1206046 TTGACCGTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.16, C:0.44, G:0.22, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1206045 original size:8 final size:8
Alignment explanation
Indices: 1206032--1206078 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 8
1206022 CCGTTGACTC
1206032 GACCCGTT
1 GACCCGTT
1206040 GACCCGTT
1 GACCCGTT
1206048 GA-CCGTT
1 GACCCGTT
1206055 GACCGTCGTT
1 GACC--CGTT
1206065 GACCTCTGTT
1 GACC-C-GTT
1206075 GACC
1 GACC
1206079 AAAACTTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.20
8 11 0.31
9 2 0.06
10 15 0.43
ACGTcount: A:0.13, C:0.34, G:0.26, T:0.28
Consensus pattern (8 bp):
GACCCGTT
Found at i:1206055 original size:15 final size:16
Alignment explanation
Indices: 1206035--1206068 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
1206025 TTGACTCGAC
1206035 CCGTTGACC-CGTTGA
1 CCGTTGACCGCGTTGA
1206050 CCGTTGACCGTCGTTGA
1 CCGTTGACCG-CGTTGA
1206067 CC
1 CC
1206069 TCTGTTGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.12, C:0.35, G:0.26, T:0.26
Consensus pattern (16 bp):
CCGTTGACCGCGTTGA
Found at i:1207022 original size:262 final size:270
Alignment explanation
Indices: 1206692--1207228 Score: 966
Period size: 271 Copynumber: 2.0 Consensus size: 270
1206682 AGTATGAATA
*
1206692 GTGATAAAGAAATCAGACATGGATTTGTAATTATATTTTATATCATCAAAGGTTAAATGTTAAAG
1 GTGAAAAAGAAATCAGACATGGATTTGTAATTATATTTTATATCATCAAAGGTTAAATGTTAAAG
*
1206757 GAACTTGGATGAG-AATTAT-AGAATACTCTGGTAGGGT-AAATTACG-AAA-ACTCTTATGTTA
66 GAACTTGGATGAGAAATTATGAGAATACTCTGGTAGGGTAAAATTACGAAAATACCCTTATGTTA
1206817 TAAAAAGACAAGATTTGAATAT-GAAGTTAGATAAGAGGATTTTACAGACATA-TGATCTGATAA
131 TAAAAAGACAAGATTTGAATATGGAAGTTAGATAAGAGGATTTTACAGACATATTGATCTGATAA
* *
1206880 AATATTGATG-GCATAGGAAATGTTAG-TTTCTTTGGAAATTATGGATAACCGGTTTTTAATCCT
196 AATATTGATGTGCATAAGAAATGTTAGTTTTCTTTGGAAATTATGGATAACCGATTTTTAATCCT
1206943 ATGAGAGTTT
261 ATGAGAGTTT
1206953 GTGAAAAAGAAATCAGACATGGATTTGTAAATTATATTTTATATCATCAAAGGTTAAATGTTAAA
1 GTGAAAAAGAAATCAGACATGGATTTGT-AATTATATTTTATATCATCAAAGGTTAAATGTTAAA
1207018 GGAACTTGGATGAGAAATTATGAGAATACTCTGGTAGGGTAAAATTACGAAAATACCCTTATGTT
65 GGAACTTGGATGAGAAATTATGAGAATACTCTGGTAGGGTAAAATTACGAAAATACCCTTATGTT
1207083 ATAAAAAGACAAGATTTGAATATGGAAGTTAGATAAGAGGATTTTACAGACATATTGATCTGATA
130 ATAAAAAGACAAGATTTGAATATGGAAGTTAGATAAGAGGATTTTACAGACATATTGATCTGATA
1207148 AAATATTGATGTGCATAAGAAATGTTAGTTTTCTTTGGAAATTATGGATAACCGATTTTTAATCC
195 AAATATTGATGTGCATAAGAAATGTTAGTTTTCTTTGGAAATTATGGATAACCGATTTTTAATCC
1207213 TATGAGAGTTT
260 TATGAGAGTTT
1207224 GTGAA
1 GTGAA
1207229 GAATACTAGA
Statistics
Matches: 262, Mismatches: 4, Indels: 10
0.95 0.01 0.04
Matches are distributed among these distances:
261 27 0.10
262 50 0.19
263 6 0.02
264 18 0.07
265 8 0.03
266 3 0.01
267 33 0.13
268 30 0.11
269 21 0.08
270 15 0.06
271 51 0.19
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.34
Consensus pattern (270 bp):
GTGAAAAAGAAATCAGACATGGATTTGTAATTATATTTTATATCATCAAAGGTTAAATGTTAAAG
GAACTTGGATGAGAAATTATGAGAATACTCTGGTAGGGTAAAATTACGAAAATACCCTTATGTTA
TAAAAAGACAAGATTTGAATATGGAAGTTAGATAAGAGGATTTTACAGACATATTGATCTGATAA
AATATTGATGTGCATAAGAAATGTTAGTTTTCTTTGGAAATTATGGATAACCGATTTTTAATCCT
ATGAGAGTTT
Found at i:1207781 original size:9 final size:9
Alignment explanation
Indices: 1207767--1207792 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
1207757 AAAACTGAAC
1207767 ACCAAAATT
1 ACCAAAATT
1207776 ACCAAAATT
1 ACCAAAATT
1207785 ACCAAAAT
1 ACCAAAAT
1207793 AACCTTATGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.23, G:0.00, T:0.19
Consensus pattern (9 bp):
ACCAAAATT
Found at i:1208768 original size:12 final size:11
Alignment explanation
Indices: 1208733--1208817 Score: 64
Period size: 12 Copynumber: 7.3 Consensus size: 11
1208723 TTCGAATTAA
1208733 ATTCTGTTCTG
1 ATTCTGTTCTG
*
1208744 ATAC-GTTACCTG
1 ATTCTGTT--CTG
1208756 AATTCTGTTCTG
1 -ATTCTGTTCTG
*
1208768 ATTCTGATCTGG
1 ATTCTGTTCT-G
1208780 ATTCTGTTCTG
1 ATTCTGTTCTG
* *
1208791 ATATCTGATATG
1 AT-TCTGTTCTG
*
1208803 AATTCTGTTTTG
1 -ATTCTGTTCTG
1208815 ATT
1 ATT
1208818 TCTAATATCT
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
10 3 0.05
11 18 0.31
12 30 0.51
13 5 0.08
14 3 0.05
ACGTcount: A:0.19, C:0.15, G:0.18, T:0.48
Consensus pattern (11 bp):
ATTCTGTTCTG
Found at i:1208807 original size:24 final size:24
Alignment explanation
Indices: 1208732--1208825 Score: 95
Period size: 24 Copynumber: 4.0 Consensus size: 24
1208722 TTTCGAATTA
*
1208732 AATTCTGTTCTGATA-C-GTTACCTG
1 AATTCTGTTCTGATATCTGATA--TG
*
1208756 AATTCTGTTCTGAT-TCTGATCTG
1 AATTCTGTTCTGATATCTGATATG
*
1208779 GATTCTGTTCTGATATCTGATATG
1 AATTCTGTTCTGATATCTGATATG
* * *
1208803 AATTCTGTTTTGATTTCTAATAT
1 AATTCTGTTCTGATATCTGATAT
1208826 CTCCGTTTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
23 15 0.25
24 42 0.71
25 2 0.03
ACGTcount: A:0.21, C:0.15, G:0.16, T:0.48
Consensus pattern (24 bp):
AATTCTGTTCTGATATCTGATATG
Found at i:1211137 original size:21 final size:21
Alignment explanation
Indices: 1211111--1211154 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 21
1211101 GCATAAACCA
1211111 AAGCTGGCTGTCTAGCCTCAG
1 AAGCTGGCTGTCTAGCCTCAG
1211132 AA----GCTGTCTAGCCTCAG
1 AAGCTGGCTGTCTAGCCTCAG
1211149 AAGCTG
1 AAGCTG
1211155 TTGGCCCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 8
0.70 0.00 0.30
Matches are distributed among these distances:
17 17 0.89
21 2 0.11
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (21 bp):
AAGCTGGCTGTCTAGCCTCAG
Found at i:1211163 original size:17 final size:17
Alignment explanation
Indices: 1211117--1211155 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
1211107 ACCAAAGCTG
1211117 GCTGTCTAGCCTCAGAA
1 GCTGTCTAGCCTCAGAA
1211134 GCTGTCTAGCCTCAGAA
1 GCTGTCTAGCCTCAGAA
1211151 GCTGT
1 GCTGT
1211156 TGGCCCTCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.26
Consensus pattern (17 bp):
GCTGTCTAGCCTCAGAA
Found at i:1215138 original size:14 final size:14
Alignment explanation
Indices: 1215121--1215154 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1215111 TCGGTCCAGG
*
1215121 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
1215135 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
*
1215149 TGGCTC
1 CGGCTC
1215155 CCTAGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:1215702 original size:32 final size:31
Alignment explanation
Indices: 1215664--1215736 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1215654 TGGGACCACG
*
1215664 GGGCCTACCTGAGAACACATCTCAAGGCCGTA
1 GGGCCTACCTGAGAA-ACATCTCAAGGCCATA
* ** *
1215696 GGGCCTACCCGAGAATGATCTCAGGGCCATA
1 GGGCCTACCTGAGAAACATCTCAAGGCCATA
*
1215727 GAGCCTACCT
1 GGGCCTACCT
1215737 AAGAGTGACA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTGAGAAACATCTCAAGGCCATA
Found at i:1218908 original size:18 final size:18
Alignment explanation
Indices: 1218875--1218909 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1218865 TCCGTCCAAT
*
1218875 CTTATTATTTAATTCAAA
1 CTTATTATCTAATTCAAA
*
1218893 CTTATTATCTATTTCAA
1 CTTATTATCTAATTCAA
1218910 TCTTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
CTTATTATCTAATTCAAA
Found at i:1229342 original size:10 final size:11
Alignment explanation
Indices: 1229318--1229351 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1229308 TTTGAAATTC
*
1229318 TTCTTTTTCTT
1 TTCTTCTTCTT
1229329 TTCTTCTT-TT
1 TTCTTCTTCTT
1229339 TTCTTCTTCTT
1 TTCTTCTTCTT
1229350 TT
1 TT
1229352 TGTTTTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.48
11 11 0.52
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTCTTCTT
Found at i:1243078 original size:3 final size:3
Alignment explanation
Indices: 1243060--1243163 Score: 99
Period size: 3 Copynumber: 35.3 Consensus size: 3
1243050 TATTTGTTCT
* * * *
1243060 TTA TTT TTA ATA TTA TTA TTA ATA TTA TTA TTA TTA TTA TCA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
1243107 -TA CTA TT- TTA TTTA TT- TTA TTA TTA TTA CTTT TTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
*
1243151 ATA TTA TTA TTA T
1 TTA TTA TTA TTA T
1243164 AACAGGCCCA
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
2 8 0.10
3 69 0.84
4 5 0.06
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1245048 original size:17 final size:17
Alignment explanation
Indices: 1244995--1245060 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
1244985 GAAATATAAG
*
1244995 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
1245011 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
1245027 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
1245044 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
1245060 T
1 T
1245061 ATCCAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:1256207 original size:5 final size:5
Alignment explanation
Indices: 1256197--1256267 Score: 56
Period size: 5 Copynumber: 13.8 Consensus size: 5
1256187 AACGGTCAAC
* * * *
1256197 GGTCG GGTCG GGTCAAC GGTCC GATCG GGTCG GGTCG GGTCAAT GGTCG
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTC--G GGTCG
1256246 GGTCG GGTC- GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTC
1256268 AGACCGGTCA
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
4 8 0.15
5 39 0.71
7 8 0.15
ACGTcount: A:0.07, C:0.23, G:0.49, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1256212 original size:17 final size:17
Alignment explanation
Indices: 1256190--1256227 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1256180 AACAGTCAAC
* *
1256190 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCCGATCG
1256207 GGTCAACGGTCCGATCG
1 GGTCAACGGTCCGATCG
1256224 GGTC
1 GGTC
1256228 GGGTCGGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.13, C:0.26, G:0.42, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCCGATCG
Found at i:1256227 original size:22 final size:23
Alignment explanation
Indices: 1256184--1256232 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
1256174 AAAGTCAACA
*
1256184 GTCAACGGTCAACGGTCGGGTCGG
1 GTCAACGGTC-ACGATCGGGTCGG
1256208 GTCAACGGTC-CGATCGGGTCGG
1 GTCAACGGTCACGATCGGGTCGG
1256230 GTC
1 GTC
1256233 GGGTCAATGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 14 0.58
24 10 0.42
ACGTcount: A:0.14, C:0.27, G:0.41, T:0.18
Consensus pattern (23 bp):
GTCAACGGTCACGATCGGGTCGG
Found at i:1256233 original size:27 final size:27
Alignment explanation
Indices: 1256197--1256260 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
1256187 AACGGTCAAC
1256197 GGTCGGGTCGGGTCAACGGTCCGATCG
1 GGTCGGGTCGGGTCAACGGTCCGATCG
* * *
1256224 GGTCGGGTCGGGTCAATGGTCGGGTCG
1 GGTCGGGTCGGGTCAACGGTCCGATCG
1256251 GGTC-GGTCGG
1 GGTCGGGTCGG
1256261 TCGGGTCAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 6 0.18
27 28 0.82
ACGTcount: A:0.08, C:0.22, G:0.50, T:0.20
Consensus pattern (27 bp):
GGTCGGGTCGGGTCAACGGTCCGATCG
Found at i:1256310 original size:10 final size:9
Alignment explanation
Indices: 1256264--1256320 Score: 69
Period size: 9 Copynumber: 6.1 Consensus size: 9
1256254 CGGTCGGTCG
*
1256264 GGTCAGACC
1 GGTCAAACC
1256273 GGTCAAACC
1 GGTCAAACC
*
1256282 GGTCAAATC
1 GGTCAAACC
*
1256291 GGTTCGAACC
1 GG-TCAAACC
1256301 GGTCGAAACC
1 GGTC-AAACC
1256311 GGTCAAACC
1 GGTCAAACC
1256320 G
1 G
1256321 ATTAAAAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 26 0.63
10 15 0.37
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1256319 original size:19 final size:18
Alignment explanation
Indices: 1256264--1256320 Score: 69
Period size: 19 Copynumber: 3.1 Consensus size: 18
1256254 CGGTCGGTCG
*
1256264 GGTCAGACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
* *
1256282 GGTCAAATCGGTTCGAACC
1 GGTCAAACCGG-TCAAACC
1256301 GGTCGAAACCGGTCAAACC
1 GGTC-AAACCGGTCAAACC
1256320 G
1 G
1256321 ATTAAAAACT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
18 9 0.28
19 17 0.53
20 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:1257883 original size:32 final size:31
Alignment explanation
Indices: 1257845--1257917 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
1257835 TGGGACCACG
*
1257845 GGGCCTACCTGAGAACACATCTCAAGGCCGTA
1 GGGCCTACCTGAGAA-ACATCTCAAGGCCATA
* ** *
1257877 GGGCCTACCCGAGAATGATCTCAGGGCCATA
1 GGGCCTACCTGAGAAACATCTCAAGGCCATA
*
1257908 GAGCCTACCT
1 GGGCCTACCT
1257918 AAGAGTGACA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.16
Consensus pattern (31 bp):
GGGCCTACCTGAGAAACATCTCAAGGCCATA
Found at i:1260105 original size:13 final size:13
Alignment explanation
Indices: 1260087--1260114 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1260077 TAACTTTTTT
1260087 GTCAAAGTCAACG
1 GTCAAAGTCAACG
1260100 GTCAAAGTCAACG
1 GTCAAAGTCAACG
1260113 GT
1 GT
1260115 AAACACTCAA
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:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (13 bp):
GTCAAAGTCAACG
Found at i:1260163 original size:14 final size:14
Alignment explanation
Indices: 1260146--1260179 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1260136 TCGATACAGG
*
1260146 CGGCTCGGCTTAAA
1 CGGCTCGGCTCAAA
1260160 CGGCTCGGCTCAAA
1 CGGCTCGGCTCAAA
*
1260174 TGGCTC
1 CGGCTC
1260180 CCCAGGCTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.32, G:0.29, T:0.21
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:1267617 original size:18 final size:18
Alignment explanation
Indices: 1267584--1267618 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1267574 TCCGTCCGAT
*
1267584 CTTATTATTTAATTCAAA
1 CTTATTATCTAATTCAAA
*
1267602 CTTATTATCTATTTCAA
1 CTTATTATCTAATTCAA
1267619 TCTTTTTAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.51
Consensus pattern (18 bp):
CTTATTATCTAATTCAAA
Found at i:1292781 original size:20 final size:20
Alignment explanation
Indices: 1292750--1292788 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1292740 TGAGCAAAAT
1292750 AGGAAAATTAAAAGCAGAGTG
1 AGGAAAATTAAAAG-AGAGTG
1292771 AGGAAAA-TAAAAGAGAGT
1 AGGAAAATTAAAAGAGAGT
1292789 ATAGAACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 6 0.33
21 7 0.39
ACGTcount: A:0.56, C:0.03, G:0.28, T:0.13
Consensus pattern (20 bp):
AGGAAAATTAAAAGAGAGTG
Found at i:1293002 original size:3 final size:3
Alignment explanation
Indices: 1292984--1293079 Score: 76
Period size: 3 Copynumber: 33.3 Consensus size: 3
1292974 TATTTGTTCT
* * * * *
1292984 TTA TTT TTA ATA TTA TTA TTA ATA TTA TTA TCA TT- TTA -TA CTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1293029 TTA TTTA TT- TTA TTA TTA -TA TTA TTA TTT TTT TTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1293073 TTA TTA T
1 TTA TTA T
1293080 AATAGGCCCA
Statistics
Matches: 74, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
2 10 0.14
3 61 0.82
4 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1294959 original size:17 final size:17
Alignment explanation
Indices: 1294906--1294971 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 17
1294896 GAAATATAAG
*
1294906 TTCAAAC-ATCCATAAA
1 TTCAAACAATCCACAAA
*
1294922 TTCAAACAAAT--TCAAA
1 TTCAAAC-AATCCACAAA
*
1294938 GTCAAACAATCCACAAA
1 TTCAAACAATCCACAAA
*
1294955 TTCAAACATTCCA-AAA
1 TTCAAACAATCCACAAA
1294971 T
1 T
1294972 ATCCAAAATG
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
15 3 0.08
16 20 0.50
17 15 0.38
18 2 0.05
ACGTcount: A:0.52, C:0.24, G:0.02, T:0.23
Consensus pattern (17 bp):
TTCAAACAATCCACAAA
Found at i:1302476 original size:20 final size:19
Alignment explanation
Indices: 1302434--1302474 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1302424 TTTTTGAAAC
*
1302434 TTTGGCTTTTTTTTTGTTT
1 TTTGCCTTTTTTTTTGTTT
1302453 TTTGCCTTTTTTTTTGTTT
1 TTTGCCTTTTTTTTTGTTT
1302472 TTT
1 TTT
1302475 TGAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.80
Consensus pattern (19 bp):
TTTGCCTTTTTTTTTGTTT
Found at i:1304618 original size:22 final size:21
Alignment explanation
Indices: 1304579--1304627 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1304569 ACAGAACCCC
*
1304579 AGGGGGTATCGATTCCCTT-A
1 AGGGGGAATCGATTCCCTTCA
*
1304599 TAGGGGGAATCGGTTCCCCTTCA
1 -AGGGGGAATCGATT-CCCTTCA
1304622 AGGGGG
1 AGGGGG
1304628 GGGGTATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 11 0.46
23 1 0.04
ACGTcount: A:0.18, C:0.20, G:0.37, T:0.24
Consensus pattern (21 bp):
AGGGGGAATCGATTCCCTTCA
Found at i:1317063 original size:21 final size:22
Alignment explanation
Indices: 1317037--1317096 Score: 72
Period size: 21 Copynumber: 2.8 Consensus size: 22
1317027 TTTTTGTGCA
1317037 GAGGGAATCGATCCCCCC-CAT
1 GAGGGAATCGATCCCCCCACAT
*
1317058 GAGGGAACCGATTCCCCCCACAT
1 GAGGGAATCGA-TCCCCCCACAT
*
1317081 --GGGAATCGATACCCCC
1 GAGGGAATCGATCCCCCC
1317097 TGGGGTTCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 6 0.18
21 18 0.53
22 7 0.21
23 3 0.09
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.13
Consensus pattern (22 bp):
GAGGGAATCGATCCCCCCACAT
Found at i:1317817 original size:12 final size:12
Alignment explanation
Indices: 1317784--1317809 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1317774 TAGTCGTCAA
1317784 CCAAATCCTCCT
1 CCAAATCCTCCT
1317796 CCAAATCCTCCT
1 CCAAATCCTCCT
1317808 CC
1 CC
1317810 TATTCCTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.54, G:0.00, T:0.23
Consensus pattern (12 bp):
CCAAATCCTCCT
Found at i:1325826 original size:10 final size:10
Alignment explanation
Indices: 1325811--1325865 Score: 51
Period size: 10 Copynumber: 5.3 Consensus size: 10
1325801 AAAGAAGAAG
1325811 AAAAAAATGA
1 AAAAAAATGA
1325821 AAAAAAATGA
1 AAAAAAATGA
1325831 AAATGAAAA--A
1 AAA--AAAATGA
*
1325841 AAATGAAATGA
1 AAA-AAAATGA
1325852 AAAAAAATAGA
1 AAAAAAAT-GA
1325863 AAA
1 AAA
1325866 TGAGGGTCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
9 3 0.08
10 21 0.57
11 9 0.24
12 4 0.11
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (10 bp):
AAAAAAATGA
Found at i:1325841 original size:15 final size:16
Alignment explanation
Indices: 1325814--1325868 Score: 94
Period size: 16 Copynumber: 3.4 Consensus size: 16
1325804 GAAGAAGAAA
1325814 AAAATGAAAAAAAATG
1 AAAATGAAAAAAAATG
1325830 AAAATGAAAAAAAATG
1 AAAATGAAAAAAAATG
1325846 -AAATGAAAAAAAATAG
1 AAAATGAAAAAAAAT-G
1325862 AAAATGA
1 AAAATGA
1325869 GGGTCAAGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
15 14 0.38
16 17 0.46
17 6 0.16
ACGTcount: A:0.75, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAATGAAAAAAAATG
Found at i:1325864 original size:26 final size:25
Alignment explanation
Indices: 1325811--1325865 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
1325801 AAAGAAGAAG
1325811 AAAAAAATGAAAAAAAATGAAAATGA
1 AAAAAAATGAAAAAAAA-GAAAATGA
*
1325837 AAAAAAATGAAATGAAAA-AAAATAGA
1 AAAAAAATGAAA-AAAAAGAAAAT-GA
1325863 AAA
1 AAA
1325866 TGAGGGTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
27 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (25 bp):
AAAAAAATGAAAAAAAAGAAAATGA
Found at i:1326515 original size:20 final size:20
Alignment explanation
Indices: 1326487--1326532 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1326477 AATGTTTTAC
* * *
1326487 GAACAAGTAATTATGGTGCT
1 GAACCAGTAATTATAGTGAT
1326507 GAACCAGTAATTATAGTGAT
1 GAACCAGTAATTATAGTGAT
1326527 GAACCA
1 GAACCA
1326533 ATGTTGTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (20 bp):
GAACCAGTAATTATAGTGAT
Found at i:1326884 original size:22 final size:22
Alignment explanation
Indices: 1326858--1326937 Score: 106
Period size: 22 Copynumber: 3.6 Consensus size: 22
1326848 TACATTCTTT
1326858 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
* *
1326880 AAAGATGATATATTCTCTCTTC
1 AAAGATGATAGATTCTCTTTTC
* *
1326902 AAATATGATACATTCTCTTTTC
1 AAAGATGATAGATTCTCTTTTC
* *
1326924 AAAGAAGAAAGATT
1 AAAGATGATAGATT
1326938 TATTGGATTT
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (22 bp):
AAAGATGATAGATTCTCTTTTC
Found at i:1326920 original size:20 final size:20
Alignment explanation
Indices: 1326848--1326920 Score: 69
Period size: 22 Copynumber: 3.5 Consensus size: 20
1326838 TACGAACATC
1326848 TACATTCT-TT-AAAGATGA
1 TACATTCTCTTCAAAGATGA
*
1326866 TAGATTCTCTTTTCAAAGATGA
1 TACATTCTC--TTCAAAGATGA
* *
1326888 TATATTCTCTCTTCAAATATGA
1 TACA-T-TCTCTTCAAAGATGA
1326910 TACATTCTCTT
1 TACATTCTCTT
1326921 TTCAAAGAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
18 7 0.16
20 6 0.13
21 3 0.07
22 24 0.53
23 1 0.02
24 4 0.09
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (20 bp):
TACATTCTCTTCAAAGATGA
Found at i:1327389 original size:20 final size:20
Alignment explanation
Indices: 1327326--1327390 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 20
1327316 TTCCAGAGAA
1327326 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * *
1327346 ATCTGAAGAATGAAGAAGAA---
1 GT-T-CATAATG-AGAAGAACTT
1327366 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1327386 GTTCA
1 GTTCA
1327391 ACCTTTCGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 12
0.65 0.12 0.24
Matches are distributed among these distances:
17 7 0.21
18 5 0.15
19 1 0.03
20 7 0.21
21 1 0.03
22 5 0.15
23 7 0.21
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1327492 original size:112 final size:112
Alignment explanation
Indices: 1327295--1327614 Score: 563
Period size: 112 Copynumber: 2.9 Consensus size: 112
1327285 GATTTGAATC
*
1327295 CATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAATGAA
1 CATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAA
1327360 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCAAATT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCAAATT
*
1327407 CATCACTCAATGGATCAACATTTCTAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAA
1 CATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAA
*
1327472 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCGAATT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCAAATT
* * * *
1327519 CATCACTCGATGGATCAGCATTGCCAG-GAAGTTCATAATGAGAAGAACTTATCT-AAAAAGGAA
1 CATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAA
1327582 GAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAAC
1327615 ATTTTGTATG
Statistics
Matches: 200, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
110 41 0.20
111 27 0.14
112 132 0.66
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (112 bp):
CATCACTCAATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTCGCTCAAATT
Found at i:1327611 original size:20 final size:20
Alignment explanation
Indices: 1327549--1327612 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 20
1327539 TTGCCAGGAA
1327549 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* * * *
1327569 ATCTAAAAAGGAAGAAGAA---
1 GT-TCATAATG-AGAAGAACTT
1327588 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
1327608 GTTCA
1 GTTCA
1327613 ACATTTTGTA
Statistics
Matches: 31, Mismatches: 8, Indels: 10
0.63 0.16 0.20
Matches are distributed among these distances:
17 7 0.23
18 5 0.16
19 1 0.03
20 6 0.19
21 5 0.16
22 7 0.23
ACGTcount: A:0.45, C:0.09, G:0.20, T:0.25
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:1328120 original size:3 final size:3
Alignment explanation
Indices: 1328102--1328201 Score: 100
Period size: 3 Copynumber: 34.0 Consensus size: 3
1328092 CATTTGTTCT
* * * * *
1328102 TTA TTT TTA ATA TTA TTA TTA ATA TTA TTA TTA TCA TT- TTA -TA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
1328148 TTTA TTTA TT- TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA ATA TTA
1 -TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1328193 TTA TTA TTA
1 TTA TTA TTA
1328202 CAAACTGGCC
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
2 8 0.10
3 67 0.83
4 6 0.07
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1328153 original size:32 final size:32
Alignment explanation
Indices: 1328115--1328199 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
1328105 TTTTTAATAT
*
1328115 TATTATTAATATTATTATTATCATTTTA-TAC
1 TATTATTAATATTATTATTATCATATTATTAC
* * * *
1328146 TATTTATTTATTTTATTATTATTATATTATTAT
1 TA-TTATTAATATTATTATTATCATATTATTAC
1328179 TATTATTAATATTATTATTAT
1 TATTATTAATATTATTATTAT
1328200 TACAAACTGG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.04
32 39 0.87
33 4 0.09
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (32 bp):
TATTATTAATATTATTATTATCATATTATTAC
Found at i:1342243 original size:24 final size:24
Alignment explanation
Indices: 1342219--1342321 Score: 122
Period size: 24 Copynumber: 4.3 Consensus size: 24
1342209 TTTATCTGAT
*
1342219 TTTC-GATTTGAATTTTGTTTTGA
1 TTTCTGATCTGAATTTTGTTTTGA
*
1342242 TTTCTGATCTG-ATTTCTGTTCTGA
1 TTTCTGATCTGAATTT-TGTTTTGA
* *
1342266 TTTCTGATCTGGATTCTGTTATT-A
1 TTTCTGATCTGAATTTTGTT-TTGA
*
1342290 TATCTGATCTGAATTTTGTTTTGA
1 TTTCTGATCTGAATTTTGTTTTGA
1342314 TTTCTGAT
1 TTTCTGAT
1342322 ATCCGTTTAC
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
23 10 0.15
24 53 0.79
25 4 0.06
ACGTcount: A:0.17, C:0.11, G:0.17, T:0.56
Consensus pattern (24 bp):
TTTCTGATCTGAATTTTGTTTTGA
Found at i:1342254 original size:12 final size:12
Alignment explanation
Indices: 1342239--1342321 Score: 71
Period size: 12 Copynumber: 6.9 Consensus size: 12
1342229 AATTTTGTTT
1342239 TGATTTCTGATC
1 TGATTTCTGATC
*
1342251 TGATTTCTGTTC
1 TGATTTCTGATC
1342263 TGATTTCTGATC
1 TGATTTCTGATC
* *
1342275 TGGA-TTCTGTTA
1 T-GATTTCTGATC
* *
1342287 TTATATCTGATC
1 TGATTTCTGATC
* *
1342299 TGAATTT-TGTTT
1 TG-ATTTCTGATC
1342311 TGATTTCTGAT
1 TGATTTCTGAT
1342322 ATCCGTTTAC
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
11 5 0.09
12 44 0.81
13 5 0.09
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (12 bp):
TGATTTCTGATC
Found at i:1353057 original size:14 final size:13
Alignment explanation
Indices: 1353034--1353072 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1353024 ACTTTTTTGG
1353034 TCAAAGTCAACGA
1 TCAAAGTCAACGA
* *
1353047 TCAACAGTCAATGG
1 TCAA-AGTCAACGA
1353061 TCAAAGTCAACG
1 TCAAAGTCAACG
1353073 GGATGAATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (13 bp):
TCAAAGTCAACGA
Found at i:1353122 original size:15 final size:14
Alignment explanation
Indices: 1353086--1353124 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1353076 TGAATCGGAT
*
1353086 GAGTTGAATCAGAC
1 GAGTTGACTCAGAC
*
1353100 GGGTTGACTCAGACC
1 GAGTTGACTCAGA-C
1353115 GAGTTGACTC
1 GAGTTGACTC
1353125 GGTGACTGGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (14 bp):
GAGTTGACTCAGAC
Found at i:1356255 original size:13 final size:13
Alignment explanation
Indices: 1356237--1356295 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
1356227 GTCATAAATC
*
1356237 TATGACGCGTATT
1 TATGACACGTATT
1356250 TATGACACGTATT
1 TATGACACGTATT
* *
1356263 TATAACACATATT
1 TATGACACGTATT
*
1356276 TATGACGC-TCATT
1 TATGACACGT-ATT
1356289 TATGACA
1 TATGACA
1356296 TGCATTGAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
12 1 0.03
13 38 0.97
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (13 bp):
TATGACACGTATT
Found at i:1356463 original size:2 final size:2
Alignment explanation
Indices: 1356456--1356483 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1356446 TATTTCGTAA
1356456 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
1356484 TGTAGATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1360685 original size:9 final size:9
Alignment explanation
Indices: 1360671--1360744 Score: 58
Period size: 9 Copynumber: 7.8 Consensus size: 9
1360661 GGCTGCTGGA
1360671 AACCGGTTT
1 AACCGGTTT
1360680 AACCGGTTTT
1 AACCGG-TTT
1360690 CAACCGGTTT
1 -AACCGGTTT
* **
1360700 GACCGGTCCG
1 AACCGGT-TT
1360710 AACCGGTTT
1 AACCGGTTT
* *
1360719 GACCGGTCTG
1 AACCGGT-TT
1360729 AACCGGTTT
1 AACCGGTTT
*
1360738 GACCGGT
1 AACCGGT
1360745 CTGACCCGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
9 25 0.50
10 19 0.38
11 6 0.12
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1360746 original size:19 final size:19
Alignment explanation
Indices: 1360671--1360748 Score: 111
Period size: 19 Copynumber: 4.1 Consensus size: 19
1360661 GGCTGCTGGA
* * *
1360671 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
*
1360691 AACCGGTTTGACCGGTCCG
1 AACCGGTTTGACCGGTCTG
1360710 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
1360729 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
1360748 A
1 A
1360749 CCCGACCGAC
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
19 39 0.74
20 14 0.26
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1360749 original size:9 final size:9
Alignment explanation
Indices: 1360692--1360750 Score: 64
Period size: 9 Copynumber: 6.3 Consensus size: 9
1360682 CCGGTTTTCA
*
1360692 ACCGGTTTG
1 ACCGGTCTG
*
1360701 ACCGGTCCG
1 ACCGGTCTG
*
1360710 AACCGGTTTG
1 -ACCGGTCTG
1360720 ACCGGTCTG
1 ACCGGTCTG
*
1360729 AACCGGTTTG
1 -ACCGGTCTG
1360739 ACCGGTCTG
1 ACCGGTCTG
1360748 ACC
1 ACC
1360751 CGACCGACCC
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 26 0.63
10 15 0.37
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.24
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:1360781 original size:22 final size:21
Alignment explanation
Indices: 1360752--1360799 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 21
1360742 GGTCTGACCC
1360752 GACCGACCCAACCCGACCGTT
1 GACCGACCCAACCCGACCGTT
*
1360773 GACCTGACCCGACCCGACCGTT
1 GACC-GACCCAACCCGACCGTT
1360795 GACCG
1 GACCG
1360800 TTAACCGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.21, C:0.46, G:0.23, T:0.10
Consensus pattern (21 bp):
GACCGACCCAACCCGACCGTT
Found at i:1367970 original size:5 final size:5
Alignment explanation
Indices: 1367951--1368009 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
1367941 AGTGACTGTT
* * * *
1367951 GACCC GA-CC GA-CC GACCC GACGC GACCC GACCGTT GACCC GACCT GACGC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACC--C GACCC GACCC GACCC
1368001 GACCC GACC
1 GACCC GACC
1368010 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
4 8 0.19
5 31 0.72
7 4 0.09
ACGTcount: A:0.20, C:0.49, G:0.25, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:1367992 original size:27 final size:27
Alignment explanation
Indices: 1367962--1368016 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
1367952 ACCCGACCGA
1367962 CCGACCCGACGCGACCCGACCGTTGAC
1 CCGACCCGACGCGACCCGACCGTTGAC
*
1367989 CCGACCTGACGCGACCCGACCGTTGAC
1 CCGACCCGACGCGACCCGACCGTTGAC
1368016 C
1 C
1368017 GTTGACCGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.18, C:0.47, G:0.25, T:0.09
Consensus pattern (27 bp):
CCGACCCGACGCGACCCGACCGTTGAC
Found at i:1375012 original size:12 final size:12
Alignment explanation
Indices: 1374995--1375045 Score: 84
Period size: 12 Copynumber: 4.2 Consensus size: 12
1374985 TAAGCGCAGG
1374995 GAGAAAGGAAGA
1 GAGAAAGGAAGA
1375007 GAGAAAGGAAGA
1 GAGAAAGGAAGA
*
1375019 CAGAAAGGAAGA
1 GAGAAAGGAAGA
*
1375031 CAGAAAGGAAGA
1 GAGAAAGGAAGA
1375043 GAG
1 GAG
1375046 GAAAATAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.57, C:0.04, G:0.39, T:0.00
Consensus pattern (12 bp):
GAGAAAGGAAGA
Found at i:1375683 original size:13 final size:13
Alignment explanation
Indices: 1375665--1375693 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1375655 TTTATACTCA
1375665 TATAAGCATGCAT
1 TATAAGCATGCAT
1375678 TATAAGCATGCAT
1 TATAAGCATGCAT
1375691 TAT
1 TAT
1375694 TTGAAATCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (13 bp):
TATAAGCATGCAT
Found at i:1383302 original size:20 final size:20
Alignment explanation
Indices: 1383273--1383311 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1383263 TTTCTACCAT
1383273 ATGCAACTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
*
1383293 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
1383312 TATGGGCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:1396646 original size:18 final size:19
Alignment explanation
Indices: 1396623--1396676 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 19
1396613 CTAAATTCGG
1396623 TATCGATACTCAGCCA-AA
1 TATCGATACTCAGCCAGAA
* *
1396641 TATCGATACCCAACACCAGAA
1 TATCGATACTC-A-GCCAGAA
1396662 TATCGATACTCAGCC
1 TATCGATACTCAGCC
1396677 TGGGGTATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 10 0.34
19 3 0.10
20 4 0.14
21 12 0.41
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (19 bp):
TATCGATACTCAGCCAGAA
Found at i:1396785 original size:20 final size:19
Alignment explanation
Indices: 1396743--1396792 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
1396733 CATAAGGAGG
* *
1396743 GTATCGATACCAAGGTTTG
1 GTATCGATACCAAGGGTTA
*
1396762 GTATCGATACTGAAGGGTTA
1 GTATCGATAC-CAAGGGTTA
*
1396782 GTATCGGTACC
1 GTATCGATACC
1396793 CACGAGCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (19 bp):
GTATCGATACCAAGGGTTA
Found at i:1409914 original size:16 final size:15
Alignment explanation
Indices: 1409884--1409917 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1409874 CACGTGAGGA
1409884 TTATTTTCTTCTTAT
1 TTATTTTCTTCTTAT
*
1409899 TTATTTATCTTTTTAT
1 TTATTT-TCTTCTTAT
1409915 TTA
1 TTA
1409918 CTGTTTTACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTCTTCTTAT
Found at i:1411098 original size:81 final size:81
Alignment explanation
Indices: 1410963--1411196 Score: 369
Period size: 81 Copynumber: 2.9 Consensus size: 81
1410953 AATTTTCTAA
* * *
1410963 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGTAGAAAGATGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1411028 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
1411044 AGTAAAAGATTAATGGCCTAGTTTTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1411109 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * ** *
1411125 AGTAAAAGATTAATGGCCTAGATGTGCATTTTGCATAAAGGTGTCAATTATGATAGTTAGGTGAA
1 AGTAAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1411190 AGGTTAA
66 AGGTTAA
1411197 TGACCTAGTT
Statistics
Matches: 141, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
81 141 1.00
ACGTcount: A:0.35, C:0.09, G:0.24, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGATGTGCATTTGGAAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:1411210 original size:59 final size:59
Alignment explanation
Indices: 1411129--1411251 Score: 174
Period size: 59 Copynumber: 2.1 Consensus size: 59
1411119 CCTTTGAGTA
* * * * * *
1411129 AAAGATTAATGGCCTAGATGTGCATTTTGCATAAAGGTGTCAATTATGATAGTTAGGTG
1 AAAGGTTAATGACCTAGATGTGCAATTGGCAGAAAGGTGTCAATTAAGATAGTTAGGTG
* *
1411188 AAAGGTTAATGACCTAGTTGTGCAATTGGCAGAAAGGTGTCAATTAAGCTAGTTAGGTG
1 AAAGGTTAATGACCTAGATGTGCAATTGGCAGAAAGGTGTCAATTAAGATAGTTAGGTG
1411247 AAAGG
1 AAAGG
1411252 CTAAATGCTA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (59 bp):
AAAGGTTAATGACCTAGATGTGCAATTGGCAGAAAGGTGTCAATTAAGATAGTTAGGTG
Found at i:1415257 original size:17 final size:17
Alignment explanation
Indices: 1415235--1415269 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1415225 TATTAGAACA
1415235 TTAAGTATTATGGAAGC
1 TTAAGTATTATGGAAGC
1415252 TTAAGTATTATGGAAGC
1 TTAAGTATTATGGAAGC
1415269 T
1 T
1415270 AATGAAGGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.06, G:0.23, T:0.37
Consensus pattern (17 bp):
TTAAGTATTATGGAAGC
Found at i:1416293 original size:55 final size:56
Alignment explanation
Indices: 1416199--1416308 Score: 186
Period size: 55 Copynumber: 2.0 Consensus size: 56
1416189 ATTATCAAAT
*
1416199 GGCATTATGTGTGCAAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCATTATGTGTGCAAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCCGTATG
* *
1416255 GGCATTGTGTGTGC-AAAACTAAGAAATTTATAAGAAGTTTATGAATTTCCGTAT
1 GGCATTATGTGTGCAAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCCGTAT
1416309 TGTAGTGGGG
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
55 38 0.75
56 13 0.25
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (56 bp):
GGCATTATGTGTGCAAAAACTAAGAAATTCATAAGAAGTTTATGAATTTCCGTATG
Found at i:1416552 original size:81 final size:81
Alignment explanation
Indices: 1416451--1416864 Score: 641
Period size: 81 Copynumber: 5.1 Consensus size: 81
1416441 AGTGTTATAA
* *
1416451 AGTAAAAGATTAATGGCCTAGATGTGCATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
*
1416516 AGGTTAAATACATTTG
66 AGGTTAAATACCTTTG
* * * * *
1416532 ACTAAAAGATTAATGACCTAGTTGTGCATTTGGAAGAAAGGTGTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1416597 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* *
1416613 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGGGTCAATTATGCTAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1416678 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
1416694 AGAAAAAGATTAATGGCCTAGTTGTGCATTTGGCAGAAAGGTGTCAATTATGCGAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1416759 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
1416775 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGAAGAAATGTGTCAATTATGACAGTTAGATTG-
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGA-TGA
* *
1416839 AAGGCTAAATGCCTTTG
65 AAGGTTAAATACCTTTG
*
1416856 GGTAAAAGA
1 AGTAAAAGA
1416865 CTAAATGCTT
Statistics
Matches: 305, Mismatches: 27, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
81 303 0.99
82 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.30
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:1416977 original size:45 final size:46
Alignment explanation
Indices: 1416920--1417029 Score: 136
Period size: 45 Copynumber: 2.4 Consensus size: 46
1416910 TATTTGAAAC
*
1416920 AAAAGGCTTGAAAGGAT-TCCATAAATGAAATGT-ATAACGGTGCAT-
1 AAAAGGCATGAAAGGATGT-CATAAATGAAAT-TAATAACGGTGCATA
* *
1416965 CAAAGGCATGAAAGGATGTCATAAATGAAATTAATAATGGTGCATAA
1 AAAAGGCATGAAAGGATGTCATAAATGAAATTAATAACGGTGCAT-A
*
1417012 AAAACGCATGAAAGGATG
1 AAAAGGCATGAAAGGATG
1417030 CCACAGAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
44 1 0.02
45 38 0.68
46 1 0.02
47 16 0.29
ACGTcount: A:0.45, C:0.10, G:0.23, T:0.22
Consensus pattern (46 bp):
AAAAGGCATGAAAGGATGTCATAAATGAAATTAATAACGGTGCATA
Found at i:1417740 original size:19 final size:19
Alignment explanation
Indices: 1417716--1417754 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1417706 CTCTTCATTT
1417716 TTCTTGAAATAATTCTATA
1 TTCTTGAAATAATTCTATA
1417735 TTCTTGAAATAATTCTATA
1 TTCTTGAAATAATTCTATA
1417754 T
1 T
1417755 GATATTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (19 bp):
TTCTTGAAATAATTCTATA
Found at i:1417915 original size:31 final size:31
Alignment explanation
Indices: 1417880--1417970 Score: 155
Period size: 31 Copynumber: 2.9 Consensus size: 31
1417870 TACTTGAACC
* * *
1417880 CAAGTAACATAGATTATCTTGCACATTGCTT
1 CAAGTAGCATAGATTTTCTTACACATTGCTT
1417911 CAAGTAGCATAGATTTTCTTACACATTGCTT
1 CAAGTAGCATAGATTTTCTTACACATTGCTT
1417942 CAAGTAGCATAGATTTTCTTACACATTGC
1 CAAGTAGCATAGATTTTCTTACACATTGC
1417971 ACTTCTAAAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (31 bp):
CAAGTAGCATAGATTTTCTTACACATTGCTT
Found at i:1420591 original size:21 final size:21
Alignment explanation
Indices: 1420540--1420592 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1420530 ATTCTGACTA
1420540 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * *
1420561 CCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
1420582 TCGCAATGCGA
1 TCGCATTGCGA
1420593 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1420607 original size:20 final size:20
Alignment explanation
Indices: 1420582--1420714 Score: 248
Period size: 20 Copynumber: 6.7 Consensus size: 20
1420572 TTTTCCTAAT
1420582 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1420602 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1420622 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1420642 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
1420662 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
1420682 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATACGTAAA
*
1420702 TCGCAACGCGAAT
1 TCGCAATGCGAAT
1420715 CTGACTATCG
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 111 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:1420941 original size:22 final size:22
Alignment explanation
Indices: 1420915--1420976 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1420905 ACATCCGTCC
1420915 CCATCTCCGACGAAATCACTC-
1 CCATCTCCGACGAAATCACTCT
* *
1420936 CTCATCTCCGACGATATCAGTCT
1 C-CATCTCCGACGAAATCACTCT
* *
1420959 CCATCTTCGGCGAAATCA
1 CCATCTCCGACGAAATCA
1420977 TTCATGATCA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.26, C:0.37, G:0.13, T:0.24
Consensus pattern (22 bp):
CCATCTCCGACGAAATCACTCT
Found at i:1421394 original size:13 final size:13
Alignment explanation
Indices: 1421376--1421400 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1421366 CGATAGTCAT
1421376 TTTCGTGTTGCGG
1 TTTCGTGTTGCGG
1421389 TTTCGTGTTGCG
1 TTTCGTGTTGCG
1421401 ATTTAAAGTT
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:0.00, C:0.16, G:0.36, T:0.48
Consensus pattern (13 bp):
TTTCGTGTTGCGG
Found at i:1423284 original size:20 final size:20
Alignment explanation
Indices: 1423256--1423309 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1423246 GAAGAATAGT
*
1423256 TTACTATCGCAATGCGAAAA
1 TTACTATCGCAACGCGAAAA
*
1423276 TTACAATCGCAACGCGAAAA
1 TTACTATCGCAACGCGAAAA
*
1423296 TGACTATCGCAACG
1 TTACTATCGCAACG
1423310 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
TTACTATCGCAACGCGAAAA
Found at i:1423349 original size:53 final size:54
Alignment explanation
Indices: 1423261--1423447 Score: 159
Period size: 53 Copynumber: 3.5 Consensus size: 54
1423251 ATAGTTTACT
* * *
1423261 ATCGCAATGCGAAAATTACAATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCAAAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGAGAGA
* * ** **
1423315 ATCGCAATGC-AAAATGAAAATCGCAACAAC-AAAATCG-C-AACGCAAAAATGACT
1 ATCGCAATGCAAAAATGAAAATCGCAAC-GCGAAAAT-GACTATCGCAACGA-GAGA
** * ** *
1423368 ATCGCAATGCAAAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGA
1 ATCGCAATGC-AAAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGAGAGA
*
1423423 ATCGCAATGC-GAAATGAAAATCGCA
1 ATCGCAATGCAAAAATGAAAATCGCA
1423448 TTGCGATTCT
Statistics
Matches: 102, Mismatches: 23, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
52 7 0.07
53 45 0.44
54 14 0.14
55 29 0.28
56 7 0.07
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (54 bp):
ATCGCAATGCAAAAATGAAAATCGCAACGCGAAAATGACTATCGCAACGAGAGA
Found at i:1423384 original size:21 final size:20
Alignment explanation
Indices: 1423348--1423415 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1423338 CAACAACAAA
*
1423348 ATCGCAACGCAAAAATGACT
1 ATCGCAATGCAAAAATGACT
1423368 ATCGCAATGCAAAAAATGACT
1 ATCGCAATGC-AAAAATGACT
* **
1423389 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCAAAAATGACT
1423409 ATCGCAA
1 ATCGCAA
1423416 CGAAAGAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
20 23 0.53
21 20 0.47
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCAAAAATGACT
Done.