Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006985.1 Hibiscus syriacus cultivar Beakdansim tig00017996_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: 663392
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 5 of 5
Found at i:561485 original size:10 final size:10
Alignment explanation
Indices: 561442--561570 Score: 127
Period size: 10 Copynumber: 12.4 Consensus size: 10
561432 AGAAATAAAG
*
561442 AAAAAAG-AG
1 AAAAAAGAAA
561451 AAAAAAGAAA
1 AAAAAAGAAA
*
561461 AGAAGAAGAAGA
1 A-AAAAAGAA-A
* *
561473 AAAAAACAGA
1 AAAAAAGAAA
561483 AAAAAA-AAA
1 AAAAAAGAAA
*
561492 GAAAAAGAAAA
1 AAAAAAG-AAA
561503 AAAAAAGAAA
1 AAAAAAGAAA
561513 AAAAAAGAAA
1 AAAAAAGAAA
561523 AAAAAAGAAA
1 AAAAAAGAAA
561533 AAAAAAGAAA
1 AAAAAAGAAA
561543 AAAAAGAGGAAA
1 AAAAA-A-GAAA
*
561555 ATGAAAAGAAA
1 A-AAAAAGAAA
561566 GAAAA
1 -AAAA
561571 CTGATCAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 16
0.80 0.08 0.13
Matches are distributed among these distances:
9 14 0.14
10 47 0.47
11 28 0.28
12 9 0.09
13 3 0.03
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.01
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:561538 original size:41 final size:41
Alignment explanation
Indices: 561442--561570 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 41
561432 AGAAATAAAG
* * * * *
561442 AAAAAAG-AGAAAAAAGAAAAGAAGAAGAAGAAAAAAACAGA
1 AAAAAAGAAAAAAAAAGAAAAAAAAAAGAA-AAAAAAAGAAA
*
561483 AAAAAA-AAAGAAAAAGAAAAAAAAAAGAAAAAAAAAGAAA
1 AAAAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAGAAA
* *
561523 AAAAAAGAAAAAAAAAGAAAAAAAAGAGGAAAATGAAAAGAAA
1 AAAAAAGAAAAAAAAAGAAAAAAAA-AAGAAAA-AAAAAGAAA
*
561566 GAAAA
1 AAAAA
561571 CTGATCAAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 15 0.20
41 41 0.55
42 6 0.08
43 12 0.16
ACGTcount: A:0.83, C:0.01, G:0.16, T:0.01
Consensus pattern (41 bp):
AAAAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAGAAA
Found at i:561560 original size:6 final size:5
Alignment explanation
Indices: 561427--561570 Score: 86
Period size: 5 Copynumber: 28.2 Consensus size: 5
561417 AAAAAAGGGT
*
561427 AGAAA AGAAA TA-AAGA A-AAA AGAGA A-AAA AGAAA AG--A AGAAGA
1 AGAAA AGAAA -AGAA-A AGAAA AGAAA AGAAA AGAAA AGAAA AGAA-A
* * *
561470 AGAAA A-AAA CAGAAAA AAAAA AGAAAA AGAAAA AAAAA AGAAA AAAAA
1 AGAAA AGAAA -AG-AAA AGAAA AG-AAA AG-AAA AGAAA AGAAA AGAAA
* * *
561518 AGAAA AAAAA AGAAA AAAAA AGAAA AAAAA GAGGAAA ATGAAA AG-AA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA -A-GAAA A-GAAA AGAAA
561565 AGAAA A
1 AGAAA A
561571 CTGATCAAAT
Statistics
Matches: 110, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
3 3 0.03
4 12 0.11
5 64 0.58
6 25 0.23
7 6 0.05
ACGTcount: A:0.82, C:0.01, G:0.16, T:0.01
Consensus pattern (5 bp):
AGAAA
Found at i:561561 original size:27 final size:28
Alignment explanation
Indices: 561429--561570 Score: 139
Period size: 29 Copynumber: 5.0 Consensus size: 28
561419 AAAAGGGTAG
*
561429 AAAAGAA-ATAAAGAAAAAAGAGAA-AAAA
1 AAAAGAAGAAAAAGAAAAAA-A-AAGAAAA
* *
561457 GAAAAGAAGAAGAAGAAAAAAACAGAAAA
1 -AAAAGAAGAAAAAGAAAAAAAAAGAAAA
561486 AAAA-AAGAAAAAGAAAAAAAAAAGAAAAA
1 AAAAGAAGAAAAAG-AAAAAAAAAG-AAAA
*
561515 AAAAGAAAAAAAAAGAAAAAAAAAGAAAA
1 AAAAG-AAGAAAAAGAAAAAAAAAGAAAA
* * *
561544 AAAAGAGGAAAATG-AAAAGAAAGAAAA
1 AAAAGAAGAAAAAGAAAAAAAAAGAAAA
561571 CTGATCAAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
27 20 0.21
28 20 0.21
29 29 0.30
30 20 0.21
31 8 0.08
ACGTcount: A:0.82, C:0.01, G:0.15, T:0.01
Consensus pattern (28 bp):
AAAAGAAGAAAAAGAAAAAAAAAGAAAA
Found at i:565001 original size:7 final size:6
Alignment explanation
Indices: 564985--565092 Score: 71
Period size: 6 Copynumber: 17.8 Consensus size: 6
564975 AAAAAAGGGT
* * * *
564985 AGAAAA AGAATAA AGAAAA A-AGAG A-AAAA AGAAAGA AGAAGA AGAATA
1 AGAAAA AGAA-AA AGAAAA AGAAAA AGAAAA AGAAA-A AGAAAA AGAAAA
* * * *
565033 AGAAAA A-AACAGA AAAAAA AGAAAA AAAAAA GAGAAAA AGGAAA AGAAAG
1 AGAAAA AGAA-A-A AGAAAA AGAAAA AGAAAA -AGAAAA AGAAAA AGAAAA
565083 A-AAAA AGAAA
1 AGAAAA AGAAA
565093 GGAAACTGAT
Statistics
Matches: 80, Mismatches: 14, Indels: 16
0.73 0.13 0.15
Matches are distributed among these distances:
5 12 0.15
6 47 0.59
7 19 0.24
8 2 0.03
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:565012 original size:9 final size:9
Alignment explanation
Indices: 564998--565090 Score: 59
Period size: 9 Copynumber: 10.1 Consensus size: 9
564988 AAAAGAATAA
564998 AGAAAAAAG
1 AGAAAAAAG
565007 AGAAAAAAG
1 AGAAAAAAG
565016 A-AAGAAGAAG
1 AGAA-AA-AAG
*
565026 A-AGAATAAG
1 AGA-AAAAAG
*
565035 AAAAAAACAG
1 AGAAAAA-AG
*
565045 AAAAAAAAG
1 AGAAAAAAG
* *
565054 AAAAAAAAA
1 AGAAAAAAG
565063 AGAGAAAAAG
1 AGA-AAAAAG
565073 -GAAAAGAA-
1 AGAAAA-AAG
565081 AGAAAAAAG
1 AGAAAAAAG
565090 A
1 A
565091 AAGGAAACTG
Statistics
Matches: 70, Mismatches: 5, Indels: 18
0.75 0.05 0.19
Matches are distributed among these distances:
8 7 0.10
9 41 0.59
10 21 0.30
11 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (9 bp):
AGAAAAAAG
Found at i:565021 original size:20 final size:20
Alignment explanation
Indices: 564996--565081 Score: 79
Period size: 19 Copynumber: 4.3 Consensus size: 20
564986 GAAAAAGAAT
564996 AAAGAAAAAAGAGAAAAAAG
1 AAAGAAAAAAGAGAAAAAAG
* *
565016 AAAG-AAGAAGA-AGAATAAG
1 AAAGAAAAAAGAGA-AAAAAG
* *
565035 AAA-AAAACAGAAAAAAAAG
1 AAAGAAAAAAGAGAAAAAAG
* *
565054 AAAAAAAAAAGAGAAAAAGG
1 AAAGAAAAAAGAGAAAAAAG
565074 AAAAGAAA
1 -AAAGAAA
565082 GAAAAAAGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.02
19 27 0.52
20 18 0.35
21 6 0.12
ACGTcount: A:0.79, C:0.01, G:0.19, T:0.01
Consensus pattern (20 bp):
AAAGAAAAAAGAGAAAAAAG
Found at i:565040 original size:36 final size:36
Alignment explanation
Indices: 564985--565093 Score: 107
Period size: 38 Copynumber: 3.0 Consensus size: 36
564975 AAAAAAGGGT
564985 AGAAAAAGAATAA-AGAAAAAAGAGAAAAAAGAAAGA
1 AGAAAAAGAATAAGA-AAAAAAGAGAAAAAAGAAAGA
* *
565021 AGAAGAAGAATAAGAAAAAAACAGAAAAAAAAGAAA-A
1 AGAAAAAGAATAAG-AAAAAA-AGAGAAAAAAGAAAGA
* * *
565058 AAAAAAGAGAAAAAGGAAAAGAA-AGAAAAAAGAAAG
1 AGAAAA-AGAATAA-GAAAAAAAGAGAAAAAAGAAAG
565094 GAAACTGATC
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
36 23 0.38
37 11 0.18
38 25 0.42
39 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.02
Consensus pattern (36 bp):
AGAAAAAGAATAAGAAAAAAAGAGAAAAAAGAAAGA
Found at i:565046 original size:19 final size:18
Alignment explanation
Indices: 564990--565092 Score: 70
Period size: 19 Copynumber: 5.7 Consensus size: 18
564980 AGGGTAGAAA
*
564990 AAGAATAAAGAAAAAAGAG
1 AAGAAT-AAGAAAAAAAAG
*
565009 AA-AA-AAGAAAGAAGAAG
1 AAGAATAAGAAA-AAAAAG
565026 AAGAATAAGAAAAAAACAG
1 AAGAATAAGAAAAAAA-AG
* * *
565045 AAAAAAAAGAAAAAAAAA
1 AAGAATAAGAAAAAAAAG
* *
565063 AGAGAAAAAGGAAAAGAAAG
1 A-AGAATAA-GAAAAAAAAG
565083 AA-AA-AAGAAA
1 AAGAATAAGAAA
565093 GGAAACTGAT
Statistics
Matches: 69, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
16 10 0.14
17 8 0.12
18 11 0.16
19 31 0.45
20 9 0.13
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (18 bp):
AAGAATAAGAAAAAAAAG
Found at i:565065 original size:45 final size:45
Alignment explanation
Indices: 564989--565092 Score: 131
Period size: 45 Copynumber: 2.3 Consensus size: 45
564979 AAGGGTAGAA
* * * *
564989 AAAGAATAAAGAAAAAAGAGAAAAAAGAAAGAAGAAGAA-GAATAAG
1 AAAGAAAAAAGAAAAAAAAGAAAAAAAAAAG-AGAAAAAGGAA-AAG
*
565035 AAA-AAAACAGAAAAAAAAGAAAAAAAAAAGAGAAAAAGGAAAAG
1 AAAGAAAAAAGAAAAAAAAGAAAAAAAAAAGAGAAAAAGGAAAAG
565079 AAAGAAAAAAGAAA
1 AAAGAAAAAAGAAA
565093 GGAAACTGAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
44 12 0.24
45 35 0.70
46 3 0.06
ACGTcount: A:0.79, C:0.01, G:0.18, T:0.02
Consensus pattern (45 bp):
AAAGAAAAAAGAAAAAAAAGAAAAAAAAAAGAGAAAAAGGAAAAG
Found at i:565759 original size:28 final size:28
Alignment explanation
Indices: 565718--565781 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
565708 CGCAAGAAGC
*
565718 CAACCTGAAACACATTACCTCCCCAAAT
1 CAACCTAAAACACATTACCTCCCCAAAT
* * *
565746 TAACCTAAAACACATTACCTTCCCAAGT
1 CAACCTAAAACACATTACCTCCCCAAAT
565774 CAACCTAA
1 CAACCTAA
565782 GCCTTTTATC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.41, C:0.36, G:0.03, T:0.20
Consensus pattern (28 bp):
CAACCTAAAACACATTACCTCCCCAAAT
Found at i:567593 original size:275 final size:275
Alignment explanation
Indices: 567092--567756 Score: 1041
Period size: 275 Copynumber: 2.4 Consensus size: 275
567082 AGGGTTTCTT
* * * *
567092 GATGTTCTCAAATGATTTTTTTAGAAACTAAGCC-AATTTTCAGGGGTTTCTTGATGATTATTTT
1 GATGTTTTCAAATGA-GTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTC
*
567156 CAAAGAATTTTTAAAATGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAACT
65 CAAAGAATTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCC-T--TGACAACTAAGAAACT
*
567221 AAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGTGCCATCATTAAATCTTTCGAGCA
127 AAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGTGCCATCAGTAAATCTTTCGAGCA
* *
567286 TGATGTTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCTAGATGATA-AGTCATTCGGGCCA
192 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACA-TCATTCGGGCCA
567350 TCCATAAGACCTTCGGACAG
256 TCCATAAGACCTTCGGACAG
*
567370 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
* * *
567435 AAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTAAGGGCTTCCTTGACAACTAAGAAACTAAGC
66 AAAGAATTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGC
* *
567500 TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTAG-GCCATCAGTAAGTCTTTCGAGCGTGA
131 TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTT-GTGCCATCAGTAAATCTTTCGAGCATGA
* * *
567564 TGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCTAGCAAGATGATACATCCTTCGGTCCATCCA
195 TGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACATCATTCGGGCCATCCA
** *
567629 TAAGACCTTCGGGTAT
260 TAAGACCTTCGGACAG
*
567645 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGTGGTTTCTTGATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
* *
567710 AAATAATTTTT-AAAGGAAGCTAAGCCTAATTTTTAGGGGGTCCTTGA
66 AAAGAATTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGA
567757 TGACAACTGA
Statistics
Matches: 357, Mismatches: 27, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
274 33 0.09
275 222 0.62
276 2 0.01
277 18 0.05
278 82 0.23
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (275 bp):
GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
AAAGAATTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGC
TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTTGTGCCATCAGTAAATCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACATCATTCGGGCCATCCAT
AAGACCTTCGGACAG
Found at i:567889 original size:55 final size:55
Alignment explanation
Indices: 567784--567895 Score: 127
Period size: 54 Copynumber: 2.0 Consensus size: 55
567774 ATATTTTTAA
* * *** * *
567784 AAACTAAGCCTGATTTTTAGGGGTTTCTTGATGTTTTTAAAAGATTTTTTGAAAG
1 AAACTAAGCCTGAATTGTAGGGGTTTCTTGATAACTGTAAAAGATCTTTTGAAAG
* *
567839 AAACTAAGCCT-AATTGTAGGGGTTTCTTGATAACTGTAAATGAATCTTTTGGAAG
1 AAACTAAGCCTGAATTGTAGGGGTTTCTTGATAACTGTAAAAG-ATCTTTTGAAAG
567894 AA
1 AA
567896 GCAAAATTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
54 24 0.51
55 23 0.49
ACGTcount: A:0.32, C:0.09, G:0.21, T:0.38
Consensus pattern (55 bp):
AAACTAAGCCTGAATTGTAGGGGTTTCTTGATAACTGTAAAAGATCTTTTGAAAG
Found at i:568813 original size:117 final size:117
Alignment explanation
Indices: 568595--568919 Score: 470
Period size: 117 Copynumber: 2.8 Consensus size: 117
568585 AAGATAAATT
* *
568595 GATCAACATTTCAAGTGGAGGGTTCATAATGAGAAGAACGCATCCGACAGAGGGAGAAGAAGTTC
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGAC-GAGGGAGAAGAAGTTC
* * *
568660 ATAATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATAACAGAATGAGGTG
65 ATAATGAGAAGAACTTGTTCAACCTCGGTTCCATTCCATAACAGAAGGAGGTG
* * * *
568713 GATCAACGTTTCCAGTGGAGAGTTCATAACGAGAAGAACTCATCTGACGAGGGAGAAGAAGTTCA
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
* *
568778 TAATGAGAAGAACTTGTTCAACCTCGTTTCCATTCCATCACAGAAGGAGGTG
66 TAATGAGAAGAACTTGTTCAACCTCGGTTCCATTCCATAACAGAAGGAGGTG
** * *
568830 GATCAACATTTCAAAAGGAGAGTTCATAATGAGAATAACTCATCCGAAAGAGGGAGAAGAAGTTC
1 GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCG-ACGAGGGAGAAGAAGTTC
* * *
568895 ATAATAAGAAGATCTTGTTCGACCT
65 ATAATGAGAAGAACTTGTTCAACCT
568920 ATCACTTGAT
Statistics
Matches: 184, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
117 103 0.56
118 81 0.44
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (117 bp):
GATCAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTCGGTTCCATTCCATAACAGAAGGAGGTG
Found at i:569136 original size:139 final size:137
Alignment explanation
Indices: 568845--569473 Score: 743
Period size: 139 Copynumber: 4.6 Consensus size: 137
568835 ACATTTCAAA
* * * *
568845 AGGAGAGTTCATAATGAGAATAACTCATCCGAAAGAGGGAGAAGAAGTTCATAATAAGAAGATCT
1 AGGAGAGTTCATAATGAGAAGAACTCATCCG-ATGAGGGAGAAGAAGTTCATAATGAGAAGAACT
* * * * ** * * *
568910 TGTTCGACCTATCA-CTTGATTCA-CGACCT-T----TCGAATCAGTGACGCCTCGC-CTGATGG
65 TGTTCAACCT-T-AGCTCGATTCATC-ACATATGGAGTTGAATCAGCAACACCTCACTC-GAGGG
* **
568967 ATTAACATTTCAA
126 ATCAACATTT-TG
* * *
568980 ATGGAGAGTTCATAATGAGAAGAAATCGTCCGATGAGGGAGAATAAGTTCATAATGAGAAGAACT
1 A-GGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACT
*
569045 TGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATTA
65 TGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCA
569110 ACATTTTG
130 ACATTTTG
* * *
569118 AGAAAAGAGTTCATAATGAGAATAACTCGTCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAAC
1 AG--GAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAAC
* * * *
569183 TTGTTCAACCTTAGCTCAATTTATCGCATATGGAGTTGAATCAGCAACACCTCACTTGAGGGATC
64 TTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATC
*
569248 AACATTTCCAG
129 AACATTT--TG
* * *
569259 TGGACAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTCATAATGAGAAGAACTT
1 AGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
* * *
569324 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGATCAGCAACACATTACTCGAGGGATCAA
66 GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAA
569389 CATTTCCTG
131 CATTT--TG
* * * *
569398 TGGTGAGTTCATAATGAGAATAACTCATCCGATGAGAGAGAAGAAGTTCATAATGAGAAGAACTT
1 AGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
569463 GTTCAACCTTA
66 GTTCAACCTTA
569474 ACAGTTGTCT
Statistics
Matches: 434, Mismatches: 47, Indels: 22
0.86 0.09 0.04
Matches are distributed among these distances:
133 1 0.00
134 12 0.03
135 41 0.09
136 27 0.06
137 1 0.00
138 1 0.00
139 348 0.80
140 1 0.00
141 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (137 bp):
AGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAGAAGAACTT
GTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACCTCACTCGAGGGATCAA
CATTTTG
Found at i:569328 original size:278 final size:271
Alignment explanation
Indices: 568829--569473 Score: 844
Period size: 278 Copynumber: 2.3 Consensus size: 271
568819 AGAAGGAGGT
** * *
568829 GGATCAACATTTCAAAAGGAGAGTTCATAATGAGAATAACTCATCCGAAAGAGGGAGAAGAAGTT
1 GGATCAACATTTC-TGAGAAGAGTTCATAATGAGAATAACTCATCCG-ATGAGGGAGAAGAAGTT
* * * ** * ** * *
568894 CATAATAAGAAGATCTTGTTCGACCTATCACTTGATTCACGACCTTTCGAATCAGTGACGCCTCG
64 CATAATGAGAAGAACTTGTTCAACCT-T-ACTCAATTCACGACATTTCGAATCAGCAACACCTCA
* * * * *
568959 CCTGATGGATTAACATTTCAAATGGAGAGTTCATAATGAGAAGAAATCGTCCGATGAGGGAGAAT
127 CCTGAGGGATCAACATTTCAAATGGACAGTTCATAATGAGAAGAAATCATCCGATGAGGGAGAAA
569024 AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGC
192 AAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGC
*
569089 AACACCTCACTCGAG
257 AACACATCACTCGAG
* *
569104 GGATTAACATTT-TGAGAAAAGAGTTCATAATGAGAATAACTCGTCCGATGAGGGAGAAGAAGTT
1 GGATCAACATTTCTGAG--AAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTT
* *
569168 CATAATGAGAAGAACTTGTTCAACCTTAGCTCAATTTATCG-CATATGGAGTTGAATCAGCAACA
64 CATAATGAGAAGAACTTGTTCAACCTTA-CTCAATTCA-CGACAT-T----TCGAATCAGCAACA
* * * *
569232 CCTCACTTGAGGGATCAACATTTCCAGTGGACAGTTCATAATGAGAAGAACTCATCCGATGAGGG
122 CCTCACCTGAGGGATCAACATTTCAAATGGACAGTTCATAATGAGAAGAAATCATCCGATGAGGG
*
569297 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGGA
187 AGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAA
*
569362 TCAGCAACACATTACTCGAG
252 TCAGCAACACATCACTCGAG
* ** *
569382 GGATCAACATTTCCTGTGGTGAGTTCATAATGAGAATAACTCATCCGATGAGAGAGAAGAAGTTC
1 GGATCAACATTT-CTGAGAAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTC
569447 ATAATGAGAAGAACTTGTTCAACCTTA
65 ATAATGAGAAGAACTTGTTCAACCTTA
569474 ACAGTTGTCT
Statistics
Matches: 323, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
272 1 0.00
273 11 0.03
274 42 0.13
275 38 0.12
278 228 0.71
280 3 0.01
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (271 bp):
GGATCAACATTTCTGAGAAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCA
TAATGAGAAGAACTTGTTCAACCTTACTCAATTCACGACATTTCGAATCAGCAACACCTCACCTG
AGGGATCAACATTTCAAATGGACAGTTCATAATGAGAAGAAATCATCCGATGAGGGAGAAAAAGT
TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACA
CATCACTCGAG
Found at i:574885 original size:7 final size:7
Alignment explanation
Indices: 574855--574916 Score: 54
Period size: 7 Copynumber: 8.6 Consensus size: 7
574845 AAAAGGGTAG
574855 AAAAGAA
1 AAAAGAA
574862 ATAAAGAAA
1 A-AAAG-AA
574871 AAATAGAA
1 AAA-AGAA
574879 AAAAGAA
1 AAAAGAA
*
574886 TAAAGAA
1 AAAAGAA
*
574893 GAAA-AA
1 AAAAGAA
* *
574899 AACATAA
1 AAAAGAA
574906 AAAAGAA
1 AAAAGAA
574913 AAAA
1 AAAA
574917 AAGGAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 4 0.09
7 25 0.56
8 11 0.24
9 5 0.11
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (7 bp):
AAAAGAA
Found at i:574910 original size:20 final size:20
Alignment explanation
Indices: 574875--574936 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
574865 AAGAAAAAAT
574875 AGAAAAAAGAAT---AAAGA
1 AGAAAAAAGAATAAAAAAGA
574892 AGAAAAAA-ACATAAAAAAGA
1 AGAAAAAAGA-ATAAAAAAGA
574912 A-AAAAAAGGAATAAAAAAG-
1 AGAAAAAA-GAATAAAAAAGA
574931 AGAAAA
1 AGAAAA
574937 TGTAACACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
16 1 0.03
17 10 0.26
19 7 0.18
20 19 0.50
21 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.15, T:0.05
Consensus pattern (20 bp):
AGAAAAAAGAATAAAAAAGA
Found at i:574917 original size:17 final size:16
Alignment explanation
Indices: 574855--574918 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 16
574845 AAAAGGGTAG
574855 AAAAGAAATAAAGAA-AA
1 AAAAGAAA-AAA-AATAA
*
574872 AATAGAAAAAAGAATAA
1 AAAAGAAAAAA-AATAA
*
574889 AGAAGAAAAAAACATAA
1 AAAAGAAAAAAA-ATAA
574906 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
574919 GGAATAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 8 0.20
17 33 0.80
ACGTcount: A:0.81, C:0.02, G:0.11, T:0.06
Consensus pattern (16 bp):
AAAAGAAAAAAAATAA
Found at i:575735 original size:22 final size:22
Alignment explanation
Indices: 575710--575782 Score: 55
Period size: 22 Copynumber: 3.2 Consensus size: 22
575700 AAGCTTATTT
575710 TACCAATATACTTACCATTTAA
1 TACCAATATACTTACCATTTAA
*
575732 TACC-ATA-AGCTCGTAAGCTTATTT--
1 TACCAATATA-CT--T-A-C-CATTTAA
575756 TACCAATATACTTACCATTTAA
1 TACCAATATACTTACCATTTAA
575778 TACCA
1 TACCA
575783 TAAGCTCGTA
Statistics
Matches: 39, Mismatches: 2, Indels: 20
0.64 0.03 0.33
Matches are distributed among these distances:
20 5 0.13
21 6 0.15
22 10 0.26
23 2 0.05
24 5 0.13
25 6 0.15
26 5 0.13
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.36
Consensus pattern (22 bp):
TACCAATATACTTACCATTTAA
Found at i:575748 original size:46 final size:46
Alignment explanation
Indices: 575678--575891 Score: 353
Period size: 46 Copynumber: 4.7 Consensus size: 46
575668 AAAATTTCTC
* *
575678 ACCATTT-ATCCCATAAGCTTGTAAGCTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
575723 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
*
575769 ACCATTTAATACCATAAGCTCGTAAGTTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
*
575815 ACAATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
* *
575861 GCCA-TT-ATATCATAAGCTCGTAAGCTTATTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTT
575892 GCATGGTTAC
Statistics
Matches: 160, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
44 24 0.15
45 9 0.06
46 127 0.79
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (46 bp):
ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
Found at i:579604 original size:13 final size:12
Alignment explanation
Indices: 579586--579691 Score: 97
Period size: 13 Copynumber: 8.3 Consensus size: 12
579576 GTGAAATATT
579586 TTTTTCTTTTCTG
1 TTTTTCTTTT-TG
*
579599 TTTTTCTTTATTC
1 TTTTTCTTT-TTG
*
579612 TTTTTCTTTATTC
1 TTTTTCTTT-TTG
*
579625 TTTTTCTTTATTC
1 TTTTTCTTT-TTG
579638 TTTTTCTTTTT-
1 TTTTTCTTTTTG
* *
579649 CTTTTCTTCTTG
1 TTTTTCTTTTTG
579661 TTTCTTCTTTTTG
1 TTT-TTCTTTTTG
579674 TTTTCTTCTTTTTG
1 -TTT-TTCTTTTTG
579688 TTTT
1 TTTT
579692 CTTCTTTTTT
Statistics
Matches: 84, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
11 9 0.11
12 5 0.06
13 56 0.67
14 14 0.17
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (12 bp):
TTTTTCTTTTTG
Found at i:579615 original size:26 final size:25
Alignment explanation
Indices: 579582--579653 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 25
579572 AAAAGTGAAA
*
579582 TATT-TTTTTCTTTTCTGTTTTTCTT
1 TATTCTTTTTCTTTT-TCTTTTTCTT
579607 TATTCTTTTTCTTTATTCTTTTTCTT
1 TATTCTTTTTCTTT-TTCTTTTTCTT
579633 TATTCTTTTTCTTTTTCTTTT
1 TATTCTTTTTCTTTTTCTTTT
579654 CTTCTTGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
25 11 0.25
26 32 0.73
27 1 0.02
ACGTcount: A:0.06, C:0.14, G:0.01, T:0.79
Consensus pattern (25 bp):
TATTCTTTTTCTTTTTCTTTTTCTT
Found at i:579620 original size:6 final size:6
Alignment explanation
Indices: 579586--579691 Score: 97
Period size: 6 Copynumber: 16.7 Consensus size: 6
579576 GTGAAATATT
*
579586 TTTTTC TTTTCTG TTTTTC TTTATTC TTTTTC TTTATTC TTTTTC TTTATTC
1 TTTTTC TTTT-TC TTTTTC TTT-TTC TTTTTC TTT-TTC TTTTTC TTT-TTC
* * * *
579638 TTTTTC TTTTTC -TTTTC TTCTTG TTTCTTC TTTTTGT TTTCTTC TTTTTG
1 TTTTTC TTTTTC TTTTTC TTTTTC TTT-TTC TTTTT-C TTT-TTC TTTTTC
579688 TTTT
1 TTTT
579692 CTTCTTTTTT
Statistics
Matches: 83, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
5 5 0.06
6 42 0.51
7 34 0.41
8 2 0.02
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:579668 original size:24 final size:22
Alignment explanation
Indices: 579635--579701 Score: 57
Period size: 24 Copynumber: 3.0 Consensus size: 22
579625 TTTTTCTTTA
*
579635 TTCTTTTTC-TTT-TTCTTTTC
1 TTCTTTTTCTTTTCTTCTTTTT
* * *
579655 TTCTTGTTTCTTCTTTTTGTTTTC
1 TTCTT-TTTCTT-TTCTTCTTTTT
*
579679 TTCTTTTTGTTTTCTTCTTTTT
1 TTCTTTTTCTTTTCTTCTTTTT
579701 T
1 T
579702 ATATATAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 5 0.13
21 4 0.11
22 10 0.26
23 7 0.18
24 12 0.32
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.79
Consensus pattern (22 bp):
TTCTTTTTCTTTTCTTCTTTTT
Found at i:579699 original size:13 final size:14
Alignment explanation
Indices: 579641--579700 Score: 83
Period size: 14 Copynumber: 4.6 Consensus size: 14
579631 TTTATTCTTT
*
579641 TTCTTTTTCTTTTC
1 TTCTTTTTGTTTTC
579655 TTC---TTG-TTTC
1 TTCTTTTTGTTTTC
579665 TTCTTTTTGTTTTC
1 TTCTTTTTGTTTTC
579679 TTCTTTTTGTTTTC
1 TTCTTTTTGTTTTC
579693 TTCTTTTT
1 TTCTTTTT
579701 TATATATAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
10 7 0.17
11 2 0.05
13 3 0.07
14 29 0.71
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (14 bp):
TTCTTTTTGTTTTC
Found at i:582670 original size:46 final size:46
Alignment explanation
Indices: 582600--582813 Score: 353
Period size: 46 Copynumber: 4.7 Consensus size: 46
582590 AAAATTTCTC
* *
582600 ACCATTT-ATCCCATAAGCTTGTAAGCTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
582645 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
582691 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
*
582737 ACCATTTAATACCATAAGCTCATAAGCTTATTTTACCAATATACTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
* * *
582783 GCCA-TT-ATATCATAAGCTCGTCAGCTTATTT
1 ACCATTTAATACCATAAGCTCGTAAGCTTATTT
582814 GCATGGTTAC
Statistics
Matches: 161, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
44 22 0.14
45 9 0.06
46 130 0.81
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (46 bp):
ACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATACTT
Found at i:582682 original size:24 final size:24
Alignment explanation
Indices: 582654--582728 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
582644 TACCATTTAA
582654 TACCATAAGCTCGTAAGCTTATTT
1 TACCATAAGCTCGTAAGCTTATTT
*
582678 TACCAATATA-CT--T-A-C-CATTT
1 TACC-ATA-AGCTCGTAAGCTTATTT
582698 AATACCATAAGCTCGTAAGCTTATTT
1 --TACCATAAGCTCGTAAGCTTATTT
582724 TACCA
1 TACCA
582729 ATATACTTAC
Statistics
Matches: 39, Mismatches: 2, Indels: 20
0.64 0.03 0.33
Matches are distributed among these distances:
20 5 0.13
21 6 0.15
22 5 0.13
23 2 0.05
24 10 0.26
25 6 0.15
26 5 0.13
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (24 bp):
TACCATAAGCTCGTAAGCTTATTT
Found at i:585341 original size:28 final size:28
Alignment explanation
Indices: 585279--585342 Score: 74
Period size: 28 Copynumber: 2.3 Consensus size: 28
585269 TGCAAGAAGC
* *
585279 CAACCTGAAGCACATTACCTCCCCAAAT
1 CAACCTAAAACACATTACCTCCCCAAAT
* * *
585307 TAACCTAAAACACATTACCTTCCCAAGT
1 CAACCTAAAACACATTACCTCCCCAAAT
*
585335 CAGCCTAA
1 CAACCTAA
585343 GCCTTTTATC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.38, C:0.36, G:0.06, T:0.20
Consensus pattern (28 bp):
CAACCTAAAACACATTACCTCCCCAAAT
Found at i:586851 original size:42 final size:42
Alignment explanation
Indices: 586805--586887 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
586795 AAGGGTTTCT
* *
586805 TGATGAGTAAGTCCTTCGTGTCATC-ATTAAGTCTTTCGAGCA
1 TGATGAGTAAATCCTTCGGGTCATCTA-TAAGTCTTTCGAGCA
**
586847 TGATGTTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGC
1 TGATGAGTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGC
586888 TAGATGATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 35 0.97
43 1 0.03
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (42 bp):
TGATGAGTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
Found at i:587154 original size:275 final size:275
Alignment explanation
Indices: 586653--587316 Score: 1014
Period size: 275 Copynumber: 2.4 Consensus size: 275
586643 AGGGTTTCTT
* *
586653 GATGTTCTCAAATGAGTTTTTAGAAACTAAG-C-GAATTTTCAGGGGTTTCTTGATGATTATTTT
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTG-ATTTTCAGGGGTTTCTTGATGATTA-TCT
* ** * *
586716 CAAAAAAAAGTTTAAAATGAAGCTAAACCTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAAC
64 CCAAAAAATTTTTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTCC-T--TGACAACTAAGAAAC
* * *
586781 TAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGTGTCATCATTAAGTCTTTCGAGC
126 TAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGC
* *
586846 ATGATGTTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCTAGATGATA-AGCCATTCGGGCC
191 ATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACAGCC-TTCGGGCC
586910 ATCCATAAGACCTTCGGGCAG
255 ATCCATAAGACCTTCGGGCAG
586931 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
* * *
586996 AAAGAGTTTTTAAAAAAAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGC
66 AAAAAATTTTTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGC
* **
587061 TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTCAGTCTTTCGAGTGTGAT
131 TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
* *
587126 GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACATCCTTCGGTCCATCCAT
196 GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACAGCCTTCGGGCCATCCAT
*
587191 AAGACCTTTGGGCAG
261 AAGACCTTCGGGCAG
*
587206 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCC
1 GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
* * *
587271 AAATAATTTTT-AAAGGAAGCTAAG-CTAATTTTTAGGGGGTCCTTGA
66 AAAAAATTTTTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGA
587317 TGACAACTGA
Statistics
Matches: 356, Mismatches: 27, Indels: 11
0.90 0.07 0.03
Matches are distributed among these distances:
273 21 0.06
274 11 0.03
275 223 0.63
276 3 0.01
277 1 0.00
278 70 0.20
279 26 0.07
280 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (275 bp):
GATGTTTTCAAATGAGTTTTTAGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATCTCC
AAAAAATTTTTAAAAAGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGACAACTAAGAAACTAAGC
TTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGAT
GCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATACAGCCTTCGGGCCATCCAT
AAGACCTTCGGGCAG
Found at i:587301 original size:57 final size:56
Alignment explanation
Indices: 587222--587429 Score: 180
Period size: 57 Copynumber: 3.7 Consensus size: 56
587212 TTCAAATGAG
* ** *
587222 TTTTTAGA-AACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTCCAAATAA
1 TTTTTAAAGAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTAAAAAAAA
* * * * *
587277 TTTTTAAAGGAAGCTAAG-CTAATTTTTAGGGGGTCCTTGATGA-CAACTGAAAACGAAAGA
1 TTTTTAAA-GAA-CTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCT-AAAA--AAA-A
* * *
587337 TTTTTAAA-AACTAAGCCTGATTTTCAGGGGTTTCTTGATG-TT-T-TTAAAAGAA
1 TTTTTAAAGAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTAAAAAAAA
587389 TTTTTGAAAGAAACTAAGCCTAATTTT-AGGGGTTTCTTGAT
1 TTTTT-AAAG-AACTAAGCCTAATTTTCAGGGGTTTCTTGAT
587430 AACTGTAAAT
Statistics
Matches: 123, Mismatches: 18, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
52 6 0.05
53 5 0.04
54 14 0.11
55 25 0.20
56 4 0.03
57 31 0.25
58 27 0.22
59 2 0.02
60 9 0.07
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (56 bp):
TTTTTAAAGAACTAAGCCTAATTTTCAGGGGTTTCTTGATGATTATCTAAAAAAAA
Found at i:588374 original size:117 final size:117
Alignment explanation
Indices: 588157--588478 Score: 509
Period size: 117 Copynumber: 2.7 Consensus size: 117
588147 ATAAACTGAT
*
588157 CAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGAC-GAGGGAGAAGAAGTTCATA
* *
588222 ATGAGAAGAACTTGTTCAACCTTGGTTCGATTCCATCACAGAATGAGGTGGAC
65 ATGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAGGAGGTGGAC
* * * *
588275 CAACGTTTCCAGTGGAGGGTTCATAACGAGAAGAACTCATCTGACGAGGGAGAAGAAGTTCATAA
1 CAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGACGAGGGAGAAGAAGTTCATAA
*
588340 TGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAGGAGGTGGAT
66 TGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAGGAGGTGGAC
* * *
588392 CAACATTTCAAATGGAGAGTTCATAATAAGAAGAACTCATCTGAAAGAGGGAGAAGAAGTTCATA
1 CAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTG-ACGAGGGAGAAGAAGTTCATA
* *
588457 ATGAGAAGATCTTGTTCGACCT
65 ATGAGAAGAACTTGTTCAACCT
588479 ATCACTTGAT
Statistics
Matches: 186, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
117 106 0.57
118 80 0.43
ACGTcount: A:0.36, C:0.16, G:0.25, T:0.23
Consensus pattern (117 bp):
CAACATTTCAAGTGGAGAGTTCATAATGAGAAGAACTCATCTGACGAGGGAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTCGGTTCGATTCCATCACAGAAGGAGGTGGAC
Found at i:588690 original size:139 final size:139
Alignment explanation
Indices: 588388--589030 Score: 813
Period size: 139 Copynumber: 4.6 Consensus size: 139
588378 AGAAGGAGGT
* * *
588388 GGATCAACATTT-CA-AATGGAGAGTTCATAATAAGAAGAACTCATCTGAAAGAGGGAGAAGAAG
1 GGATCAACATTTCCAGAA--GAGAGTTCATAATGAGAAGAACTCATCCG-ATGAGGGAGAAGAAG
* * * * * *
588451 TTCATAATGAGAAGATCTTGTTCGACCTATCA-CTTGATTCA-CGACCT-T----TCGAATCAGT
63 TTCATAATGAGAAGAACTTGTTCAACCT-T-AGCTCGATTCATC-ACATATGGAGTTGAATCAGC
* * * *
588509 GACACCTCGCTTGAT
125 AACACCTCACTCGAG
* * *
588524 GGATTAACATTT-CA-AATGGAGAGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAATAAGT
1 GGATCAACATTTCCAGAA--GAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGT
588587 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACA
64 TCATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACA
588652 CCTCACTCGAG
129 CCTCACTCGAG
* *
588663 GGATCAACATTTCCAGAAAAGAGTTCATAATGAGAAGAACTCGTCCGATGAGGGAGAAGAAGTTC
1 GGATCAACATTTCCAGAAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* *
588728 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTTATCGCATATGGAGTTGAATCAGCAACACC
66 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
*
588793 TCACTTGAG
131 TCACTCGAG
** * *
588802 GGATCAACATTTCCAGTGGACAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAAAAGTTC
1 GGATCAACATTTCCAGAAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* ** * * *
588867 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGCAAATGGATCAACAACACA
66 ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
*
588932 TTACTCGAG
131 TCACTCGAG
** * *
588941 GGATCAACATTTCCAGTGGTGAGTTCATAATGAGAAGAACTCATCCGATGAGAGAGAAGAAGTTC
1 GGATCAACATTTCCAGAAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
589006 ATAATGAGAAGAACTTGTTCAACCT
66 ATAATGAGAAGAACTTGTTCAACCT
589031 CAGCAGTTGC
Statistics
Matches: 456, Mismatches: 42, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
133 1 0.00
134 12 0.03
135 41 0.09
136 43 0.09
139 355 0.78
140 2 0.00
141 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (139 bp):
GGATCAACATTTCCAGAAGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTAGCTCGATTCATCACATATGGAGTTGAATCAGCAACACC
TCACTCGAG
Found at i:588747 original size:20 final size:19
Alignment explanation
Indices: 588685--588748 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
588675 CCAGAAAAGA
588685 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* **
588704 CGTCCGATGAGGGAGAAGAA--
1 -GTTC-AT-AATGAGAAGAACT
588724 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
588744 GTTCA
1 GTTCA
588749 ACCTTAGCTC
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 9 0.27
18 2 0.06
19 3 0.09
20 8 0.24
21 2 0.06
22 9 0.27
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:591191 original size:30 final size:31
Alignment explanation
Indices: 591127--591201 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 31
591117 GATTTTAAAC
* *
591127 CTAG-CCCTAAA-TTTAAACTTCTTTTAGAT
1 CTAGTCCCTAAACTTTAAACTTCTTTGAAAT
591156 CTAGTCCCTAAACTTTATAAC-TCTTTGAAAT
1 CTAGTCCCTAAACTTTA-AACTTCTTTGAAAT
*
591187 -TAGT-CCTCAACTTTA
1 CTAGTCCCTAAACTTTA
591202 GAAATTATCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 14 0.35
30 11 0.28
31 12 0.30
32 3 0.08
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.40
Consensus pattern (31 bp):
CTAGTCCCTAAACTTTAAACTTCTTTGAAAT
Found at i:592655 original size:2 final size:2
Alignment explanation
Indices: 592648--592672 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
592638 TGAGAAATAG
592648 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
592673 GATGTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:601448 original size:74 final size:74
Alignment explanation
Indices: 601323--601524 Score: 228
Period size: 74 Copynumber: 2.7 Consensus size: 74
601313 AACTCCATTA
* * ** * * **
601323 ATTTTAAAAGTTA-CAATGACCTAAAA-ATAATTATACCAAAAAAAATAGGGAGGAATAAGGGCT
1 ATTTTATAA-TTATCAATGACCTAAAATATAATTAGACC-ATCAAAGTTGGGAGGAATAAAAGCT
601386 CAATTATAATG
64 CAATTATAATG
* * * ** *
601397 ATTTTATAATTATCAGTGACCTAAAATATAATTAGATCATCAAATTTGGGAGGGGTAAAAGCTTA
1 ATTTTATAATTATCAATGACCTAAAATATAATTAGACCATCAAAGTTGGGAGGAATAAAAGCTCA
601462 ATTATAATG
66 ATTATAATG
* *
601471 ATTTTATAATTATCAATGATCTAAAATGTAATTAGACCATCAAAGTTGGGAGGA
1 ATTTTATAATTATCAATGACCTAAAATATAATTAGACCATCAAAGTTGGGAGGA
601525 GCAATTGCTC
Statistics
Matches: 107, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
73 3 0.03
74 95 0.89
75 9 0.08
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (74 bp):
ATTTTATAATTATCAATGACCTAAAATATAATTAGACCATCAAAGTTGGGAGGAATAAAAGCTCA
ATTATAATG
Found at i:605360 original size:23 final size:23
Alignment explanation
Indices: 605334--605380 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
605324 TATATAACAC
605334 TATTAGATAAATAAATATTTATA
1 TATTAGATAAATAAATATTTATA
* * *
605357 TATTATATACATAACTATTTATA
1 TATTAGATAAATAAATATTTATA
605380 T
1 T
605381 TTATTTAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTAGATAAATAAATATTTATA
Found at i:605414 original size:29 final size:29
Alignment explanation
Indices: 605340--605415 Score: 84
Period size: 29 Copynumber: 2.7 Consensus size: 29
605330 ACACTATTAG
* * *
605340 ATAAATAA--ATATTTATATATTATATAC
1 ATAAATAATTATATTTATTTAGTATATAA
* * *
605367 ATAACTATTTATATTTATTTAGTATGTAA
1 ATAAATAATTATATTTATTTAGTATATAA
605396 ATAAATAATTATATTTATTT
1 ATAAATAATTATATTTATTT
605416 TTACATAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 6 0.15
29 33 0.85
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (29 bp):
ATAAATAATTATATTTATTTAGTATATAA
Found at i:605512 original size:31 final size:29
Alignment explanation
Indices: 605477--605538 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
605467 TTTTTACTAC
*
605477 ATATAATTA-AATTAAAATTAAAATATTGTGT
1 ATATAATTACAA-T-AAATTAAAAT-TTATGT
605508 ATATAATTACAATAAATTAAAATTTATGT
1 ATATAATTACAATAAATTAAAATTTATGT
605537 AT
1 AT
605539 TACACCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 10 0.34
31 10 0.34
32 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATAATTACAATAAATTAAAATTTATGT
Found at i:606605 original size:24 final size:24
Alignment explanation
Indices: 606553--606615 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 24
606543 ATTTTTATTA
606553 TTACTATTATATTTATCATTATT-T
1 TTACTATTATATTTATCATT-TTAT
*
606577 TTACTATTATATTTTTC-TTTTAT
1 TTACTATTATATTTATCATTTTAT
606600 TCTACTTATTTATATT
1 T-TAC-TA-TTATATT
606616 ATATATGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 2 0.06
23 4 0.12
24 19 0.56
25 2 0.06
26 7 0.21
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (24 bp):
TTACTATTATATTTATCATTTTAT
Found at i:606930 original size:22 final size:22
Alignment explanation
Indices: 606886--606931 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
606876 GTTATTGTTA
*
606886 TTTTTTTATTTTGTTTATTTAT
1 TTTTTTTATTTTGTTTATATAT
*
606908 TTTTTTTCTTTT-TTATATATAT
1 TTTTTTTATTTTGTT-TATATAT
606930 TT
1 TT
606932 ATCTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.15, C:0.02, G:0.02, T:0.80
Consensus pattern (22 bp):
TTTTTTTATTTTGTTTATATAT
Found at i:611441 original size:24 final size:24
Alignment explanation
Indices: 611414--611469 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
611404 AGATCGAGAG
611414 GTCAACAATGTCAACACCTATAAC
1 GTCAACAATGTCAACACCTATAAC
611438 GTCAACAATGTCAACACCTATAAC
1 GTCAACAATGTCAACACCTATAAC
611462 GTCAACAA
1 GTCAACAA
611470 GGGCGTTACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.43, C:0.29, G:0.09, T:0.20
Consensus pattern (24 bp):
GTCAACAATGTCAACACCTATAAC
Found at i:611443 original size:15 final size:15
Alignment explanation
Indices: 611423--611468 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
611413 GGTCAACAAT
611423 GTCAACACCTATAAC
1 GTCAACACCTATAAC
611438 GTCAACA---AT---
1 GTCAACACCTATAAC
611447 GTCAACACCTATAAC
1 GTCAACACCTATAAC
611462 GTCAACA
1 GTCAACA
611469 AGGGCGTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 7 0.28
12 4 0.16
15 14 0.56
ACGTcount: A:0.41, C:0.30, G:0.09, T:0.20
Consensus pattern (15 bp):
GTCAACACCTATAAC
Found at i:618422 original size:98 final size:98
Alignment explanation
Indices: 618189--618840 Score: 847
Period size: 98 Copynumber: 6.6 Consensus size: 98
618179 ATATCGTACC
* * * * *
618189 ACTCAAGACAATACAAGTTCAACTTCACAACGAAGGGACGGCTGATTGTCAACAACAAATTTCCC
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGT---CAACAAA-----C
*
618254 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
58 AATTTCGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
618295 ACTCAAGACAACACATGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGG
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGG
618360 AGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AGCCAATTTCAACTTCACAACGAAGGATATTGG
*
618393 ACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGG
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGG
* * *
618458 AGCCAATCTCAATTTCACAGCGAAGGATATTGG
66 AGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * **
618491 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCAG
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTC-G
*
618555 G-GCCAATTTCAACTTCACATCGAAGGATATTGG
65 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
618588 ACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAGTTTTGG
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGG
* *
618653 AGCCAATCTCAACTT--C-AC--A-GATATTGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * **
618680 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCAG
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTC-G
618744 G-GCCAATTTCAACTTCACAACGAAGGATATTGG
65 GAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
618777 ACCCAAGACAGCACAAGCTCAACTTCACAGCGAAAGGGCGGCTGACTGTCAACAAAACAATTTC
1 ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAAC-AAACAATTTC
618841 CCAGTTCCAG
Statistics
Matches: 480, Mismatches: 54, Indels: 31
0.85 0.10 0.05
Matches are distributed among these distances:
91 20 0.04
92 55 0.11
93 2 0.00
94 2 0.00
95 1 0.00
96 2 0.00
97 137 0.29
98 202 0.42
99 9 0.02
103 7 0.01
106 43 0.09
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (98 bp):
ACTCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCGG
AGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:618617 original size:195 final size:194
Alignment explanation
Indices: 618253--618840 Score: 945
Period size: 189 Copynumber: 3.0 Consensus size: 194
618243 ACAAATTTCC
* * * *
618253 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACATGCTCAAC
1 CAATTTCGGAGCCAATCTCAACTTCAC-ACGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
* * **
618318 TTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTC-GGAGCCAATTTCAACTTCACAACG
65 TTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTCAGG-GCCAATTTCAACTTCACAACG
*
618382 AAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACA
128 AAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACA
618447 AA
193 AA
* *
618449 CAATTTCGGAGCCAATCTCAATTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAAC
1 CAATTTCGGAGCCAATCTCAACTTCACA-CGAAGGATATTGGACTCAAGACAACACAAGTTCAAC
*
618514 TTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCAGGGCCAATTTCAACTTCACATCGAA
65 TTCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCAGGGCCAATTTCAACTTCACAACGAA
618579 GGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAA
130 GGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAA
* * *
618644 CAGTTTTGGAGCCAATCTCAACTT--CAC--A-GATATTGAACTCAAGACAACACAAGTTCAACT
1 CAATTTCGGAGCCAATCTCAACTTCACACGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
618704 TCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCAGGGCCAATTTCAACTTCACAACGAAG
66 TCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCAGGGCCAATTTCAACTTCACAACGAAG
*
618769 GATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAAGGGCGGCTGACTGTCAACAAAA
131 GATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAAC-AAA
618834 CAATTTC
1 CAATTTC
618841 CCAGTTCCAG
Statistics
Matches: 368, Mismatches: 21, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
189 154 0.42
190 9 0.02
192 1 0.00
193 2 0.01
195 117 0.32
196 85 0.23
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (194 bp):
CAATTTCGGAGCCAATCTCAACTTCACACGAAGGATATTGGACTCAAGACAACACAAGTTCAACT
TCACAACGAAGGGACGGCTGGTTGTCAACAACAATTTCAGGGCCAATTTCAACTTCACAACGAAG
GATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAA
Found at i:620168 original size:24 final size:24
Alignment explanation
Indices: 620116--620178 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 24
620106 ATTTTTATTA
620116 TTACTATTATATTTATCATTATT-T
1 TTACTATTATATTTATCATT-TTAT
*
620140 TTACTATTATATTTTTC-TTTTAT
1 TTACTATTATATTTATCATTTTAT
620163 TCTACTTATTTATATT
1 T-TAC-TA-TTATATT
620179 ATATATGTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
22 2 0.06
23 4 0.12
24 19 0.56
25 2 0.06
26 7 0.21
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (24 bp):
TTACTATTATATTTATCATTTTAT
Found at i:624402 original size:31 final size:29
Alignment explanation
Indices: 624365--624426 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
624355 TTTTTACTAC
*
624365 ATATAATTA-AATTAAAATTAAAATATTGTGT
1 ATATAATTACAA-T-AAATTAAAAT-TTATGT
624396 ATATAATTACAATAAATTAAAATTTATGT
1 ATATAATTACAATAAATTAAAATTTATGT
624425 AT
1 AT
624427 TACACCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 10 0.34
31 10 0.34
32 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATAATTACAATAAATTAAAATTTATGT
Found at i:624727 original size:2 final size:2
Alignment explanation
Indices: 624720--624768 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
624710 GTTTTCGTGC
624720 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
624762 AT AT AT A
1 AT AT AT A
624769 ATTTATGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:625012 original size:2 final size:2
Alignment explanation
Indices: 625005--625032 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
624995 TAAAGATCAG
625005 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
625033 TTATGTAAAA
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:625236 original size:261 final size:263
Alignment explanation
Indices: 624742--625274 Score: 980
Period size: 262 Copynumber: 2.0 Consensus size: 263
624732 ATATATATAT
*
624742 ATATATATATATATATATATATATATAATTTATGTAAAAAGGTGTGAACTTAAGAAGTTATATTA
1 ATATATATATATATATATATATATATAATTTATGTAAAAAGGTATGAACTTAAGAAGTTATATTA
*
624807 AAATTTTTAAGGGGTGCGAAGTTGTAAAATTTTAGGGAGTGTAAAACTAAATAATCAATAGAAAA
66 AAATTTTTAAGGGGTGCGAAGTTGTAAAATTTTAGGGAGTGCAAAACTAAATAATCAATAGAAAA
* *
624872 AACTTAAAATATAAGGGAGTTTAAAATTTTTAGTAGGTATGACTGACCCCATTACCCCTCGGTCC
131 AACTTAAAATATAAGGGAGATTAAAATTTTTAGTAGGTATAACTGACCCCATTACCCCTCGGTCC
624937 ATCTTTATATATAAGTTTAAATAGTATTCAACAGTATAATTTTGATACTTTTAGTTCATAAAGAT
196 ATCTTTATATATAAGTTTAAATAGTATTCAACAGTATAATTTTGATACTTTTAGTTCATAAAGAT
625002 CAG
261 CAG
625005 ATATATATATATATATATATATATAT-ATTTATGTAAAAAGGTATGAACTTAAGAAGTTATATTA
1 ATATATATATATATATATATATATATAATTTATGTAAAAAGGTATGAACTTAAGAAGTTATATTA
*
625069 AAATTTTTAAGGGGTGCGAAGTTGTAAAATTTTAGGGAGTGCAAAACTAGATAATCAATAGAAAA
66 AAATTTTTAAGGGGTGCGAAGTTGTAAAATTTTAGGGAGTGCAAAACTAAATAATCAATAGAAAA
*
625134 AACTTAAAATATAAGGGAGATTAAAATTTTTAGTGGGTATAACTGA-CCCATTACCCCTCGGTCC
131 AACTTAAAATATAAGGGAGATTAAAATTTTTAGTAGGTATAACTGACCCCATTACCCCTCGGTCC
*
625198 ATCTTTATATATAAGTTTAAGTAGTATTCAACAGTATAATTTTGATACTTTTAGTTCATAAAGAT
196 ATCTTTATATATAAGTTTAAATAGTATTCAACAGTATAATTTTGATACTTTTAGTTCATAAAGAT
625263 CAG
261 CAG
*
625266 AGATATATA
1 ATATATATA
625275 CTCCACACTG
Statistics
Matches: 262, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
261 93 0.35
262 143 0.55
263 26 0.10
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.36
Consensus pattern (263 bp):
ATATATATATATATATATATATATATAATTTATGTAAAAAGGTATGAACTTAAGAAGTTATATTA
AAATTTTTAAGGGGTGCGAAGTTGTAAAATTTTAGGGAGTGCAAAACTAAATAATCAATAGAAAA
AACTTAAAATATAAGGGAGATTAAAATTTTTAGTAGGTATAACTGACCCCATTACCCCTCGGTCC
ATCTTTATATATAAGTTTAAATAGTATTCAACAGTATAATTTTGATACTTTTAGTTCATAAAGAT
CAG
Found at i:627081 original size:18 final size:18
Alignment explanation
Indices: 627058--627100 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
627048 CTTTAGATTA
*
627058 TTTATTTAATTATTTTCT
1 TTTATTTAATTATTATCT
*
627076 TTTATTTAATTCTTATCT
1 TTTATTTAATTATTATCT
627094 TTTATTT
1 TTTATTT
627101 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTATTTAATTATTATCT
Found at i:627208 original size:28 final size:28
Alignment explanation
Indices: 627146--627200 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
627136 TAATACTATT
627146 ATTTATTATTTTATTATATTTTCCTTTC
1 ATTTATTATTTTATTATATTTTCCTTTC
*
627174 ATTTATTATTATT-TTAT-TTTTTCTTTC
1 ATTTATTATT-TTATTATATTTTCCTTTC
627201 CTTTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 9 0.36
28 14 0.56
29 2 0.08
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (28 bp):
ATTTATTATTTTATTATATTTTCCTTTC
Found at i:627271 original size:11 final size:11
Alignment explanation
Indices: 627251--627282 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
627241 TCCCGTTTCT
627251 TTTTTATTTTA
1 TTTTTATTTTA
*
627262 TTTTTCTTTTA
1 TTTTTATTTTA
627273 TTTTTATTTT
1 TTTTTATTTT
627283 TCTCTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:627314 original size:17 final size:16
Alignment explanation
Indices: 627250--627317 Score: 61
Period size: 17 Copynumber: 4.3 Consensus size: 16
627240 TTCCCGTTTC
627250 TTTTTTATTTTATT-T
1 TTTTTTATTTTATTAT
627265 TTCTTTTA-TTT-TTAT
1 TT-TTTTATTTTATTAT
* * **
627280 TTTTCTCTTTTAACAT
1 TTTTTTATTTTATTAT
627296 TTTTTATATTTTATTAT
1 TTTTT-TATTTTATTAT
627313 TTTTT
1 TTTTT
627318 CCTGAAATTT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
14 5 0.12
15 11 0.28
16 11 0.28
17 13 0.32
ACGTcount: A:0.16, C:0.06, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTTATTAT
Found at i:631050 original size:29 final size:29
Alignment explanation
Indices: 631017--631073 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
631007 CTAAATTAAT
631017 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
631046 TTGATGTCATTGCTTACATCAATTTAGT
1 TTGATGTCATTGCTTACATCAATTTAGT
631074 TAGGTGAAAA
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:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:635728 original size:29 final size:29
Alignment explanation
Indices: 635695--635751 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
635685 CTAAATTAAT
635695 TTGATGTCATTGCTTACATCAATTTAGTA
1 TTGATGTCATTGCTTACATCAATTTAGTA
635724 TTGATGTCATTGCTTACATCAATTTAGT
1 TTGATGTCATTGCTTACATCAATTTAGT
635752 TAGGTGAAAA
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:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (29 bp):
TTGATGTCATTGCTTACATCAATTTAGTA
Found at i:637645 original size:23 final size:23
Alignment explanation
Indices: 637619--637668 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
637609 ATATAACACC
637619 ATTATATAAATAAATATTTATAT
1 ATTATATAAATAAATATTTATAT
* *
637642 ATTATATACATAACTATTTATAT
1 ATTATATAAATAAATATTTATAT
637665 -TTAT
1 ATTAT
637669 TTAGTATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 4 0.16
23 21 0.84
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATATAAATAAATATTTATAT
Found at i:637664 original size:29 final size:29
Alignment explanation
Indices: 637624--637696 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
637614 ACACCATTAT
* *
637624 ATAAATAA--ATATTTATATATTATATAC
1 ATAAATAATTATATTTATATAGTATATAA
* * * *
637651 ATAACTATTTATATTTATTTAGTATGTAA
1 ATAAATAATTATATTTATATAGTATATAA
637680 ATAAATAATTATATTTA
1 ATAAATAATTATATTTA
637697 CTTTTATATA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
27 6 0.17
29 30 0.83
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
ATAAATAATTATATTTATATAGTATATAA
Found at i:637797 original size:31 final size:29
Alignment explanation
Indices: 637762--637823 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 29
637752 TTTTTACTAC
*
637762 ATATAATTA-AATTAAAATTAAAATATTGTGT
1 ATATAATTACAA-T-AAATTAAAAT-TTATGT
637793 ATATAATTACAATAAATTAAAATTTATGT
1 ATATAATTACAATAAATTAAAATTTATGT
637822 AT
1 AT
637824 TACACCAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 7 0.24
30 10 0.34
31 10 0.34
32 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (29 bp):
ATATAATTACAATAAATTAAAATTTATGT
Found at i:642063 original size:38 final size:37
Alignment explanation
Indices: 642021--642152 Score: 117
Period size: 37 Copynumber: 3.6 Consensus size: 37
642011 ACAAAGTGTC
* * * *
642021 GTCTCGGTAGAGACAGGTTTTCTTTAAAAATG-AATTTT
1 GTCTCGCTTGAGACA-GTTTTCTCT-AAAAGGAAATTTT
*
642059 GTCTCGTTTGAGACAGTTTTCTCTAAAAGGAAATTTT
1 GTCTCGCTTGAGACAGTTTTCTCTAAAAGGAAATTTT
* * *
642096 GTCTCGCTTGAGACAATTTT-TCTCAAAA-CAAATTTC
1 GTCTCGCTTGAGACAGTTTTCTCT-AAAAGGAAATTTT
* * *
642132 ATCTCGCTTGAGGCATTTTTC
1 GTCTCGCTTGAGACAGTTTTC
642153 CTTTGAGATG
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
36 31 0.39
37 36 0.45
38 13 0.16
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.39
Consensus pattern (37 bp):
GTCTCGCTTGAGACAGTTTTCTCTAAAAGGAAATTTT
Found at i:642137 original size:36 final size:37
Alignment explanation
Indices: 642060--642152 Score: 109
Period size: 36 Copynumber: 2.5 Consensus size: 37
642050 ATGAATTTTG
* * * **
642060 TCTCGTTTGAGACAGTTTTCTCTAAAAGGAAATTTTG
1 TCTCGCTTGAGACATTTTTCTCTAAAAGCAAATTTCA
642097 TCTCGCTTGAGACAATTTTTCTC-AAAA-CAAATTTCA
1 TCTCGCTTGAGAC-ATTTTTCTCTAAAAGCAAATTTCA
*
642133 TCTCGCTTGAGGCATTTTTC
1 TCTCGCTTGAGACATTTTTC
642153 CTTTGAGATG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
35 7 0.14
36 18 0.37
37 16 0.33
38 8 0.16
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (37 bp):
TCTCGCTTGAGACATTTTTCTCTAAAAGCAAATTTCA
Found at i:642193 original size:20 final size:21
Alignment explanation
Indices: 642170--642208 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
642160 ATGCAAATTT
*
642170 CAAATTTG-TTTCACTTGAAA
1 CAAAGTTGATTTCACTTGAAA
642190 CAAAGTTGATTTCACTTGA
1 CAAAGTTGATTTCACTTGA
642209 GATTGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (21 bp):
CAAAGTTGATTTCACTTGAAA
Found at i:642485 original size:37 final size:36
Alignment explanation
Indices: 642444--642534 Score: 112
Period size: 36 Copynumber: 2.5 Consensus size: 36
642434 AAATTTGGAA
* *
642444 ATTGTTTCACTTGAAACAAA-ATTGATAAACCTTTGAG
1 ATTGTTTCTCTTGAAACAAATATTG-T-AACCCTTGAG
* **
642481 ATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAG
1 ATTGTTTCTCTTGAAACAAATATTGTAACCCTTGAG
642517 ATTGTTTCTCTTGAAACA
1 ATTGTTTCTCTTGAAACA
642535 CAAAATCTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 25 0.52
37 20 0.42
38 3 0.06
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (36 bp):
ATTGTTTCTCTTGAAACAAATATTGTAACCCTTGAG
Found at i:642516 original size:36 final size:36
Alignment explanation
Indices: 642476--642601 Score: 124
Period size: 36 Copynumber: 3.6 Consensus size: 36
642466 TGATAAACCT
642476 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCC
1 TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCC
**
642512 TTGAGATTGTTTCTCTTGAAACACAA---AATCT---
1 TTGAGATTGTTTCTCTTGAAACA-AATTTTGTCTCCC
*
642543 TTGA-ATATGTTTCCCTTGAAACAAATTTTGTCTCCC
1 TTGAGAT-TGTTTCTCTTGAAACAAATTTTGTCTCCC
* *
642579 TTGAGACAT-TTTCTTTTGAAACA
1 TTGAGA-TTGTTTCTCTTGAAACA
642602 TAAATCTTTG
Statistics
Matches: 72, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
30 4 0.06
31 19 0.26
33 3 0.04
34 3 0.04
36 39 0.54
37 4 0.06
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (36 bp):
TTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCC
Found at i:642650 original size:66 final size:66
Alignment explanation
Indices: 642474--642863 Score: 500
Period size: 66 Copynumber: 5.9 Consensus size: 66
642464 ATTGATAAAC
* * **
642474 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGATTGTTTCTCTTGAAACACAAA
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAC-AA
642539 AT
65 AT
* * * *
642541 CTTTGA-ATATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCTTTTGAAACATAA
1 CTTTGAGAT-CGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
642605 AT
65 AT
* * * * *
642607 CTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCATGAGACAGTTTCCCTTGAAACACCAA
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
642672 T
66 T
*
642673 CTTTGA-A-CTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAA
1 CTTTGAGATC-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
642736 AT
65 AT
* * *
642738 CTTTGAGATCGTTTCCCTTGAAA-AGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCA
1 CTTTGAGATCGTTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAA
*
642802 AC
65 AT
* ** ** *
642804 CTTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTCTTTTGAGACGGTTTCTCTTGAAAC
1 CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
642864 CATCATATCC
Statistics
Matches: 284, Mismatches: 32, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
64 1 0.00
65 58 0.20
66 168 0.59
67 57 0.20
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (66 bp):
CTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAA
T
Found at i:642738 original size:131 final size:131
Alignment explanation
Indices: 642474--642863 Score: 555
Period size: 131 Copynumber: 3.0 Consensus size: 131
642464 ATTGATAAAC
* * * * ** * *
642474 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGATTGTTTCTCTTGAAACACAAA
1 CTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAC-CA
* * *
642539 ATCTTTGAATATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCTTTTGAAACATA
65 ATCTTTGAA-ATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACA
642604 AAT
129 AAT
*
642607 CTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCATGAGACAGTTTCCCTTGAAACACCAA
1 CTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCAA
*
642672 TCTTTGAACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAA
66 TCTTTGAAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAA
642737 T
131 T
*
642738 CTTTGAGATCGTTTCCCTTGAAAAGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCAA
1 CTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCAA
* * ** ** **
642803 CCTTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTCTTTTGAGACGGTTTCTCTTGAAAC
66 TCTTTGA-AATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC
642864 CATCATATCC
Statistics
Matches: 233, Mismatches: 23, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
131 123 0.53
132 56 0.24
133 54 0.23
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (131 bp):
CTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACACCAA
TCTTTGAAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAA
T
Found at i:642758 original size:30 final size:30
Alignment explanation
Indices: 642719--642828 Score: 80
Period size: 30 Copynumber: 3.5 Consensus size: 30
642709 CTTGAGACAA
*
642719 TTTCTCTTGAAACACAAATCTTTGAGATCG
1 TTTCCCTTGAAACACAAATCTTTGAGATCG
* *
642749 TTTCCCTTGAAA-AGAATTTTGTCTCTCTTGAGA-CAG
1 TTTCCCTTGAAACACAA------ATCT-TTGAGATC-G
* * *
642785 TTTCCCTTGAAACACCAACCTTTGAGATTG
1 TTTCCCTTGAAACACAAATCTTTGAGATCG
642815 TTTCCCTTGAAACA
1 TTTCCCTTGAAACA
642829 TGTTTTGTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
29 3 0.05
30 32 0.52
31 2 0.03
35 4 0.06
36 19 0.31
37 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (30 bp):
TTTCCCTTGAAACACAAATCTTTGAGATCG
Found at i:642826 original size:197 final size:199
Alignment explanation
Indices: 642474--642863 Score: 547
Period size: 197 Copynumber: 2.0 Consensus size: 199
642464 ATTGATAAAC
* * ***
642474 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCTCCCTTGAGATTGTTTCTCTTGAAACACAAA
1 CTTTGAGACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAA
* * ** *
642539 ATCTTTGAATATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACATTTTCTTTTGAAACATA
66 ATCTTTGAATACGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACA
*
642604 AATCTTTGAGATCGTTTCCCTTGAAACGA-ATTTTGTCTCTCATGAGACAGTTTCCCTTGAAACA
131 AACCTTTGAGATCGTTTCCCTTGAAAC-ATATTTTGTCTCTCATGAGACAGTTTCCCTTGAAACA
642668 CCAAT
195 CCAAT
642673 CTTTGA-ACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAC-AA
1 CTTTGAGACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAA
*
642736 ATCTTTGAGAT-CGTTTCCCTTGAAA-AGAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
66 ATCTTTGA-ATACGTTTCCCTTGAAACA-AATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACA
* * * ** * *
642799 CCAACCTTTGAGATTGTTTCCCTTGAAACATGTTTTGTCTCTTTTGAGACGGTTTCTCTTGAAAC
129 CAAACCTTTGAGATCGTTTCCCTTGAAACATATTTTGTCTCTCATGAGACAGTTTCCCTTGAAAC
642864 CATCATATCC
Statistics
Matches: 169, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
196 2 0.01
197 109 0.64
198 52 0.31
199 6 0.04
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (199 bp):
CTTTGAGACTGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAA
ATCTTTGAATACGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACACA
AACCTTTGAGATCGTTTCCCTTGAAACATATTTTGTCTCTCATGAGACAGTTTCCCTTGAAACAC
CAAT
Found at i:644457 original size:4 final size:4
Alignment explanation
Indices: 644448--644479 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
644438 TAATCATTGC
644448 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
644480 GTTTCTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:644786 original size:129 final size:131
Alignment explanation
Indices: 644462--644829 Score: 423
Period size: 131 Copynumber: 2.8 Consensus size: 131
644452 TATTTATTTA
* *
644462 TTTATTTATTTATTTATTGTTTCTAATATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATG
1 TTTATTTATTTATTTATTGTTTCGAATATTCGATTCGACCTTGTGGTGACCAGATCTGGGGTATG
* * * *
644527 ATCTACATTATTATGGTTCGAACTCTGCTAACTACTGACTTTTATTTTATTGCACTCTAACCATT
66 ATCTACATTATTATGGTTCGGACTCTGCTAACCACTAACTTTTATTATATTGCACTCTAACCATT
644592 G
131 G
* * *
644593 TTTATTTATTTATTTATTGTTTCTAATATTTGAATCGACCTTGTGGTGATCC-GATCTGGGGTAT
1 TTTATTTATTTATTTATTGTTTCGAATATTCGATTCGACCTTGTGGTGA-CCAGATCTGGGGTAT
** * **
644657 GATCCGCATTATTATGGTTCGGACTCTGCTAACCACTAACGTTTT-TTATATT----T-TTATTA
65 GATCTACATTATTATGGTTCGGACTCTGCTAACCACTAAC-TTTTATTATATTGCACTCTAACCA
644716 TAT-
129 T-TG
*
644719 TTTATTTTACTTT-TTTAATTTGTTT-GAATTATTCGATTCAACCTTGTGGTGACCAGATCTGGG
1 TTTA-TTTA-TTTATTT-A-TTGTTTCGAA-TATTCGATTCGACCTTGTGGTGACCAGATCTGGG
* * * *
644782 GTATGATCTATATTATTATGGCTCGGACTCTGCTAATCGCTAACTTTT
61 GTATGATCTACATTATTATGGTTCGGACTCTGCTAACCACTAACTTTT
644830 CTAACATCTA
Statistics
Matches: 206, Mismatches: 22, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
126 8 0.04
127 9 0.04
128 12 0.06
129 72 0.35
131 99 0.48
132 6 0.03
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (131 bp):
TTTATTTATTTATTTATTGTTTCGAATATTCGATTCGACCTTGTGGTGACCAGATCTGGGGTATG
ATCTACATTATTATGGTTCGGACTCTGCTAACCACTAACTTTTATTATATTGCACTCTAACCATT
G
Found at i:644856 original size:16 final size:17
Alignment explanation
Indices: 644820--644856 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
644810 TCTGCTAATC
*
644820 GCTAACTTTTCTAACAT
1 GCTAACCTTTCTAACAT
644837 -CTAACCTTTCTAAC-T
1 GCTAACCTTTCTAACAT
644852 GCTAA
1 GCTAA
644857 TTACTAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.30, C:0.27, G:0.05, T:0.38
Consensus pattern (17 bp):
GCTAACCTTTCTAACAT
Found at i:650687 original size:28 final size:28
Alignment explanation
Indices: 650647--650709 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
650637 AGTTTACAAA
*
650647 ATTTGAAGTTTATGATATAATTCATAGG
1 ATTTGGAGTTTATGATATAATTCATAGG
* *
650675 ATTTGGAGTTTATGATGTAATTTATAGG
1 ATTTGGAGTTTATGATATAATTCATAGG
*
650703 GTTTGGA
1 ATTTGGA
650710 TTAAATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.02, G:0.24, T:0.44
Consensus pattern (28 bp):
ATTTGGAGTTTATGATATAATTCATAGG
Found at i:652723 original size:69 final size:69
Alignment explanation
Indices: 652468--652731 Score: 280
Period size: 69 Copynumber: 3.8 Consensus size: 69
652458 TACGATAATA
* * * * * *
652468 TGCTCCCTTGTGATTCACTCTAATCCTT-TGGAGCTCCCGTGCGAGTCAACCAAAATAATTACGA
1 TGCTCCCGTGCGAGTCACTCTAATCATTCTGG-GCTCCCGTGCGAGTCACCCAGAATAATTACGA
652532 TTAGG
65 TTAGG
* * * * *
652537 TGCTCTCGTGCAAGTCACTCTAATCATTCGGGGCTCCCGTGCAAGTCATCC-GAAATAATTACGA
1 TGCTCCCGTGCGAGTCACTCTAATCATTCTGGGCTCCCGTGCGAGTCACCCAG-AATAATTACGA
652601 TTAGG
65 TTAGG
* * *** *
652606 TGCTCCCGTGTGAGTCACTCTATTCATTCTGGGCTTTTGTGCGAGTCACCCAGAATAATCACGAT
1 TGCTCCCGTGCGAGTCACTCTAATCATTCTGGGCTCCCGTGCGAGTCACCCAGAATAATTACGAT
*
652671 TTGG
66 TAGG
* * ** * *
652675 TGCTCCCTTGCGAGTCACTCTAATCCTTCAAGGCTCCTGTGCGAGTCACTCAGAATA
1 TGCTCCCGTGCGAGTCACTCTAATCATTCTGGGCTCCCGTGCGAGTCACCCAGAATA
652732 CACATTATTA
Statistics
Matches: 161, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
69 158 0.98
70 3 0.02
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (69 bp):
TGCTCCCGTGCGAGTCACTCTAATCATTCTGGGCTCCCGTGCGAGTCACCCAGAATAATTACGAT
TAGG
Found at i:652971 original size:25 final size:26
Alignment explanation
Indices: 652938--652986 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
652928 TGAAATGAAT
*
652938 ACATAATTTTAGCACT-AAACTTATG
1 ACATAATTTCAGCACTGAAACTTATG
* *
652963 ACATGATTTCAGCAGTGAAACTTA
1 ACATAATTTCAGCACTGAAACTTA
652987 ACATTGACTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (26 bp):
ACATAATTTCAGCACTGAAACTTATG
Found at i:652986 original size:76 final size:76
Alignment explanation
Indices: 652862--653720 Score: 1071
Period size: 76 Copynumber: 11.3 Consensus size: 76
652852 ACATTAACAT
* * * *
652862 GTAATTCCAGCACTAAA-TTAAACACATACAATTCTAGCAGTGAAACTTAACAATGACTTGCACC
1 GTAATTCCAGCACTAAACTT-ATCACAT--AATTCCAGCAGTGAAACTTAACATTGACTTACACC
652926 AGTGAAATGAATAC
63 AGTGAAATGAATAC
* ** * * *
652940 ATAATTTTAGCACTAAACTTATGACATGATTTCAGCAGTGAAACTTAACATTGACTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
653005 GAAATGAATAC
66 GAAATGAATAC
* * * * * * * *
653016 GTAATTCAAGCACCAAACTTATCACATCATTTCAGTAGTGAAATTTAACATTGACCTACACCAGA
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
653081 AAAATGAATAC
66 GAAATGAATAC
* * * **
653092 GTAATTCCAGAACTAAACTTATCACATAATTCCAGTAGTGAAACTTAACATTAACTTACACCAAC
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
653157 GAAATGAATAT
66 GAAATGAATAC
* * *
653168 GCAATTCCAACACTAAACTTATCACATAATTCCAACAGTGAAACTTAACATTGACTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
653233 GAAATGAATAT
66 GAAATGAATAC
* * * *
653244 GTAATTTCAGCACTAAACTTATCACCTAATTCCAGCAATGAAATTTAACATTGACTTACACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
* * *
653309 AAAATAAATAT
66 GAAATGAATAC
* * * *
653320 GTAATTCCAACACTAAACTTATCACATAATTCCAGTAGCGAAACTTAACATTGACTTACATCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
653385 GAAATGAATAC
66 GAAATGAATAC
* * *
653396 GTAATTCTAGCACTAAACTTATCACATAATTCCCA-CAGTGAAATTTAACATTGACTTACACCAA
1 GTAATTCCAGCACTAAACTTATCACATAATT-CCAGCAGTGAAACTTAACATTGACTTACACCAG
*
653460 TGAAACGAATAC
65 TGAAATGAATAC
* * * *
653472 GTAATTCCAGCACTAAACTTATCACATAATTTCTGCAGTGAAACTTGACATTGACTTACACCAGC
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
653537 GAAATGAATAC
66 GAAATGAATAC
* * * * * * * *
653548 ATGATTCCAACATTAAATTTATCACCTAATTCCAGTAGTGAAACTTAACATTGACTTAAACCAGT
1 GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
*
653613 GAAATGAATAT
66 GAAATGAATAC
* * * *
653624 GTAATTCCAGCACTAAACGTT-TCACATAAGTCAAGGAGTG-AA-TTGAACATTGACTTACACTA
1 GTAATTCCAGCACTAAAC-TTATCACATAATTCCAGCAGTGAAACTT-AACATTGACTTACACCA
653686 GTGAAATGAATAC
64 GTGAAATGAATAC
*
653699 GTAATTCCATCACTAAACTTAT
1 GTAATTCCAGCACTAAACTTAT
653721 GATTTCACAT
Statistics
Matches: 672, Mismatches: 103, Indels: 15
0.85 0.13 0.02
Matches are distributed among these distances:
74 4 0.01
75 48 0.07
76 594 0.88
77 5 0.01
78 19 0.03
79 2 0.00
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (76 bp):
GTAATTCCAGCACTAAACTTATCACATAATTCCAGCAGTGAAACTTAACATTGACTTACACCAGT
GAAATGAATAC
Found at i:662345 original size:18 final size:18
Alignment explanation
Indices: 662322--662364 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
662312 CAGTCCGATC
662322 GTTGACCATTGATCGACT
1 GTTGACCATTGATCGACT
662340 GTTGACCATTGATCGACT
1 GTTGACCATTGATCGACT
662358 GTTGACC
1 GTTGACC
662365 GTGACCGTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (18 bp):
GTTGACCATTGATCGACT
Found at i:662369 original size:24 final size:24
Alignment explanation
Indices: 662342--662390 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
662332 GATCGACTGT
* *
662342 TGACCATTGATCGACTGTTGACCG
1 TGACCATTGATCGACCGTTAACCG
*
662366 TGACCGTTGATCGACCGTTAACCG
1 TGACCATTGATCGACCGTTAACCG
662390 T
1 T
662391 AAGCTGTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.24, T:0.29
Consensus pattern (24 bp):
TGACCATTGATCGACCGTTAACCG
Found at i:663234 original size:38 final size:38
Alignment explanation
Indices: 663183--663276 Score: 136
Period size: 38 Copynumber: 2.4 Consensus size: 38
663173 CTTTCCGCAG
663183 GCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTAC-AGCA
1 GCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTA-CA
*
663221 GCTCCTCGGCTTTGTGTTTAGGGTAAGTCCTTACTACA
1 GCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTACA
* *
663259 GACTCATCTGCTTTGTGC
1 G-CTCCTCGGCTTTGTGC
663277 ACAGGATAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 36 0.72
39 14 0.28
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.35
Consensus pattern (38 bp):
GCTCCTCGGCTTTGTGCTTAGGGTAAGTCCTTACTACA
Done.