Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_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: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 30
Found at i:2561811 original size:510 final size:510
Alignment explanation
Indices: 2560831--2561853 Score: 1609
Period size: 510 Copynumber: 2.0 Consensus size: 510
2560821 AGATGACAGA
* *
2560831 ATTCTGAATGTCAAGGCATTACAAAATGTTAGACATGCTAATAGGCCTCATGTTATTCGTGATCA
1 ATTCCGAATGTCAAGGCATTACAAAATATTAGACATGCTAATAGGCCTCATGTTATTCGTGATCA
* * *
2560896 TTTAAATCCGATGCTAGATGATTTTAATCCTGGAATAGTGGCACCCGAAATTCAAACTGTACATT
66 TTTAAATCCGATGCTAGATGACTTTAATCCTGGAATAGTGGCACCCAAAATTCAAACTGCACATT
* * * * *
2560961 TTGAGCTTAAACTAGTAATGTTTAATATGTTGAATTCTATATAGAAGATTGGAGGCATGCCAACT
131 TTGAGCTTAAACTAATAATATTTAATATGTTGAATTCTATAGAGAAGATTCGAGGCATGACAACT
* * * * *
2561026 GAAGATGCTAGGTAGCATATTCGTAATTTTTTAGAGGTTTATGATTCTTTTCTCCAAGAATGAGT
196 GAAGATGCTAGGCAACATATTCGTAATTTTTTAGAGGTTTATGATTCTTTTCACCAAGAAGGACT
* * *
2561091 GCACGATGATGTTATGAAATTAAAGTTGTTGTCATATTCTTTGTGTGACTGAAGAAGGGCTTGGT
261 GCACGAGGATGTTATAAAATTAAAGTTGTTGTCATATTCTTTGTGTGACCGAAGAAGGGCTTGGT
* * *
2561156 TGAGTTGTGTTCCATCCGGTTCAATGGAATCATGGGTTGATCTTTGCAAGAGTTTCTTATTGCGG
326 TGAGTGGTGTTCCATCCGATTCAATGGAATCATGGGCTGATCTTTGCAAGAGTTTCTTATTGCGG
* * * *
2561221 TATAACGCACCGAACATAATTACTCAACTAAGGAATAACACAACATCAACTTTTTGGTGACATTG
391 TATAACGCACCGAACATAAATACTCAACTAAGGAATAAAACAACATCAACTTTTTGGCGACATTA
**
2561286 CCAGGGATTATTGGTTTTACTTTAGAGTTTTATTTTATTGTTTACTTATTTGTTT
456 CCAGGGAGCATTGGTTTTACTTTAGAGTTTTATTTTATTGTTTACTTATTTGTTT
* * * * *
2561341 ATTCCGAATGT-AGAGGCATTACAAAATATTGGACCTGCTGATAGGCCTCGTGTTATTTGTGATC
1 ATTCCGAATGTCA-AGGCATTACAAAATATTAGACATGCTAATAGGCCTCATGTTATTCGTGATC
*
2561405 ATTTAAATCCGATGCTAGATGACTTTAATCCTGGAATTGTGGCACCCAAAATTCAAACTGCACAT
65 ATTTAAATCCGATGCTAGATGACTTTAATCCTGGAATAGTGGCACCCAAAATTCAAACTGCACAT
* * *
2561470 TTTGAGCTTAAACTAATTATATTTAATATGTTGAATTCTATAGGGAAGTTTCGAGGCATGACAAC
130 TTTGAGCTTAAACTAATAATATTTAATATGTTGAATTCTATAGAGAAGATTCGAGGCATGACAAC
* *
2561535 TGAAGATGCTAGGCAACATATTCGTATTTTTTTAGAGGTTTGTGATTCTTTTCACCAAGAAGGAC
195 TGAAGATGCTAGGCAACATATTCGTAATTTTTTAGAGGTTTATGATTCTTTTCACCAAGAAGGAC
*
2561600 TGCACGAGGATGTTCTAAAATTAAAGTTGTTGTCATATTCTTTGTGTGACCG-AGCAAGGGCTTG
260 TGCACGAGGATGTTATAAAATTAAAGTTGTTGTCATATTCTTTGTGTGACCGAAG-AAGGGCTTG
** *
2561664 GTTGAGTGGTGTTCCATCTTATTCAATGGAATCATGGGCTGATCTTTGCATGAGTTTCTTATTGC
324 GTTGAGTGGTGTTCCATCCGATTCAATGGAATCATGGGCTGATCTTTGCAAGAGTTTCTTATTGC
* *
2561729 GGTATAACGCACCGAATATAAATACTCAACTAAGGAATAAAACAACATCAAGTTTTTGGCGACAT
389 GGTATAACGCACCGAACATAAATACTCAACTAAGGAATAAAACAACATCAACTTTTTGGCGACAT
*
2561794 TACCAGGGAGCATTGGTTTTACTTTAGAGTTTTATTTTATTGTTTACTTTTTTGTTT
454 TACCAGGGAGCATTGGTTTTACTTTAGAGTTTTATTTTATTGTTTACTTATTTGTTT
2561851 ATT
1 ATT
2561854 TCTTTTTGTA
Statistics
Matches: 466, Mismatches: 45, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
509 3 0.01
510 463 0.99
ACGTcount: A:0.29, C:0.14, G:0.20, T:0.37
Consensus pattern (510 bp):
ATTCCGAATGTCAAGGCATTACAAAATATTAGACATGCTAATAGGCCTCATGTTATTCGTGATCA
TTTAAATCCGATGCTAGATGACTTTAATCCTGGAATAGTGGCACCCAAAATTCAAACTGCACATT
TTGAGCTTAAACTAATAATATTTAATATGTTGAATTCTATAGAGAAGATTCGAGGCATGACAACT
GAAGATGCTAGGCAACATATTCGTAATTTTTTAGAGGTTTATGATTCTTTTCACCAAGAAGGACT
GCACGAGGATGTTATAAAATTAAAGTTGTTGTCATATTCTTTGTGTGACCGAAGAAGGGCTTGGT
TGAGTGGTGTTCCATCCGATTCAATGGAATCATGGGCTGATCTTTGCAAGAGTTTCTTATTGCGG
TATAACGCACCGAACATAAATACTCAACTAAGGAATAAAACAACATCAACTTTTTGGCGACATTA
CCAGGGAGCATTGGTTTTACTTTAGAGTTTTATTTTATTGTTTACTTATTTGTTT
Found at i:2564745 original size:21 final size:21
Alignment explanation
Indices: 2564719--2564788 Score: 122
Period size: 21 Copynumber: 3.3 Consensus size: 21
2564709 TTTCATGCAT
*
2564719 TTAGGTCCTCTACCAATAATA
1 TTAGGTCATCTACCAATAATA
2564740 TTAGGTCATCTACCAATAATA
1 TTAGGTCATCTACCAATAATA
*
2564761 TTAGGTCATCTGCCAATAATA
1 TTAGGTCATCTACCAATAATA
2564782 TTAGGTC
1 TTAGGTC
2564789 CTCAGAAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.34
Consensus pattern (21 bp):
TTAGGTCATCTACCAATAATA
Found at i:2566222 original size:19 final size:20
Alignment explanation
Indices: 2566200--2566237 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2566190 AATATTGTGT
2566200 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
*
2566219 TTCGCATTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
2566238 CGCACTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:2566273 original size:20 final size:20
Alignment explanation
Indices: 2566248--2566291 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
2566238 CGCACTTTGG
* *
2566248 GAATTTGACTTATGTGTTGC
1 GAATTTAACTTATATGTTGC
*
2566268 GAATTTAACTTCTATGTTGC
1 GAATTTAACTTATATGTTGC
2566288 GAAT
1 GAAT
2566292 ACGCGAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.43
Consensus pattern (20 bp):
GAATTTAACTTATATGTTGC
Found at i:2569608 original size:22 final size:22
Alignment explanation
Indices: 2569580--2569626 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
2569570 ATCCATTCAT
2569580 GCACATTCTGAATTTTTAAAAG
1 GCACATTCTGAATTTTTAAAAG
2569602 GCACATTCTGAATTTTTAAAAG
1 GCACATTCTGAATTTTTAAAAG
2569624 GCA
1 GCA
2569627 GGGTGCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (22 bp):
GCACATTCTGAATTTTTAAAAG
Found at i:2570612 original size:2 final size:2
Alignment explanation
Indices: 2570605--2570685 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
2570595 GAAAATTTGA
2570605 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
2570647 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2570686 ACCAACCAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2571455 original size:6 final size:6
Alignment explanation
Indices: 2571444--2571532 Score: 115
Period size: 6 Copynumber: 14.8 Consensus size: 6
2571434 AACTCAGAAA
* * * *
2571444 GAGAGT GAGAGT GAGAGG GAGAGT GAGAGT GAGAGG GAGAGG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
* * *
2571492 GAGAGG GAGAGG GAGAGG GAGAGG GACAGA GAGAGA GAGAG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAG
2571533 CTGACTGGTT
Statistics
Matches: 77, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 77 1.00
ACGTcount: A:0.36, C:0.01, G:0.58, T:0.04
Consensus pattern (6 bp):
GAGAGG
Found at i:2571783 original size:24 final size:25
Alignment explanation
Indices: 2571756--2571804 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2571746 ATGAGTTTAA
*
2571756 TATTTACATAAT-TATACAATAATC
1 TATTTACATAATATATAAAATAATC
* *
2571780 TATTTATATTATATATAAAATAATC
1 TATTTACATAATATATAAAATAATC
2571805 GATTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.45
Consensus pattern (25 bp):
TATTTACATAATATATAAAATAATC
Found at i:2573782 original size:9 final size:9
Alignment explanation
Indices: 2573768--2573798 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2573758 TAAAGTTCAG
2573768 TGAATAAAT
1 TGAATAAAT
2573777 TGAATAAAT
1 TGAATAAAT
*
2573786 TGAAAAAAT
1 TGAATAAAT
2573795 TGAA
1 TGAA
2573799 AATACAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.13, T:0.29
Consensus pattern (9 bp):
TGAATAAAT
Found at i:2574644 original size:31 final size:30
Alignment explanation
Indices: 2574566--2574651 Score: 100
Period size: 30 Copynumber: 2.8 Consensus size: 30
2574556 TATTTTATAC
* * *
2574566 AAATTCAATGGTCAAATTAACATTTTATCTC
1 AAATTCAA-GGTCAAGTTAAAATTTTATCTA
* * *
2574597 AAGTTTAAGGTCAAGTTAATATTTTATCTA
1 AAATTCAAGGTCAAGTTAAAATTTTATCTA
2574627 AAATTCAAGAGTCAAGTTAAAATTT
1 AAATTCAAG-GTCAAGTTAAAATTT
2574652 AAATATTTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 26 0.57
31 20 0.43
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (30 bp):
AAATTCAAGGTCAAGTTAAAATTTTATCTA
Found at i:2575792 original size:3 final size:3
Alignment explanation
Indices: 2575784--2575823 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2575774 TTTAATATTG
2575784 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
2575824 TATCTCACAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2583407 original size:17 final size:16
Alignment explanation
Indices: 2583385--2583424 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
2583375 GTTGAAGTTT
2583385 ATTCTTTGGATGTTGAA
1 ATTCTTTGGATGTT-AA
*
2583402 ATTCTTTTGATGTTAA
1 ATTCTTTGGATGTTAA
2583418 ATTCTTT
1 ATTCTTT
2583425 TGATTGATCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.55
Consensus pattern (16 bp):
ATTCTTTGGATGTTAA
Found at i:2583421 original size:16 final size:17
Alignment explanation
Indices: 2583385--2583428 Score: 72
Period size: 16 Copynumber: 2.6 Consensus size: 17
2583375 GTTGAAGTTT
*
2583385 ATTCTTTGGATGTTGAA
1 ATTCTTTTGATGTTGAA
2583402 ATTCTTTTGATGTT-AA
1 ATTCTTTTGATGTTGAA
2583418 ATTCTTTTGAT
1 ATTCTTTTGAT
2583429 TGATCGAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (17 bp):
ATTCTTTTGATGTTGAA
Found at i:2584214 original size:13 final size:13
Alignment explanation
Indices: 2584196--2584228 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2584186 TCATGTCCAA
*
2584196 TTTCTTTCTTTAT
1 TTTCTTTCATTAT
2584209 TTTCTTTCATTAT
1 TTTCTTTCATTAT
2584222 TTTCTTT
1 TTTCTTT
2584229 TCACAATGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTCTTTCATTAT
Found at i:2590825 original size:26 final size:28
Alignment explanation
Indices: 2590792--2590843 Score: 90
Period size: 26 Copynumber: 1.9 Consensus size: 28
2590782 ATATTTTAAA
2590792 TTTCAAAGTT-AAAAT-AATTTCAAATG
1 TTTCAAAGTTCAAAATAAATTTCAAATG
2590818 TTTCAAAGTTCAAAATAAATTTCAAA
1 TTTCAAAGTTCAAAATAAATTTCAAA
2590844 GTTAAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.42
27 5 0.21
28 9 0.38
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (28 bp):
TTTCAAAGTTCAAAATAAATTTCAAATG
Found at i:2590852 original size:18 final size:19
Alignment explanation
Indices: 2590818--2590853 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2590808 ATTTCAAATG
2590818 TTTCAAAGTTCAAAATAAA
1 TTTCAAAGTTCAAAATAAA
2590837 TTTCAAAGTT-AAAATAA
1 TTTCAAAGTTCAAAATAA
2590854 TTTAAGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (19 bp):
TTTCAAAGTTCAAAATAAA
Found at i:2590934 original size:39 final size:40
Alignment explanation
Indices: 2590848--2590939 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 40
2590838 TTCAAAGTTA
* * **
2590848 AAATAATTTAAGAAATTTAGAATTTAGAATGTTATGGTTG
1 AAATAATTTAAGAAATTAAGAATTTAAAATGTTATGAATG
* *
2590888 TAA-AATTTATGAAATTAAGAATTTAAAATGTTA-GAATG
1 AAATAATTTAAGAAATTAAGAATTTAAAATGTTATGAATG
*
2590926 AAATAATTTGAGAA
1 AAATAATTTAAGAA
2590940 TTATAAATAA
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
38 5 0.12
39 35 0.83
40 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.37
Consensus pattern (40 bp):
AAATAATTTAAGAAATTAAGAATTTAAAATGTTATGAATG
Found at i:2591768 original size:13 final size:13
Alignment explanation
Indices: 2591729--2591776 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
2591719 GCCGCCCATG
2591729 CTCC-TCCCCTCTC
1 CTCCTTCCCCT-TC
*
2591742 CCCCTTCTCCCTTC
1 CTCCTTC-CCCTTC
2591756 CTCCTTCCCCTTC
1 CTCCTTCCCCTTC
2591769 CTCCTTCC
1 CTCCTTCC
2591777 ATAGTTTTCG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 17 0.55
14 10 0.32
15 4 0.13
ACGTcount: A:0.00, C:0.65, G:0.00, T:0.35
Consensus pattern (13 bp):
CTCCTTCCCCTTC
Found at i:2592168 original size:22 final size:22
Alignment explanation
Indices: 2592143--2592197 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
2592133 TAAAAAATTA
2592143 AAAAATATAACGGTTTACACCT
1 AAAAATATAACGGTTTACACCT
2592165 AAAAATATAACGGTTTACACCT
1 AAAAATATAACGGTTTACACCT
2592187 AAAAATATAAC
1 AAAAATATAAC
2592198 TGAGAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.25
Consensus pattern (22 bp):
AAAAATATAACGGTTTACACCT
Found at i:2596201 original size:29 final size:29
Alignment explanation
Indices: 2596152--2596227 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
2596142 GATAGGGATT
* *
2596152 TAATCCCATGTAAAATTAGGACACAGATA
1 TAATCCCATGCAAAATCAGGACACAGATA
* ***
2596181 TAATCCCATGCAGAATCAGGACGGGGATA
1 TAATCCCATGCAAAATCAGGACACAGATA
* *
2596210 CAATCCCATGCATAATCA
1 TAATCCCATGCAAAATCA
2596228 AGAATGCATC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (29 bp):
TAATCCCATGCAAAATCAGGACACAGATA
Found at i:2621690 original size:54 final size:54
Alignment explanation
Indices: 2621623--2621892 Score: 380
Period size: 54 Copynumber: 5.0 Consensus size: 54
2621613 GGTCATTCAT
* * *
2621623 AAACGGTTGTTCATCAACATATGTTGAATTTCGTGAATTGCACACATAGTGCCG
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACCTAGTGCCG
* * * *
2621677 AAACGGTTATTCATTAACATATGATGAATTTTTGTGAGTTACACACCTAGTGCCG
1 AAACGGTTGTTCATCAACATATGATGAA-TTTCGTGAGTTGCACACCTAGTGCCG
* *
2621732 AAATGGTTGTTCATCAACATATGATGAATTCCGTGAGTTGCACACCTAGTGCCG
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACCTAGTGCCG
* * *
2621786 AAAAGGTTGTTCATCAACATATGATGACTTCCGTGAGTTGCACACCTAGTGCCG
1 AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACCTAGTGCCG
* * *
2621840 AAATGGTTGTTCATCAACATATGATGAACTTT-GTGAGTTGCGCACTTAGTGCC
1 AAACGGTTGTTCATCAACATATGATGAA-TTTCGTGAGTTGCACACCTAGTGCC
2621893 CATTTGGTAA
Statistics
Matches: 194, Mismatches: 20, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
54 145 0.75
55 49 0.25
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (54 bp):
AAACGGTTGTTCATCAACATATGATGAATTTCGTGAGTTGCACACCTAGTGCCG
Found at i:2628761 original size:25 final size:25
Alignment explanation
Indices: 2628733--2628795 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
2628723 TCACTATAAT
2628733 TTTATAA-ACAAAAAAATAATAAGAG
1 TTTATAATAC-AAAAAATAATAAGAG
* *
2628758 TTTATAATACACACAATAATAAGAG
1 TTTATAATACAAAAAATAATAAGAG
* *
2628783 TTTAAAATCCAAA
1 TTTATAATACAAA
2628796 GTAGATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 30 0.94
26 2 0.06
ACGTcount: A:0.57, C:0.10, G:0.06, T:0.27
Consensus pattern (25 bp):
TTTATAATACAAAAAATAATAAGAG
Found at i:2629284 original size:29 final size:29
Alignment explanation
Indices: 2629249--2629318 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
2629239 CAGGATAAAG
*
2629249 ATATAATCCCATGCAAAATCATGACGAGG-
1 ATATAATCCCATGCAAAATCAGGAC-AGGA
* * *
2629278 ATTTAATCTCATGCATAATCAGGACAGGA
1 ATATAATCCCATGCAAAATCAGGACAGGA
2629307 ATATAATCCCAT
1 ATATAATCCCAT
2629319 ATACAATCAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.26
Consensus pattern (29 bp):
ATATAATCCCATGCAAAATCAGGACAGGA
Found at i:2629343 original size:22 final size:24
Alignment explanation
Indices: 2629302--2629345 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2629292 ATAATCAGGA
*
2629302 CAGGAATATAATCCCATATACAAT
1 CAGGAATATAATCACATATACAAT
2629326 CAGGAATA-AATCAC-TATACA
1 CAGGAATATAATCACATATACA
2629346 TATTAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 6 0.32
23 5 0.26
24 8 0.42
ACGTcount: A:0.48, C:0.20, G:0.09, T:0.23
Consensus pattern (24 bp):
CAGGAATATAATCACATATACAAT
Found at i:2632591 original size:19 final size:19
Alignment explanation
Indices: 2632567--2632609 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
2632557 AAATATTTTA
2632567 GAACCGACTGAACCAGTTT
1 GAACCGACTGAACCAGTTT
2632586 GAACCGACTGAACCAGTTT
1 GAACCGACTGAACCAGTTT
2632605 GAACC
1 GAACC
2632610 ACCTAAGTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.19
Consensus pattern (19 bp):
GAACCGACTGAACCAGTTT
Found at i:2639177 original size:32 final size:32
Alignment explanation
Indices: 2639098--2639187 Score: 108
Period size: 32 Copynumber: 2.8 Consensus size: 32
2639088 GGATAGCAAC
** *
2639098 ATAAGGGGGACAAAGCATAATTAATCATAGAAA
1 ATAA-GGGGACAAAATATAATTAACCATAGAAA
*
2639131 ATAAGGGGACAAAATATATTTAACCATAGAAA
1 ATAAGGGGACAAAATATAATTAACCATAGAAA
* *
2639163 ATGAGGGGACAAAATTAAAATTAAC
1 ATAAGGGGACAAAA-TATAATTAAC
2639188 TAAATTAGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 37 0.76
33 12 0.24
ACGTcount: A:0.52, C:0.09, G:0.19, T:0.20
Consensus pattern (32 bp):
ATAAGGGGACAAAATATAATTAACCATAGAAA
Found at i:2642916 original size:44 final size:44
Alignment explanation
Indices: 2642867--2642984 Score: 122
Period size: 44 Copynumber: 2.7 Consensus size: 44
2642857 GGCGCCTATT
*
2642867 TTTTTTTCAA-TTCTACCTTT-TATCTTTATAATTGAGAGCC-TTAA
1 TTTTTTTCAATTTC-A-CTTTCTACCTTTATAATTGAGA-CCATTAA
* *
2642911 TTTTTTTTAATTTCATTTTCTACCTTTATAATTGAGACCATTAA
1 TTTTTTTCAATTTCACTTTCTACCTTTATAATTGAGACCATTAA
*
2642955 TTTTTTT--ATTTCA-TTCTCTTCCTTTATAAT
1 TTTTTTTCAATTTCACTT-TCTACCTTTATAAT
2642985 GAGCCCTTTA
Statistics
Matches: 66, Mismatches: 4, Indels: 10
0.82 0.05 0.12
Matches are distributed among these distances:
41 2 0.03
42 19 0.29
43 5 0.08
44 37 0.56
45 3 0.05
ACGTcount: A:0.24, C:0.15, G:0.04, T:0.57
Consensus pattern (44 bp):
TTTTTTTCAATTTCACTTTCTACCTTTATAATTGAGACCATTAA
Found at i:2642979 original size:42 final size:44
Alignment explanation
Indices: 2642890--2642984 Score: 142
Period size: 42 Copynumber: 2.2 Consensus size: 44
2642880 TACCTTTTAT
*
2642890 CTTTATAATTGAGAGCCTTAATTTTTTTTAATTTCATTTTCTAC
1 CTTTATAATTGAGAGCCTTAATTTTTTTTAATTTCATTCTCTAC
*
2642934 CTTTATAATTGAGA-CCATTAA-TTTTTTT-ATTTCATTCTCTTC
1 CTTTATAATTGAGAGCC-TTAATTTTTTTTAATTTCATTCTCTAC
2642976 CTTTATAAT
1 CTTTATAAT
2642985 GAGCCCTTTA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
42 21 0.44
43 9 0.19
44 18 0.38
ACGTcount: A:0.25, C:0.15, G:0.05, T:0.55
Consensus pattern (44 bp):
CTTTATAATTGAGAGCCTTAATTTTTTTTAATTTCATTCTCTAC
Found at i:2642994 original size:14 final size:15
Alignment explanation
Indices: 2642975--2643006 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
2642965 TCATTCTCTT
2642975 CCTTTATAATGA-GC
1 CCTTTATAATGAGGC
2642989 CCTTTATAATGAGGC
1 CCTTTATAATGAGGC
2643004 CCT
1 CCT
2643007 AATTTTTGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (15 bp):
CCTTTATAATGAGGC
Found at i:2643114 original size:44 final size:42
Alignment explanation
Indices: 2642989--2643228 Score: 209
Period size: 42 Copynumber: 5.6 Consensus size: 42
2642979 TATAATGAGC
** * *
2642989 CCTTTATAA-TGAGGC-CCTAATTTTTGCGATCTCACATTTTA
1 CCTTTATAATTGAGGCTCCTAATTTTT-TAATCTCTCTTTTTA
* * * * *
2643030 TCTTTATAATTGATGCACCTAATTTTCTCT-GTCTCATTTTTTTA
1 CCTTTATAATTGAGGCTCCTAATTTT-T-TAATCTC-TCTTTTTA
* * *
2643074 CCTTTACAATTGAGGCTCATAATTTTTTAATCTTTCTTTTTA
1 CCTTTATAATTGAGGCTCCTAATTTTTTAATCTCTCTTTTTA
** *
2643116 TTTTTATAATTGAGGCTCCTAATTTTTTTTAATCTCTCTTTCTA
1 CCTTTATAATTGAGGCTCCTAA--TTTTTTAATCTCTCTTTTTA
* * *
2643160 CATTTATAATTGAGGACT-CTAATTTGTTAATCTCACTTTTTA
1 CCTTTATAATTGAGG-CTCCTAATTTTTTAATCTCTCTTTTTA
* *
2643202 CCTTTATAAATGAGGCTCCTCATTTTT
1 CCTTTATAATTGAGGCTCCTAATTTTT
2643229 GAGTTCGAAT
Statistics
Matches: 159, Mismatches: 31, Indels: 17
0.77 0.15 0.08
Matches are distributed among these distances:
41 10 0.06
42 68 0.43
43 17 0.11
44 62 0.39
45 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (42 bp):
CCTTTATAATTGAGGCTCCTAATTTTTTAATCTCTCTTTTTA
Found at i:2643171 original size:86 final size:86
Alignment explanation
Indices: 2643017--2643228 Score: 239
Period size: 86 Copynumber: 2.5 Consensus size: 86
2643007 AATTTTTGCG
* * * * * * * *
2643017 ATCTCACATTTTATCTTTATAATTGATGCACCTAATTTTCTCTGTCTCATTTTTTTACCTTTACA
1 ATCTCACTTTTTATCTTTATAATTGAGGCTCCTAATTTTTTCTATCTCATCTTTCTACATTTACA
*
2643082 ATTGAGG-CTCATAATTTTTTA
66 ATTGAGGACTC-TAATTTGTTA
** * * *
2643103 ATCTTTCTTTTTATTTTTATAATTGAGGCTCCTAATTTTTTTTAATCTC-TCTTTCTACATTTAT
1 ATCTCACTTTTTATCTTTATAATTGAGGCTCCTAATTTTTTCT-ATCTCATCTTTCTACATTTAC
2643167 AATTGAGGACTCTAATTTGTTA
65 AATTGAGGACTCTAATTTGTTA
* * *
2643189 ATCTCACTTTTTACCTTTATAAATGAGGCTCCTCATTTTT
1 ATCTCACTTTTTATCTTTATAATTGAGGCTCCTAATTTTT
2643229 GAGTTCGAAT
Statistics
Matches: 104, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
86 97 0.93
87 7 0.07
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (86 bp):
ATCTCACTTTTTATCTTTATAATTGAGGCTCCTAATTTTTTCTATCTCATCTTTCTACATTTACA
ATTGAGGACTCTAATTTGTTA
Found at i:2644364 original size:17 final size:17
Alignment explanation
Indices: 2644339--2644388 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
2644329 TTTAAATTAA
2644339 TAAAAATAAAAAAAACT
1 TAAAAATAAAAAAAACT
* **
2644356 TAAATATAAACTAAACT
1 TAAAAATAAAAAAAACT
*
2644373 GAAAAATAAAGAAAAA
1 TAAAAATAAA-AAAAA
2644389 TATTATTTAA
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
17 22 0.88
18 3 0.12
ACGTcount: A:0.72, C:0.06, G:0.04, T:0.18
Consensus pattern (17 bp):
TAAAAATAAAAAAAACT
Found at i:2645237 original size:21 final size:22
Alignment explanation
Indices: 2645211--2645271 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 22
2645201 AAATACATCG
2645211 TATTATTATTTTATTTATATAA
1 TATTATTATTTTATTTATATAA
2645233 T-TTATTA---TACTTTA-ATAA
1 TATTATTATTTTA-TTTATATAA
2645251 TATTA-TATTTTATCTTATATA
1 TATTATTATTTTAT-TTATATA
2645272 TTATATTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 14
0.70 0.00 0.30
Matches are distributed among these distances:
18 9 0.28
19 7 0.22
20 1 0.03
21 11 0.34
22 4 0.12
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (22 bp):
TATTATTATTTTATTTATATAA
Found at i:2645802 original size:3 final size:3
Alignment explanation
Indices: 2645796--2645827 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2645786 GAAAAAAAAA
2645796 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2645828 ACAAAAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2647464 original size:30 final size:30
Alignment explanation
Indices: 2647406--2647481 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
2647396 TATTTTTTCT
* *
2647406 ATTTTAGTCCTTAAAAATTATATTTTTGCA
1 ATTTTAGTCCTTTAAAATTATATATTTGCA
** * *
2647436 ATTTTAGTCCTTTAAGTTTATGTATTTGCT
1 ATTTTAGTCCTTTAAAATTATATATTTGCA
*
2647466 ATTTTGGTCCTTTAAA
1 ATTTTAGTCCTTTAAA
2647482 TCGAATATGA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAAATTATATATTTGCA
Found at i:2652904 original size:16 final size:16
Alignment explanation
Indices: 2652880--2652918 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
2652870 CCATTCCCCT
* *
2652880 CATAGATCAACATATA
1 CATACATCAACACATA
2652896 CATACATCAACACATA
1 CATACATCAACACATA
2652912 CATACAT
1 CATACAT
2652919 GACACATGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.49, C:0.26, G:0.03, T:0.23
Consensus pattern (16 bp):
CATACATCAACACATA
Found at i:2653517 original size:31 final size:31
Alignment explanation
Indices: 2653450--2653525 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
2653440 CTTGAGGCAG
* * * * *
2653450 TTTCTCTAGAAGCACAAAATCTTTGAGTTTG
1 TTTCTCTTGAAACACAAAAACTTTGAGTATA
*
2653481 GTTCTCTTGAAACACAAAAACTTTGAGTATA
1 TTTCTCTTGAAACACAAAAACTTTGAGTATA
2653512 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
2653526 AAGTTTTGTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (31 bp):
TTTCTCTTGAAACACAAAAACTTTGAGTATA
Found at i:2653654 original size:66 final size:65
Alignment explanation
Indices: 2653482--2653725 Score: 233
Period size: 66 Copynumber: 3.7 Consensus size: 65
2653472 TTGAGTTTGG
* * * *
2653482 TTCTCTTGAAACACAAAAACTTTGAGTAT-ATTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGA
1 TTCTCTTGAAACAC-CATA-TTTGAG-ATCATTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGA
*
2653546 CGGT
62 CAGT
* * * *
2653550 TTCCCTTGAAACA-CATATCTTCA-AGTCATTTCCCTTGAAACGAATTTTGTCTCTCTTGAGGCA
1 TTCTCTTGAAACACCATAT-TTGAGA-TCATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA
2653613 GT
64 GT
* *
2653615 TTCTCTTGAAACACCCATATTTGAGATCATTTCCCTTGAAACAAATTTTTTCTCTCTTGAGACAA
1 TTCTCTTGAAACA-CCATATTTGAGATCATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
2653680 C
65 T
* * * * ** *
2653681 TTCTCTTGAAGCATCATCTTTGAGTTTGTTTCCCTCGAAACAAAT
1 TTCTCTTGAAACACCATATTTGAGATCATTTCCCTTGAAACAAAT
2653726 CCCTAAAGAT
Statistics
Matches: 147, Mismatches: 23, Indels: 15
0.79 0.12 0.08
Matches are distributed among these distances:
64 1 0.01
65 58 0.39
66 70 0.48
67 6 0.04
68 12 0.08
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.38
Consensus pattern (65 bp):
TTCTCTTGAAACACCATATTTGAGATCATTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGT
Found at i:2653931 original size:131 final size:133
Alignment explanation
Indices: 2653774--2654026 Score: 350
Period size: 131 Copynumber: 1.9 Consensus size: 133
2653764 GTATCATCCC
**
2653774 CCGACCAGACCTCATCATCACATAGGAGCCGTGTCACCTTTAGATAA-CAAGTCATCCTCATCAC
1 CCGACCAGACCTCATCATCACATAGGAGCCGTGTCACCCCTAGATAATC-AGTCATCCTCATCAC
*
2653838 GTAGAAACCTTGTTATCATCC-C-TAAACATGGCATGCCATCCTCATCACATAGGAACCGTGTCA
65 GTAGAAACCGTGTTATCATCCTCTTAAACATGGCATGCCATCCTCATCACATAGGAACCGTGTCA
2653901 TCTA
130 TCTA
* * * * * *
2653905 CCGACTAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAATCATTCGTCCTCATCGCG
1 CCGACCAGACCTCATCATCACATAGGAGCCGTGTCACCCCTAGATAATCAGTCATCCTCATCACG
* * **
2653970 TAGGAACCGTGTTATCATCCTTCTTAAAGATGGCATGCCATCCTCATTGCATAGGAA
66 TAGAAACCGTGTTATCATCC-TCTTAAACATGGCATGCCATCCTCATCACATAGGAA
2654027 TTGGGCCATC
Statistics
Matches: 105, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
131 73 0.70
132 1 0.01
133 1 0.01
134 30 0.29
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (133 bp):
CCGACCAGACCTCATCATCACATAGGAGCCGTGTCACCCCTAGATAATCAGTCATCCTCATCACG
TAGAAACCGTGTTATCATCCTCTTAAACATGGCATGCCATCCTCATCACATAGGAACCGTGTCAT
CTA
Found at i:2654056 original size:134 final size:131
Alignment explanation
Indices: 2653774--2654065 Score: 343
Period size: 131 Copynumber: 2.2 Consensus size: 131
2653764 GTATCATCCC
* * **
2653774 CCGACCAGACCTCATCATCACATAGGAGCCGTGTCACCTTTAGATAACAAGTCATCCTCATCACG
1 CCGACCAAACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGATAACAAGTCATCCTCATCACG
* * *
2653839 TAGAAACCTTGTTATCATCCCTAAACATGGCATGCCATCCTCATCACATAGGAACCGTGTCATCT
66 TAGAAACCGTGTTATCATCCCTAAACATGGCATGCCATCCTCATCACATAGGAACCGGGCCATCT
2653904 A
131 A
* * * * * *
2653905 CCGACTAGACCTCCTCATCACGTAGGAGCCGTGTCACCCCTAGATAATC-ATTCGTCCTCATCGC
1 CCGACCAAACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGATAA-CAAGTCATCCTCATCAC
* * ** **
2653969 GTAGGAACCGTGTTATCATCCTTCTTAAAGATGGCATGCCATCCTCATTGCATAGGAATTGGGCC
65 GTAGAAACCGTGTTATCATCC--C-TAAACATGGCATGCCATCCTCATCACATAGGAACCGGGCC
2654034 ATCTA
127 ATCTA
* * *
2654039 CCGGCCAAATCTCCTCATCGCATAGGA
1 CCGACCAAACCTCCTCATCACATAGGA
2654066 ATTGTGTCAC
Statistics
Matches: 134, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
131 73 0.54
132 1 0.01
133 1 0.01
134 59 0.44
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (131 bp):
CCGACCAAACCTCCTCATCACATAGGAGCCGTGTCACCCCTAGATAACAAGTCATCCTCATCACG
TAGAAACCGTGTTATCATCCCTAAACATGGCATGCCATCCTCATCACATAGGAACCGGGCCATCT
A
Found at i:2654276 original size:3 final size:3
Alignment explanation
Indices: 2654270--2654295 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2654260 AAAAAAATAC
2654270 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
2654296 ACAAAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2656194 original size:13 final size:13
Alignment explanation
Indices: 2656194--2656238 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2656184 CCGTTGACCC
*
2656194 GACCCAACCCGTT
1 GACCCGACCCGTT
*
2656207 AACCCGACCCGTT
1 GACCCGACCCGTT
* *
2656220 GACTCGACCTGTT
1 GACCCGACCCGTT
2656233 GACCCG
1 GACCCG
2656239 TTGACCGTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.18
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:2656195 original size:18 final size:18
Alignment explanation
Indices: 2656171--2656217 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
2656161 GACCGGTAAC
2656171 AACCCGACCCGACCCGTT
1 AACCCGACCCGACCCGTT
* *
2656189 GACCCGACCCAACCCGTT
1 AACCCGACCCGACCCGTT
2656207 AACCCGACCCG
1 AACCCGACCCG
2656218 TTGACTCGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.51, G:0.17, T:0.09
Consensus pattern (18 bp):
AACCCGACCCGACCCGTT
Found at i:2656241 original size:8 final size:8
Alignment explanation
Indices: 2656225--2656279 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
2656215 CCGTTGACTC
*
2656225 GACCTGTT
1 GACCCGTT
2656233 GACCCGTT
1 GACCCGTT
2656241 GA-CCGTT
1 GACCCGTT
2656248 GACCCGTT
1 GACCCGTT
2656256 GACCAGCGTT
1 GACC--CGTT
2656266 GACCACTGTT
1 GACC-C-GTT
2656276 GACC
1 GACC
2656280 AAAACTTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
7 7 0.17
8 18 0.44
9 1 0.02
10 15 0.37
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.25
Consensus pattern (8 bp):
GACCCGTT
Found at i:2656250 original size:15 final size:16
Alignment explanation
Indices: 2656225--2656259 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
2656215 CCGTTGACTC
2656225 GACCTGTTGACCCGTT
1 GACCTGTTGACCCGTT
2656241 GACC-GTTGACCCGTT
1 GACCTGTTGACCCGTT
2656256 GACC
1 GACC
2656260 AGCGTTGACC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.14, C:0.34, G:0.26, T:0.26
Consensus pattern (16 bp):
GACCTGTTGACCCGTT
Found at i:2656267 original size:10 final size:9
Alignment explanation
Indices: 2656230--2656280 Score: 56
Period size: 10 Copynumber: 5.9 Consensus size: 9
2656220 GACTCGACCT
2656230 GTTGACC-C
1 GTTGACCAC
2656238 GTTGA-C-C
1 GTTGACCAC
2656245 GTTGACC-C
1 GTTGACCAC
2656253 GTTGACCAGC
1 GTTGACCA-C
2656263 GTTGACCAC
1 GTTGACCAC
2656272 TGTTGACCA
1 -GTTGACCA
2656281 AAACTTTGAC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
7 7 0.18
8 14 0.36
9 1 0.03
10 17 0.44
ACGTcount: A:0.18, C:0.31, G:0.25, T:0.25
Consensus pattern (9 bp):
GTTGACCAC
Found at i:2656278 original size:20 final size:18
Alignment explanation
Indices: 2656230--2656280 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 18
2656220 GACTCGACCT
2656230 GTTGACCCGTTGA-C--C
1 GTTGACCCGTTGACCAGC
2656245 GTTGACCCGTTGACCAGC
1 GTTGACCCGTTGACCAGC
2656263 GTTGACCACTGTTGACCA
1 GTTGACC-C-GTTGACCA
2656281 AAACTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 13 0.42
16 1 0.03
18 8 0.26
19 1 0.03
20 8 0.26
ACGTcount: A:0.18, C:0.31, G:0.25, T:0.25
Consensus pattern (18 bp):
GTTGACCCGTTGACCAGC
Found at i:2657563 original size:18 final size:18
Alignment explanation
Indices: 2657537--2657572 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
2657527 TCGAAAGGAC
*
2657537 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
2657555 TGAATTAAATAATAAGAT
1 TGAAGTAAATAATAAGAT
2657573 CGGATGGAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:2658751 original size:12 final size:12
Alignment explanation
Indices: 2658736--2658792 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
2658726 GATACATTAC
*
2658736 CTGAATTCTGTT
1 CTGAATTCTGAT
*
2658748 CTGATTTCTGAT
1 CTGAATTCTGAT
* *
2658760 CTGGATTCTGTT
1 CTGAATTCTGAT
2658772 CTG-ATATCTGAT
1 CTGAAT-TCTGAT
2658784 CTGAATTCT
1 CTGAATTCT
2658793 ATTTTGATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (12 bp):
CTGAATTCTGAT
Found at i:2658767 original size:24 final size:24
Alignment explanation
Indices: 2658713--2658807 Score: 111
Period size: 24 Copynumber: 4.0 Consensus size: 24
2658703 ATTTCCGACT
* * *
2658713 TGAATTCTGTTCTGA-TACATTACC
1 TGAATTCTGTTCTGATTTC-TGATC
2658737 TGAATTCTGTTCTGATTTCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* *
2658761 TGGATTCTGTTCTGATATCTGATC
1 TGAATTCTGTTCTGATTTCTGATC
* *
2658785 TGAATTCTATTTTGATTTCTGAT
1 TGAATTCTGTTCTGATTTCTGAT
2658808 ATCTCCGTTT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
24 59 0.97
25 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (24 bp):
TGAATTCTGTTCTGATTTCTGATC
Found at i:2658768 original size:48 final size:48
Alignment explanation
Indices: 2658716--2658807 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
2658706 TCCGACTTGA
* *
2658716 ATTCTGTTCTGATA-CATTACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATATC-TGACCTGAATTCTATTCTGATTTCTGATCTGG
* *
2658764 ATTCTGTTCTGATATCTGATCTGAATTCTATTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGACCTGAATTCTATTCTGATTTCTGAT
2658808 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.20, C:0.16, G:0.15, T:0.49
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGACCTGAATTCTATTCTGATTTCTGATCTGG
Found at i:2660963 original size:18 final size:18
Alignment explanation
Indices: 2660940--2660996 Score: 96
Period size: 18 Copynumber: 3.2 Consensus size: 18
2660930 ACCGGTCACA
*
2660940 ACCCGACCTGACCCGTTG
1 ACCCGACCCGACCCGTTG
*
2660958 ACCCGACCCGACCCGTTA
1 ACCCGACCCGACCCGTTG
2660976 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
2660994 ACC
1 ACC
2660997 ACTGTTGACC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.19, C:0.49, G:0.19, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:2663498 original size:12 final size:12
Alignment explanation
Indices: 2663483--2663539 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
2663473 GATACATTAC
*
2663483 CTGAATTCTGTT
1 CTGAATTCTGAT
*
2663495 CTGATTTCTGAT
1 CTGAATTCTGAT
* *
2663507 CTGGATTCTGTT
1 CTGAATTCTGAT
2663519 CTG-ATATCTGAT
1 CTGAAT-TCTGAT
2663531 CTGAATTCT
1 CTGAATTCT
2663540 ATTTTTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (12 bp):
CTGAATTCTGAT
Found at i:2663514 original size:24 final size:24
Alignment explanation
Indices: 2663446--2663554 Score: 114
Period size: 24 Copynumber: 4.5 Consensus size: 24
2663436 AAATATTTTA
2663446 TCTGATTTCTGA-CTTGAATTCTGT
1 TCTGATTTCTGATC-TGAATTCTGT
* * *
2663470 TCTGA-TACATTACCTGAATTCTGT
1 TCTGATTTC-TGATCTGAATTCTGT
*
2663494 TCTGATTTCTGATCTGGATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* *
2663518 TCTGATATCTGATCTGAATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
* *
2663542 TTTTATTTCTGAT
1 TCTGATTTCTGAT
2663555 ATCTCCGTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
23 2 0.03
24 65 0.93
25 3 0.04
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:2663535 original size:48 final size:49
Alignment explanation
Indices: 2663446--2663554 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
2663436 AAATATTTTA
* *
2663446 TCTGATTTCTGA-CTTGAATTCTGTTCTGATACATTACCTGAATTCTGT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATACATGACCTGAATTCTAT
* *
2663494 TCTGATTTCTGATC-TGGATTCTGTTCTGATATC-TGATCTGAATTCTAT
1 TCTGATTTCTGATCTTGAATTCTGTTCTGATA-CATGACCTGAATTCTAT
* *
2663542 TTTTATTTCTGAT
1 TCTGATTTCTGAT
2663555 ATCTCCGTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 51 0.96
49 2 0.04
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.50
Consensus pattern (49 bp):
TCTGATTTCTGATCTTGAATTCTGTTCTGATACATGACCTGAATTCTAT
Found at i:2665230 original size:19 final size:20
Alignment explanation
Indices: 2665200--2665250 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2665190 CAGCCAAGAG
* *
2665200 CATGTATCTTCATT-AAAGT
1 CATGTATTTTCATTAAAAAT
*
2665219 CATGTTTTTTCATTAAAAAT
1 CATGTATTTTCATTAAAAAT
2665239 CATGTATTTTCA
1 CATGTATTTTCA
2665251 AAGGGATTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTAAAAAT
Found at i:2666676 original size:30 final size:30
Alignment explanation
Indices: 2666642--2666764 Score: 165
Period size: 30 Copynumber: 4.1 Consensus size: 30
2666632 CAGCCCTCTG
* *
2666642 AATTTCTATTTTTGCTATTTTAGTACTTAA
1 AATTTCTATTTTTGCTATTTTAGTCCTTTA
* *
2666672 AATTTTTATTTTTGCTATTTTAGTCCATTA
1 AATTTCTATTTTTGCTATTTTAGTCCTTTA
* * * *
2666702 ATTTTTTGTATTTGCTATTTTAGTCCTTTA
1 AATTTCTATTTTTGCTATTTTAGTCCTTTA
*
2666732 AATTTCTATTTTTACTATTTTAGTCCTTTA
1 AATTTCTATTTTTGCTATTTTAGTCCTTTA
2666762 AAT
1 AAT
2666765 CGAATATGAT
Statistics
Matches: 80, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 80 1.00
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.59
Consensus pattern (30 bp):
AATTTCTATTTTTGCTATTTTAGTCCTTTA
Found at i:2668174 original size:2 final size:2
Alignment explanation
Indices: 2668167--2668195 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2668157 TATGCACTGT
2668167 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2668196 TCATTTATGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2668900 original size:26 final size:25
Alignment explanation
Indices: 2668836--2669379 Score: 327
Period size: 26 Copynumber: 23.5 Consensus size: 25
2668826 TTATTCGTTA
2668836 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
* *
2668862 ----C-TTAATGCATCCTTTTATGC
1 ATTTCATTTATGCATCCTTTCATGC
2668882 ATTTCATTTATGACATCCTTTCATGC
1 ATTTCATTTATG-CATCCTTTCATGC
2668908 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
* *
2668934 ----C-TTAATGCATCTTTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
* *
2668954 ATTTCATTTATTACATCATTTCATG-
1 ATTTCATTTA-TGCATCCTTTCATGC
*
2668979 ---TC-TTAATGCATCCTTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
*
2669000 ATTTCTTTTATGGCATCCTTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
*
2669026 ----C-TTAATGCATCCTTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
2669046 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
* * *
2669072 ----C-TTAATGCATCATTTCATTC
1 ATTTCATTTATGCATCCTTTCATGC
* *
2669092 ATTTCAATTATGGTATCCTTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
* *
2669118 ----C-TTAATGTATCCTTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
*
2669138 ATTTCATTTATGGCAT-ATGTTCATGC
1 ATTTCATTTAT-GCATCCT-TTCATGC
*
2669164 --CTCA---ATGCATCCTTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
*
2669184 ATTTCATTTATGGCATCCGTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
* *
2669210 ----C-TTAATGCATCATTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
*
2669230 ATTTCATTTATGGCATCCATTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
*
2669256 ----C-TTAATGCATCCTTTCATG-
1 ATTTCATTTATGCATCCTTTCATGC
*
2669275 ---TC-TTAATGCATCCTTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
* *
2669296 ATTTCATTTATAGAATCATTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
* *
2669322 ----C-TTAATGTATCCTTTCATGC
1 ATTTCATTTATGCATCCTTTCATGC
2669342 ATTTCATTTATGGCATCCTTTCATGC
1 ATTTCATTTAT-GCATCCTTTCATGC
2669368 ATTTCATTTATG
1 ATTTCATTTATG
2669380 GATTTGTTTT
Statistics
Matches: 406, Mismatches: 48, Indels: 129
0.70 0.08 0.22
Matches are distributed among these distances:
20 144 0.35
21 37 0.09
22 13 0.03
24 14 0.03
25 39 0.10
26 158 0.39
27 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (25 bp):
ATTTCATTTATGCATCCTTTCATGC
Found at i:2668950 original size:46 final size:46
Alignment explanation
Indices: 2668895--2669274 Score: 600
Period size: 46 Copynumber: 8.3 Consensus size: 46
2668885 TCATTTATGA
2668895 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
* ** * *
2668941 CATCTTTTCATGCATTTCATTTATTACATCATTTCATGTCTTAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
*
2668987 CATCCTTTCATGCATTTCTTTTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
2669033 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
* * * *
2669079 CATCATTTCATTCATTTCAATTATGGTATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
* * *
2669125 TATCCTTTCATGCATTTCATTTATGGCAT-ATGTTCATGCCTCAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCT-TTCATGCCTTAATG
*
2669171 CATCCTTTCATGCATTTCATTTATGGCATCCGTTCATGCCTTAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
* *
2669217 CATCATTTCATGCATTTCATTTATGGCATCCATTCATGCCTTAATG
1 CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
2669263 CATCCTTTCATG
1 CATCCTTTCATG
2669275 TCTTAATGCA
Statistics
Matches: 302, Mismatches: 30, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.00
46 301 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATG
Found at i:2668953 original size:92 final size:90
Alignment explanation
Indices: 2668848--2669380 Score: 353
Period size: 92 Copynumber: 5.8 Consensus size: 90
2668838 TTCATTTATG
* *
2668848 GCATCCTTTCATGCCTTAATGCATCCTTTTATGCATTTCATTTATGACATCCTTTCATGCATTTC
1 GCATCCTTTCATGCCTT-ATGCATCCTTTCATGCATTTCATTAATG-CATCCTTTCATGCATTTC
2668913 ATTTATGGCATCCTTTCATGCCTTAAT
64 ATTTATGGCATCCTTTCATGCCTTAAT
* * *
2668940 GCATCTTTTCATGCATT-T-CAT-TTATTACAT-CATTTCATGTCTTAATGCATCCTTTCATGCA
1 GCATCCTTTCATGCCTTATGCATCCT-TT-CATGCATTTCA----TTAATGCATCCTTTCATGCA
*
2669001 TTTCTTTTATGGCATCCTTTCATGCCTTAAT
60 TTTCATTTATGGCATCCTTTCATGCCTTAAT
* *
2669032 GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC----C-TTAATGCATCATTTCATTC
1 GCATCCTTTCATGC----C--TTAT-GCATCCTTTCATGCATTTCATTAATGCATCCTTTCATGC
* *
2669092 ATTTCAATTATGGTATCCTTTCATGCCTTAAT
59 ATTTCATTTATGGCATCCTTTCATGCCTTAAT
* *
2669124 GTATCCTTTCATGCATT-T-CA---TTT-ATGGCATATGTTCATGCCTCAATGCATCCTTTCATG
1 GCATCCTTTCATGCCTTATGCATCCTTTCAT-GC--AT-TTCAT---T-AATGCATCCTTTCATG
*
2669183 CATTTCATTTATGGCATCCGTTCATGCCTTAAT
58 CATTTCATTTATGGCATCCTTTCATGCCTTAAT
* *
2669216 GCATCATTTCATGCATTTCATTTATGGCATCCATTCATGC----C-TTAATGCATCCTTTCATG-
1 GCATCCTTTCATGC----C--TTAT-GCATCCTTTCATGCATTTCATTAATGCATCCTTTCATGC
* *
2669275 ---TC-TTAAT-GCATCCTTTCATGCATTTCATTTAT
59 ATTTCATTTATGGCATCCTTTCATGC----C-TTAAT
* * * *
2669307 AGAATCATTTCATGCCTTAATGTATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGCATTT
1 -GCATCCTTTCATGCCTT-ATGCATCCTTTCATGCATTTCATTAAT-GCATCCTTTCATGCATTT
2669372 CATTTATGG
63 CATTTATGG
2669381 ATTTGTTTTA
Statistics
Matches: 346, Mismatches: 33, Indels: 118
0.70 0.07 0.24
Matches are distributed among these distances:
79 2 0.01
80 5 0.01
83 2 0.01
85 1 0.00
86 29 0.08
87 7 0.02
88 5 0.01
89 12 0.03
90 5 0.01
91 9 0.03
92 229 0.66
93 6 0.02
96 3 0.01
97 6 0.02
98 5 0.01
99 2 0.01
100 3 0.01
101 8 0.02
102 1 0.00
104 4 0.01
105 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (90 bp):
GCATCCTTTCATGCCTTATGCATCCTTTCATGCATTTCATTAATGCATCCTTTCATGCATTTCAT
TTATGGCATCCTTTCATGCCTTAAT
Found at i:2669020 original size:13 final size:12
Alignment explanation
Indices: 2668984--2669071 Score: 60
Period size: 12 Copynumber: 7.3 Consensus size: 12
2668974 TCATGTCTTA
2668984 ATGCATCCTTTC
1 ATGCATCCTTTC
* *
2668996 ATGCATTTCTTTT
1 ATGCA-TCCTTTC
2669009 ATGGCATCCTTTC
1 AT-GCATCCTTTC
*
2669022 ATG---CC-TTA
1 ATGCATCCTTTC
2669030 ATGCATCCTTTC
1 ATGCATCCTTTC
*
2669042 ATGCATTTCATTT-
1 ATGCA--TCCTTTC
2669055 ATGGCATCCTTTC
1 AT-GCATCCTTTC
2669068 ATGC
1 ATGC
2669072 CTTAATGCAT
Statistics
Matches: 58, Mismatches: 8, Indels: 20
0.67 0.09 0.23
Matches are distributed among these distances:
8 5 0.09
9 2 0.03
11 2 0.03
12 20 0.34
13 18 0.31
14 11 0.19
ACGTcount: A:0.18, C:0.26, G:0.11, T:0.44
Consensus pattern (12 bp):
ATGCATCCTTTC
Found at i:2669226 original size:112 final size:113
Alignment explanation
Indices: 2668836--2669380 Score: 267
Period size: 112 Copynumber: 4.7 Consensus size: 113
2668826 TTATTCGTTA
* * ** * * * *
2668836 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTTATGCATTTCATTTATGACATCCT
1 ATTTCATTTATAGAATCAGTTCATGCCTTAATGCATCATTTCATGC---TC-TTAATG-TATCCT
* * *
2668901 TTCATGCATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGC
61 TTCATGCATTTCATTTATGGCATCATTTCATGCCTCAATGCATCCTTTCATGC
* * * * * *
2668954 ATTTCATTTATTA-CATCATTTCATGTCTTAATGCATCCTTTCATGCATTTCTTTTATGGCATCC
1 ATTTCATTTA-TAGAATCAGTTCATGCCTTAATGCATCATTTCATGC---TC-TTAAT-GTATCC
* * *
2669018 TTTCATGC----C-TTAAT-GCATCCTTTCATGCATTTCATTTATGGCATCCTTTCATGC
60 TTTCATGCATTTCATTTATGGCATCATTTCATGC--CTCA---AT-GCATCCTTTCATGC
* * ** ** * * * *
2669072 -CTTAATGCATCA-TTTCA-TTCATTTCAATT-ATGGTATCCTTTCATGC-CTTAATGTATCCTT
1 ATTTCATTTAT-AGAATCAGTTCA-TGC-CTTAAT-GCATCATTTCATGCTCTTAATGTATCCTT
2669132 TCATGCATTTCATTTATGGCAT-ATGTTCATGCCTCAATGCATCCTTTCATGC
62 TCATGCATTTCATTTATGGCATCAT-TTCATGCCTCAATGCATCCTTTCATGC
* * * * * * * *
2669184 ATTTCATTTATGGCATCCGTTCATGCCTTAATGCATCATTTCATGCAT-TTCATTTATGGCATCC
1 ATTTCATTTATAGAATCAGTTCATGCCTTAATGCATCATTTCATGC-TCTTAATGTAT-CCTTTC
* * * * * * *
2669248 ATTCA-TGCCTTAAT-GCATCCTTTCATGTCTTAATGCATCCTTTCATGC
64 ATGCATTTCATTTATGGCATCATTTCATGCCTCAATGCATCCTTTCATGC
* * * * *
2669296 ATTTCATTTATAGAATCATTTCATGCCTTAATGTATCCTTTCATGCATTTCATTTATGGCATCCT
1 ATTTCATTTATAGAATCAGTTCATGCCTTAATGCATCATTTCATGC---TC-TTAAT-GTATCCT
2669361 TTCATGCATTTCATTTATGG
61 TTCATGCATTTCATTTATGG
2669381 ATTTGTTTTA
Statistics
Matches: 328, Mismatches: 65, Indels: 68
0.71 0.14 0.15
Matches are distributed among these distances:
112 124 0.38
113 36 0.11
114 16 0.05
116 20 0.06
117 27 0.08
118 103 0.31
119 2 0.01
ACGTcount: A:0.21, C:0.23, G:0.10, T:0.45
Consensus pattern (113 bp):
ATTTCATTTATAGAATCAGTTCATGCCTTAATGCATCATTTCATGCTCTTAATGTATCCTTTCAT
GCATTTCATTTATGGCATCATTTCATGCCTCAATGCATCCTTTCATGC
Found at i:2669318 original size:46 final size:46
Alignment explanation
Indices: 2669268--2669367 Score: 155
Period size: 46 Copynumber: 2.2 Consensus size: 46
2669258 TAATGCATCC
*
2669268 TTTCATGTCTTAATGCATCCTTTCATGCATTTCATTTATAGAATCA
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATAGAATCA
* * * *
2669314 TTTCATGCCTTAATGTATCCTTTCATGCATTTCATTTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATAGAATCA
2669360 TTTCATGC
1 TTTCATGC
2669368 ATTTCATTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTCATTTATAGAATCA
Found at i:2669318 original size:138 final size:138
Alignment explanation
Indices: 2668848--2669321 Score: 535
Period size: 138 Copynumber: 3.4 Consensus size: 138
2668838 TTCATTTATG
* *
2668848 GCATCCTTTCATG--CCTTAAT-GCATCCTTTTATGCATTTCATTTATGACATCCTTTCATGCAT
1 GCATCCTTTCATGTTCATTAATGGCATCCTTTCATGC--TTCATTTATGA-ATCCTTTCATGCAT
* **
2668910 TTCATTTATGGCATCCTTTCATGCCTTAATGCATCTTTTCATGCATTTCATTTATTACAT-CATT
63 TTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCA-T
*
2668974 TCATGTCTTAAT
127 TCATGCCTTAAT
* * * *
2668986 GCATCCTTTCATGCATTTCTTTTATGGCATCCTTTCATGC--C-TTAATGCATCCTTTCATGCAT
1 GCATCCTTTCATG---TTCATTAATGGCATCCTTTCATGCTTCATTTATGAATCCTTTCATGCAT
* * * *
2669048 TTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATTCATTTCAATTATGGTATCCTTT
63 TTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCATT
2669113 CATGCCTTAAT
128 CATGCCTTAAT
* * * * *
2669124 GTATCCTTTCATGCATTTCATTTATGGCAT-ATGTTCATGCCTCA---ATGCATCCTTTCATGCA
1 GCATCCTTTCATG---TTCATTAATGGCATCCT-TTCATGCTTCATTTATGAATCCTTTCATGCA
*
2669185 TTTCATTTATGGCATCCGTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCAT
62 TTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCAT
2669250 TCATGCCTTAAT
127 TCATGCCTTAAT
*
2669262 GCATCCTTTCATG-TC-TTAAT-GCATCCTTTCATGCATTTCATTTATAGAATCATTTCATGC
1 GCATCCTTTCATGTTCATTAATGGCATCCTTTCATGC--TTCATTTAT-GAATCCTTTCATGC
2669322 CTTAATGTAT
Statistics
Matches: 291, Mismatches: 27, Indels: 36
0.82 0.08 0.10
Matches are distributed among these distances:
132 11 0.04
133 5 0.02
134 5 0.02
137 3 0.01
138 241 0.83
139 6 0.02
140 2 0.01
143 5 0.02
144 13 0.04
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (138 bp):
GCATCCTTTCATGTTCATTAATGGCATCCTTTCATGCTTCATTTATGAATCCTTTCATGCATTTC
ATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGCATTTCATTTATGGCATCCATTCAT
GCCTTAAT
Found at i:2670748 original size:8 final size:8
Alignment explanation
Indices: 2670735--2670789 Score: 110
Period size: 8 Copynumber: 6.9 Consensus size: 8
2670725 TTTCTCTAAC
2670735 CATACATG
1 CATACATG
2670743 CATACATG
1 CATACATG
2670751 CATACATG
1 CATACATG
2670759 CATACATG
1 CATACATG
2670767 CATACATG
1 CATACATG
2670775 CATACATG
1 CATACATG
2670783 CATACAT
1 CATACAT
2670790 ATATTTAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 47 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.25
Consensus pattern (8 bp):
CATACATG
Found at i:2681018 original size:20 final size:19
Alignment explanation
Indices: 2680971--2681018 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
2680961 ATTATAATAA
*
2680971 TAATAATATTTTTATTTTTT
1 TAATAA-ATTCTTATTTTTT
*
2680991 TAGCTAAATTCTTATTTTATT
1 TA-ATAAATTCTTATTTT-TT
2681012 TAATAAA
1 TAATAAA
2681019 AATAATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (19 bp):
TAATAAATTCTTATTTTTT
Found at i:2683159 original size:19 final size:19
Alignment explanation
Indices: 2683135--2683183 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
2683125 AATACCTAGG
2683135 CTTCAAAGACTTTTTATGT
1 CTTCAAAGACTTTTTATGT
2683154 CTTCAAAGACTTTTTATGT
1 CTTCAAAGACTTTTTATGT
2683173 CTTCAAAGACT
1 CTTCAAAGACT
2683184 ACAGAGTCTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.10, T:0.43
Consensus pattern (19 bp):
CTTCAAAGACTTTTTATGT
Found at i:2686672 original size:43 final size:42
Alignment explanation
Indices: 2686625--2686733 Score: 139
Period size: 42 Copynumber: 2.6 Consensus size: 42
2686615 GGTTACGACT
*
2686625 TTTGTGACTAAAAACGACGCTAAATGACCAACCTATTACAGCG
1 TTTGTGACT-AAAACGACGCTAAATGACCAACCTATTACAACG
* * *
2686668 TTTGTGCCTGAAACGACGCTAAATGACCAACCTATTGCAACG
1 TTTGTGACTAAAACGACGCTAAATGACCAACCTATTACAACG
* *
2686710 TTTGTGCCTGAAAC-ACCGCTAAAT
1 TTTGTGACTAAAACGA-CGCTAAAT
2686734 ATCAAATATG
Statistics
Matches: 61, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 1 0.02
42 52 0.85
43 8 0.13
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (42 bp):
TTTGTGACTAAAACGACGCTAAATGACCAACCTATTACAACG
Found at i:2686691 original size:42 final size:42
Alignment explanation
Indices: 2686636--2686733 Score: 162
Period size: 42 Copynumber: 2.3 Consensus size: 42
2686626 TTGTGACTAA
*
2686636 AAACGACGCTAAATGACCAACCTATTACAGCGTTTGTGCCTG
1 AAACGACGCTAAATGACCAACCTATTACAACGTTTGTGCCTG
*
2686678 AAACGACGCTAAATGACCAACCTATTGCAACGTTTGTGCCTG
1 AAACGACGCTAAATGACCAACCTATTACAACGTTTGTGCCTG
2686720 AAAC-ACCGCTAAAT
1 AAACGA-CGCTAAAT
2686734 ATCAAATATG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 52 0.98
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (42 bp):
AAACGACGCTAAATGACCAACCTATTACAACGTTTGTGCCTG
Found at i:2687313 original size:42 final size:42
Alignment explanation
Indices: 2687254--2687415 Score: 288
Period size: 42 Copynumber: 3.9 Consensus size: 42
2687244 TTTCCCCGAA
*
2687254 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCTGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
*
2687296 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGCT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
*
2687338 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATGTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
*
2687380 TTCCCGTGTTTGTTTCACGTAATTGGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
2687416 TGTAATTCAT
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 114 1.00
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATGTT
Found at i:2687615 original size:34 final size:31
Alignment explanation
Indices: 2687575--2687640 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
2687565 CATTTTCATC
2687575 AAAATAT--TATT-TATTTATTAATATT-TAT
1 AAAATATAATATTATATTT-TTAATATTATAT
2687603 AATAATATAATATTATATTTTTAATATTATAT
1 AA-AATATAATATTATATTTTTAATATTATAT
2687635 AAAATA
1 AAAATA
2687641 ATCGATTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
28 2 0.06
29 5 0.15
31 16 0.48
32 10 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAAATATAATATTATATTTTTAATATTATAT
Found at i:2687621 original size:22 final size:23
Alignment explanation
Indices: 2687590--2687633 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2687580 ATTATTTATT
2687590 TATTAATATTTATAATAATATAA
1 TATTAATATTTATAATAATATAA
* *
2687613 TATT-ATATTTTTAATATTATA
1 TATTAATATTTATAATAATATA
2687634 TAAAATAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TATTAATATTTATAATAATATAA
Found at i:2687630 original size:31 final size:31
Alignment explanation
Indices: 2687582--2687751 Score: 87
Period size: 29 Copynumber: 5.9 Consensus size: 31
2687572 ATCAAAATAT
2687582 TATT-TATTTATTAATATTTATAATAATATAA
1 TATTATATTT-TTAATATTTATAATAATATAA
*
2687613 TATTATATTTTTAATA-TTAT-ATAAAATAA
1 TATTATATTTTTAATATTTATAATAATATAA
2687642 TCGATTATA---TT-ATA---ATAAT-ATA-AGA
1 T--ATTATATTTTTAATATTTATAATAATATA-A
2687667 TATTATATTTTT-AT-TTTAATAAT-ATATAA
1 TATTATATTTTTAATATTT-ATAATAATATAA
* *
2687696 TA-AATTTTTTTAA-ATATT-TAATAAT-TAA
1 TATTATATTTTTAATAT-TTATAATAATATAA
2687724 TA--ATATTATTTATATATTTA-AATAATAT
1 TATTATATT-TTTA-ATATTTATAATAATAT
2687752 TTTAATAAAG
Statistics
Matches: 112, Mismatches: 5, Indels: 45
0.69 0.03 0.28
Matches are distributed among these distances:
23 6 0.05
24 1 0.01
25 6 0.05
26 6 0.05
27 7 0.06
28 22 0.20
29 33 0.29
30 10 0.09
31 16 0.14
32 5 0.04
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (31 bp):
TATTATATTTTTAATATTTATAATAATATAA
Found at i:2687749 original size:22 final size:20
Alignment explanation
Indices: 2687710--2687752 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2687700 TTTTTTTAAA
2687710 TATTTAATAATTAATAATAT
1 TATTTAATAATTAATAATAT
*
2687730 TATTTATATATTTAAATAATAT
1 TATTTA-ATAATT-AATAATAT
2687752 T
1 T
2687753 TTAATAAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTAATAATTAATAATAT
Found at i:2687780 original size:23 final size:23
Alignment explanation
Indices: 2687754--2687798 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2687744 AATAATATTT
2687754 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
2687777 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
2687799 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:2687950 original size:21 final size:20
Alignment explanation
Indices: 2687926--2687998 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 20
2687916 ATAAATTATT
*
2687926 TTAATATTTAAAATAATAATA
1 TTAAT-TTTATAATAATAATA
*
2687947 TTAAGTTTTATGATAATAATA
1 TTAA-TTTTATAATAATAATA
*
2687968 TT-ATTTTATAATAATAAGA
1 TTAATTTTATAATAATAATA
2687987 TTTATATTTTAT
1 -TTA-ATTTTAT
2687999 TTTAATATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 14 0.32
20 3 0.07
21 19 0.43
22 8 0.18
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (20 bp):
TTAATTTTATAATAATAATA
Found at i:2688065 original size:22 final size:20
Alignment explanation
Indices: 2688026--2688068 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2688016 AAAATTTATA
2688026 TATTTAATAATTAATAATAT
1 TATTTAATAATTAATAATAT
*
2688046 TATTTATATATTTAAATAATAT
1 TATTTA-ATAATT-AATAATAT
2688068 T
1 T
2688069 TAATAAAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TATTTAATAATTAATAATAT
Found at i:2688082 original size:32 final size:29
Alignment explanation
Indices: 2687990--2688083 Score: 97
Period size: 28 Copynumber: 3.2 Consensus size: 29
2687980 AATAAGATTT
*
2687990 ATATTT-TAT-TTTAATATATATAATAAA
1 ATATTTATATATTTAATATATTTAATAAA
*
2688017 AAATTTATATATTTAATA-A-TTAATAATA
1 ATATTTATATATTTAATATATTTAATAA-A
*
2688045 TTATTTATATATTTAAATAATATTTAATAAA
1 ATATTTATATATTT-AAT-ATATTTAATAAA
2688076 GATATTTA
1 -ATATTTA
2688084 AAATATACTA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
27 11 0.20
28 17 0.31
29 10 0.19
30 1 0.02
31 2 0.04
32 13 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
ATATTTATATATTTAATATATTTAATAAA
Found at i:2688208 original size:21 final size:21
Alignment explanation
Indices: 2688182--2688252 Score: 142
Period size: 21 Copynumber: 3.4 Consensus size: 21
2688172 AAATATACAA
2688182 AAAATTATTATTTTTATTAAT
1 AAAATTATTATTTTTATTAAT
2688203 AAAATTATTATTTTTATTAAT
1 AAAATTATTATTTTTATTAAT
2688224 AAAATTATTATTTTTATTAAT
1 AAAATTATTATTTTTATTAAT
2688245 AAAATTAT
1 AAAATTAT
2688253 AAAAATAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
AAAATTATTATTTTTATTAAT
Found at i:2688309 original size:22 final size:22
Alignment explanation
Indices: 2688272--2688330 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2688262 ATGTAATAAT
* *
2688272 AAATAAATTATTTTAATATTTTA
1 AAATAAATAATATTAA-ATTTTA
2688295 AAAT-AATAATATTAAATTTTA
1 AAATAAATAATATTAAATTTTA
**
2688316 TGATAAATAATATTA
1 AAATAAATAATATTA
2688331 TTTATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 8 0.26
22 19 0.61
23 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
AAATAAATAATATTAAATTTTA
Found at i:2688400 original size:315 final size:309
Alignment explanation
Indices: 2687704--2688346 Score: 818
Period size: 315 Copynumber: 2.0 Consensus size: 309
2687694 AATAAATTTT
* * * **
2687704 TTTAAATATTTAATAATTAATAATATTATTTATATATTTAAATAATATTTTAATAAAGATATTTA
1 TTTATATATTTAATAATTAATAATATTATTTAAAAATTTAAATAATA-TGGAATAAAGATATTTA
2687769 AAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATATA
65 AAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATATA
2687834 ATTTATAATATTTTATTTCACTAAAATATACAAAAATTATTATTTTTATTAATAAAATTATAAAA
130 ATTTATAATATTTTATTTCACTAAAATATACAAAAATTATTATTTTTATTAATAAAATTAT----
* * * *
2687899 ATAATATTTAATAATAAATAAATTATTTTAATATTTAAAATAATAATATTAAGTTTTATGATAAT
191 ATAATATTTAATAATAAATAAATTATTTT-ATATTTAAAATAATAAAAATAAGTTTAATAATAAT
* * ** *
2687964 AATATTATTTTATAATAATAAGATTTATATTTTATTTTAATATATATAATAAAAAA
255 AATATTATTTTATAATAATAAGAATAATATTAAATTTTAATATAAATAAT-AAAAA
* * **
2688020 TTTATATATTTAATAATTAATAATATTATTTATATATTTAAATAATATTTAATAAAGATATTTAA
1 TTTATATATTTAATAATTAATAATATTATTTAAAAATTTAAATAATATGGAATAAAGATATTTAA
2688085 AATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATATAA
66 AATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATATAA
2688150 TTTATAATATTTTATTTCACTAAAATATACAAAAAATTATTATTTTTATTAATAAAATTAT-T-A
131 TTTATAATATTTTATTTCACTAAAATATAC-AAAAATTATTATTTTTATTAATAAAATTATATAA
* * * *
2688213 TTTTTATTAATAAA-ATTATTATTTT-TATTAATAAAATTATAAAAATAA-TATGTAATAATAAA
195 TATTTAATAATAAATA-AATTATTTTATATT--TAAAATAATAAAAATAAGT-T-TAATAAT-AA
* * **
2688275 TAA-ATTATTTTAATATTTTAA-AATAATAATATTAAATTTT-ATGATAAATAAT-ATTA
254 TAATATTATTTT-ATA--ATAATAAGAATAATATTAAATTTTAAT-ATAAATAATAAAAA
2688331 TTTATTATATTTAATA
1 TTTA-TATATTTAATA
2688347 TTTGTAATAA
Statistics
Matches: 297, Mismatches: 18, Indels: 28
0.87 0.05 0.08
Matches are distributed among these distances:
308 4 0.01
309 2 0.01
310 36 0.12
311 20 0.07
312 21 0.07
313 22 0.07
314 3 0.01
315 113 0.38
316 76 0.26
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (309 bp):
TTTATATATTTAATAATTAATAATATTATTTAAAAATTTAAATAATATGGAATAAAGATATTTAA
AATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATATAA
TTTATAATATTTTATTTCACTAAAATATACAAAAATTATTATTTTTATTAATAAAATTATATAAT
ATTTAATAATAAATAAATTATTTTATATTTAAAATAATAAAAATAAGTTTAATAATAATAATATT
ATTTTATAATAATAAGAATAATATTAAATTTTAATATAAATAATAAAAA
Found at i:2688567 original size:21 final size:21
Alignment explanation
Indices: 2688525--2688567 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2688515 AGAATTCAAA
** *
2688525 TTCCAGTAATTCATTTTTCAG
1 TTCCAGTAATTCAAATTCCAG
*
2688546 TTCCAGTAATTTAAATTCCAG
1 TTCCAGTAATTCAAATTCCAG
2688567 T
1 T
2688568 AATTCATTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (21 bp):
TTCCAGTAATTCAAATTCCAG
Found at i:2688579 original size:15 final size:15
Alignment explanation
Indices: 2688502--2688546 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
2688492 TTCAGAAATT
2688502 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
**
2688517 -AATTCAAATTCCAG
1 TAATTCATTTTCCAG
*
2688531 TAATTCATTTTTCAG
1 TAATTCATTTTCCAG
2688546 T
1 T
2688547 TCCAGTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:2689964 original size:37 final size:36
Alignment explanation
Indices: 2689889--2689964 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
2689879 TTTTTATATT
*
2689889 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
2689925 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
2689962 TTT
1 TTT
2689965 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:2689972 original size:17 final size:18
Alignment explanation
Indices: 2689950--2689988 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2689940 AAAATATATA
* *
2689950 AATATTTTAC-AATTTGT
1 AATATTATACAAATATGT
2689967 AATATTATACAAATATGT
1 AATATTATACAAATATGT
2689985 AATA
1 AATA
2689989 AGGATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (18 bp):
AATATTATACAAATATGT
Found at i:2690984 original size:5 final size:5
Alignment explanation
Indices: 2690974--2691019 Score: 56
Period size: 5 Copynumber: 8.8 Consensus size: 5
2690964 AATATAGTAC
* *
2690974 ATTTA ATTTA ATTAA ATTTA ATTTA ATTTA ATCTTA TATTTT ATTT
1 ATTTA ATTTA ATTTA ATTTA ATTTA ATTTA AT-TTA -ATTTA ATTT
2691020 TTGTTACAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 29 0.81
6 5 0.14
7 2 0.06
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (5 bp):
ATTTA
Found at i:2691909 original size:17 final size:18
Alignment explanation
Indices: 2691887--2691920 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2691877 CATTCTCTAA
2691887 TATTAA-AAATATATTTT
1 TATTAAGAAATATATTTT
*
2691904 TATTAAGAATTATATTT
1 TATTAAGAAATATATTT
2691921 ATCTCATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATTAAGAAATATATTTT
Found at i:2692846 original size:24 final size:24
Alignment explanation
Indices: 2692818--2692866 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
2692808 AGCATAATAT
2692818 ATATAATA-AATATAGTTTTTGAAA
1 ATAT-ATAGAATATAGTTTTTGAAA
*
2692842 ATATATAGTATATAGTTTTTGAAA
1 ATATATAGAATATAGTTTTTGAAA
2692866 A
1 A
2692867 CGTATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.43
Consensus pattern (24 bp):
ATATATAGAATATAGTTTTTGAAA
Found at i:2692954 original size:73 final size:72
Alignment explanation
Indices: 2692872--2693138 Score: 210
Period size: 75 Copynumber: 3.7 Consensus size: 72
2692862 GAAAACGTAT
* * * *
2692872 TTTTTAAAACATATATAATATAATTTTTAAAATAGTTTTGAAAACGTGTAATATGTATGGTTTTT
1 TTTTGAAAACATATATAATAT-ATTTTTAAAATAGTTTTGAAAACATATAATATGTATGATTTTT
2692937 TAAAATGG
65 TAAAATGG
* * * *
2692945 TTTTGAAAACATACA-ATATATAGTTTTTAAAAAATGGTTTTGAAAATATATAGTATATG-AT-T
1 TTTTGAAAACATATATA-ATATA-TTTTT--AAAATAGTTTTGAAAACATATA--ATATGTATGA
*
2693007 TTTTTTAAAACGG
60 TTTTTTAAAATGG
* *
2693020 TTTTGAAAACACAGTAT-ATGAT-TTTTTAAAA-ACGGTTTTGAAAACATATAGTA--TATGATT
1 TTTTGAAAACATA-TATAAT-ATATTTTTAAAATA--GTTTTGAAAACATATAATATGTATGATT
2693080 TTTTAAAAATGG
62 TTTT-AAAATGG
* * ** *
2693092 TTTTGAAAACGTATACT-ATATTTTTTTAAACGATTTTTGAAAACATA
1 TTTTGAAAACATATA-TAATATATTTTTAAAATAGTTTTGAAAACATA
2693139 ATTTTGAAAA
Statistics
Matches: 158, Mismatches: 19, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
70 2 0.01
71 25 0.16
72 34 0.22
73 38 0.24
74 5 0.03
75 44 0.28
76 5 0.03
77 5 0.03
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (72 bp):
TTTTGAAAACATATATAATATATTTTTAAAATAGTTTTGAAAACATATAATATGTATGATTTTTT
AAAATGG
Found at i:2692963 original size:38 final size:36
Alignment explanation
Indices: 2692872--2693138 Score: 219
Period size: 37 Copynumber: 7.4 Consensus size: 36
2692862 GAAAACGTAT
* * *
2692872 TTTTTAAAACATAT-ATAATAT-AATTTTTAAAATAG
1 TTTTGAAAACATATAAT-ATATGATTTTTTAAAATGG
* * *
2692907 TTTTGAAAACGTGTAATATGTATGGTTTTTTAAAATGG
1 TTTTGAAAACATATAATA--TATGATTTTTTAAAATGG
* *
2692945 TTTTGAAAACATACAATATAT-AGTTTTTAAAAAATGG
1 TTTTGAAAACATATAATATATGA-TTTTT-TAAAATGG
* * *
2692982 TTTTGAAAATATATAGTATATGATTTTTTTTAAAACGG
1 TTTTGAAAACATATAATATATGA--TTTTTTAAAATGG
* * *
2693020 TTTTGAAAAC--ACAGTATATGATTTTTTAAAAACGG
1 TTTTGAAAACATATAATATATGATTTTTT-AAAATGG
*
2693055 TTTTGAAAACATATAGTATATGATTTTTTAAAAATGG
1 TTTTGAAAACATATAATATATGATTTTTT-AAAATGG
* *
2693092 TTTTGAAAACGTATACTATAT--TTTTTTAAACGAT--
1 TTTTGAAAACATATAATATATGATTTTTTAAA--ATGG
2693126 TTTTGAAAACATA
1 TTTTGAAAACATA
2693139 ATTTTGAAAA
Statistics
Matches: 195, Mismatches: 24, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
34 21 0.11
35 35 0.18
36 22 0.11
37 70 0.36
38 42 0.22
39 5 0.03
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (36 bp):
TTTTGAAAACATATAATATATGATTTTTTAAAATGG
Found at i:2693192 original size:23 final size:24
Alignment explanation
Indices: 2693166--2693215 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
2693156 TTATATAGTT
2693166 TTTA-CTAGTATATTTATA-TTTTA
1 TTTATCTA-TATATTTATATTTTTA
* *
2693189 TTTATTTATTTATTTATATTTTTA
1 TTTATCTATATATTTATATTTTTA
2693213 TTT
1 TTT
2693216 TATTATTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTATCTATATATTTATATTTTTA
Found at i:2699571 original size:29 final size:29
Alignment explanation
Indices: 2699531--2699588 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2699521 AAATAATCAA
2699531 TTTGGCCCTTATTCTTTTTTATGGAATAT
1 TTTGGCCCTTATTCTTTTTTATGGAATAT
2699560 TTTGGCCCTTATTCTTTTTTATGGAATAT
1 TTTGGCCCTTATTCTTTTTTATGGAATAT
2699589 ATATACCCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (29 bp):
TTTGGCCCTTATTCTTTTTTATGGAATAT
Found at i:2699597 original size:29 final size:29
Alignment explanation
Indices: 2699536--2699597 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
2699526 ATCAATTTGG
* *
2699536 CCCTTATTCTTTTTTATGGAATATTTTGG
1 CCCTTATTCTTTTTTATGGAATATTATGA
2699565 CCCTTATTCTTTTTTATGGAATATATAT-A
1 CCCTTATTCTTTTTTATGGAATAT-TATGA
2699594 CCCT
1 CCCT
2699598 CAACGTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.93
30 2 0.07
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.52
Consensus pattern (29 bp):
CCCTTATTCTTTTTTATGGAATATTATGA
Found at i:2704753 original size:29 final size:30
Alignment explanation
Indices: 2704713--2704771 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
2704703 AAATAATCAA
*
2704713 TTTGGCCCTTATTC-TTTTTTGTGGAATAT
1 TTTGGCCCTTATTCTTTTTTTATGGAATAT
2704742 TTTGGCCCTTATTCTTTTTTTATGGAATAT
1 TTTGGCCCTTATTCTTTTTTTATGGAATAT
2704772 ATATACCCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.15, C:0.14, G:0.15, T:0.56
Consensus pattern (30 bp):
TTTGGCCCTTATTCTTTTTTTATGGAATAT
Found at i:2705728 original size:77 final size:77
Alignment explanation
Indices: 2705590--2705737 Score: 203
Period size: 77 Copynumber: 1.9 Consensus size: 77
2705580 TTATCCCATA
*
2705590 ATCTCAAATGGGGATGATAAATTCATGAGCATTATTTGGCTAGAGTTGTGATACTAGAGATTTAA
1 ATCTCAAATGGGGATGATAAATTCATCAGCATTATTTGGCTAGAGTTGTGATACTAGAGATTTAA
2705655 ATCATGCCATCT
66 ATCATGCCATCT
* * * *
2705667 ATCTCATATGGGGATGATATATTCGTCAGCATTATTTGG-TGAGAGTTGT-AGTA-TCATAGATT
1 ATCTCAAATGGGGATGATAAATTCATCAGCATTATTTGGCT-AGAGTTGTGA-TACT-AGAGATT
2705729 TAAATCATG
63 TAAATCATG
2705738 GTTAAATATT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
76 3 0.05
77 60 0.95
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (77 bp):
ATCTCAAATGGGGATGATAAATTCATCAGCATTATTTGGCTAGAGTTGTGATACTAGAGATTTAA
ATCATGCCATCT
Found at i:2706111 original size:21 final size:21
Alignment explanation
Indices: 2706060--2706112 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
2706050 ATTATGACTA
2706060 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
2706081 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
2706102 TCGCAATGCGA
1 TCGCAATGCGA
2706113 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:2706127 original size:20 final size:21
Alignment explanation
Indices: 2706102--2706153 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
2706092 TTTTCCCAAT
*
2706102 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
2706122 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
2706143 TCGCAATGCGA
1 TCGCAATGCGA
2706154 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:2706171 original size:20 final size:20
Alignment explanation
Indices: 2706142--2706269 Score: 132
Period size: 20 Copynumber: 6.3 Consensus size: 20
2706132 AATTTGGAAA
*
2706142 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * *
2706162 ATCTCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
2706183 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
2706203 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
2706223 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
2706243 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
2706263 ATCGCAA
1 ATCGCAA
2706270 TGAGATAATA
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 78 0.82
21 13 0.14
22 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:2706215 original size:41 final size:42
Alignment explanation
Indices: 2706139--2706255 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 42
2706129 GCGAATTTGG
* * * *
2706139 AAAATCGCAATGCGATACTGACTATCTCAATGCGATAAT-AC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
**
2706180 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGAC
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
** *
2706222 --TTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGCGATACTGACTTTCGCAACGCGAT
2706256 TCTGACTATC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
40 31 0.47
41 33 0.50
42 2 0.03
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
AAAATCGCAACGCGATACTGACTTTCGCAACGCGATAATGAC
Found at i:2706241 original size:40 final size:40
Alignment explanation
Indices: 2706183--2706269 Score: 156
Period size: 40 Copynumber: 2.2 Consensus size: 40
2706173 ATAATACAAA
2706183 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
* *
2706223 TTCGCAACGCGATTCTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
2706263 ATCGCAA
1 ATCGCAA
2706270 TGAGATAATA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (40 bp):
ATCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACT
Found at i:2706877 original size:20 final size:20
Alignment explanation
Indices: 2706822--2706868 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2706812 CAACGGGGAA
2706822 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
2706842 ATCGTAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGACT
2706862 ATCGCAA
1 ATCGCAA
2706869 TGAGAAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.21, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:2706937 original size:19 final size:19
Alignment explanation
Indices: 2706896--2706998 Score: 171
Period size: 19 Copynumber: 5.7 Consensus size: 19
2706886 GAAATGAAAA
2706896 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
2706912 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2706929 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2706948 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2706967 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2706986 TCGCATTGCGATT
1 TCGCATTGCGATT
2706999 CTCTCGTTGC
Statistics
Matches: 82, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
14 11 0.13
16 3 0.04
17 3 0.04
19 65 0.79
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2708639 original size:41 final size:41
Alignment explanation
Indices: 2708555--2708676 Score: 145
Period size: 42 Copynumber: 2.9 Consensus size: 41
2708545 GTGAATCAGG
* * * * * *
2708555 CTCTGGAATGGTGGGAGGGACCTCTTCAGCGATGACAGTGGC
1 CTCTTGAACGGTGGGGGGGA-CTCTTGAGGGATGACAGGGGC
*
2708597 CTCTTGAACGGTGGGGGGGACTCTTGAGGGATGATAGGGGC
1 CTCTTGAACGGTGGGGGGGACTCTTGAGGGATGACAGGGGC
* *
2708638 CTCTTGAACGATTGGAGGGGACTCTTGAGGGATGACAGG
1 CTCTTGAACG-GTGGGGGGGACTCTTGAGGGATGACAGG
2708677 TGAGTCGGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
41 27 0.39
42 42 0.61
ACGTcount: A:0.20, C:0.17, G:0.41, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGGGGGACTCTTGAGGGATGACAGGGGC
Found at i:2708641 original size:21 final size:21
Alignment explanation
Indices: 2708612--2708672 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
2708602 GAACGGTGGG
*
2708612 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
2708633 GGGGCCTCTTGAACGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
2708654 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
2708673 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.13, G:0.43, T:0.23
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:2709064 original size:40 final size:40
Alignment explanation
Indices: 2709020--2709105 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
2709010 TAGTTTACTT
* *
2709020 TCGCAACAC-GAAACTTACTTTCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAA-TGACTATCGCAACGCGAAAATGACTA
* * *
2709060 TCGCAACACGGAAATGGCTATCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
2709100 TCGCAA
1 TCGCAA
2709106 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 36 0.90
41 4 0.10
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (40 bp):
TCGCAACACGGAAATGACTATCGCAACGCGAAAATGACTA
Found at i:2709075 original size:20 final size:20
Alignment explanation
Indices: 2709020--2709105 Score: 93
Period size: 20 Copynumber: 4.3 Consensus size: 20
2709010 TAGTTTACTT
* *
2709020 TCGCAACAC-GAAACTTACTT
1 TCGCAACACGGAAA-TGACTA
* *
2709040 TCGCAACGCGAAAATGACTA
1 TCGCAACACGGAAATGACTA
*
2709060 TCGCAACACGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
* *
2709080 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGGAAATGACTA
2709100 TCGCAA
1 TCGCAA
2709106 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 54 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (20 bp):
TCGCAACACGGAAATGACTA
Found at i:2709121 original size:19 final size:19
Alignment explanation
Indices: 2709099--2709157 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
2709089 GGAAATGGCT
2709099 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
2709118 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
2709132 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
2709151 ATCGCAA
1 ATCGCAA
2709158 CGATAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:2709141 original size:33 final size:33
Alignment explanation
Indices: 2709099--2709178 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
2709089 GGAAATGGCT
2709099 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
2709132 ATCGCAATGCGAAATGAAAATCGCAACGATAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
2709165 ATCGAAACGCGAAA
1 ATCGCAATGCGAAA
2709179 CACAAATCGC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.49, C:0.20, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:2709167 original size:14 final size:14
Alignment explanation
Indices: 2709115--2709173 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
2709105 ATGCGAAATG
*
2709115 AAAATCGCAACGAC
1 AAAATCGCAACGAT
2709129 AAAATCGCAATGCGAAAT
1 AAAATCGCAA--CG--AT
2709147 GAAAATCGCAACGAT
1 -AAAATCGCAACGAT
*
2709162 AAAATCGAAACG
1 AAAATCGCAACG
2709174 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.55
15 2 0.05
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.51, C:0.20, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAT
Found at i:2709186 original size:33 final size:33
Alignment explanation
Indices: 2709107--2709189 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
2709097 CTATCGCAAT
* * *
2709107 GCGAAATGAAAATCGCAACGACAAAATCGCAAT
1 GCGAAATCAAAATCGCAACGACAAAATCGAAAC
* *
2709140 GCGAAATGAAAATCGCAACGATAAAATCGAAAC
1 GCGAAATCAAAATCGCAACGACAAAATCGAAAC
2709173 GCGAAA-CACAAATCGCA
1 GCGAAATCA-AAATCGCA
2709190 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.02
33 44 0.98
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (33 bp):
GCGAAATCAAAATCGCAACGACAAAATCGAAAC
Found at i:2709207 original size:19 final size:19
Alignment explanation
Indices: 2709185--2709281 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
2709175 GAAACACAAA
2709185 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
2709204 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2709220 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
2709237 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
2709253 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
2709270 TCGCATTGCGAT
1 TCGCATTGCGAT
2709282 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 12 0.19
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 23 0.37
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:2709226 original size:14 final size:14
Alignment explanation
Indices: 2709207--2709265 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
2709197 TTTCATTTCG
2709207 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
2709221 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
2709238 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
2709254 CGTTGCGATTTT
1 CGTTGCGATTTT
2709266 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2709232 original size:33 final size:33
Alignment explanation
Indices: 2709190--2709281 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
2709180 ACAAATCGCA
*
2709190 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2709223 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
2709256 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
2709282 AGCCATTTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:2709300 original size:20 final size:19
Alignment explanation
Indices: 2709266--2709320 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
2709256 TTGCGATTTT
*
2709266 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
2709285 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
2709305 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
2709321 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:2709873 original size:18 final size:18
Alignment explanation
Indices: 2709850--2709897 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
2709840 CGGGTCGATC
2709850 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
2709868 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
2709886 AGGTGATGGCTC
1 AGGTGATGGCTC
2709898 CTGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:2711265 original size:20 final size:20
Alignment explanation
Indices: 2711217--2711275 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
2711207 AATAGTTTCT
* *
2711217 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
2711237 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
** *
2711257 GAATTTGACTATCGCAACG
1 GAAAATGACAATCGCAACG
2711276 AGAGAATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.15
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:2711564 original size:22 final size:22
Alignment explanation
Indices: 2711537--2711580 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2711527 GATGGAGATA
2711537 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
2711559 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
2711581 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:2711881 original size:20 final size:20
Alignment explanation
Indices: 2711767--2711880 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
2711757 GATTATATAT
*
2711767 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2711787 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *
2711807 TGTCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
2711827 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
2711848 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
2711868 TATCGCATTGCGA
1 TATCGCGTTGCGA
2711881 TTTTCCAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 59 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:2711884 original size:41 final size:41
Alignment explanation
Indices: 2711747--2711882 Score: 159
Period size: 41 Copynumber: 3.3 Consensus size: 41
2711737 CGCTTTGAAA
* *
2711747 ATCGCATTGCGATTATATATTATCTCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
* * * * *
2711788 ATCGCGTTGCGA--AAGTAAGTGTCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGT
* * *
2711828 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
2711869 ATCGCATTGCGATT
1 ATCGCATTGCGATT
2711883 TTCCAAATTC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.03
40 31 0.40
41 43 0.55
42 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGT
Done.