Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 51
Found at i:5149489 original size:10 final size:10
Alignment explanation
Indices: 5149428--5149495 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
5149418 ATTGGAGTGC
*
5149428 AAAAAGAAAG
1 AAAAAGAAAA
5149438 AAAAAGAAAAA
1 AAAAAG-AAAA
5149449 AAAGAAGAAAA
1 AAA-AAGAAAA
*** *
5149460 CAAAATTCATA
1 -AAAAAGAAAA
*
5149471 AAGAAGAAAA
1 AAAAAGAAAA
5149481 AAAAAGAAAA
1 AAAAAGAAAA
5149491 AAAAA
1 AAAAA
5149496 TTCAAAAAAA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
10 25 0.57
11 13 0.30
12 6 0.14
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:5152416 original size:25 final size:24
Alignment explanation
Indices: 5152388--5152441 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
5152378 CTTTACACAT
*
5152388 ATATATGTT-TATTTCAAATGTTATA
1 ATATATGTTAT-TTTCAAAT-ATATA
*
5152413 ATATA-GTTATTTTCATATATATA
1 ATATATGTTATTTTCAAATATATA
5152436 ATATAT
1 ATATAT
5152442 ATGGTTATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
23 9 0.36
24 10 0.40
25 6 0.24
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATATATGTTATTTTCAAATATATA
Found at i:5157654 original size:167 final size:173
Alignment explanation
Indices: 5157375--5157715 Score: 631
Period size: 167 Copynumber: 2.0 Consensus size: 173
5157365 TGGTGCCAAG
5157375 ATGAACCATAAGAAGACCATTCGGCCAAGAACATTTTCTTTCATCGAAGCATTATGCATTTTTAA
1 ATGAACCATAAGAAGACCATTCGGCCAAGAACATTTTCTTTCATCGAAGCATTATGCATTTTTAA
5157440 TTTAAATCATGTACTTTCCTGAAAAGGCATGTATCTATTCGACCAAGCCTTTACAAATAT-AAAT
66 TTTAAATCATGTACTTTCCTGAAAAGGCATGTATCTATTCGACCAAGCCTTTACAAATATAAAAT
5157504 AGGTATTGGCATTCATTTGTAAA-TCAACCA-TTGATAATATA
131 AGGTATTGGCATTCATTTGTAAACTCAACCATTTGATAATATA
5157545 ATGAACCATAAGAAGACCATTCGGCC-A-AACATTTTCTTTCATCGAAGCATTATGCA-TTTTAA
1 ATGAACCATAAGAAGACCATTCGGCCAAGAACATTTTCTTTCATCGAAGCATTATGCATTTTTAA
*
5157607 TTTAAATCATGTACTTTCCTGAAAAGGCATGTATCTATTCGACCAAGCCTTTACAAATCTAAAAT
66 TTTAAATCATGTACTTTCCTGAAAAGGCATGTATCTATTCGACCAAGCCTTTACAAATATAAAAT
5157672 AGGTATTGGCATTCATTTGTAAACTCAACCATTTGATAATATA
131 AGGTATTGGCATTCATTTGTAAACTCAACCATTTGATAATATA
5157715 A
1 A
5157716 AATCCTTGTG
Statistics
Matches: 167, Mismatches: 1, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
167 65 0.39
168 56 0.34
169 8 0.05
170 38 0.23
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (173 bp):
ATGAACCATAAGAAGACCATTCGGCCAAGAACATTTTCTTTCATCGAAGCATTATGCATTTTTAA
TTTAAATCATGTACTTTCCTGAAAAGGCATGTATCTATTCGACCAAGCCTTTACAAATATAAAAT
AGGTATTGGCATTCATTTGTAAACTCAACCATTTGATAATATA
Found at i:5161378 original size:24 final size:24
Alignment explanation
Indices: 5161349--5161404 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5161339 AAAATTAGCA
*
5161349 AAGAAAAGTCAAGCACTCCAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
** *
5161373 AAGAAATTTCCAGCACTCAAAAAG
1 AAGAAAAGTCAAGCACTCAAAAAG
*
5161397 AAAAAAAG
1 AAGAAAAG
5161405 AAAAGAAAGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.18, G:0.14, T:0.11
Consensus pattern (24 bp):
AAGAAAAGTCAAGCACTCAAAAAG
Found at i:5161404 original size:8 final size:8
Alignment explanation
Indices: 5161391--5161425 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
5161381 TCCAGCACTC
5161391 AAAAAGAA
1 AAAAAGAA
5161399 AAAAAGAA
1 AAAAAGAA
5161407 AAGAAAGAA
1 AA-AAAGAA
*
5161416 ATAAAGAA
1 AAAAAGAA
5161424 AA
1 AA
5161426 GTTGAAAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5161415 original size:17 final size:17
Alignment explanation
Indices: 5161393--5161426 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5161383 CAGCACTCAA
5161393 AAAGAAAAAAAGAAAAG
1 AAAGAAAAAAAGAAAAG
*
5161410 AAAGAAATAAAGAAAAG
1 AAAGAAAAAAAGAAAAG
5161427 TTGAAAGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (17 bp):
AAAGAAAAAAAGAAAAG
Found at i:5163311 original size:60 final size:60
Alignment explanation
Indices: 5163245--5163364 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
5163235 TGTATTCTTT
5163245 TGTAGGTACATGTTCGGCCACATGATGGGAGCTGACTTAAAGCTAGAATTGGAGTCATTG
1 TGTAGGTACATGTTCGGCCACATGATGGGAGCTGACTTAAAGCTAGAATTGGAGTCATTG
5163305 TGTAGGTACATGTTCGGCCACATGATGGGAGCTGACTTAAAGCTAGAATTGGAGTCATTG
1 TGTAGGTACATGTTCGGCCACATGATGGGAGCTGACTTAAAGCTAGAATTGGAGTCATTG
5163365 AGCTAAGGAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.28
Consensus pattern (60 bp):
TGTAGGTACATGTTCGGCCACATGATGGGAGCTGACTTAAAGCTAGAATTGGAGTCATTG
Found at i:5164897 original size:6 final size:6
Alignment explanation
Indices: 5164846--5164899 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
5164836 GTGCTGCAAC
* *
5164846 AAAAGA AACAA-A AAGAGA AAAAGA AAGAAGA AAAACA AAAAG- AAAAGA
1 AAAAGA AA-AAGA AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA
5164894 AAAAGA
1 AAAAGA
5164900 TTCCTACATC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 6 0.15
6 26 0.65
7 8 0.20
ACGTcount: A:0.80, C:0.04, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:5165955 original size:127 final size:126
Alignment explanation
Indices: 5165729--5165982 Score: 483
Period size: 127 Copynumber: 2.0 Consensus size: 126
5165719 AACGATTTAT
5165729 TAATGTTCACTATCACCGGGACTTGTTTCAAAAGTTACAGAATCTTAAACAAGGCCAAAGGAGGT
1 TAATGTTCACTATCACCGGGACTTGTTTCAAAAGTTACAGAATCTTAAACAAGGCCAAAGGAGGT
5165794 GGAGGACTACTACAAAGAAATGGAAAGTCGCAATGATCTGAGTCAACATTGAGGAGGGGTCG
66 GGAGGACTACTACAAAGAAATGGAAAGTCGCAATGATCTGAGTCAACATTGAGGA-GGGTCG
5165856 TAATGTTCACTATCACCGGGACTTGTTTCAAAAGTTACAGAATCTTAAACAAGGCCAAAGGAGTG
1 TAATGTTCACTATCACCGGGACTTGTTTCAAAAGTTACAGAATCTTAAACAAGGCCAAAGGAG-G
5165921 TGGAGGACTACTACAAAGAAATGG-AAGTCGCAATGATCTGAGTCAACATTGAGGAGGGTCG
65 TGGAGGACTACTACAAAGAAATGGAAAGTCGCAATGATCTGAGTCAACATTGAGGAGGGTCG
5165982 T
1 T
5165983 GAAGCAACTA
Statistics
Matches: 126, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
126 7 0.06
127 94 0.75
128 25 0.20
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (126 bp):
TAATGTTCACTATCACCGGGACTTGTTTCAAAAGTTACAGAATCTTAAACAAGGCCAAAGGAGGT
GGAGGACTACTACAAAGAAATGGAAAGTCGCAATGATCTGAGTCAACATTGAGGAGGGTCG
Found at i:5172619 original size:17 final size:18
Alignment explanation
Indices: 5172597--5172636 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
5172587 ATTCCACATC
*
5172597 TATTTCTTTTC-TATCTT
1 TATTTCATTTCTTATCTT
*
5172614 TATTTCATTTCTTATTTT
1 TATTTCATTTCTTATCTT
5172632 TATTT
1 TATTT
5172637 AATCATTACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTTCATTTCTTATCTT
Found at i:5186350 original size:38 final size:38
Alignment explanation
Indices: 5186279--5186389 Score: 161
Period size: 38 Copynumber: 2.9 Consensus size: 38
5186269 TGACTTTTAT
* *
5186279 CGACTTATCAAGTAA-TTCATTTACTTGTGGCGTCAAACA
1 CGACTTATCAAGTAACTT--GTTACTTGTCGCGTCAAACA
* *
5186318 TGACTTATCAAGTAACTTGTTACTTGTCGCGTCAAACC
1 CGACTTATCAAGTAACTTGTTACTTGTCGCGTCAAACA
5186356 CGACTTATCAAGTAACTTGTTACTTGTCGCGTCA
1 CGACTTATCAAGTAACTTGTTACTTGTCGCGTCA
5186390 TTTCTTTTCA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
38 50 0.76
39 14 0.21
40 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (38 bp):
CGACTTATCAAGTAACTTGTTACTTGTCGCGTCAAACA
Found at i:5190886 original size:44 final size:45
Alignment explanation
Indices: 5190763--5190888 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
5190753 TATAAAATCC
*
5190763 CTTACCATTTATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
5190808 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTACCCATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* * *
5190855 CTTTCCA-TTATTCCAAAAGCTCGTAATCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
5190889 ATATGCTTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
44 23 0.32
45 10 0.14
46 2 0.03
47 38 0.52
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:5191089 original size:59 final size:59
Alignment explanation
Indices: 5190997--5191125 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 59
5190987 CATAGTGTTA
* * **
5190997 TCCCGAATATGACACATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
* ** *
5191056 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
5191115 TCCCGAATATG
1 TCCCGAATATG
5191126 CAGCCTGCGG
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.28
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCCTTAAGTACAG
Found at i:5197336 original size:22 final size:25
Alignment explanation
Indices: 5197309--5197361 Score: 76
Period size: 22 Copynumber: 2.2 Consensus size: 25
5197299 AAAATCAGCA
*
5197309 AAGAAATTG-AAGTACTC-AAAA-G
1 AAGAAATTGAAAGAACTCAAAAAGG
5197331 AAGAAATTGAAAGAACTCAAAAAGG
1 AAGAAATTGAAAGAACTCAAAAAGG
5197356 AAGAAA
1 AAGAAA
5197362 AAGAAAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.33
23 7 0.26
24 4 0.15
25 7 0.26
ACGTcount: A:0.60, C:0.08, G:0.19, T:0.13
Consensus pattern (25 bp):
AAGAAATTGAAAGAACTCAAAAAGG
Found at i:5197367 original size:25 final size:23
Alignment explanation
Indices: 5197322--5197367 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
5197312 AAATTGAAGT
**
5197322 ACTCAAAAGAAGAAATTGAAAGA
1 ACTCAAAAGAAGAAAAAGAAAGA
5197345 ACTCAAAAAGGAAGAAAAAGAAA
1 ACTC-AAAA-GAAGAAAAAGAAA
5197368 AGAAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 4 0.21
25 11 0.58
ACGTcount: A:0.65, C:0.09, G:0.17, T:0.09
Consensus pattern (23 bp):
ACTCAAAAGAAGAAAAAGAAAGA
Found at i:5198566 original size:30 final size:30
Alignment explanation
Indices: 5198530--5198588 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
5198520 CTACTATTTC
* * *
5198530 TTTTTTCATGCAGGATATTCAAGAGACATA
1 TTTTTTCAAGCAGGAGATTCAAGAAACATA
*
5198560 TTTTTTCAAGCTGGAGATTCAAGAAACAT
1 TTTTTTCAAGCAGGAGATTCAAGAAACAT
5198589 GTCTTTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (30 bp):
TTTTTTCAAGCAGGAGATTCAAGAAACATA
Found at i:5200522 original size:19 final size:18
Alignment explanation
Indices: 5200494--5200529 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
5200484 CATTCAGCCA
5200494 AGAGCATGTATTTTCATT
1 AGAGCATGTATTTTCATT
5200512 AGAGTCATGTATTTTCAT
1 AGAG-CATGTATTTTCAT
5200530 AAAAAAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (18 bp):
AGAGCATGTATTTTCATT
Found at i:5200850 original size:14 final size:14
Alignment explanation
Indices: 5200831--5200858 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5200821 TTCTAGTTCC
5200831 TAGTTCTTATAACT
1 TAGTTCTTATAACT
5200845 TAGTTCTTATAACT
1 TAGTTCTTATAACT
5200859 AGTGGGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.14, G:0.07, T:0.50
Consensus pattern (14 bp):
TAGTTCTTATAACT
Found at i:5202808 original size:24 final size:25
Alignment explanation
Indices: 5202781--5202829 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
5202771 GCCTATTTTT
* * *
5202781 GACGAGGAACCTGAA-ACAATACAA
1 GACGAAGAAACTGAAGAAAATACAA
5202805 GACGAAGAAACTGAAGAAAATACAA
1 GACGAAGAAACTGAAGAAAATACAA
5202830 ACCATGGCGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.55, C:0.16, G:0.20, T:0.08
Consensus pattern (25 bp):
GACGAAGAAACTGAAGAAAATACAA
Found at i:5209523 original size:59 final size:58
Alignment explanation
Indices: 5209463--5209705 Score: 162
Period size: 58 Copynumber: 4.2 Consensus size: 58
5209453 TTGTTACCAT
* * * *
5209463 TTTAGCACATAATATACCCTATCTGGAAATCCATATTTTCAATAAGATTTCCTTATCA
1 TTTAGCACATAATATGCCATATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
* ** * * * *
5209521 TTTAGCACCCT--TAGTGCTTTACCTGGAAA-CCAATACA-CTCAGTATGATTCCCTTA-CAA
1 TTTAGCA-CATAATA-TGCCATATCTGGAAATCC-ATA-ATTTCAATATGATTTCCTTATC-A
* *
5209579 TTTTAGCACATAATATGCCATATTTGGAAATCCATAATTTCAATATGATTTCCTTATTA
1 -TTTAGCACATAATATGCCATATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
* ** * *
5209638 TTTAGCACACTCA-GGGCTCCATA--TGGAAATCCATACA-CTCAGTATGATTTCCTTATCA
1 TTTAGCACA-TAATATG--CCATATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCA
5209696 TTCTAGCACA
1 TT-TAGCACA
5209706 CAAAGTTCCA
Statistics
Matches: 144, Mismatches: 25, Indels: 31
0.72 0.12 0.16
Matches are distributed among these distances:
57 5 0.03
58 81 0.56
59 49 0.34
60 9 0.06
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (58 bp):
TTTAGCACATAATATGCCATATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
Found at i:5209613 original size:117 final size:116
Alignment explanation
Indices: 5209460--5209705 Score: 323
Period size: 117 Copynumber: 2.1 Consensus size: 116
5209450 ATTTTGTTAC
* *
5209460 CATTTTAGCACATAATATACCCTATCTGGAAATCCATATTTTCAATAAGATTTCCTTATCATTTA
1 CATTTTAGCACATAATATACCATATCTGGAAATCCATAATTTCAATAAGATTTCCTTATCATTTA
* * * ** *
5209525 GCACCCTTAGTGCTTTACCTGGAAA-CCAATACACTCAGTATGATTCCCTTA
66 GCACACTCAGGGCTCCACATGGAAATCC-ATACACTCAGTATGATTCCCTTA
* * * *
5209576 CAATTTTAGCACATAATATGCCATATTTGGAAATCCATAATTTCAATATGATTTCCTTATTATTT
1 C-ATTTTAGCACATAATATACCATATCTGGAAATCCATAATTTCAATAAGATTTCCTTATCATTT
* *
5209641 AGCACACTCAGGGCTCCATATGGAAATCCATACACTCAGTATGATTTCCTTA
65 AGCACACTCAGGGCTCCACATGGAAATCCATACACTCAGTATGATTCCCTTA
*
5209693 TCATTCTAGCACA
1 -CATTTTAGCACA
5209706 CAAAGTTCCA
Statistics
Matches: 112, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
116 1 0.01
117 108 0.96
118 3 0.03
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (116 bp):
CATTTTAGCACATAATATACCATATCTGGAAATCCATAATTTCAATAAGATTTCCTTATCATTTA
GCACACTCAGGGCTCCACATGGAAATCCATACACTCAGTATGATTCCCTTA
Found at i:5219110 original size:42 final size:42
Alignment explanation
Indices: 5219064--5219199 Score: 263
Period size: 42 Copynumber: 3.2 Consensus size: 42
5219054 AAAAGGATTT
5219064 AAAGAAGTATTTGTATATGGAACAATGTTATGGTGATGGAAG
1 AAAGAAGTATTTGTATATGGAACAATGTTATGGTGATGGAAG
*
5219106 AAAGAAGTATTTGTATATGGAACAATGTTATGGTGATCGAAG
1 AAAGAAGTATTTGTATATGGAACAATGTTATGGTGATGGAAG
5219148 AAAGAAGTATTTGTATATGGAACAATGTTATGGTGATGGAAG
1 AAAGAAGTATTTGTATATGGAACAATGTTATGGTGATGGAAG
5219190 AAAGAAGTAT
1 AAAGAAGTAT
5219200 GGAAATGGTA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 92 1.00
ACGTcount: A:0.40, C:0.03, G:0.27, T:0.30
Consensus pattern (42 bp):
AAAGAAGTATTTGTATATGGAACAATGTTATGGTGATGGAAG
Found at i:5224831 original size:24 final size:24
Alignment explanation
Indices: 5224804--5224855 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
5224794 CAGTTCGTAT
*
5224804 AAATTACACCAAAGTGCCACATGG
1 AAATTACACCAAAGTGCCACATAG
* ** *
5224828 AAATTGCATTAAAGTGCCATATAG
1 AAATTACACCAAAGTGCCACATAG
5224852 AAAT
1 AAAT
5224856 GTCTCGAAGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.23
Consensus pattern (24 bp):
AAATTACACCAAAGTGCCACATAG
Found at i:5224910 original size:23 final size:23
Alignment explanation
Indices: 5224860--5224942 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
5224850 AGAAATGTCT
* * *
5224860 CGAAGAACCACATAGTATTATCC
1 CGAAGGACCGCATAGAATTATCC
* *
5224883 TGAAGGACCGCATAGAATTGTCC
1 CGAAGGACCGCATAGAATTATCC
* * *
5224906 CGAAGGACAGCGTAGAATTATCT
1 CGAAGGACCGCATAGAATTATCC
*
5224929 CGAAAGACCGCATA
1 CGAAGGACCGCATA
5224943 CAACCCTCGA
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.22, T:0.19
Consensus pattern (23 bp):
CGAAGGACCGCATAGAATTATCC
Found at i:5226005 original size:58 final size:58
Alignment explanation
Indices: 5225938--5226150 Score: 207
Period size: 58 Copynumber: 3.7 Consensus size: 58
5225928 ATAATATACC
*** *
5225938 CTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCACTTAGCACCCTTAGTGCT
1 CTATCTGGAAATCCATACACTCAATATGATTTCCTTATCAATTAGCACCCTTAGTGCT
* * * * * * * *
5225996 TTATCTGGAAACCCATACACTCAGTATGATTCCCTTACCATTTTAGCA-CATAATA-TGCC
1 CTATCTGGAAATCCATACACTCAATATGATTTCCTTATCA-ATTAGCACCCT--TAGTGCT
* * *
5226055 CTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCAATTAGCACACTCAGTGCT
1 CTATCTGGAAATCCATACA-CTCAATATGATTTCCTTATCAATTAGCACCCTTAGTGCT
* * *
5226113 CCATATGGAAATCCATACACTCAGTATGATTTCCTTAT
1 CTATCTGGAAATCCATACACTCAATATGATTTCCTTAT
5226151 TATTCTAGTA
Statistics
Matches: 122, Mismatches: 26, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
57 1 0.01
58 76 0.62
59 43 0.35
60 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (58 bp):
CTATCTGGAAATCCATACACTCAATATGATTTCCTTATCAATTAGCACCCTTAGTGCT
Found at i:5226057 original size:117 final size:117
Alignment explanation
Indices: 5225913--5226149 Score: 375
Period size: 117 Copynumber: 2.0 Consensus size: 117
5225903 GTATGTTTTG
* *
5225913 TTACCATTTTAGTACATAATATACCCTATCTGGAAATCCATATTTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATACCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
* * * ** *
5225978 CTTAGCACCCTTAGTGCTTTATCTGGAAACCCATACACTCAGTATGATTCCC
66 ATTAGCACACTCAGTGCTCCATATGGAAACCCATACACTCAGTATGATTCCC
*
5226030 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATACCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
* *
5226095 ATTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGATTTCC
66 ATTAGCACACTCAGTGCTCCATATGGAAACCCATACACTCAGTATGATTCCC
5226147 TTA
1 TTA
5226150 TTATTCTAGT
Statistics
Matches: 109, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
117 109 1.00
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (117 bp):
TTACCATTTTAGCACATAATATACCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
ATTAGCACACTCAGTGCTCCATATGGAAACCCATACACTCAGTATGATTCCC
Found at i:5226065 original size:59 final size:58
Alignment explanation
Indices: 5225913--5226149 Score: 196
Period size: 58 Copynumber: 4.1 Consensus size: 58
5225903 GTATGTTTTG
* * ***
5225913 TTACCATTTTAGTACATAATATACCCTATCTGGAAATCCATATTTTCAATATGATTTCC
1 TTACCA-TTTAGCACATAATATGCCCTATCTGGAAATCCATACACTCAATATGATTTCC
* * * ** * * *
5225972 TTATCACTTAGCACCCT--TAGTGCTTTATCTGGAAACCCATACACTCAGTATGATTCCC
1 TTACCATTTAGCA-CATAATA-TGCCCTATCTGGAAATCCATACACTCAATATGATTTCC
*
5226030 TTACCATTTTAGCACATAATATGCCCTATCTGGAAATCCATA-ATTTCAATATGATTTCC
1 TTACCA-TTTAGCACATAATATGCCCTATCTGGAAATCCATACA-CTCAATATGATTTCC
* * * * * *
5226089 TTATCAATTAGCACACTCA-GTGCTCC-ATATGGAAATCCATACACTCAGTATGATTTCC
1 TTACCATTTAGCACA-TAATATGC-CCTATCTGGAAATCCATACACTCAATATGATTTCC
5226147 TTA
1 TTA
5226150 TTATTCTAGT
Statistics
Matches: 140, Mismatches: 29, Indels: 19
0.74 0.15 0.10
Matches are distributed among these distances:
57 2 0.01
58 83 0.59
59 53 0.38
60 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (58 bp):
TTACCATTTAGCACATAATATGCCCTATCTGGAAATCCATACACTCAATATGATTTCC
Found at i:5232254 original size:7 final size:7
Alignment explanation
Indices: 5232242--5232279 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
5232232 TTTTTTAAAA
5232242 TGAATAG
1 TGAATAG
5232249 TGAATAG
1 TGAATAG
*
5232256 TGAATAA
1 TGAATAG
5232263 TGAATAG
1 TGAATAG
*
5232270 TAAATAG
1 TGAATAG
5232277 TGA
1 TGA
5232280 TTGTACCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.24, T:0.29
Consensus pattern (7 bp):
TGAATAG
Found at i:5232266 original size:21 final size:21
Alignment explanation
Indices: 5232240--5232279 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5232230 TATTTTTTAA
*
5232240 AATGAATAGTGAATAGTGAAT
1 AATGAATAGTAAATAGTGAAT
5232261 AATGAATAGTAAATAGTGA
1 AATGAATAGTAAATAGTGA
5232280 TTGTACCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.28
Consensus pattern (21 bp):
AATGAATAGTAAATAGTGAAT
Found at i:5232597 original size:23 final size:23
Alignment explanation
Indices: 5232558--5232618 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
5232548 TATTATCCTA
* * * *
5232558 AAAGACCGCGTAAAATTGTCTCG
1 AAAGACAGCGTAGAATTATCACG
*
5232581 AAGGACAGCGTAGAATTATCACG
1 AAAGACAGCGTAGAATTATCACG
*
5232604 AAAGACCGCGTAGAA
1 AAAGACAGCGTAGAA
5232619 CCCTCGACTA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (23 bp):
AAAGACAGCGTAGAATTATCACG
Found at i:5233656 original size:58 final size:58
Alignment explanation
Indices: 5233568--5233791 Score: 229
Period size: 58 Copynumber: 3.8 Consensus size: 58
5233558 ATAATATGCC
* *** *
5233568 CTATATGGAAATCCATATTTTCAATATGATTTCCTTATCATTTAGCACCCTTAGTGCT
1 CTATCTGGAAATCCATACACTCAATATGATTTCCTTATCATTTAGCACCCTAAGTGCT
* * * * * * *
5233626 TTATCTGGAAA-CCAATACACTCAGTATGATTCCCTTACCATTTTAGCA-CATAATTTGCC
1 CTATCTGGAAATCC-ATACACTCAATATGATTTCCTTATCA-TTTAGCACCCTAA-GTGCT
* * *
5233685 CTATCTGGAAATCCATA-ATTTCAATATGATTTCCTTATCATTTAGCACACTCAGTGCT
1 CTATCTGGAAATCCATACA-CTCAATATGATTTCCTTATCATTTAGCACCCTAAGTGCT
* *
5233743 CCATATGGAAATCCATACACTCAATATGATTTCCTTATCATTCTAGCAC
1 CTATCTGGAAATCCATACACTCAATATGATTTCCTTATCATT-TAGCAC
5233792 AAAAAGTACC
Statistics
Matches: 133, Mismatches: 25, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
57 2 0.02
58 80 0.60
59 49 0.37
60 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.37
Consensus pattern (58 bp):
CTATCTGGAAATCCATACACTCAATATGATTTCCTTATCATTTAGCACCCTAAGTGCT
Found at i:5233665 original size:117 final size:117
Alignment explanation
Indices: 5233543--5233792 Score: 360
Period size: 117 Copynumber: 2.1 Consensus size: 117
5233533 TATGATTTTG
*
5233543 TTACCATTTTA-CGACATAATATGCCCTATATGGAAATCCATATTTTCAATATGATTTCCTTATC
1 TTACCATTTTAGC-ACATAATATGCCCTATATGGAAATCCATAATTTCAATATGATTTCCTTATC
* * ** * *
5233607 ATTTAGCACCCTTAGTGCTTTATCTGGAAA-CCAATACACTCAGTATGATTCCC
65 ATTTAGCACACTCAGTGCTCCATATGGAAATCC-ATACACTCAATATGATTCCC
* *
5233660 TTACCATTTTAGCACATAATTTGCCCTATCTGGAAATCCATAATTTCAATATGATTTCCTTATCA
1 TTACCATTTTAGCACATAATATGCCCTATATGGAAATCCATAATTTCAATATGATTTCCTTATCA
*
5233725 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAATATGATTTCC
66 TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAATATGATTCCC
* *
5233777 TTATCATTCTAGCACA
1 TTACCATTTTAGCACA
5233793 AAAAGTACCA
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
117 116 0.97
118 3 0.03
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (117 bp):
TTACCATTTTAGCACATAATATGCCCTATATGGAAATCCATAATTTCAATATGATTTCCTTATCA
TTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAATATGATTCCC
Found at i:5236043 original size:30 final size:28
Alignment explanation
Indices: 5235985--5236043 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 28
5235975 ATCATATTAG
5235985 GGATTTATTGAAAAGATTTAAAAAATGA
1 GGATTTATTGAAAAGATTTAAAAAATGA
*
5236013 GGATTTATTTGAATAA-ATGTTAAAAGATGA
1 GGATTTA-TTGAA-AAGAT-TTAAAAAATGA
5236043 G
1 G
5236044 AAAATGATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
28 7 0.26
29 7 0.26
30 13 0.48
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (28 bp):
GGATTTATTGAAAAGATTTAAAAAATGA
Found at i:5240413 original size:17 final size:18
Alignment explanation
Indices: 5240388--5240423 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
5240378 TTAGTAATAA
5240388 AAAATAACCTCACAAAAC
1 AAAATAACCTCACAAAAC
*
5240406 AAAA-AACCTCACCAAAC
1 AAAATAACCTCACAAAAC
5240423 A
1 A
5240424 CTCCAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.61, C:0.31, G:0.00, T:0.08
Consensus pattern (18 bp):
AAAATAACCTCACAAAAC
Found at i:5243136 original size:19 final size:20
Alignment explanation
Indices: 5243098--5243140 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
5243088 AAAACCCCTT
5243098 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
5243118 TGAAAATACATTA-TTTTAA
1 TGAAAATACATGATTTTTAA
5243137 TGAA
1 TGAA
5243141 GATATATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:5246462 original size:35 final size:35
Alignment explanation
Indices: 5246421--5246501 Score: 108
Period size: 35 Copynumber: 2.3 Consensus size: 35
5246411 TACTATATGT
*
5246421 TCATCACTATCTTCCATCACTATTGCACGCCTATA
1 TCATCACTATCTTCCATCACCATTGCACGCCTATA
* * *
5246456 TCATCACTATCTTCTATCCCCATTTCACGCCTATA
1 TCATCACTATCTTCCATCACCATTGCACGCCTATA
* *
5246491 TAATCATTATC
1 TCATCACTATC
5246502 CCATTACCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (35 bp):
TCATCACTATCTTCCATCACCATTGCACGCCTATA
Found at i:5246966 original size:15 final size:16
Alignment explanation
Indices: 5246946--5246983 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
5246936 TTTGGAGTAC
5246946 AAAAGAAAG-AAAAGA
1 AAAAGAAAGAAAAAGA
5246961 AAAAG-AAGAAAAAGA
1 AAAAGAAAGAAAAAGA
5246976 AAAAGAAA
1 AAAAGAAA
5246984 AGTGAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 16 0.76
16 2 0.10
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAAAGA
Found at i:5247142 original size:15 final size:15
Alignment explanation
Indices: 5247112--5247169 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
5247102 GAGTTGTAAG
5247112 TTATCTTCACTTTCTTA
1 TTAT-TTCA-TTTCTTA
*
5247129 CTATTTCATTTCTTTA
1 TTATTTCATTTC-TTA
*
5247145 TTCTTTCATATT-TTA
1 TTATTTCAT-TTCTTA
5247160 TTATTTCATT
1 TTATTTCATT
5247170 ACCATATCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 1 0.03
15 15 0.43
16 14 0.40
17 5 0.14
ACGTcount: A:0.19, C:0.17, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATTTCATTTCTTA
Found at i:5251817 original size:20 final size:20
Alignment explanation
Indices: 5251789--5251843 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
5251779 CATCCAAGCA
*
5251789 TCATCTATTTTCATTTTAAG
1 TCATGTATTTTCATTTTAAG
5251809 TCATGTATTTTCATTTTAAG
1 TCATGTATTTTCATTTTAAG
5251829 TCATGTATTTTCATT
1 TCATGTATTTTCATT
5251844 AAAAAGATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (20 bp):
TCATGTATTTTCATTTTAAG
Found at i:5252374 original size:23 final size:23
Alignment explanation
Indices: 5252347--5252398 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
5252337 AGGTGAGCTA
5252347 TAGCTTGATGAACTCAAGCTAGT
1 TAGCTTGATGAACTCAAGCTAGT
5252370 TAGCTTGATGAACTCAAGCTAGT
1 TAGCTTGATGAACTCAAGCTAGT
5252393 TAGCTT
1 TAGCTT
5252399 TGGTCTTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (23 bp):
TAGCTTGATGAACTCAAGCTAGT
Found at i:5259293 original size:18 final size:18
Alignment explanation
Indices: 5259270--5259306 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5259260 CTTGTTAACA
*
5259270 TGTAAATGGTAAAGTATG
1 TGTAAATGGTAAAGAATG
5259288 TGTAAATGGTAAAGAATG
1 TGTAAATGGTAAAGAATG
5259306 T
1 T
5259307 CTTGTAGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (18 bp):
TGTAAATGGTAAAGAATG
Found at i:5259838 original size:14 final size:11
Alignment explanation
Indices: 5259808--5259837 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5259798 ATAGTATCTT
5259808 AAAGAAGACTC
1 AAAGAAGACTC
5259819 AAAGAAGACTC
1 AAAGAAGACTC
5259830 AAAGAAGA
1 AAAGAAGA
5259838 ACCAATGCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.60, C:0.13, G:0.20, T:0.07
Consensus pattern (11 bp):
AAAGAAGACTC
Found at i:5268283 original size:24 final size:24
Alignment explanation
Indices: 5268256--5268303 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5268246 ATGTCAACGA
5268256 ACACAACTCTTGGAACTTAAAGTG
1 ACACAACTCTTGGAACTTAAAGTG
** * *
5268280 ACACTTCTTTTGGAACTTTAAGTG
1 ACACAACTCTTGGAACTTAAAGTG
5268304 GCATAATTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (24 bp):
ACACAACTCTTGGAACTTAAAGTG
Found at i:5276918 original size:5 final size:5
Alignment explanation
Indices: 5276903--5276940 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
5276893 GTGCTTCAAT
5276903 TTTTC -TTTC TTTTC TTTTC TTTTC TTTT- TTTTCC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT-C TTTT
5276941 TGAGTGCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.27
5 18 0.60
6 4 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:5276941 original size:10 final size:9
Alignment explanation
Indices: 5276902--5276941 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
5276892 AGTGCTTCAA
5276902 TTTTTCTTT
1 TTTTTCTTT
*
5276911 CTTTTCTTT
1 TTTTTCTTT
5276920 TCTTTTCTTT
1 T-TTTTCTTT
*
5276930 TTTTTCCTT
1 TTTTTCTTT
5276939 TTT
1 TTT
5276942 GAGTGCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:5276974 original size:22 final size:23
Alignment explanation
Indices: 5276938--5276981 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
5276928 TTTTTTTCCT
5276938 TTTTGAGTGCTTTCAATTTCTTC
1 TTTTGAGTGCTTTCAATTTCTTC
5276961 TTTTGAGTGC-TTCAATTTCTT
1 TTTTGAGTGCTTTCAATTTCTT
5276982 TGCTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.14, C:0.16, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTTGAGTGCTTTCAATTTCTTC
Found at i:5282123 original size:23 final size:24
Alignment explanation
Indices: 5282078--5282127 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
5282068 TTGTTTTTTC
*
5282078 TTCTTTTTGAGTGCTTTTAATTTA
1 TTCTTTTTAAGTGCTTTTAATTTA
* * *
5282102 TTCTTTTTAAGTTCTTTGATTTTA
1 TTCTTTTTAAGTGCTTTTAATTTA
5282126 TT
1 TT
5282128 TGCTATATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.16, C:0.08, G:0.10, T:0.66
Consensus pattern (24 bp):
TTCTTTTTAAGTGCTTTTAATTTA
Found at i:5282944 original size:21 final size:21
Alignment explanation
Indices: 5282920--5282973 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 21
5282910 GTCTCCTTCA
*
5282920 AGCTAGCTTGAGTGTGGAGCT
1 AGCTAGCATGAGTGTGGAGCT
5282941 AGCTAGCAAGCATGAGTGTGGAGCT
1 AGCT----AGCATGAGTGTGGAGCT
5282966 AGCTAGCA
1 AGCTAGCA
5282974 AGCATAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
21 8 0.29
25 20 0.71
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.22
Consensus pattern (21 bp):
AGCTAGCATGAGTGTGGAGCT
Found at i:5282956 original size:25 final size:25
Alignment explanation
Indices: 5282928--5282978 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
5282918 CAAGCTAGCT
5282928 TGAGTGTGGAGCTAGCTAGCAAGCA
1 TGAGTGTGGAGCTAGCTAGCAAGCA
5282953 TGAGTGTGGAGCTAGCTAGCAAGCA
1 TGAGTGTGGAGCTAGCTAGCAAGCA
5282978 T
1 T
5282979 AGGGTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (25 bp):
TGAGTGTGGAGCTAGCTAGCAAGCA
Found at i:5285781 original size:23 final size:23
Alignment explanation
Indices: 5285741--5285793 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5285731 TTCTTTTCTT
*
5285741 TTTCTTCTTTTTGAGTGCTTTTAA
1 TTTCTTCTTTTT-AGTGCTTTGAA
*
5285765 TTTCTTC-TTTTATGTGCTTTGAT
1 TTTCTTCTTTTTA-GTGCTTTGAA
5285788 TTTCTT
1 TTTCTT
5285794 TGCTAGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 18 0.69
24 7 0.27
ACGTcount: A:0.09, C:0.13, G:0.11, T:0.66
Consensus pattern (23 bp):
TTTCTTCTTTTTAGTGCTTTGAA
Found at i:5286802 original size:51 final size:50
Alignment explanation
Indices: 5286744--5286839 Score: 147
Period size: 51 Copynumber: 1.9 Consensus size: 50
5286734 AGCTTCAGCT
* *
5286744 TGGAGCTAGCTAGCCAGCATGAGTGCGAAAGCTAGGTAGCAAGCATGAGTG
1 TGGAGCTAGCTAGCAAGCATGAGTGCG-AAGCTAGCTAGCAAGCATGAGTG
* *
5286795 TGGAGCTAGCTAGCAAGCATGAGTGTGGAGCTAGCTAGCAAGCAT
1 TGGAGCTAGCTAGCAAGCATGAGTGCGAAGCTAGCTAGCAAGCAT
5286840 AGGGTTGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
50 16 0.39
51 25 0.61
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (50 bp):
TGGAGCTAGCTAGCAAGCATGAGTGCGAAGCTAGCTAGCAAGCATGAGTG
Found at i:5286808 original size:25 final size:25
Alignment explanation
Indices: 5286744--5286839 Score: 147
Period size: 25 Copynumber: 3.8 Consensus size: 25
5286734 AGCTTCAGCT
*
5286744 TGGAGCTAGCTAGCCAGCATGAGTG
1 TGGAGCTAGCTAGCAAGCATGAGTG
* * *
5286769 CGAAAGCTAGGTAGCAAGCATGAGTG
1 TG-GAGCTAGCTAGCAAGCATGAGTG
5286795 TGGAGCTAGCTAGCAAGCATGAGTG
1 TGGAGCTAGCTAGCAAGCATGAGTG
5286820 TGGAGCTAGCTAGCAAGCAT
1 TGGAGCTAGCTAGCAAGCAT
5286840 AGGGTTGTTT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
25 42 0.67
26 21 0.33
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (25 bp):
TGGAGCTAGCTAGCAAGCATGAGTG
Found at i:5287803 original size:160 final size:160
Alignment explanation
Indices: 5287626--5287944 Score: 638
Period size: 160 Copynumber: 2.0 Consensus size: 160
5287616 TGATAGAATA
5287626 GAATGTATAAATGATATAATATAAGATAAGGTAAGAAAGTACTCCCTTAGAATTAGCTTTGAATA
1 GAATGTATAAATGATATAATATAAGATAAGGTAAGAAAGTACTCCCTTAGAATTAGCTTTGAATA
5287691 ACATTCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCTTGTCATCTTCCCCT
66 ACATTCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCTTGTCATCTTCCCCT
5287756 TCTTTTAGGTGATTTGTCTTCAAATCAATT
131 TCTTTTAGGTGATTTGTCTTCAAATCAATT
5287786 GAATGTATAAATGATATAATATAAGATAAGGTAAGAAAGTACTCCCTTAGAATTAGCTTTGAATA
1 GAATGTATAAATGATATAATATAAGATAAGGTAAGAAAGTACTCCCTTAGAATTAGCTTTGAATA
5287851 ACATTCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCTTGTCATCTTCCCCT
66 ACATTCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCTTGTCATCTTCCCCT
5287916 TCTTTTAGGTGATTTGTCTTCAAATCAAT
131 TCTTTTAGGTGATTTGTCTTCAAATCAAT
5287945 GTAGTTTTTC
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 159 1.00
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (160 bp):
GAATGTATAAATGATATAATATAAGATAAGGTAAGAAAGTACTCCCTTAGAATTAGCTTTGAATA
ACATTCATGGTGTGTTCAAGTCATGGAGAAAGTTGGAGCTTGTTTGGATCTTGTCATCTTCCCCT
TCTTTTAGGTGATTTGTCTTCAAATCAATT
Found at i:5295883 original size:15 final size:14
Alignment explanation
Indices: 5295856--5295887 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
5295846 GATAACATAG
5295856 ATATATTCATCTAT
1 ATATATTCATCTAT
5295870 ATATATTACATCTAT
1 ATATATT-CATCTAT
5295885 ATA
1 ATA
5295888 GATATATTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (14 bp):
ATATATTCATCTAT
Found at i:5295894 original size:19 final size:18
Alignment explanation
Indices: 5295852--5295902 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 18
5295842 TTATGATAAC
5295852 ATAGATATATT-CATC-T
1 ATAGATATATTACATCTT
5295868 AT--ATATATTACATCTAT
1 ATAGATATATTACATCT-T
5295885 ATAGATATATTACATCTT
1 ATAGATATATTACATCTT
5295903 GTTTATGAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
14 7 0.23
15 4 0.13
16 2 0.07
17 3 0.10
18 1 0.03
19 13 0.43
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.45
Consensus pattern (18 bp):
ATAGATATATTACATCTT
Found at i:5296064 original size:23 final size:23
Alignment explanation
Indices: 5296034--5296089 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
5296024 AGGTGCTGGA
5296034 AACAAGATAAGAAATAAGTTTAG
1 AACAAGATAAGAAATAAGTTTAG
5296057 AACAAGATAAGAAATAAGTTTAG
1 AACAAGATAAGAAATAAGTTTAG
5296080 AACAAGATAA
1 AACAAGATAA
5296090 ACAAAAGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.59, C:0.05, G:0.16, T:0.20
Consensus pattern (23 bp):
AACAAGATAAGAAATAAGTTTAG
Found at i:5301121 original size:23 final size:25
Alignment explanation
Indices: 5301091--5301144 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
5301081 AATTTTGTAA
* * *
5301091 CTTTTTTTTG-CTTTTTGTT-TTTT
1 CTTTTTTTGGCCTTTTTCTTCTCTT
5301114 CTTTTTTTGGCCTTTTTCTTCTCTT
1 CTTTTTTTGGCCTTTTTCTTCTCTT
5301139 CTTTTT
1 CTTTTT
5301145 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 9 0.35
24 8 0.31
25 9 0.35
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (25 bp):
CTTTTTTTGGCCTTTTTCTTCTCTT
Found at i:5302074 original size:12 final size:12
Alignment explanation
Indices: 5302057--5302096 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5302047 TTAGGTGATG
*
5302057 GAAACAAGGTAA
1 GAAACAAGATAA
5302069 GAAACAAGATAA
1 GAAACAAGATAA
5302081 -AAACAAGATAAA
1 GAAACAAGAT-AA
5302093 GAAA
1 GAAA
5302097 AGATAAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 9 0.36
12 13 0.52
13 3 0.12
ACGTcount: A:0.68, C:0.07, G:0.17, T:0.07
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:5302086 original size:11 final size:11
Alignment explanation
Indices: 5302058--5302103 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
5302048 TAGGTGATGG
*
5302058 AAACAAGGTAA
1 AAACAAGATAA
5302069 GAAACAAGATAA
1 -AAACAAGATAA
5302081 AAACAAGATAA
1 AAACAAGATAA
5302092 AGAA-AAGATAA
1 A-AACAAGATAA
5302103 A
1 A
5302104 GGAATTGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 20 0.62
12 12 0.38
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.09
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:5302662 original size:34 final size:35
Alignment explanation
Indices: 5302615--5302705 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 35
5302605 TTATAAGTTG
*
5302615 GGTGATAATATAGGCGTGATA-CCAGATGGAATAT
1 GGTGATGATATAGGCGTGATATCCAGATGGAATAT
*** *
5302649 GGTG-TGATGATAGGCGTGATAATGGTGATGGACTAT
1 GGTGATGAT-ATAGGCGTGAT-ATCCAGATGGAATAT
5302685 GGTGATGATATAGGCGTGATA
1 GGTGATGATATAGGCGTGATA
5302706 ATGGTGATGG
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
33 3 0.06
34 15 0.31
35 2 0.04
36 24 0.50
37 4 0.08
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.29
Consensus pattern (35 bp):
GGTGATGATATAGGCGTGATATCCAGATGGAATAT
Found at i:5302717 original size:36 final size:36
Alignment explanation
Indices: 5302639--5302717 Score: 133
Period size: 36 Copynumber: 2.2 Consensus size: 36
5302629 CGTGATACCA
*
5302639 GATGGAATATGGTGTGATGATAGGCGTGATAATGGT
1 GATGGACTATGGTGTGATGATAGGCGTGATAATGGT
5302675 GATGGACTATGGTGATGAT-ATAGGCGTGATAATGGT
1 GATGGACTATGGTG-TGATGATAGGCGTGATAATGGT
5302711 GATGGAC
1 GATGGAC
5302718 AGATTGTAGC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
36 37 0.90
37 4 0.10
ACGTcount: A:0.28, C:0.05, G:0.38, T:0.29
Consensus pattern (36 bp):
GATGGACTATGGTGTGATGATAGGCGTGATAATGGT
Found at i:5303101 original size:19 final size:20
Alignment explanation
Indices: 5303054--5303104 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5303044 GAAACCCCTT
**
5303054 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
5303074 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
5303093 TGAAGATACATG
1 TGAAAATACATG
5303105 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:5306302 original size:12 final size:12
Alignment explanation
Indices: 5306280--5306320 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
5306270 TTAGATAATG
5306280 CAAAA-GAAAAA
1 CAAAAGGAAAAA
*
5306291 TAAAAGGAAAAA
1 CAAAAGGAAAAA
5306303 CAAAAGGAAAAA
1 CAAAAGGAAAAA
5306315 CAAAAG
1 CAAAAG
5306321 AACCTAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.02
Consensus pattern (12 bp):
CAAAAGGAAAAA
Found at i:5306886 original size:23 final size:25
Alignment explanation
Indices: 5306856--5306909 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
5306846 AATTTTGTAA
* * *
5306856 CTTTTTTTTG-CTTTTTGTT-TTTT
1 CTTTTTTTGGCCTTTTTCTTCTCTT
5306879 CTTTTTTTGGCCTTTTTCTTCTCTT
1 CTTTTTTTGGCCTTTTTCTTCTCTT
5306904 CTTTTT
1 CTTTTT
5306910 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 9 0.35
24 8 0.31
25 9 0.35
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (25 bp):
CTTTTTTTGGCCTTTTTCTTCTCTT
Found at i:5307838 original size:12 final size:12
Alignment explanation
Indices: 5307821--5307860 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
5307811 TTAGGTGATG
*
5307821 GAAACAAGGTAA
1 GAAACAAGATAA
5307833 GAAACAAGATAA
1 GAAACAAGATAA
5307845 -AAACAAGATAAA
1 GAAACAAGAT-AA
5307857 GAAA
1 GAAA
5307861 AGATAAAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 9 0.36
12 13 0.52
13 3 0.12
ACGTcount: A:0.68, C:0.07, G:0.17, T:0.07
Consensus pattern (12 bp):
GAAACAAGATAA
Found at i:5307850 original size:11 final size:11
Alignment explanation
Indices: 5307822--5307867 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
5307812 TAGGTGATGG
*
5307822 AAACAAGGTAA
1 AAACAAGATAA
5307833 GAAACAAGATAA
1 -AAACAAGATAA
5307845 AAACAAGATAA
1 AAACAAGATAA
5307856 AGAA-AAGATAA
1 A-AACAAGATAA
5307867 A
1 A
5307868 GGAATTGCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
11 20 0.62
12 12 0.38
ACGTcount: A:0.70, C:0.07, G:0.15, T:0.09
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:5308454 original size:36 final size:36
Alignment explanation
Indices: 5308382--5308485 Score: 149
Period size: 36 Copynumber: 2.9 Consensus size: 36
5308372 ATTTATAAGT
* *** *
5308382 TGGTGATAATATAGGCGTGAT-A-CCAGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5308416 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
5308452 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
5308486 AGATTGTAGC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
34 20 0.32
35 1 0.02
36 42 0.67
ACGTcount: A:0.30, C:0.07, G:0.35, T:0.29
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:5308872 original size:19 final size:20
Alignment explanation
Indices: 5308825--5308875 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
5308815 GAAACCCCTT
**
5308825 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
5308845 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
5308864 TGAATATACATG
1 TGAAAATACATG
5308876 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:5312388 original size:22 final size:23
Alignment explanation
Indices: 5312360--5312411 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
5312350 ATTTATAAGT
5312360 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
5312382 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
5312405 TGGTGAT
1 TGGTGAT
5312412 GGACTATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:5312403 original size:36 final size:38
Alignment explanation
Indices: 5312362--5312441 Score: 98
Period size: 36 Copynumber: 2.2 Consensus size: 38
5312352 TTATAAGTTG
*
5312362 GTGATAATATAGGCG-T-GA-TATGGTGATGATATAGGC
1 GTGATAATAT-GGCGATGGACTATGATGATGATATAGGC
*
5312398 GTGAT-A-ATGGTGATGGACTATGATGATGATATAGGC
1 GTGATAATATGGCGATGGACTATGATGATGATATAGGC
5312434 GTGATAAT
1 GTGATAAT
5312442 GGTGATGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
33 3 0.08
34 3 0.08
35 3 0.08
36 27 0.73
37 1 0.03
ACGTcount: A:0.31, C:0.05, G:0.33, T:0.31
Consensus pattern (38 bp):
GTGATAATATGGCGATGGACTATGATGATGATATAGGC
Found at i:5312442 original size:36 final size:36
Alignment explanation
Indices: 5312380--5312451 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
5312370 ATAGGCGTGA
*
5312380 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGATGATGATATAGGCGTGATAATGGTGATGGAC
5312416 TATGATGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGATGATGATATAGGCGTGATAATGGTGATGGAC
5312452 ATATTGTATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.29, C:0.06, G:0.35, T:0.31
Consensus pattern (36 bp):
TATGATGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:5312838 original size:19 final size:20
Alignment explanation
Indices: 5312791--5312841 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
5312781 GAAACCCCTT
**
5312791 TGAAAATACATGATTTGTTA
1 TGAAAATACATGATTTGAAA
5312811 TGAAAATACATGATTT-AAA
1 TGAAAATACATGATTTGAAA
*
5312830 TGAAGATACATG
1 TGAAAATACATG
5312842 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTGAAA
Found at i:5317639 original size:16 final size:16
Alignment explanation
Indices: 5317614--5317648 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5317604 TAATTCCTAA
*
5317614 TAAAATAATAATAATT
1 TAAAAAAATAATAATT
*
5317630 TAAAAAAATAATATTT
1 TAAAAAAATAATAATT
5317646 TAA
1 TAA
5317649 CCCAACCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAAAAAATAATAATT
Found at i:5321599 original size:35 final size:37
Alignment explanation
Indices: 5321530--5321609 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
5321520 ATACTATTTC
*
5321530 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
5321567 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
5321602 CATCACCA
1 CATCACCA
5321610 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:5322021 original size:23 final size:21
Alignment explanation
Indices: 5321990--5322034 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
5321980 ATACAACAAT
*
5321990 AAAAGCAAAAAGAAAGAAGAAAA
1 AAAAACAAAAAG-AA-AAGAAAA
5322013 AAAAACAAAAAGAAAAGAAAA
1 AAAAACAAAAAGAAAAGAAAA
5322034 A
1 A
5322035 GACTCATACA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
22 2 0.10
23 11 0.52
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.00
Consensus pattern (21 bp):
AAAAACAAAAAGAAAAGAAAA
Found at i:5322025 original size:16 final size:18
Alignment explanation
Indices: 5321990--5322034 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5321980 ATACAACAAT
*
5321990 AAAAGCAAAAAGAAAGAAG
1 AAAAG-AAAAACAAAGAAG
5322009 AAAA-AAAAACAAA-AAG
1 AAAAGAAAAACAAAGAAG
5322025 AAAAGAAAAA
1 AAAAGAAAAA
5322035 GACTCATACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.29
17 13 0.54
19 4 0.17
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAACAAAGAAG
Found at i:5322035 original size:11 final size:11
Alignment explanation
Indices: 5321990--5322036 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
5321980 ATACAACAAT
5321990 AAAAGCAAAAAG
1 AAAAG-AAAAAG
5322002 AAAGAAGAAAAA-
1 -AA-AAGAAAAAG
*
5322014 AAAACAAAAAG
1 AAAAGAAAAAG
5322025 AAAAGAAAAAG
1 AAAAGAAAAAG
5322036 A
1 A
5322037 CTCATACAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
10 7 0.23
11 13 0.43
13 7 0.23
14 3 0.10
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:5322265 original size:16 final size:16
Alignment explanation
Indices: 5322246--5322284 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5322236 TTTCTTACTA
5322246 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
* * *
5322262 TTTCATTTTTTTCTTG
1 TTTCATTTCTTTATTC
5322278 TTTCATT
1 TTTCATT
5322285 ACCATATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:5325613 original size:35 final size:37
Alignment explanation
Indices: 5325544--5325623 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
5325534 ATACTATTTC
*
5325544 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
5325581 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
5325616 CATCACCA
1 CATCACCA
5325624 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:5335380 original size:23 final size:23
Alignment explanation
Indices: 5335329--5335381 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
5335319 TTCTTTGTTT
5335329 TTTTCTTCTTTTTGAGTGTTTCA
1 TTTTCTTCTTTTTGAGTGTTTCA
** *
5335352 AATTCTTC-TTTTGAGTGCTTTGA
1 TTTTCTTCTTTTTGAGTG-TTTCA
5335375 TTTTCTT
1 TTTTCTT
5335382 TGCTGGATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.62
Consensus pattern (23 bp):
TTTTCTTCTTTTTGAGTGTTTCA
Found at i:5339728 original size:30 final size:30
Alignment explanation
Indices: 5339638--5339733 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 30
5339628 CACATTTGGG
* * ** *
5339638 ACAGCTTGATGAAGCATTTGTAAGACAAAA
1 ACAGCTTGGTGGAGCATTTGGGAGACACAA
* * * *
5339668 ACAACTTAGTGGAGCATTTTTGGA-AGACAA
1 ACAGCTTGGTGGAGCA-TTTGGGAGACACAA
*
5339698 ATAGCTTGGTGGAGCATTTGGGAGACACAA
1 ACAGCTTGGTGGAGCATTTGGGAGACACAA
5339728 ACAGCT
1 ACAGCT
5339734 CACAAGAATC
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
29 6 0.12
30 39 0.80
31 4 0.08
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (30 bp):
ACAGCTTGGTGGAGCATTTGGGAGACACAA
Found at i:5340544 original size:29 final size:29
Alignment explanation
Indices: 5340512--5340576 Score: 130
Period size: 29 Copynumber: 2.2 Consensus size: 29
5340502 AGTCTTAAGA
5340512 GAAATGCAATTACCTTGTTCTTTAACATT
1 GAAATGCAATTACCTTGTTCTTTAACATT
5340541 GAAATGCAATTACCTTGTTCTTTAACATT
1 GAAATGCAATTACCTTGTTCTTTAACATT
5340570 GAAATGC
1 GAAATGC
5340577 TTTGATTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.38
Consensus pattern (29 bp):
GAAATGCAATTACCTTGTTCTTTAACATT
Found at i:5342988 original size:11 final size:11
Alignment explanation
Indices: 5342972--5343003 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
5342962 CGTCATACAT
5342972 AGCTCACAAAC
1 AGCTCACAAAC
5342983 AGCTCACAAAC
1 AGCTCACAAAC
5342994 AGCTCACAAA
1 AGCTCACAAA
5343004 GTACAAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.34, G:0.09, T:0.09
Consensus pattern (11 bp):
AGCTCACAAAC
Found at i:5347201 original size:11 final size:11
Alignment explanation
Indices: 5347185--5347216 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
5347175 CGTCATACAT
5347185 AGCTCACAAAC
1 AGCTCACAAAC
5347196 AGCTCACAAAC
1 AGCTCACAAAC
5347207 AGCTCACAAA
1 AGCTCACAAA
5347217 GTACAAGGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.34, G:0.09, T:0.09
Consensus pattern (11 bp):
AGCTCACAAAC
Found at i:5351879 original size:30 final size:30
Alignment explanation
Indices: 5351801--5351881 Score: 83
Period size: 30 Copynumber: 2.7 Consensus size: 30
5351791 AGCGTGATGA
** *
5351801 AGCATTTGTAAGACAAAAACAACTTAGTGG
1 AGCATTTGGGAGACACAAACAACTTAGTGG
* * * *
5351831 AGCATTTTTGGA-AGACAAATAACTTGGTGG
1 AGCA-TTTGGGAGACACAAACAACTTAGTGG
5351861 AGCATTTGGGAGACACAAACA
1 AGCATTTGGGAGACACAAACA
5351882 GCTCACAATC
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
29 6 0.15
30 29 0.74
31 4 0.10
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (30 bp):
AGCATTTGGGAGACACAAACAACTTAGTGG
Found at i:5352659 original size:5 final size:5
Alignment explanation
Indices: 5352649--5352673 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5352639 GTTAAATAAA
5352649 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
5352674 TTCTAGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5358343 original size:15 final size:15
Alignment explanation
Indices: 5358323--5358365 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
5358313 CCTACTTTGA
5358323 TATCATTTCTTTTCT
1 TATCATTTCTTTTCT
**
5358338 TATCATTTCCATTCT
1 TATCATTTCTTTTCT
5358353 TATTCCATTTCTT
1 TA-T-CATTTCTT
5358366 ATTTCATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 15 0.68
16 1 0.05
17 6 0.27
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.60
Consensus pattern (15 bp):
TATCATTTCTTTTCT
Found at i:5360997 original size:35 final size:34
Alignment explanation
Indices: 5360907--5361018 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 34
5360897 ATAAGATACT
*
5360907 ACCTA-AACATTACCATCTTCCATCACCATTTTCAC
1 ACCTATAACATTACCATCTTCCAT-ACCA-TTGCAC
* * *
5360942 GCCTATAACATCACCGTCTTCCACTACCATTGCAC
1 ACCTATAACATTACCATCTTCCA-TACCATTGCAC
* *
5360977 ACTTATAACATTACCATCTTCCATTACCATTTCAC
1 ACCTATAACATTACCATCTTCCA-TACCATTGCAC
*
5361012 GCCTATA
1 ACCTATA
5361019 TAACCACCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
35 43 0.68
36 19 0.30
37 1 0.02
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.31
Consensus pattern (34 bp):
ACCTATAACATTACCATCTTCCATACCATTGCAC
Found at i:5361744 original size:25 final size:26
Alignment explanation
Indices: 5361716--5361778 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
5361706 ATCCATTTCT
*
5361716 TAACCTTTTCTATCCTA-CCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
5361741 TAACCATTTCTATCCTACCCCTATCA
1 TAACCATTTCTATCCTACCCCTATCA
5361767 TAACCATTTCTA
1 TAACCATTTCTA
5361779 GACCCTAACC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (26 bp):
TAACCATTTCTATCCTACCCCTATCA
Found at i:5365531 original size:35 final size:35
Alignment explanation
Indices: 5365452--5365557 Score: 122
Period size: 35 Copynumber: 3.0 Consensus size: 35
5365442 ACTACCTAAC
* * * * * *
5365452 CATCACCATCTTTCATCACCATTTTCACGCATATAA
1 CATCACCATCTTCCATTACCA-CTGCACGCCTATAT
5365488 CATCACCATCTTCCATTACCACTGCACGCCTATAT
1 CATCACCATCTTCCATTACCACTGCACGCCTATAT
* * *
5365523 CATTACCATCTTCCATTACCATTTCACGCCTATAT
1 CATCACCATCTTCCATTACCACTGCACGCCTATAT
5365558 AACCACCAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 42 0.69
36 19 0.31
ACGTcount: A:0.27, C:0.36, G:0.04, T:0.33
Consensus pattern (35 bp):
CATCACCATCTTCCATTACCACTGCACGCCTATAT
Found at i:5372221 original size:14 final size:14
Alignment explanation
Indices: 5372202--5372228 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5372192 TAAGATATTA
5372202 TTTCCATCACCATC
1 TTTCCATCACCATC
5372216 TTTCCATCACCAT
1 TTTCCATCACCAT
5372229 TCACGCCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
TTTCCATCACCATC
Found at i:5372673 original size:20 final size:22
Alignment explanation
Indices: 5372638--5372679 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
5372628 CAAGTGCTGC
5372638 AACAAAAGCAAAAAGAA-AAAA
1 AACAAAAGCAAAAAGAAGAAAA
*
5372659 AACAAAA-CGAAAAGAAGAAAA
1 AACAAAAGCAAAAAGAAGAAAA
5372680 GACTCCTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.79, C:0.10, G:0.12, T:0.00
Consensus pattern (22 bp):
AACAAAAGCAAAAAGAAGAAAA
Found at i:5378126 original size:15 final size:15
Alignment explanation
Indices: 5378106--5378141 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
5378096 ATCCATCAGG
*
5378106 ACCATCATTTTCGCA
1 ACCATCATTTCCGCA
5378121 ACCATCATTTCCGCA
1 ACCATCATTTCCGCA
*
5378136 GCCATC
1 ACCATC
5378142 TCTATCCCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.25, C:0.39, G:0.08, T:0.28
Consensus pattern (15 bp):
ACCATCATTTCCGCA
Found at i:5382366 original size:14 final size:14
Alignment explanation
Indices: 5382347--5382375 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5382337 TATAAGATAT
5382347 TATTTCCATCACCA
1 TATTTCCATCACCA
5382361 TATTTCCATCACCA
1 TATTTCCATCACCA
5382375 T
1 T
5382376 TCACGCCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.00, T:0.38
Consensus pattern (14 bp):
TATTTCCATCACCA
Found at i:5383920 original size:12 final size:12
Alignment explanation
Indices: 5383903--5383934 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
5383893 GAACAAAATA
5383903 AAAGAAAATTGC
1 AAAGAAAATTGC
5383915 AAAGAAAATTGC
1 AAAGAAAATTGC
5383927 AAAGAAAA
1 AAAGAAAA
5383935 GTTTAAAGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.66, C:0.06, G:0.16, T:0.12
Consensus pattern (12 bp):
AAAGAAAATTGC
Found at i:5385403 original size:2 final size:2
Alignment explanation
Indices: 5385387--5385428 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
5385377 TTTCATATGT
* *
5385387 TA TA -A TA TA TT TA TA TA TA TA TA TA TA TA TA T- TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5385427 TA
1 TA
5385429 GTTATTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5385404 original size:10 final size:11
Alignment explanation
Indices: 5385381--5385433 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 11
5385371 TTCTTATTTC
*
5385381 ATATGTTATA-
1 ATATATTATAT
5385391 ATATATT-TAT
1 ATATATTATAT
5385401 ATATATATATAT
1 ATATAT-TATAT
5385413 ATATATTATAT
1 ATATATTATAT
*
5385424 CTATAGTTAT
1 ATATA-TTAT
5385434 TATGATAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 2 0.05
10 12 0.32
11 10 0.27
12 13 0.35
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (11 bp):
ATATATTATAT
Found at i:5394646 original size:36 final size:36
Alignment explanation
Indices: 5394593--5394730 Score: 224
Period size: 36 Copynumber: 3.9 Consensus size: 36
5394583 ACAATCTGTT
*
5394593 CATCACCATTATGACGCCTATATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
5394629 CATCTCCATTATCACGCCTATATCATCACCATAGTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
* *
5394665 CATCACTATTATCACGCCTATATCATCACCATATTC
1 CATCACCATTATCACGCCTATATCATCACCATAGTC
*
5394701 CATCACCA-TATCACGCCTATATTATCACCA
1 CATCACCATTATCACGCCTATATCATCACCA
5394731 ACTTATAAAT
Statistics
Matches: 95, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
35 21 0.22
36 74 0.78
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
CATCACCATTATCACGCCTATATCATCACCATAGTC
Found at i:5394670 original size:13 final size:11
Alignment explanation
Indices: 5394612--5394713 Score: 64
Period size: 11 Copynumber: 8.5 Consensus size: 11
5394602 TATGACGCCT
5394612 ATATCATCACC
1 ATATCATCACC
*
5394623 ATAGTCCATCTCC
1 ATA-T-CATCACC
*
5394636 ATTATCA-CGCC
1 A-TATCATCACC
5394647 TATATCATCACC
1 -ATATCATCACC
*
5394659 ATAGTCCATCACT
1 ATA-T-CATCACC
*
5394672 ATTATCA-CGCC
1 A-TATCATCACC
5394683 TATATCATCACC
1 -ATATCATCACC
5394695 ATATTCCATCACC
1 ATA-T-CATCACC
5394708 ATATCA
1 ATATCA
5394714 CGCCTATATT
Statistics
Matches: 72, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
11 26 0.36
12 16 0.22
13 26 0.36
14 4 0.06
ACGTcount: A:0.31, C:0.34, G:0.04, T:0.30
Consensus pattern (11 bp):
ATATCATCACC
Found at i:5401600 original size:15 final size:16
Alignment explanation
Indices: 5401577--5401617 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
5401567 AAACAACAAA
*
5401577 AAGAGAAAAAGAAA-G
1 AAGAAAAAAAGAAAGG
5401592 AAGAAAAAAA-AAAGG
1 AAGAAAAAAAGAAAGG
5401607 AA-AAAAAAAGA
1 AAGAAAAAAAGA
5401618 CTCCTACATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAGAAAGG
Found at i:5401609 original size:12 final size:12
Alignment explanation
Indices: 5401574--5401615 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 12
5401564 CAAAAACAAC
5401574 AAAAAGAGAAAAA
1 AAAAAG-GAAAAA
5401587 GAAAGAA-GAAAAA
1 -AAA-AAGGAAAAA
5401600 AAAAAGGAAAAA
1 AAAAAGGAAAAA
5401612 AAAA
1 AAAA
5401616 GACTCCTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 13 0.50
13 6 0.23
14 3 0.12
15 2 0.08
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGGAAAAA
Found at i:5416780 original size:18 final size:18
Alignment explanation
Indices: 5416738--5416783 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5416728 TAGTTTGATT
*
5416738 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
5416756 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
5416774 AATGAACTAA
1 AATGAACTAA
5416784 ACACATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:5416859 original size:17 final size:18
Alignment explanation
Indices: 5416839--5416880 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5416829 ACTACTTCCC
5416839 TAAATGAAATACATGC-T
1 TAAATGAAATACATGCAT
* *
5416856 TAAATGCAATGCATGCAT
1 TAAATGAAATACATGCAT
5416874 T-AATGAA
1 TAAATGAA
5416881 CAACATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (18 bp):
TAAATGAAATACATGCAT
Found at i:5417070 original size:25 final size:25
Alignment explanation
Indices: 5417042--5417098 Score: 60
Period size: 28 Copynumber: 2.2 Consensus size: 25
5417032 AGTAAGGTAA
*
5417042 AACTCCCTTTGAATCATCCTTGGTG
1 AACTACCTTTGAATCATCCTTGGTG
**
5417067 AACTTATATGTTTGAATCATCCTTGGTG
1 AAC---TACCTTTGAATCATCCTTGGTG
5417095 AACT
1 AACT
5417099 TTTTTTACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
25 4 0.15
28 22 0.85
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (25 bp):
AACTACCTTTGAATCATCCTTGGTG
Found at i:5420651 original size:18 final size:18
Alignment explanation
Indices: 5420625--5420663 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5420615 ATTAATCAAA
5420625 TAACATTATTCAATGAAC
1 TAACATTATTCAATGAAC
* *
5420643 TAACTTTATTTAATGAAC
1 TAACATTATTCAATGAAC
5420661 TAA
1 TAA
5420664 ATGCATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (18 bp):
TAACATTATTCAATGAAC
Found at i:5420739 original size:17 final size:18
Alignment explanation
Indices: 5420719--5420760 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5420709 ACTACTTCCC
5420719 TAAATGAAATACATGC-T
1 TAAATGAAATACATGCAT
* *
5420736 TAAATGTAATGCATGCAT
1 TAAATGAAATACATGCAT
5420754 T-AATGAA
1 TAAATGAA
5420761 CAACATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.45, C:0.10, G:0.14, T:0.31
Consensus pattern (18 bp):
TAAATGAAATACATGCAT
Found at i:5420950 original size:25 final size:25
Alignment explanation
Indices: 5420922--5420978 Score: 60
Period size: 28 Copynumber: 2.2 Consensus size: 25
5420912 AGTAAGGTAA
*
5420922 AACTCCCTTTGAATCATCCTTGGTG
1 AACTACCTTTGAATCATCCTTGGTG
**
5420947 AACTTATATGTTTGAATCATCCTTGGTG
1 AAC---TACCTTTGAATCATCCTTGGTG
5420975 AACT
1 AACT
5420979 TTTTTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
25 4 0.15
28 22 0.85
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (25 bp):
AACTACCTTTGAATCATCCTTGGTG
Found at i:5424559 original size:18 final size:18
Alignment explanation
Indices: 5424517--5424562 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
5424507 AAGTTTGATT
*
5424517 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
*
5424535 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
5424553 AATGAACTAA
1 AATGAACTAA
5424563 ATGCATGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:5424638 original size:17 final size:18
Alignment explanation
Indices: 5424618--5424659 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5424608 GCTACTTCCC
5424618 TAAATGAAATACATGC-T
1 TAAATGAAATACATGCAT
* *
5424635 TAAATGCAATGCATGCAT
1 TAAATGAAATACATGCAT
5424653 T-AATGAA
1 TAAATGAA
5424660 CAACATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (18 bp):
TAAATGAAATACATGCAT
Found at i:5432737 original size:18 final size:18
Alignment explanation
Indices: 5432711--5432749 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5432701 ATTAATGAAA
5432711 TAACATTATTCAATCAAC
1 TAACATTATTCAATCAAC
* *
5432729 TAACTTTATTCAATGAAC
1 TAACATTATTCAATCAAC
5432747 TAA
1 TAA
5432750 ATACATGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (18 bp):
TAACATTATTCAATCAAC
Found at i:5436120 original size:18 final size:18
Alignment explanation
Indices: 5436097--5436143 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
5436087 TAGTTTGATT
*
5436097 AATGAAATAAAATTATTC
1 AATGAACTAAAATTATTC
**
5436115 AATGAACTAACTTTATTC
1 AATGAACTAAAATTATTC
5436133 AATGAACTAAA
1 AATGAACTAAA
5436144 TGCATGAATG
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:0.51, C:0.11, G:0.06, T:0.32
Consensus pattern (18 bp):
AATGAACTAAAATTATTC
Found at i:5436218 original size:17 final size:18
Alignment explanation
Indices: 5436198--5436239 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
5436188 ATTACTTCCC
5436198 TAAATGAAATACATGC-T
1 TAAATGAAATACATGCAT
* *
5436215 TAAATGCAATGCATGCAT
1 TAAATGAAATACATGCAT
5436233 T-AATGAA
1 TAAATGAA
5436240 CAACATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 19 0.90
18 2 0.10
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.29
Consensus pattern (18 bp):
TAAATGAAATACATGCAT
Found at i:5436429 original size:25 final size:25
Alignment explanation
Indices: 5436401--5436457 Score: 60
Period size: 28 Copynumber: 2.2 Consensus size: 25
5436391 AGGAAAGTAA
*
5436401 AACTCCCTTTGAATCATCCTTGGTG
1 AACTACCTTTGAATCATCCTTGGTG
**
5436426 AACTTATATGTTTGAATCATCCTTGGTG
1 AAC---TACCTTTGAATCATCCTTGGTG
5436454 AACT
1 AACT
5436458 TTTTTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
25 4 0.15
28 22 0.85
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.39
Consensus pattern (25 bp):
AACTACCTTTGAATCATCCTTGGTG
Found at i:5437155 original size:29 final size:29
Alignment explanation
Indices: 5437108--5437199 Score: 98
Period size: 29 Copynumber: 3.2 Consensus size: 29
5437098 ATCAATGTTA
*
5437108 GAACGTGGAACACTATTAATAAAATAAAT
1 GAACATGGAACACTATTAATAAAATAAAT
* * *
5437137 GAATATGGAACACTATTAATATAAGT-TA-
1 GAACATGGAACACTATTAATA-AAATAAAT
* *
5437165 GAACAAGGAACACTATAAATAAAATAAAT
1 GAACATGGAACACTATTAATAAAATAAAT
*
5437194 AAACAT
1 GAACAT
5437200 AGAAAATTCA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
27 3 0.06
28 19 0.39
29 24 0.49
30 3 0.06
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (29 bp):
GAACATGGAACACTATTAATAAAATAAAT
Found at i:5437633 original size:19 final size:19
Alignment explanation
Indices: 5437584--5437640 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
5437574 AATGTACTCA
5437584 TTTTC-ACTCTCAATTCTC
1 TTTTCAACTCTCAATTCTC
*
5437602 TTTTTAATGCTCTCAATGTCT-
1 TTTTCAA--CTCTCAAT-TCTC
*
5437623 TTTTCAACTCTCATTTCT
1 TTTTCAACTCTCAATTCT
5437641 TTATCTTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 7 0.22
19 8 0.25
21 14 0.44
22 3 0.09
ACGTcount: A:0.18, C:0.26, G:0.04, T:0.53
Consensus pattern (19 bp):
TTTTCAACTCTCAATTCTC
Found at i:5440066 original size:18 final size:18
Alignment explanation
Indices: 5440033--5440078 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
5440023 TAGTTTGATT
*
5440033 AATGAAATAACATTATTC
1 AATGAACTAACATTATTC
* *
5440051 AATTAACTAACTTTATTC
1 AATGAACTAACATTATTC
5440069 AATGAACTAA
1 AATGAACTAA
5440079 ATGCATGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:5440153 original size:17 final size:18
Alignment explanation
Indices: 5440133--5440175 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
5440123 ACTACTTCCC
5440133 TAAATGAAATACATGC-T
1 TAAATGAAATACATGCAT
* *
5440150 TAAATGCAATGCATGCAT
1 TAAATGAAATACATGCAT
5440168 T-AATGAAA
1 TAAATGAAA
5440176 AACACACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 20 0.91
18 2 0.09
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.28
Consensus pattern (18 bp):
TAAATGAAATACATGCAT
Found at i:5440944 original size:29 final size:29
Alignment explanation
Indices: 5440902--5440964 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
5440892 ATCAATGTTA
*
5440902 GAACATGGAACACTATTAATAAAATAAAT
1 GAACAAGGAACACTATTAATAAAATAAAT
5440931 GAACAAGGAACACTATTAATAAAATAAAT
1 GAACAAGGAACACTATTAATAAAATAAAT
5440960 GAACA
1 GAACA
5440965 TAGAAAATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.57, C:0.11, G:0.11, T:0.21
Consensus pattern (29 bp):
GAACAAGGAACACTATTAATAAAATAAAT
Found at i:5441399 original size:19 final size:20
Alignment explanation
Indices: 5441351--5441399 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
5441341 AATGTGCTCG
*
5441351 TTTTC-ACTGTCAATTGTCT
1 TTTTCAACTCTCAATTGTCT
5441370 TTTT-AATCTCTCAA-TGTCT
1 TTTTCAA-CTCTCAATTGTCT
5441389 TTTTCAACTCT
1 TTTTCAACTCT
5441400 TGTTTCTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.18, C:0.22, G:0.06, T:0.53
Consensus pattern (20 bp):
TTTTCAACTCTCAATTGTCT
Found at i:5443831 original size:18 final size:18
Alignment explanation
Indices: 5443808--5443849 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
5443798 TAGTTTGATT
5443808 AATGAAATAACATTATTC
1 AATGAAATAACATTATTC
*
5443826 AATGAAATAACTTTATTC
1 AATGAAATAACATTATTC
5443844 AATGAA
1 AATGAA
5443850 CTAAATGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.50, C:0.10, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAAATAACATTATTC
Done.