Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008209.1 Hibiscus syriacus cultivar Beakdansim tig00110831_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: 6561538
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 30
Found at i:3253727 original size:24 final size:24
Alignment explanation
Indices: 3253677--3253731 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
3253667 AATAAAGATA
*
3253677 AAAATAATAAATAAAATAGTATTT
1 AAAATAATAAATAAAATAGTATAT
* *
3253701 AAAATAATATAT-ATATA-TATAT
1 AAAATAATAAATAAAATAGTATAT
3253723 ATAAATAAT
1 A-AAATAAT
3253732 TAATTAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.19
23 11 0.41
24 11 0.41
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATAATAAATAAAATAGTATAT
Found at i:3254669 original size:13 final size:11
Alignment explanation
Indices: 3254630--3254660 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
3254620 TTTTTGTATG
3254630 ATTTCTCTCGT
1 ATTTCTCTCGT
*
3254641 ATTTCTCTCAT
1 ATTTCTCTCGT
3254652 ATTTCTCTC
1 ATTTCTCTC
3254661 TTGTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.29, G:0.03, T:0.55
Consensus pattern (11 bp):
ATTTCTCTCGT
Found at i:3258080 original size:24 final size:24
Alignment explanation
Indices: 3258052--3258107 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
3258042 AGAACGGTTC
3258052 AGCGGTTCTGGCCGGTTCATTAGT
1 AGCGGTTCTGGCCGGTTCATTAGT
3258076 AGCGGTTCTGGCCGGTTCATTAGT
1 AGCGGTTCTGGCCGGTTCATTAGT
3258100 AGCGGTTC
1 AGCGGTTC
3258108 AACCGGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.12, C:0.21, G:0.34, T:0.32
Consensus pattern (24 bp):
AGCGGTTCTGGCCGGTTCATTAGT
Found at i:3259597 original size:570 final size:569
Alignment explanation
Indices: 3258479--3259618 Score: 2253
Period size: 570 Copynumber: 2.0 Consensus size: 569
3258469 TCCTCTTTCA
3258479 TGGGTGACTTCTCAACTGGCACAGGAATAGCAACATTCGTATGATGTTACTAAGTCAATTTATAT
1 TGGGTGACTTCTCAACTGGCACAGGAATAGCAACATTCGTATGATGTTACTAAGTCAATTTATAT
3258544 TTGACAAATACGGATGGGGAGGTGCTGCAAGAATTACACCCACCGTCTTGCTTCTGACCGGAGTC
66 TTGACAAATACGGATGGGGAGGTGCTGCAAGAATTACACCCACCGTCTTGCTTCTGACCGGAGTC
3258609 GGTTTCTTTTCGTTGATTCTATTCAGTGATCCACTCGTACCAGCTCTAGCTAAATTCGGCATGAC
131 GGTTTCTTTTCGTTGATTCTATTCAGTGATCCACTCGTACCAGCTCTAGCTAAATTCGGCATGAC
3258674 CCCTCTTCTTGCAGCTGTATACGTTGGTGCCATGCAGAACATTTTCAGCAAGGGTGCAAAGTACA
196 CCCTCTTCTTGCAGCTGTATACGTTGGTGCCATGCAGAACATTTTCAGCAAGGGTGCAAAGTACA
* *
3258739 GTTTATTTTATCCATGCAAATAAATGGCCTATATTCCTTTAGACGAGGAGACAAGGTTCGGAATC
261 GTTTATTTTATCCATGCAAAGAAATGGCCTATAGTCCTTTAGACGAGGAGACAAGGTTCGGAATC
3258804 TTTACCCTAAACTCCGAATCTTTTTTCAAACTTATCGATCATTTATGAATAACTTACTCGATATA
326 TTTACCCTAAACTCCGAATCTTTTTTCAAACTTATCGATCATTTATGAATAACTTACTCGATATA
3258869 TGTTATCTCTAGGTTAAAGGGAGGGCTGCCACTGATGTTGTAATCAATCCATTAGGGAAATCAGG
391 TGTTATCTCTAGGTTAAAGGGAGGGCTGCCACTGATGTTGTAATCAATCCATTAGGGAAATCAGG
3258934 GGGTGCTCTGATTCAGCAGTTTATGATCTTGACCTTTAGATCGCTTGCAAACTCTACCCCATACT
456 GGGTGCTCTGATTCAGCAGTTTATGATCTTGACCTTTAGATCGCTTGCAAACTCTACCCCATACT
3258999 TCGGAGGCATACTCTGATCATTGTTTTCGCATGGTTGTCGGCGGCCAAG
521 TCGGAGGCATACTCTGATCATTGTTTTCGCATGGTTGTCGGCGGCCAAG
3259048 TGGGTGACTTCTCAACTGGCACAGGAATAGCAACATTCGCTATGATGTTACTAAGTCAATTTATA
1 TGGGTGACTTCTCAACTGGCACAGGAATAGCAACATTCG-TATGATGTTACTAAGTCAATTTATA
3259113 TTTGACAAATACGGATGGGGAGGTGCTGCAAGAATTACACCCACCGTCTTGCTTCTGACCGGAGT
65 TTTGACAAATACGGATGGGGAGGTGCTGCAAGAATTACACCCACCGTCTTGCTTCTGACCGGAGT
3259178 CGGTTTCTTTTCGTTGATTCTATTCAGTGATCCACTCGTACCAGCTCTAGCTAAATTCGGCATGA
130 CGGTTTCTTTTCGTTGATTCTATTCAGTGATCCACTCGTACCAGCTCTAGCTAAATTCGGCATGA
3259243 CCCCTCTTCTTGCAGCTGTATACGTTGGTGCCATGCAGAACATTTTCAGCAAGGGTGCAAAGTAC
195 CCCCTCTTCTTGCAGCTGTATACGTTGGTGCCATGCAGAACATTTTCAGCAAGGGTGCAAAGTAC
3259308 AGTTTATTTTATCCATGCAAAGAAATGGCCTATAGTCCTTTAGACGAGGAGACAAGGTTCGGAAT
260 AGTTTATTTTATCCATGCAAAGAAATGGCCTATAGTCCTTTAGACGAGGAGACAAGGTTCGGAAT
3259373 CTTTACCCTAAACTCCGAATCTTTTTTCAAACTTATCGATCATTTATGAATAACTTACTCGATAT
325 CTTTACCCTAAACTCCGAATCTTTTTTCAAACTTATCGATCATTTATGAATAACTTACTCGATAT
3259438 ATGTTATCTCTAGGTTAAAGGGAGGGCTGCCACTGATGTTGTAATCAATCCATTAGGGAAATCAG
390 ATGTTATCTCTAGGTTAAAGGGAGGGCTGCCACTGATGTTGTAATCAATCCATTAGGGAAATCAG
3259503 GGGGTGCTCTGATTCAGCAGTTTATGATCTTGACCTTTAGATCGCTTGCAAACTCTACCCCATAC
455 GGGGTGCTCTGATTCAGCAGTTTATGATCTTGACCTTTAGATCGCTTGCAAACTCTACCCCATAC
3259568 TTCGGAGGCATACTCTGATCATTGTTTTCGCATGGTTGTCGGCGGCCAAG
520 TTCGGAGGCATACTCTGATCATTGTTTTCGCATGGTTGTCGGCGGCCAAG
3259618 T
1 T
3259619 CGTTGGATAT
Statistics
Matches: 568, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
569 39 0.07
570 529 0.93
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (569 bp):
TGGGTGACTTCTCAACTGGCACAGGAATAGCAACATTCGTATGATGTTACTAAGTCAATTTATAT
TTGACAAATACGGATGGGGAGGTGCTGCAAGAATTACACCCACCGTCTTGCTTCTGACCGGAGTC
GGTTTCTTTTCGTTGATTCTATTCAGTGATCCACTCGTACCAGCTCTAGCTAAATTCGGCATGAC
CCCTCTTCTTGCAGCTGTATACGTTGGTGCCATGCAGAACATTTTCAGCAAGGGTGCAAAGTACA
GTTTATTTTATCCATGCAAAGAAATGGCCTATAGTCCTTTAGACGAGGAGACAAGGTTCGGAATC
TTTACCCTAAACTCCGAATCTTTTTTCAAACTTATCGATCATTTATGAATAACTTACTCGATATA
TGTTATCTCTAGGTTAAAGGGAGGGCTGCCACTGATGTTGTAATCAATCCATTAGGGAAATCAGG
GGGTGCTCTGATTCAGCAGTTTATGATCTTGACCTTTAGATCGCTTGCAAACTCTACCCCATACT
TCGGAGGCATACTCTGATCATTGTTTTCGCATGGTTGTCGGCGGCCAAG
Found at i:3263646 original size:23 final size:21
Alignment explanation
Indices: 3263599--3263640 Score: 66
Period size: 23 Copynumber: 1.9 Consensus size: 21
3263589 AATAAAAACT
3263599 AGAAAATAAAGAAGATTAATG
1 AGAAAATAAAGAAGATTAATG
3263620 AGAAAAGTAAAAGAAGATTAA
1 AGAAAA-T-AAAGAAGATTAA
3263641 GAAGAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (21 bp):
AGAAAATAAAGAAGATTAATG
Found at i:3272481 original size:21 final size:20
Alignment explanation
Indices: 3272453--3272509 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
3272443 TTTGCTTTAG
*
3272453 AATTTCTCCTAGGAAGTAATC
1 AATTTCTCCT-GGAAGTAACC
* *
3272474 AGTTTCTCTTGGGAAGTAACC
1 AATTTCTCCT-GGAAGTAACC
*
3272495 AATTTTTCCTGGAAG
1 AATTTCTCCTGGAAG
3272510 ATCAACAACT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 5 0.17
21 24 0.83
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (20 bp):
AATTTCTCCTGGAAGTAACC
Found at i:3274042 original size:12 final size:11
Alignment explanation
Indices: 3273991--3274043 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
3273981 AAAAGAAAAT
3273991 AAAGAAGATTA
1 AAAGAAGATTA
* * *
3274002 AAGATAAAAGTA
1 AA-AGAAGATTA
3274014 AAAGAAGATTA
1 AAAGAAGATTA
3274025 AGAAGAAGATTTA
1 A-AAGAAGA-TTA
3274038 AAAGAA
1 AAAGAA
3274044 ATAAATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
11 9 0.27
12 20 0.61
13 4 0.12
ACGTcount: A:0.64, C:0.00, G:0.19, T:0.17
Consensus pattern (11 bp):
AAAGAAGATTA
Found at i:3277251 original size:11 final size:11
Alignment explanation
Indices: 3277235--3277281 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
3277225 TTCTATTAAT
3277235 TATAATTTATA
1 TATAATTTATA
*
3277246 TATAATATATA
1 TATAATTTATA
3277257 TAATATATTTA-A
1 T-ATA-ATTTATA
3277269 TATAATATTATA
1 TATAAT-TTATA
3277281 T
1 T
3277282 GTATATACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
10 2 0.07
11 17 0.57
12 7 0.23
13 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
TATAATTTATA
Found at i:3277254 original size:9 final size:9
Alignment explanation
Indices: 3277242--3277281 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
3277232 AATTATAATT
3277242 TATATATAA
1 TATATATAA
3277251 TATATATAA
1 TATATATAA
*
3277260 TATATTTAA
1 TATATATAA
*
3277269 TATA-ATAT
1 TATATATAA
3277277 TATAT
1 TATAT
3277282 GTATATACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 6 0.22
9 21 0.78
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TATATATAA
Found at i:3277927 original size:14 final size:14
Alignment explanation
Indices: 3277910--3277938 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3277900 GTAGCTTTCC
3277910 TTAATTAGCATTCT
1 TTAATTAGCATTCT
3277924 TTAATTAGCATTCT
1 TTAATTAGCATTCT
3277938 T
1 T
3277939 AGCTTATTCC
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:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTAATTAGCATTCT
Found at i:3278279 original size:14 final size:14
Alignment explanation
Indices: 3278262--3278289 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3278252 TAACATAATC
3278262 TAATTTCTATAAAA
1 TAATTTCTATAAAA
3278276 TAATTTCTATAAAA
1 TAATTTCTATAAAA
3278290 CATAATCAAT
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATTTCTATAAAA
Found at i:3278988 original size:139 final size:140
Alignment explanation
Indices: 3278781--3279066 Score: 547
Period size: 139 Copynumber: 2.0 Consensus size: 140
3278771 GGTCACTCAA
3278781 CTTTACCAATATTTGCATTTTGATCTAAAAAAAATGTTCTAACTTCAAATTTAGCATTTGAACCT
1 CTTTACCAATATTTGCATTTTGATC-AAAAAAAATGTTCTAACTTCAAATTTAGCATTTGAACCT
3278846 CAATTTCCAGCATTGTTCATAATTAAACAATTATACATAAATGTCCTAAAATTCCCAAAAACTTA
65 CAATTTCCAGCATTGTTCATAATTAAACAATTATACATAAATGTCCTAAAATTCCCAAAAACTTA
3278911 CAACATAGTCC
130 CAACATAGTCC
*
3278922 CTTTACCAATATTTGCATTTTGATC-AAAAAAATGTTCTAACTTCAAATTTAGCATTTGAACTTC
1 CTTTACCAATATTTGCATTTTGATCAAAAAAAATGTTCTAACTTCAAATTTAGCATTTGAACCTC
3278986 AATTTCCAGCATTGTTCATAATTAAACAATTATACATAAATGTCCTAAAATTCCCAAAAACTTAC
66 AATTTCCAGCATTGTTCATAATTAAACAATTATACATAAATGTCCTAAAATTCCCAAAAACTTAC
3279051 AACATAGTCC
131 AACATAGTCC
3279061 CTTTAC
1 CTTTAC
3279067 TATTACAATG
Statistics
Matches: 144, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
139 119 0.83
141 25 0.17
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.35
Consensus pattern (140 bp):
CTTTACCAATATTTGCATTTTGATCAAAAAAAATGTTCTAACTTCAAATTTAGCATTTGAACCTC
AATTTCCAGCATTGTTCATAATTAAACAATTATACATAAATGTCCTAAAATTCCCAAAAACTTAC
AACATAGTCC
Found at i:3280668 original size:21 final size:21
Alignment explanation
Indices: 3280642--3280696 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
3280632 TCGAGGTGGA
3280642 ACGGAATAATTAACATTTTAG
1 ACGGAATAATTAACATTTTAG
3280663 ACGGAATAATTAACATTTTAG
1 ACGGAATAATTAACATTTTAG
* *
3280684 ATGGATTAATTAA
1 ACGGAATAATTAA
3280697 TGACATTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.44, C:0.07, G:0.15, T:0.35
Consensus pattern (21 bp):
ACGGAATAATTAACATTTTAG
Found at i:3297514 original size:3 final size:3
Alignment explanation
Indices: 3297506--3297543 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
3297496 TTAGAGAAAG
*
3297506 AAT AAT AAT AAT AAT AAT AGT AA- AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3297544 TTTTTGATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3304018 original size:21 final size:21
Alignment explanation
Indices: 3303990--3304052 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
3303980 CATTTTGGTG
3303990 CAGAGGGAATCGATCCCCCCC
1 CAGAGGGAATCGATCCCCCCC
* * *
3304011 CTGAGGGAACCGATTCCCCCCA
1 CAGAGGGAATCGA-TCCCCCCC
*
3304033 CAG-GGGAATCGATACCCCCC
1 CAGAGGGAATCGATCCCCCCC
3304053 TGGGGTTCTG
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
20 6 0.18
21 19 0.56
22 9 0.26
ACGTcount: A:0.24, C:0.41, G:0.24, T:0.11
Consensus pattern (21 bp):
CAGAGGGAATCGATCCCCCCC
Found at i:3309003 original size:18 final size:20
Alignment explanation
Indices: 3308980--3309020 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3308970 GGACGGGTGA
3308980 TTTAAATT-TATC-ATATAT
1 TTTAAATTATATCTATATAT
*
3308998 TTTAAATTATTTCTATATAT
1 TTTAAATTATATCTATATAT
3309018 TTT
1 TTT
3309021 CTATTGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 3 0.15
20 9 0.45
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTAAATTATATCTATATAT
Found at i:3309398 original size:25 final size:24
Alignment explanation
Indices: 3309359--3309407 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
3309349 AATTTAAAGA
3309359 AAAATTAAATTAAATTGAAATAAT
1 AAAATTAAATTAAATTGAAATAAT
3309383 AAAATTAAATTGAAATTGAAATAAT
1 AAAATTAAATT-AAATTGAAATAAT
3309408 TTAAACAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (24 bp):
AAAATTAAATTAAATTGAAATAAT
Found at i:3311627 original size:13 final size:13
Alignment explanation
Indices: 3311609--3311644 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
3311599 AGCGTTTTAC
3311609 CAAAAATATTAAT
1 CAAAAATATTAAT
3311622 CAAAAATATT-A-
1 CAAAAATATTAAT
3311633 -AAAAATATTAAT
1 CAAAAATATTAAT
3311645 ATTTCTGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 9 0.43
11 1 0.05
12 1 0.05
13 10 0.48
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (13 bp):
CAAAAATATTAAT
Found at i:3314363 original size:70 final size:74
Alignment explanation
Indices: 3314253--3314398 Score: 246
Period size: 70 Copynumber: 2.0 Consensus size: 74
3314243 ACCAAATGAT
3314253 TTTTAGAATTATTTTTTAATTAATTTTAATATTTTAATATAATATTTTTATCCACCAACCAAGTG
1 TTTTAGAATTATTTTTT-ATTAATTTTAATATTTTAATATAATATTTTTATCCACCAACCAAGTG
3314318 GTAACGCGTG
65 GTAACGCGTG
3314328 TTTTAGAATTA-TTTTT-TTAATTTT-A-ATTTTAATATAATATTTTTATCCACCAACCAAGTGG
1 TTTTAGAATTATTTTTTATTAATTTTAATATTTTAATATAATATTTTTATCCACCAACCAAGTGG
*
3314389 TAATGCGTG
66 TAACGCGTG
3314398 T
1 T
3314399 CACCACCTAA
Statistics
Matches: 70, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
70 45 0.64
71 1 0.01
72 8 0.11
74 5 0.07
75 11 0.16
ACGTcount: A:0.32, C:0.10, G:0.10, T:0.48
Consensus pattern (74 bp):
TTTTAGAATTATTTTTTATTAATTTTAATATTTTAATATAATATTTTTATCCACCAACCAAGTGG
TAACGCGTG
Found at i:3314741 original size:12 final size:12
Alignment explanation
Indices: 3314713--3314745 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3314703 ATAACTATTT
3314713 TTAAATAATTATA
1 TTAAA-AATTATA
3314726 -TAAAAATTATA
1 TTAAAAATTATA
3314737 TTAAAAATT
1 TTAAAAATT
3314746 CATTAGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAAAAATTATA
Found at i:3315728 original size:2 final size:2
Alignment explanation
Indices: 3315723--3315747 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3315713 TTACTCTCTT
3315723 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3315748 CAATTCACAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3319370 original size:14 final size:14
Alignment explanation
Indices: 3319351--3319380 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3319341 TTAAATGATA
3319351 AACGAACACAAACG
1 AACGAACACAAACG
*
3319365 AACGAACATAAACG
1 AACGAACACAAACG
3319379 AA
1 AA
3319381 TATAATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.23, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:3319398 original size:23 final size:23
Alignment explanation
Indices: 3319348--3319435 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
3319338 TCATTAAATG
3319348 ATAAACGAACACAA-ACGAACGAAC
1 ATAAACGAACACAATA--AACGAAC
* * *
3319372 ATAAACGAATATAATAAATGAAC
1 ATAAACGAACACAATAAACGAAC
3319395 ATAAACGAACACAATAAACGAAC
1 ATAAACGAACACAATAAACGAAC
* * *
3319418 A-ACACAAACACAAAAAAC
1 ATAAACGAACACAATAAAC
3319436 AAACTTATTC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
22 14 0.26
23 27 0.50
24 12 0.22
25 1 0.02
ACGTcount: A:0.62, C:0.20, G:0.08, T:0.09
Consensus pattern (23 bp):
ATAAACGAACACAATAAACGAAC
Found at i:3319430 original size:22 final size:23
Alignment explanation
Indices: 3319348--3319457 Score: 80
Period size: 23 Copynumber: 4.8 Consensus size: 23
3319338 TCATTAAATG
*
3319348 ATAAACGAACACAA-ACGAACGAAC
1 ATAAACAAACACAATA--AACGAAC
* * * *
3319372 ATAAACGAATATAATAAATGAAC
1 ATAAACAAACACAATAAACGAAC
*
3319395 ATAAACGAACACAATAAACGAAC
1 ATAAACAAACACAATAAACGAAC
* * *
3319418 A-ACACAAACACAAAAAACAAAC
1 ATAAACAAACACAATAAACGAAC
* **
3319440 TTATTCAAACACAATAAA
1 ATAAACAAACACAATAAA
3319458 TGAATGTAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 5
0.79 0.16 0.06
Matches are distributed among these distances:
22 17 0.24
23 40 0.57
24 12 0.17
25 1 0.01
ACGTcount: A:0.62, C:0.20, G:0.06, T:0.12
Consensus pattern (23 bp):
ATAAACAAACACAATAAACGAAC
Found at i:3319783 original size:43 final size:41
Alignment explanation
Indices: 3319734--3319834 Score: 107
Period size: 40 Copynumber: 2.4 Consensus size: 41
3319724 TTCACGAACG
* ** *
3319734 TAAATGAACGAACGAGCCCTTTGTTCGTGTTCGTTCATTTAA
1 TAAATGAACGAACAAAACC-TTGTTCATGTTCGTTCATTTAA
*
3319776 TTAAATGAAC--ACAAAATCTTGTTCATGTTCGTTCATTTAA
1 -TAAATGAACGAACAAAACCTTGTTCATGTTCGTTCATTTAA
*
3319816 TAAATAAACGAACATAAAC
1 TAAATGAACGAACA-AAAC
3319835 GAACTTACCG
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
39 8 0.17
40 21 0.44
41 7 0.15
42 3 0.06
43 9 0.19
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.34
Consensus pattern (41 bp):
TAAATGAACGAACAAAACCTTGTTCATGTTCGTTCATTTAA
Found at i:3321122 original size:16 final size:18
Alignment explanation
Indices: 3321101--3321141 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3321091 TAAATTTGTT
3321101 ATTTTAA-TAAAAT-ATA
1 ATTTTAATTAAAATAATA
3321117 ATTTTAATTAAAATAATA
1 ATTTTAATTAAAATAATA
*
3321135 TTTTTAA
1 ATTTTAA
3321142 GGTTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTTTAATTAAAATAATA
Found at i:3322636 original size:20 final size:20
Alignment explanation
Indices: 3322611--3322692 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 20
3322601 AACAAACACA
3322611 ATAAACGAACGTAAATGAAC
1 ATAAACGAACGTAAATGAAC
3322631 ATAAACGAACG--AATG---
1 ATAAACGAACGTAAATGAAC
*
3322646 -TAAACGAACACAATAAATGAAC
1 ATAAACG-A-AC-GTAAATGAAC
* *
3322668 ATAAAAGAACGTAAATGAAT
1 ATAAACGAACGTAAATGAAC
3322688 ATAAA
1 ATAAA
3322693 TGAAAATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
14 6 0.12
15 1 0.02
16 2 0.04
18 4 0.08
19 4 0.08
20 24 0.49
21 2 0.04
22 1 0.02
23 5 0.10
ACGTcount: A:0.59, C:0.12, G:0.13, T:0.16
Consensus pattern (20 bp):
ATAAACGAACGTAAATGAAC
Found at i:3322671 original size:10 final size:10
Alignment explanation
Indices: 3322658--3322696 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
3322648 AACGAACACA
3322658 ATAAATGAAC
1 ATAAATGAAC
*
3322668 ATAAAAGAAC
1 ATAAATGAAC
* *
3322678 GTAAATGAAT
1 ATAAATGAAC
3322688 ATAAATGAA
1 ATAAATGAA
3322697 AATATTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.62, C:0.05, G:0.13, T:0.21
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:3322897 original size:14 final size:14
Alignment explanation
Indices: 3322875--3322904 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3322865 AATGAATGCT
3322875 TAAACGAACGAACA
1 TAAACGAACGAACA
*
3322889 TAAATGAACGAACA
1 TAAACGAACGAACA
3322903 TA
1 TA
3322905 TTACTGAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.17, G:0.13, T:0.13
Consensus pattern (14 bp):
TAAACGAACGAACA
Found at i:3333520 original size:25 final size:26
Alignment explanation
Indices: 3333492--3333576 Score: 74
Period size: 25 Copynumber: 3.4 Consensus size: 26
3333482 ATATATTTTA
*
3333492 AATA-AAAATATTTTTAAATTATGTT
1 AATATAAAATATTTTTAAATTAAGTT
* *
3333517 AATAATAAAATATATTT--AGTAAGTT
1 AAT-ATAAAATATTTTTAAATTAAGTT
3333542 AATATAAAA-ATATTTTAAATTAA--T
1 AATATAAAATAT-TTTTAAATTAAGTT
3333566 ATATATAAAAT
1 A-ATATAAAAT
3333577 TATATTAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
23 2 0.04
24 11 0.23
25 20 0.42
26 5 0.10
27 10 0.21
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (26 bp):
AATATAAAATATTTTTAAATTAAGTT
Found at i:3333566 original size:21 final size:23
Alignment explanation
Indices: 3333515--3333568 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 23
3333505 TTAAATTATG
*
3333515 TTAATAATAAAATATATTTAGTAAG
1 TTAAT-ATAAAATATATTTA-TAAA
3333540 TTAATATAAAA-ATATTT-TAAA
1 TTAATATAAAATATATTTATAAA
3333561 TTAATATA
1 TTAATATA
3333569 TATAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.39
23 6 0.21
24 6 0.21
25 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAATATAAAATATATTTATAAA
Found at i:3333584 original size:25 final size:26
Alignment explanation
Indices: 3333543--3333591 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3333533 TAGTAAGTTA
*
3333543 ATATAAAAATATTTTAAAT-TAATAT
1 ATATAAAAATATATTAAATATAATAT
*
3333568 ATATAAAATTATATTAAATATAAT
1 ATATAAAAATATATTAAATATAAT
3333592 CTAGGTCACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.81
26 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATAAAAATATATTAAATATAATAT
Found at i:3349285 original size:48 final size:48
Alignment explanation
Indices: 3349214--3349314 Score: 175
Period size: 48 Copynumber: 2.1 Consensus size: 48
3349204 TAAAACTGAC
3349214 TGAAATCGACTCGAGTCAAAATCGTTTGTAACCTGAGCAATGATGATA
1 TGAAATCGACTCGAGTCAAAATCGTTTGTAACCTGAGCAATGATGATA
* * *
3349262 TGAAATCGACTCGAGTCAAAATCGTTTGTAACCTGAGCAGTGTTGATC
1 TGAAATCGACTCGAGTCAAAATCGTTTGTAACCTGAGCAATGATGATA
3349310 TGAAA
1 TGAAA
3349315 CCAACTAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.28
Consensus pattern (48 bp):
TGAAATCGACTCGAGTCAAAATCGTTTGTAACCTGAGCAATGATGATA
Found at i:3349326 original size:48 final size:48
Alignment explanation
Indices: 3349226--3349326 Score: 148
Period size: 48 Copynumber: 2.1 Consensus size: 48
3349216 AAATCGACTC
* * *
3349226 GAGTCAAAATCGTTTGTAACCTGAGCAATGATGATATGAAATCGACTC
1 GAGTCAAAATCGTTTGTAACCTGAGCAATGATGATATGAAACCAACTA
* * *
3349274 GAGTCAAAATCGTTTGTAACCTGAGCAGTGTTGATCTGAAACCAACTA
1 GAGTCAAAATCGTTTGTAACCTGAGCAATGATGATATGAAACCAACTA
3349322 GAGTC
1 GAGTC
3349327 TGAACTGGTG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (48 bp):
GAGTCAAAATCGTTTGTAACCTGAGCAATGATGATATGAAACCAACTA
Found at i:3349530 original size:16 final size:16
Alignment explanation
Indices: 3349509--3349558 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
3349499 TGGTATTATC
3349509 TGACATGTTATCAACT
1 TGACATGTTATCAACT
3349525 TGACATGTTATCAACT
1 TGACATGTTATCAACT
*
3349541 TGACATGTTATGAACT
1 TGACATGTTATCAACT
3349557 TG
1 TG
3349559 GCCTGTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (16 bp):
TGACATGTTATCAACT
Found at i:3349573 original size:32 final size:32
Alignment explanation
Indices: 3349509--3349578 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
3349499 TGGTATTATC
*
3349509 TGACATGTTATCAACTTGACATGTTATCAACT
1 TGACATGTTATCAACTTGACATGTAATCAACT
* * * *
3349541 TGACATGTTATGAACTTGGCCTGTAATTAACT
1 TGACATGTTATCAACTTGACATGTAATCAACT
*
3349573 TTACAT
1 TGACAT
3349579 TTAAATGATC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (32 bp):
TGACATGTTATCAACTTGACATGTAATCAACT
Found at i:3350235 original size:2 final size:2
Alignment explanation
Indices: 3350228--3350379 Score: 102
Period size: 2 Copynumber: 76.0 Consensus size: 2
3350218 TTCACTTTTG
*
3350228 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* *
3350271 TA TA CT- TA TA CT- TA TA CT- TA TA CTT TA TA CA TA TA TA TA TA
1 TA TA -TA TA TA -TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA
* * * * * *
3350312 TG TA CA CA CA TA TA TA TA TA TA TA TG TA CT- TG TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
*
3350353 TA TA T- TA TA TA CT- TT TA TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
3350380 CAAAGTAGAT
Statistics
Matches: 122, Mismatches: 14, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
1 7 0.06
2 108 0.89
3 7 0.06
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3350568 original size:2 final size:2
Alignment explanation
Indices: 3350561--3350675 Score: 144
Period size: 2 Copynumber: 58.5 Consensus size: 2
3350551 TTTCAAAATA
* * ** * *
3350561 AT AT AT AT TT AT AT AC AT AT GC AT AT AT AT AT TT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3350603 AT GT AT TT 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
3350645 AT AT AT AT AT AT A- AT AT AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3350676 CATAACGCAT
Statistics
Matches: 95, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
1 2 0.02
2 93 0.98
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3352644 original size:116 final size:117
Alignment explanation
Indices: 3352439--3352713 Score: 383
Period size: 116 Copynumber: 2.4 Consensus size: 117
3352429 TGGCACTTTG
* * * * * ** *
3352439 TGTGCTAGAATGATAAGGAAATCATACTGAGTGTATGGATTTCCATATGGAGCACTGGGTGTGCT
1 TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTTCCAGATAAAGCACTAGGTGTGCT
* * *
3352504 AAATGATAAGGAAATCATTTTGAAATTATGGATTTCCAGATAGGGCATATTA
66 AAATGATAAGGAAATCATATTGAAAATATAGATTTCCAGATAGGGCATATTA
*
3352556 TGTGCTAAAATGGTAAGGAAATCATACT-ATTGTATGGGTTTCCAGATAAAGCACTAAGG-GTGC
1 TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTTCCAGATAAAGCACT-AGGTGTGC
*
3352619 TAAATGATAAGGAAATCATATTGAAAATATAGATTTCCATATAGGGCATATTA
65 TAAATGATAAGGAAATCATATTGAAAATATAGATTTCCAGATAGGGCATATTA
** *
3352672 TGTGCTAAAATGGTAACAAAATCATACTAATGGTATGGATTT
1 TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTT
3352714 TCGAATAGGG
Statistics
Matches: 140, Mismatches: 16, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
116 101 0.72
117 39 0.28
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (117 bp):
TGTGCTAAAATGGTAAGGAAATCATACTAATTGTATGGATTTCCAGATAAAGCACTAGGTGTGCT
AAATGATAAGGAAATCATATTGAAAATATAGATTTCCAGATAGGGCATATTA
Found at i:3352713 original size:59 final size:60
Alignment explanation
Indices: 3352430--3352786 Score: 235
Period size: 59 Copynumber: 6.1 Consensus size: 60
3352420 ATTACCGAAT
* * * * *
3352430 GGCACT-TTGTGTGCTAGAATGATAAGGAAATCATACTGAGT-GTATGGATTTCCATAT-G
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACT-AATAGTATGGATTTCCAGATAG
*** * ** *
3352488 GAGCACT-GGGTGTGCT-AAATGATAAGGAAATCATTTTGAA-ATTATGGATTTCCAGATAG
1 G-GCACTATTATGTGCTAAAATGGTAAGGAAATCATACT-AATAGTATGGATTTCCAGATAG
* * *
3352547 GGCA-TATTATGTGCTAAAATGGTAAGGAAATCATACT-ATTGTATGGGTTTCCAGATAA
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAATAGTATGGATTTCCAGATAG
* * * * * * *
3352605 AGCACTA--AGGGTGCT-AAATGATAAGGAAATCATATTGAA-AATATAGATTTCCATATAG
1 GGCACTATTA-TGTGCTAAAATGGTAAGGAAATCATACT-AATAGTATGGATTTCCAGATAG
** * *
3352663 GGCA-TATTATGTGCTAAAATGGTAACAAAATCATACTAATGGTATGGATTTTC-GAATAG
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAATAGTATGGATTTCCAG-ATAG
* ** * *
3352722 GGCACT-TTGTGTGCTAAAATGAAAAGGGAAGCATACTAAGT-GTAT-GATTTTCCAGATAG
1 GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAA-TAGTATGGA-TTTCCAGATAG
*
3352781 AGCACT
1 GGCACT
3352787 GATAGTGCTA
Statistics
Matches: 232, Mismatches: 48, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
57 24 0.10
58 92 0.40
59 113 0.49
60 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (60 bp):
GGCACTATTATGTGCTAAAATGGTAAGGAAATCATACTAATAGTATGGATTTCCAGATAG
Found at i:3353994 original size:20 final size:20
Alignment explanation
Indices: 3353956--3353994 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3353946 ATTCATAATA
*
3353956 AATAATTATGATATTAATTT
1 AATAATTATGATATAAATTT
**
3353976 AATAATTATTTTATAAATT
1 AATAATTATGATATAAATT
3353995 CCAAAACATC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
AATAATTATGATATAAATTT
Found at i:3354193 original size:23 final size:22
Alignment explanation
Indices: 3354147--3354195 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
3354137 AATAACATAT
**
3354147 TAGGTAGCGTTATATAATGTAA
1 TAGGTAGCGTTATATAATAAAA
3354169 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCG-TTATATAATAAAA
3354192 TAGG
1 TAGG
3354196 CATTTAACCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (22 bp):
TAGGTAGCGTTATATAATAAAA
Found at i:3357951 original size:200 final size:198
Alignment explanation
Indices: 3357294--3358053 Score: 1130
Period size: 199 Copynumber: 3.8 Consensus size: 198
3357284 CATTTGGTTG
* * * *
3357294 TAATTATGTTTTTTGATGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTT-GTG
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TTAGTG
* * * * *
3357358 CACTTGGTTTTTAAAATATAGTCTGGACAAAAATGTATCGAAACTTGATGTATTTGTGTCGATAC
65 CACTTGG-TTTTGAAATACATTCTGGACAAAAA-GTATCGACACTTGTTG-ATTTGTGTCGATAC
** * * * * *
3357423 TTCATGTATACCTGTTTTCTCATAAACCGATACATTTAGACTGGTTACATTGTTAATTTACCTAT
127 TTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATTGATAATTTACCTAT
3357488 TACATTA
192 TACATTA
*
3357495 TAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
* *
3357560 ACTTGGTTTTGAAATACATTCTGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGATACTTT
66 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTT-GATTTGTGTCGATACTTT
* * *
3357625 TTATACACATGTTTTCTCAAAAACCGGTATATTTAGACTGTTTACA-TGAATAATTTACCTATTA
130 TTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATTG-ATAATTTACCTATTA
3357689 CATTA
194 CATTA
* * *
3357694 TAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACAC-TTTTATGTG
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTA-GTG
* * *
3357758 CACTTGGTTCTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTCGATTTGTGTCAATACTT
65 CACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTT-GATTTGTGTCGATACTT
* * *
3357823 TTTGTACACCTGTTTTCTCAAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATT
129 TTTGTACACCTGTTTTCTC-AAAAACCGGTATATTTAGACTGGTTACATTGATAATTTACCTATT
3357888 ACATTA
193 ACATTA
3357894 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
3357959 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTT
66 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTG-TTGATTTGTGTCGATACTTT
3358024 TTGTACACCTGTTTTCTCAAAAACCGGTAT
130 TTGTACACCTGTTTTCTCAAAAACCGGTAT
3358054 TAATTATGGT
Statistics
Matches: 507, Mismatches: 44, Indels: 18
0.89 0.08 0.03
Matches are distributed among these distances:
198 7 0.01
199 228 0.45
200 200 0.39
201 72 0.14
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (198 bp):
TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTGATTTGTGTCGATACTTTT
TGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGTTACATTGATAATTTACCTATTACA
TTA
Found at i:3358039 original size:399 final size:400
Alignment explanation
Indices: 3357294--3358053 Score: 1215
Period size: 399 Copynumber: 1.9 Consensus size: 400
3357284 CATTTGGTTG
* *
3357294 TAATTATGTTTTTTGATGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTTGTGC
1 TAATTATGTTTTTCGATGTTTTCGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTTGTGC
* * *
3357359 ACTTGGTTTTTAAAATATAGTCTGGACAAAAATGTATCGAAACTTGATGTATTTGTGTCGATACT
66 ACTTGGTTTCTAAAATACAGTCTGGACAAAAATGTATCGAAACTTGATGTATTTGTGTCAATACT
* * * *
3357424 TCATGTATACCTGTTTTCTCATAAACCGATACATTTAGACTGGTTACATTGTTAATTTACCTATT
131 TCATGTACACCTGTTTTCTCAAAAACCGATACATTTAGACCGGTTACATTGCTAATTTACCTATT
3357489 ACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTT
196 ACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTT
*
3357554 TAGTGCACTTGGTTTTGAAATACATTCTGGAGAAAAAGTATCGACACTTGTTATATTTGTGTCGA
261 TAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGA
3357619 TACTTTTTATACACATGTTTTCTCAAAAACCGGTATATTTAGACTGTTTACATGAATAATTTACC
326 TACTTTTTATACACATGTTTTCTCAAAAACCGGTATATTTAGACTGTTTACATGAATAATTTACC
3357684 TATTACATTA
391 TATTACATTA
* * *
3357694 TAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTTTAAATGTATCGACACTTT-TATGTG
1 TAATTATGTTTTTCGATGTTTTCGGGATCGACAATTGTTATAAATGTATCGAAACTTTGT-TGTG
* * * * *
3357758 CACTTGG-TTCTGAAATACATTCTGGACCAAAA-GTATCGACACTTGTTCG-ATTTGTGTCAATA
65 CACTTGGTTTCTAAAATACAGTCTGGACAAAAATGTATCGAAACTTGAT-GTATTTGTGTCAATA
** * * *
3357820 CTTTTTGTACACCTGTTTTCTCAAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCT
129 CTTCATGTACACCTGTTTTCTC-AAAAACCGATACATTTAGACCGGTTACATTGCTAATTTACCT
*
3357885 ATTACATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACT
193 ATTACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACT
3357950 TTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTT-TGATTTGTG
258 TTTTAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTAT-ATTTGTG
* *
3358014 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCGGTAT
322 TCGATACTTTTTATACACATGTTTTCTCAAAAACCGGTAT
3358054 TAATTATGGT
Statistics
Matches: 330, Mismatches: 26, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
398 45 0.14
399 221 0.67
400 64 0.19
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (400 bp):
TAATTATGTTTTTCGATGTTTTCGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTTGTGC
ACTTGGTTTCTAAAATACAGTCTGGACAAAAATGTATCGAAACTTGATGTATTTGTGTCAATACT
TCATGTACACCTGTTTTCTCAAAAACCGATACATTTAGACCGGTTACATTGCTAATTTACCTATT
ACATTATAATTATAGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTT
TAGTGCACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTATATTTGTGTCGA
TACTTTTTATACACATGTTTTCTCAAAAACCGGTATATTTAGACTGTTTACATGAATAATTTACC
TATTACATTA
Found at i:3358158 original size:160 final size:160
Alignment explanation
Indices: 3357894--3358213 Score: 579
Period size: 160 Copynumber: 2.0 Consensus size: 160
3357884 TATTACATTA
3357894 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
3357959 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTT-
66 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTG
*
3358023 TTTGTACACCTGTTTTCTCAAAAACCGGTAT
131 TTT-TACACATGTTTTCTCAAAAACCGGTAT
*
3358054 TAATTATGGTTTTCGATGTTTTTTGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
1 TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
* *
3358119 ACTTGGTTTTGAAATACATTCTGGACCAAAAGTATCGACACTTGTTTTATTTGTGTCGATACTTG
66 ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTG
*
3358184 TTTTACACATGTTTTCTCAAAATCCGGTAT
131 TTTTACACATGTTTTCTCAAAAACCGGTAT
3358214 ATTTAGACCG
Statistics
Matches: 154, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
160 151 0.98
161 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.42
Consensus pattern (160 bp):
TAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGTGC
ACTTGGTTTTGAAATACATTCTGGACAAAAAGTATCGACACTTGTTTGATTTGTGTCGATACTTG
TTTTACACATGTTTTCTCAAAAACCGGTAT
Found at i:3358700 original size:18 final size:19
Alignment explanation
Indices: 3358657--3358701 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
3358647 ATTCACATAA
*
3358657 AAAATTATAAATCGTATAC
1 AAAATTAAAAATCGTATAC
*
3358676 AAAATTAAAAATCTTATAC
1 AAAATTAAAAATCGTATAC
3358695 -AAATTAA
1 AAAATTAA
3358702 CCATGCATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAATTAAAAATCGTATAC
Found at i:3360206 original size:21 final size:18
Alignment explanation
Indices: 3360168--3360206 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3360158 TTCTCCTCAT
3360168 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
3360186 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTTTCTTC
3360204 TTC
1 TTC
3360207 AAAATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:3361891 original size:18 final size:18
Alignment explanation
Indices: 3361868--3361906 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3361858 TACTGTCAAC
3361868 ATTTAAAATTTGTAAT-CA
1 ATTTAAAATTT-TAATCCA
*
3361886 ATTTAAAGTTTTAATCCA
1 ATTTAAAATTTTAATCCA
3361904 ATT
1 ATT
3361907 ATCATTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (18 bp):
ATTTAAAATTTTAATCCA
Found at i:3362211 original size:19 final size:20
Alignment explanation
Indices: 3362164--3362212 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
3362154 CATTTATACA
3362164 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
3362183 ACCTAT-AATATCATTTT-T
1 ACCTATAAATATCATTTTCT
3362201 ACCTATAAATAT
1 ACCTATAAATAT
3362213 TAACTAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:3362891 original size:180 final size:179
Alignment explanation
Indices: 3362592--3363919 Score: 1383
Period size: 177 Copynumber: 7.6 Consensus size: 179
3362582 TACGCGTATT
* * *
3362592 TATTAAAGTATCGACACTTTCAACATATCTGGTATC-TATTTACCGG-TTTGTCA-TTTTGAGAC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACGT-TTTACCGGTTTTGTCATTTTTGAGAC
*
3362654 C-GATTTTATCATA-TTTTACTG-TATATTGTTCTGGATCGATACATTTTCATAAAGTGTCGACA
65 CTG-TTTTATCATATTTTTACTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
*
3362716 CTTTTTAAGCGTTATACTTCTTCTCTTTTAAATTCA-AAAGTGTCGATACTTA
129 CTTTTTAAGCGCTATA--TCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * *
3362768 TATTAAATTATCAAAACTTTCAACATATCGGGTAAC-TTTCT-CCGGTTTTGTCATTTTTGAGAC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACGTTT-TACCGGTTTTGTCATTTTTGAGAC
* * *
3362831 CTGTTTTATCATATTTTTACATGTTATATTGGTAAGGATCGATACATTTTAATAAAGTGTCGACA
65 CTGTTTTATCATATTTTTAC-TGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
*
3362896 CTTTTTAAGCGCTATAACTTCTCTTTTAAATTCAGAAAGTGTCGATA-TTAA
129 CTTTTTAAGCGCTATATCTTCTCTTTTAAATTCAGAAAGTGTCGATACTT-A
* * ** * * * *
3362947 TATTAAATTATCGACAATTTCAATATATCCGACAACTTTTTTCCGGTTTTGTCATTTTTTAGA-T
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACGTTTTACCGGTTTTGTCATTTTTGAGACC
3363011 TAGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
66 T-GTTTTATCATATTTTTA-CTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACA
*
3363076 CTTTTT-A--G-------------TTTAATTTCAGAAAGTGTCGATACTTA
129 CTTTTTAAGCGCTATATCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * ** * * *
3363111 TATTAAATTATC-A-ACTTTCAAC--ATCCGATATCGTTTTACTAGTTTTGACAATTTTGGGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACGTTTTACCGGTTTTGTCATTTTTGAGACC
* * * *
3363172 TGTTTTATCATATTTTTACTTGTTATATTGTTGTGGATCGATATATTTT-TTAAAGTATCGACAC
66 TGTTTTATCATATTTTTAC-TGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * * *
3363236 TTTATAGGCGCTATAACTTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
130 TTTTTAAGCGCTATATC-TTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* * * * *
3363287 TATTAAATTATCG-CACTTTC-A-ATATCCGGTAGCGTTTTACTGGTTTTGTAAATTTTGAGACA
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACGTTTTACCGGTTTTGTCATTTTTGAGACC
* *
3363349 TGTTTTATCATATTTTTACTGTTATATTGTTATAGATCGATACA-TTTCATTAAGTGTCGACAC-
66 TGTTTTATCATATTTTTACTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
* *
3363412 TTTTAAGCGCAATAATTTTTTCTCTTTTAAATTCAGAAAGTGTCGATAC-TA
131 TTTTAAGCGC--T-ATATCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* *
3363463 TATTAAATTATCGACACTTTTAACATATCCGGTAAC-TTTTTCCGGTTTTGTCATTTTT-AGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACGTTTTACCGGTTTTGTCATTTTTGAGACC
* * * * *
3363526 TG-TTTATCATA-TTTTATCTATTAT-TTGGTAAGG-TCGAAACATTTTCATAAAGTG-CGACAT
66 TGTTTTATCATATTTTTA-CTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * *
3363586 TTTTTAGGCG-TATAACTTCTATCTTTTAAATTCAGAAAGTGTCGATACTAA
130 TTTTTAAGCGCTATATCTTC--TCTTTTAAATTCAGAAAGTGTCGATACTTA
* * ** *
3363637 TATTAAATTATCGACACTTTCAATATATCCGATAAC-TTTTTTCGATTTTGTCATTTTT-AGACC
1 TATTAAATTATCGACACTTTCAACATATCCGGTAACGTTTTACCGGTTTTGTCATTTTTGAGACC
* * * ** *
3363700 AGTTTTATCATATTTTTACCTGTTATATTGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACAC
66 TGTTTTATCATATTTTTA-CTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACAC
* * * * *
3363764 TTTATAGGCGTTATAACTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
130 TTTTTAAGCGCTATATCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
* *
3363814 TATTAAATTATCGACAC--TCGACACATATCCGGTAGCGTTTTACCGGTTTTGTCA-TTTTGGGA
1 TATTAAATTATCGACACTTTC-A-ACATATCCGGTAACGTTTTACCGGTTTTGTCATTTTTGAGA
* * * * * * *
3363876 CCGGTTTTGTCTTATTTGTACCTGTAATATTGCTATGGAGCGAT
64 CCTGTTTTATCATATTTTTA-CTGTTATATTGTTATGGATCGAT
3363920 CTATTTTTCA
Statistics
Matches: 974, Mismatches: 118, Indels: 118
0.80 0.10 0.10
Matches are distributed among these distances:
159 18 0.02
160 71 0.07
161 1 0.00
162 8 0.01
163 1 0.00
164 35 0.04
165 2 0.00
171 5 0.01
172 1 0.00
173 27 0.03
174 72 0.07
175 58 0.06
176 154 0.16
177 196 0.20
178 118 0.12
179 67 0.07
180 139 0.14
181 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (179 bp):
TATTAAATTATCGACACTTTCAACATATCCGGTAACGTTTTACCGGTTTTGTCATTTTTGAGACC
TGTTTTATCATATTTTTACTGTTATATTGTTATGGATCGATACATTTTCATAAAGTGTCGACACT
TTTTAAGCGCTATATCTTCTCTTTTAAATTCAGAAAGTGTCGATACTTA
Found at i:3364920 original size:22 final size:22
Alignment explanation
Indices: 3364893--3364936 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3364883 TGAGACAAAC
3364893 CTCTCAACCAAGTTTGCTCCGT
1 CTCTCAACCAAGTTTGCTCCGT
*
3364915 CTCTCAACCAAGTTTGTTCCGT
1 CTCTCAACCAAGTTTGCTCCGT
3364937 GCACAATGAC
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:0.34, G:0.14, T:0.34
Consensus pattern (22 bp):
CTCTCAACCAAGTTTGCTCCGT
Found at i:3368837 original size:84 final size:87
Alignment explanation
Indices: 3368687--3368846 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 87
3368677 GGATTGACTT
*
3368687 ACTTAATAATACCCCTAGTAGGCTCTTATGAAAGGATTGCAATGGGTGGAGTTAGGGTCAGGTTT
1 ACTTAATAATACCCCTAGTAGACTCTTATGAAAGGATTGCAATGGGTGGAGTTAGGGTCAGGTTT
*
3368752 TTGTTCAAACCAACCCGAGCCC
66 TTGATCAAACCAACCCGAGCCC
*
3368774 ACTTAATAATA-CCC-AGTAGACTCTTATGTAAGGATTG-AATGGGTTGGA-TTAGGGTC-GGAT
1 ACTTAATAATACCCCTAGTAGACTCTTATGAAAGGATTGCAATGGG-TGGAGTTAGGGTCAGG-T
3368834 TTTTGATCAAACC
64 TTTTGATCAAACC
3368847 GACCTAACCC
Statistics
Matches: 68, Mismatches: 3, Indels: 7
0.87 0.04 0.09
Matches are distributed among these distances:
83 2 0.03
84 27 0.40
85 25 0.37
86 3 0.04
87 11 0.16
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (87 bp):
ACTTAATAATACCCCTAGTAGACTCTTATGAAAGGATTGCAATGGGTGGAGTTAGGGTCAGGTTT
TTGATCAAACCAACCCGAGCCC
Found at i:3369688 original size:22 final size:21
Alignment explanation
Indices: 3369654--3369694 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3369644 ATAATTATTT
3369654 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
3369675 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
3369695 ATTTTATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:3370588 original size:26 final size:26
Alignment explanation
Indices: 3370557--3370643 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
3370547 TTAAGTTAAA
*
3370557 ATATTTAAAAAAGATAAGAATTAAAT
1 ATATTTAAAAAAGATAAGAATAAAAT
*
3370583 ATATTTTAATTTAAA-ATAAGAATAAAAT
1 ATA-TTTAA--AAAAGATAAGAATAAAAT
* ***
3370611 ATTTTTATGTAAGATAAGAATAAAAT
1 ATATTTAAAAAAGATAAGAATAAAAT
*
3370637 ATTTTTA
1 ATATTTA
3370644 TATTAAATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
25 2 0.04
26 23 0.45
27 9 0.18
28 14 0.27
29 3 0.06
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (26 bp):
ATATTTAAAAAAGATAAGAATAAAAT
Found at i:3370644 original size:26 final size:26
Alignment explanation
Indices: 3370567--3370644 Score: 111
Period size: 26 Copynumber: 2.9 Consensus size: 26
3370557 ATATTTAAAA
* *
3370567 AAGATAAGAATTAAATATATTTTAATTT
1 AAGATAAGAA-TAAA-ATATTTTTATGT
*
3370595 AAAATAAGAATAAAATATTTTTATGT
1 AAGATAAGAATAAAATATTTTTATGT
3370621 AAGATAAGAATAAAATATTTTTAT
1 AAGATAAGAATAAAATATTTTTAT
3370645 ATTAAATTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 33 0.72
27 4 0.09
28 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.40
Consensus pattern (26 bp):
AAGATAAGAATAAAATATTTTTATGT
Found at i:3370662 original size:27 final size:25
Alignment explanation
Indices: 3370570--3370663 Score: 107
Period size: 26 Copynumber: 3.5 Consensus size: 25
3370560 TTTAAAAAAG
*
3370570 ATAAGAATTAAATATATTTTAATTTAAA
1 ATAAGAA-TAAA-ATATTTTTATTT-AA
*
3370598 ATAAGAATAAAATATTTTTATGTAA
1 ATAAGAATAAAATATTTTTATTTAA
3370623 GATAAGAATAAAATATTTTTATATTAA
1 -ATAAGAATAAAATATTTTTAT-TTAA
*
3370650 ATTAATAATAAAAT
1 A-TAAGAATAAAAT
3370664 TTAAACATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
25 2 0.03
26 32 0.54
27 18 0.31
28 7 0.12
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.40
Consensus pattern (25 bp):
ATAAGAATAAAATATTTTTATTTAA
Found at i:3370722 original size:2 final size:2
Alignment explanation
Indices: 3370715--3370801 Score: 51
Period size: 2 Copynumber: 46.0 Consensus size: 2
3370705 AATAAAGATG
* * * *
3370715 AT AT AT AT AT AT AT AT AT AT CAC AT -T AT A- AT AA AA AT AA AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT
* * * *
3370756 -T AT AT TT A- AT AA AT -T A- AA AT AA 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
3370794 AT AT AT AT
1 AT AT AT AT
3370802 TTGTTTTCCA
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
1 6 0.09
2 58 0.89
3 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3374691 original size:69 final size:68
Alignment explanation
Indices: 3374572--3374702 Score: 201
Period size: 69 Copynumber: 1.9 Consensus size: 68
3374562 TGGCGGGACC
* * *
3374572 TCCCTCCTCGATCAGCTGCCGGCAATGTTTGACGGATAGCGTAGATCTGAGAAGTGTGGCCTGCC
1 TCCCTCCTCGATCAGCCGCC-GCAATGTTTGACGGATAGCATAGACCTGAGAAGTGTGGCCTGCC
3374637 TTGG
65 TTGG
3374641 TCCCTCCTCGGATCAGCCGCC-CAATGATTTGACGGATAGCATAGACCTGAGAAGTGTGGCCT
1 TCCCTCCTC-GATCAGCCGCCGCAATG-TTTGACGGATAGCATAGACCTGAGAAGTGTGGCCT
3374703 CCGCCTTTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
68 5 0.09
69 42 0.74
70 10 0.18
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.24
Consensus pattern (68 bp):
TCCCTCCTCGATCAGCCGCCGCAATGTTTGACGGATAGCATAGACCTGAGAAGTGTGGCCTGCCT
TGG
Found at i:3376129 original size:33 final size:33
Alignment explanation
Indices: 3376092--3376158 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 33
3376082 CCAGGAGGAA
3376092 AAATTAGA-GACTGATGAGAAGAAAAGGGGAAAC
1 AAATTAGAGGA-TGATGAGAAGAAAAGGGGAAAC
* *
3376125 AAATTAGAGGATGATGAGGAGAAAGGGGGAAAC
1 AAATTAGAGGATGATGAGAAGAAAAGGGGAAAC
3376158 A
1 A
3376159 CGGGGAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 29 0.94
34 2 0.06
ACGTcount: A:0.49, C:0.04, G:0.34, T:0.12
Consensus pattern (33 bp):
AAATTAGAGGATGATGAGAAGAAAAGGGGAAAC
Found at i:3381976 original size:46 final size:46
Alignment explanation
Indices: 3381922--3382026 Score: 201
Period size: 46 Copynumber: 2.3 Consensus size: 46
3381912 AATTAATAAC
3381922 AAAATTTTATTTTGGTAAACTATACCAATTATCATTAATTTTTGCG
1 AAAATTTTATTTTGGTAAACTATACCAATTATCATTAATTTTTGCG
3381968 AAAATTTTATTTTGGTAAACTATACCAATTATCATTAATTTTTGCG
1 AAAATTTTATTTTGGTAAACTATACCAATTATCATTAATTTTTGCG
*
3382014 AAAATTTTCTTTT
1 AAAATTTTATTTT
3382027 TTCCCACTAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.34, C:0.10, G:0.08, T:0.48
Consensus pattern (46 bp):
AAAATTTTATTTTGGTAAACTATACCAATTATCATTAATTTTTGCG
Found at i:3385697 original size:15 final size:15
Alignment explanation
Indices: 3385677--3385705 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3385667 ACTTTGGGTC
3385677 ATTCTTCTTCTTCTT
1 ATTCTTCTTCTTCTT
3385692 ATTCTTCTTCTTCT
1 ATTCTTCTTCTTCT
3385706 ACGATCTCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.28, G:0.00, T:0.66
Consensus pattern (15 bp):
ATTCTTCTTCTTCTT
Found at i:3400945 original size:26 final size:25
Alignment explanation
Indices: 3400893--3400945 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3400883 TATCCAAAAA
*
3400893 TATTAAATATTAATAAATATTTATT
1 TATTAAATATTAATAAATATTAATT
*
3400918 TATTAAATTATTTATAAAT-TTAAGTT
1 TATTAAA-TATTAATAAATATTAA-TT
3400944 TA
1 TA
3400946 AAGAGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TATTAAATATTAATAAATATTAATT
Found at i:3408220 original size:2 final size:2
Alignment explanation
Indices: 3408213--3408255 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3408203 TAACTATAGG
3408213 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3408255 T
1 T
3408256 GAAAATAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3411176 original size:6 final size:6
Alignment explanation
Indices: 3411167--3411225 Score: 57
Period size: 6 Copynumber: 9.5 Consensus size: 6
3411157 CTCTTTTGAA
* * *
3411167 TTTCTT TTTCTTT TCTTTTT TTTCTT ATTCTT TTTTTT TTGTCTT TTTC-T
1 TTTCTT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TT-TCTT TTTCTT
3411217 TTTCTT TTT
1 TTTCTT TTT
3411226 GCTCTCCAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 5 0.12
6 25 0.58
7 11 0.26
8 2 0.05
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTCTT
Found at i:3411197 original size:15 final size:14
Alignment explanation
Indices: 3411171--3411224 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 14
3411161 TTTGAATTTC
3411171 TTTTTCTTTTCTTT
1 TTTTTCTTTTCTTT
3411185 TTTTTCTTATTCTTT
1 TTTTTCTT-TTCTTT
*
3411200 TTTTT-TTGTCTTTT
1 TTTTTCTTTTC-TTT
3411214 TCTTTTCTTTT
1 T-TTTTCTTTT
3411225 TGCTCTCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
13 2 0.06
14 14 0.41
15 15 0.44
16 3 0.09
ACGTcount: A:0.02, C:0.13, G:0.02, T:0.83
Consensus pattern (14 bp):
TTTTTCTTTTCTTT
Found at i:3411206 original size:19 final size:20
Alignment explanation
Indices: 3411167--3411225 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
3411157 CTCTTTTGAA
3411167 TTTCTTTTTCTTTTCTTTTT
1 TTTCTTTTTCTTTTCTTTTT
*
3411187 TTTCTTATTCTTTT-TTTTT
1 TTTCTTTTTCTTTTCTTTTT
*
3411206 TGTCTTTTTCTTTTCTTTTT
1 TTTCTTTTTCTTTTCTTTTT
3411226 GCTCTCCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTCTTTTTCTTTTCTTTTT
Found at i:3411226 original size:19 final size:19
Alignment explanation
Indices: 3411169--3411226 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 19
3411159 CTTTTGAATT
*
3411169 TCTTTTTCTTTTCTTTTTTT
1 TCTTTTTCTTTTC-TTTTTG
* *
3411189 TCTTATTCTTTTTTTTTTG
1 TCTTTTTCTTTTCTTTTTG
3411208 TCTTTTTCTTTTCTTTTTG
1 TCTTTTTCTTTTCTTTTTG
3411227 CTCTCCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
19 22 0.67
20 11 0.33
ACGTcount: A:0.02, C:0.14, G:0.03, T:0.81
Consensus pattern (19 bp):
TCTTTTTCTTTTCTTTTTG
Found at i:3413055 original size:16 final size:16
Alignment explanation
Indices: 3413036--3413066 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3413026 CATTTAACCC
*
3413036 TTTATAAATTTAAATT
1 TTTATAAATTAAAATT
3413052 TTTATAAATTAAAAT
1 TTTATAAATTAAAAT
3413067 AATAATATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTATAAATTAAAATT
Found at i:3414471 original size:17 final size:16
Alignment explanation
Indices: 3414429--3414467 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3414419 TATATTTTAA
*
3414429 AATTTTAAATTATTATT
1 AATTTTAATTTATT-TT
*
3414446 TATTTTAATTTATTTT
1 AATTTTAATTTATTTT
3414462 AATTTT
1 AATTTT
3414468 TAATGATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTTTAATTTATTTT
Found at i:3415882 original size:39 final size:39
Alignment explanation
Indices: 3415821--3415912 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 39
3415811 TCATAATTGT
*
3415821 TTTTCGAATTGAATAATCAATATGATCATATC-ATAAAA
1 TTTTCGAATTGAATAATCAATATGATCATATCAAGAAAA
* * *
3415859 TTTGTTGAATTGAATAATTAATATGGTCATATCAAGAAAA
1 TTT-TCGAATTGAATAATCAATATGATCATATCAAGAAAA
3415899 TTTTCGAATTGAAT
1 TTTTCGAATTGAAT
3415913 CAAACAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
38 3 0.06
39 36 0.77
40 8 0.17
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (39 bp):
TTTTCGAATTGAATAATCAATATGATCATATCAAGAAAA
Found at i:3420374 original size:45 final size:46
Alignment explanation
Indices: 3420288--3420376 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 46
3420278 AAAAAAGCCA
* *
3420288 GAGTGCATCGATGCATGGTCTTGTGCATCGATGCATCAAATGCACT
1 GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACT
3420334 GAGTGCATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCA
3420377 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (46 bp):
GAGTGCATCGATGCATGGTCATGTGCATCGATGCATAAAATGCACT
Found at i:3426054 original size:220 final size:215
Alignment explanation
Indices: 3425715--3426118 Score: 664
Period size: 220 Copynumber: 1.9 Consensus size: 215
3425705 CGAATTAGAT
3425715 TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCGAACCGACC
1 TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCGAACCGACC
*
3425780 CGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTT
66 CGAAAATATATATAATTCAGGTCGGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAATAATTT
* * * *
3425845 TTTATTATTTCGGGTCGGGTTGGATTTCTAATTCATATATTCGGATTGGGTCGGATGAAACTTTA
131 TTTATTATTTCAGGTCGAGTCGGATTTCTAATTCATATATTCGGATCGGGTCGGATGAAACTTTA
3425910 TTTTGTTCGGGTCGGTCGGG
196 TTTTGTTCGGGTCGGTCGGG
* * *
3425930 TTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTCGGGTTTGAGTTTAGGGTGAAAAAAATCGGAC
1 TTTTTTAAGTGTGATATTC--G--G-GTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCGAAC
* *
3425995 CGACCCGAAAATATATATAATTCGGGTCGGGTCGAATTAAGTCATTGTTTTTATTAAATAAAAAT
61 CGACCCGAAAATATATATAATTCAGGTCGGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAAT
*
3426060 AATTTTTTATTATTTCAGGTCGAGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGG
126 AATTTTTTATTATTTCAGGTCGAGTCGGATTTCTAATTCATATATTCGGATCGGGTCGG
3426119 GTTTTTTTAA
Statistics
Matches: 173, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
215 19 0.11
217 1 0.01
219 1 0.01
220 152 0.88
ACGTcount: A:0.26, C:0.12, G:0.25, T:0.37
Consensus pattern (215 bp):
TTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGAGTTTAGGGTGAAAAAAACCGAACCGACC
CGAAAATATATATAATTCAGGTCGGGTCGAATTAAGTCACTGTTTTTATTAAATAAAAATAATTT
TTTATTATTTCAGGTCGAGTCGGATTTCTAATTCATATATTCGGATCGGGTCGGATGAAACTTTA
TTTTGTTCGGGTCGGTCGGG
Found at i:3426753 original size:16 final size:15
Alignment explanation
Indices: 3426732--3426774 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
3426722 ATATGAAATT
3426732 AATTTCAATTCCTAC
1 AATTTCAATTCCTAC
3426747 AAATTTCAATT-CTAC
1 -AATTTCAATTCCTAC
3426762 AATTTCAATTCCT
1 AATTTCAATTCCT
3426775 TCAGAGATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.38
15 6 0.23
16 10 0.38
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (15 bp):
AATTTCAATTCCTAC
Found at i:3429997 original size:28 final size:27
Alignment explanation
Indices: 3429912--3429998 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
3429902 TCTCATTCTA
*
3429912 AATTGATCTCTAAATTTTT-TAATTCC
1 AATTGATCCCTAAATTTTTATAATTCC
* * ** **
3429938 GAATTCATCCCTAAACTACTACCATTCTC
1 -AATTGATCCCTAAATTTTTATAATTC-C
3429967 AATTGATCCCTAAATTTTTTATAATTCC
1 AATTGATCCCTAAA-TTTTTATAATTCC
3429995 AATT
1 AATT
3429999 TTATTTGTAA
Statistics
Matches: 44, Mismatches: 13, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
27 14 0.32
28 22 0.50
29 8 0.18
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (27 bp):
AATTGATCCCTAAATTTTTATAATTCC
Found at i:3430991 original size:2 final size:2
Alignment explanation
Indices: 3430984--3431019 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
3430974 TTTTAAAATA
3430984 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
3431020 TTTTTAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3433824 original size:2 final size:2
Alignment explanation
Indices: 3433819--3433845 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3433809 TTTTTTAATT
3433819 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 T
3433846 TATTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3435683 original size:12 final size:12
Alignment explanation
Indices: 3435663--3435761 Score: 74
Period size: 12 Copynumber: 8.2 Consensus size: 12
3435653 CAAGCGCCTC
3435663 CAGGTGATTTAG
1 CAGGTGATTTAG
* *
3435675 CAGGCGATTTGG
1 CAGGTGATTTAG
** **
3435687 CAAATGGCTTAG
1 CAGGTGATTTAG
3435699 CAGGTGATTTAG
1 CAGGTGATTTAG
* *
3435711 CAGGCGATTTTG
1 CAGGTGATTTAG
*
3435723 CATGTGATTTAG
1 CAGGTGATTTAG
3435735 -AGGGTGATTTAG
1 CA-GGTGATTTAG
** *
3435747 TGGGTGACTTAG
1 CAGGTGATTTAG
3435759 CAG
1 CAG
3435762 TACCCTTACG
Statistics
Matches: 63, Mismatches: 22, Indels: 4
0.71 0.25 0.04
Matches are distributed among these distances:
11 1 0.02
12 62 0.98
ACGTcount: A:0.23, C:0.11, G:0.34, T:0.31
Consensus pattern (12 bp):
CAGGTGATTTAG
Found at i:3435741 original size:36 final size:36
Alignment explanation
Indices: 3435663--3435746 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
3435653 CAAGCGCCTC
*
3435663 CAGGTGATTTAGCAGGCGATTTGGCAAATGGCTTAG
1 CAGGTGATTTAGCAGGCGATTTGGCAAATGACTTAG
* ** *
3435699 CAGGTGATTTAGCAGGCGATTTTGCATGTGATTTAG
1 CAGGTGATTTAGCAGGCGATTTGGCAAATGACTTAG
3435735 -AGGGTGATTTAG
1 CA-GGTGATTTAG
3435747 TGGGTGACTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
35 1 0.02
36 41 0.98
ACGTcount: A:0.24, C:0.11, G:0.33, T:0.32
Consensus pattern (36 bp):
CAGGTGATTTAGCAGGCGATTTGGCAAATGACTTAG
Found at i:3438341 original size:27 final size:27
Alignment explanation
Indices: 3438311--3438366 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
3438301 ACTTTTTTGT
*
3438311 ATACCATTTGGTAAACTTTGAGAATCA
1 ATACCATTTGGTAAACTTCGAGAATCA
3438338 ATACCATTTGGTAAACTTCGAGAATCA
1 ATACCATTTGGTAAACTTCGAGAATCA
3438365 AT
1 AT
3438367 CTGTTGTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (27 bp):
ATACCATTTGGTAAACTTCGAGAATCA
Found at i:3442247 original size:20 final size:20
Alignment explanation
Indices: 3442222--3442259 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3442212 TGGGTTAGAG
3442222 TATCGATACTGGATGAATAA
1 TATCGATACTGGATGAATAA
*
3442242 TATCGATATTGGATGAAT
1 TATCGATACTGGATGAAT
3442260 TAGGAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (20 bp):
TATCGATACTGGATGAATAA
Found at i:3442447 original size:19 final size:21
Alignment explanation
Indices: 3442411--3442458 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
3442401 ACGAATGGTC
3442411 TCCATACCGAAGGGCTTG-TA
1 TCCATACCGAAGGGCTTGATA
*
3442431 TCCATACTGAA-GGCTTGATA
1 TCCATACCGAAGGGCTTGATA
*
3442451 TCAATACC
1 TCCATACC
3442459 TAAAGTGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (21 bp):
TCCATACCGAAGGGCTTGATA
Found at i:3443320 original size:27 final size:27
Alignment explanation
Indices: 3443282--3443344 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
3443272 ATCAGGGTTA
*
3443282 GAGACCCTTTAAATATGTACTCATGGT
1 GAGACCCTTTAAATATGTACTCATAGT
*
3443309 GAGACCCTTTAAATGTGTACTCATAGT
1 GAGACCCTTTAAATATGTACTCATAGT
3443336 GAGACCCTT
1 GAGACCCTT
3443345 AATAGAGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (27 bp):
GAGACCCTTTAAATATGTACTCATAGT
Found at i:3445038 original size:20 final size:18
Alignment explanation
Indices: 3445013--3445049 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
3445003 CATAGACCAG
3445013 GAGTATCGATACTCAAACTA
1 GAGTATC-ATACT-AAACTA
3445033 GAGTATCATACTAAACT
1 GAGTATCATACTAAACT
3445050 TTTGCTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 5 0.29
20 7 0.41
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (18 bp):
GAGTATCATACTAAACTA
Found at i:3445132 original size:168 final size:170
Alignment explanation
Indices: 3444928--3445265 Score: 662
Period size: 168 Copynumber: 2.0 Consensus size: 170
3444918 TAAGGGTAGA
3444928 GTACAGATACCCCTAGTAGGGGTATCAATACTAAGGTATTTTTCAAAGCATCAAAGGCGATTTTG
1 GTACAGATACCCCTAGTAGGGGTATCAATACTAAGGTATTTTTCAAAGCATCAAAGGCGATTTTG
3444993 GTATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATC-ATACTAAACTTTTGCTA
66 GTATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTA
3445057 GTAGTCTTCAATAAGTTAGTAAAATCGATACCAAGAGGGT
131 GTAGTCTTCAATAAGTTAGTAAAATCGATACCAAGAGGGT
3445097 GTACAGATACCCCTAGTA-GGGTATCAATACTAAGGTATTTTTCAAAGCATCAAAGGCGATTTTG
1 GTACAGATACCCCTAGTAGGGGTATCAATACTAAGGTATTTTTCAAAGCATCAAAGGCGATTTTG
3445161 GTATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTA
66 GTATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTA
3445226 GTAGTCTTCAATAAGTTAGTAAAATCGATACCAAGAGGGT
131 GTAGTCTTCAATAAGTTAGTAAAATCGATACCAAGAGGGT
3445266 AGTATCGATA
Statistics
Matches: 168, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
168 93 0.55
169 75 0.45
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.28
Consensus pattern (170 bp):
GTACAGATACCCCTAGTAGGGGTATCAATACTAAGGTATTTTTCAAAGCATCAAAGGCGATTTTG
GTATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTA
GTAGTCTTCAATAAGTTAGTAAAATCGATACCAAGAGGGT
Found at i:3445206 original size:20 final size:19
Alignment explanation
Indices: 3445181--3445218 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3445171 CATAGACCAG
*
3445181 GAGTATCGATACTCAAACTA
1 GAGTATCAATACT-AAACTA
3445201 GAGTATCAATACTAAACT
1 GAGTATCAATACTAAACT
3445219 TTTGCTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.26
Consensus pattern (19 bp):
GAGTATCAATACTAAACTA
Found at i:3445253 original size:86 final size:86
Alignment explanation
Indices: 3444995--3445258 Score: 253
Period size: 86 Copynumber: 3.1 Consensus size: 86
3444985 CGATTTTGGT
3444995 ATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATC-ATACTAAACTTTTGCTAGT
1 ATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTAGT
3445059 AGTCTTCAATAAGTTAGTAAA
66 AGTCTTCAATAAGTTAGTAAA
* * * ** * * *
3445080 ATCGATACCA-AGA--GGGTGTA-CAGATACCCCTAGTAGGGTATCAATACTAAGGTA-TTTTTC
1 ATCGATACCATAGACCAGGAGTATC-GATACTCAAACTAGAGTATCAATACTAA---ACTTTTGC
* * * * ***
3445140 -A-AAG-CATCAA-AGGCGATT-TTGGT
62 TAGTAGTCTTCAATA--AG-TTAGTAAA
3445163 ATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTAGT
1 ATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTAGT
3445228 AGTCTTCAATAAGTTAGTAAA
66 AGTCTTCAATAAGTTAGTAAA
3445249 ATCGATACCA
1 ATCGATACCA
3445259 AGAGGGTAGT
Statistics
Matches: 131, Mismatches: 30, Indels: 35
0.67 0.15 0.18
Matches are distributed among these distances:
81 2 0.02
82 25 0.19
83 22 0.17
84 14 0.11
85 18 0.14
86 43 0.33
87 6 0.05
88 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.28
Consensus pattern (86 bp):
ATCGATACCATAGACCAGGAGTATCGATACTCAAACTAGAGTATCAATACTAAACTTTTGCTAGT
AGTCTTCAATAAGTTAGTAAA
Found at i:3447427 original size:16 final size:16
Alignment explanation
Indices: 3447406--3447439 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3447396 GGAATGGTCC
*
3447406 GTAAGGATAAGACTTA
1 GTAAGGACAAGACTTA
3447422 GTAAGGACAAGACTTA
1 GTAAGGACAAGACTTA
3447438 GT
1 GT
3447440 TCGTGAGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.09, G:0.26, T:0.24
Consensus pattern (16 bp):
GTAAGGACAAGACTTA
Found at i:3448405 original size:32 final size:31
Alignment explanation
Indices: 3448364--3448527 Score: 186
Period size: 32 Copynumber: 5.1 Consensus size: 31
3448354 ACTTGTATGT
*
3448364 TGCATAGTAGTATTAGTATTGTATTCAAATAA
1 TGCATAGTAG-ATTAGTATTGCATTCAAATAA
*
3448396 TGCATAGTAGAGTTAGTATTGCATTCAGATAA
1 TGCATAGTAGA-TTAGTATTGCATTCAAATAA
*
3448428 TGCATAGTAGATTCAATATTGCATTCAAATAA
1 TGCATAGTAGATT-AGTATTGCATTCAAATAA
* * * *
3448460 TGCATAACATAGA-CAATATTGCATTCAGATAA
1 TGCAT-A-GTAGATTAGTATTGCATTCAAATAA
* *
3448492 TGCATAGCAGAGTCAGTATTGCATTCAAATAA
1 TGCATAGTAGA-TTAGTATTGCATTCAAATAA
3448524 TGCA
1 TGCA
3448528 CATGAGCATC
Statistics
Matches: 115, Mismatches: 11, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
30 3 0.03
31 4 0.03
32 103 0.90
33 1 0.01
34 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (31 bp):
TGCATAGTAGATTAGTATTGCATTCAAATAA
Found at i:3448465 original size:64 final size:64
Alignment explanation
Indices: 3448364--3448527 Score: 222
Period size: 64 Copynumber: 2.6 Consensus size: 64
3448354 ACTTGTATGT
* ** ** *
3448364 TGCATAGTAGTATT-AGTATTGTATTCAAATAATGCATAGTAGAGTTAGTATTGCATTCAGATAA
1 TGCATAGTAG-ATTCAGTATTGCATTCAAATAATGCATAACAGAGACAATATTGCATTCAGATAA
* *
3448428 TGCATAGTAGATTCAATATTGCATTCAAATAATGCATAACATAGACAATATTGCATTCAGATAA
1 TGCATAGTAGATTCAGTATTGCATTCAAATAATGCATAACAGAGACAATATTGCATTCAGATAA
* *
3448492 TGCATAGCAGAGTCAGTATTGCATTCAAATAATGCA
1 TGCATAGTAGATTCAGTATTGCATTCAAATAATGCA
3448528 CATGAGCATC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
63 3 0.03
64 85 0.97
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.33
Consensus pattern (64 bp):
TGCATAGTAGATTCAGTATTGCATTCAAATAATGCATAACAGAGACAATATTGCATTCAGATAA
Found at i:3453373 original size:52 final size:52
Alignment explanation
Indices: 3453295--3453398 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
3453285 TGCTCAAAGA
*
3453295 CTACGACTGTGTGATTGACTACCACCCAAGGACTACGAAATGTGAAAGTTGT
1 CTACGACTGTGTGATTGACTACCACCCAAGCACTACGAAATGTGAAAGTTGT
3453347 CTACGACTGTGTGATTGACTACCACCCAAGCACTACGAAATGTGAAAGTTGT
1 CTACGACTGTGTGATTGACTACCACCCAAGCACTACGAAATGTGAAAGTTGT
3453399 TTTCTCATGA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (52 bp):
CTACGACTGTGTGATTGACTACCACCCAAGCACTACGAAATGTGAAAGTTGT
Found at i:3456889 original size:39 final size:39
Alignment explanation
Indices: 3456815--3456956 Score: 177
Period size: 39 Copynumber: 3.8 Consensus size: 39
3456805 CCCACCATAA
* * * *
3456815 TACACATAAGGTCGTG--CACTATATGTAACGAAGTGCT
1 TACACATAAGGTCGTGCCCACCATATGCACCAAAGTGCT
3456852 TACACATAAGGTCGTGCCCACCATATGCACCAAAGTGCT
1 TACACATAAGGTCGTGCCCACCATATGCACCAAAGTGCT
*
3456891 T--ACA-AAGGTCGTGCCCACCATATGCACCTAAGTGCT
1 TACACATAAGGTCGTGCCCACCATATGCACCAAAGTGCT
* * *
3456927 TACACATAAGGTCATGCACACCATACGCAC
1 TACACATAAGGTCGTGCCCACCATATGCAC
3456957 TAGGTATCCT
Statistics
Matches: 92, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
36 32 0.35
37 19 0.21
38 3 0.03
39 38 0.41
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (39 bp):
TACACATAAGGTCGTGCCCACCATATGCACCAAAGTGCT
Found at i:3464773 original size:143 final size:144
Alignment explanation
Indices: 3464514--3464805 Score: 561
Period size: 143 Copynumber: 2.0 Consensus size: 144
3464504 TACTCCATCT
3464514 TATACAGATACCTCAGTGGAAATGGGATAGGGTGACATGGACTTTGTGACATTTTTACTAATAAC
1 TATACAGATACCTCAGTGGAAATGGGATAGGGTGACATGGACTTTGTGACATTTTTACTAATAAC
3464579 CAAGCACATACACAATGCAGTTTGGGTTACAGTAGGCCGCTTAACCAAATTAGCTCATTTTATCC
66 CAAGCACATACACAATGCAGTTTGGGTTACAGTAGGCCGCTTAACCAAATTAGCTCATTTTATCC
3464644 CAGTTCGCATGGAC
131 CAGTTCGCATGGAC
3464658 TATACAGATACCTCAGTGGAAATGGGATA-GG-GACCATGGACTTTGTGACATTTTTACTAATAA
1 TATACAGATACCTCAGTGGAAATGGGATAGGGTGA-CATGGACTTTGTGACATTTTTACTAATAA
3464721 CCAAGCACATACACAATGCAGTTTGGGTTACAGTAGGCCGCTTAACCAAATTAGCTCATTTTATC
65 CCAAGCACATACACAATGCAGTTTGGGTTACAGTAGGCCGCTTAACCAAATTAGCTCATTTTATC
3464786 CCAGTTCGCATGGAC
130 CCAGTTCGCATGGAC
3464801 TATAC
1 TATAC
3464806 CTTAGAGCGG
Statistics
Matches: 147, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
142 2 0.01
143 116 0.79
144 29 0.20
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (144 bp):
TATACAGATACCTCAGTGGAAATGGGATAGGGTGACATGGACTTTGTGACATTTTTACTAATAAC
CAAGCACATACACAATGCAGTTTGGGTTACAGTAGGCCGCTTAACCAAATTAGCTCATTTTATCC
CAGTTCGCATGGAC
Found at i:3472127 original size:17 final size:16
Alignment explanation
Indices: 3472101--3472133 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3472091 AGCCATTGAT
3472101 CAATAACAAGAATCAA
1 CAATAACAAGAATCAA
3472117 CAATCAACAAGAATCAA
1 CAAT-AACAAGAATCAA
3472134 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (16 bp):
CAATAACAAGAATCAA
Found at i:3480464 original size:17 final size:16
Alignment explanation
Indices: 3480438--3480470 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
3480428 AGCCATTAAT
3480438 CAATAACAAGAATCAA
1 CAATAACAAGAATCAA
3480454 CAATCAACAAGAATCAA
1 CAAT-AACAAGAATCAA
3480471 GAGAGAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.61, C:0.21, G:0.06, T:0.12
Consensus pattern (16 bp):
CAATAACAAGAATCAA
Found at i:3483598 original size:16 final size:17
Alignment explanation
Indices: 3483564--3483596 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
3483554 AAAAAAAGAG
3483564 TATTTTATCTTCATTTT
1 TATTTTATCTTCATTTT
3483581 TATTTT-TCTT-ATTTT
1 TATTTTATCTTCATTTT
3483596 T
1 T
3483597 TAAAGAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 4 0.25
17 6 0.38
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TATTTTATCTTCATTTT
Found at i:3491674 original size:135 final size:135
Alignment explanation
Indices: 3491432--3491702 Score: 533
Period size: 135 Copynumber: 2.0 Consensus size: 135
3491422 CCCCCAACTT
3491432 TCAAAAAATTATATAAGGGTTCCTATAACTTTCTAAGGCTTGTAGAATCCTTCCCACATCATTTA
1 TCAAAAAATTATATAAGGGTTCCTATAACTTTCTAAGGCTTGTAGAATCCTTCCCACATCATTTA
3491497 CAACCCTTACATAATTTTTTCACAATTTTCTCACTCATTCAAGCCATGGTCAAATATTTTAGTGC
66 CAACCCTTACATAATTTTTTCACAATTTTCTCACTCATTCAAGCCATGGTCAAATATTTTAGTGC
3491562 TATGG
131 TATGG
*
3491567 TCAAAAAATTATGTAAGGGTTCCTATAACTTTCTAAGGCTTGTAGAATCCTTCCCACATCATTTA
1 TCAAAAAATTATATAAGGGTTCCTATAACTTTCTAAGGCTTGTAGAATCCTTCCCACATCATTTA
3491632 CAACCCTTACATAATTTTTTCACAATTTTCTCACTCATTCAAGCCATGGTCAAATATTTTAGTGC
66 CAACCCTTACATAATTTTTTCACAATTTTCTCACTCATTCAAGCCATGGTCAAATATTTTAGTGC
3491697 TATGG
131 TATGG
3491702 T
1 T
3491703 TCCATAATTT
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
135 135 1.00
ACGTcount: A:0.31, C:0.21, G:0.11, T:0.37
Consensus pattern (135 bp):
TCAAAAAATTATATAAGGGTTCCTATAACTTTCTAAGGCTTGTAGAATCCTTCCCACATCATTTA
CAACCCTTACATAATTTTTTCACAATTTTCTCACTCATTCAAGCCATGGTCAAATATTTTAGTGC
TATGG
Found at i:3495175 original size:163 final size:160
Alignment explanation
Indices: 3494984--3495307 Score: 621
Period size: 163 Copynumber: 2.0 Consensus size: 160
3494974 AAATATTTAA
3494984 AAAACTAAAATAATCATTATAATGTTTAGTGATATAATAATTAATATTAATAAATTAATTATTGA
1 AAAACTAAAATAATCATTATAATGTTTAGTGATATAATAATTAATATTAATAAATTAATTATTGA
3495049 GAAAAGTATTTCAATTAAAAGAGGAATCTTCCTTGAAGTCAATAAGAATAATTAACCGTAATAGC
66 GAAAAGTATTTCAATTAAAAGAGGAATCTTCCTTGAAGTCAATAAGAATAATTAACCGTAATAGC
3495114 TACGTTTTCCCTGTTTGATTGAAACACTCTTCC
131 TACG-TTTCCCTGTTTGATTG-AA-ACTCTTCC
3495147 AAAACTAAAATAATCATTATAATGTTTAGTGATATAATAATTAATATTAATAAATTAATTATTGA
1 AAAACTAAAATAATCATTATAATGTTTAGTGATATAATAATTAATATTAATAAATTAATTATTGA
3495212 GAAAAGTATTTCAATTAAAAGAGGAATCTTCCTTGAAGTCAATAAGAATAATTAACCGTAATAGC
66 GAAAAGTATTTCAATTAAAAGAGGAATCTTCCTTGAAGTCAATAAGAATAATTAACCGTAATAGC
3495277 TACGTTTCCCTGTTTGATTGAAACTCTTCC
131 TACGTTTCCCTGTTTGATTGAAACTCTTCC
3495307 A
1 A
3495308 TCAAACCTTT
Statistics
Matches: 161, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
160 9 0.06
161 2 0.01
162 16 0.10
163 134 0.83
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.35
Consensus pattern (160 bp):
AAAACTAAAATAATCATTATAATGTTTAGTGATATAATAATTAATATTAATAAATTAATTATTGA
GAAAAGTATTTCAATTAAAAGAGGAATCTTCCTTGAAGTCAATAAGAATAATTAACCGTAATAGC
TACGTTTCCCTGTTTGATTGAAACTCTTCC
Found at i:3509662 original size:21 final size:22
Alignment explanation
Indices: 3509622--3509663 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
3509612 ATATATATAT
*
3509622 ATAATATAAAAGACTTATTTAC
1 ATAATATAAAAGAATTATTTAC
3509644 ATAATATAAAA-AATTATTTA
1 ATAATATAAAAGAATTATTTA
3509664 GTTTTATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (22 bp):
ATAATATAAAAGAATTATTTAC
Found at i:3509876 original size:44 final size:44
Alignment explanation
Indices: 3509798--3509886 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
3509788 TGACCCTATT
*
3509798 CCCATATGTAATGGGGTAAAGGGATGTATAATAGTAGGCTGCCC
1 CCCATATATAATGGGGTAAAGGGATGTATAATAGTAGGCTGCCC
* * *
3509842 CCCATATATAATGGGGTAAGGGGA-GATATGATAGTAGGTTGCCC
1 CCCATATATAATGGGGTAAAGGGATG-TATAATAGTAGGCTGCCC
3509886 C
1 C
3509887 AACGCCAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
43 1 0.03
44 39 0.98
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (44 bp):
CCCATATATAATGGGGTAAAGGGATGTATAATAGTAGGCTGCCC
Found at i:3514036 original size:43 final size:43
Alignment explanation
Indices: 3513970--3514098 Score: 240
Period size: 43 Copynumber: 3.0 Consensus size: 43
3513960 TGTAATTGTT
*
3513970 CATCGACATTAAATTTATTAAATTGTTACAAAATAGTGATTAA
1 CATCGACATTAAATTTATCAAATTGTTACAAAATAGTGATTAA
3514013 CATCGACATTAAATTTATCAAATTGTTACAAAATAGTGATTAA
1 CATCGACATTAAATTTATCAAATTGTTACAAAATAGTGATTAA
*
3514056 CATCGACATTAAATTTATCAAATTGTTACAAAATGGTGATTAA
1 CATCGACATTAAATTTATCAAATTGTTACAAAATAGTGATTAA
3514099 ATCTATCAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 84 1.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (43 bp):
CATCGACATTAAATTTATCAAATTGTTACAAAATAGTGATTAA
Found at i:3516226 original size:12 final size:12
Alignment explanation
Indices: 3516209--3516247 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3516199 TTTAGATAAA
3516209 ATTAATTTAATT
1 ATTAATTTAATT
3516221 ATTAA-TTAATT
1 ATTAATTTAATT
3516232 ATTTAATTTATATT
1 A-TTAATTTA-ATT
3516246 AT
1 AT
3516248 GTTAGAGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 9 0.38
13 4 0.17
14 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTAATTTAATT
Found at i:3516775 original size:3 final size:3
Alignment explanation
Indices: 3516754--3516806 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
3516744 TTTGTCCGGG
* *
3516754 TTA TTA ATA TTA ATA TTA TTA TTA TTA TTA TTA -TA TT- TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
3516798 TTA TTA TTA
1 TTA TTA TTA
3516807 GAGAAAATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
2 3 0.07
3 39 0.91
4 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3516935 original size:20 final size:20
Alignment explanation
Indices: 3516910--3516964 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
3516900 GCGAAATAAA
3516910 AATCGCAACACGA-TCTCCAG
1 AATCGCAACACGATTC-CCAG
*
3516930 AATCGCAA-ATCAATTCCCAG
1 AATCGCAACA-CGATTCCCAG
*
3516950 AATCGCAACGCGATT
1 AATCGCAACACGATT
3516965 ATGAAGAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
19 1 0.03
20 26 0.90
21 2 0.07
ACGTcount: A:0.36, C:0.31, G:0.15, T:0.18
Consensus pattern (20 bp):
AATCGCAACACGATTCCCAG
Found at i:3516974 original size:21 final size:21
Alignment explanation
Indices: 3516948--3517042 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
3516938 ATCAATTCCC
3516948 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
3516969 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
** * **
3516989 CA-AATTCGCATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
*
3517011 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
3517032 A-AATCGCAACG
1 AGAATCGCAACG
3517043 AGTATCCGTA
Statistics
Matches: 57, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.02
20 15 0.26
21 38 0.67
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:3517038 original size:20 final size:20
Alignment explanation
Indices: 3517013--3517222 Score: 161
Period size: 20 Copynumber: 10.5 Consensus size: 20
3517003 GATTTTCCAG
*
3517013 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGTA
* * **
3517033 AATCGCAACGAGTATCCGTA
1 AATCGCAACGCGAATATGTA
*
3517053 AATCGCAACGAC-AATACGTA
1 AATCGCAACG-CGAATATGTA
* * *
3517073 AATCGCAACGTGTATCTGTA
1 AATCGCAACGCGAATATGTA
* * *
3517093 AATCACAAGGAGAATATGTA
1 AATCGCAACGCGAATATGTA
* * * **
3517113 AATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATATGTA
* * **
3517133 AATCACAATGCGAATACATA
1 AATCGCAACGCGAATATGTA
* *
3517153 AATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATATGTA
*
3517173 AATCGCAATGCGAATATGTA
1 AATCGCAACGCGAATATGTA
* * *
3517193 AATCGCAATGTGAATCTGTA
1 AATCGCAACGCGAATATGTA
3517213 AATCGCAACG
1 AATCGCAACG
3517223 AGATTCTGAC
Statistics
Matches: 154, Mismatches: 34, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
20 154 1.00
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22
Consensus pattern (20 bp):
AATCGCAACGCGAATATGTA
Found at i:3517062 original size:40 final size:40
Alignment explanation
Indices: 3517013--3517222 Score: 233
Period size: 40 Copynumber: 5.2 Consensus size: 40
3517003 GATTTTCCAG
* * *
3517013 AATCGCAACGCGAATATGAAAATCGCAACGAGTATCCGTA
1 AATCGCAACGCGAATATGTAAATCGCAATGTGTATCCGTA
* * *
3517053 AATCGCAACGAC-AATACGTAAATCGCAACGTGTATCTGTA
1 AATCGCAACG-CGAATATGTAAATCGCAATGTGTATCCGTA
* * *
3517093 AATCACAAGGAGAATATGTAAATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATATGTAAATCGCAATGTGTATCCGTA
* * ** * * *
3517133 AATCACAATGCGAATACATAAATCGCAATGCGAATACGTA
1 AATCGCAACGCGAATATGTAAATCGCAATGTGTATCCGTA
* * *
3517173 AATCGCAATGCGAATATGTAAATCGCAATGTGAATCTGTA
1 AATCGCAACGCGAATATGTAAATCGCAATGTGTATCCGTA
3517213 AATCGCAACG
1 AATCGCAACG
3517223 AGATTCTGAC
Statistics
Matches: 144, Mismatches: 24, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
40 143 0.99
41 1 0.01
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.22
Consensus pattern (40 bp):
AATCGCAACGCGAATATGTAAATCGCAATGTGTATCCGTA
Found at i:3517096 original size:60 final size:59
Alignment explanation
Indices: 3517013--3517225 Score: 194
Period size: 60 Copynumber: 3.6 Consensus size: 59
3517003 GATTTTCCAG
* * * * *
3517013 AATCGCAACGCGAATATGAAAATCGCAACGAGTATCCGTAAATCGCAACGACAATACGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAATG-CAATACGTA
* * * * * ** *
3517073 AATCGCAACGTGTATCTGTAAATCACAAGGAGAATATGTAAATCGCAATGTGTATCCGTA
1 AATCGCAACGCGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAATG-CAATACGTA
* * * * * *
3517133 AATCACAATGCGAATAC-ATAAATCGCAATGCGAATACGTAAATCGCAATGCGAATATGTA
1 AATCGCAACGCGAAT-CTGTAAATCGCAACGAGAATACGTAAATCGCAATGC-AATACGTA
* *
3517193 AATCGCAATGTGAATCTGTAAATCGCAACGAGA
1 AATCGCAACGCGAATCTGTAAATCGCAACGAGA
3517226 TTCTGACTAT
Statistics
Matches: 118, Mismatches: 32, Indels: 6
0.76 0.21 0.04
Matches are distributed among these distances:
59 1 0.01
60 116 0.98
61 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (59 bp):
AATCGCAACGCGAATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCAATACGTA
Found at i:3518104 original size:24 final size:24
Alignment explanation
Indices: 3518077--3518123 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
3518067 AGTCAGTATT
3518077 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
*
3518101 CGAACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
3518124 TCAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:3518135 original size:24 final size:24
Alignment explanation
Indices: 3518082--3518128 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
3518072 GTATTCGAAA
*
3518082 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
3518106 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
3518129 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Found at i:3520715 original size:33 final size:33
Alignment explanation
Indices: 3520673--3520766 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
3520663 GGAAATTACT
*
3520673 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3520706 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
3520739 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3520767 CGAATTTAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3520769 original size:19 final size:19
Alignment explanation
Indices: 3520673--3520770 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
3520663 GGAAATTACT
*
3520673 ATCGCAATGCAAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3520692 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3520706 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
3520725 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
3520739 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3520758 ATCGCAACGCGAA
1 ATCGCAATGCGAA
3520771 TTTAGTTTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.07
17 3 0.05
18 2 0.03
19 31 0.51
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3520795 original size:14 final size:14
Alignment explanation
Indices: 3520776--3520820 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
3520766 GCGAATTTAG
3520776 TTTGGCGTTGCGAT
1 TTTGGCGTTGCGAT
3520790 TTTGGCGTTGCGAT
1 TTTGGCGTTGCGAT
*
3520804 TTTGTCGTTGCGAT
1 TTTGGCGTTGCGAT
3520818 TTT
1 TTT
3520821 AATTTCGCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.07, C:0.13, G:0.31, T:0.49
Consensus pattern (14 bp):
TTTGGCGTTGCGAT
Found at i:3520835 original size:19 final size:18
Alignment explanation
Indices: 3520811--3520869 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
3520801 GATTTTGTCG
3520811 TTGCGATTTTAATTTCGCA
1 TTGCGATTTT-ATTTCGCA
* *
3520830 TTGCGA--TTCTCTCG--
1 TTGCGATTTTATTTCGCA
3520844 TTGCGATTTTCATTTCGCA
1 TTGCGATTTT-ATTTCGCA
3520863 TTGCGAT
1 TTGCGAT
3520870 AGTCATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 6 0.19
16 6 0.19
17 6 0.19
19 13 0.42
ACGTcount: A:0.15, C:0.20, G:0.19, T:0.46
Consensus pattern (18 bp):
TTGCGATTTTATTTCGCA
Found at i:3520845 original size:33 final size:33
Alignment explanation
Indices: 3520797--3520869 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
3520787 GATTTTGGCG
* *
3520797 TTGCGATTTTGTCGTTGCGATTTTAATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTAATTTCGCA
*
3520830 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTAATTTCGCA
3520863 TTGCGAT
1 TTGCGAT
3520870 AGTCATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTAATTTCGCA
Found at i:3520995 original size:14 final size:14
Alignment explanation
Indices: 3520976--3521012 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3520966 CATCAATTAA
3520976 ACAAATCAACTTTT
1 ACAAATCAACTTTT
* *
3520990 ACAAATGATCTTTT
1 ACAAATCAACTTTT
3521004 ACAAATCAA
1 ACAAATCAA
3521013 TTAAACAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.19, G:0.03, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3522429 original size:21 final size:21
Alignment explanation
Indices: 3522363--3522429 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3522353 GTGAATCGGG
*
3522363 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
3522383 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
3522405 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
3522426 CTCT
1 CTCT
3522430 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:3524509 original size:19 final size:19
Alignment explanation
Indices: 3524445--3524562 Score: 164
Period size: 19 Copynumber: 6.1 Consensus size: 19
3524435 TCTTTTGGTT
*
3524445 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
3524464 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
3524484 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
3524504 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
3524523 GAAATGAAAATCGAAACGC
1 GAAATGAAAATCGCAACGC
* *
3524542 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAACGC
3524561 GA
1 GA
3524563 TTTTGGTTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
19 55 0.62
20 31 0.35
21 2 0.02
ACGTcount: A:0.47, C:0.18, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:3524627 original size:21 final size:20
Alignment explanation
Indices: 3524608--3524679 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
3524598 TGATTCTCTC
3524608 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
3524628 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
3524649 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
3524669 GTTGCGATTTT
1 GTTGCGATTTT
3524680 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:3525266 original size:20 final size:20
Alignment explanation
Indices: 3525241--3525412 Score: 193
Period size: 20 Copynumber: 8.5 Consensus size: 20
3525231 TTTAAAAACT
3525241 GCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
* *
3525261 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAC
* *
3525281 GTCGTTGCAATTTATGGATAC
1 G-CGTTGCGATTTACGGATAC
* * *
3525302 GCATTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
* *
3525322 TCGTTGCGATTTACAGATAC
1 GCGTTGCGATTTACGGATAC
* *
3525342 GCGTTGCGATTTACGTATTC
1 GCGTTGCGATTTACGGATAC
*
3525362 TCGTTGCGATTTACGGATAC
1 GCGTTGCGATTTACGGATAC
3525382 GCGTTGCGATTTTACGGATAC
1 GCGTTGCGA-TTTACGGATAC
*
3525403 TCGTTGCGAT
1 GCGTTGCGAT
3525413 AGTCAGAATC
Statistics
Matches: 123, Mismatches: 25, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
20 88 0.72
21 35 0.28
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAC
Found at i:3525326 original size:40 final size:41
Alignment explanation
Indices: 3525242--3525412 Score: 265
Period size: 40 Copynumber: 4.2 Consensus size: 41
3525232 TTAAAAACTG
*
3525242 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
3525283 CGTTGCAATTTATGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
3525323 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
3525363 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
3525404 CGTTGCGAT
1 CGTTGCGAT
3525413 AGTCAGAATC
Statistics
Matches: 118, Mismatches: 11, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 74 0.63
41 44 0.37
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Done.