Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007708.1 Hibiscus syriacus cultivar Beakdansim tig00109923_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: 882274
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:435171 original size:30 final size:30
Alignment explanation
Indices: 435137--435197 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
435127 TTTTTTACAT
*
435137 TTATACATCCTTTGTATCCTTATATTTTCA
1 TTATACATCCCTTGTATCCTTATATTTTCA
435167 TTATACATCCCTTGTATCCTTATATTTTCA
1 TTATACATCCCTTGTATCCTTATATTTTCA
435197 T
1 T
435198 ACTGTTCGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.03, T:0.52
Consensus pattern (30 bp):
TTATACATCCCTTGTATCCTTATATTTTCA
Found at i:443827 original size:38 final size:37
Alignment explanation
Indices: 443785--443858 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
443775 TAATTTTAGA
443785 TATAATATAATT-AAATAATATT-TTTATATCAAAAAAGT
1 TATAATA-AATTCAAATAAT-TTATTT-TATCAAAAAAGT
*
443823 TATAATAAATTCAAATAATTTATTTTATCAACAAAG
1 TATAATAAATTCAAATAATTTATTTTATCAAAAAAG
443859 AATTATACGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
37 16 0.48
38 17 0.52
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (37 bp):
TATAATAAATTCAAATAATTTATTTTATCAAAAAAGT
Found at i:452930 original size:3 final size:3
Alignment explanation
Indices: 452922--452955 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
452912 CTTCAAAAAG
452922 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
452956 AATACAACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:458617 original size:21 final size:21
Alignment explanation
Indices: 458571--458627 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
458561 ACTTTGACGA
*
458571 AGAAGATAAAGCTAAAAAAAT
1 AGAAGATAAAGATAAAAAAAT
* *
458592 GGAAGA-AAAGATAAAAATATT
1 AGAAGATAAAGATAAAAA-AAT
*
458613 AGAAGATCAA-ATAAA
1 AGAAGATAAAGATAAA
458628 GATGGTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.34
21 17 0.59
22 2 0.07
ACGTcount: A:0.65, C:0.04, G:0.16, T:0.16
Consensus pattern (21 bp):
AGAAGATAAAGATAAAAAAAT
Found at i:465223 original size:14 final size:14
Alignment explanation
Indices: 465206--465232 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
465196 AAAAAATATG
465206 AAAAAAACAAAAAC
1 AAAAAAACAAAAAC
465220 AAAAAAACAAAAA
1 AAAAAAACAAAAA
465233 AACGCTTAGG
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:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAACAAAAAC
Found at i:466191 original size:105 final size:105
Alignment explanation
Indices: 466009--466690 Score: 1238
Period size: 105 Copynumber: 6.5 Consensus size: 105
465999 AGGTTTTACC
466009 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
466074 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
466114 CAGAGCCAATTTCAACTTCACAACGAAGGACATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
466179 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
466219 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
466284 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
466324 CAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
466389 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
466429 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
466494 ACGAAGGGACCGCTAGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
466534 CAGAGCCGATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
466599 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTTAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ** * * *
466639 CAGAGCCAATTGCTGCTTCACAACGAAGGATATTGGCCTCGAAACAACGCAA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
466691 CTTGTATGGG
Statistics
Matches: 559, Mismatches: 18, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
105 559 1.00
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:468489 original size:18 final size:17
Alignment explanation
Indices: 468448--468489 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
468438 GTTCATATTC
468448 TTAT-TTCATTTTTTTT
1 TTATATTCATTTTTTTT
*
468464 TCTCTATTCATTTTTTTCT
1 T-TATATTCATTTTTTT-T
468483 TTATATT
1 TTATATT
468490 TATTCATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 1 0.05
17 2 0.10
18 16 0.76
19 2 0.10
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATATTCATTTTTTTT
Found at i:470818 original size:17 final size:17
Alignment explanation
Indices: 470796--470832 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
470786 CTAAGAAAAA
*
470796 TTATTATTTTAGAGAGT
1 TTATTAATTTAGAGAGT
*
470813 TTATTAATTTATAGAGT
1 TTATTAATTTAGAGAGT
470830 TTA
1 TTA
470833 CGGGAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (17 bp):
TTATTAATTTAGAGAGT
Found at i:472377 original size:30 final size:28
Alignment explanation
Indices: 472285--472388 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 28
472275 ATTTAGATGA
* ** *
472285 AAAAAATAATTTAATTACAGATTTTAACT
1 AAAAAATAATTTAAATACTTATTTTGA-T
*
472314 AAAAAAT-ATTTAAATATTTATTTTGAT
1 AAAAAATAATTTAAATACTTATTTTGAT
*
472341 AAAAAATAACTTTAAATACTTATTTTTAT
1 AAAAAATAA-TTTAAATACTTATTTTGAT
*
472370 GAAAAAATATTTTTAAATA
1 -AAAAAATA-ATTTAAATA
472389 ATTTTAAAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
27 8 0.13
28 15 0.24
29 24 0.38
30 16 0.25
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (28 bp):
AAAAAATAATTTAAATACTTATTTTGAT
Found at i:474435 original size:3 final size:3
Alignment explanation
Indices: 474427--474453 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
474417 ATCAAATGTG
474427 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
474454 GCAGGGGGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:490476 original size:32 final size:31
Alignment explanation
Indices: 490440--490536 Score: 97
Period size: 32 Copynumber: 3.0 Consensus size: 31
490430 ATTAATGAAC
490440 TATTATAAAATGAATATTAAATTTTATCAATT
1 TATTATAAAAT-AATATTAAATTTTATCAATT
* * *
490472 TATTATAAAATAGTCGTTAAATTTTATCAAAT
1 TATTATAAAATAAT-ATTAAATTTTATCAATT
* * *
490504 TGTTACAAAATAAGCATTAAA-TTTATCATATT
1 TATTATAAAATAA-TATTAAATTTTATCA-ATT
490536 T
1 T
490537 TACACTTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
31 9 0.17
32 44 0.83
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (31 bp):
TATTATAAAATAATATTAAATTTTATCAATT
Found at i:491865 original size:16 final size:17
Alignment explanation
Indices: 491844--491877 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
491834 TAGTGTTCAT
491844 ATTTTG-GAAAGAGATG
1 ATTTTGAGAAAGAGATG
491860 ATTTTGATGAAAGAGATG
1 ATTTTGA-GAAAGAGATG
491878 TTAATTATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.29, T:0.32
Consensus pattern (17 bp):
ATTTTGAGAAAGAGATG
Found at i:518541 original size:20 final size:21
Alignment explanation
Indices: 518516--518556 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
518506 TATATAGTAT
518516 ATTATT-AAGTTTTAT-TTTTA
1 ATTATTGAA-TTTTATCTTTTA
518536 ATTATTGAATTTTATCTTTTA
1 ATTATTGAATTTTATCTTTTA
518557 TTTCAAGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.63
Consensus pattern (21 bp):
ATTATTGAATTTTATCTTTTA
Found at i:521576 original size:16 final size:16
Alignment explanation
Indices: 521563--521594 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
521553 TTTTCTCTGC
521563 AATCTCCATTCTCTCA
1 AATCTCCATTCTCTCA
521579 AATCTCCATTCTCTCA
1 AATCTCCATTCTCTCA
521595 TTGGAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (16 bp):
AATCTCCATTCTCTCA
Found at i:524597 original size:14 final size:14
Alignment explanation
Indices: 524578--524605 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
524568 AAGTGAAAGA
524578 ATAGTTATATAATT
1 ATAGTTATATAATT
524592 ATAGTTATATAATT
1 ATAGTTATATAATT
524606 TTGTTATGAT
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:528782 original size:2 final size:2
Alignment explanation
Indices: 528771--528827 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
528761 AGGGGGGGGG
* *
528771 GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GG GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
528812 GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA
528828 TAGTGATATA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
GA
Found at i:533438 original size:25 final size:25
Alignment explanation
Indices: 533404--533454 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
533394 TGAAGAGACA
533404 ACTAATACTTAATTGTCTGAGTTTG
1 ACTAATACTTAATTGTCTGAGTTTG
*
533429 ACTAATACTTAATTGTCTGCGTTTG
1 ACTAATACTTAATTGTCTGAGTTTG
533454 A
1 A
533455 ATCCGAGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (25 bp):
ACTAATACTTAATTGTCTGAGTTTG
Found at i:539465 original size:400 final size:400
Alignment explanation
Indices: 538725--539524 Score: 1600
Period size: 400 Copynumber: 2.0 Consensus size: 400
538715 ATTAGCTTGA
538725 GACTTAAATATGATGTTAATATTCATATGCAATCGTGCATGTTTGCACATCAACACTAATTACTA
1 GACTTAAATATGATGTTAATATTCATATGCAATCGTGCATGTTTGCACATCAACACTAATTACTA
538790 ATTAGAGATTGGAAGCTCAGCTTTTTCAACCTTTGAAGAAAACGAAATGCCCTGAATGTTCCGTA
66 ATTAGAGATTGGAAGCTCAGCTTTTTCAACCTTTGAAGAAAACGAAATGCCCTGAATGTTCCGTA
538855 CATGTACTATCCATCTACAAAGTTACCTCATTAAATTAAAATTAACATAATCAAGAATTTTAATT
131 CATGTACTATCCATCTACAAAGTTACCTCATTAAATTAAAATTAACATAATCAAGAATTTTAATT
538920 TATTAATTTAAATTGTATATCATAAAGATTTGTTTTGAGGAGGATCTCTTTAACTTAGCTTAATT
196 TATTAATTTAAATTGTATATCATAAAGATTTGTTTTGAGGAGGATCTCTTTAACTTAGCTTAATT
538985 CATTCATAACGCCAAGATTTAAATTCTAGATGTTGTTTAAAAAATCTAATATATTGTTTAACTAA
261 CATTCATAACGCCAAGATTTAAATTCTAGATGTTGTTTAAAAAATCTAATATATTGTTTAACTAA
539050 ATTAATCAATAACTGATGAATACGAGAATATTTAATAATACGTTCTATTTCTATAAATAAAAAAA
326 ATTAATCAATAACTGATGAATACGAGAATATTTAATAATACGTTCTATTTCTATAAATAAAAAAA
539115 ATCAAGACTT
391 ATCAAGACTT
539125 GACTTAAATATGATGTTAATATTCATATGCAATCGTGCATGTTTGCACATCAACACTAATTACTA
1 GACTTAAATATGATGTTAATATTCATATGCAATCGTGCATGTTTGCACATCAACACTAATTACTA
539190 ATTAGAGATTGGAAGCTCAGCTTTTTCAACCTTTGAAGAAAACGAAATGCCCTGAATGTTCCGTA
66 ATTAGAGATTGGAAGCTCAGCTTTTTCAACCTTTGAAGAAAACGAAATGCCCTGAATGTTCCGTA
539255 CATGTACTATCCATCTACAAAGTTACCTCATTAAATTAAAATTAACATAATCAAGAATTTTAATT
131 CATGTACTATCCATCTACAAAGTTACCTCATTAAATTAAAATTAACATAATCAAGAATTTTAATT
539320 TATTAATTTAAATTGTATATCATAAAGATTTGTTTTGAGGAGGATCTCTTTAACTTAGCTTAATT
196 TATTAATTTAAATTGTATATCATAAAGATTTGTTTTGAGGAGGATCTCTTTAACTTAGCTTAATT
539385 CATTCATAACGCCAAGATTTAAATTCTAGATGTTGTTTAAAAAATCTAATATATTGTTTAACTAA
261 CATTCATAACGCCAAGATTTAAATTCTAGATGTTGTTTAAAAAATCTAATATATTGTTTAACTAA
539450 ATTAATCAATAACTGATGAATACGAGAATATTTAATAATACGTTCTATTTCTATAAATAAAAAAA
326 ATTAATCAATAACTGATGAATACGAGAATATTTAATAATACGTTCTATTTCTATAAATAAAAAAA
539515 ATCAAGACTT
391 ATCAAGACTT
539525 TACACCATAT
Statistics
Matches: 400, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
400 400 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (400 bp):
GACTTAAATATGATGTTAATATTCATATGCAATCGTGCATGTTTGCACATCAACACTAATTACTA
ATTAGAGATTGGAAGCTCAGCTTTTTCAACCTTTGAAGAAAACGAAATGCCCTGAATGTTCCGTA
CATGTACTATCCATCTACAAAGTTACCTCATTAAATTAAAATTAACATAATCAAGAATTTTAATT
TATTAATTTAAATTGTATATCATAAAGATTTGTTTTGAGGAGGATCTCTTTAACTTAGCTTAATT
CATTCATAACGCCAAGATTTAAATTCTAGATGTTGTTTAAAAAATCTAATATATTGTTTAACTAA
ATTAATCAATAACTGATGAATACGAGAATATTTAATAATACGTTCTATTTCTATAAATAAAAAAA
ATCAAGACTT
Found at i:541333 original size:25 final size:25
Alignment explanation
Indices: 541305--541376 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
541295 ATATTATAAC
541305 AATATTCTTATTTTAATAAGTAATT
1 AATATTCTTATTTTAATAAGTAATT
*
541330 AATA----TA-ATTAAT-AGT-A-T
1 AATATTCTTATTTTAATAAGTAATT
*
541347 AATATTCTTATTTTAATAAATAATT
1 AATATTCTTATTTTAATAAGTAATT
541372 AATAT
1 AATAT
541377 AATTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 16
0.65 0.05 0.29
Matches are distributed among these distances:
17 5 0.14
18 1 0.03
19 3 0.08
20 5 0.14
21 4 0.11
22 5 0.14
23 2 0.06
24 1 0.03
25 10 0.28
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (25 bp):
AATATTCTTATTTTAATAAGTAATT
Found at i:541369 original size:21 final size:21
Alignment explanation
Indices: 541305--541370 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 21
541295 ATATTATAAC
*
541305 AATATTCTTATTTTAATAAGT
1 AATATTCTTATTTTAATAAAT
** * *
541326 -A-ATTAATATAATTAATAGTAT
1 AATATTCTTAT-TTTAATA-AAT
541347 AATATTCTTATTTTAATAAAT
1 AATATTCTTATTTTAATAAAT
541368 AAT
1 AAT
541371 TAATATAATT
Statistics
Matches: 32, Mismatches: 9, Indels: 8
0.65 0.18 0.16
Matches are distributed among these distances:
19 6 0.19
20 7 0.22
21 6 0.19
22 7 0.22
23 6 0.19
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (21 bp):
AATATTCTTATTTTAATAAAT
Found at i:541382 original size:21 final size:21
Alignment explanation
Indices: 541316--541386 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 21
541306 ATATTCTTAT
*
541316 TTTAATAAGTAATTAATATAA
1 TTTAATAAATAATTAATATAA
* * * *
541337 -TTAATAGTATAA-TATTCTTAT
1 TTTAATA-AATAATTAAT-ATAA
541358 TTTAATAAATAATTAATATAA
1 TTTAATAAATAATTAATATAA
541379 TTT-ATAAA
1 TTTAATAAA
541387 ATTTTATTTT
Statistics
Matches: 37, Mismatches: 9, Indels: 9
0.67 0.16 0.16
Matches are distributed among these distances:
20 14 0.38
21 14 0.38
22 9 0.24
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
TTTAATAAATAATTAATATAA
Found at i:541423 original size:32 final size:37
Alignment explanation
Indices: 541305--541435 Score: 100
Period size: 42 Copynumber: 3.6 Consensus size: 37
541295 ATATTATAAC
*
541305 AATATTCTTATTTTAATAAGTAATTAATATAAT-TAATAGTAT
1 AATATT-TTATTTTAATAA--AA-TAAT-TAATATAAT-CTAT
*
541347 AATATTCTTATTTTAAT-AAATAATTAATATAATTTAT
1 AATATT-TTATTTTAATAAAATAATTAATATAATCTAT
*
541384 AAAATTTTATTTTAATAAAAT-A-T-A-ATAATCT-T
1 AATATTTTATTTTAATAAAATAATTAATATAATCTAT
541416 AATATTTT-TATTT-ATAAAAT
1 AATATTTTAT-TTTAATAAAAT
541436 TTTAGAAATA
Statistics
Matches: 82, Mismatches: 4, Indels: 17
0.80 0.04 0.17
Matches are distributed among these distances:
31 8 0.10
32 11 0.13
33 6 0.07
34 1 0.01
35 1 0.01
36 11 0.13
37 16 0.20
38 8 0.10
39 2 0.02
41 1 0.01
42 17 0.21
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (37 bp):
AATATTTTATTTTAATAAAATAATTAATATAATCTAT
Found at i:541459 original size:14 final size:14
Alignment explanation
Indices: 541391--541464 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
541381 TATAAAATTT
541391 TATTTTAATAA-AA
1 TATTTTAATAATAA
** **
541404 TATAATAATCTTAA
1 TATTTTAATAATAA
* *
541418 TATTTTTATTTATAA
1 TA-TTTTAATAATAA
*
541433 AATTTTAGA-AATAA
1 TATTTTA-ATAATAA
541447 TATTTTAATAATAA
1 TATTTTAATAATAA
541461 TATT
1 TATT
541465 GACAAAAAAT
Statistics
Matches: 44, Mismatches: 13, Indels: 7
0.69 0.20 0.11
Matches are distributed among these distances:
13 8 0.18
14 28 0.64
15 8 0.18
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:548596 original size:2 final size:2
Alignment explanation
Indices: 548589--548620 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
548579 AGCTAATGAT
548589 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
548621 AATTAGAGGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:549858 original size:18 final size:18
Alignment explanation
Indices: 549835--549869 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
549825 TCTTTGAATA
549835 ATATTAGATAATTAAAAG
1 ATATTAGATAATTAAAAG
* *
549853 ATATTATATATTTAAAA
1 ATATTAGATAATTAAAA
549870 AATTTCTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (18 bp):
ATATTAGATAATTAAAAG
Found at i:556300 original size:2 final size:2
Alignment explanation
Indices: 556293--556331 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
556283 ATTAAACGTG
556293 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
556332 CATGTGATTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:557075 original size:18 final size:18
Alignment explanation
Indices: 557049--557084 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
557039 ATAATGTACC
*
557049 AAATATAAAGAAGAATTA
1 AAATATAAAAAAGAATTA
*
557067 AAATCTAAAAAAGAATTA
1 AAATATAAAAAAGAATTA
557085 CCTGGAGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.08, T:0.22
Consensus pattern (18 bp):
AAATATAAAAAAGAATTA
Found at i:559172 original size:20 final size:20
Alignment explanation
Indices: 559132--559172 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
559122 ATAATGGGCA
*
559132 TCGAAACCCAACACTTGGTT
1 TCGAAACCCAACACTTAGTT
559152 TCGAAACCCAA-ACATTAGTT
1 TCGAAACCCAACAC-TTAGTT
559172 T
1 T
559173 TGGCCAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (20 bp):
TCGAAACCCAACACTTAGTT
Found at i:563358 original size:51 final size:51
Alignment explanation
Indices: 563282--563384 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
563272 TGAGTTAAGA
*
563282 AGAGTTTGAACTTAAAATCTCTAAGGAAGTTAACACTCGATCAATAATCAC
1 AGAGTTTGAACTTAAAATCTCTAAGGAAGTTAACACTCAATCAATAATCAC
* *
563333 AGAGTTTGAACTTAAAATCTCTAAGGAAGTTAACACTTAATCAGTAATCAC
1 AGAGTTTGAACTTAAAATCTCTAAGGAAGTTAACACTCAATCAATAATCAC
563384 A
1 A
563385 ACACTAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (51 bp):
AGAGTTTGAACTTAAAATCTCTAAGGAAGTTAACACTCAATCAATAATCAC
Found at i:567341 original size:2 final size:2
Alignment explanation
Indices: 567334--567412 Score: 106
Period size: 2 Copynumber: 39.5 Consensus size: 2
567324 CAGTAAAAAG
* * * *
567334 AT AT AT AT AT AT AT AT AT AT AT -T TT TT AA AGC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
567376 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
567413 CACTCCCATC
Statistics
Matches: 71, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.01
2 69 0.97
3 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (2 bp):
AT
Found at i:567602 original size:24 final size:24
Alignment explanation
Indices: 567575--567645 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 24
567565 GTAAACGGAG
567575 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
*
567599 ATATCA-AATATCAGAAA-AGAATCC
1 ATATCAGAA-ATCA-AAACAGAATTC
* *
567623 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
567646 TGGTAACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 2 0.05
23 12 0.31
24 22 0.56
25 3 0.08
ACGTcount: A:0.52, C:0.17, G:0.11, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:567682 original size:24 final size:24
Alignment explanation
Indices: 567582--567684 Score: 61
Period size: 24 Copynumber: 4.3 Consensus size: 24
567572 GAGATATCAG
*
567582 AAATCAAAACAGAATTC-ATATCAA
1 AAATCAGAACAGAATTCAAT-TCAA
* * *
567606 ATATCAGAAAAGAATCCAGA-TC-A
1 AAATCAGAACAGAATTCA-ATTCAA
* ***
567629 GAATCAGAACAGAATTCTGGT-AA
1 AAATCAGAACAGAATTCAATTCAA
**
567652 CGTATCAGAACAGAATTCAATTCAA
1 -AAATCAGAACAGAATTCAATTCAA
567677 AAATCAGA
1 AAATCAGA
567685 TAAAATATTT
Statistics
Matches: 57, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
23 16 0.28
24 38 0.67
25 2 0.04
26 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAATTCAA
Found at i:570131 original size:18 final size:18
Alignment explanation
Indices: 570108--570146 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
570098 GCCGGTCAAC
*
570108 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCAGGTCG
570126 GGTCAACGGGTCAGGTCG
1 GGTCAACGGGTCAGGTCG
570144 GGT
1 GGT
570147 TGTGACCGGT
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:0.13, C:0.21, G:0.49, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCAGGTCG
Found at i:571446 original size:23 final size:22
Alignment explanation
Indices: 571402--571446 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
571392 AATGTCATGG
*
571402 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
571424 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
571447 AGAAATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:573018 original size:100 final size:100
Alignment explanation
Indices: 572835--573023 Score: 252
Period size: 100 Copynumber: 1.9 Consensus size: 100
572825 GAGTCGAGGG
*
572835 TCTACGCGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGCGACACGT
1 TCTACGCGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGT
* *
572900 ATTTGGTCCTTAGCATATGTATATTTAAGGAATTT
66 ACTTGATCCTTAGCATATGTATATTTAAGGAATTT
* * * * * * * * *
572935 TCTACGTGGTCCTTCGGGACGTATATGTATTCTTTGGAGCATGTATGAGGTCTTTTGAGACACTT
1 TCTACGCGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGT
* *
573000 ACTTGATCCTTGGTATATGTATAT
66 ACTTGATCCTTAGCATATGTATAT
573024 GGTTCTTAAG
Statistics
Matches: 75, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
100 75 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (100 bp):
TCTACGCGGTCCTTCGGGACATATAGGTATCCTATGGAACATCTATGAGGTCCTTTGAGACACGT
ACTTGATCCTTAGCATATGTATATTTAAGGAATTT
Found at i:574431 original size:2 final size:2
Alignment explanation
Indices: 574424--574466 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
574414 AACATAAAAT
574424 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
574466 T
1 T
574467 TTGAATTAAA
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:575466 original size:25 final size:23
Alignment explanation
Indices: 575434--575511 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 23
575424 AAATTTTTAG
575434 CCGTCATTGGCAGTCAATTTACCA
1 CCGTCATTGG-AGTCAATTTACCA
** *
575458 CCGATCATT-GA-TCTTTTTA--G
1 CCG-TCATTGGAGTCAATTTACCA
575478 CCGTCATTGGTAGTCAATTTACCA
1 CCGTCATTGG-AGTCAATTTACCA
575502 CCGGTCATTG
1 CC-GTCATTG
575512 ATCATCATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
19 5 0.12
20 4 0.10
21 1 0.02
22 12 0.29
23 1 0.02
24 6 0.15
25 12 0.29
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (23 bp):
CCGTCATTGGAGTCAATTTACCA
Found at i:575475 original size:44 final size:44
Alignment explanation
Indices: 575427--575514 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 44
575417 CACTGCCAAA
575427 TTTTTAGCCGTCATTGGCAGTCAATTTACCACCGATCATTGATC
1 TTTTTAGCCGTCATTGGCAGTCAATTTACCACCGATCATTGATC
* *
575471 TTTTTAGCCGTCATTGGTAGTCAATTTACCACCGGTCATTGATC
1 TTTTTAGCCGTCATTGGCAGTCAATTTACCACCGATCATTGATC
575515 ATCATTTGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.38
Consensus pattern (44 bp):
TTTTTAGCCGTCATTGGCAGTCAATTTACCACCGATCATTGATC
Found at i:592677 original size:37 final size:36
Alignment explanation
Indices: 592602--592677 Score: 93
Period size: 36 Copynumber: 2.1 Consensus size: 36
592592 TTTTTATATT
*
592602 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
*
592638 TTTAATATTT-TAAAGAAAA-TATATAAATATTTTACAA
1 TTTAAT-TTTGTAAA-AAAATTATATAAATATTAT-CAA
592675 TTT
1 TTT
592678 GTAATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 23 0.66
37 12 0.34
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:592858 original size:20 final size:20
Alignment explanation
Indices: 592822--592859 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
592812 AATCTATTCC
**
592822 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
592842 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
592860 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:603753 original size:30 final size:30
Alignment explanation
Indices: 603719--603780 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
603709 GACTGATGTG
* *
603719 CATTCTTTACTTCTCTTTCTTTAATGGGAT
1 CATTCTTTACTTCTCTCTCTTGAATGGGAT
603749 CATTCTTTACTTCTCTCTCTTGAATGGGAT
1 CATTCTTTACTTCTCTCTCTTGAATGGGAT
603779 CA
1 CA
603781 AGTAATATGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (30 bp):
CATTCTTTACTTCTCTCTCTTGAATGGGAT
Found at i:606996 original size:49 final size:49
Alignment explanation
Indices: 606930--607120 Score: 294
Period size: 49 Copynumber: 3.9 Consensus size: 49
606920 TCCTTACCTT
*
606930 TTTTATGACTAATATTAAATATGGCAGATTTTGGTTACCTTTTTTACCG
1 TTTTATTACTAATATTAAATATGGCAGATTTTGGTTACCTTTTTTACCG
* * *
606979 TTTTATTACTAATATTAACTACGGCAGATTTTGGTTACCTTTTTTACTAG
1 TTTTATTACTAATATTAAATATGGCAGATTTTGGTTACCTTTTTTAC-CG
* * * *
607029 -TTTATTACCAATATTAAATATGGCAGATTTCGGCTACCTTTTTTACCA
1 TTTTATTACTAATATTAAATATGGCAGATTTTGGTTACCTTTTTTACCG
607077 TTTTATTACTAATATTAAATATGGCAGATTTTGGTTACCTTTTT
1 TTTTATTACTAATATTAAATATGGCAGATTTTGGTTACCTTTTT
607121 ATTATTTTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
49 125 0.99
50 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (49 bp):
TTTTATTACTAATATTAAATATGGCAGATTTTGGTTACCTTTTTTACCG
Found at i:607173 original size:16 final size:19
Alignment explanation
Indices: 607140--607176 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
607130 TCTTATATTA
607140 AATATTTGTTGATATAAAT
1 AATATTTGTTGATATAAAT
607159 AATATTT-TT-AT-TAAAT
1 AATATTTGTTGATATAAAT
607175 AA
1 AA
607177 AAGGAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 2 0.11
19 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
AATATTTGTTGATATAAAT
Found at i:614478 original size:5 final size:5
Alignment explanation
Indices: 614468--614496 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
614458 TAAGAAAGAG
614468 TATCC TATCC TATCC TATCC TATCC TATC
1 TATCC TATCC TATCC TATCC TATCC TATC
614497 ATACACGTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.38, G:0.00, T:0.41
Consensus pattern (5 bp):
TATCC
Found at i:623151 original size:2 final size:2
Alignment explanation
Indices: 623144--623187 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
623134 AAAAATGAGA
623144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
623186 AT
1 AT
623188 GGGTCGGGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:628428 original size:99 final size:99
Alignment explanation
Indices: 628257--628457 Score: 339
Period size: 99 Copynumber: 2.0 Consensus size: 99
628247 TTATGATGGC
* ** * *
628257 AAGAGGGATAGATGGAGTGGTTATGATGCATCTACATATGCTCGTGTCATTCAAAGGTATGAGGC
1 AAGAGCGATAGATGGAACGGTTATGATGCATCTACATATGCTCATGTCATTCAAAGGTACGAGGC
628322 TAGAAGGAAGTATTTGAAGGAACAACAGCTGAAG
66 TAGAAGGAAGTATTTGAAGGAACAACAGCTGAAG
* *
628356 AAGAGCGATAGATGGAACGGTTATGATGCATCTACATATGCTCATGTCATTTAAAGGTACGGGGC
1 AAGAGCGATAGATGGAACGGTTATGATGCATCTACATATGCTCATGTCATTCAAAGGTACGAGGC
628421 TAGAAGGAAGTATTTGAAGGAACAACAGCTGAAG
66 TAGAAGGAAGTATTTGAAGGAACAACAGCTGAAG
628455 AAG
1 AAG
628458 TTGGAGGAGA
Statistics
Matches: 95, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
99 95 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.23
Consensus pattern (99 bp):
AAGAGCGATAGATGGAACGGTTATGATGCATCTACATATGCTCATGTCATTCAAAGGTACGAGGC
TAGAAGGAAGTATTTGAAGGAACAACAGCTGAAG
Found at i:630221 original size:17 final size:17
Alignment explanation
Indices: 630199--630231 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
630189 TTAATATTTG
*
630199 CATAATTTCTTTAACAC
1 CATAATGTCTTTAACAC
630216 CATAATGTCTTTAACA
1 CATAATGTCTTTAACA
630232 AAAGCATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.39
Consensus pattern (17 bp):
CATAATGTCTTTAACAC
Found at i:630467 original size:6 final size:6
Alignment explanation
Indices: 630456--630487 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
630446 ATTCATGAGC
630456 ATCAAT ATCAAT ATCAAT ATCAAT ATCAAT AT
1 ATCAAT ATCAAT ATCAAT ATCAAT ATCAAT AT
630488 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (6 bp):
ATCAAT
Found at i:633125 original size:37 final size:38
Alignment explanation
Indices: 633020--633371 Score: 271
Period size: 37 Copynumber: 9.7 Consensus size: 38
633010 ATATAGTTTG
* * *
633020 AAAACATTTTT-AATA-TATATATAATATATAATTTTGA
1 AAAACATTTTTGAAAATTA-ATATAATATATAGTTTTTA
* * * * *
633057 AAAGCATGTTTGAAAACATTTATATATTATATAGTTCTT-
1 AAAACATTTTTG-AAA-ATTAATATAATATATAGTTTTTA
** * *
633096 AAGTCATTTTTGAAAATTAATATAATATAT-GGTTTTC
1 AAAACATTTTTGAAAATTAATATAATATATAGTTTTTA
*
633133 AAAACATTTTTGAAAA-TATATATATTATATAGTTTTTA
1 AAAACATTTTTGAAAATTA-ATATAATATATAGTTTTTA
633171 AAAACATTTTTGAAAATTAATATAATATATAGTTTTT-
1 AAAACATTTTTGAAAATTAATATAATATATAGTTTTTA
* **
633208 AAAACATTTTTGAAAA-TACT-TGTTATATAGTTTTT-
1 AAAACATTTTTGAAAATTAATATAATATATAGTTTTTA
**
633243 AAAACA-TTTT---AA--AATAT-ATATATAGTTTAAA
1 AAAACATTTTTGAAAATTAATATAATATATAGTTTTTA
* * *
633274 AAAACA-TTTTGAAAACATAAATATATTATATAGTTTTTG
1 AAAACATTTTTG-AAA-ATTAATATAATATATAGTTTTTA
* *
633313 AAATCA-TTTTGAAAA--CATATAATATATAG-TTTTA
1 AAAACATTTTTGAAAATTAATATAATATATAGTTTTTA
* *
633347 AAAACATTTTTAAAAACT-ATATAAT
1 AAAACATTTTTGAAAATTAATATAAT
633372 TTTGAAAACA
Statistics
Matches: 256, Mismatches: 38, Indels: 43
0.76 0.11 0.13
Matches are distributed among these distances:
30 12 0.05
31 13 0.05
34 13 0.05
35 40 0.16
36 17 0.07
37 63 0.25
38 49 0.19
39 33 0.13
40 15 0.06
41 1 0.00
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (38 bp):
AAAACATTTTTGAAAATTAATATAATATATAGTTTTTA
Found at i:633185 original size:75 final size:73
Alignment explanation
Indices: 632999--633369 Score: 354
Period size: 75 Copynumber: 5.1 Consensus size: 73
632989 ACATATATAT
* * * * * *
632999 ATATATACAGTATATAG-TTTGAAAACATTTTT-AATATATATATAATATATAATTTTGAAAAGC
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAAATA-ATATAATATATAGTTTT-AAAAAC
*
633062 ATGTTTGAAAA
64 ATTTTTG-AAA
* * ** * *
633073 CATTTATATATTATATAGTTCTTAAGTCATTTTTGAAAATTAATATAATATATGGTTTTCAAAAC
1 -ATATATATATTATATAGTTTTTAAAACATTTTTGAAAA-TAATATAATATATAGTTTTAAAAAC
633138 ATTTTTGAAA
64 ATTTTTGAAA
*
633148 ATATATATATTATATAGTTTTTAAAAACATTTTTGAAAATTAATATAATATATAGTTTTTAAAAC
1 ATATATATATTATATAGTTTTT-AAAACATTTTTGAAAA-TAATATAATATATAGTTTTAAAAAC
633213 ATTTTTGAAA
64 ATTTTTGAAA
* * *
633223 ATA-CT-TGTTATATAGTTTTTAAAACA-TTTT---AA-AATAT-ATATATAGTTTAAAAAAACA
1 ATATATATATTATATAGTTTTTAAAACATTTTTGAAAATAATATAATATATAGTTT-TAAAAACA
633280 -TTTTGAAAA
65 TTTTTG-AAA
* * *
633289 CATAAATATATTATATAGTTTTTGAAATCA-TTTTGAAAA-CATATAATATATAGTTTTAAAAAC
1 -ATATATATATTATATAGTTTTT-AAAACATTTTTGAAAATAATATAATATATAGTTTTAAAAAC
*
633352 ATTTTTAAAA
64 ATTTTTGAAA
633362 ACTATATA
1 A-TATATA
633370 ATTTTGAAAA
Statistics
Matches: 250, Mismatches: 30, Indels: 34
0.80 0.10 0.11
Matches are distributed among these distances:
65 16 0.06
66 14 0.06
67 3 0.01
68 3 0.01
69 14 0.06
70 9 0.04
71 4 0.02
72 7 0.03
73 35 0.14
74 36 0.14
75 68 0.27
76 21 0.08
77 18 0.07
78 2 0.01
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (73 bp):
ATATATATATTATATAGTTTTTAAAACATTTTTGAAAATAATATAATATATAGTTTTAAAAACAT
TTTTGAAA
Found at i:633306 original size:39 final size:37
Alignment explanation
Indices: 633254--633361 Score: 132
Period size: 39 Copynumber: 2.9 Consensus size: 37
633244 AAACATTTTA
*
633254 AAATATATATATAGTTTAAAAAAACATTTTGAAAACAT
1 AAATATATATATAGTTT-TAAAAACATTTTGAAAACAT
* *
633292 AAATATATTATATAGTTTTTGAAATCATTTTGAAAACAT
1 AAATATA-TATATAG-TTTTAAAAACATTTTGAAAACAT
*
633331 --ATA-ATATATAGTTTTAAAAACATTTTTAAAA
1 AAATATATATATAGTTTTAAAAACATTTTGAAAA
633362 ACTATATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
34 17 0.27
35 7 0.11
36 1 0.02
37 3 0.05
38 7 0.11
39 24 0.39
40 3 0.05
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.40
Consensus pattern (37 bp):
AAATATATATATAGTTTTAAAAACATTTTGAAAACAT
Found at i:633379 original size:29 final size:28
Alignment explanation
Indices: 633335--633389 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
633325 AAACATATAA
*
633335 TATATAGTTTTAAAAACATTTTTAAAAAC
1 TATATAATTTTAAAAACA-TTTTAAAAAC
*
633364 TATATAATTTTGAAAACATTTTAAAA
1 TATATAATTTTAAAAACATTTTAAAA
633390 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (28 bp):
TATATAATTTTAAAAACATTTTAAAAAC
Found at i:636698 original size:19 final size:19
Alignment explanation
Indices: 636674--636719 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
636664 ATTTAGACAT
636674 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
636693 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
636712 TTTGCATT
1 TTTGCATT
636720 CACATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:640075 original size:165 final size:164
Alignment explanation
Indices: 639803--640670 Score: 1349
Period size: 165 Copynumber: 5.3 Consensus size: 164
639793 TAAACAAACT
* *
639803 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * *
639868 GCTTCGATGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACC
639933 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* **
639968 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * *
640033 GCTTCAAGGACATAACATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCAGCAAAGACCT
66 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
640098 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
131 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
640132 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * * * * * *
640197 GCTACGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAGACC
640262 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* *
640297 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGACCCCCAAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * * * * *
640362 ACTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACC
66 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACC-AAAGACC
*
640427 TTCGAGTTCGACTACGCTCAGCTCCAAGGCACATC
130 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
* **
640462 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
* * *
640527 GCTTCAAGGGCATAACATTTACATCATAACTCAAAGCTAGAAGGGTTATCTGTCAGCAAAGACCT
66 GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
*
640592 TTGAGTTCGACTACGCTCAGCTCCAAGGCATATC
131 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
*
640626 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCTAAAGACC
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
640671 TTCGAGTTCA
Statistics
Matches: 641, Mismatches: 60, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
164 232 0.36
165 409 0.64
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (164 bp):
ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCA
GCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCT
TTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
Found at i:640401 original size:329 final size:327
Alignment explanation
Indices: 639803--640746 Score: 1390
Period size: 329 Copynumber: 2.9 Consensus size: 327
639793 TAAACAAACT
*
639803 ATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * *
639868 GCTTCGATGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACT-AAAGCTAGAAGGGTTATCTG-CACC-AAAGACC
*
639933 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGC
128 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGC
* * * * * *
639998 TATCTGCCAAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGACATAA-CATTTACAGTATAA
193 TATCTGCTAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCA-AATCATTTACAGCATAA
* *
640062 CTCAAGGCTAGAAGGGTTATCTGTCAGC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGG
257 CTCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGG
640126 CACATC
322 CACATC
640132 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * *
640197 GCTACGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACC
66 GCTTCGAGGGCACATCATTTACAGCATAACTAAAG-CTAGAAGGGTTATCTG-C-ACCAAAGACC
*
640262 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGC
128 TTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGC
* *
640327 TATCTGCTAAAGACCCCCAAGTTCGATTACACTCAACTTCGAGGGCACATCATTTACAGCATAAC
193 TATCTGCTAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCAAATCATTTACAGCATAAC
* *
640392 TCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
258 TCAAGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGC
640457 ACATC
323 ACATC
* ***
640462 ATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGACCCTTAAGTTCGATTACACTCA
1 ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
* * * * *
640527 GCTTCAAGGGCATAACATTTACATCATAACTCAAAGCTAGAAGGGTTATCTGTCAGCAAAGACCT
66 GCTTCGAGGGCACATCATTTACAGCATAACT-AAAGCTAGAAGGGTTATCTG-CACCAAAGACCT
*
640592 TTGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCT
129 TTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCT
* * * * * * *
640657 ATCTGCTAAAGACCTTCGAGTTCAATTATATTCAACTTAGA-GGCAAATCAAGTTTACAGCATAG
194 ATCTGCTAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCAAATC-A-TTTACAGCATAA
* * *
640721 CTCAAGGCAAGAAGGGCTATATGTCA
257 CTCAAGGCTAGAAGGGTTATCTGTCA
640747 ATAAAATTGT
Statistics
Matches: 555, Mismatches: 53, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
328 10 0.02
329 364 0.66
330 178 0.32
331 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (327 bp):
ATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCA
GCTTCGAGGGCACATCATTTACAGCATAACTAAAGCTAGAAGGGTTATCTGCACCAAAGACCTTT
GAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTAT
CTGCTAAAGACCCTCAAGTTCGATTACACTCAACTTCGAGGGCAAATCATTTACAGCATAACTCA
AGGCTAGAAGGGTTATCTGTCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACA
TC
Found at i:641424 original size:37 final size:38
Alignment explanation
Indices: 641341--641675 Score: 255
Period size: 37 Copynumber: 9.3 Consensus size: 38
641331 GAAAACATTT
* * * *
641341 TTAATAT-ATATATAATTTTGAAAAGCATGTTTGAAAACA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTG-AAA-A
* * * **
641380 TTTATATATTATATAGTTCTT-AAGTCATTTTTGAAAA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTGAAAA
* *
641417 TTAATATAATATAT-GGTTTTCAAAACATTTTTGAAAA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTGAAAA
*
641454 -TATATATATTATATAGTTTTTAAAAACATTTTTGAAAA
1 TTA-ATATAATATATAGTTTTTAAAAACATTTTTGAAAA
641492 TTAATATAATATATAGTTTTT-AAAACATTTTTGAAAA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTGAAAA
* **
641529 -TACT-TGTTATATAGTTTTT-AAAACA-TTTT---AA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTGAAAA
**
641560 --AA-AT-ATATATAGTTTAAAAAAACA-TTTTGAAAACA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTG-AAA-A
* * * *
641595 TAAATATATTATATAGTTTTTGAAATCA-TTTTGAAAA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTGAAAA
* *
641632 --CATATAATATATAG-TTTTAAAAACATTTTTAAAAA
1 TTAATATAATATATAGTTTTTAAAAACATTTTTGAAAA
*
641667 CT-ATATAAT
1 TTAATATAAT
641676 TTTGAAAACA
Statistics
Matches: 242, Mismatches: 35, Indels: 41
0.76 0.11 0.13
Matches are distributed among these distances:
29 10 0.04
30 12 0.05
31 2 0.01
34 14 0.06
35 40 0.17
36 16 0.07
37 56 0.23
38 46 0.19
39 37 0.15
40 9 0.04
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.44
Consensus pattern (38 bp):
TTAATATAATATATAGTTTTTAAAAACATTTTTGAAAA
Found at i:641571 original size:102 final size:106
Alignment explanation
Indices: 641321--641689 Score: 307
Period size: 103 Copynumber: 3.5 Consensus size: 106
641311 ATATATACAG
* * * * * * **
641321 TATATAG-TTTGAAAACATTTTT-AATA-TATATATAATTTTGAAAAGCATGTTTGAAAACATTT
1 TATATAGTTTTAAAAACATTTTTAAAAACTATATATAGTTTTTAAAAACATTTTTGAAAACATAA
* * ** *
641383 ATATATTATATAGTTCTT-AAGTCATTTTTGAAAATTAATATAA
66 ATATAATATATAGTTTTTGAAAACA-TTTTGAAAA--CATATAA
* * *
641426 TATATGGTTTTCAAAACATTTTTGAAAATATATATATTATATAGTTTTTAAAAACATTTTTG-AA
1 TATATAGTTTTAAAAACATTTTT--AAA-A-A-CTA-TATATAGTTTTTAAAAACATTTTTGAAA
* * **
641490 A-ATTAATATAATATATAGTTTTT-AAAACATTTTTGAAAATACT-TGT
60 ACATAAATATAATATATAGTTTTTGAAAACA-TTTTGAAAACA-TATAA
* **
641536 TATATAGTTTTTAAAACA-TTTTAAAAA-TATATATAGTTTAAAAAAACA-TTTTGAAAACATAA
1 TATATAGTTTTAAAAACATTTTTAAAAACTATATATAGTTTTTAAAAACATTTTTGAAAACATAA
* *
641598 ATATATTATATAGTTTTTGAAATCATTTTGAAAACATATAA
66 ATATAATATATAGTTTTTGAAAACATTTTGAAAACATATAA
*
641639 TATATAGTTTTAAAAACATTTTTAAAAACTATATA-A--TTTTGAAAACATTTT
1 TATATAGTTTTAAAAACATTTTTAAAAACTATATATAGTTTTTAAAAACATTTT
641690 AAAATATTTT
Statistics
Matches: 218, Mismatches: 29, Indels: 36
0.77 0.10 0.13
Matches are distributed among these distances:
101 5 0.02
102 29 0.13
103 53 0.24
104 15 0.07
105 13 0.06
106 15 0.07
107 3 0.01
109 6 0.03
110 18 0.08
111 2 0.01
112 33 0.15
113 5 0.02
114 21 0.10
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (106 bp):
TATATAGTTTTAAAAACATTTTTAAAAACTATATATAGTTTTTAAAAACATTTTTGAAAACATAA
ATATAATATATAGTTTTTGAAAACATTTTGAAAACATATAA
Found at i:641683 original size:29 final size:28
Alignment explanation
Indices: 641639--641693 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
641629 AAACATATAA
*
641639 TATATAGTTTTAAAAACATTTTTAAAAAC
1 TATATAATTTTAAAAACA-TTTTAAAAAC
*
641668 TATATAATTTTGAAAACATTTTAAAA
1 TATATAATTTTAAAAACATTTTAAAA
641694 TATTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (28 bp):
TATATAATTTTAAAAACATTTTAAAAAC
Found at i:641692 original size:215 final size:211
Alignment explanation
Indices: 641321--641724 Score: 492
Period size: 215 Copynumber: 1.9 Consensus size: 211
641311 ATATATACAG
* * ** * **
641321 TATATAGTTTGAAAACATTTTTAATATATATATAATTTTGAAAAGCATGTTTGAAAACATTTATA
1 TATATAGTTTGAAAACATTTTAAAAATATATATAATTTAAAAAAACATGTTTGAAAACATAAATA
* * * *
641386 TATTATATAGTTCTTAAGTCATTTTTGAAAATTAATATAATATATGGTTTTCAAAACATTTTTGA
66 TATTATATAGTTCTTAAATCATTTTTGAAAA-TAATATAATATATAGTTTTAAAAACATTTTTAA
* ** * *
641451 AAATATATATATTATATAGTTTTTAAAAACATTTTTGAAAATTAATATAATATATAGTTTTTAAA
130 AAATATATATATTATAAACATTTT-AAAACATTTTT-AAAAGT-ATATAATATATAGGTTTTAAA
641516 ACATTTTTGAAAATACTTGT
192 ACATTTTTGAAAATACTTGT
* *
641536 TATATAGTTTTTAAAACATTTTAAAAATATATATAGTTTAAAAAAACAT-TTTGAAAACATAAAT
1 TATATAG-TTTGAAAACATTTTAAAAATATATATAATTTAAAAAAACATGTTTGAAAACATAAAT
* *
641600 ATATTATATAGTTTTTGAAATCA-TTTTGAAAA-CATATAATATATAGTTTTAAAAACATTTTTA
65 ATATTATATAGTTCTT-AAATCATTTTTGAAAATAATATAATATATAGTTTTAAAAACATTTTTA
* * *
641663 AAAACTATATA-ATTTTGAAAACATTTTAAAATATTTTTAAAAGTATATATTATATAGGTTTT
129 AAAA-TATATATATTAT--AAACATTTTAAAACATTTTTAAAAGTATATAATATATAGGTTTT
641725 GGGAAATTAT
Statistics
Matches: 161, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
212 16 0.10
213 40 0.25
214 16 0.10
215 50 0.31
216 39 0.24
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (211 bp):
TATATAGTTTGAAAACATTTTAAAAATATATATAATTTAAAAAAACATGTTTGAAAACATAAATA
TATTATATAGTTCTTAAATCATTTTTGAAAATAATATAATATATAGTTTTAAAAACATTTTTAAA
AATATATATATTATAAACATTTTAAAACATTTTTAAAAGTATATAATATATAGGTTTTAAAACAT
TTTTGAAAATACTTGT
Found at i:649883 original size:21 final size:21
Alignment explanation
Indices: 649854--649893 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
649844 TTTTTATTAT
* *
649854 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
649875 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
649894 CATTTAGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:651435 original size:30 final size:25
Alignment explanation
Indices: 651406--651458 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
651396 AATGATTAAT
*
651406 TTAAATTTAAATATGGTAAAAATTA
1 TTAATTTTAAATATGGTAAAAATTA
651431 TTAATTTTAAATATGGTAAAAATTA
1 TTAATTTTAAATATGGTAAAAATTA
651456 TTA
1 TTA
651459 TACAGCGATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (25 bp):
TTAATTTTAAATATGGTAAAAATTA
Found at i:660574 original size:53 final size:55
Alignment explanation
Indices: 660475--660577 Score: 147
Period size: 53 Copynumber: 1.9 Consensus size: 55
660465 AAAAAGAGAA
* * **
660475 ATATAATGTTAATGTACAAGATTTTTAAATCCCAGGCATCTATTTAGAGTTATAT
1 ATATAATGCTAATGCACAAGATTTTTAAATCCCAACCATCTATTTAGAGTTATAT
*
660530 ATATAATGCTAATGCACAAGA-TTTT-AATCTCAACCATCTATTTAGAGT
1 ATATAATGCTAATGCACAAGATTTTTAAATCCCAACCATCTATTTAGAGT
660578 CATCCAATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
53 20 0.47
54 4 0.09
55 19 0.44
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (55 bp):
ATATAATGCTAATGCACAAGATTTTTAAATCCCAACCATCTATTTAGAGTTATAT
Found at i:661790 original size:3 final size:3
Alignment explanation
Indices: 661782--661823 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
661772 AAGGCATATA
661782 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
661824 CAAATTTCTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:661976 original size:27 final size:27
Alignment explanation
Indices: 661922--661976 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
661912 TTATCAAACT
**
661922 ATTACAAAATAGACATTTTTTTGGATA
1 ATTACAAAATAGACATTTTCATGGATA
661949 ATTACAAAATAGACA-TTTCATGGTATA
1 ATTACAAAATAGACATTTTCATGG-ATA
661976 A
1 A
661977 AAAAATGATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.24
27 19 0.76
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (27 bp):
ATTACAAAATAGACATTTTCATGGATA
Found at i:674319 original size:21 final size:23
Alignment explanation
Indices: 674274--674321 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
674264 TGGTAAAAAA
*
674274 TTACCTAAAATATTATTATTATTT
1 TTACCTAAAACATTA-TATTATTT
674298 TTACCTAAAACATTA-ATT-TTT
1 TTACCTAAAACATTATATTATTT
674319 TTA
1 TTA
674322 ATATTTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 6 0.26
22 3 0.13
24 14 0.61
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (23 bp):
TTACCTAAAACATTATATTATTT
Found at i:685826 original size:23 final size:23
Alignment explanation
Indices: 685796--685839 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
685786 AATTTATTAT
685796 TAAATATTAAATTAAAAATAATG
1 TAAATATTAAATTAAAAATAATG
* *
685819 TAAATATTTAATTAATAATAA
1 TAAATATTAAATTAAAAATAA
685840 AAGAACAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (23 bp):
TAAATATTAAATTAAAAATAATG
Found at i:688721 original size:17 final size:18
Alignment explanation
Indices: 688689--688722 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
688679 ATCATTTAGA
*
688689 TTTTAAATTGATTATAAG
1 TTTTAAAATGATTATAAG
688707 TTTTAAAAT-ATTATAA
1 TTTTAAAATGATTATAA
688723 TTGAACCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTAAAATGATTATAAG
Found at i:693713 original size:3 final size:3
Alignment explanation
Indices: 693705--693748 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
693695 GGACGAACCC
693705 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
693749 GTTTTAAGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:693900 original size:13 final size:13
Alignment explanation
Indices: 693855--693902 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
693845 CGACCATTAA
693855 TATTTTTTATTTT
1 TATTTTTTATTTT
* * *
693868 TATATTGTATCTT
1 TATTTTTTATTTT
*
693881 TACTTTTTATTTTT
1 TATTTTTTA-TTTT
693895 TATTTTTT
1 TATTTTTT
693903 TAGTTTTAAC
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:694254 original size:14 final size:15
Alignment explanation
Indices: 694229--694264 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
694219 TGTATATATA
694229 TTTTA-TTT-AAGTT
1 TTTTATTTTCAAGTT
694242 TTTT-TTTTCAAGTT
1 TTTTATTTTCAAGTT
694256 TTTTATTTT
1 TTTTATTTT
694265 TTATATGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 7 0.35
14 9 0.45
15 4 0.20
ACGTcount: A:0.17, C:0.03, G:0.06, T:0.75
Consensus pattern (15 bp):
TTTTATTTTCAAGTT
Found at i:694995 original size:435 final size:433
Alignment explanation
Indices: 694182--695056 Score: 1583
Period size: 435 Copynumber: 2.0 Consensus size: 433
694172 ATTTGATCTC
694182 ATATTGTGGTTTGTCTATCGATACCGTCAGATTTGTTTGTATATATATTTTATTTAAGTTTTTTT
1 ATATTGTGGTTTGTCTATCGATACCGTCAGATTTGTTTGTATATATATTTTATTTAAG--TTTTT
694247 TTTCAAGTTTTTTATTTTTTATATGGTCCTTATATGATTCAGAGTGAATAGTTTATTGAGTCAAT
64 TTTCAAGTTTTTTATTTTTTATATGGTCCTTATATGATTCAGAGTGAATAGTTTATTGAGTCAAT
* * * *
694312 AGTAATAGAAAATATCCTAATTATGTGTTTAATTTATGTGTACGGTTGTAAACTTTAATTTTAAT
129 AGTAATAGAAAATATCCTAATTATGTATTTAATTTACGTGTACGATTGTAAACTTTAATTGTAAT
**
694377 TTTAATTTTTTTAATAAAACTAGCAATTACTTAAAAATATAATTTTTAAGTTAATTCAGTTAAAA
194 TTTAATAATTTTAATAAAACTAGCAATTACTTAAAAATATAATTTTTAAGTTAATTCAGTTAAAA
694442 CAATAATAATACAATGTTATTAAATTGTTTTATATTTTTTATAAATATAATAATATTCATGTTAC
259 CAATAATAATACAATGTTATTAAATTGTTTTATATTTTTTATAAATATAATAATATTCATGTTAC
694507 ATTTTTAAATTGTTTATTTGAAATATCACCAATTTTTTATAATTATTTTTCAAATTCATACAATT
324 ATTTTTAAATTGTTTATTTGAAATATCACCAATTTTTTATAATTATTTTTCAAATTCATACAA-T
694572 TTAATAGTAAAATAATTATATATCCAACCAAAATAATCATAAATACGA
388 TTAATAGT-AAA-AATTATATATCCAACCAAAATAATCATAAATACGA
694620 ATATTGTGGTTTGTCTATCGATACCGTCAGATTTGTTTGTATATATATTTTATTTAAG-TTTTTT
1 ATATTGTGGTTTGTCTATCGATACCGTCAGATTTGTTTGTATATATATTTTATTTAAGTTTTTTT
*
694684 TCAAGTTTTTTAATTTTTTATATTGTCCTTATATGATTCAGAGTGAATAGTTTATTGAGTCAATA
66 TCAAGTTTTTT-ATTTTTTATATGGTCCTTATATGATTCAGAGTGAATAGTTTATTGAGTCAATA
* *
694749 GTAATAGAAAATGTCCTAATTATGTATTTAATTTACGTGTACTATTGTAAACTTTAATTGTAATT
130 GTAATAGAAAATATCCTAATTATGTATTTAATTTACGTGTACGATTGTAAACTTTAATTGTAATT
*
694814 TTAA-AATTTTAATAAAATTAGCAATTACTTAAAAATATAATTTTTAAGTTAATTCAGTTAAAAC
195 TTAATAATTTTAATAAAACTAGCAATTACTTAAAAATATAATTTTTAAGTTAATTCAGTTAAAAC
694878 AATAATAATACAATGTTATTAAATTGTTTTATATTTTTTATAAATATAATAATATTCATGTTACA
260 AATAATAATACAATGTTATTAAATTGTTTTATATTTTTTATAAATATAATAATATTCATGTTACA
694943 TTTTTAAATTGTTTATTTGAAATATCACCAATTTTTTATAATTATTTTTCAAATTCATACAATTT
325 TTTTTAAATTGTTTATTTGAAATATCACCAATTTTTTATAATTATTTTTCAAATTCATACAATTT
*
695008 AATAGTAAAAATTATATATCCAACCAAAATAATCATAAATATGA
390 AATAGTAAAAATTATATATCCAACCAAAATAATCATAAATACGA
695052 ATATT
1 ATATT
695057 TTAATATGAT
Statistics
Matches: 425, Mismatches: 11, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
432 39 0.09
433 3 0.01
434 9 0.02
435 201 0.47
436 115 0.27
438 58 0.14
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (433 bp):
ATATTGTGGTTTGTCTATCGATACCGTCAGATTTGTTTGTATATATATTTTATTTAAGTTTTTTT
TCAAGTTTTTTATTTTTTATATGGTCCTTATATGATTCAGAGTGAATAGTTTATTGAGTCAATAG
TAATAGAAAATATCCTAATTATGTATTTAATTTACGTGTACGATTGTAAACTTTAATTGTAATTT
TAATAATTTTAATAAAACTAGCAATTACTTAAAAATATAATTTTTAAGTTAATTCAGTTAAAACA
ATAATAATACAATGTTATTAAATTGTTTTATATTTTTTATAAATATAATAATATTCATGTTACAT
TTTTAAATTGTTTATTTGAAATATCACCAATTTTTTATAATTATTTTTCAAATTCATACAATTTA
ATAGTAAAAATTATATATCCAACCAAAATAATCATAAATACGA
Found at i:696265 original size:63 final size:63
Alignment explanation
Indices: 696186--696307 Score: 192
Period size: 63 Copynumber: 1.9 Consensus size: 63
696176 ACAAGTTACA
*
696186 CTTTGTAGGTATTGACCACTGAGAATCTATCTACT-CTATCACTTAGGTGTTTGTGGTGGTACT
1 CTTTGTAGGCATTGACCACTGAGAATCTATCTACTGC-ATCACTTAGGTGTTTGTGGTGGTACT
* * *
696249 CTTTGTAGGCATTGACCACTGAGAATCTGTCTGCTGCATCACTTAGGTGTTTGTTGTGG
1 CTTTGTAGGCATTGACCACTGAGAATCTATCTACTGCATCACTTAGGTGTTTGTGGTGG
696308 AAAAATGGCT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 53 0.98
64 1 0.02
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (63 bp):
CTTTGTAGGCATTGACCACTGAGAATCTATCTACTGCATCACTTAGGTGTTTGTGGTGGTACT
Found at i:702457 original size:18 final size:17
Alignment explanation
Indices: 702425--702463 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
702415 AATTTAAACT
702425 AATTAAATTATAATAAA
1 AATTAAATTATAATAAA
* *
702442 AATTAGATTCATAATAGA
1 AATTAAATT-ATAATAAA
702460 AATT
1 AATT
702464 TTGATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (17 bp):
AATTAAATTATAATAAA
Found at i:702777 original size:18 final size:19
Alignment explanation
Indices: 702754--702789 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
702744 ATTAGCAGTA
702754 AAAGGATTCAA-CTAATTT
1 AAAGGATTCAATCTAATTT
*
702772 AAAGGATTTAATCTAATT
1 AAAGGATTCAATCTAATT
702790 ATACATTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (19 bp):
AAAGGATTCAATCTAATTT
Found at i:712726 original size:15 final size:15
Alignment explanation
Indices: 712706--712750 Score: 72
Period size: 15 Copynumber: 3.0 Consensus size: 15
712696 TAATAAGGTT
712706 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
712721 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
712736 AATTATTATAAAATA
1 ATTTATTTTAAAATA
712751 TGAATTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:712762 original size:37 final size:34
Alignment explanation
Indices: 712721--712804 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 34
712711 TTTTAAAATA
712721 ATTTATTTTAAAATAAATTATTATAAAATATGAATTG
1 ATTTATTTTAAAATAAA-T-TTAT-AAATATGAATTG
* * *
712758 ATTTATTTT-AAAT-AATTTATTAGTATGGATTG
1 ATTTATTTTAAAATAAATTTATAAATATGAATTG
712790 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
712805 TTGATTGATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 18 0.43
33 8 0.19
34 1 0.02
35 2 0.05
36 4 0.10
37 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (34 bp):
ATTTATTTTAAAATAAATTTATAAATATGAATTG
Found at i:712883 original size:31 final size:31
Alignment explanation
Indices: 712848--712906 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
712838 AGTTGTATGG
* *
712848 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
712879 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
712907 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:715039 original size:79 final size:79
Alignment explanation
Indices: 714908--715065 Score: 289
Period size: 79 Copynumber: 2.0 Consensus size: 79
714898 TAGTTTTGAT
714908 TTCATTTTGATCAATCGGTTAAAAAATTATCAACTGTCACTATAATATAATATTATTTCATTTTT
1 TTCATTTTGATCAATCGGTTAAAAAATTATCAACTGTCACTATAATATAATATTATTTCATTTTT
714973 AATAATATAAAAAA
66 AATAATATAAAAAA
* * *
714987 TTCATTTTGATCAATGGGTTAAAAAATTATCGACTGTGACTATAATATAATATTATTTCATTTTT
1 TTCATTTTGATCAATCGGTTAAAAAATTATCAACTGTCACTATAATATAATATTATTTCATTTTT
715052 AATAATATAAAAAA
66 AATAATATAAAAAA
715066 ATATCACATT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.42, C:0.09, G:0.07, T:0.42
Consensus pattern (79 bp):
TTCATTTTGATCAATCGGTTAAAAAATTATCAACTGTCACTATAATATAATATTATTTCATTTTT
AATAATATAAAAAA
Found at i:715692 original size:2 final size:2
Alignment explanation
Indices: 715685--715712 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
715675 TAGTGTAATC
715685 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
715713 TTTACGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:727310 original size:127 final size:127
Alignment explanation
Indices: 727084--727330 Score: 458
Period size: 127 Copynumber: 1.9 Consensus size: 127
727074 AAAATTCAGT
727084 GGGTTGAGTTGGAAGTTTTGAAGGAGAAGATAGGGTCTAGGTTTAGGGTGGAAAATACAAGATTG
1 GGGTTGAGTTGGAAGTTTTGAAGGAGAAGATAGGGTCTAGGTTTAGGGTGGAAAATACAAGATTG
* *
727149 AATTGGGGAATAATGGTATAATTGGCCTTCATATAGTTAAAGGATATTTATATAGCAGGTTC
66 AATTGGGGAATAATGGTATAACTGACCTTCATATAGTTAAAGGATATTTATATAGCAGGTTC
* *
727211 GGGTTGAGTTGGAATTTTTGAAGGAGAAGATAGGGTCTAGGTTTAGGGTGGAAAATTCAAGATTG
1 GGGTTGAGTTGGAAGTTTTGAAGGAGAAGATAGGGTCTAGGTTTAGGGTGGAAAATACAAGATTG
727276 AATTGGGGAATAATGGTATAACTGACCTTCATATAGTTAAAGGATATTTATATAG
66 AATTGGGGAATAATGGTATAACTGACCTTCATATAGTTAAAGGATATTTATATAG
727331 TTAGAGATAA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
127 116 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (127 bp):
GGGTTGAGTTGGAAGTTTTGAAGGAGAAGATAGGGTCTAGGTTTAGGGTGGAAAATACAAGATTG
AATTGGGGAATAATGGTATAACTGACCTTCATATAGTTAAAGGATATTTATATAGCAGGTTC
Found at i:732781 original size:7 final size:7
Alignment explanation
Indices: 732769--732797 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
732759 TAGTGAATTC
732769 CCTCACT
1 CCTCACT
732776 CCTCACT
1 CCTCACT
732783 CCTCACT
1 CCTCACT
732790 CCTCACT
1 CCTCACT
732797 C
1 C
732798 AATTCCCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.59, G:0.00, T:0.28
Consensus pattern (7 bp):
CCTCACT
Found at i:732884 original size:6 final size:6
Alignment explanation
Indices: 732873--732919 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
732863 CAGCGATCAT
* * *
732873 CATGAC CATGAC CATCAT CATGAC CATGAC CAT-ACC CATGCC CATGA
1 CATGAC CATGAC CATGAC CATGAC CATGAC CATGA-C CATGAC CATGA
732920 TGAGTAAGTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 1 0.03
6 32 0.97
ACGTcount: A:0.32, C:0.36, G:0.13, T:0.19
Consensus pattern (6 bp):
CATGAC
Found at i:732891 original size:18 final size:18
Alignment explanation
Indices: 732868--732905 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
732858 GCTTCCAGCG
732868 ATCATCATGACCATGACC
1 ATCATCATGACCATGACC
732886 ATCATCATGACCATGACC
1 ATCATCATGACCATGACC
732904 AT
1 AT
732906 ACCCATGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.24
Consensus pattern (18 bp):
ATCATCATGACCATGACC
Found at i:732912 original size:18 final size:18
Alignment explanation
Indices: 732868--732919 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
732858 GCTTCCAGCG
*
732868 ATCATCATGACCATGACC
1 ATCACCATGACCATGACC
*
732886 ATCATCATGACCATGACC
1 ATCACCATGACCATGACC
*
732904 AT-ACCCATGCCCATGA
1 ATCA-CCATGACCATGA
732920 TGAGTAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 1 0.03
18 30 0.97
ACGTcount: A:0.33, C:0.35, G:0.12, T:0.21
Consensus pattern (18 bp):
ATCACCATGACCATGACC
Found at i:740547 original size:23 final size:22
Alignment explanation
Indices: 740517--740560 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
740507 GTAAATATAT
740517 TAATAATACAA-ATATAAGAAAA
1 TAATAATACAATA-ATAAGAAAA
740539 TAATGAATACAATAATAAGAAA
1 TAAT-AATACAATAATAAGAAA
740561 CATTATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 15 0.75
24 1 0.05
ACGTcount: A:0.66, C:0.05, G:0.07, T:0.23
Consensus pattern (22 bp):
TAATAATACAATAATAAGAAAA
Found at i:746122 original size:19 final size:20
Alignment explanation
Indices: 746098--746148 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
746088 AATGACCAAT
746098 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
746117 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
746137 AAAATCGCAACG
1 AAAATCGCAACG
746149 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:746142 original size:20 final size:20
Alignment explanation
Indices: 746098--746395 Score: 147
Period size: 20 Copynumber: 14.6 Consensus size: 20
746088 AATGACCAAT
*
746098 AAAATCGCAACGCGA-T-ATC
1 AAAATCGCAACGCGATTGA-G
*
746117 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
** ***
746137 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTGAG
**
746157 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TGAG
**
746177 AAAATCGCAACGCGAGCTT-CC
1 AAAATCGCAACGCGA--TTGAG
**
746198 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* *
746221 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTGAG
** *
746241 TGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
746261 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA-TT-G-AG
* * *
746284 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * * *
746304 AGATTCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* * * *
746324 AGAATCGAAATGCGACTGAG
1 AAAATCGCAACGCGATTGAG
* *
746344 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTGAG
* *
746364 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAG
746384 AAAATCGCAACG
1 AAAATCGCAACG
746396 TTAAAAAGAA
Statistics
Matches: 228, Mismatches: 37, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
19 15 0.07
20 162 0.71
21 19 0.08
22 4 0.02
23 27 0.12
24 1 0.00
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTGAG
Found at i:746277 original size:40 final size:40
Alignment explanation
Indices: 746223--746393 Score: 207
Period size: 40 Copynumber: 4.2 Consensus size: 40
746213 TTTAGAAGAA
** *
746223 AATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
* *
746263 AGTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGA-TT-G-AGAGAATCGCAATGCGACTGAGAG
* * *
746306 ATTCGCAATGCGACTGAGAGAATCGAAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
* * * *
746346 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
746386 AATCGCAA
1 AATCGCAA
746394 CGTTAAAAAG
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
40 75 0.67
41 3 0.03
42 2 0.02
43 32 0.29
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAG
Found at i:746290 original size:63 final size:63
Alignment explanation
Indices: 746202--746395 Score: 250
Period size: 63 Copynumber: 3.1 Consensus size: 63
746192 GCTTCCAAGT
* ** *
746202 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
* * *
746265 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
* * * * * *
746328 TCGAAATGCGA-CT-G-AGAGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAA
1 TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
746388 TCGCAACG
1 TCGCAACG
746396 TTAAAAAGAA
Statistics
Matches: 113, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
60 46 0.41
61 1 0.01
62 1 0.01
63 65 0.58
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.19
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAGAATCGCAATGCGATTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:746405 original size:20 final size:20
Alignment explanation
Indices: 746382--746425 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
746372 AACGCGATTT
*
746382 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
746402 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
746422 AGAA
1 AGAA
746426 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:746410 original size:60 final size:60
Alignment explanation
Indices: 746098--746413 Score: 190
Period size: 60 Copynumber: 5.2 Consensus size: 60
746088 AATGACCAAT
* *
746098 AAAATCGCAACGCGATATCA-A-AATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
1 AAAATCGCAATGCGAT-TGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
* ** * * ** ** * *
746157 AAAATCGCAA--CGGTCAAAAGAAAATCGCAACGCGAGCTTCCAAGTTCGCAACGCGATTTAGAA
1 AAAATCGCAATGCGAT--TGAGAGAATCGCAACGCGA-TTTAGAAAATCGCAA--CG-TTAAAAA
746220 G
60 G
** * * * * * *
746221 AAAATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAA--CG-TTAAAAAG
* * * * * * * * * ** ***
746284 AGAATCGCAATGCGACTGAGAGATTCGCAATGCGACTGAGAGAATCGAAATGCGACTGAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
*
746344 AGAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
1 AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
746404 AAAATCGCAA
1 AAAATCGCAA
746414 CGGTCAAAAG
Statistics
Matches: 195, Mismatches: 53, Indels: 17
0.74 0.20 0.06
Matches are distributed among these distances:
57 3 0.02
58 2 0.01
59 11 0.06
60 71 0.36
61 11 0.06
63 65 0.33
64 29 0.15
66 3 0.02
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (60 bp):
AAAATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAAAATCGCAACGTTAAAAAG
Found at i:746514 original size:6 final size:6
Alignment explanation
Indices: 746503--746579 Score: 95
Period size: 6 Copynumber: 12.5 Consensus size: 6
746493 GACACGTATT
746503 ACCACG ACCACG ACCACG A-CACG TATTACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ----ACCACG ACCACG ACCACG ACCACG
*
746554 ACCACG ACCACG ACCCCG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
746580 CGAGACGAGA
Statistics
Matches: 65, Mismatches: 1, Indels: 11
0.84 0.01 0.14
Matches are distributed among these distances:
5 9 0.14
6 51 0.78
9 1 0.02
10 4 0.06
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.04
Consensus pattern (6 bp):
ACCACG
Found at i:746523 original size:27 final size:27
Alignment explanation
Indices: 746493--746573 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
746483 ACGTGTCGAA
746493 GACACGTATTACCACGACCACGACCAC
1 GACACGTATTACCACGACCACGACCAC
746520 GACACGTATTACCACGACCACGACCAC
1 GACACGTATTACCACGACCACGACCAC
*
746547 GACCACG----ACCACGACCACGACCCC
1 GA-CACGTATTACCACGACCACGACCAC
746571 GAC
1 GAC
746574 CCGACCCGAG
Statistics
Matches: 52, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
23 1 0.02
24 18 0.35
27 29 0.56
28 4 0.08
ACGTcount: A:0.32, C:0.44, G:0.16, T:0.07
Consensus pattern (27 bp):
GACACGTATTACCACGACCACGACCAC
Found at i:746535 original size:15 final size:15
Alignment explanation
Indices: 746493--746537 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
746483 ACGTGTCGAA
746493 GACACGTATTACCAC
1 GACACGTATTACCAC
746508 GACCACG----ACCAC
1 GA-CACGTATTACCAC
746520 GACACGTATTACCAC
1 GACACGTATTACCAC
746535 GAC
1 GAC
746538 CACGACCACG
Statistics
Matches: 25, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 4 0.16
12 7 0.28
15 10 0.40
16 4 0.16
ACGTcount: A:0.33, C:0.38, G:0.16, T:0.13
Consensus pattern (15 bp):
GACACGTATTACCAC
Found at i:747316 original size:6 final size:6
Alignment explanation
Indices: 747275--747385 Score: 180
Period size: 6 Copynumber: 19.5 Consensus size: 6
747265 TCTCGGATCG
747275 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
747317 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
747365 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
747386 AATACGTGTC
Statistics
Matches: 105, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 30 0.29
6 75 0.71
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:747488 original size:20 final size:20
Alignment explanation
Indices: 747463--747506 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
747453 TTTTTAACTA
*
747463 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
747483 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
747503 TTCT
1 TTCT
747507 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:747516 original size:20 final size:20
Alignment explanation
Indices: 747493--747727 Score: 134
Period size: 20 Copynumber: 11.6 Consensus size: 20
747483 TTCTTTTTAA
747493 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
747513 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *
747533 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
747553 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
747573 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
747593 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
747616 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
747637 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
747655 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
* *
747677 CGTTGCGATTTTTTAAATCA
1 CGTTGCGATTTTCTAAATCG
* *
747697 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
747716 CGTTGCGATTTT
1 CGTTGCGATTTT
747728 ATTGGTCATT
Statistics
Matches: 174, Mismatches: 33, Indels: 17
0.78 0.15 0.08
Matches are distributed among these distances:
18 2 0.01
19 16 0.09
20 126 0.72
21 13 0.07
22 4 0.02
23 13 0.07
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:747537 original size:40 final size:40
Alignment explanation
Indices: 747493--747623 Score: 163
Period size: 40 Copynumber: 3.2 Consensus size: 40
747483 TTCTTTTTAA
* * * *
747493 CGTTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCG
*
747533 CGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCG
* **
747573 CATTGCGATTCAATCAATCGCATTGCGATTTTCTTCTAAATCG
1 CGTTGCGATTCTCTCAATCGCATTGCGA--TTC-TCTAAATCG
747616 CGTTGCGA
1 CGTTGCGA
747624 ACTTGGAAGC
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
40 60 0.77
42 3 0.04
43 15 0.19
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (40 bp):
CGTTGCGATTCTCTCAATCGCATTGCGATTCTCTAAATCG
Found at i:747719 original size:19 final size:19
Alignment explanation
Indices: 747676--747727 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
747666 TTTCTTTTTA
*
747676 ACGTTGCGATTTTTTAAATC
1 ACGTTGCGA-TTTTGAAATC
*
747696 ACGTTGCGATTTTGATATC
1 ACGTTGCGATTTTGAAATC
*
747715 GCGTTGCGATTTT
1 ACGTTGCGATTTT
747728 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.44
Consensus pattern (19 bp):
ACGTTGCGATTTTGAAATC
Found at i:752326 original size:46 final size:46
Alignment explanation
Indices: 752274--752364 Score: 164
Period size: 46 Copynumber: 2.0 Consensus size: 46
752264 GATCTTAAGA
*
752274 GATCTTAAGAGATATAATGTCTTATTTCACTATATATAAATTAAAG
1 GATCTTAAGAGATATAATGTCTTATTTAACTATATATAAATTAAAG
*
752320 GATCTTAAGAGATATAGTGTCTTATTTAACTATATATAAATTAAA
1 GATCTTAAGAGATATAATGTCTTATTTAACTATATATAAATTAAA
752365 ACAAAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (46 bp):
GATCTTAAGAGATATAATGTCTTATTTAACTATATATAAATTAAAG
Found at i:752837 original size:37 final size:37
Alignment explanation
Indices: 752803--752872 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
752793 TACAAATTGT
752803 AAAAAATTTATAT-ATTTTATTTAAAAAATTAAATTC
1 AAAAAATTTATATAATTTTATTTAAAAAATTAAATTC
* * * *
752839 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAAAATTTATATAATTTTATTTAAAAAATTAAA
752873 AATATAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
36 11 0.38
37 18 0.62
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (37 bp):
AAAAAATTTATATAATTTTATTTAAAAAATTAAATTC
Found at i:754880 original size:25 final size:25
Alignment explanation
Indices: 754846--754895 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
754836 TAAAAGTTAA
*
754846 TAAGTTTACTCTATCACCAGATTAG
1 TAAGTTTACTCAATCACCAGATTAG
*
754871 TAAGTTTACTCAATCCCCAGATTAG
1 TAAGTTTACTCAATCACCAGATTAG
754896 CTGTGCTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (25 bp):
TAAGTTTACTCAATCACCAGATTAG
Found at i:762773 original size:21 final size:21
Alignment explanation
Indices: 762752--762790 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
762742 TGAAATGAGA
*
762752 AAAAATG-AATTTAATTTAAG
1 AAAAATGAAATTCAATTTAAG
*
762772 AATAATGAAATTCAATTTA
1 AAAAATGAAATTCAATTTA
762791 TTTGTTGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.36
Consensus pattern (21 bp):
AAAAATGAAATTCAATTTAAG
Found at i:763177 original size:31 final size:30
Alignment explanation
Indices: 763142--763256 Score: 117
Period size: 28 Copynumber: 3.6 Consensus size: 30
763132 CTTTATTTTG
763142 TTCGGGTCGGGTCGGGTTTTTAAGTGTGATA
1 TTCGGGTCGGGTC-GGTTTTTAAGTGTGATA
763173 TTCGGGTCGAGTCGGTCGGTTTTTTTAAGTGTGATA
1 TTCGGGTC--G--GGTCGG--TTTTTAAGTGTGATA
* *
763209 TTCGGGTCGGATC--TTTTTAAGTTTGATA
1 TTCGGGTCGGGTCGGTTTTTAAGTGTGATA
*
763237 TTTGGGTCGGGTTCGGTTTT
1 TTCGGGTCGGG-TCGGTTTT
763257 ATGGTGAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 18
0.76 0.04 0.19
Matches are distributed among these distances:
28 23 0.32
29 2 0.03
31 12 0.17
32 3 0.04
33 1 0.01
34 3 0.04
35 4 0.06
36 23 0.32
ACGTcount: A:0.12, C:0.10, G:0.34, T:0.43
Consensus pattern (30 bp):
TTCGGGTCGGGTCGGTTTTTAAGTGTGATA
Found at i:763187 original size:62 final size:61
Alignment explanation
Indices: 763072--763187 Score: 135
Period size: 62 Copynumber: 1.9 Consensus size: 61
763062 AAATAATTTT
* * *
763072 TTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTTGGCTCGGGTCGGGTGAAAC
1 TTTATTATTTCGGGTCGGGTCGGATTTCTAAGTCATATATTCGGCTCGAGTCGGGTGAAAC
* * * * *
763133 TTTATTTTGTTCGGGTCGGGTCGGGTTTTTAAGT-GTGATATTCGGGTCGAGTCGG
1 TTTATTAT-TTCGGGTCGGGTCGGATTTCTAAGTCAT-ATATTCGGCTCGAGTCGG
763188 TCGGTTTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
61 8 0.18
62 37 0.82
ACGTcount: A:0.15, C:0.13, G:0.32, T:0.41
Consensus pattern (61 bp):
TTTATTATTTCGGGTCGGGTCGGATTTCTAAGTCATATATTCGGCTCGAGTCGGGTGAAAC
Found at i:763800 original size:17 final size:18
Alignment explanation
Indices: 763778--763824 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
763768 TATGAAATTG
*
763778 GATTCCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
763795 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
763813 TATTCCAATTCC
1 GATTCCAATTCC
763825 CTCATAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 12 0.44
18 15 0.56
ACGTcount: A:0.28, C:0.32, G:0.06, T:0.34
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:764372 original size:20 final size:21
Alignment explanation
Indices: 764347--764386 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
764337 AATACAAGAA
764347 AATAAAAGTTAACT-ATTTTT
1 AATAAAAGTTAACTAATTTTT
*
764367 AATAAATGTTAACTAATTTT
1 AATAAAAGTTAACTAATTTT
764387 GAAGCAGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (21 bp):
AATAAAAGTTAACTAATTTTT
Found at i:778376 original size:19 final size:19
Alignment explanation
Indices: 778354--778391 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
778344 GATAATAATG
778354 AGATTATATGTATTCAAAC
1 AGATTATATGTATTCAAAC
778373 AGATTATATGTATTCAAAC
1 AGATTATATGTATTCAAAC
778392 TAAGAACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (19 bp):
AGATTATATGTATTCAAAC
Found at i:780254 original size:2 final size:2
Alignment explanation
Indices: 780247--780283 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
780237 ATTTTCATCC
*
780247 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
780284 GAACTTTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:787749 original size:60 final size:61
Alignment explanation
Indices: 787651--787823 Score: 208
Period size: 60 Copynumber: 2.9 Consensus size: 61
787641 AACTATAACC
* * * *
787651 CTCATT-TCAAATTAGTCTTTAAACTTTTGATTACTTTAATTTCATCCCTAAATC-ATGACT
1 CTCATTCT-AAATTAGTCTTTAAACTTTTGAATATTTTAATTTCATCCCTAAATCTACGACA
*
787711 CTCATTCTAAATTAGTCTTTAAACTTTTGAACATTTTAATTTCATCCCTAAA-CTACGACA
1 CTCATTCTAAATTAGTCTTTAAACTTTTGAATATTTTAATTTCATCCCTAAATCTACGACA
* * *** * *
787771 CTCTTTCTAGATTAGTCCCCAAAATTTTGAATATTTTAATTTCATCCCAAAAT
1 CTCATTCTAAATTAGTCTTTAAACTTTTGAATATTTTAATTTCATCCCTAAAT
787824 TCATCCTAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
59 1 0.01
60 95 0.98
61 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.42
Consensus pattern (61 bp):
CTCATTCTAAATTAGTCTTTAAACTTTTGAATATTTTAATTTCATCCCTAAATCTACGACA
Found at i:791584 original size:17 final size:16
Alignment explanation
Indices: 791524--791630 Score: 61
Period size: 16 Copynumber: 6.9 Consensus size: 16
791514 AGATCCAATC
791524 AAGAACAAAAG--A-A
1 AAGAACAAAAGAAACA
791537 AAGAAGCAAAA-AAAGCA
1 AAGAA-CAAAAGAAA-CA
* *
791554 AA-AAAAAAAAAAACA
1 AAGAACAAAAGAAACA
*
791569 AAGAAGCAAGAGAAAC-
1 AAGAA-CAAAAGAAACA
*
791585 AAGAACAAAAGAAAAA
1 AAGAACAAAAGAAACA
791601 AAGAGA-AAAAGAGAA-A
1 AAGA-ACAAAAGA-AACA
791617 AA-AATCAAAAGAAA
1 AAGAA-CAAAAGAAA
791631 AAGGGACAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 24
0.71 0.06 0.23
Matches are distributed among these distances:
13 5 0.07
14 6 0.08
15 20 0.27
16 31 0.41
17 13 0.17
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.01
Consensus pattern (16 bp):
AAGAACAAAAGAAACA
Found at i:791602 original size:8 final size:8
Alignment explanation
Indices: 791524--791620 Score: 70
Period size: 9 Copynumber: 11.2 Consensus size: 8
791514 AGATCCAATC
*
791524 AAGAACAA
1 AAGAAAAA
*
791532 AAGAAAAG
1 AAGAAAAA
791540 AAGCAAAAA
1 AAG-AAAAA
791549 AAGCAAAAA
1 AAG-AAAAA
791558 AA-AAAAA
1 AAGAAAAA
*
791565 AACAAAGAA
1 AAGAAA-AA
*
791574 GCAAGAGAAAC
1 --AAGA-AAAA
*
791585 AAGAACAA
1 AAGAAAAA
791593 AAGAAAAA
1 AAGAAAAA
791601 AAGAGAAAA
1 AAGA-AAAA
791610 AGAGAAAAA
1 A-AGAAAAA
791619 AA
1 AA
791621 TCAAAAGAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 16
0.75 0.08 0.16
Matches are distributed among these distances:
7 7 0.10
8 26 0.36
9 31 0.42
10 3 0.04
11 4 0.05
12 2 0.03
ACGTcount: A:0.77, C:0.07, G:0.15, T:0.00
Consensus pattern (8 bp):
AAGAAAAA
Found at i:791642 original size:32 final size:33
Alignment explanation
Indices: 791523--791643 Score: 96
Period size: 32 Copynumber: 3.8 Consensus size: 33
791513 AAGATCCAAT
* *
791523 CAAGAACAAAAGAAAAGAAG-CAAAAAAAGCAAA
1 CAAGAACAAAAGAAAAAAAGACAAAAAGAG-AAA
* **
791556 -AA-AA-AAAA-AAACAAAGA-AGCAAGAGAAA
1 CAAGAACAAAAGAAAAAAAGACAAAAAGAGAAA
*
791584 CAAGAACAAAAGAAAAAAAGAGAAAAAGAGAAA
1 CAAGAACAAAAGAAAAAAAGACAAAAAGAGAAA
**
791617 -AA-AATCAAAAGAAAAAGGGACAAAAAG
1 CAAGAA-CAAAAGAAAAAAAGACAAAAAG
791644 CACATGCAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
28 3 0.04
29 13 0.19
30 6 0.09
31 8 0.11
32 31 0.44
33 9 0.13
ACGTcount: A:0.74, C:0.08, G:0.17, T:0.01
Consensus pattern (33 bp):
CAAGAACAAAAGAAAAAAAGACAAAAAGAGAAA
Found at i:792292 original size:22 final size:22
Alignment explanation
Indices: 792264--792314 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
792254 CCCCATCAAT
792264 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
* *
792286 CCTTTGAGCATCAAATGCTAAA
1 CCTTTGAGCATCAAATACCAAA
792308 CCTTTGA
1 CCTTTGA
792315 CCAAACACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.27
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:793331 original size:36 final size:36
Alignment explanation
Indices: 793215--793346 Score: 160
Period size: 36 Copynumber: 3.7 Consensus size: 36
793205 AACATAAACA
* * *
793215 TTGAAACA-TTTCCCTTGAAATAAATTTCGTCTCTC
1 TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
* *
793250 TTGAGATAGTTTCCCTTGGAACTAAGTTTT-GTCTCTC
1 TTGAGACAGTTTCCCTTGAAAC-AA-TTTTCGTCTCTC
* * *
793287 TTAAGACAGTTTCTCTTGAAACAATTTTCGTCTATC
1 TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
793323 TTGAGACAGTTTCCCTTGAAACAA
1 TTGAGACAGTTTCCCTTGAAACAA
793347 AACCTTTGAA
Statistics
Matches: 81, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
35 10 0.12
36 41 0.51
37 27 0.33
38 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (36 bp):
TTGAGACAGTTTCCCTTGAAACAATTTTCGTCTCTC
Found at i:793456 original size:67 final size:64
Alignment explanation
Indices: 793305--793460 Score: 156
Period size: 64 Copynumber: 2.4 Consensus size: 64
793295 GTTTCTCTTG
** * **
793305 AAACAATTTTCG-TCTATCTTGAGACAGTTTCCCTTGAAACAAAACCTTTGAATTATTTCCCCTA
1 AAACAATTTT-GTTCTCCCTTGAGACAGTTACCCTTGAAACAAAACCTTCAAATTATTTCCCCTA
* * * *
793369 AAACAATTTTTTTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAATTTTGTTCTCCCTTGAGACAGTTACCCTTG-AA-ACAAAACCTTCAAA-TTATTTCCCC
793434 TA
63 TA
793436 AAACATAATTTTGTT-T-CCTTGAGAC
1 AAAC--AATTTTGTTCTCCCTTGAGAC
793461 CGTTTCTCAT
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
64 30 0.39
65 2 0.03
66 11 0.14
67 24 0.32
68 1 0.01
69 8 0.11
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (64 bp):
AAACAATTTTGTTCTCCCTTGAGACAGTTACCCTTGAAACAAAACCTTCAAATTATTTCCCCTA
Found at i:794349 original size:104 final size:105
Alignment explanation
Indices: 794109--794824 Score: 1070
Period size: 104 Copynumber: 7.0 Consensus size: 105
794099 GCACTCGAGG
* * ** *
794109 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTC-ACAACAAAACTTCTCAATTTCA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAAC--AACTTCTCAATTTCA
*
794173 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG-
64 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
*
794214 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGTCAACAACAACTTCTC-ATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
794278 GCCAATTTCAACTTCACAATGAAGGATATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
*
794318 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT---CAACAACTTCTCAATTTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
* *
794380 ACCAATTTCAACTTCACAATGAAGG--ATTGGACTTCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
* *
794418 CAATGCAAGTTCAAATTCACGACGAAGGGACCGCTGCTTGTCAACAAACAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAG
794483 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
65 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
* **
794524 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
*
794589 GCCAATTTCAACTTCACAACG-AGGATATTGGACTCCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
* * *
794628 CAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
794693 GCCAATTTCAACTTCACAACGAAGGATATTGGAC-TCAGA
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
794732 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-AC-A-AA-TT-TC-A-TTCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
** * *
794790 TTCAATTTCAACTTCACGACGGAGGATATTGGACT
66 GCCAATTTCAACTTCACAACGAAGGATATTGGACT
794825 CTGAACAATG
Statistics
Matches: 570, Mismatches: 30, Indels: 29
0.91 0.05 0.05
Matches are distributed among these distances:
97 35 0.06
98 1 0.00
99 1 0.00
100 53 0.09
101 14 0.02
102 33 0.06
103 48 0.08
104 238 0.42
105 86 0.15
106 61 0.11
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (105 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGA
GCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGA
Found at i:794717 original size:209 final size:209
Alignment explanation
Indices: 794109--794825 Score: 1102
Period size: 209 Copynumber: 3.5 Consensus size: 209
794099 GCACTCGAGG
* * ** *
794109 CAACACAAGTTCAACTTCACAACGAAGGGACAACTGGTTGTCACAACAAAACTTCTCAATTTCAG
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCACAAC--AACTTCTCAATTTCAG
*
794174 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAG-CAACGCAAGTTCAACTTCACGACG
64 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACG
* *
794238 AAGGGACCGCTGCCTGTCAACAACAACTTCTC-ATTTCAGAGCCAATTTCAACTTCACAATGAAG
129 AAGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
794302 GATATTGGACTTCAGA
194 GATATTGGACTTCAGA
* *
794318 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCCTGT--CAACAACTTCTCAATTTCAGAA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCACAACAACTTCTCAATTTCAGAG
* * *
794381 CCAATTTCAACTTCACAATGAAGG--ATTGGACTTCAGACAATGCAAGTTCAAATTCACGACGAA
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAA
794444 GGGACCGCTGCTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
131 GGGACCGCTGCTTGTCAAC-AACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
794509 ATATTGGACTTCAGA
195 ATATTGGACTTCAGA
* **
794524 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGA
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTC-ACAACAACTTCTCAATTTCAGA
794589 GCCAATTTCAACTTCACAACG-AGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGA
65 GCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGA
* *
794653 AGGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
130 AGGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
794718 ATATTGGAC-TCAGA
195 ATATTGGACTTCAGA
*
794732 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAC-A-AA-TT-TC-A-TTCAGAT
1 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCACAACAACTTCTCAATTTCAGAG
* * *
794791 TCAATTTCAACTTCACGACGGAGGATATTGGACTC
66 CCAATTTCAACTTCACAACGAAGGATATTGGACTC
794826 TGAACAATGC
Statistics
Matches: 470, Mismatches: 29, Indels: 25
0.90 0.06 0.05
Matches are distributed among these distances:
201 22 0.05
202 15 0.03
203 12 0.03
204 44 0.09
205 53 0.11
206 88 0.19
207 6 0.01
208 50 0.11
209 124 0.26
210 56 0.12
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (209 bp):
CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCACAACAACTTCTCAATTTCAGAG
CCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAA
GGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGA
TATTGGACTTCAGA
Found at i:795899 original size:2 final size:2
Alignment explanation
Indices: 795892--795956 Score: 75
Period size: 2 Copynumber: 34.5 Consensus size: 2
795882 ATTGTATTAT
* *
795892 TA TA TA TA TA TG T- TT TA T- 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
*
795932 TA TA TA TA TC TA TA -A TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
795957 TTATTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
1 4 0.07
2 51 0.93
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:795909 original size:18 final size:19
Alignment explanation
Indices: 795888--795961 Score: 81
Period size: 16 Copynumber: 4.3 Consensus size: 19
795878 CTTAATTGTA
*
795888 TTATTATATATATATGT-T
1 TTATTATATATATATATAT
795906 TTATTATATATATATATA-
1 TTATTATATATATATATAT
795924 -TA-TATATATATATATAT
1 TTATTATATATATATATAT
*
795941 CTA-TA-ATATAT-TATAT
1 TTATTATATATATATATAT
795957 TTATT
1 TTATT
795962 TTTTTTTTGA
Statistics
Matches: 50, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
16 21 0.42
17 9 0.18
18 20 0.40
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (19 bp):
TTATTATATATATATATAT
Done.