Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007729.1 Hibiscus syriacus cultivar Beakdansim tig00109980_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: 1111098
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 7
Found at i:456794 original size:23 final size:23
Alignment explanation
Indices: 456764--456813 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
456754 AGCTATCCTG
456764 CTCCTCCACCCCTCCACCACCTA
1 CTCCTCCACCCCTCCACCACCTA
*
456787 CTCCTCCACCCCTCCACCACCTG
1 CTCCTCCACCCCTCCACCACCTA
456810 CTCC
1 CTCC
456814 ACCAACTCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.14, C:0.66, G:0.02, T:0.18
Consensus pattern (23 bp):
CTCCTCCACCCCTCCACCACCTA
Found at i:457504 original size:3 final size:3
Alignment explanation
Indices: 457492--457540 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
457482 TAATATTTAT
457492 TAA TAA -AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
457536 TAA TA
1 TAA TA
457541 TTCAAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 37 0.86
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:457983 original size:113 final size:113
Alignment explanation
Indices: 457866--458356 Score: 811
Period size: 113 Copynumber: 4.3 Consensus size: 113
457856 ATAGGGTCAT
* * ** * *
457866 ACAAAAGGTCGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
457931 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
*
457979 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTCTTCAGATGAGTTCTTCTC
1 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
*
458044 ATTATGAACTTTCTCTAGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
*
458092 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTGCTTCTTCAGATGAGTTCTTCTC
1 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
458157 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
66 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
458205 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * * **
458270 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA
66 ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
* * **
458318 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTTCT
1 ACAAAAAGTTGAACAAATTCTTCTCATTATGAA-TTTCT
458357 CTGGAAAAGC
Statistics
Matches: 356, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
113 351 0.99
114 5 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (113 bp):
ACAAAAAGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAA
Found at i:458382 original size:73 final size:73
Alignment explanation
Indices: 458263--458426 Score: 328
Period size: 73 Copynumber: 2.2 Consensus size: 73
458253 TCAGATGAGT
458263 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
1 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
458328 GAACAAGC
66 GAACAAGC
458336 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
1 TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
458401 GAACAAGC
66 GAACAAGC
458409 TCTTCTCATTATGAACTT
1 TCTTCTCATTATGAACTT
458427 CTTCTTCCTT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 91 1.00
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.32
Consensus pattern (73 bp):
TCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGAGCAAAAGGTT
GAACAAGC
Found at i:458675 original size:123 final size:123
Alignment explanation
Indices: 458390--458836 Score: 449
Period size: 123 Copynumber: 3.7 Consensus size: 123
458380 GATGGATTTG
* * *
458390 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAAATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCT
* * * * *
458455 CATTATGAAC-TTCACCTGGAAATAGCTCTGCTGCTCTATCTCTTTTTGGAAATGGAGTCA
65 CATTATGAACTTTC-TCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGG-AATAGAGTCA
* *
458515 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCATCTTCCTCTTCAGATAAGTTCTTCTC
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
* * * * *
458580 ATTATGAACTTTCTTTGGAAA-AGTTGGTGTTGATCTATCTCCTTCTGTG-ATAGATTCA
66 ATTATGAACTTTCTCTGGAAATAGCT-CTGCTGATCTATCTCCTTCTG-GAATAGAGTCA
* * * *
458638 TGCAAAAGGTTGAACAACCTCTTCTCATTATGAACTTCTTATTCCTCTTCAGATAAATTCTTCTC
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
* * *** ** **
458703 ATTATGAACTTTCTCTGG-CA-A---C-GCTGATCCATCGGGTGAT-GAAT----TTG
66 ATTATGAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGGAATAGAGTCA
* *
458750 AGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCCTTCCTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTT-CTTCCTCTTCAGATAAGTTCTTCT
*
458814 CATTATGAACTCT-TCTGGAAATA
65 CATTATGAACTTTCTCTGGAAATA
458837 TTGAAAACAT
Statistics
Matches: 274, Mismatches: 41, Indels: 26
0.80 0.12 0.08
Matches are distributed among these distances:
111 7 0.03
112 69 0.25
113 1 0.00
115 1 0.00
116 2 0.01
117 11 0.04
122 2 0.01
123 86 0.31
124 48 0.18
125 47 0.17
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (123 bp):
AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTC
ATTATGAACTTTCTCTGGAAATAGCTCTGCTGATCTATCTCCTTCTGGAATAGAGTCA
Found at i:459117 original size:77 final size:73
Alignment explanation
Indices: 458885--459134 Score: 356
Period size: 73 Copynumber: 3.4 Consensus size: 73
458875 GAGGTCTTAT
* * *
458885 CATCTTGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTTCTGAAGGCTT
1 CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
*
458950 TTTGAGAA
66 TTTGAAAA
*
458958 CATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
1 CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
459023 TTTGAAAA
66 TTTGAAAA
* * * *
459031 CATCATGCACTGTAGGTCTTACAGATAACCCTGAGGGTTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCATGCACTGTAGGGCTTACAGATGACCCTGA-GGCTTT---AAGATCAAAAAGCTCCCGAAG
459096 GCTTTTTGAAAA
62 GCTTTTTGAAAA
* * *
459108 CATCCTGCACTGCAGGGCTTACGGATG
1 CATCATGCACTGTAGGGCTTACAGATG
459135 TTGGAAATAG
Statistics
Matches: 160, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
73 101 0.63
74 5 0.03
77 54 0.34
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (73 bp):
CATCATGCACTGTAGGGCTTACAGATGACCCTGAGGCTTTAAGATCAAAAAGCTCCCGAAGGCTT
TTTGAAAA
Found at i:459852 original size:22 final size:22
Alignment explanation
Indices: 459801--459858 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
459791 GATAAAGCTT
* *
459801 TCATCTTCGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
459823 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
459845 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
459859 TGTAGATGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:460309 original size:54 final size:54
Alignment explanation
Indices: 460227--460381 Score: 157
Period size: 55 Copynumber: 2.9 Consensus size: 54
460217 AATTACTGGT
* ** * **
460227 TCGTAAAACACTTGACAATGCATTCATCATTTCACGTGGCTTATGCTTAGAGGC
1 TCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTATGCCCAGAGGC
* * * * * *
460281 TCGTAAAACATTTGACAACACGTTCATCATTCTCATGCGGTTTCTGCCCAGATGT
1 TCGTAAAACATTTGACAACACATTCATCATT-TCATGTGGCTTATGCCCAGAGGC
* * * *
460336 TCATAAAACATTTAATAACACATTCATCTTTTCATGTGGCTTATGC
1 TCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTATGC
460382 ACAAATTTAT
Statistics
Matches: 80, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
54 39 0.49
55 41 0.51
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (54 bp):
TCGTAAAACATTTGACAACACATTCATCATTTCATGTGGCTTATGCCCAGAGGC
Found at i:467283 original size:16 final size:16
Alignment explanation
Indices: 467264--467298 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
467254 GATCTTGTAG
467264 TCCCTCATAAGATTGC
1 TCCCTCATAAGATTGC
467280 TCCCTCATAAGATTGC
1 TCCCTCATAAGATTGC
467296 TCC
1 TCC
467299 ATTGTTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.31
Consensus pattern (16 bp):
TCCCTCATAAGATTGC
Found at i:470384 original size:20 final size:19
Alignment explanation
Indices: 470345--470386 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
470335 TTTCTTCGAT
470345 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
470364 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
470384 ATT
1 ATT
470387 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:470497 original size:120 final size:120
Alignment explanation
Indices: 470258--470490 Score: 321
Period size: 120 Copynumber: 2.0 Consensus size: 120
470248 TATATTAATT
* * *
470258 TATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCT
1 TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
*
470323 TAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAA
66 TAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
** * *
470378 TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGACATCCAGTTGT
1 TATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGTGC
* * *
470442 TTTAAGACTGC-CTTTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
64 CTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
470491 GGATTAAAAT
Statistics
Matches: 100, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
118 9 0.09
119 25 0.25
120 47 0.47
121 19 0.19
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (120 bp):
TATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGCCT
TAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAA
Found at i:471995 original size:3 final size:3
Alignment explanation
Indices: 471983--472025 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
471973 TAATATTTAT
* * *
471983 TAA TAA -AA TAA TAA TAA TAA TAA TTA TAA TTA TAA GAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
472026 TAAACAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:472823 original size:19 final size:21
Alignment explanation
Indices: 472799--472840 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
472789 TGATTTAATC
*
472799 TATATATG-TTAGT-TTTTAT
1 TATATATGAATAGTATTTTAT
472818 TATATATGAATAGTATTTTAT
1 TATATATGAATAGTATTTTAT
472839 TA
1 TA
472841 AATCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TATATATGAATAGTATTTTAT
Found at i:480033 original size:18 final size:18
Alignment explanation
Indices: 480010--480052 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
480000 GATCATCCTT
480010 TAACAATAGTAATGACAA
1 TAACAATAGTAATGACAA
480028 TAACAATAGTAATGACAA
1 TAACAATAGTAATGACAA
*
480046 TGACAAT
1 TAACAAT
480053 GGAAAAGCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (18 bp):
TAACAATAGTAATGACAA
Found at i:480225 original size:30 final size:30
Alignment explanation
Indices: 480190--480248 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
480180 AACTCTATGA
480190 CATGTCAATTGTATCTGAAACTCGATAAGG
1 CATGTCAATTGTATCTGAAACTCGATAAGG
480220 CATGTCAATTGTATCTGAAACTCGATAAG
1 CATGTCAATTGTATCTGAAACTCGATAAG
480249 ATACGTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
CATGTCAATTGTATCTGAAACTCGATAAGG
Found at i:481653 original size:28 final size:29
Alignment explanation
Indices: 481621--481676 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
481611 TTCTCAAATT
* *
481621 TTTGAACATTTCACTTTTATCCT-AAACC
1 TTTGAACATTTCAATTTCATCCTCAAACC
*
481649 TTTGAATATTTCAATTTCATCCTCAAAC
1 TTTGAACATTTCAATTTCATCCTCAAAC
481677 TATTAGGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.30, C:0.23, G:0.04, T:0.43
Consensus pattern (29 bp):
TTTGAACATTTCAATTTCATCCTCAAACC
Found at i:482352 original size:20 final size:20
Alignment explanation
Indices: 482327--482366 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
482317 TTGCTTCTGG
*
482327 TTCTCTTTCTTTCTTTATTT
1 TTCTCTTTCTTTCTTGATTT
*
482347 TTCTCTTTGTTTCTTGATTT
1 TTCTCTTTCTTTCTTGATTT
482367 ATTTGCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.72
Consensus pattern (20 bp):
TTCTCTTTCTTTCTTGATTT
Found at i:487276 original size:25 final size:25
Alignment explanation
Indices: 487242--487290 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
487232 AAACCCTTAA
487242 AATTGTATAACTTCGTCTCTAACAT
1 AATTGTATAACTTCGTCTCTAACAT
* * *
487267 AATTTTATAAGTTCGTTTCTAACA
1 AATTGTATAACTTCGTCTCTAACA
487291 CAAAATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (25 bp):
AATTGTATAACTTCGTCTCTAACAT
Found at i:489036 original size:13 final size:13
Alignment explanation
Indices: 489018--489045 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
489008 ACATGATACA
489018 TACATTAATAAAT
1 TACATTAATAAAT
489031 TACATTAATAAAT
1 TACATTAATAAAT
489044 TA
1 TA
489046 TAAATTATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (13 bp):
TACATTAATAAAT
Found at i:489088 original size:27 final size:27
Alignment explanation
Indices: 489056--489123 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
489046 TAAATTATAC
*
489056 ATACATATGTACATAAATACATGCATG
1 ATACATACGTACATAAATACATGCATG
489083 ATACATACGTACATAAATACATGCATG
1 ATACATACGTACATAAATACATGCATG
* *
489110 ATGCATACATACAT
1 ATACATACGTACAT
489124 TTCATATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.44, C:0.18, G:0.10, T:0.28
Consensus pattern (27 bp):
ATACATACGTACATAAATACATGCATG
Found at i:489531 original size:18 final size:18
Alignment explanation
Indices: 489487--489534 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
489477 AATACATCAT
*
489487 TTAATAAAATT-AATTTA
1 TTAATATAATTAAATTTA
* *
489504 ATGATCATAATTAAATTTA
1 TTAAT-ATAATTAAATTTA
489523 TTAATATAATTA
1 TTAATATAATTA
489535 TCATAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAATATAATTAAATTTA
Found at i:489584 original size:27 final size:27
Alignment explanation
Indices: 489554--489619 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
489544 ATATGGAAAG
*
489554 TAAATTTATTAATCTAATAATCATAGT
1 TAAATTTATTAATCTAATAATCATACT
*
489581 TAAATTTATTAATCTAATATTCATACT
1 TAAATTTATTAATCTAATAATCATACT
489608 TAATAATTTATT
1 T-A-AATTTATT
489620 CTAAATTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 26 0.74
28 1 0.03
29 8 0.23
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.48
Consensus pattern (27 bp):
TAAATTTATTAATCTAATAATCATACT
Found at i:489629 original size:66 final size:66
Alignment explanation
Indices: 489495--489638 Score: 166
Period size: 66 Copynumber: 2.2 Consensus size: 66
489485 ATTTAATAAA
* *
489495 ATTAATTTAATGATCATAATTAAATTTATTAATATAATTATCATAATTAATATGGAAAGTAAATT
1 ATTAATTTAATAATCATAATTAAATTTATTAATATAATTATCATAATTAATATGGAAACTAAATT
489560 T
66 T
* * * * ** **
489561 ATTAATCTAATAATCATAGTTAAATTTATTAATCTAA-TATTCATACTTAATAATTTATTCTAAA
1 ATTAATTTAATAATCATAATTAAATTTATTAATATAATTA-TCATAATTAAT-ATGGAAACTAAA
489625 -TT
64 TTT
489627 ATTAATTTAATA
1 ATTAATTTAATA
489639 GATCTTTTGA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
65 2 0.03
66 56 0.86
67 7 0.11
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (66 bp):
ATTAATTTAATAATCATAATTAAATTTATTAATATAATTATCATAATTAATATGGAAACTAAATT
T
Found at i:495760 original size:28 final size:26
Alignment explanation
Indices: 495705--495762 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 26
495695 AAACATTAAT
*
495705 AAAATAATATACATATAAATATTATG
1 AAAATAATATACATATAAAAATTATG
* *
495731 AAAATAATAGGTATATATAAAAATTTTG
1 AAAATAATA--TACATATAAAAATTATG
495759 AAAA
1 AAAA
495763 GAAAGAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (26 bp):
AAAATAATATACATATAAAAATTATG
Found at i:496256 original size:29 final size:29
Alignment explanation
Indices: 496224--496282 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
496214 AATTCAAAAT
*
496224 TATAATTATGAAA-AAAATATATTAATTTATA
1 TATATTTAT-AAATAAAATAT-TT-ATTTATA
496255 TATATTTATAAATAAAATATTTATTTAT
1 TATATTTATAAATAAAATATTTATTTAT
496283 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 6 0.23
30 5 0.19
31 15 0.58
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TATATTTATAAATAAAATATTTATTTATA
Found at i:496377 original size:20 final size:19
Alignment explanation
Indices: 496338--496379 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
496328 TTTCTTCGAT
496338 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
496357 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
496377 ATT
1 ATT
496380 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:496490 original size:120 final size:122
Alignment explanation
Indices: 496237--496490 Score: 304
Period size: 120 Copynumber: 2.1 Consensus size: 122
496227 AATTATGAAA
*
496237 AAAATATATTAATTTATATATATTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGG
1 AAAATATATTAA-TTATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGG
* * *
496302 ACTTCTAGGTACCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATT
65 ACATCCAGGTACCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATT
* ** *
496360 AAAACA-ATTAA-TATATA-ATTTATAAAATAGGATATTTATTTATTTAAAAATATCGGAAAATG
1 AAAATATATTAATTATATATATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-G
* *** * *
496422 GACATCCAGTTGTTTTAAGACTGC-CTTTTCTT-AATATTGAAAAATAAATAAAT-ATT
64 GACATCCAGGTACCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATT
496478 AAAATATGATTAA
1 AAAATAT-ATTAA
496491 AATAAGTTAA
Statistics
Matches: 112, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
118 8 0.07
119 25 0.22
120 51 0.46
121 18 0.16
122 5 0.04
123 5 0.04
ACGTcount: A:0.46, C:0.07, G:0.08, T:0.38
Consensus pattern (122 bp):
AAAATATATTAATTATATATATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGA
CATCCAGGTACCTTAAGACAGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATT
Found at i:497992 original size:3 final size:3
Alignment explanation
Indices: 497980--498019 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
497970 TAATATTTAT
* *
497980 TAA TAA -AA TAA TAA TAA TAA TTA TAA TTA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
498020 TACACAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:498002 original size:21 final size:21
Alignment explanation
Indices: 497967--498019 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
497957 ATTGGGCCTG
*
497967 TAATAATATTTATTAATAAAATAA
1 TAATAATAATTA-TAAT--AATAA
*
497991 TAATAATAATTATAATTATAA
1 TAATAATAATTATAATAATAA
498012 TAATAATA
1 TAATAATA
498020 TACACAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 12 0.44
23 4 0.15
24 11 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATAATAATTATAATAATAA
Found at i:498818 original size:19 final size:21
Alignment explanation
Indices: 498794--498835 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 21
498784 TGATTTAATC
*
498794 TATATATG-TTAGT-TTTTAT
1 TATATATGAATAGTATTTTAT
498813 TATATATGAATAGTATTTTAT
1 TATATATGAATAGTATTTTAT
498834 TA
1 TA
498836 AATCATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TATATATGAATAGTATTTTAT
Found at i:506004 original size:18 final size:18
Alignment explanation
Indices: 505981--506023 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
505971 GATCATCCTT
505981 TAACAATAGTAATGACAA
1 TAACAATAGTAATGACAA
505999 TAACAATAGTAATGACAA
1 TAACAATAGTAATGACAA
*
506017 TGACAAT
1 TAACAAT
506024 GGAAAAGCCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.23
Consensus pattern (18 bp):
TAACAATAGTAATGACAA
Found at i:506197 original size:30 final size:30
Alignment explanation
Indices: 506162--506220 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
506152 AACTCTATGA
506162 CATGTCAATTGTATCTGAAACTCGATAAGG
1 CATGTCAATTGTATCTGAAACTCGATAAGG
506192 CATGTCAATTGTATCTGAAACTCGATAAG
1 CATGTCAATTGTATCTGAAACTCGATAAG
506221 ATACGTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
CATGTCAATTGTATCTGAAACTCGATAAGG
Found at i:508321 original size:20 final size:20
Alignment explanation
Indices: 508296--508335 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
508286 TTGCTTCTGG
*
508296 TTCTCTTTCTTTCTTTATTT
1 TTCTCTTTCTTTCTTGATTT
*
508316 TTCTCTTTGTTTCTTGATTT
1 TTCTCTTTCTTTCTTGATTT
508336 ATTTGCATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.05, C:0.17, G:0.05, T:0.72
Consensus pattern (20 bp):
TTCTCTTTCTTTCTTGATTT
Found at i:513250 original size:25 final size:25
Alignment explanation
Indices: 513216--513264 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
513206 AAACCCTTAA
513216 AATTGTATAACTTCGTCTCTAACAT
1 AATTGTATAACTTCGTCTCTAACAT
* * *
513241 AATTTTATAAGTTCGTTTCTAACA
1 AATTGTATAACTTCGTCTCTAACA
513265 CAAAATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (25 bp):
AATTGTATAACTTCGTCTCTAACAT
Found at i:514748 original size:15 final size:15
Alignment explanation
Indices: 514728--514768 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
514718 TTTAAGGACT
514728 AAATTAAAAAACATG
1 AAATTAAAAAACATG
*
514743 AAATT-ATAAAC-TG
1 AAATTAAAAAACATG
*
514756 AAATTAAACAACA
1 AAATTAAAAAACA
514769 CAGAGATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
13 7 0.33
14 9 0.43
15 5 0.24
ACGTcount: A:0.63, C:0.10, G:0.05, T:0.22
Consensus pattern (15 bp):
AAATTAAAAAACATG
Found at i:515454 original size:18 final size:18
Alignment explanation
Indices: 515410--515457 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
515400 AATACATCAT
*
515410 TTAATAAAATT-AATTTA
1 TTAATATAATTAAATTTA
* *
515427 ATGATCATAATTAAATTTA
1 TTAAT-ATAATTAAATTTA
515446 TTAATATAATTA
1 TTAATATAATTA
515458 TCATAATTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 3 0.12
18 12 0.50
19 9 0.38
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (18 bp):
TTAATATAATTAAATTTA
Found at i:516863 original size:14 final size:13
Alignment explanation
Indices: 516842--516868 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
516832 TTTTTTTTCT
516842 TTTGAAAAATTAC
1 TTTGAAAAATTAC
516855 TTTGAAAAATTAC
1 TTTGAAAAATTAC
516868 T
1 T
516869 CCTCCTTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TTTGAAAAATTAC
Found at i:525197 original size:13 final size:13
Alignment explanation
Indices: 525179--525203 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
525169 TCGAATATAA
525179 AATCTTAAAATTT
1 AATCTTAAAATTT
525192 AATCTTAAAATT
1 AATCTTAAAATT
525204 CATTAACACT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATCTTAAAATTT
Found at i:528374 original size:2 final size:2
Alignment explanation
Indices: 528369--528404 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
528359 TGTTTGTTCT
528369 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
528405 ATACATTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:531564 original size:739 final size:747
Alignment explanation
Indices: 530116--531612 Score: 2651
Period size: 739 Copynumber: 2.0 Consensus size: 747
530106 AAGAAATACA
530116 CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACAATTCAATATGCACATATAAG
1 CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACAATTCAATATGCACATATAAG
* *
530181 CTAATTTCATTAAGCTCTTCAAATCATGGAATTAATATGTATTAAATTATAATGTTAGACCCTAT
66 CTAATTCCATTAAGCTCTTCAAATCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTAT
* *
530246 AGTTTTATTTTTTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGTGCCTGTCCTTACGTG
131 AGTTTTA--TTGTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTG
*
530311 GCACCAGCTCGGATAAGGCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGTTCGAGCAAA
194 GCACCAGCTCGGATAAGGCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGCTCGAGCAAA
*
530376 GGCGTGAATGACGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGGT
259 GGCGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGGT
530441 GTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATCAAGGCAATT
324 GTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATAT--AGGCAATT
530506 TAATGGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTATTTTAGGTTGATT
387 TAATGGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTATTTTAGGTTGATT
530571 TTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAGGT
452 TTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAGGT
* *
530636 TGAAATGGTTCGGGTTTGAATAAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTTGAGTC
517 TAAAATGGTTCGGGTTTG-A-AAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTCGAGTC
530701 GAGTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTTTCA
580 GAGTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTTTCA
530766 GGTAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTCGGGTGAAT
645 GGTAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTCGGGTGAAT
530831 TATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
710 TATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
*
530869 CATTTTAGCTTTTATCCCACATTGACAAGAAACATAAACCTAAACACTTCAATATGCACATATAA
1 CATTTTAGCTTTTATCCCACATTGACAAGAAACAT-AACCTAAACAATTCAATATGCACATATAA
530934 GCTAATTCCATT-AGCTCTTCAAATCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTA
65 GCTAATTCCATTAAGCTCTTCAAATCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTA
530998 TAG-TTTA-TGTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTGG
130 TAGTTTTATTGTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTGG
* * *
531061 CACCAGCTCGGATAAGACGCGGATGACCATTCATGTCTTTCATGATGTGGCGCC-GCTCGGGC-A
195 CACCAGCTCGGATAAG--GCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGCTCGAGCAA
531124 AGGCGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGG
258 AGGCGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGG
531189 TGTCTGATATGTAATTA-TTCATGTCAGAGTGATTTTTGGGTAAAAATGCC-A-AT-GGCAATTT
323 TGTCTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATAGGCAATTT
* * *
531250 AATGGTTCAAATTA-ACTAGATCGAGTCTAGGTTGACTCAGATTCGAGTTATTTTTAGGTTGATT
388 AATGGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTA-TTTTAGGTTGATT
531314 TTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAGGT
452 TTAAATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAGGT
*
531379 TAAAATGGTTC-GGTTTG-AAGTTAAATATCATGTTAATTTAGGTTCATATGGACTTCGAGTCGA
517 TAAAATGGTTCGGGTTTGAAAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTCGAGTCGA
*
531442 GTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATTGGTTTCAGG
582 GTCCTGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTTTCAGG
531507 TAAACTTCAAGTCGGGTCTTACTTAATACAAATAGAC-TTTGGTTGGATCATTTTCGGGTGAATT
647 TAAACTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCA-TTTCGGGTGAATT
531571 ATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
711 ATTTTCCACCTTTCACGAACGTTTAATGCCTTTGTAG
531608 CATTT
1 CATTT
531613 CCATGACTTC
Statistics
Matches: 722, Mismatches: 17, Indels: 24
0.95 0.02 0.03
Matches are distributed among these distances:
738 13 0.02
739 200 0.28
742 40 0.06
743 109 0.15
746 2 0.00
747 1 0.00
748 33 0.05
749 152 0.21
750 6 0.01
751 34 0.05
752 4 0.01
753 89 0.12
754 39 0.05
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (747 bp):
CATTTTAGCTTTTATCCCACATTGACAAGAAACATAACCTAAACAATTCAATATGCACATATAAG
CTAATTCCATTAAGCTCTTCAAATCATGGAATTAATATGTATTAAATTACAATGTTAGACCCTAT
AGTTTTATTGTTTAATTTTAAAATGCTAAGGCGCAGATGGTGATCTGCGCCTGTCCTTACGTGGC
ACCAGCTCGGATAAGGCGGATGACCATTCACGCCTTTCATGATGTGGCGCCAGCTCGAGCAAAGG
CGTGAATGAAGATCCGCGCCTTGTTAGAAAGGGTGCTAGATCGGTAAAATTTGACAAAACGGTGT
CTGATATGTAATTATTTCATGTCAGAGTGATTTTTGGGTAAAAATGCCAATATAGGCAATTTAAT
GGTTCAAATCAGACTAGATCGAGTCCAGGTTAACTCAGATTCGAGTTATTTTAGGTTGATTTTAA
ATCAGATTCAGTTTGAGTTCGGATCGACTTAATTACAAGTCAGATCAATATTTGTTTAGGTTAAA
ATGGTTCGGGTTTGAAAGTTAAATATCATGTTAATTTAGGTTCAGATGGACTTCGAGTCGAGTCC
TGTTCAAATCGAGTCATATCATTGACGAATACAATTTAGGTTAGGTAATATCGGTTTCAGGTAAA
CTTCAAGTCGGGTCTTACTTAATACAAATAGACTTTTGGTTGGATCATTTCGGGTGAATTATTTT
CCACCTTTCACGAACGTTTAATGCCTTTGTAG
Found at i:533108 original size:8 final size:8
Alignment explanation
Indices: 533095--533153 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
533085 ATAATAAATT
533095 ATACATGC
1 ATACATGC
*
533103 ATACATAC
1 ATACATGC
*
533111 ATACATAC
1 ATACATGC
*
533119 ATACATAC
1 ATACATGC
533127 ATACATGAAC
1 ATACATG--C
533137 ATACATG-
1 ATACATGC
*
533144 GTACATGC
1 ATACATGC
533152 AT
1 AT
533154 CAATAGATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
7 6 0.14
8 30 0.68
10 8 0.18
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.25
Consensus pattern (8 bp):
ATACATGC
Found at i:533111 original size:4 final size:4
Alignment explanation
Indices: 533095--533142 Score: 69
Period size: 4 Copynumber: 11.5 Consensus size: 4
533085 ATAATAAATT
*
533095 ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATGAAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT--AC ATAC AT
533143 GGTACATGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
4 36 0.90
6 4 0.10
ACGTcount: A:0.48, C:0.23, G:0.04, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:544269 original size:2 final size:2
Alignment explanation
Indices: 544262--544299 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
544252 GTAACATGTT
544262 TA TA TA TA TA TA TA TA TA TA -A 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
544300 TCGTACTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:544287 original size:17 final size:17
Alignment explanation
Indices: 544265--544298 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
544255 ACATGTTTAT
544265 ATATATATATATATATA
1 ATATATATATATATATA
544282 ATATATATATATATATA
1 ATATATATATATATATA
544299 TTCGTACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:545175 original size:131 final size:131
Alignment explanation
Indices: 544954--545440 Score: 657
Period size: 131 Copynumber: 3.7 Consensus size: 131
544944 TTAATATTGA
* * * * *
544954 AAATAGTAATATCTTTTCATTTCTG-TTGGAGTAATAAATGTA-TGCTTAAAGGCATAAAAGGTC
1 AAATAGTGATATCTCTTCATTTC-GATTGGAGTAATAAATG-ACTGCTTTAAGGCATGAGAGGTC
* *
545017 ATTTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAGTCAATATTGAATTTTAAG
64 ATGTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAG
545082 ACG
129 ACG
* *
545085 AAACAATGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
*
545150 GTATTCTTGATTGGAAATAATTAGATATTACT-GTTTTCTCTCGAATCAATATTGAATTTTAAGA
66 GTATTCTCGATTGGAAATAATTAGATATTA-TGGTTTTCTCTCGAATCAATATTGAATTTTAAGA
*
545214 TG
130 CG
* * * * *
545216 AAATAGTGATATCTCTTCATTTTGATTGGAGTAGTAAATGAATGTTTTAAGGCAT-A-A-G--AG
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
* * *
545276 GTATTCTCGATTGGAAATAATTAGATATTATCGTTTTTTTTTCTTGAATCAATATTGAATTTTAA
66 GTATTCTCGATTGGAAATAATTAGATATTAT-G--GTTTTCTCTCGAATCAATATTGAATTTTAA
545341 GACG
128 GACG
*
545345 AAATAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
1 AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
* * *
545410 TTATTCTCAATTGTAAATAATTAGATATTAT
66 GTATTCTCGATTGGAAATAATTAGATATTAT
545441 CATAAATAGC
Statistics
Matches: 312, Mismatches: 32, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
125 1 0.00
126 30 0.10
128 1 0.00
129 81 0.26
130 4 0.01
131 164 0.53
132 2 0.01
134 29 0.09
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (131 bp):
AAATAGTGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCAT
GTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGAC
G
Found at i:545430 original size:260 final size:258
Alignment explanation
Indices: 544954--545439 Score: 724
Period size: 260 Copynumber: 1.9 Consensus size: 258
544944 TTAATATTGA
* *
544954 AAATAGTAATATCTTTTCATTTCTGTTGGAGTAATAAATGTATGCTTAAAGGCATAAAAGGTCAT
1 AAATAGTAATATCTCTTCATTTCTGTTGGAGTAATAAATGAATGCTTAAAGGCATAAAAGG----
*
545019 TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAGTCAATATTGAATTTTAAGAC
62 TTATTCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGAC
*
545084 GAAACAATGATATCTCTTCATTTCGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
127 GAAACAATGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
**
545149 TGTATTCTTGATTGGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGA
192 TGTATTCTCAATTGGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGA
545214 TG
257 TG
* * * * *
545216 AAATAGTGATATCTCTTCATTT-TGATTGGAGTAGTAAATGAATGTTTTAAGGCATAAGAGG-TA
1 AAATAGTAATATCTCTTCATTTCTG-TTGGAGTAATAAATGAATGCTTAAAGGCATAAAAGGTTA
* * *
545279 TTCTCGATTGGAAATAATTAGATATTATCGTTTTTTTTTCTTGAATCAATATTGAATTTTAAGAC
65 TTCTCGATTGGAAATAATTAGATATTAT-G--GTTTTCTCTCGAATCAATATTGAATTTTAAGAC
* *
545344 GAAATAGTGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
127 GAAACAATGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCA
* *
545409 TTTATTCTCAATTGTAAATAATTAGATATTA
192 TGTATTCTCAATTGGAAATAATTAGATATTA
545440 TCATAAATAG
Statistics
Matches: 202, Mismatches: 18, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
257 30 0.15
258 1 0.00
260 118 0.58
261 2 0.01
262 51 0.25
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (258 bp):
AAATAGTAATATCTCTTCATTTCTGTTGGAGTAATAAATGAATGCTTAAAGGCATAAAAGGTTAT
TCTCGATTGGAAATAATTAGATATTATGGTTTTCTCTCGAATCAATATTGAATTTTAAGACGAAA
CAATGATATCTCTTCATTTCGATTGAAGTAATAAATGACTGCTTTAAGGCATGAGAGGTCATGTA
TTCTCAATTGGAAATAATTAGATATTACTGTTTTCTCTCGAATCAATATTGAATTTTAAGATG
Found at i:553121 original size:3 final size:3
Alignment explanation
Indices: 553113--553177 Score: 105
Period size: 3 Copynumber: 21.7 Consensus size: 3
553103 AAAAACCCAA
*
553113 AAT AAT AAT AAT AAT -AT AAT ATAT AAA AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
553158 AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AA
553178 GCTTAATATA
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 53 0.91
4 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:553246 original size:21 final size:21
Alignment explanation
Indices: 553216--553255 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
553206 AAACTATATA
*
553216 ATATATTATATTTTCAAAATC
1 ATATAATATATTTTCAAAATC
553237 ATATAATATATTTTCAAAA
1 ATATAATATATTTTCAAAA
553256 CATTATGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAATATATTTTCAAAATC
Found at i:553319 original size:14 final size:14
Alignment explanation
Indices: 553297--553326 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
553287 ATTACATATT
*
553297 ATACGTTTTCAAAA
1 ATACATTTTCAAAA
553311 ATACATTTTCAAAA
1 ATACATTTTCAAAA
553325 AT
1 AT
553327 TATATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (14 bp):
ATACATTTTCAAAA
Found at i:553369 original size:38 final size:38
Alignment explanation
Indices: 553262--553391 Score: 151
Period size: 38 Copynumber: 3.4 Consensus size: 38
553252 AAAACATTAT
*
553262 GTTTTCAAAAA-ATAAGTTTTTAAAAATTACATATTATAC
1 GTTTTCAAAAATAT-A-TTTTTAAAAATTATATATTATAC
* *
553301 GTTTTCAAAAATACATTTTCAAAAATTATATATTATAC
1 GTTTTCAAAAATATATTTTTAAAAATTATATATTATAC
**
553339 GTTTTCAAAAATATATTTTTAAAACCTATAT-TATATA-
1 GTTTTCAAAAATATATTTTTAAAAATTATATAT-TATAC
553376 -TTTTCAAAAACTATAT
1 GTTTTCAAAAA-TATAT
553392 GTTATATAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
36 10 0.12
37 6 0.07
38 52 0.64
39 12 0.15
40 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (38 bp):
GTTTTCAAAAATATATTTTTAAAAATTATATATTATAC
Found at i:553399 original size:24 final size:22
Alignment explanation
Indices: 553349--553391 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
553339 GTTTTCAAAA
* *
553349 ATATATTTTTAAAACCTATATT
1 ATATATTTTCAAAAACTATATT
553371 ATATATTTTCAAAAACTATAT
1 ATATATTTTCAAAAACTATAT
553392 GTTATATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATATTTTCAAAAACTATATT
Found at i:555111 original size:19 final size:19
Alignment explanation
Indices: 555060--555112 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
555050 TTCGAGAATG
* *
555060 AAAATCGCAACGCGAAATA
1 AAAATCGCAATGCGAAACA
*
555079 AAAATCGCAATGCGAAACC
1 AAAATCGCAATGCGAAACA
*
555098 AAAATCGCATTGCGA
1 AAAATCGCAATGCGA
555113 TTTTCATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.17, T:0.13
Consensus pattern (19 bp):
AAAATCGCAATGCGAAACA
Found at i:555124 original size:19 final size:19
Alignment explanation
Indices: 555102--555214 Score: 92
Period size: 20 Copynumber: 6.1 Consensus size: 19
555092 GAAACCAAAA
*
555102 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
555121 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
555140 TCGTGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
555154 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
555173 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
555193 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
555213 TC
1 TC
555215 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
14 9 0.12
16 2 0.03
17 2 0.03
19 29 0.39
20 31 0.42
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:555166 original size:33 final size:34
Alignment explanation
Indices: 555124--555189 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
555114 TTTCATTTCG
*
555124 CGTTGCGATAGTCATTT-CGTGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
555157 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
555190 ATTATCTCGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 17 0.55
34 14 0.45
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.39
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:555191 original size:20 final size:19
Alignment explanation
Indices: 555102--555214 Score: 92
Period size: 19 Copynumber: 6.1 Consensus size: 19
555092 GAAACCAAAA
* *
555102 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTCTCATT
**
555121 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
*
555140 TCGTGTTGCGATTCTC---
1 TCGCGTTGCGATTCTCATT
**
555156 T--CGTTGCGATAGTCATT
1 TCGCGTTGCGATTCTCATT
555173 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTCTCATT
* *
555193 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTCTCATT
555213 TC
1 TC
555215 AACCAAAAGA
Statistics
Matches: 74, Mismatches: 13, Indels: 14
0.73 0.13 0.14
Matches are distributed among these distances:
14 10 0.14
16 1 0.01
17 1 0.01
19 31 0.42
20 30 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTCTCATT
Found at i:558801 original size:14 final size:14
Alignment explanation
Indices: 558782--558817 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
558772 ATTGTTTAAT
*
558782 TGATTTGTAAAAGG
1 TGATTTGTAAAACG
*
558796 TGATTTGTAAAACT
1 TGATTTGTAAAACG
558810 TGATTTGT
1 TGATTTGT
558818 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.03, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAACG
Found at i:558961 original size:14 final size:14
Alignment explanation
Indices: 558942--558998 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
558932 GCGAAATGAA
558942 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
558956 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
558975 AATCGCAACGAGAG
1 AATCGCAACGAGAG
558989 AATCGCAACG
1 AATCGCAACG
558999 CGAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:558974 original size:33 final size:33
Alignment explanation
Indices: 558927--559013 Score: 147
Period size: 33 Copynumber: 2.6 Consensus size: 33
558917 AAGTACTATT
*
558927 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
558960 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAACGCGAAATGAAAATCGCAACGAGAGAATC
* *
558993 GCAACGCGAAATTAAATTCGC
1 GCAACGCGAAATGAAAATCGC
559014 GTTGCGATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (33 bp):
GCAACGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:558980 original size:19 final size:19
Alignment explanation
Indices: 558927--558984 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
558917 AAGTACTATT
*
558927 GCAATGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
558946 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
558960 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
558979 GCAACG
1 GCAACG
558985 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.50
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:559020 original size:19 final size:19
Alignment explanation
Indices: 558998--559058 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
558988 GAATCGCAAC
558998 GCGAAATTAAATTCGCGTT
1 GCGAAATTAAATTCGCGTT
** * * *
559017 GCGATTTTCATTTCGCATT
1 GCGAAATTAAATTCGCGTT
559036 GCGAAATTAAATTCGCGTT
1 GCGAAATTAAATTCGCGTT
559055 GCGA
1 GCGA
559059 TTTTCATTTC
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (19 bp):
GCGAAATTAAATTCGCGTT
Found at i:559042 original size:38 final size:38
Alignment explanation
Indices: 558998--559110 Score: 173
Period size: 38 Copynumber: 3.1 Consensus size: 38
558988 GAATCGCAAC
558998 GCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATT
1 GCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATT
559036 GCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATT
1 GCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATT
* *
559074 GCG--ATT---CTCTCGTTGCGATTTTCATTTCGCATT
1 GCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATT
559107 GCGA
1 GCGA
559111 TAGTAATTTC
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
33 28 0.39
36 3 0.04
38 41 0.57
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (38 bp):
GCGAAATTAAATTCGCGTTGCGATTTTCATTTCGCATT
Found at i:559069 original size:19 final size:19
Alignment explanation
Indices: 559009--559111 Score: 108
Period size: 19 Copynumber: 5.7 Consensus size: 19
558999 CGAAATTAAA
*
559009 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
** * *
559028 TTCGCATTGCGAAATTAAA
1 TTCGCATTGCGATTTTCAT
*
559047 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
559066 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
559082 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
559099 TTCGCATTGCGAT
1 TTCGCATTGCGAT
559112 AGTAATTTCC
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
14 6 0.09
16 7 0.11
17 7 0.11
19 46 0.70
ACGTcount: A:0.17, C:0.21, G:0.19, T:0.43
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:559093 original size:33 final size:34
Alignment explanation
Indices: 559010--559111 Score: 143
Period size: 33 Copynumber: 2.9 Consensus size: 34
559000 GAAATTAAAT
*
559010 TCGCGTTGCGATTTTCATTTCGCATTGCGAAATTAAAT
1 TCGCGTTGCGATTTTCATTTCGCATTGCG--ATT--AC
559048 TCGCGTTGCGATTTTCATTTCGCATTGCGATT-C
1 TCGCGTTGCGATTTTCATTTCGCATTGCGATTAC
*
559081 TCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCGTTGCGATTTTCATTTCGCATTGCGAT
559112 AGTAATTTCC
Statistics
Matches: 62, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
33 30 0.48
36 3 0.05
38 29 0.47
ACGTcount: A:0.17, C:0.22, G:0.20, T:0.42
Consensus pattern (34 bp):
TCGCGTTGCGATTTTCATTTCGCATTGCGATTAC
Found at i:561420 original size:12 final size:12
Alignment explanation
Indices: 561403--561427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
561393 TCTTCGGGGA
561403 CTTTTTCTTCTT
1 CTTTTTCTTCTT
561415 CTTTTTCTTCTT
1 CTTTTTCTTCTT
561427 C
1 C
561428 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:562465 original size:20 final size:21
Alignment explanation
Indices: 562440--562491 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
562430 TTTTCCTAAT
*
562440 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
562460 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
562481 TCGCAATGCGA
1 TCGCAATGCGA
562492 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:562513 original size:20 final size:20
Alignment explanation
Indices: 562480--562558 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
562470 AATTTGGAAA
* *
562480 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
562500 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
562521 ATCGCAACGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
* *
562541 TTCGCAACGAGATTCTGA
1 ATCGCAACGAGATACTGA
562559 AAAATCGCAA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
19 2 0.04
20 30 0.62
21 14 0.29
22 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:562568 original size:21 final size:21
Alignment explanation
Indices: 562500--562568 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
562490 GATACTGACT
**
562500 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATTCTGA-AAA
**
562521 ATCGCAACGAGATTCTG-ACT
1 ATCGCAACGAGATTCTGAAAA
*
562541 TTCGCAACGAGATTCTGAAAA
1 ATCGCAACGAGATTCTGAAAA
562562 ATCGCAA
1 ATCGCAA
562569 TCATATTCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 17 0.45
21 21 0.55
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAGATTCTGAAAA
Found at i:562814 original size:20 final size:20
Alignment explanation
Indices: 562791--562835 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
562781 AATCGCAACG
*
562791 CGAAAATGGCTATTGCAATT
1 CGAAAATGGCTATCGCAATT
562811 CGAAAATGGCTATCGCAATT
1 CGAAAATGGCTATCGCAATT
562831 CGAAA
1 CGAAA
562836 TGAAAAATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (20 bp):
CGAAAATGGCTATCGCAATT
Found at i:562869 original size:20 final size:20
Alignment explanation
Indices: 562782--562869 Score: 79
Period size: 20 Copynumber: 4.4 Consensus size: 20
562772 CAACGGGGAA
562782 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
* **
562802 ATTGCAATTCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
562822 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
562842 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
562862 ATCACAAC
1 ATCGCAAC
562870 TAGAAAATCG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
19 5 0.09
20 43 0.81
21 5 0.09
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:565040 original size:19 final size:18
Alignment explanation
Indices: 564976--565108 Score: 86
Period size: 20 Copynumber: 7.5 Consensus size: 18
564966 ACGAAACTTA
*
564976 AAATCGCAACGCGAAAATG
1 AAATCGCAATGCG-AAATG
* *
564995 ACTATCGCAACGCGGAAATGG
1 A-AATCGCAATGC-GAAAT-G
**
565016 CTATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
565034 CAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
565049 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
565067 AAAATCGCAA--CGACAA-G
1 -AAATCGCAATGCGA-AATG
565084 --ATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
565100 AAATCGCAA
1 AAATCGCAA
565109 CGACAAAATC
Statistics
Matches: 92, Mismatches: 7, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
14 16 0.17
15 2 0.02
16 8 0.09
17 8 0.09
18 10 0.11
19 22 0.24
20 24 0.26
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.21, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:565054 original size:14 final size:14
Alignment explanation
Indices: 565035--565124 Score: 72
Period size: 14 Copynumber: 5.8 Consensus size: 14
565025 TGCGAAATGC
565035 AAATCGCAACGACA
1 AAATCGCAACGACA
*
565049 AAATCGCAATGCGAAATGA
1 AAATCGCAA--CG--A-CA
565068 AAATCGCAACGACA
1 AAATCGCAACGACA
* *
565082 AGATCGCAATGCGAAA
1 AAATCGCAA--CGACA
565098 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
565114 AAATCGCAACG
1 AAATCGCAACG
565125 CGAAACACAA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 29 0.48
15 1 0.02
16 10 0.16
17 2 0.03
18 9 0.15
19 10 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:565060 original size:33 final size:33
Alignment explanation
Indices: 565018--565140 Score: 194
Period size: 33 Copynumber: 3.8 Consensus size: 33
565008 GGAAATGGCT
565018 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* *
565051 ATCGCAATGCGAAATGAAAATCGCAACGACAAG
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
565084 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAA
* **
565116 ATCGCAACGCGAAACACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCA
565141 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
32 28 0.34
33 55 0.66
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAA
Found at i:565137 original size:65 final size:66
Alignment explanation
Indices: 565018--565140 Score: 205
Period size: 65 Copynumber: 1.9 Consensus size: 66
565008 GGAAATGGCT
* *
565018 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
565083 G
66 G
565084 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATCGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCA-AAATCGCA
565141 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 1 0.02
65 37 0.69
66 16 0.30
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (66 bp):
ATCGCAATGCGAAATGCAAATCGCAACGACAAAATCGCAACGCGAAATCAAAATCGCAACGACAA
G
Found at i:565158 original size:19 final size:19
Alignment explanation
Indices: 565136--565265 Score: 121
Period size: 19 Copynumber: 7.6 Consensus size: 19
565126 GAAACACAAA
565136 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
565155 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
565171 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
565188 TCGCATTGCGA---TC-TT
1 TCGCATTGCGATTTTCATT
565203 GTCG--TTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
*
565221 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
565237 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
565254 TCGCATTGCGAT
1 TCGCATTGCGAT
565266 AGCCATTTCC
Statistics
Matches: 90, Mismatches: 4, Indels: 34
0.70 0.03 0.27
Matches are distributed among these distances:
14 18 0.20
15 8 0.09
16 13 0.14
17 13 0.14
18 8 0.09
19 30 0.33
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:565179 original size:14 final size:14
Alignment explanation
Indices: 565160--565249 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
565150 TCATTTCGCA
565160 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
565174 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
*
565191 CATTGCGATCTTGTCG
1 --TTGCGATTTTGTCG
*
565207 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
565224 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
565240 TTGCGATTTT
1 TTGCGATTTT
565250 CATTTCGCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 22 0.37
15 5 0.08
16 8 0.13
17 8 0.13
18 5 0.08
19 12 0.20
ACGTcount: A:0.11, C:0.18, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:565183 original size:33 final size:33
Alignment explanation
Indices: 565141--565265 Score: 241
Period size: 33 Copynumber: 3.8 Consensus size: 33
565131 ACAAATCGCA
565141 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
565174 TTGCGATTTTCATTTCGCATTGCGATCTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
565207 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
565240 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
565266 AGCCATTTCC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:565284 original size:20 final size:19
Alignment explanation
Indices: 565250--565304 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
565240 TTGCGATTTT
*
565250 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
565269 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
565289 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
565305 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:565816 original size:18 final size:18
Alignment explanation
Indices: 565793--565832 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
565783 TCAGATGTTG
565793 GCTCTGGGTGAGGTGATA
1 GCTCTGGGTGAGGTGATA
*
565811 GCTCTGGGTGAGGTGATG
1 GCTCTGGGTGAGGTGATA
565829 GCTC
1 GCTC
565833 CCGAAGTGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.15, G:0.45, T:0.28
Consensus pattern (18 bp):
GCTCTGGGTGAGGTGATA
Found at i:567176 original size:20 final size:20
Alignment explanation
Indices: 567151--567224 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
567141 AATAGTTTCT
*
567151 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
567171 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** **
567191 GAATTTGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
567211 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
567225 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 6 0.13
20 39 0.87
ACGTcount: A:0.43, C:0.23, G:0.18, T:0.16
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:567485 original size:22 final size:22
Alignment explanation
Indices: 567458--567501 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
567448 GATGGAGATA
567458 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
567480 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
567502 TGAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.45, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:567775 original size:20 final size:20
Alignment explanation
Indices: 567669--567803 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
567659 CGCTTTGAAA
*
567669 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
567690 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
567710 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
567730 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
567751 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
567771 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
567791 ATCGCATTGCGAT
1 ATCGCATTGCGAT
567804 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:567775 original size:61 final size:61
Alignment explanation
Indices: 567669--567806 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
567659 CGCTTTGAAA
* * * *
567669 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
567730 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
567791 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
567807 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:567822 original size:61 final size:61
Alignment explanation
Indices: 567669--567824 Score: 161
Period size: 61 Copynumber: 2.6 Consensus size: 61
567659 CGCTTTGAAA
* ** * * * *
567669 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
* * ** * * * *
567730 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
567791 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
567825 TTACTTATTC
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
61 77 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:570452 original size:12 final size:12
Alignment explanation
Indices: 570421--570459 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
570411 ACCCACTATA
*
570421 CCCGCAATAGAG
1 CCCGCAATAGCG
570433 -CC-CAATAGCG
1 CCCGCAATAGCG
570443 CCCGCAATAGCG
1 CCCGCAATAGCG
570455 CCCGC
1 CCCGC
570460 GATGACCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 7 0.29
11 4 0.17
12 13 0.54
ACGTcount: A:0.26, C:0.44, G:0.23, T:0.08
Consensus pattern (12 bp):
CCCGCAATAGCG
Found at i:578403 original size:16 final size:16
Alignment explanation
Indices: 578378--578408 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
578368 TATTGTTTCC
578378 CCCCTCTTTCTCTTTT
1 CCCCTCTTTCTCTTTT
*
578394 CCCCTTTTTCTCTTT
1 CCCCTCTTTCTCTTT
578409 GCATCTGTCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (16 bp):
CCCCTCTTTCTCTTTT
Found at i:582922 original size:12 final size:12
Alignment explanation
Indices: 582905--582929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
582895 GTCAATCTAC
582905 AATATATATATA
1 AATATATATATA
582917 AATATATATATA
1 AATATATATATA
582929 A
1 A
582930 TTTACGACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATATATATATA
Found at i:583120 original size:13 final size:13
Alignment explanation
Indices: 583098--583140 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
583088 AATGACGCAC
*
583098 AATGCGCGTCATA
1 AATGCACGTCATA
583111 AATGCACGTCATA
1 AATGCACGTCATA
*
583124 AATGCATGTCATA
1 AATGCACGTCATA
583137 AATG
1 AATG
583141 TGCATCATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (13 bp):
AATGCACGTCATA
Found at i:585013 original size:21 final size:21
Alignment explanation
Indices: 584987--585068 Score: 119
Period size: 21 Copynumber: 3.9 Consensus size: 21
584977 CGAGGGTTTC
584987 ATAGGTCCTTCGGGACAACTT
1 ATAGGTCCTTCGGGACAACTT
*
585008 ATAGGTCCTTCAGGACAACTT
1 ATAGGTCCTTCGGGACAACTT
* *
585029 ATAGGTCATTCGGGACATACTC
1 ATAGGTCCTTCGGGACA-ACTT
*
585051 ACAGGTCCTTCGGGACAA
1 ATAGGTCCTTCGGGACAA
585069 ATTTCATATG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
21 36 0.67
22 18 0.33
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (21 bp):
ATAGGTCCTTCGGGACAACTT
Found at i:586316 original size:17 final size:17
Alignment explanation
Indices: 586274--586328 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
586264 TAAGCTTAAT
586274 TAAAATAAAAAAATAA-A
1 TAAAAT-AAAAAATAACA
*
586291 -AAGAGTAAAAAATAACA
1 TAA-AATAAAAAATAACA
586308 TAAAAT-AAAAATAAACA
1 TAAAATAAAAAAT-AACA
586325 TAAA
1 TAAA
586329 TACAAGGAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 17 0.53
17 13 0.41
18 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (17 bp):
TAAAATAAAAAATAACA
Found at i:588551 original size:206 final size:206
Alignment explanation
Indices: 588185--588591 Score: 627
Period size: 206 Copynumber: 2.0 Consensus size: 206
588175 CTTATGGATG
*
588185 GCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATGGATGACCCGAAGGATTTAAGCATCATAC
1 GCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATAC
* * * * *
588250 TCAAAAGGTTACTAATGGCCTGAAGGACTTAAGTTGATTCGAAGTATTGTGAATCGAGAAATAGG
66 TCAAAAGCTTACTAATGGCCCGAAGGACTTAAGCTGATTCGAACTATTGTGAATCAAGAAATAGG
* * *
588315 AAATGTTAACCCCTCTTGTGGGGTGTTGCTGATTCGAAGTGTTGTGAATAGAGAAAAGGAAATGT
131 AAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCAAAGTGTTGTGAATAGAGAAAAGGAAATGT
588380 TGAAAAATATT
196 TGAAAAATATT
* * *
588391 GCCCGAAGGACTTATCATCTTTCTCGAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATGC
1 GCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATAC
* * * * *
588456 TCGAAAGACTTACTGATGGCCCGAAGGACTTAAGCTGATTTGAACTGTTGTGAATCAAGCAA-AG
66 TCAAAAG-CTTACTAATGGCCCGAAGGACTTAAGCTGATTCGAACTATTGTGAATCAAGAAATAG
* *
588520 GAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCAAAGTGTTGTGAATCGAGCAAAGGAAATG
130 GAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCAAAGTGTTGTGAATAGAGAAAAGGAAATG
588585 TTGAAAA
195 TTGAAAA
588592 TATCCTACCT
Statistics
Matches: 181, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
206 136 0.75
207 45 0.25
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (206 bp):
GCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCGAAGGATTTAAGCATCATAC
TCAAAAGCTTACTAATGGCCCGAAGGACTTAAGCTGATTCGAACTATTGTGAATCAAGAAATAGG
AAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCAAAGTGTTGTGAATAGAGAAAAGGAAATGT
TGAAAAATATT
Found at i:590820 original size:7 final size:7
Alignment explanation
Indices: 590810--590924 Score: 79
Period size: 7 Copynumber: 15.1 Consensus size: 7
590800 TCTTTTCCAT
590810 TTTTTTC
1 TTTTTTC
590817 TTTTTTC
1 TTTTTTC
*
590824 TTTTCTC
1 TTTTTTC
590831 TCTTTTTC
1 T-TTTTTC
590839 TTTTTTC
1 TTTTTTC
*
590846 TTTTTCTT
1 TTTTT-TC
590854 TTTGCTTTC
1 TTT--TTTC
*
590863 TTTTATC
1 TTTTTTC
*
590870 TATTTTC
1 TTTTTTC
**
590877 TTTTCCC
1 TTTTTTC
590884 TTTTTTC
1 TTTTTTC
590891 TCCCTTTTT-
1 T---TTTTTC
590900 TGTTTTTC
1 T-TTTTTC
590908 TTTTTGTTC
1 -TTTT-TTC
590917 TTTTTTC
1 TTTTTTC
590924 T
1 T
590925 CTTTGTGTTA
Statistics
Matches: 85, Mismatches: 13, Indels: 20
0.72 0.11 0.17
Matches are distributed among these distances:
7 52 0.61
8 17 0.20
9 9 0.11
10 7 0.08
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:590826 original size:22 final size:22
Alignment explanation
Indices: 590798--590861 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
590788 ATCGGTTTTC
*
590798 TTTCTTTTC-CATTTTTTTCTTT
1 TTTCTTTTCTC-TCTTTTTCTTT
590820 TTTCTTTTCTCTCTTTTTCTTT
1 TTTCTTTTCTCTCTTTTTCTTT
*
590842 TTTCTTTT-TCT-TTTTGCTTT
1 TTTCTTTTCTCTCTTTTTCTTT
590862 CTTTTATCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.21
21 3 0.08
22 27 0.69
23 1 0.03
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (22 bp):
TTTCTTTTCTCTCTTTTTCTTT
Found at i:593253 original size:87 final size:87
Alignment explanation
Indices: 593107--593278 Score: 290
Period size: 87 Copynumber: 2.0 Consensus size: 87
593097 TCTTGATAGA
* * * * *
593107 CAACTTAGGATGTTTTCCATAGATACTTTATCATACCCATATAAGGAAACTCAATGCTCCTCGTG
1 CAACTTAGGATATTTTCCAGAGATACTTTATCATACCCACACAAGGAAACTCAATGCTCCTCATG
593172 AGGTATGACGTTTCTCCCTAGG
66 AGGTATGACGTTTCTCCCTAGG
593194 CAACTTAGGATATTTTCCAGAGATACTTTATCATACCCACACAAGGAAACTCAATGCTCCTCATG
1 CAACTTAGGATATTTTCCAGAGATACTTTATCATACCCACACAAGGAAACTCAATGCTCCTCATG
*
593259 AGGTGTGACGTTTCTCCCTA
66 AGGTATGACGTTTCTCCCTA
593279 CTTAGGTAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.31
Consensus pattern (87 bp):
CAACTTAGGATATTTTCCAGAGATACTTTATCATACCCACACAAGGAAACTCAATGCTCCTCATG
AGGTATGACGTTTCTCCCTAGG
Found at i:594763 original size:26 final size:27
Alignment explanation
Indices: 594734--594793 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
594724 AAGCTTAATT
* *
594734 AAAATAATAAAATAGCAA-ATAATAA-A
1 AAAATAATAAAAAAACAACATAA-AATA
*
594760 AAAATAGTAAAAAAACAACATAAAATA
1 AAAATAATAAAAAAACAACATAAAATA
594787 AAAATAA
1 AAAATAA
594794 AATAAACATA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.75, C:0.05, G:0.03, T:0.17
Consensus pattern (27 bp):
AAAATAATAAAAAAACAACATAAAATA
Found at i:594784 original size:11 final size:11
Alignment explanation
Indices: 594776--594805 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
594766 GTAAAAAAAC
594776 AACATAAAATA
1 AACATAAAATA
*
594787 AAAATAAAATA
1 AACATAAAATA
594798 AACATAAA
1 AACATAAA
594806 TTCAAGGACC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (11 bp):
AACATAAAATA
Found at i:598942 original size:16 final size:16
Alignment explanation
Indices: 598923--599016 Score: 55
Period size: 16 Copynumber: 5.5 Consensus size: 16
598913 AATTTAGCGA
598923 AACCAAAATTAACCAG
1 AACCAAAATTAACCAG
*
598939 AACCGAAATTAACCTGAATCG
1 AACCAAAATTAACC---A--G
* *
598960 AAACCGAAATTAACCTG
1 -AACCAAAATTAACCAG
598977 AACCAAAATTAACTC-G
1 AACCAAAATTAAC-CAG
* * *
598993 AACCGAATTTAACCCG
1 AACCAAAATTAACCAG
*
599009 ACCCAAAA
1 AACCAAAA
599017 GCAACCCGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
15 1 0.02
16 43 0.69
17 2 0.03
19 1 0.02
21 1 0.02
22 14 0.23
ACGTcount: A:0.48, C:0.27, G:0.10, T:0.16
Consensus pattern (16 bp):
AACCAAAATTAACCAG
Found at i:599772 original size:32 final size:32
Alignment explanation
Indices: 599730--599828 Score: 114
Period size: 32 Copynumber: 3.1 Consensus size: 32
599720 ACCTAAATTG
*
599730 AAAATC-AACTGATTCGATATTGACCCGACCC
1 AAAATCTAACTGATTCGGTATTGACCCGACCC
* *
599761 GAAATCTAACTGA-TCTGGTATTAACCCGACCC
1 AAAATCTAACTGATTC-GGTATTGACCCGACCC
* *
599793 AAAAT-TCAACTGATCCGGTATTGACCCGATCC
1 AAAATCT-AACTGATTCGGTATTGACCCGACCC
599825 AAAA
1 AAAA
599829 ATAACCGATC
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
31 8 0.14
32 48 0.84
33 1 0.02
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.23
Consensus pattern (32 bp):
AAAATCTAACTGATTCGGTATTGACCCGACCC
Found at i:601146 original size:16 final size:16
Alignment explanation
Indices: 601116--601161 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
601106 GATATCAATA
601116 ATAATAATATATTATC
1 ATAATAATATATTATC
601132 ATAA-AATATATTTAT-
1 ATAATAATATA-TTATC
*
601147 ATACATATTATATTA
1 ATA-ATAATATATTA
601162 ATTAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
15 9 0.35
16 12 0.46
17 5 0.19
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
ATAATAATATATTATC
Found at i:601177 original size:14 final size:15
Alignment explanation
Indices: 601158--601200 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
601148 TACATATTAT
601158 ATTAAT-TAATTTAA
1 ATTAATATAATTTAA
*
601172 ATTAATATATTTTAA
1 ATTAATATAATTTAA
*
601187 ATT-TTATAATTTAA
1 ATTAATATAATTTAA
601201 TGTCTAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTAATATAATTTAA
Found at i:602534 original size:19 final size:19
Alignment explanation
Indices: 602484--602538 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
602474 TTATCATTAT
*
602484 TTTATTTAT-ATTAACTTTA
1 TTTATTTATCATTTA-TTTA
*
602503 TTT-TTTCATCATTTATTTG
1 TTTATTT-ATCATTTATTTA
602522 TTTATTTATCATTTATT
1 TTTATTTATCATTTATT
602539 ATTATTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 3 0.10
19 21 0.68
20 7 0.23
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTATTTATCATTTATTTA
Found at i:604397 original size:103 final size:103
Alignment explanation
Indices: 604146--604407 Score: 332
Period size: 103 Copynumber: 2.5 Consensus size: 103
604136 AGCAATGATT
* * * * *
604146 AATTTTAGTTTAAATAAGTCTTTTAGGGATCGAATCTAAATTAAATATTATAATATTAAAATTAT
1 AATTTTAGTTTAAATAATTCTTTTAGAGATCGAATCCAACTCAAATATTATAATATTAAAATTAT
* *
604211 TAGATTAAATTATGAGATATTGAACAAAAATAAGGGTC
66 TAGACTAAATAATGAGATATTGAACAAAAATAAGGGTC
* * *
604249 AATTTTAGTTTAAATAATTCTTTTA-AGGATCCAATACAACCCAAATATTATAATATTAATAA-T
1 AATTTTAGTTTAAATAATTCTTTTAGA-GATCGAATCCAACTCAAATATTATAATATTAA-AATT
*
604312 ATTAGACTAAATAATGAGATATTTAACAAAAAT-AGGGATC
64 ATTAGACTAAATAATGAGATATTGAACAAAAATAAGGG-TC
* * * * *
604352 AATTTTAATTTGAATAATTCTTTCAGAAATCGAATCCAACTCAAATATTATTATAT
1 AATTTTAGTTTAAATAATTCTTTTAGAGATCGAATCCAACTCAAATATTATAATAT
604408 ATTGTAATAA
Statistics
Matches: 136, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
102 4 0.03
103 129 0.95
104 3 0.02
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (103 bp):
AATTTTAGTTTAAATAATTCTTTTAGAGATCGAATCCAACTCAAATATTATAATATTAAAATTAT
TAGACTAAATAATGAGATATTGAACAAAAATAAGGGTC
Found at i:606254 original size:18 final size:17
Alignment explanation
Indices: 606224--606257 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
606214 TTATTTATTT
*
606224 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
606241 ATATGAAAAAATAATAT
1 ATAT-AAAAAATAATAT
606258 TGTAGTCTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:607276 original size:65 final size:64
Alignment explanation
Indices: 607151--607351 Score: 221
Period size: 65 Copynumber: 3.1 Consensus size: 64
607141 TTTTTCAAAG
* * * **
607151 TGATGCACCGATTCACCAATCCATGCATCGATGCAC-CATGAATCAAATTG-AACATCGAATGCA
1 TGATGCATCGATGCACC-ATCCATGCATCGATGCACTCA-GGAT-ATTTTGAAACATCGAATGCA
607214 TT
63 TT
* *
607216 TCATGCATCGATGCA-CATACCATGCATCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCA
1 TGATGCATCGATGCACCAT-CCATGCATCGATGCACTCAGGATATTT-TG-AAACATCGAATGCA
607279 TT
63 TT
* * * *
607281 TGATGCATCGATGCACCATCCATGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCATCCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
607345 TGATGCA
1 TGATGCA
607352 CTTTTAGTGC
Statistics
Matches: 116, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 42 0.36
65 63 0.54
66 6 0.05
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (64 bp):
TGATGCATCGATGCACCATCCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:613170 original size:21 final size:22
Alignment explanation
Indices: 613141--613198 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
613131 TTGTGCTTAA
613141 TGCATCGAT-ACACCATGAAGG
1 TGCATCGATCACACCATGAAGG
* * *
613162 TGCACCGATGCACACCTTGAATG
1 TGCATCGAT-CACACCATGAAGG
613185 TGCATCGATGCACA
1 TGCATCGAT-CACA
613199 AGGCCATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 8 0.26
23 23 0.74
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.21
Consensus pattern (22 bp):
TGCATCGATCACACCATGAAGG
Found at i:613182 original size:23 final size:23
Alignment explanation
Indices: 613150--613198 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
613140 ATGCATCGAT
613150 ACACCATGAAGGTGCACCGATGC
1 ACACCATGAAGGTGCACCGATGC
* * *
613173 ACACCTTGAATGTGCATCGATGC
1 ACACCATGAAGGTGCACCGATGC
613196 ACA
1 ACA
613199 AGGCCATGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.18
Consensus pattern (23 bp):
ACACCATGAAGGTGCACCGATGC
Found at i:615924 original size:64 final size:62
Alignment explanation
Indices: 615843--616043 Score: 201
Period size: 65 Copynumber: 3.1 Consensus size: 62
615833 TTTTCAAAGT
* *
615843 GATGCACCAATCCATGCATCGATGCACCATGAATCAAATTG-AACATCGAATGCATTTCATGCAT
1 GATGCA-CAA-CCATGCATCGATGCACC-TGAAT-ATATTGAAACATCGAATGCATTTGATGCAT
615907 C
62 C
* *
615908 GATGCACATACCATGCATCAATGCA-CTGAGGAT-TTTATGAAAACATCGAATGCATTTGATGCA
1 GATGCACA-ACCATGCATCGATGCACCTGA--ATATAT-TG-AAACATCGAATGCATTTGATGCA
615971 TC
61 TC
* ** * *
615973 GATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTGATGCATC
1 GATGCA-CAACCATGCATCGATGCAC-CTGAATATATTGAAACATCGAATGCATTTGATGCATC
616037 GATGCAC
1 GATGCAC
616044 TCTTAGTGCA
Statistics
Matches: 117, Mismatches: 9, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
62 4 0.03
63 4 0.03
64 48 0.41
65 53 0.45
66 5 0.04
67 3 0.03
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (62 bp):
GATGCACAACCATGCATCGATGCACCTGAATATATTGAAACATCGAATGCATTTGATGCATC
Found at i:615956 original size:65 final size:63
Alignment explanation
Indices: 615884--616043 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
615874 AATCAAATTG
* *
615884 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCAATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCAATGCACTCAGGATATTT-TG-
615948 A
63 A
* * * *
615949 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCAATGCACTCAGGATATTTTGA
*
616013 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
616044 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 50 0.58
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCAATGCACTCAGGATATTTTGA
Found at i:616043 original size:17 final size:19
Alignment explanation
Indices: 616015--616063 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
616005 TATTTTGAAA
616015 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
616033 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
616052 CACCGATGCACT
1 CATCGATGCACT
616064 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:617161 original size:2 final size:2
Alignment explanation
Indices: 617154--617190 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
617144 AAAATATTAA
617154 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
617191 ATAATTTTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:624295 original size:27 final size:27
Alignment explanation
Indices: 624257--624319 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
624247 ATGGAGTTAC
624257 AGAGAGTCCAAAATCTCCATTTTGAAA
1 AGAGAGTCCAAAATCTCCATTTTGAAA
624284 AGAGAGTCCAAAATCTCCATTTTGAAA
1 AGAGAGTCCAAAATCTCCATTTTGAAA
624311 AGAGAGTCC
1 AGAGAGTCC
624320 TTACTCTGCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (27 bp):
AGAGAGTCCAAAATCTCCATTTTGAAA
Found at i:628031 original size:8 final size:8
Alignment explanation
Indices: 628023--628116 Score: 152
Period size: 8 Copynumber: 11.5 Consensus size: 8
628013 GTATGAATGT
*
628023 ATGTGTGT
1 ATGTGTGC
628031 ATGTGTGC
1 ATGTGTGC
628039 ATGTGTGC
1 ATGTGTGC
628047 ATGTGTGTGC
1 A--TGTGTGC
628057 ATGTGTGC
1 ATGTGTGC
628065 ATGTGTGC
1 ATGTGTGC
628073 ATGTGTGC
1 ATGTGTGC
628081 ATGTGTGC
1 ATGTGTGC
628089 ATGTGTGC
1 ATGTGTGC
628097 ATGTGTGC
1 ATGTGTGC
*
628105 ATGTGTGT
1 ATGTGTGC
628113 ATGT
1 ATGT
628117 ATGTATGTAT
Statistics
Matches: 82, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
8 74 0.90
10 8 0.10
ACGTcount: A:0.13, C:0.10, G:0.37, T:0.40
Consensus pattern (8 bp):
ATGTGTGC
Found at i:629764 original size:16 final size:16
Alignment explanation
Indices: 629743--629780 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
629733 CGAATAAAAG
629743 CATGCGAACTAGATAC
1 CATGCGAACTAGATAC
629759 CATGCGAACTAGATAC
1 CATGCGAACTAGATAC
629775 CATGCG
1 CATGCG
629781 GTTAAGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.18
Consensus pattern (16 bp):
CATGCGAACTAGATAC
Found at i:629825 original size:16 final size:17
Alignment explanation
Indices: 629804--629836 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
629794 TCTTGAAAAT
*
629804 AAATCAT-TTTGGGTAG
1 AAATCATGTTCGGGTAG
629820 AAATCATGTTCGGGTAG
1 AAATCATGTTCGGGTAG
629837 GATTACTATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.09, G:0.27, T:0.33
Consensus pattern (17 bp):
AAATCATGTTCGGGTAG
Found at i:635894 original size:16 final size:17
Alignment explanation
Indices: 635861--635894 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
635851 CCATCCATTT
*
635861 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
635878 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
635894 T
1 T
635895 AATAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:637086 original size:27 final size:27
Alignment explanation
Indices: 637053--637140 Score: 176
Period size: 27 Copynumber: 3.3 Consensus size: 27
637043 TTCTTTTAAG
637053 GATGAAATTAGATAAGATTAGGTTTAT
1 GATGAAATTAGATAAGATTAGGTTTAT
637080 GATGAAATTAGATAAGATTAGGTTTAT
1 GATGAAATTAGATAAGATTAGGTTTAT
637107 GATGAAATTAGATAAGATTAGGTTTAT
1 GATGAAATTAGATAAGATTAGGTTTAT
637134 GATGAAA
1 GATGAAA
637141 AAAACTTAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (27 bp):
GATGAAATTAGATAAGATTAGGTTTAT
Found at i:639760 original size:59 final size:61
Alignment explanation
Indices: 639697--639822 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 61
639687 TTAATAGAAT
* *
639697 AATAATTAAATTA-TATTTTTTTATTAAAAATCCTAATTCT-AAAAAAATAAATTACTTAA
1 AATAATTAAATTATTATTATTTAATTAAAAATCCTAATTCTAAAAAAAATAAATTACTTAA
*
639756 AATAA-T-AATTATTATTATTTAATTAAAAATCCTAATTCTAAAAAAAATTAATTACTTAA
1 AATAATTAAATTATTATTATTTAATTAAAAATCCTAATTCTAAAAAAAATAAATTACTTAA
639815 AATAATTA
1 AATAATTA
639823 TTATTTTTAA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
57 5 0.08
58 26 0.43
59 28 0.47
60 1 0.02
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.41
Consensus pattern (61 bp):
AATAATTAAATTATTATTATTTAATTAAAAATCCTAATTCTAAAAAAAATAAATTACTTAA
Found at i:639816 original size:17 final size:17
Alignment explanation
Indices: 639736--639822 Score: 50
Period size: 17 Copynumber: 4.6 Consensus size: 17
639726 ATCCTAATTC
*
639736 TAAAAAAATAAATTACT
1 TAAAAAAATTAATTACT
*
639753 TAAAATAATAATTATTATTATT
1 T-AAA-AA-AATTA--ATTACT
639775 TAATTAAAAATCCTAATT-CT
1 TAA--AAAAAT--TAATTACT
*
639795 AAAAAAAATTAATTACT
1 TAAAAAAATTAATTACT
*
639812 TAAAATAATTA
1 TAAAAAAATTA
639823 TTATTTTTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 20
0.68 0.08 0.25
Matches are distributed among these distances:
16 5 0.09
17 12 0.22
18 9 0.17
19 2 0.04
20 7 0.13
21 8 0.15
22 8 0.15
23 3 0.06
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAAAAAATTAATTACT
Found at i:640736 original size:18 final size:17
Alignment explanation
Indices: 640699--640742 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
640689 ATAAATTAAT
* *
640699 TAATATTTAATATCAAA
1 TAATATTTAAAATAAAA
640716 TAATATTTAAAATAAAAA
1 TAATATTTAAAAT-AAAA
*
640734 TAAAATTTA
1 TAATATTTA
640743 TAATTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
TAATATTTAAAATAAAA
Found at i:641872 original size:31 final size:31
Alignment explanation
Indices: 641833--641899 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
641823 ATGAAAGTTG
** *
641833 AGGTACTAAATCGGAACAAAAGTGATAGTTT
1 AGGTACTAAATCAAAACAAAAGTGATAATTT
*
641864 GGGTACTAAATCAAAACAAAAGTGATAATTT
1 AGGTACTAAATCAAAACAAAAGTGATAATTT
641895 AGGTA
1 AGGTA
641900 TTGAACATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (31 bp):
AGGTACTAAATCAAAACAAAAGTGATAATTT
Found at i:642767 original size:15 final size:17
Alignment explanation
Indices: 642736--642767 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
642726 ATGTATTTTT
642736 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
642753 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
642768 TTATATTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Done.