Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005819.1 Hibiscus syriacus cultivar Beakdansim tig00013636_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: 637054
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 3
Found at i:535427 original size:10 final size:10
Alignment explanation
Indices: 535412--535518 Score: 85
Period size: 10 Copynumber: 10.6 Consensus size: 10
535402 ACTTGATCGA
535412 TTTTCTTTCT
1 TTTTCTTTCT
535422 TTTTCTTT-T
1 TTTTCTTTCT
535431 TCTTTCTTTC-
1 T-TTTCTTTCT
535441 TTTTCTTT-T
1 TTTTCTTTCT
*
535450 TTATCTTTCT
1 TTTTCTTTCT
*
535460 TTTGCTTTCT
1 TTTTCTTTCT
*
535470 TTTCCTTTCT
1 TTTTCTTTCT
* *
535480 TATTTTTTATGT
1 T-TTTCTT-TCT
*
535492 TTTTTTTTCT
1 TTTTCTTTCT
* *
535502 ATATCTTTTCT
1 TTTTC-TTTCT
535513 TTTTCT
1 TTTTCT
535519 CTGTGTCGTC
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
9 16 0.21
10 40 0.52
11 18 0.23
12 3 0.04
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.77
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:535462 original size:32 final size:30
Alignment explanation
Indices: 535437--535516 Score: 61
Period size: 33 Copynumber: 2.5 Consensus size: 30
535427 TTTTTCTTTC
*
535437 TTTCTTTTCTTTTTTATCTTTCTTTTGCTTTC
1 TTTCTTTTCTTTTTT-T-TTTCTTTTTCTTTC
* * * *
535469 TTTTCCTTTCTTATTTTTTATGTTTTTTTTTC
1 -TTTCTTTTCTT-TTTTTTTTCTTTTTCTTTC
535501 TATATCTTTTCTTTTT
1 T-T-TCTTTTCTTTTT
535517 CTCTGTGTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
31 1 0.03
32 14 0.37
33 19 0.50
34 4 0.11
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (30 bp):
TTTCTTTTCTTTTTTTTTTCTTTTTCTTTC
Found at i:543481 original size:23 final size:24
Alignment explanation
Indices: 543450--543495 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
543440 TGACTGGACT
*
543450 GGACTAGGCGGGTCGGGTCAGGTC
1 GGACTAGGCGGATCGGGTCAGGTC
*
543474 GGAC-AGGCTGATCGGGTCAGGT
1 GGACTAGGCGGATCGGGTCAGGT
543496 TGACCGGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.15, C:0.20, G:0.48, T:0.17
Consensus pattern (24 bp):
GGACTAGGCGGATCGGGTCAGGTC
Found at i:551381 original size:18 final size:18
Alignment explanation
Indices: 551358--551428 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
551348 GTTCTTAAGG
* *
551358 AGTGGTACTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
*
551376 AGTGGTCCATCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
551394 AGTAGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
551412 AGTAGTCATTCGGGACA
1 AGTGGTCCTTCGGGACA
551429 AATTCATATG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:556585 original size:3 final size:3
Alignment explanation
Indices: 556567--556661 Score: 77
Period size: 3 Copynumber: 31.3 Consensus size: 3
556557 TTCTTTTAAA
* * * * *
556567 ATT ATT TTT AATT ATT ATT ATT ATC AAT ATT AAT A-T AGT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
556612 ATT ATT ATT ATT ATT ATT AAT ATT A-T ATAC ATT ATAT CTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT
556658 ATT A
1 ATT A
556662 AATAATTACA
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
2 4 0.05
3 63 0.86
4 6 0.08
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:558099 original size:20 final size:18
Alignment explanation
Indices: 558074--558110 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
558064 TTTTATTATT
558074 TATATA-AATAAATATATA
1 TATATATAATAAATA-ATA
558092 TATATATAATAAATAATA
1 TATATATAATAAATAATA
558110 T
1 T
558111 TTGTTTATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TATATATAATAAATAATA
Found at i:558284 original size:22 final size:23
Alignment explanation
Indices: 558259--558308 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
558249 ATAAATATTC
558259 TATTTTATAAATTATATA-TTAT
1 TATTTTATAAATTATATATTTAT
* *
558281 TATTTT-TTAATTATTTATTTAT
1 TATTTTATAAATTATATATTTAT
558303 T-TTTTA
1 TATTTTA
558309 ATATCAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TATTTTATAAATTATATATTTAT
Found at i:558306 original size:120 final size:121
Alignment explanation
Indices: 558172--558397 Score: 296
Period size: 121 Copynumber: 1.9 Consensus size: 121
558162 TTTTAATATA
* * * * *
558172 TATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAATAACTGGATGTCCATTTTATG
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCC-TTTTATG
*
558235 ATATTTTTAAATAAATAAATATTCTATTTTATAAAT-TATATATTATTATTTTTTAAT
65 ATATTTCTAAATAAATAAATATTCTA-TTTATAAATATATATATTATTATTTTTTAAT
* * ** * *
558292 TATTTATTTATTTTTTAATATCAAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCTTTTCTGA
1 TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTATGA
*
558357 TATTTCTAAATAAATAAATATTTTATTTATAAATATATATA
66 TATTTCTAAATAAATAAATATTCTATTTATAAATATATATA
558398 AATTAATATA
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
120 29 0.32
121 39 0.43
122 22 0.24
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (121 bp):
TATTTATTTATTTTTCAATATCAAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCCTTTTATGA
TATTTCTAAATAAATAAATATTCTATTTATAAATATATATATTATTATTTTTTAAT
Found at i:560527 original size:9 final size:9
Alignment explanation
Indices: 560515--560546 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
560505 TTTACATTCC
560515 CATTTTTTA
1 CATTTTTTA
560524 CATTTTTTA
1 CATTTTTTA
*
560533 CATTTTTCA
1 CATTTTTTA
560542 CATTT
1 CATTT
560547 ACATTTCAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (9 bp):
CATTTTTTA
Found at i:564963 original size:114 final size:114
Alignment explanation
Indices: 564763--564980 Score: 364
Period size: 114 Copynumber: 1.9 Consensus size: 114
564753 TGTTCTCGTA
* *
564763 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTCGG
* * *
564828 TATGAACCCCAAAACCAATCATTAGATTTGAAAGATGAATTTGCTCATC
66 TAGGAACCCCAAAACCAATCATTAGAATAGAAAGATGAATTTGCTCATC
564877 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTCGG
1 GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTCGG
* * *
564942 TAGGAACCCCAGAACTAATCATTGGAATAGAAAGATGAA
66 TAGGAACCCCAAAACCAATCATTAGAATAGAAAGATGAA
564981 CTGCATGATC
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (114 bp):
GTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTCGG
TAGGAACCCCAAAACCAATCATTAGAATAGAAAGATGAATTTGCTCATC
Found at i:565197 original size:31 final size:31
Alignment explanation
Indices: 565159--565221 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
565149 GCACATATAA
* *
565159 AATCTGTCAACTCTGCAATTGATGAATTCAG
1 AATCTGTCAACTCTGAAATTAATGAATTCAG
565190 AATCTGTCAACTCTGAAATTAATGAATTCAG
1 AATCTGTCAACTCTGAAATTAATGAATTCAG
565221 A
1 A
565222 CCACATCTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (31 bp):
AATCTGTCAACTCTGAAATTAATGAATTCAG
Found at i:568506 original size:37 final size:36
Alignment explanation
Indices: 568419--568765 Score: 241
Period size: 37 Copynumber: 9.6 Consensus size: 36
568409 CAAATAGCAA
** ** * *
568419 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAT
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACAAAC
* * *
568455 TTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAC
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACA-AAC
** ** *
568492 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACAAAC
* * *
568527 TTTGTCTCGCTTGAGACAGTTTCACTCGAAACAGAAC
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACA-AAC
** ** *
568564 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACAAAC
* * *
568599 TTTGTCTCGCTTGAGACAGTTTCACTCGAAACATAAC
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACA-AAC
** ** *
568636 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACAAAC
* * * *
568671 TTTGTCTCGCTTGAGACAGTTTCACTCGAAACTGAAC
1 TTTATCTCACTTGAGACAGTTTCACTCAAAAC-AAAC
* ** ** * *
568708 TTTATATCACTTGAGATTGTTTTTCTTAAAACAAAGA
1 TTTATCTCACTTGAGACAGTTTCACTCAAAACAAA-C
* *
568745 TTTGTCTCGCTTGAGACAGTT
1 TTTATCTCACTTGAGACAGTT
568766 ATTTCGAGTT
Statistics
Matches: 229, Mismatches: 74, Indels: 15
0.72 0.23 0.05
Matches are distributed among these distances:
35 74 0.32
36 39 0.17
37 116 0.51
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (36 bp):
TTTATCTCACTTGAGACAGTTTCACTCAAAACAAAC
Found at i:568564 original size:72 final size:72
Alignment explanation
Indices: 568419--568765 Score: 640
Period size: 72 Copynumber: 4.8 Consensus size: 72
568409 CAAATAGCAA
568419 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTTGTCTCGCTTGAGACAGTTTCACTCGA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAA-TTTGTCTCGCTTGAGACAGTTTCACTCGA
568484 AACAGAAC
65 AACAGAAC
568492 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA
568557 ACAGAAC
66 ACAGAAC
568564 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA
*
568629 ACATAAC
66 ACAGAAC
568636 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA
*
568701 ACTGAAC
66 ACAGAAC
*
568708 TTTATATCACTTGAGATTGTTTTTCTTAAAACAAAGATTTGTCTCGCTTGAGACAGTT
1 TTTATCTCACTTGAGATTGTTTTTCTTAAAAC-AA-ATTTGTCTCGCTTGAGACAGTT
568766 ATTTCGAGTT
Statistics
Matches: 268, Mismatches: 4, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
72 209 0.78
73 37 0.14
74 22 0.08
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (72 bp):
TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTTGTCTCGCTTGAGACAGTTTCACTCGAA
ACAGAAC
Found at i:568782 original size:13 final size:13
Alignment explanation
Indices: 568764--568791 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
568754 CTTGAGACAG
568764 TTATTTCGAGTTA
1 TTATTTCGAGTTA
568777 TTATTTCGAGTTA
1 TTATTTCGAGTTA
568790 TT
1 TT
568792 TGGGGGCATG
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:0.21, C:0.07, G:0.14, T:0.57
Consensus pattern (13 bp):
TTATTTCGAGTTA
Found at i:569069 original size:76 final size:76
Alignment explanation
Indices: 568943--569200 Score: 435
Period size: 76 Copynumber: 3.4 Consensus size: 76
568933 CTATTTCCCA
* * *
568943 CATCTGTAAGTCTTGCAGTGCATGATGTTTCCAAAAAGACTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
569008 AGCCTTAGGGT
66 AGCCTTAGGGT
569019 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
569084 AACCTTATGGT
66 AGCCTTAGGGT
* *
569095 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAACGCCTTCGGGAGCTTTTTGATGATTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
569160 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
569171 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
569201 TTAAGACCTC
Statistics
Matches: 171, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 171 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:569375 original size:3 final size:3
Alignment explanation
Indices: 569357--569449 Score: 98
Period size: 3 Copynumber: 30.3 Consensus size: 3
569347 TTCTTTTAAA
* * * * *
569357 ATT ATT TTT AATT ATT ATT ATT ATC AAT ATT AAT A-T AGT ATT ATT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
569402 ATT ATT ATT ATT ATT ATT ATAC ATT ATAT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT AT-T ATT AT-T ATT ATT ATT ATT ATT ATT
569449 A
1 A
569450 AATAATTACA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
2 2 0.03
3 67 0.88
4 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:569439 original size:29 final size:29
Alignment explanation
Indices: 569367--569449 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
569357 ATTATTTTTA
* * * *
569367 ATTATTATTATTATCAATATTAATATAGT
1 ATTATTATTATTATTATTATTATTATAGC
569396 ATTATTATTATTATTATTATTATTATA-C
1 ATTATTATTATTATTATTATTATTATAGC
569424 ATTATATATTATTATTATTATTATTA
1 ATTAT-TATTATTATTATTATTATTA
569450 AATAATTACA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.10
29 44 0.90
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (29 bp):
ATTATTATTATTATTATTATTATTATAGC
Found at i:569460 original size:35 final size:35
Alignment explanation
Indices: 569367--569461 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 35
569357 ATTATTTTTA
*
569367 ATTATTATTATTATCAAT-ATTA-A-TATAGTATT
1 ATTATTATTATTATTAATAATTACATTATAGTATT
* *
569399 ATTATTATTATTATTATTATTATACATTATA-TATT
1 ATTATTATTATTATTAATAAT-TACATTATAGTATT
569434 ATTATTATTATTATTAAATAATTACATT
1 ATTATTATTATTATT-AATAATTACATT
569462 GCAAGACCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
32 16 0.30
33 1 0.02
34 2 0.04
35 26 0.49
36 8 0.15
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (35 bp):
ATTATTATTATTATTAATAATTACATTATAGTATT
Found at i:570900 original size:16 final size:16
Alignment explanation
Indices: 570866--570897 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
570856 ATTATTTTTT
570866 TATATAAATAAATAAA
1 TATATAAATAAATAAA
570882 TATATATAATAAATAA
1 TATATA-AATAAATAA
570898 TATTTGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TATATAAATAAATAAA
Found at i:571083 original size:20 final size:19
Alignment explanation
Indices: 571058--571099 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
571048 CTATTTTATA
571058 AATTATATATATAATTTTTT
1 AATTATATAT-TAATTTTTT
* *
571078 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
571097 AAT
1 AAT
571100 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:571095 original size:119 final size:117
Alignment explanation
Indices: 570962--571190 Score: 293
Period size: 120 Copynumber: 1.9 Consensus size: 117
570952 TTTTAATATA
* * * *
570962 TATTTATTTATTTTTCAATAT-TAAG-AAAGGGC-AGTCTTAAAACAACTGGATGTCCATTTTCT
1 TATTTATTTATTTTTCAATATCGAAGAAAAGAGCTA-TCTTAAAACAACTAGAAGTCC-TTTTCT
*
571024 GATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATATAATTTTTTAAT
64 GATATTTCTAAATAAATAAATATCCTA-TTTATAAA-TATATATA-AATTTTTTAAT
* ** *
571081 TATTTATTTATTTTTTAATATCGAAGAAAAGAGCTATCTTAAGGCACCTAGAAGTCCTTTTCTGA
1 TATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGTCCTTTTCTGA
**
571146 TATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATT
66 TATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATT
571191 AAAATATATT
Statistics
Matches: 96, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
117 4 0.04
118 8 0.08
119 28 0.29
120 33 0.34
121 22 0.23
122 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.45
Consensus pattern (117 bp):
TATTTATTTATTTTTCAATATCGAAGAAAAGAGCTATCTTAAAACAACTAGAAGTCCTTTTCTGA
TATTTCTAAATAAATAAATATCCTATTTATAAATATATATAAATTTTTTAAT
Found at i:578183 original size:2 final size:2
Alignment explanation
Indices: 578176--578205 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
578166 AAATTATTGT
578176 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
578206 CATTGTAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:581879 original size:8 final size:8
Alignment explanation
Indices: 581863--581904 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
581853 GGGCTGATGT
581863 AAAGAGAA
1 AAAGAGAA
*
581871 AAAGGGAA
1 AAAGAGAA
581879 AAAGAGAA
1 AAAGAGAA
*
581887 AAAG-GGA
1 AAAGAGAA
581894 AAAGAGAA
1 AAAGAGAA
581902 AAA
1 AAA
581905 ATGGGGGAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
7 6 0.21
8 23 0.79
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (8 bp):
AAAGAGAA
Found at i:581896 original size:15 final size:16
Alignment explanation
Indices: 581863--581904 Score: 77
Period size: 16 Copynumber: 2.7 Consensus size: 16
581853 GGGCTGATGT
581863 AAAGAGAAAAAGGGAA
1 AAAGAGAAAAAGGGAA
581879 AAAGAGAAAAAGGG-A
1 AAAGAGAAAAAGGGAA
581894 AAAGAGAAAAA
1 AAAGAGAAAAA
581905 ATGGGGGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AAAGAGAAAAAGGGAA
Found at i:584258 original size:133 final size:133
Alignment explanation
Indices: 584011--584371 Score: 431
Period size: 133 Copynumber: 2.7 Consensus size: 133
584001 CTTTGCTGCC
* * * *
584011 CTTTAGGGAAGATTGAATTGAACTTGATTTGCTTCACT-TCTCTTCAGAAATATC-AATTTGAAA
1 CTTTAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGT-TATTCAGAAAGACCAAATTTGAAA
* * * * * * * *
584074 GAAAT-AGTATCTTCTCCACTACTCTGTAGGGGATATTAGACTCGAAAAACTTTGATCTACTTCG
65 G-AATGAGGATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAAAAACTTAGATCCACTTCA
584138 TAGCT
129 TAGCT
**
584143 CTTTAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGTTATTCATTAAGACCAAATTTGAAAG
1 CTTTAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGTTATTCAGAAAGACCAAATTTGAAAG
* * *
584208 AATGAGGATCTGCTCCACTACTATTTAGGGGAGATCAGACTTGAAAAACTTAGATCCACTTCATT
66 AATGAGGATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAAAAACTTAGATCCACTTCATA
584273 GCT
131 GCT
* * * ** * *
584276 CTTTAAGGAAGATTTAATCGAACTTGATTTGCTTCACTGGTATTCAGGCAGACCAAATCTAAAAC
1 CTTTAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGTTATTCAGAAAGACCAAATTTGAAA-
* * *
584341 AAATGATGATATGCTCCACTACTCTTTAGGG
65 GAATGAGGATCTGCTCCACTACTCTTTAGGG
584372 AAAACCAAAT
Statistics
Matches: 196, Mismatches: 29, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
132 49 0.25
133 120 0.61
134 27 0.14
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (133 bp):
CTTTAGGGAAGATTGAATCGAACTTGATTTGCTTCACTGTTATTCAGAAAGACCAAATTTGAAAG
AATGAGGATCTGCTCCACTACTCTTTAGGGGAGATCAGACTCGAAAAACTTAGATCCACTTCATA
GCT
Found at i:585765 original size:8 final size:7
Alignment explanation
Indices: 585752--585850 Score: 51
Period size: 7 Copynumber: 13.4 Consensus size: 7
585742 CCTATATTTA
585752 TTTTTTCC
1 TTTTTT-C
585760 TTTTTTC
1 TTTTTTC
585767 TTTTCTT-
1 TTTT-TTC
585774 TTTTTATC
1 TTTTT-TC
* *
585782 ATTATT-
1 TTTTTTC
*
585788 ATTTTTC
1 TTTTTTC
585795 TTCTTTT-
1 TT-TTTTC
*
585802 TTATTTC
1 TTTTTTC
*
585809 TTTTTTA
1 TTTTTTC
*
585816 TTCTTTC
1 TTTTTTC
585823 TTCTTCTTC
1 TT-TT-TTC
585832 TTCTTCTTC
1 TT-TT-TTC
585841 TTTTTTC
1 TTTTTTC
585848 TTT
1 TTT
585851 CTTTAGGCAA
Statistics
Matches: 73, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
6 9 0.12
7 32 0.44
8 18 0.25
9 14 0.19
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:585792 original size:28 final size:29
Alignment explanation
Indices: 585761--585830 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 29
585751 ATTTTTTCCT
585761 TTTTTCTTTTCTTTTTT-TATCATTATTA
1 TTTTTCTTTTCTTTTTTATATCATTATTA
* * *
585789 TTTTTC--TTCTTTTTTATTTCTTTTTTA
1 TTTTTCTTTTCTTTTTTATATCATTATTA
585816 TTCTTTCTTCTTCTT
1 TT-TTTCTT-TTCTT
585831 CTTCTTCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
26 9 0.26
27 10 0.29
28 10 0.29
31 5 0.15
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTTCTTTTCTTTTTTATATCATTATTA
Found at i:585809 original size:11 final size:10
Alignment explanation
Indices: 585789--585846 Score: 53
Period size: 10 Copynumber: 5.5 Consensus size: 10
585779 ATCATTATTA
*
585789 TTTTTCTTCT
1 TTTTTATTCT
585799 TTTTTATTTCT
1 TTTTTA-TTCT
585810 TTTTTATTCT
1 TTTTTATTCT
* *
585820 TTCTTCTTCT
1 TTTTTATTCT
*
585830 TCTTCTTCTTCT
1 T-TT-TTATTCT
585842 TTTTT
1 TTTTT
585847 CTTTCTTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
10 20 0.49
11 13 0.32
12 8 0.20
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTATTCT
Found at i:607774 original size:134 final size:134
Alignment explanation
Indices: 607479--608087 Score: 700
Period size: 134 Copynumber: 4.5 Consensus size: 134
607469 TGATTCATTC
* * * * * * *
607479 CACTGTTCTTCAAGGAAGATTGAATCGGAATTGATTTGTTTCA-TTGCTATTCAAGAATACCAAA
1 CACTGCTCTTCAGGGAAGATTGAATCAGAATTGATTTGCTTCACTT-CTCTTCAGGAAGACCAAA
* *
607543 TCTGAAAGAAAAAGAGTATGCTCCACTACTCTTTAGGGGGAGATCAAACTCGAGAAAACTTTGAT
65 TCTGAAAGAAAAAGAATCTGCTCCACTACTCTTTA-GGGGAGATCAAACTCGAGAAAACTTTGAT
*
607608 CCACTT
129 CTACTT
** * *
607614 CACTATTCTTCATGGAAGATTGAATCAGAATCGATTTGCTTCACTTCTCTTCAGGAAGACCAAAT
1 CACTGCTCTTCAGGGAAGATTGAATCAGAATTGATTTGCTTCACTTCTCTTCAGGAAGACCAAAT
* * ** * * **
607679 CTAAAAGAAGAAGCGTCTGCTCCACTACTCTTTAGGGGAGATCAGACTTGAGAAAACTTTGATAG
66 CTGAAAGAAAAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCT
607744 ACTT
131 ACTT
* * * * *
607748 CACTGCTCTTCACGAAAGATTGAATCAGAATTGATTTACTTCACTGCTCTTCAGGAAGACCAAGT
1 CACTGCTCTTCAGGGAAGATTGAATCAGAATTGATTTGCTTCACTTCTCTTCAGGAAGACCAAAT
* * *
607813 CTGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGGATATCAAACTCGAGAATACTTTGATCT
66 CTGAAAGAAAAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCT
607878 ACTT
131 ACTT
* * * *
607882 CACTGCTCTTTAGGGAATATTGAATCAGAATTGATTTGTTTCACTTCTCTTTAGGAAGACCAAAT
1 CACTGCTCTTCAGGGAAGATTGAATCAGAATTGATTTGCTTCACTTCTCTTCAGGAAGACCAAAT
* * * * * *
607947 CTGAAAGAAAAAAAAATCTACTCCAATACTCTTTAGGGGAGATTAAATTCGAGAAATCTTTGATC
66 CTGAAAG-AAAAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATC
*
608012 TATTT
130 TACTT
* * * * * * * * * *
608017 TAATTCTCTTCAGGAAAGATTGAATC-GAATGTGGTTTGTTTTACTTCTTTTTAGAAAGACCAAA
1 CACTGCTCTTCAGGGAAGATTGAATCAGAAT-TGATTTGCTTCACTTCTCTTCAGGAAGACCAAA
*
608081 TTTGAAA
65 TCTGAAA
608088 ATCAAAACAT
Statistics
Matches: 408, Mismatches: 63, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
134 215 0.53
135 191 0.47
136 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (134 bp):
CACTGCTCTTCAGGGAAGATTGAATCAGAATTGATTTGCTTCACTTCTCTTCAGGAAGACCAAAT
CTGAAAGAAAAAGAATCTGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCT
ACTT
Found at i:608010 original size:269 final size:268
Alignment explanation
Indices: 607479--608046 Score: 717
Period size: 269 Copynumber: 2.1 Consensus size: 268
607469 TGATTCATTC
* * ** * *
607479 CACTGTTCTTCAAGGAAGATTGAATCGGAATTGATTTGTTTCATTGCTATTCAAGAATACCAAAT
1 CACTGCTCTTCAAGAAAGATTGAATC-GAATTGATTTACTTCACTGCTATTCAAGAAGACCAAAT
*
607544 CTGAAAGAAAAAGAGTATGCTCCACTACTCTTTAGGGGGAGATCAAACTCGAGAAAACTTTGATC
65 CTGAAAGAAAAAGAATATGCTCCACTACTCTTTAGGGGGAGATCAAACTCGAGAAAACTTTGATC
* *
607609 CACTTCACTATTCTTCATGGAAGATTGAATCAGAATCGATTTGCTTCACTTCTCTTCAGGAAGAC
130 CACTTCACTACTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTTCTCTTCAGGAAGAC
* *** * * *
607674 CAAATCTAAAAGAAGAAGCGTCTGCTCCACTACTCTTTAGGGGAGATCAGACTTGAGAAAACTTT
195 CAAATCTAAAAGAAAAAAAATCTACTCCAATACTCTTTAGGGGAGATCAGAATTGAGAAAACTTT
607739 GATAGACTT
260 GATAGACTT
* * * *
607748 CACTGCTCTTCACGAAAGATTGAATCAGAATTGATTTACTTCACTGCTCTTCAGGAAGACCAAGT
1 CACTGCTCTTCAAGAAAGATTGAATC-GAATTGATTTACTTCACTGCTATTCAAGAAGACCAAAT
* * * *
607813 CTGAAAGAAGAAGAATCTGCTCCACTACTCTTTA-GGGGATATCAAACTCGAGAATACTTTGATC
65 CTGAAAGAAAAAGAATATGCTCCACTACTCTTTAGGGGGAGATCAAACTCGAGAAAACTTTGATC
* * * * * * *
607877 TACTTCACTGCTCTTTAGGGAATATTGAATCAGAATTGATTTGTTTCACTTCTCTTTAGGAAGAC
130 CACTTCACTACTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTTCTCTTCAGGAAGAC
* * *
607942 CAAATCTGAAAGAAAAAAAAATCTACTCCAATACTCTTTAGGGGAGATTA-AATTCGAGAAATCT
195 CAAATCTAAAAG-AAAAAAAATCTACTCCAATACTCTTTAGGGGAGATCAGAATT-GAGAAAACT
** *
608006 TTGATCTATTT
258 TTGATAGACTT
* * * *
608017 TAATTCTCTTCAGGAAAGATTGAATCGAAT
1 CACTGCTCTTCAAGAAAGATTGAATCGAAT
608047 GTGGTTTGTT
Statistics
Matches: 255, Mismatches: 42, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
268 102 0.40
269 153 0.60
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (268 bp):
CACTGCTCTTCAAGAAAGATTGAATCGAATTGATTTACTTCACTGCTATTCAAGAAGACCAAATC
TGAAAGAAAAAGAATATGCTCCACTACTCTTTAGGGGGAGATCAAACTCGAGAAAACTTTGATCC
ACTTCACTACTCTTCAGGGAAGATTGAATCAGAATCGATTTGCTTCACTTCTCTTCAGGAAGACC
AAATCTAAAAGAAAAAAAATCTACTCCAATACTCTTTAGGGGAGATCAGAATTGAGAAAACTTTG
ATAGACTT
Found at i:608784 original size:45 final size:43
Alignment explanation
Indices: 608685--608861 Score: 167
Period size: 45 Copynumber: 4.0 Consensus size: 43
608675 TCAAGTTGAA
* * *
608685 AATGACATCACTAAAAGGTTGACTCATCTTTC-TGAAAAAGTCAAG
1 AATGACAACACT-AAAGATTGACTC-TC-TTCATGAGAAAGTCAAG
* * *
608730 AATCACAACACTGAAAGATTGACTTCTCTTCATGAGAAATTCAAT
1 AATGACAACACT-AAAGATTGAC-TCTCTTCATGAGAAAGTCAAG
* * * * *
608775 AATGACAACAATAAAGGTTGACTCCCTTCACGAGAAAGTAAAG
1 AATGACAACACTAAAGATTGACTCTCTTCATGAGAAAGTCAAG
* *
608818 AATGACATCACTTAAAGATTGACTTCTCTTCATGAGAAATTCAA
1 AATGACAACAC-TAAAGATTGAC-TCTCTTCATGAGAAAGTCAA
608862 AAATAATATT
Statistics
Matches: 106, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
43 25 0.24
44 22 0.21
45 57 0.54
46 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (43 bp):
AATGACAACACTAAAGATTGACTCTCTTCATGAGAAAGTCAAG
Found at i:609016 original size:42 final size:42
Alignment explanation
Indices: 608722--609509 Score: 481
Period size: 38 Copynumber: 19.4 Consensus size: 42
608712 CTTTCTGAAA
* * * *
608722 AAGTCAAGAATCACAACACTGAAAGATTGACTTCTCTTCATGAGA
1 AAGTCAAGAAT---AACATTGAAAGATTGACTCCTCTTCACGAGG
* * * * *
608767 AATTCAATAATGACAACAAT-AAAGGTTGACTCC-CTTCACGAGA
1 AAGTCAAGAAT---AACATTGAAAGATTGACTCCTCTTCACGAGG
* * * *
608810 AAGTAAAGAATGACATCACTT-AAAGATTGACTTCTCTTCATGAGA
1 AAGTCAAGAAT-A-A-CA-TTGAAAGATTGACTCCTCTTCACGAGG
* * * * *
608855 AATTCAAAAATAATATTGAAATATTGACTCATCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* ** * * *
608897 GAGTCAAG-ATAA-A-AAAAATATTAACTTCTCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* ** * *
608936 AAGTTAAGAATAA-A---AAAGATCAACTTCTCTTCAAGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* * *
608974 AAGTCAATAATAACATTGAAAAATTGACTCCACTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* * *
609016 AAGTCAAGAATAATATTGAAAGATTGACTCTTCTTTACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* * *
609058 GAGTCAAGAATAACA---AAA-ATTTACTTCTCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
*
609096 AAGTCGAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* * * * * *
609138 GAGTCAAGAA-AGGCAATACCGAAAGATTAACTTCTCTTCACGAAG
1 AAGTCAAGAATA-AC-AT--TGAAAGATTGACTCCTCTTCACGAGG
* *
609183 AAGTCAAGAATAACATTGAAAGAATGACTCATCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* * * *
609225 GAGTTAAGAATAAC----AAAGATTGATTTCTCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
*
609263 AAGTGAAGAATAAC----AAAGATTGAC-CTCTCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTC-CTCTTCACGAGG
* * * * *
609301 AAGTCAATAAT-A-A-T-AAATATTGGCTTCTCTTCACAAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
*
609339 AAGTTAAGAATAAC----AAAGA-TGAAC-CTCTCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTG-ACTC-CTCTTCACGAGG
* *
609377 AAGTCAAGAAAAACATTGAAATATTGACTCCTCTTCACGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* * * ** * *
609419 GAGTAAAGAATAAC----AAAGATTGATTTTTCTTCACAATG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
* * * * *
609457 AATTTAAGAATAAC----AAAGATCGACTTCTCTTCATGAGG
1 AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
609495 AAGTCAAGAATAACA
1 AAGTCAAGAATAACA
609510 AATATTGAAG
Statistics
Matches: 588, Mismatches: 121, Indels: 74
0.75 0.15 0.09
Matches are distributed among these distances:
37 3 0.01
38 238 0.40
39 32 0.05
40 6 0.01
41 11 0.02
42 181 0.31
43 25 0.04
44 26 0.04
45 65 0.11
46 1 0.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.26
Consensus pattern (42 bp):
AAGTCAAGAATAACATTGAAAGATTGACTCCTCTTCACGAGG
Found at i:609017 original size:80 final size:77
Alignment explanation
Indices: 608787--609517 Score: 487
Period size: 80 Copynumber: 9.1 Consensus size: 77
608777 TGACAACAAT
* * * * * *
608787 AAAGGTTGACTCCCTTCACGAGAAAGTAAAGAATGACATCACTTAAAGATTGACTTCTCTTCATG
1 AAAGATTGACTCTCTTCACGAGGAAGTCAAGAAT-A-A-CA--TAAAAATTGACTTCTCTTCACG
* * *
608852 AGAAATTCAAAAATAATA
61 AGGAAGTCAAGAATAA-A
* * * *
608870 TTGAAATATTGACTCATCTTCACGAGGGAGTCAAG-ATAA-AAAAAATATTAACTTCTCTTCACG
1 ---AAAGATTGACTC-TCTTCACGAGGAAGTCAAGAATAACATAAAA-ATTGACTTCTCTTCACG
*
608933 AGGAAGTTAAGAATAAA
61 AGGAAGTCAAGAATAAA
** * * * *
608950 AAAGATCAACTTCTCTTCAAGAGGAAGTCAATAATAACATTGAAAAATTGACTCCACTTCACGAG
1 AAAGATTGAC-TCTCTTCACGAGGAAGTCAAGAATAACA-T-AAAAATTGACTTCTCTTCACGAG
609015 GAAGTCAAGAATAATA
63 GAAGTCAAGAATAA-A
* * *
609031 TTGAAAGATTGACTCTTCTTTACGAGGGAGTCAAGAATAAC--AAAAATTTACTTCTCTTCACGA
1 ---AAAGATTGACTC-TCTTCACGAGGAAGTCAAGAATAACATAAAAATTGACTTCTCTTCACGA
*
609094 GGAAGTCGAGAATAACA
62 GGAAGTCAAGAATAA-A
* * *
609111 TTGAAAGATTGACTCCTCTTCACGAGGGAGTCAAGAA-AGGCAATACCGAAAGATTAACTTCTCT
1 ---AAAGATTGACT-CTCTTCACGAGGAAGTCAAGAATA-AC-ATA---AAA-ATTGACTTCTCT
*
609175 TCACGAAGAAGTCAAGAATAACA
56 TCACGAGGAAGTCAAGAATAA-A
* * * * *
609198 TTGAAAGAATGACTCATCTTCACGAGGGAGTTAAGAATAAC--AAAGATTGATTTCTCTTCACGA
1 ---AAAGATTGACTC-TCTTCACGAGGAAGTCAAGAATAACATAAAAATTGACTTCTCTTCACGA
* *
609261 GGAAGTGAAGAATAAC
62 GGAAGTCAAGAATAAA
* * * *
609277 AAAGATTGACCTCTCTTCACGAGGAAGTCAATAAT-A-ATAAATATTGGCTTCTCTTCACAAGGA
1 AAAGATTGA-CTCTCTTCACGAGGAAGTCAAGAATAACATAAAAATTGACTTCTCTTCACGAGGA
* *
609340 AGTTAAGAATAAC
65 AGTCAAGAATAAA
* * *
609353 AAAGA-TGAACCTCTCTTCACGAGGAAGTCAAGAAAAACATTGAAATATTGACTCCTCTTCACGA
1 AAAGATTG-A-CTCTCTTCACGAGGAAGTCAAGAATAACA-T-AAAAATTGACTTCTCTTCACGA
* * *
609417 GGGAGTAAAGAATAAC
62 GGAAGTCAAGAATAAA
* * * * * * * * *
609433 AAAGATTGATTTTTCTTCACAATGAATTTAAGAATAAC--AAAGATCGACTTCTCTTCATGAGGA
1 AAAGATTGA-CTCTCTTCACGAGGAAGTCAAGAATAACATAAAAATTGACTTCTCTTCACGAGGA
*
609496 AGTCAAGAATAAC
65 AGTCAAGAATAAA
*
609509 AAATATTGA
1 AAAGATTGA
609518 AGTTTATAGG
Statistics
Matches: 532, Mismatches: 81, Indels: 74
0.77 0.12 0.11
Matches are distributed among these distances:
75 3 0.01
76 130 0.24
77 27 0.05
78 7 0.01
79 3 0.01
80 191 0.36
81 37 0.07
82 1 0.00
83 3 0.01
84 31 0.06
85 1 0.00
86 16 0.03
87 81 0.15
88 1 0.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.26
Consensus pattern (77 bp):
AAAGATTGACTCTCTTCACGAGGAAGTCAAGAATAACATAAAAATTGACTTCTCTTCACGAGGAA
GTCAAGAATAAA
Found at i:611372 original size:19 final size:19
Alignment explanation
Indices: 611350--611394 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
611340 ATTTAATTTA
*
611350 TTTTTTTCTCATTTTT-TTC
1 TTTTTCTCTC-TTTTTGTTC
611369 TTTTTCTCTCTTTTTGTTC
1 TTTTTCTCTCTTTTTGTTC
*
611388 TTCTTCT
1 TTTTTCT
611395 TTTTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTCTCTCTTTTTGTTC
Found at i:611382 original size:17 final size:17
Alignment explanation
Indices: 611352--611462 Score: 62
Period size: 16 Copynumber: 6.9 Consensus size: 17
611342 TTAATTTATT
611352 TTTTTCTCAT-TTTTTTC
1 TTTTTCTC-TCTTTTTTC
*
611369 TTTTTCTCTC-TTTTTG
1 TTTTTCTCTCTTTTTTC
* *
611385 TTCTTCT-TCTTTTTATA
1 TTTTTCTCTCTTTTT-TC
611402 TATTTTC-C-C--TTTTC
1 T-TTTTCTCTCTTTTTTC
* *
611416 TTTTTCTATCTTTTCTC
1 TTTTTCTCTCTTTTTTC
611433 -TTTTC-CTCTTTTTTC
1 TTTTTCTCTCTTTTTTC
*
611448 -TTCTCTCTCCTTTTT
1 TTTTTCTCT-CTTTTT
611463 ATCTCTATAT
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
13 5 0.07
14 2 0.03
15 18 0.25
16 23 0.32
17 21 0.29
18 4 0.05
ACGTcount: A:0.05, C:0.23, G:0.01, T:0.71
Consensus pattern (17 bp):
TTTTTCTCTCTTTTTTC
Found at i:611419 original size:22 final size:22
Alignment explanation
Indices: 611391--611437 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
611381 TTTGTTCTTC
611391 TTCTTTTTATATATTTTCCCTT
1 TTCTTTTTATATATTTTCCCTT
* * *
611413 TTCTTTTTCTATCTTTTCTCTT
1 TTCTTTTTATATATTTTCCCTT
611435 TTC
1 TTC
611438 CTCTTTTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (22 bp):
TTCTTTTTATATATTTTCCCTT
Found at i:619365 original size:2 final size:2
Alignment explanation
Indices: 619358--619387 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
619348 TAGAAAGAAA
619358 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
619388 TTCTAATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:625211 original size:14 final size:16
Alignment explanation
Indices: 625192--625228 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
625182 AAATAATAAT
625192 AATAATAA-TATT-TA
1 AATAATAATTATTATA
*
625206 AATAATAATTATTATT
1 AATAATAATTATTATA
625222 AATAATA
1 AATAATA
625229 TTAATGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 8 0.40
15 4 0.20
16 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATAATAATTATTATA
Found at i:626764 original size:2 final size:2
Alignment explanation
Indices: 626757--626786 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
626747 ATGCTAAGTA
626757 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
626787 TTTCGGTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:635777 original size:13 final size:13
Alignment explanation
Indices: 635759--635853 Score: 80
Period size: 12 Copynumber: 7.7 Consensus size: 13
635749 ACTCATCATC
635759 AGAAAAAAAAGAA
1 AGAAAAAAAAGAA
635772 AG-AAAAAAAGAA
1 AGAAAAAAAAGAA
635784 A-AAGAAAAAAG-A
1 AGAA-AAAAAAGAA
*
635796 A-AAAGAAAA-AA
1 AGAAAAAAAAGAA
635807 AG-AAAAAAAGAA
1 AGAAAAAAAAGAA
*
635819 A-AAAAAGAAGAGA
1 AGAAAAAAAAGA-A
*
635832 TGAAAAAAGAA-AA
1 AGAAAAAA-AAGAA
635845 AGAAAAAAA
1 AGAAAAAAA
635854 TTGAATCAAG
Statistics
Matches: 67, Mismatches: 6, Indels: 19
0.73 0.07 0.21
Matches are distributed among these distances:
11 13 0.19
12 28 0.42
13 18 0.27
14 6 0.09
15 2 0.03
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (13 bp):
AGAAAAAAAAGAA
Found at i:635783 original size:8 final size:8
Alignment explanation
Indices: 635762--635853 Score: 79
Period size: 8 Copynumber: 11.9 Consensus size: 8
635752 CATCATCAGA
635762 AAAAAAAG
1 AAAAAAAG
*
635770 AAAGAAAAA
1 AAA-AAAAG
635779 AAGAAAAAG
1 AA-AAAAAG
635788 -AAAAAAG
1 AAAAAAAG
635795 --AAAAAG
1 AAAAAAAG
635801 AAAAAAAG
1 AAAAAAAG
635809 AAAAAAAG
1 AAAAAAAG
635817 AAAAAAAAG
1 -AAAAAAAG
* * *
635826 AAGAGATG
1 AAAAAAAG
635834 -AAAAAAG
1 AAAAAAAG
635841 --AAAAAG
1 AAAAAAAG
635847 AAAAAAA
1 AAAAAAA
635854 TTGAATCAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
6 12 0.17
7 10 0.14
8 28 0.41
9 18 0.26
10 1 0.01
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (8 bp):
AAAAAAAG
Found at i:635785 original size:21 final size:20
Alignment explanation
Indices: 635759--635845 Score: 85
Period size: 21 Copynumber: 4.3 Consensus size: 20
635749 ACTCATCATC
635759 AGAAAAAAAAGAAAGAAAAAA
1 AGAAAAAAAAGAAAG-AAAAA
635780 AGAAAAAGAAA-AAAG-AAAA
1 AGAAAAA-AAAGAAAGAAAAA
635799 AG-AAAAAAAGAAA-AAAAGA
1 AGAAAAAAAAGAAAGAAAA-A
*
635818 A-AAAAAAGAAGAGATGAAAAA
1 AGAAAAAA-AAGA-AAGAAAAA
635839 AGAAAAA
1 AGAAAAA
635846 GAAAAAAATT
Statistics
Matches: 56, Mismatches: 1, Indels: 17
0.76 0.01 0.23
Matches are distributed among these distances:
17 3 0.05
18 10 0.18
19 13 0.23
20 4 0.07
21 14 0.25
22 12 0.21
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (20 bp):
AGAAAAAAAAGAAAGAAAAA
Found at i:635824 original size:46 final size:47
Alignment explanation
Indices: 635762--635853 Score: 143
Period size: 46 Copynumber: 2.0 Consensus size: 47
635752 CATCATCAGA
635762 AAAAAAAGAAAGAAAAA-AAGAAAAAGAAAAAAGAAAAAGAAAAAAAG
1 AAAAAAAGAAAGAAAAAGAAG-AAAAGAAAAAAGAAAAAGAAAAAAAG
* *
635809 AAAAAAAGAAA-AAAAAGAAGAGATGAAAAAAGAAAAAGAAAAAAA
1 AAAAAAAGAAAGAAAAAGAAGAAAAGAAAAAAGAAAAAGAAAAAAA
635854 TTGAATCAAG
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
46 28 0.67
47 14 0.33
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (47 bp):
AAAAAAAGAAAGAAAAAGAAGAAAAGAAAAAAGAAAAAGAAAAAAAG
Found at i:635839 original size:1 final size:1
Alignment explanation
Indices: 635761--635824 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
635751 TCATCATCAG
* * * * * * * *
635761 AAAAAAAAGAAAGAAAAAAAGAAAAAGAAAAAAGAAAAAGAAAAAAAGAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
635825 GAAGAGATGA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:635839 original size:17 final size:17
Alignment explanation
Indices: 635764--635827 Score: 85
Period size: 17 Copynumber: 3.6 Consensus size: 17
635754 TCATCAGAAA
635764 AAAAAGAAAGAAAAAAAG
1 AAAAA-AAAGAAAAAAAG
*
635782 AAAAAGAAAAAAGAAAAAG
1 AAAAA-AAAGAA-AAAAAG
635801 -AAAAAAAGAAAAAAAG
1 AAAAAAAAGAAAAAAAG
635817 AAAAAAAAGAA
1 AAAAAAAAGAA
635828 GAGATGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
16 6 0.14
17 15 0.36
18 15 0.36
19 6 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAG
Found at i:635846 original size:21 final size:21
Alignment explanation
Indices: 635759--635853 Score: 93
Period size: 22 Copynumber: 4.3 Consensus size: 21
635749 ACTCATCATC
*
635759 AGAAAAAAAAGAAAGAAAAA-A
1 AGAAAAGAAA-AAAGAAAAAGA
635780 AGAAAAAGAAAAAAGAAAAAGA
1 AG-AAAAGAAAAAAGAAAAAGA
* *
635802 AAAAAAGAAAAAAAGAAAAAAA
1 AGAAAAG-AAAAAAGAAAAAGA
635824 AGAAGAGATGAAAAAAGAAAAAGA
1 AGAA-A-A-GAAAAAAGAAAAAGA
*
635848 AAAAAA
1 AGAAAA
635854 TTGAATCAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
21 16 0.26
22 26 0.42
23 2 0.03
24 17 0.27
25 1 0.02
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (21 bp):
AGAAAAGAAAAAAGAAAAAGA
Done.