Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008489.1 Hibiscus syriacus cultivar Beakdansim tig00111331_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: 1108073
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 6
Found at i:520578 original size:39 final size:39
Alignment explanation
Indices: 520502--520584 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 39
520492 GGCGATAACA
* * *
520502 CCTAAGGTGAGGATGTTGAGTGCAATGAAGGCAATAATG
1 CCTAAGGTGAGGATGTCGAGTGCAATAAAGACAATAATG
* * **
520541 CCTAGGGTGAGGATGTCGAGTGCAGTAAAGATGATAATG
1 CCTAAGGTGAGGATGTCGAGTGCAATAAAGACAATAATG
520580 CCTAA
1 CCTAA
520585 AGAGAGGGCG
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.33, C:0.12, G:0.33, T:0.23
Consensus pattern (39 bp):
CCTAAGGTGAGGATGTCGAGTGCAATAAAGACAATAATG
Found at i:523941 original size:21 final size:20
Alignment explanation
Indices: 523891--523942 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
523881 TAAATAATTT
523891 AAAATTAACAAC-CATATATA
1 AAAATTAA-AACACATATATA
* *
523911 ATAATT-AAACACATTTAATA
1 AAAATTAAAACACATAT-ATA
523931 AAAATTAAAACA
1 AAAATTAAAACA
523943 AATGGTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.12
19 5 0.19
20 13 0.50
21 5 0.19
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATTAAAACACATATATA
Found at i:525600 original size:18 final size:18
Alignment explanation
Indices: 525577--525614 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
525567 TTTTGAATCA
525577 AAGAATCCAGATACTCAC
1 AAGAATCCAGATACTCAC
525595 AAGAATCCAGATACTCAC
1 AAGAATCCAGATACTCAC
525613 AA
1 AA
525615 TAATGCATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (18 bp):
AAGAATCCAGATACTCAC
Found at i:528146 original size:24 final size:22
Alignment explanation
Indices: 528113--528199 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 22
528103 TCCTTTTATG
*
528113 AAAAAGGTTAAGTCTTTTCAGGA
1 AAAAATGTTAAGTCTTTTCA-GA
* * *
528136 AAAAATTGTTAAGCCCTTTCATA
1 AAAAA-TGTTAAGTCTTTTCAGA
528159 AAAAATGTTAAGTCTTTT-A-A
1 AAAAATGTTAAGTCTTTTCAGA
* *
528179 TCAAAATGTTAAGTCCTTTCA
1 -AAAAATGTTAAGTCTTTTCA
528200 TTGAAAGATC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 17 0.32
22 12 0.23
23 11 0.21
24 12 0.23
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.36
Consensus pattern (22 bp):
AAAAATGTTAAGTCTTTTCAGA
Found at i:528960 original size:45 final size:45
Alignment explanation
Indices: 528911--529267 Score: 474
Period size: 45 Copynumber: 8.2 Consensus size: 45
528901 TATTCATTAT
*
528911 TTTCATTTATGGCATTCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
528956 TTTCATTTATGGCATCCTTTCATTCCTTTAATGCACCTTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * * *
529001 TTTCATTTATGGCATCCTTTCATACCTTTAATGTATCTTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* *
529046 --TC-CTT-T--CATTCCTTTAATG-C---A-----CCGTTATGCA
1 TTTCATTTATGGCA-TCCTTTCATGCCTTTAATGCACCGTTATGCA
529077 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
529122 TTTCATTTATGGTATCCTTTCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
*
529167 TTTCATTTATGGCATCCTTCCATGCCTTTAATGCACCGTTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
* * *
529212 TTTCATTTATGGCATCATTTCATGCCTTTAATGCTCCATTATGCA
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
529257 TTTCATTTATG
1 TTTCATTTATG
529268 TAATAAAACA
Statistics
Matches: 276, Mismatches: 20, Indels: 32
0.84 0.06 0.10
Matches are distributed among these distances:
31 8 0.03
33 2 0.01
34 2 0.01
35 1 0.00
36 10 0.04
37 3 0.01
39 3 0.01
40 9 0.03
41 1 0.00
42 2 0.01
43 2 0.01
45 233 0.84
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.45
Consensus pattern (45 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCA
Found at i:529049 original size:76 final size:77
Alignment explanation
Indices: 528961--529109 Score: 273
Period size: 76 Copynumber: 1.9 Consensus size: 77
528951 ATGCATTTCA
*
528961 TTTATGGCATCCTTTCATTCCTTTAATGCACCTTTATGCATTTCATTTATGGCATCCTTTCATAC
1 TTTATGGCATCCTTTCATTCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATAC
529026 CTTTAATGTATC
66 CTTTAATGTATC
*
529038 TTTAT-GCATCCTTTCATTCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATGC
1 TTTATGGCATCCTTTCATTCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATAC
529102 CTTTAATG
66 CTTTAATG
529110 CACCGTTATG
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
76 65 0.93
77 5 0.07
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.46
Consensus pattern (77 bp):
TTTATGGCATCCTTTCATTCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTTCATAC
CTTTAATGTATC
Found at i:529074 original size:31 final size:31
Alignment explanation
Indices: 529007--529077 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
528997 TGCATTTCAT
* * *
529007 TTATGGCATCCTTTCATACCTTTAATGTATCT
1 TTAT-GCATCCTTTCATACCTTTAATGCACCG
*
529039 TTATGCATCCTTTCATTCCTTTAATGCACCG
1 TTATGCATCCTTTCATACCTTTAATGCACCG
529070 TTATGCAT
1 TTATGCAT
529078 TTCATTTATG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.21, C:0.24, G:0.10, T:0.45
Consensus pattern (31 bp):
TTATGCATCCTTTCATACCTTTAATGCACCG
Found at i:529211 original size:166 final size:166
Alignment explanation
Indices: 528911--529212 Score: 523
Period size: 166 Copynumber: 1.8 Consensus size: 166
528901 TATTCATTAT
*
528911 TTTCATTTATGGCATTCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
* * * * * *
528976 CATTCCTTTAATGCACCTTTATGCATTTCATTTATGGCATCCTTTCATACCTTTAATGTATCTTT
66 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTCCATACCTTTAATGCACCGTT
529041 ATGCATCCTTTCATTCCTTTAATGCACCGTTATGCA
131 ATGCATCCTTTCATTCCTTTAATGCACCGTTATGCA
*
529077 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGTATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
*
529142 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTCCATGCCTTTAATGCACCGTT
66 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTCCATACCTTTAATGCACCGTT
529207 ATGCAT
131 ATGCAT
529213 TTCATTTATG
Statistics
Matches: 127, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
166 127 1.00
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (166 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTT
CATGCCTTTAATGCACCGTTATGCATTTCATTTATGGCATCCTTCCATACCTTTAATGCACCGTT
ATGCATCCTTTCATTCCTTTAATGCACCGTTATGCA
Found at i:529265 original size:24 final size:24
Alignment explanation
Indices: 529193--529265 Score: 57
Period size: 24 Copynumber: 3.2 Consensus size: 24
529183 CTTCCATGCC
* *
529193 TTTAATGCACCGTTATGCATTTCA
1 TTTAATGCTCCATTATGCATTTCA
* *
529217 TTT-ATGGCAT-CATT-T-CA-TGCC
1 TTTAAT-GC-TCCATTATGCATTTCA
529238 TTTAATGCTCCATTATGCATTTCA
1 TTTAATGCTCCATTATGCATTTCA
529262 TTTA
1 TTTA
529266 TGTAATAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 1 0.03
21 11 0.31
22 5 0.14
23 5 0.14
24 14 0.39
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (24 bp):
TTTAATGCTCCATTATGCATTTCA
Found at i:534354 original size:2 final size:2
Alignment explanation
Indices: 534347--534417 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
534337 AATGAATTGT
534347 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
534389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
534418 TGTATATGAT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:536921 original size:20 final size:19
Alignment explanation
Indices: 536879--536921 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
536869 CCTATATTGT
*
536879 AAACATAACTTAAAACCCT
1 AAACATAACTTAAAACCCA
*
536898 AAACACTAACTTAAAACTCA
1 AAACA-TAACTTAAAACCCA
536918 AAAC
1 AAAC
536922 CCAAATAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.56, C:0.26, G:0.00, T:0.19
Consensus pattern (19 bp):
AAACATAACTTAAAACCCA
Found at i:542430 original size:23 final size:23
Alignment explanation
Indices: 542404--542449 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
542394 AATTTTAAAG
542404 TAATATTATTTCAAATAAATAAT
1 TAATATTATTTCAAATAAATAAT
*
542427 TAATATTGTTTCAAATAAATAAT
1 TAATATTATTTCAAATAAATAAT
542450 ATGATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (23 bp):
TAATATTATTTCAAATAAATAAT
Found at i:543604 original size:21 final size:21
Alignment explanation
Indices: 543580--543651 Score: 85
Period size: 21 Copynumber: 3.4 Consensus size: 21
543570 ACTTCGTGCA
543580 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* * *
543601 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAAATT
543620 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGATTTATTCCAAATT
543643 CGTTGCGAT
1 CGTTGCGAT
543652 AGTCCAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 8 0.20
21 25 0.61
23 8 0.20
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:543659 original size:19 final size:19
Alignment explanation
Indices: 543593--543659 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
543583 TGCGATTTAT
543593 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* * *
543612 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
543635 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
543654 TCCAAA
1 TCCAAA
543660 ATCGCAACGA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 14 0.37
21 16 0.42
23 8 0.21
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:543759 original size:6 final size:6
Alignment explanation
Indices: 543748--543777 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
543738 GACACGTATT
543748 ACCACG ACCACG ACCACG ACCACG A-CACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
543778 GACGAGACGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.37, C:0.47, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:543782 original size:5 final size:5
Alignment explanation
Indices: 543769--543801 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
543759 GACCACGACC
*
543769 ACGAC ACGAG ACGAG ACGAG ACGAG ACGAG ACG
1 ACGAG ACGAG ACGAG ACGAG ACGAG ACGAG ACG
543802 GCGGCGGTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.39, C:0.24, G:0.36, T:0.00
Consensus pattern (5 bp):
ACGAG
Found at i:544288 original size:5 final size:5
Alignment explanation
Indices: 544278--544321 Score: 70
Period size: 5 Copynumber: 8.4 Consensus size: 5
544268 TCCGTCTGTC
544278 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TC
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TC
544322 TCGCGATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 28 0.74
6 10 0.26
ACGTcount: A:0.00, C:0.20, G:0.55, T:0.25
Consensus pattern (5 bp):
TCGGG
Found at i:544349 original size:21 final size:21
Alignment explanation
Indices: 544324--544369 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
544314 TCGTGGTCTC
*
544324 GCGATAGTCCAAGTTCGTGTT
1 GCGATAGTCCAAGTTCGCGTT
*
544345 GCGATAGTCGAAGTTCGCGTT
1 GCGATAGTCCAAGTTCGCGTT
544366 GCGA
1 GCGA
544370 ATCTGGAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.33, T:0.28
Consensus pattern (21 bp):
GCGATAGTCCAAGTTCGCGTT
Found at i:546651 original size:14 final size:13
Alignment explanation
Indices: 546613--546651 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
546603 ATTTTATTTT
*
546613 TATTTTAAATAT-
1 TATTTTAACTATA
546625 TATTTTAACTATA
1 TATTTTAACTATA
546638 T-TTTTAACTATA
1 TATTTTAACTATA
546650 TA
1 TA
546652 AAATATATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
12 23 0.96
13 1 0.04
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTTTAACTATA
Found at i:547876 original size:49 final size:53
Alignment explanation
Indices: 547813--547914 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 53
547803 GCTATTTTGA
*
547813 TCTTTTACATTTTTATTTATTTATTT-ATTTTACA-T-ATATATATATATATAT
1 TCTTTTACATTTTTATTT-TTTATTTCATTTAACATTGATATATATATATATAT
* *
547864 TCTTTTA-A-TTTTATTTTTTATTTCCTTTAACATTGTTATATATATATATAT
1 TCTTTTACATTTTTATTTTTTATTTCATTTAACATTGATATATATATATATAT
547915 ATATATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
48 7 0.16
49 14 0.31
50 2 0.04
51 22 0.49
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (53 bp):
TCTTTTACATTTTTATTTTTTATTTCATTTAACATTGATATATATATATATAT
Found at i:547907 original size:2 final size:2
Alignment explanation
Indices: 547900--547930 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
547890 TTAACATTGT
547900 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
547931 TGTTTTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:550652 original size:35 final size:35
Alignment explanation
Indices: 550590--550668 Score: 106
Period size: 35 Copynumber: 2.2 Consensus size: 35
550580 ATTTGCAGCA
**
550590 TCTTGTTTGAACTTTGTTTTTTTACTTTCTCATATT
1 TCTT-TTTGAACTTTGTTTTTGAACTTTCTCATATT
550626 TCTTTTTGTAAC-TTGTTTTTGAACTTTCTCATATT
1 TCTTTTTG-AACTTTGTTTTTGAACTTTCTCATATT
*
550661 TCATTTTG
1 TCTTTTTG
550669 CAAGGATATT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 32 0.82
36 7 0.18
ACGTcount: A:0.15, C:0.14, G:0.09, T:0.62
Consensus pattern (35 bp):
TCTTTTTGAACTTTGTTTTTGAACTTTCTCATATT
Found at i:551018 original size:20 final size:20
Alignment explanation
Indices: 550989--551027 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
550979 AAAGCTCATA
*
550989 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
551009 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
551028 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:558831 original size:13 final size:13
Alignment explanation
Indices: 558799--558824 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
558789 TAGCAGTGTT
558799 AAAAAAACAAAAA
1 AAAAAAACAAAAA
558812 AAAAAAACAAAAA
1 AAAAAAACAAAAA
558825 GGAAAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:559229 original size:20 final size:20
Alignment explanation
Indices: 559200--559238 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
559190 AAAGCTCATA
*
559200 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
559220 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
559239 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:561328 original size:99 final size:99
Alignment explanation
Indices: 561214--561410 Score: 279
Period size: 99 Copynumber: 2.0 Consensus size: 99
561204 TATTATTATA
* * * *
561214 TATACAATAAAGCTTGAGCT-GTCCCTCTAGAGCAATTGGTTAAACGCCTCAGCTTTATGGATAA
1 TATACAATAAAGCTTGAGCTAAT-CCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATAGATAA
* **
561278 GATTCAACTAGCCTGATAAATGTGATTATAATATC
65 GATTCAACTAGCCTGATAAAGGTGACAATAATATC
**
561313 TATACAATAAAGCTTGAGCTAATTTTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATAGATAAG
1 TATACAATAAAGCTTGAGCTAATCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATAGATAAG
* *
561378 ATTCAGCTAGCCTTATAAAGGTGACAATAATAT
66 ATTCAACTAGCCTGATAAAGGTGACAATAATAT
561411 TGAGCTGCCT
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
99 85 0.99
100 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (99 bp):
TATACAATAAAGCTTGAGCTAATCCTCTAAAGCAATTGGTTAAACGCCCCAGCTTTATAGATAAG
ATTCAACTAGCCTGATAAAGGTGACAATAATATC
Found at i:562559 original size:42 final size:42
Alignment explanation
Indices: 562513--562609 Score: 140
Period size: 42 Copynumber: 2.3 Consensus size: 42
562503 GAGTCACTCG
* *
562513 AAGAACATCTCACATGGCTTTCCCGTGAAGGGGAGTTATCCA
1 AAGAACATCTCACATGGATTTCCCGTGAAGGGGAGTCATCCA
* * *
562555 AAGAATATTTCACATGGATTTCCTGTGAAGGGGAGTCATCCA
1 AAGAACATCTCACATGGATTTCCCGTGAAGGGGAGTCATCCA
*
562597 AAGATCATCTCAC
1 AAGAACATCTCAC
562610 TTAGTTCAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (42 bp):
AAGAACATCTCACATGGATTTCCCGTGAAGGGGAGTCATCCA
Found at i:562657 original size:86 final size:86
Alignment explanation
Indices: 562565--562810 Score: 339
Period size: 86 Copynumber: 2.9 Consensus size: 86
562555 AAGAATATTT
* *
562565 CACATGGATTTCCTGTGAAGGGGAGTCATCCAAAGATCATCTCACTTAGTTCAGACCCGCTAAGG
1 CACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTAGTTCAGACCCGCTAAGG
* *
562630 GGAACCATCTGAGGAATATAC
66 GGAACCACCCGAGGAATATAC
* * * * * *
562651 CACATGGCTTTCCCGTGAGGGGGAGTCATCCAAAGATTATCTAACTTGGTTCAAACCTGCTAAGG
1 CACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTAGTTCAGACCCGCTAAGG
562716 GGAACCACCCGAGGAATATAC
66 GGAACCACCCGAGGAATATAC
* * * * * * *
562737 TATATGGCTTTCCCATAAAGGGGAGTCATCCAACGATCATCTCACTTTGTTCAGACCCGTTAAGG
1 CACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTAGTTCAGACCCGCTAAGG
562802 GGAACCACC
66 GGAACCACC
562811 TAAAGAATTA
Statistics
Matches: 138, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 138 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.24
Consensus pattern (86 bp):
CACATGGCTTTCCCGTGAAGGGGAGTCATCCAAAGATCATCTCACTTAGTTCAGACCCGCTAAGG
GGAACCACCCGAGGAATATAC
Found at i:563017 original size:85 final size:85
Alignment explanation
Indices: 562874--563278 Score: 494
Period size: 85 Copynumber: 4.8 Consensus size: 85
562864 GGAACTATTG
* * * *
562874 ACAGCATAGCTCAAGGCGAGAAAGGCTATTTGTCAACCAAGATCC-TCGAGTTTGATTACATTCA
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAGA-CCTTCGAGTTCGATTACATTCA
562938 GCTCAAAGGCATATCAAATTT
65 GCTCAAAGGCATATCAAATTT
* * * * *
562959 ACAGCATAGCTCAAGGCGAGAAGGGCTATCTATCAACCACGACCTTCGAGTTTGATTACATTTAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAG
* *
563024 CTTAAAGGTATATCAAATTT
66 CTCAAAGGCATATCAAATTT
* *
563044 ACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACCTAGACCTTCGAGTTCGATTACATTCAG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAG
*
563109 CTCAAAGGCATATTAAATTT
66 CTCAAAGGCATATCAAATTT
* * ** * * *
563129 ACAGAAAAACTCAAGGCGAGAAGGATTATCTGTCAACCAAGACCTTTGAGTTCGATTACACTCTG
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAG
563194 CTCAAAGGCATATCAAATTT
66 CTCAAAGGCATATCAAATTT
** * ** * * * *
563214 GTAGTATAACTCAAGGC-A-AAAAGCTATCTGTCAA-CAAAAACTGTCGAGTTCAATTCCATTCA
1 ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCT-TCGAGTTCGATTACATTCA
563276 GCT
65 GCT
563279 TGATGGTACA
Statistics
Matches: 278, Mismatches: 40, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
82 6 0.02
83 29 0.10
84 3 0.01
85 240 0.86
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (85 bp):
ACAGCATAACTCAAGGCGAGAAGGGCTATCTGTCAACCAAGACCTTCGAGTTCGATTACATTCAG
CTCAAAGGCATATCAAATTT
Found at i:565032 original size:30 final size:30
Alignment explanation
Indices: 564980--565045 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
564970 GTAATTATTG
* * *
564980 TTTAGTCATTTTAGTTTATGTTTATT-TCAT
1 TTTAGTCATTTAAATTTATGTTT-TTGCCAT
*
565010 TTTAGTCATTTAAATTTCTGTTTTTGCCAT
1 TTTAGTCATTTAAATTTATGTTTTTGCCAT
565040 TTTAGT
1 TTTAGT
565046 TTTAACCTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTAGTCATTTAAATTTATGTTTTTGCCAT
Found at i:565069 original size:28 final size:28
Alignment explanation
Indices: 564980--565070 Score: 69
Period size: 30 Copynumber: 3.1 Consensus size: 28
564970 GTAATTATTG
* * *
564980 TTTAGTCATTTTAGTTTATGTTTATTTCAT
1 TTTAGT-ATTTAAATTTCTGTTT-TTTCAT
*
565010 TTTAGTCATTTAAATTTCTGTTTTTGCCAT
1 TTTAGT-ATTTAAATTTCTGTTTTT-TCAT
*
565040 TTTAGT-TTTAACCTTT-TGTTTTTTCTAT
1 TTTAGTATTTAA-ATTTCTGTTTTTTC-AT
565068 TTT
1 TTT
565071 GATCTTTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
27 1 0.02
28 17 0.33
29 5 0.10
30 29 0.56
ACGTcount: A:0.18, C:0.10, G:0.09, T:0.64
Consensus pattern (28 bp):
TTTAGTATTTAAATTTCTGTTTTTTCAT
Found at i:565165 original size:2 final size:2
Alignment explanation
Indices: 565158--565193 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
565148 TTAACATTGT
565158 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
565194 CACTTTTTTA
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:565296 original size:26 final size:26
Alignment explanation
Indices: 565262--565323 Score: 124
Period size: 26 Copynumber: 2.4 Consensus size: 26
565252 TAACATTTTT
565262 TTTATTTTTCTCAATATATTTATTTA
1 TTTATTTTTCTCAATATATTTATTTA
565288 TTTATTTTTCTCAATATATTTATTTA
1 TTTATTTTTCTCAATATATTTATTTA
565314 TTTATTTTTC
1 TTTATTTTTC
565324 CCTCTCTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTATTTTTCTCAATATATTTATTTA
Found at i:566607 original size:18 final size:18
Alignment explanation
Indices: 566584--566622 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
566574 TAGTTGATAA
*
566584 ATTTTCTAAAAATTATTT
1 ATTTTCCAAAAATTATTT
566602 ATTTTCCAAAAATTATTT
1 ATTTTCCAAAAATTATTT
566620 ATT
1 ATT
566623 AAAACAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTTCCAAAAATTATTT
Found at i:566817 original size:34 final size:34
Alignment explanation
Indices: 566773--566839 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
566763 GACTAATATA
*
566773 TTATTGAAATAA-ATTATTATTAATTAT-TTATTAT
1 TTATTGAAATAAGAATATTA-T-ATTATATTATTAT
*
566807 TTATTTAAATAAGAATATTATATTATATTATTA
1 TTATTGAAATAAGAATATTATATTATATTATTA
566840 AAATTATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 18 0.62
35 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (34 bp):
TTATTGAAATAAGAATATTATATTATATTATTAT
Found at i:566856 original size:22 final size:23
Alignment explanation
Indices: 566831--566882 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
566821 ATATTATATT
566831 ATATTATTAAA-ATTATTAATAAA
1 ATATTATTAAATATT-TTAATAAA
*
566854 TATATT-TTAAATATTTTATTAAA
1 -ATATTATTAAATATTTTAATAAA
566877 ATATTA
1 ATATTA
566883 CTATACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.20
23 12 0.48
24 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTATTAAATATTTTAATAAA
Found at i:566864 original size:11 final size:12
Alignment explanation
Indices: 566767--566882 Score: 64
Period size: 11 Copynumber: 9.8 Consensus size: 12
566757 TATTAAGACT
566767 AATATATTATTGA
1 AATATATTATT-A
*
566780 AATAAATTATT-
1 AATATATTATTA
* *
566791 ATTA-ATTATTT
1 AATATATTATTA
*
566802 ATTAT-TTATTTA
1 AATATATTA-TTA
* *
566814 AATAAGAATATTA
1 AAT-ATATTATTA
*
566827 TATTATATTATTA
1 -AATATATTATTA
*
566840 AA-ATTATTAATA
1 AATA-TATTATTA
566852 AATATATT-TTA
1 AATATATTATTA
*
566863 AATATTTTATTA
1 AATATATTATTA
566875 AA-ATATTA
1 AATATATTA
566883 CTATACTATT
Statistics
Matches: 80, Mismatches: 14, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
10 6 0.08
11 25 0.31
12 23 0.29
13 22 0.28
14 4 0.05
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (12 bp):
AATATATTATTA
Found at i:566988 original size:24 final size:23
Alignment explanation
Indices: 566961--567015 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
566951 ATAATTTATT
566961 TAAAAATTATTTTAATA-TTATATA
1 TAAAAATTA-TTT-ATACTTATATA
566985 TAAAAATTATTTATACCTTATATA
1 TAAAAATTATTTATA-CTTATATA
567009 TAAAAAT
1 TAAAAAT
567016 ATAAGATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.10
23 3 0.10
24 23 0.79
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TAAAAATTATTTATACTTATATA
Found at i:567073 original size:249 final size:271
Alignment explanation
Indices: 566651--567172 Score: 865
Period size: 249 Copynumber: 2.0 Consensus size: 271
566641 AAATTTATTA
566651 TAAAAAATTAATATTATTAGTTTTAAAATACTAGAATAATTTATTTAATAATATTTATTTTAATA
1 TAAAAAATTAATATTATTAGTTTTAAAATACTAGAATAATTTATTTAATAATATTTATTTTAATA
566716 TTATTATGAAAATATTATTTATACCACTTTATATATAAAAATATTAAGACTAATATATTATTGAA
66 TTATTATGAAAATATTATTTATACCACTTTATATATAAAAATATTAAGACTAATATATTATTGAA
566781 ATAAATTATTATTAATTATTTATTATTTATTTAAATAAGAATATTATATTATATTATTAAAATTA
131 ATAAATTATTATTAATTATTTA-TATTTATTTAAATAAGAATATTATATTATATTATTAAAATTA
566846 TTAATAAATATATTTTAAATATTTTATTAAAATATTACTATACTA-T-TA-T-ATATTAAAT-CA
195 TTAATAAATATATTTTAAATATTTTATTAAAATATTACTATACTATTATATTAATATTAAATACA
566906 TAAGCTCCTCAC
260 TAAGCTCCTCAC
566918 TAAAAAATTAATATTATTAG-TTT-AAATACTAGAATAATTTATTTAA-AA-A-TTATTTTAATA
1 TAAAAAATTAATATTATTAGTTTTAAAATACTAGAATAATTTATTTAATAATATTTATTTTAATA
566978 TTATATAT-AAAA-ATTATTTATA-C-C-TTATATATAAAAATA-TAAGA-TAA-ATATTATTG-
66 TTAT-TATGAAAATATTATTTATACCACTTTATATATAAAAATATTAAGACTAATATATTATTGA
567034 AATAAATT-TTA-TAATTATTTA-A-TTATTTAAATAAGAATATTATATTATATTATTAAAATTA
130 AATAAATTATTATTAATTATTTATATTTATTTAAATAAGAATATTATATTATATTATTAAAATTA
567095 TTAATAAATATATTTTAAATATTTTATTAAAATATTACTATACTATTATATTAATATTAAATACA
195 TTAATAAATATATTTTAAATATTTTATTAAAATATTACTATACTATTATATTAATATTAAATACA
567160 TAAGCTCCTCAC
260 TAAGCTCCTCAC
567172 T
1 T
567173 TAGGATTTTC
Statistics
Matches: 249, Mismatches: 0, Indels: 25
0.91 0.00 0.09
Matches are distributed among these distances:
249 84 0.34
250 2 0.01
251 2 0.01
252 11 0.04
253 12 0.05
254 23 0.09
255 9 0.04
256 3 0.01
257 5 0.02
258 15 0.06
259 1 0.00
260 1 0.00
261 10 0.04
262 19 0.08
263 4 0.02
264 2 0.01
265 23 0.09
266 3 0.01
267 20 0.08
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (271 bp):
TAAAAAATTAATATTATTAGTTTTAAAATACTAGAATAATTTATTTAATAATATTTATTTTAATA
TTATTATGAAAATATTATTTATACCACTTTATATATAAAAATATTAAGACTAATATATTATTGAA
ATAAATTATTATTAATTATTTATATTTATTTAAATAAGAATATTATATTATATTATTAAAATTAT
TAATAAATATATTTTAAATATTTTATTAAAATATTACTATACTATTATATTAATATTAAATACAT
AAGCTCCTCAC
Found at i:567105 original size:22 final size:23
Alignment explanation
Indices: 567080--567131 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
567070 ATATTATATT
567080 ATATTATTAAA-ATTATTAATAAA
1 ATATTATTAAATATT-TTAATAAA
*
567103 TATATT-TTAAATATTTTATTAAA
1 -ATATTATTAAATATTTTAATAAA
567126 ATATTA
1 ATATTA
567132 CTATACTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.20
23 12 0.48
24 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTATTAAATATTTTAATAAA
Found at i:567113 original size:11 final size:12
Alignment explanation
Indices: 567079--567131 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
567069 AATATTATAT
567079 TATATTATTAAA
1 TATATTATTAAA
*
567091 -ATTATTAATAAA
1 TA-TATTATTAAA
567103 TATATT-TTAAA
1 TATATTATTAAA
*
567114 TATTTTATTAAA
1 TATATTATTAAA
567126 -ATATTA
1 TATATTA
567132 CTATACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
11 15 0.44
12 18 0.53
13 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (12 bp):
TATATTATTAAA
Found at i:572265 original size:116 final size:115
Alignment explanation
Indices: 572061--572450 Score: 586
Period size: 116 Copynumber: 3.4 Consensus size: 115
572051 ATTGAACTCG
* ** *
572061 AGATTGATTTGCTTCATTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGATTTAATCATCATG
1 AGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATG
*
572126 CTCGTAAGGCTTACTGATGAATTTGCTTCACTACTCTTTGGTGAAGGCTTA
66 CTCGGAAGGCTTACTGATGAATTTGCTTCACTACTCTTT-GTGAAGGCTTA
* * * *
572177 AGATTGATTTGCTTCACTACTATTCGGTGAAGGTTTAAGATGGCCTGGAGGACTTAATCATCATG
1 AGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATG
*
572242 CTCGGAAGGCTTACTGATGAATTTGCTTCACTACTCTTCCGTGAAGGCTTA
66 CTCGGAAGGCTTACTGATGAATTTGCTTCACTACTCTT-TGTGAAGGCTTA
* *
572293 TGA-TGAATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGCCCGGAGGACTTAATCATCAT
1 AGATTG-ATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCAT
* *
572357 GCTCGGAAGGCTTACTAATGAATTTTCTTCACTACTCTTCTGTGAAGGCTTA
65 GCTCGGAAGGCTTACTGATGAATTTGCTTCACTACTCTT-TGTGAAGGCTTA
* *
572409 AGATGGA-TTGCTTCACTCCTCTTCAGTGAAGGCTTAAGATGG
1 AGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGG
572451 TTTGCTTCAT
Statistics
Matches: 250, Mismatches: 21, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
115 35 0.14
116 214 0.86
117 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (115 bp):
AGATTGATTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATGGCCCGGAGGACTTAATCATCATG
CTCGGAAGGCTTACTGATGAATTTGCTTCACTACTCTTTGTGAAGGCTTA
Found at i:572431 original size:36 final size:36
Alignment explanation
Indices: 572148--572770 Score: 372
Period size: 36 Copynumber: 16.9 Consensus size: 36
572138 ACTGATGAAT
*
572148 TTGCTTCACTACTCTT-TGGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGGA
* * * *
572184 TTTGCTTCACTACTATTCGGTGAAGGTTTAAGATGGC
1 -TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
* **** * * * *
572221 CTGGAGGACTTAATCATCATGCTCGGAAGGCTTACTGATGAA
1 TTGCTTCAC-TACTCTTC-TG-T--GAAGGCTTA-AGATGGA
* * *
572263 TTTGCTTCACTACTCTTCCGTGAAGGCTTATGATGAA
1 -TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
* * *
572300 TTTGCTTCACTACTCTTCAGTGAAGGCTTAAGATTGC
1 -TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
** **** * * *
572337 CCGGAGGACTTAATCATCATGCTCGGAAGGCTTACTA-ATGAA
1 TTGCTTCAC-TACTCTTC-TG-T--GAAGGCTTA--AGATGGA
*
572379 TTTTCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
1 -TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
* * *
572416 TTGCTTCACTCCTCTTCAGTGAAGGCTTAAGATGGT
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
* * * * *
572452 TTGCTTCATTACTCTCCGGTGAAGGCTTCAGATGGT
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
*
572488 TTGCTTCACTACTC-TCTGGTGAAGGCTTAGGAT-GA
1 TTGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGGA
* *
572523 TTTGCTGT-ACTACTC-TCCGTTGAAGGCTTTAA-ATGGT
1 -TTGCT-TCACTACTCTTCTG-TGAAGGC-TTAAGATGGA
* * * *
572560 TTTCTTCACTATTC-TCTGGTGAAGGCTTAGGATGGC
1 TTGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGGA
* *
572596 TTGCTTCACTACT-TTCCGATGAAGGCTTAGGAT-GA
1 TTGCTTCACTACTCTTCTG-TGAAGGCTTAAGATGGA
* * ** * *
572631 TTTGCTTTACTACTCTCCAATGAAGGCTTCAGATGGT
1 -TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
* * * *
572668 TTGCTTCACTATTCTCCGGTGAAGGCTTAGGATGG-
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
* *
572703 -TGCTTCACTCCTCTT-TGGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCT-GTGAAGGCTTAAGATGGA
*
572738 TTGCTTCACTACTCTTCAGTGAAGGCTTAAGAT
1 TTGCTTCACTACTCTTCTGTGAAGGCTTAAGAT
572771 TGACTTGCCC
Statistics
Matches: 450, Mismatches: 101, Indels: 71
0.72 0.16 0.11
Matches are distributed among these distances:
34 27 0.06
35 9 0.02
36 252 0.56
37 93 0.21
38 20 0.04
39 2 0.00
40 2 0.00
41 20 0.04
42 18 0.04
43 7 0.02
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (36 bp):
TTGCTTCACTACTCTTCTGTGAAGGCTTAAGATGGA
Found at i:572547 original size:108 final size:106
Alignment explanation
Indices: 572383--572770 Score: 482
Period size: 108 Copynumber: 3.6 Consensus size: 106
572373 AATGAATTTT
*
572383 CTTCACTACTCTTCT-GTGAAGGCTTAAGATGGATTGCTTCACTCCTCTTCAGTGAAGGCTTAAG
1 CTTCACTACTC-TCTGGTGAAGGCTTAAGAT-GATTGCTTCACTACTCTTCAGTGAAGGCTTAAG
* *
572447 ATGGTTTGCTTCATTACTCTCCGGTGAAGGCTTCA-GATGGTTTG
64 ATGGTTTGCTTCACTATTCTCCGGTGAAGGCTT-AGGATGG-TTG
* *
572491 CTTCACTACTCTCTGGTGAAGGCTTAGGATGATTTGCTGT-ACTACTC-TCCGTTGAAGGCTTTA
1 CTTCACTACTCTCTGGTGAAGGCTTAAGATGA-TTGCT-TCACTACTCTTCAG-TGAAGGC-TTA
* *
572554 A-ATGGTTTTCTTCACTATTCTCTGGTGAAGGCTTAGGATGGCTTG
62 AGATGGTTTGCTTCACTATTCTCCGGTGAAGGCTTAGGATGG-TTG
* * * * * * * *
572599 CTTCACTACTTTCCGATGAAGGCTTAGGATGATTTGCTTTACTACTCTCCAATGAAGGCTTCAGA
1 CTTCACTACTCTCTGGTGAAGGCTTAAGATGA-TTGCTTCACTACTCTTCAGTGAAGGCTTAAGA
572664 TGGTTTGCTTCACTATTCTCCGGTGAAGGCTTAGGATGG-TG
65 TGGTTTGCTTCACTATTCTCCGGTGAAGGCTTAGGATGGTTG
* *
572705 CTTCACTCCTCTTTGGTGAAGGCTTAAGATTGATTGCTTCACTACTCTTCAGTGAAGGCTTAAGA
1 CTTCACTACTCTCTGGTGAAGGCTTAAGA-TGATTGCTTCACTACTCTTCAGTGAAGGCTTAAGA
572770 T
65 T
572771 TGACTTGCCC
Statistics
Matches: 243, Mismatches: 27, Indels: 22
0.83 0.09 0.08
Matches are distributed among these distances:
106 54 0.22
107 16 0.07
108 167 0.69
109 6 0.02
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (106 bp):
CTTCACTACTCTCTGGTGAAGGCTTAAGATGATTGCTTCACTACTCTTCAGTGAAGGCTTAAGAT
GGTTTGCTTCACTATTCTCCGGTGAAGGCTTAGGATGGTTG
Found at i:573627 original size:16 final size:18
Alignment explanation
Indices: 573600--573634 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
573590 ACCTCCACTA
573600 TCACTGCTTCAT-CATTT
1 TCACTGCTTCATACATTT
573617 TCACT-CTTCATACATTT
1 TCACTGCTTCATACATTT
573634 T
1 T
573635 TATCCCATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.20, C:0.29, G:0.03, T:0.49
Consensus pattern (18 bp):
TCACTGCTTCATACATTT
Found at i:580999 original size:21 final size:21
Alignment explanation
Indices: 580951--580992 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
580941 TTTATGATCC
580951 CCTACAAAACAACACATGAAT
1 CCTACAAAACAACACATGAAT
*
580972 CCGACAAAACAACACATGAAT
1 CCTACAAAACAACACATGAAT
580993 TTTACAACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.29, G:0.07, T:0.12
Consensus pattern (21 bp):
CCTACAAAACAACACATGAAT
Found at i:587231 original size:2 final size:2
Alignment explanation
Indices: 587213--587256 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
587203 GAACATGTGA
* *
587213 AT AT CT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
587255 AT
1 AT
587257 GATAAGAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:587681 original size:23 final size:23
Alignment explanation
Indices: 587647--587715 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
587637 CAACCTTATA
587647 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
587670 TTGCACTACGGTGCAATTCTATG
1 TGGCACTTCGGTGCATTTCTACG
*
587693 TGGCACTTCGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
587716 AGCTGCGGTG
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.17, C:0.23, G:0.25, T:0.35
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:588935 original size:18 final size:18
Alignment explanation
Indices: 588912--588950 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
588902 TAGTTGGTAA
*
588912 ATTTTCTAAAAATTATTT
1 ATTTTCCAAAAATTATTT
*
588930 ATTTTCCAAAATTTATTT
1 ATTTTCCAAAAATTATTT
588948 ATT
1 ATT
588951 AACAGTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTCCAAAAATTATTT
Found at i:589182 original size:23 final size:23
Alignment explanation
Indices: 589155--589200 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
589145 TATTATACCA
589155 TTAAA-ATTATTAATAAACATATT
1 TTAAATATTATTAATAAA-ATATT
*
589178 TTAAATATTATTATTAAAATATT
1 TTAAATATTATTAATAAAATATT
589201 ACTAGACTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAATATTATTAATAAAATATT
Found at i:589382 original size:23 final size:23
Alignment explanation
Indices: 589334--589384 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
589324 TTAAAATAAG
*
589334 AATATAATATAATATGTTATTAT
1 AATATAATATAATATATTATTAT
* *
589357 AATATAAT-TGAATATATTGTTTT
1 AATATAATAT-AATATATTATTAT
589380 AATAT
1 AATAT
589385 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 1 0.04
23 23 0.96
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (23 bp):
AATATAATATAATATATTATTAT
Found at i:590078 original size:15 final size:15
Alignment explanation
Indices: 590060--590089 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
590050 AAAACCATGT
590060 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
590075 TAGATAAAAAGGTAA
1 TAGATAAAAAGGTAA
590090 GAAATAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (15 bp):
TAGATAAAAAGGTAA
Found at i:590096 original size:15 final size:15
Alignment explanation
Indices: 590063--590097 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
590053 ACCATGTTAG
* *
590063 ATAAAAAGGTAATAG
1 ATAAAAAGGTAAGAA
590078 ATAAAAAGGTAAGAA
1 ATAAAAAGGTAAGAA
590093 ATAAA
1 ATAAA
590098 TAAATTAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.17, T:0.17
Consensus pattern (15 bp):
ATAAAAAGGTAAGAA
Found at i:590214 original size:21 final size:21
Alignment explanation
Indices: 590188--590239 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
590178 AAATAAATAT
*
590188 AAAAAATAAAGAAA-AAGAAGA
1 AAAAAATAAAGAAATAA-AACA
*
590209 AAAAAATATAGAAATAAAACA
1 AAAAAATAAAGAAATAAAACA
*
590230 AATAAATAAA
1 AAAAAATAAA
590240 ATAATAATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 24 0.92
22 2 0.08
ACGTcount: A:0.79, C:0.02, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAGAAATAAAACA
Found at i:590269 original size:47 final size:51
Alignment explanation
Indices: 590178--590278 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 51
590168 ATAGTAAGTA
590178 AAATAAATATAAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAATAA-AAC
1 AAATAAATATAAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAA-AATAAC
* * *
590229 AAATAAATA-AAATAATAATA-AAAAAGTA-AAAAGAA-A-AGAAAAATAAC
1 AAATAAATATAAAAAATAA-AGAAAAAGAAGAAAAAAATATAGAAAAATAAC
590276 AAA
1 AAA
590279 ACAATTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
46 2 0.04
47 11 0.24
48 1 0.02
49 6 0.13
50 15 0.33
51 10 0.22
ACGTcount: A:0.77, C:0.02, G:0.07, T:0.14
Consensus pattern (51 bp):
AAATAAATATAAAAAATAAAGAAAAAGAAGAAAAAAATATAGAAAAATAAC
Found at i:590621 original size:34 final size:34
Alignment explanation
Indices: 590578--590647 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
590568 TGAATCCTAG
590578 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
* *
590612 TAAAATTCTATCCTATTTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
590646 TA
1 TA
590648 GTAGGACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (34 bp):
TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
Found at i:591285 original size:106 final size:106
Alignment explanation
Indices: 591115--591310 Score: 331
Period size: 106 Copynumber: 1.8 Consensus size: 106
591105 TTCAAGGCCG
591115 ATATCATTCACTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGTGTTTGTTGACAACCAGCGG
1 ATATCATTCACTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGTGTTTGTTGACAACCAGCGG
591180 CCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCA
66 CCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCA
* * * * *
591221 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGGAAGTTGTTTGTTGACAGCCAGCG
1 ATATCATTCACTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAG-TGTTTGTTGACAACCAGCG
591285 GCCCCTTCGTTGTGAAGTTGAACTTG
65 GCCCCTTCGTTGTGAAGTTGAACTTG
591311 TGCTGTCTTA
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
105 7 0.08
106 77 0.92
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.33
Consensus pattern (106 bp):
ATATCATTCACTGTGAAGTTGAAATTGACTCTGAAACTTGGAAAGTGTTTGTTGACAACCAGCGG
CCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCA
Found at i:591435 original size:65 final size:64
Alignment explanation
Indices: 591225--591511 Score: 418
Period size: 64 Copynumber: 4.5 Consensus size: 64
591215 AGTCCAATAT
* * * * * *
591225 CCTTCGCTGTGAAGTTGAAATTG-G--CTCTGAAATTGGGAAGTTGTTTGTTGACAGCCAGCGGC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAA-AT-TTTGTTGACAACCAGCGGC
591287 C
64 C
* * *
591288 CCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAACTGGGAAATTTTGTTGACAACCAGCGGAC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
* * *
591352 CCTTCGTTGTGAAGTTGAACTTATGTTGTCTGATACTGGGAAATTTTTGTCGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAA-TTTTGTTGACAACCAGCGGCC
591417 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
591481 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1 CCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
591512 TGAGTGGCAC
Statistics
Matches: 203, Mismatches: 17, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
63 21 0.10
64 109 0.54
65 61 0.30
66 12 0.06
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (64 bp):
CCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAACTGGGAAATTTTGTTGACAACCAGCGGCC
Found at i:591453 original size:129 final size:130
Alignment explanation
Indices: 591258--591511 Score: 438
Period size: 129 Copynumber: 2.0 Consensus size: 130
591248 GCTCTGAAAT
* * * *
591258 TGGGAAGTTGTTTGTTGACAGCCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTTAAA
1 TGGGAAATTGTTTGTCGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAA
591323 CTGGGAAATTTTGTTGACAACCAGCGGACCCTTCGTTGTGAAGTTGAACTTATGTTGTCTGATAC
66 CTGGGAAATTTTGTTGACAACCAGCGGACCCTTCGTTGTGAAGTTGAACTTATGTTGTCTGATAC
*
591388 TGGGAAATT-TTTGTCGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTGAAA
1 TGGGAAATTGTTTGTCGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAA
* *
591452 CTGGGAAATTTTGTTGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 CTGGGAAATTTTGTTGACAACCAGCGGACCCTTCGTTGTGAAGTTGAACTTATGTTGTCT
591512 TGAGTGGCAC
Statistics
Matches: 117, Mismatches: 7, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
129 109 0.93
130 8 0.07
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (130 bp):
TGGGAAATTGTTTGTCGACAACCAGCGGCCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTGAAA
CTGGGAAATTTTGTTGACAACCAGCGGACCCTTCGTTGTGAAGTTGAACTTATGTTGTCTGATAC
Found at i:591793 original size:36 final size:36
Alignment explanation
Indices: 591756--591879 Score: 185
Period size: 36 Copynumber: 3.4 Consensus size: 36
591746 AATTGTGTTG
* * * *
591756 TTTCAAGAGAAATTGTCTCAAGGGAGATAAAATTTG
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
* *
591792 TTTGAAGAGAAACTGTCTCAAGAGAGACAAAACTTA
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
591828 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
1 TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
*
591864 TTTCAAGGGAAATTGT
1 TTTCAAGAGAAATTGT
591880 TTTCTTATGT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 79 1.00
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (36 bp):
TTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTTA
Found at i:591834 original size:21 final size:21
Alignment explanation
Indices: 591809--591870 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
591799 AGAAACTGTC
591809 TCAAGAGAGACAAAACTTATT
1 TCAAGAGAGACAAAACTTATT
* *
591830 TC-A-AGAG---AAA-TTGTC
1 TCAAGAGAGACAAAACTTATT
591845 TCAAGAGAGACAAAACTTATT
1 TCAAGAGAGACAAAACTTATT
591866 TCAAG
1 TCAAG
591871 GGAAATTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 12
0.66 0.09 0.26
Matches are distributed among these distances:
15 5 0.16
16 4 0.13
17 4 0.13
19 4 0.13
20 4 0.13
21 10 0.32
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (21 bp):
TCAAGAGAGACAAAACTTATT
Found at i:591941 original size:37 final size:37
Alignment explanation
Indices: 591892--592048 Score: 127
Period size: 37 Copynumber: 4.5 Consensus size: 37
591882 TCTTATGTTA
* *
591892 GAAACCTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGG
1 GAAA-CTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
* **
591930 GAAACTGTCTCAAGAGAGACGAAA-TTCATTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
**** * *
591966 GAAA-TGT-T------TTTTAATATTTATGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAATTT-TGTTTCAAGG
591996 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
1 GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
592033 GAAAC-GTCTCAAGAGA
1 GAAACTGTCTCAAGAGA
592049 AGCAAACTTG
Statistics
Matches: 89, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
28 2 0.02
29 2 0.02
30 11 0.12
31 3 0.03
32 1 0.01
34 1 0.01
35 3 0.03
36 25 0.28
37 31 0.35
38 10 0.11
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (37 bp):
GAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGG
Found at i:591961 original size:94 final size:98
Alignment explanation
Indices: 591799--592048 Score: 300
Period size: 94 Copynumber: 2.6 Consensus size: 98
591789 TTGTTTGAAG
* * * *
591799 AGAAACTGTCTCAAGAGAGACAAAA-CTTATTTCAAGAGAAATTGTCTCAAGAGAGACAAAACTT
1 AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
591863 ATTTCAAGGGAAA-TTGTTT-T-CTTATG-TT-
66 ATTTCAAGGGAAAGTTGTTTATACTTATGTTTA
* * *
591891 AGAAACCTGTCTCAAGGGAGGCAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAA-T
1 AGAAA-CTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACT
* *
591955 TCATTTCAAGGGAAATGTTTTTTAATATTTATGTTTCAA
65 T-ATTTCAAGGGAAA-GTTGTTT-ATACTTATGTTT--A
591994 GAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAAC-GTCTCAAGAGA
1 -AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGA
592049 AGCAAACTTG
Statistics
Matches: 134, Mismatches: 11, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
92 5 0.04
93 20 0.15
94 44 0.33
96 5 0.04
98 1 0.01
99 5 0.04
100 2 0.01
102 11 0.08
103 36 0.27
104 5 0.04
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (98 bp):
AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTT
ATTTCAAGGGAAAGTTGTTTATACTTATGTTTA
Found at i:593003 original size:22 final size:22
Alignment explanation
Indices: 592978--593020 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
592968 CATTTTTGTT
*
592978 CATTTGATGCTCAAAGGTTTGG
1 CATTGGATGCTCAAAGGTTTGG
593000 CATTGGATGCTCAAAGGTTTG
1 CATTGGATGCTCAAAGGTTTG
593021 ATGGGGTGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (22 bp):
CATTGGATGCTCAAAGGTTTGG
Found at i:593678 original size:23 final size:22
Alignment explanation
Indices: 593651--593724 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
593641 TTTTTGTCCC
593651 TTTTTCTTTTTGATTTTTGCTCT
1 TTTTTCTTTTTG-TTTTTGCTCT
* * *
593674 TTTTTCCTTTTGTTCTTGTTTCT
1 TTTTTCTTTTTGTTTTTG-CTCT
*
593697 CTTTTTCTTTGTTTTTTTTTGCT-T
1 -TTTTTC-TT-TTTGTTTTTGCTCT
593721 TTTT
1 TTTT
593725 GCTTCTTTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
22 5 0.12
23 18 0.45
24 7 0.17
25 2 0.05
26 8 0.20
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTCTTTTTGTTTTTGCTCT
Found at i:593683 original size:8 final size:7
Alignment explanation
Indices: 593671--593740 Score: 61
Period size: 8 Copynumber: 9.1 Consensus size: 7
593661 TGATTTTTGC
593671 TCTTTTT
1 TCTTTTT
593678 TCCTTTTGT
1 T-CTTTT-T
*
593687 TCTTGTT
1 TCTTTTT
593694 TCTCTTTT
1 TCT-TTTT
593702 TCTTTGTT
1 TCTTT-TT
593710 T-TTTTT
1 TCTTTTT
593716 TGCTTTTT
1 T-CTTTTT
593724 TGCTTCTTT
1 T-CTT-TTT
593733 TCTTTTT
1 TCTTTTT
593740 T
1 T
593741 GTTCTTGATT
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
6 3 0.06
7 14 0.26
8 31 0.57
9 6 0.11
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.77
Consensus pattern (7 bp):
TCTTTTT
Found at i:593684 original size:16 final size:17
Alignment explanation
Indices: 593665--593719 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
593655 TCTTTTTGAT
*
593665 TTTTGCTCTTTTTTC-C
1 TTTTGCTCTTGTTTCTC
*
593681 TTTTGTTCTTGTTTCTC
1 TTTTGCTCTTGTTTCTC
* *
593698 TTTTTCT-TTGTTT-TT
1 TTTTGCTCTTGTTTCTC
593713 TTTTGCT
1 TTTTGCT
593720 TTTTTGCTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
15 7 0.22
16 19 0.59
17 6 0.19
ACGTcount: A:0.00, C:0.16, G:0.09, T:0.75
Consensus pattern (17 bp):
TTTTGCTCTTGTTTCTC
Found at i:593739 original size:16 final size:16
Alignment explanation
Indices: 593696--593746 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 16
593686 TTCTTGTTTC
*
593696 TCTTTTTCTTTGTTT-T
1 TCTTTTGCTTT-TTTGT
593712 T-TTTTGCTTTTTTGCT
1 TCTTTTGCTTTTTTG-T
593728 TCTTTT-CTTTTTTGT
1 TCTTTTGCTTTTTTGT
593743 TCTT
1 TCTT
593747 GATTGGATCT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.10
15 13 0.42
16 11 0.35
17 4 0.13
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (16 bp):
TCTTTTGCTTTTTTGT
Found at i:596607 original size:34 final size:34
Alignment explanation
Indices: 596564--596633 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
596554 TGAATCCTAG
596564 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
* *
596598 TAAAATTCTATCCTATTTTTAGGAGTTTGAATCC
1 TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
596632 TA
1 TA
596634 GTAGGACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (34 bp):
TAAAATTCTATCATATCTTTAGGAGTTTGAATCC
Found at i:597936 original size:16 final size:16
Alignment explanation
Indices: 597906--597936 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
597896 TAATATTGAA
*
597906 ACTTGAACTCGAAAAT
1 ACTTGAACTCAAAAAT
597922 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
597937 AAATTTAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.23
Consensus pattern (16 bp):
ACTTGAACTCAAAAAT
Found at i:600302 original size:27 final size:29
Alignment explanation
Indices: 600246--600329 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
600236 ATTTCTGATT
600246 TTTTATTTCTATATAATTATATATATGAAA
1 TTTTATTT-TATATAATTATATATATGAAA
*
600276 CTTTTATTTTAT-TTATTATATA-A-GAAA
1 -TTTTATTTTATATAATTATATATATGAAA
* *
600303 TTTTGATTTTAATAAAATTATACATAT
1 TTTT-ATTTT-ATATAATTATATATAT
600330 TAAAGTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
26 4 0.09
27 9 0.20
28 3 0.07
29 16 0.36
30 4 0.09
31 8 0.18
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
TTTTATTTTATATAATTATATATATGAAA
Found at i:606939 original size:14 final size:14
Alignment explanation
Indices: 606922--606964 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
606912 AAAATAAAAT
606922 TAAAAATATAATAA
1 TAAAAATATAATAA
606936 TAAAAA-ATAATAAA
1 TAAAAATATAAT-AA
606950 TAAAAATA-AATAA
1 TAAAAATATAATAA
606963 TA
1 TA
606965 TTAATATTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 17 0.63
15 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAAATATAATAA
Found at i:606945 original size:13 final size:13
Alignment explanation
Indices: 606912--606964 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
606902 TGGAAAATCG
606912 AAAATAA-AATTAA
1 AAAATAATAA-TAA
606925 AAATATAATAATAA
1 AAA-ATAATAATAA
606939 AAAATAATAA-ATA
1 AAAATAATAATA-A
606952 AAAATAAATAATA
1 AAAAT-AATAATA
606965 TTAATATTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
12 1 0.03
13 16 0.46
14 15 0.43
15 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (13 bp):
AAAATAATAATAA
Found at i:606970 original size:13 final size:11
Alignment explanation
Indices: 606925--606962 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
606915 ATAAAATTAA
606925 AAATATAATAAT
1 AAATA-AATAAT
606937 AAA-AAATAAT
1 AAATAAATAAT
606947 AAATAAA-AAT
1 AAATAAATAAT
606957 AAATAA
1 AAATAA
606963 TATTAATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 18 0.72
11 4 0.16
12 3 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAATAAATAAT
Found at i:607032 original size:16 final size:17
Alignment explanation
Indices: 606989--607026 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
606979 ATATATAATA
606989 AAAAATAATATGTTTTC
1 AAAAATAATATGTTTTC
607006 AAAAATAATATGTTTTC
1 AAAAATAATATGTTTTC
607023 AAAA
1 AAAA
607027 TTATATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
AAAAATAATATGTTTTC
Found at i:607037 original size:38 final size:38
Alignment explanation
Indices: 606996--607177 Score: 198
Period size: 38 Copynumber: 4.8 Consensus size: 38
606986 ATAAAAAATA
* * *
606996 ATATGTTTTCAAAAATAATATGTTTTCAAAATTATATAAT
1 ATATGTTTTCAAAAATAAT-T-TTTTAAAAACTATATATT
*
607036 ATATGTTTTCAAAAACACA-TTTTTAAAAAC---ATATT
1 ATATGTTTTCAAAAATA-ATTTTTTAAAAACTATATATT
* *
607071 ATATATTTTCAAAAATCGATTTTTTAAAAACTATATATT
1 ATATGTTTTCAAAAAT-AATTTTTTAAAAACTATATATT
* *
607110 ATATGCTTTCAAAAA-ACATTTTCTAAAAACTATATATT
1 ATATGTTTTCAAAAATA-ATTTTTTAAAAACTATATATT
607148 ATATGTTTTCAAAAAT-A-TTTTTAAAAACTA
1 ATATGTTTTCAAAAATAATTTTTTAAAAACTA
607178 CATTATATTA
Statistics
Matches: 121, Mismatches: 13, Indels: 20
0.79 0.08 0.13
Matches are distributed among these distances:
35 19 0.16
36 23 0.19
37 1 0.01
38 42 0.35
39 19 0.16
40 16 0.13
41 1 0.01
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (38 bp):
ATATGTTTTCAAAAATAATTTTTTAAAAACTATATATT
Found at i:607113 original size:74 final size:73
Alignment explanation
Indices: 606996--607177 Score: 226
Period size: 74 Copynumber: 2.4 Consensus size: 73
606986 ATAAAAAATA
* * *
606996 ATATGTTTTCAAAAATAATATGTTTTCAAAATTATATAATATATGTTTTCAAAAACACATTTT-T
1 ATATGTTTTCAAAAAT-AT-T-TTTTAAAAACTATATAATATATGCTTTCAAAAA-ACATTTTCT
607060 AAAAAC-ATATT
62 AAAAACTATATT
* *
607071 ATATATTTTCAAAAATCGATTTTTTAAAAACTATATATTATATGCTTTCAAAAAACATTTTCTAA
1 ATATGTTTTCAAAAAT--ATTTTTTAAAAACTATATAATATATGCTTTCAAAAAACATTTTCTAA
607136 AAACTATATATT
64 AAAC--TATATT
607148 ATATGTTTTCAAAAATA-TTTTTAAAAACTA
1 ATATGTTTTCAAAAATATTTTTTAAAAACTA
607178 CATTATATTA
Statistics
Matches: 95, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
73 7 0.07
74 49 0.52
75 17 0.18
76 2 0.02
77 20 0.21
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (73 bp):
ATATGTTTTCAAAAATATTTTTTAAAAACTATATAATATATGCTTTCAAAAAACATTTTCTAAAA
ACTATATT
Found at i:608435 original size:96 final size:96
Alignment explanation
Indices: 608271--608463 Score: 352
Period size: 96 Copynumber: 2.0 Consensus size: 96
608261 TGATTTAAAC
*
608271 AATGGTTTTCAGTGAACTGGAACCCATTATCTCGAGTATGGTGCATAAGCCTTTATCGGCTTCCA
1 AATGGTTTTCAGTGAACTGGAACCCATTATCTCGAGTATAGTGCATAAGCCTTTATCGGCTTCCA
608336 AACACCTGTACCTTTCGAAAAACCTTTGTAT
66 AACACCTGTACCTTTCGAAAAACCTTTGTAT
608367 AATGGCTTTT-AGTGAACTGGAACCCATTATCTCGAGTATAGTGCATAAGCCTTTATCGGCTTCC
1 AATGG-TTTTCAGTGAACTGGAACCCATTATCTCGAGTATAGTGCATAAGCCTTTATCGGCTTCC
*
608431 AAACACCTGTACCTTTCGGAAAACCTTTGTAT
65 AAACACCTGTACCTTTCGAAAAACCTTTGTAT
608463 A
1 A
608464 GTAATACGCA
Statistics
Matches: 94, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
96 90 0.96
97 4 0.04
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (96 bp):
AATGGTTTTCAGTGAACTGGAACCCATTATCTCGAGTATAGTGCATAAGCCTTTATCGGCTTCCA
AACACCTGTACCTTTCGAAAAACCTTTGTAT
Found at i:619486 original size:15 final size:15
Alignment explanation
Indices: 619466--619516 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
619456 TAGATTGTAA
619466 AAATAAATAAATATT
1 AAATAAATAAATATT
*
619481 AAATAAATAAA-AGAT
1 AAATAAATAAATA-TT
* *
619496 AATTAAAAAAATATT
1 AAATAAATAAATATT
619511 AAATAA
1 AAATAA
619517 GAAATTATTA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.93
16 1 0.03
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (15 bp):
AAATAAATAAATATT
Found at i:623146 original size:55 final size:55
Alignment explanation
Indices: 622990--623250 Score: 328
Period size: 55 Copynumber: 4.7 Consensus size: 55
622980 TAAATGATAA
* *
622990 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGG
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGG
* * * * **
623045 GTTTGCTCCCTCTTTCTTTCAG-GAAGTAT-AGAACTCGAATAATCTTCTGTAATCGG
1 GTCTGCTCCCT-ATTCCTTCAGAG-AGTATAAG-ACTCGAACAATCTTCAATAATCGG
* * * * *
623101 GTCTGCTCCCTACTGCTTCAGAGAGTATGAGACTCAAACAATCTTCAATAATCGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGG
* * * *
623156 GTCTGCTCCCTATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACAATCGT
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGG
623211 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
623251 TATTCTCTTA
Statistics
Matches: 176, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
55 130 0.74
56 46 0.26
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (55 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAATCGG
Found at i:623172 original size:111 final size:110
Alignment explanation
Indices: 622990--623250 Score: 355
Period size: 111 Copynumber: 2.4 Consensus size: 110
622980 TAAATGATAA
* *
622990 GTCTGCTCCCTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGGGTTTGCTCCC
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCTGCTCCC
* * ***
623055 TCTTTCTTTCAG-GAAGTAT-AGAACTCGAATAATCTTCTGTAATCGG
66 TATTTCTTT-AGAG-AGTATAAG-ACTCGAACAATCTTCAACAATCGG
* * * * * *
623101 GTCTGCTCCCTACTGCTTCAGAGAGTATGAGACTCAAACAATCTTCAATAATCGTGTCTGCTCCC
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCTGCTCCC
*
623166 TATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACAATCGT
66 TATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACAATCGG
623211 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
1 GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACA
623251 TATTCTCTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
110 62 0.48
111 68 0.52
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.31
Consensus pattern (110 bp):
GTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCTGCTCCC
TATTTCTTTAGAGAGTATAAGACTCGAACAATCTTCAACAATCGG
Found at i:623327 original size:54 final size:54
Alignment explanation
Indices: 623242--623420 Score: 315
Period size: 54 Copynumber: 3.3 Consensus size: 54
623232 AGAGTATAAG
* *
623242 ACTCGAACATATTC-TCTTACAGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
623295 ACTCGAACATCTTCTTCTTACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
*
623349 ACTCGAACATCTTCTTCTTATAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
1 ACTCGAACATCTTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
623403 ACTCGAACATCTTCTTCT
1 ACTCGAACATCTTCTTCT
623421 GCTTTACTAC
Statistics
Matches: 120, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 13 0.11
54 107 0.89
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.36
Consensus pattern (54 bp):
ACTCGAACATCTTCTTCTTACAGGTTCGCTCCCTCTTTCTCTAGGGAGTATGGA
Found at i:623493 original size:37 final size:37
Alignment explanation
Indices: 623420--623499 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 37
623410 CATCTTCTTC
* * * *
623420 TGCTTTACTACTTTCTTGTGAAGACTTCTAGATGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
*
623457 TGCTTCACTACTCTCTCGTGAAGACTT-AAGTTTGATT
1 TGCTTCACTACTCTCTCGTGAAGACTTCAAG-ATGATT
623494 TGCTTC
1 TGCTTC
623500 GAAGGTCGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.05
37 35 0.95
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.44
Consensus pattern (37 bp):
TGCTTCACTACTCTCTCGTGAAGACTTCAAGATGATT
Found at i:623873 original size:36 final size:36
Alignment explanation
Indices: 623782--623920 Score: 163
Period size: 37 Copynumber: 3.8 Consensus size: 36
623772 TGATAGTCTG
* *
623782 ATGGTTTGCTTCAAC-ACTCTTCCGAGAAGGCTTAAAA
1 ATGGTTTGCTTC-ACTACTCTTCGGTGAAGGCTT-AAA
* * * *
623819 ATGATATGCTTCATTACTCTTCGGTGAAGGCTTAAG
1 ATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAAA
* *
623855 ATGGTTTGCTTCACTACTCTTTGGTGAAGGCTCAAA
1 ATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAAA
*
623891 ATGGATTTGCTTCACTACTCTTTGGTGAAG
1 ATGG-TTTGCTTCACTACTCTTCGGTGAAG
623921 AATTGGCTTT
Statistics
Matches: 88, Mismatches: 12, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
36 37 0.42
37 51 0.58
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (36 bp):
ATGGTTTGCTTCACTACTCTTCGGTGAAGGCTTAAA
Found at i:623902 original size:73 final size:73
Alignment explanation
Indices: 623781--623920 Score: 185
Period size: 73 Copynumber: 1.9 Consensus size: 73
623771 CTGATAGTCT
*
623781 GATGGTTTGCTTCAACACTCTTCCGAGAAGGCTTAAAAATGATATGCTTCATTACTCTTCGGTGA
1 GATGGTTTGCTTCAACACTCTTCCGAGAAGGCTTAAAAATGATATGCTTCACTACTCTTCGGTGA
623846 AGGCTTAA
66 AGGCTTAA
** * * * *
623854 GATGGTTTGCTTC-ACTACTCTTTGGTGAAGGC-TCAAAATGGATTTGCTTCACTACTCTTTGGT
1 GATGGTTTGCTTCAAC-ACTCTTCCGAGAAGGCTTAAAAAT-GATATGCTTCACTACTCTTCGGT
623917 GAAG
64 GAAG
623921 AATTGGCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
72 8 0.14
73 50 0.86
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (73 bp):
GATGGTTTGCTTCAACACTCTTCCGAGAAGGCTTAAAAATGATATGCTTCACTACTCTTCGGTGA
AGGCTTAA
Found at i:625344 original size:125 final size:125
Alignment explanation
Indices: 625145--625375 Score: 338
Period size: 125 Copynumber: 1.8 Consensus size: 125
625135 TCTTATTCAG
* * *
625145 GTACGAGCCTTCAAAATGATCCAACACCTCAAATTATAAGGCTCATTTTCAATGCCTTCTTGGTC
1 GTACGAGCCTTCAAAATGACCCAACACCTCAAATTATAAGGCTCATTTTCAATGACTCCTTGGTC
**
625210 TGAACCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCGACATTATCTCATACTA
66 CAAACCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCGACATTATCTCATACTA
* * * * *
625270 GTACGAGCCTTCAAAATGCCCCATCATCTCAATTTGTAAGGCTCATTCTTC-ATGACTCCTTGGT
1 GTACGAGCCTTCAAAATGACCCAACACCTCAAATTATAAGGCTCATT-TTCAATGACTCCTTGGT
* *
625334 CCAAATCTTATCATCTCAACATGATGTGGGTTTAGTCATGCC
65 CCAAACCTTATCATCTCAACATGATGTGGGTTCAGTCATGCC
625376 TCAATGTGGG
Statistics
Matches: 93, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
125 90 0.97
126 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (125 bp):
GTACGAGCCTTCAAAATGACCCAACACCTCAAATTATAAGGCTCATTTTCAATGACTCCTTGGTC
CAAACCTTATCATCTCAACATGATGTGGGTTCAGTCATGCCCCGACATTATCTCATACTA
Found at i:628899 original size:72 final size:72
Alignment explanation
Indices: 628780--628930 Score: 214
Period size: 72 Copynumber: 2.1 Consensus size: 72
628770 CCCCTAACAG
* * * *
628780 GTTCTTGATCAGTTTTTATCATCATATTGGCTACACCACTAATATTCAGATTCTCACTCGAAGTC
1 GTTCTTGATCAGTTTCTATCATCACATTGGCTACACCACTAACATTCAGATTCTCACCCGAAGTC
*
628845 TTCATCT
66 TTCATAT
* *
628852 GTTCTTGATCA-TTTGCTATCATCACATTGGTTGCACCACTAACATTCAGATTCTCACCCGAAGT
1 GTTCTTGATCAGTTT-CTATCATCACATTGGCTACACCACTAACATTCAGATTCTCACCCGAAGT
628916 CTTCATAT
65 CTTCATAT
*
628924 TTTCTTG
1 GTTCTTG
628931 TGTAATAGGG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
71 3 0.04
72 67 0.96
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.40
Consensus pattern (72 bp):
GTTCTTGATCAGTTTCTATCATCACATTGGCTACACCACTAACATTCAGATTCTCACCCGAAGTC
TTCATAT
Found at i:629686 original size:55 final size:55
Alignment explanation
Indices: 629615--629722 Score: 171
Period size: 55 Copynumber: 2.0 Consensus size: 55
629605 TGTGGATCAG
* *
629615 TCTTCAATCAGTTTCAAATTTCTTCATTCATCGGATGTCCTTCTTCATGAATCGT
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATCGAATGTCCTTCTTCATGAATCGT
* **
629670 TCTTCAGTCAGGTTCAAATTTCTTCATTCATCGAATGTTTTTCTTCATGAATC
1 TCTTCAATCAGGTTCAAATTTCTTCATTCATCGAATGTCCTTCTTCATGAATC
629723 ATCTGAATGC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.44
Consensus pattern (55 bp):
TCTTCAATCAGGTTCAAATTTCTTCATTCATCGAATGTCCTTCTTCATGAATCGT
Found at i:633337 original size:6 final size:6
Alignment explanation
Indices: 633328--633376 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
633318 TGGAAAACCG
*
633328 AAAAAT AAAATT AAAAAT ATAATAAT AATAAAT AATAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT A-AA-AAT AA-AAAT AA-AAAT AAAAAT AAA
633377 TTATATATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 18 0.47
7 15 0.39
8 5 0.13
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (6 bp):
AAAAAT
Found at i:633370 original size:34 final size:34
Alignment explanation
Indices: 633330--633395 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
633320 GAAAACCGAA
* *
633330 AAATAAAATTAAAA-ATATAATAATAATAAATAAT
1 AAATAAAAATAAAATATAT-ATAATAAAAAATAAT
*
633364 AAATAAAAATAAATTATATATAATAAAAAATA
1 AAATAAAAATAAAATATATATAATAAAAAATA
633396 TTACGTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (34 bp):
AAATAAAAATAAAATATATATAATAAAAAATAAT
Found at i:633388 original size:20 final size:18
Alignment explanation
Indices: 633331--633392 Score: 74
Period size: 17 Copynumber: 3.4 Consensus size: 18
633321 AAAACCGAAA
*
633331 AATAAAATTAAA-AATAT
1 AATAAAAATAAATAATAT
*
633348 AATAATAATAAATAATA-
1 AATAAAAATAAATAATAT
633365 AATAAAAATAAATTATATAT
1 AATAAAAATAAA-TA-ATAT
633385 AATAAAAA
1 AATAAAAA
633393 ATATTACGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
17 21 0.55
18 6 0.16
19 3 0.08
20 8 0.21
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAAAAATAAATAATAT
Found at i:633433 original size:16 final size:17
Alignment explanation
Indices: 633389--633426 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
633379 ATATATAATA
* *
633389 AAAAATATTACGTTTTC
1 AAAAATAATATGTTTTC
633406 AAAAATAATATGTTTTC
1 AAAAATAATATGTTTTC
633423 AAAA
1 AAAA
633427 TTATATGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (17 bp):
AAAAATAATATGTTTTC
Found at i:633475 original size:37 final size:36
Alignment explanation
Indices: 633418--633574 Score: 128
Period size: 37 Copynumber: 4.3 Consensus size: 36
633408 AAATAATATG
*
633418 TTTTCAAAA-TTATATGA-TATATGTTTTCAAAAACGTA
1 TTTTCAAAACCTATAT-ATTATATGTTTTCAAAAAC--A
633455 TTTTCAAAACC-ATAT-TATATAT-TTTT-AAAAATCGA
1 TTTTCAAAACCTATATAT-TATATGTTTTCAAAAA-C-A
* * * *
633490 TTTTTTAAAAGCTATATATTATATGCTTTAAAAAACA
1 -TTTTCAAAACCTATATATTATATGTTTTCAAAAACA
* *
633527 TTTTCTAAAAACTATATATTATATGTTTTCAAAAATA
1 TTTTC-AAAACCTATATATTATATGTTTTCAAAAACA
633564 TTTTCTAAAAC
1 TTTTC-AAAAC
633575 TACATTTTAT
Statistics
Matches: 99, Mismatches: 11, Indels: 20
0.76 0.08 0.15
Matches are distributed among these distances:
35 6 0.06
36 18 0.18
37 65 0.66
38 5 0.05
39 5 0.05
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (36 bp):
TTTTCAAAACCTATATATTATATGTTTTCAAAAACA
Found at i:633524 original size:39 final size:38
Alignment explanation
Indices: 633466--633573 Score: 139
Period size: 37 Copynumber: 2.9 Consensus size: 38
633456 TTTCAAAACC
* * * *
633466 ATATTATATATTTTTAAAAATCGATTTTTTAAAAGCTAT
1 ATATTATATGTTTTAAAAAATC-ATTTTCTAAAAACTAT
*
633505 ATATTATATGCTTTAAAAAA-CATTTTCTAAAAACTAT
1 ATATTATATGTTTTAAAAAATCATTTTCTAAAAACTAT
*
633542 ATATTATATGTTTTCAAAAAT-ATTTTCTAAAA
1 ATATTATATGTTTTAAAAAATCATTTTCTAAAA
633574 CTACATTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
37 43 0.70
38 1 0.02
39 17 0.28
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (38 bp):
ATATTATATGTTTTAAAAAATCATTTTCTAAAAACTAT
Found at i:635941 original size:34 final size:35
Alignment explanation
Indices: 635866--635942 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 35
635856 ACTGGTAATA
* * *
635866 AACAAAATTAACCAAAATACATTAACAAAAAGTCT
1 AACAAATTTAACCAAAATAAATTAACAAAAAGTCC
635901 AACAAATTTAA-CAAAATAAATTAA-AATAAA-TCC
1 AACAAATTTAACCAAAATAAATTAACAA-AAAGTCC
635934 AACCAAATT
1 AA-CAAATT
635943 AATGAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
33 6 0.16
34 21 0.57
35 10 0.27
ACGTcount: A:0.61, C:0.16, G:0.01, T:0.22
Consensus pattern (35 bp):
AACAAATTTAACCAAAATAAATTAACAAAAAGTCC
Found at i:636985 original size:19 final size:19
Alignment explanation
Indices: 636961--636998 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
636951 AGCACGCGAT
636961 CAGTGGAGTGCCACTCGAC
1 CAGTGGAGTGCCACTCGAC
636980 CAGTGGAGTGCCACTCGAC
1 CAGTGGAGTGCCACTCGAC
636999 AATCACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.32, G:0.32, T:0.16
Consensus pattern (19 bp):
CAGTGGAGTGCCACTCGAC
Found at i:638289 original size:17 final size:18
Alignment explanation
Indices: 638260--638307 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
638250 TGCAAAAGAA
*
638260 TTAATTAAA-TAAAATA-
1 TTAAATAAATTAAAATAC
*
638276 TTAAA-AAATTTAAATAC
1 TTAAATAAATTAAAATAC
638293 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
638308 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 5 0.19
18 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAATAAATTAAAATAC
Found at i:644463 original size:20 final size:21
Alignment explanation
Indices: 644441--644497 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
644431 AGAATGTCCA
644441 GGGGTACAGATTCCCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
*
644462 GGGGAACAGATT-CCCCCCAG
1 GGGGTACAGATTCCCCCCCAG
644482 GGGGTATC-GATTCCCC
1 GGGGTA-CAGATTCCCC
644498 GGGAACAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.16
Consensus pattern (21 bp):
GGGGTACAGATTCCCCCCCAG
Found at i:644525 original size:34 final size:34
Alignment explanation
Indices: 644463--644547 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 34
644453 CCCCCCCAGG
644463 GGGAACAGATTCCCCCCAGGGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCAGGGGGTATCGATTCCCC
644498 GGGAACAGATTGCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATT-CCCCCAGGGGGTATCGATTCCCC
*
644532 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
644548 TGCATGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 5 0.10
34 26 0.54
35 17 0.35
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.18
Consensus pattern (34 bp):
GGGAACAGATTCCCCCAGGGGGTATCGATTCCCC
Found at i:644542 original size:15 final size:15
Alignment explanation
Indices: 644490--644546 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
644480 AGGGGGTATC
*
644490 GATTCCCCGGGAACA
1 GATTCCCCGGGTACA
644505 GATTGCCCCCAGGGGTATC-
1 GATT--CCCC--GGGTA-CA
644524 GATTCCCCGGGTACA
1 GATTCCCCGGGTACA
644539 GATTCCCC
1 GATTCCCC
644547 CTGCATGGTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 17 0.49
17 8 0.23
19 8 0.23
20 1 0.03
ACGTcount: A:0.19, C:0.35, G:0.26, T:0.19
Consensus pattern (15 bp):
GATTCCCCGGGTACA
Found at i:644766 original size:20 final size:20
Alignment explanation
Indices: 644738--644789 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
644728 GAAAAATCAT
*
644738 TCCCAAACGGCTCCAAAACA
1 TCCCCAACGGCTCCAAAACA
644758 TCCCCAACGGCTCCAAAACA
1 TCCCCAACGGCTCCAAAACA
644778 TCCCCAACGGCT
1 TCCCCAACGGCT
644790 AGATATGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.44, G:0.12, T:0.12
Consensus pattern (20 bp):
TCCCCAACGGCTCCAAAACA
Found at i:646085 original size:3 final size:3
Alignment explanation
Indices: 646064--646122 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
646054 TAAAGAAAGG
* *
646064 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
646111 GAA GAA GAA GAA
1 GAA GAA GAA GAA
646123 TGAGGACGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.68, C:0.02, G:0.31, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:648097 original size:20 final size:20
Alignment explanation
Indices: 648072--648121 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
648062 ATCAGATTGT
648072 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
648092 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
648112 CCATGGGGTA
1 CCAGGGGGTA
648122 TCGATTCCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.14
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:648127 original size:20 final size:19
Alignment explanation
Indices: 648084--648165 Score: 73
Period size: 20 Copynumber: 4.4 Consensus size: 19
648074 AGGGGGTACA
* *
648084 GATTCCCCCCAGGGGGAAC
1 GATTCCCCCCAGGGGTATC
648103 AGATTCCCCCCATGGGGTATC
1 -GATTCCCCCCA-GGGGTATC
* * *
648124 GATT--CCTC--GGGAATA
1 GATTCCCCCCAGGGGTATC
648139 GATTCCCCCCAGGGGTATC
1 GATTCCCCCCAGGGGTATC
648158 GATTCCCC
1 GATTCCCC
648166 GGGTACAGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
15 9 0.18
17 3 0.06
18 3 0.06
19 13 0.27
20 15 0.31
21 6 0.12
ACGTcount: A:0.20, C:0.34, G:0.26, T:0.21
Consensus pattern (19 bp):
GATTCCCCCCAGGGGTATC
Found at i:648154 original size:34 final size:35
Alignment explanation
Indices: 648097--648181 Score: 136
Period size: 34 Copynumber: 2.5 Consensus size: 35
648087 TCCCCCCAGG
*
648097 GGGAACAGATTCCCCCCATGGGGTATCGATTCCTC
1 GGGAACAGATTCCCCCCATGGGGTATCGATTCCCC
*
648132 GGGAATAGATTCCCCCCA-GGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCCATGGGGTATCGATTCCCC
*
648166 GGGTACAGATTCCCCC
1 GGGAACAGATTCCCCC
648182 TGCATGGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
34 29 0.63
35 17 0.37
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.21
Consensus pattern (35 bp):
GGGAACAGATTCCCCCCATGGGGTATCGATTCCCC
Found at i:648319 original size:21 final size:21
Alignment explanation
Indices: 648293--648335 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
648283 ATTTGAATAT
*
648293 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
648314 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
648335 T
1 T
648336 CCATTCTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:649922 original size:21 final size:21
Alignment explanation
Indices: 649898--649937 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
649888 TGTGCATCTT
649898 TACATTCACAT-ATATACATCA
1 TACATT-ACATAATATACATCA
*
649919 TACATTTCATAATATACAT
1 TACATTACATAATATACAT
649938 TACATCTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (21 bp):
TACATTACATAATATACATCA
Found at i:651257 original size:29 final size:29
Alignment explanation
Indices: 651194--651277 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
651184 AAGATATAGC
*
651194 AAAAAGAAA-AAAACATAAAAAGAGAGAA
1 AAAAAGAAAGAAAACATAAAAAGAAAGAA
* *
651222 AATAAAGAAAGAATAGATAGAAAAGAAAG-A
1 AA-AAAGAAAGAAAACATA-AAAAGAAAGAA
* *
651252 AAAAAGAAAGTAAAAAATAAGAAGAA
1 AAAAAGAAAG-AAAACATAAAAAGAA
651278 GAAGAAGAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.04
29 21 0.46
30 15 0.33
31 8 0.17
ACGTcount: A:0.75, C:0.01, G:0.17, T:0.07
Consensus pattern (29 bp):
AAAAAGAAAGAAAACATAAAAAGAAAGAA
Found at i:651258 original size:11 final size:12
Alignment explanation
Indices: 651218--651268 Score: 50
Period size: 11 Copynumber: 4.1 Consensus size: 12
651208 ATAAAAAGAG
*
651218 AGAAAATAAAGAA
1 AGAAAGTAAA-AA
*
651231 AGAATAGATAGAAA
1 AGAA-AG-TAAAAA
651245 AGAAAG-AAAAA
1 AGAAAGTAAAAA
651256 AGAAAGTAAAAA
1 AGAAAGTAAAAA
651268 A
1 A
651269 TAAGAAGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 10 0.31
12 6 0.19
13 6 0.19
14 7 0.22
15 3 0.09
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.08
Consensus pattern (12 bp):
AGAAAGTAAAAA
Found at i:653368 original size:59 final size:60
Alignment explanation
Indices: 653299--653572 Score: 224
Period size: 59 Copynumber: 4.6 Consensus size: 60
653289 TAACATGATT
*
653299 TTTTTTAAGAAACTAAGTCTGATTTTCAAAGGTTTCTTGACATGATGTTCTT-AAATGAG
1 TTTTTAAAGAAACTAAGTCTGATTTTCAAAGGTTTCTTGACATGATGTTCTTCAAATGAG
* * * * * * * * *
653358 TTTTTAAAGAAGCCAAGTTTGACTTTT-AGAGGTTTTTAGATTGATATGAGGTT-TTCAAATAAA
1 TTTTTAAAGAAACTAAGTCTGA-TTTTCAAAGG--TTT--CTTGACATGATGTTCTTCAAATGAG
* * *
653421 TTTTCAAAGTAACTAAGTCTGATTTTCAGAGGTTTCTTGACATGATG-TCTTCAAATGA-
1 TTTTTAAAGAAACTAAGTCTGATTTTCAAAGGTTTCTTGACATGATGTTCTTCAAATGAG
* * * ** *
653479 ATTTTAAATAAACTAAGTATGATTTTTGGAA-GTTTCTT--TATGAT-TTCTTCAAATGAG
1 TTTTTAAAGAAACTAAGTCTGA-TTTTCAAAGGTTTCTTGACATGATGTTCTTCAAATGAG
* * * *
653536 TTTTTAAAGAATCTAAGTTTGTTTTTCATAGGTTTCT
1 TTTTTAAAGAAACTAAGTCTGATTTTCAAAGGTTTCT
653573 CGATGATTAC
Statistics
Matches: 167, Mismatches: 36, Indels: 26
0.73 0.16 0.11
Matches are distributed among these distances:
56 21 0.13
57 23 0.14
58 25 0.15
59 44 0.26
60 4 0.02
61 6 0.04
62 6 0.04
63 38 0.23
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (60 bp):
TTTTTAAAGAAACTAAGTCTGATTTTCAAAGGTTTCTTGACATGATGTTCTTCAAATGAG
Found at i:653757 original size:41 final size:42
Alignment explanation
Indices: 653665--653746 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
653655 TCCATTAGGC
* * * *
653665 CATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGT
1 CATCAATAAGTATTTCGAGCAAGATGCATAAATCCTTCGGGT
*
653707 CATCTATAAGTATTTCGAGCAAGATG-ATAAATCCTTCGGG
1 CATCAATAAGTATTTCGAGCAAGATGCATAAATCCTTCGGG
653747 CAATGAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
41 13 0.37
42 22 0.63
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (42 bp):
CATCAATAAGTATTTCGAGCAAGATGCATAAATCCTTCGGGT
Found at i:654501 original size:116 final size:116
Alignment explanation
Indices: 654317--654806 Score: 547
Period size: 116 Copynumber: 4.2 Consensus size: 116
654307 GGAAGGGTCT
* * *
654317 GTAATGAGAAGAACTCGTCCAACGAGAAAAGAAGAAGTTCATAATGAGAAGAACTTGTT-TGGAA
1 GTAATGAGAAGAACTCATCCAACGAG-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCT-AAA
* * *
654381 CTTGACACATCCATCACACAAGGAGATGGATCAACATTTCAGAAGAATGGTTC
64 CTTGACACATCCATCACACAAGGAGATGGATCAATATTTTAGAAGAAAGGTTC
* *
654434 GTAATGGGAAGAACTCATCCAACGAGGAAGAAGAAGTTCACAATGAGACA-AACTTGTTCTAAAC
1 GTAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGA-AGAACTTGTTCTAAAC
* **
654498 TTGACACATCCATCACACAAGTAGATGGATCAATATTTTAGAAGAGGGGTTC
65 TTGACACATCCATCACACAAGGAGATGGATCAATATTTTAGAAGAAAGGTTC
* ** * * * * * * *
654550 ATACCGAGAAGAGCTCATCCAACGAGGAAGAATAAGTTAATAATGCGAATACCTTGTTCAAAACT
1 GTAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCTAAACT
* * * * * *
654615 TGACACATTCGTCATACAGGGAGATGGATCAATATTTTTGAAGAAAAGTTC
66 TGACACATCCATCACACAAGGAGATGGATCAATATTTTAGAAGAAAGGTTC
* * *
654666 GTAATGAGAAGAACTCACCCAATGAGGAAGAAGGAGTTCATAATGAGAAGAACTTGTTC-AGAAC
1 GTAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCTA-AAC
** * * * * *
654730 TCAACACATCCATCACACAAGGAGATAGACCAAT-GTTTCGAAAAAAGAGTTC
65 TTGACACATCCATCACACAAGGAGATGGATCAATATTTTAGAAGAAAG-GTTC
* * *
654782 ATAATGAGAATAACTCATCCGACGA
1 GTAATGAGAAGAACTCATCCAACGA
654807 AAGGCTCATA
Statistics
Matches: 309, Mismatches: 59, Indels: 11
0.82 0.16 0.03
Matches are distributed among these distances:
115 11 0.04
116 272 0.88
117 26 0.08
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (116 bp):
GTAATGAGAAGAACTCATCCAACGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCTAAACT
TGACACATCCATCACACAAGGAGATGGATCAATATTTTAGAAGAAAGGTTC
Found at i:655054 original size:137 final size:136
Alignment explanation
Indices: 654773--655073 Score: 331
Period size: 137 Copynumber: 2.2 Consensus size: 136
654763 TGTTTCGAAA
* *
654773 AAAGAGTTCATAATGAGAATAACTCATCCGACGAAAGGCTCATAATGAGAAGAACTCATCCAACA
1 AAAGAGTTCATAATGAGAAGAACTCATCCGACGAAAGGCTCATAATGAGAAAAACTCATCCAACA
* * * * *
654838 ATGGAGAAGAAGTTCATAATGAGAATATCTTATTCAACCTGGAATCGTCCATTGCACAAGTAGGT
66 A--GAGAAGAAGTTCATAATGACAAGAGCTTATTCAACCTGGAATAGTCCATTGCACAAGGAGGT
* *
654903 GGCTAAAT
129 GGATAAAG
** * *
654911 AAAGAGTTCATAATGAGAAGAACTCATTTGACGAAGGGGGTTCATAATGAGAAAAACTCATCCAA
1 AAAGAGTTCATAATGAGAAGAACTCATCCGACGAA--AGGCTCATAATGAGAAAAACTCATCCAA
* * *
654976 CAA-AGATGAAGTTCATAATGACAAGAGCTTGTTCAACCTGGGATAGT-C--TGTCACGTAAGGA
64 CAAGAGAAGAAGTTCATAATGACAAGAGCTTATTCAACCTGGAATAGTCCATTG-CAC--AAGGA
* *
655037 GGTGTATTAAG
126 GGTGGATAAAG
**
655048 GCAGAGTTCATAATGAGAAGAACTCA
1 AAAGAGTTCATAATGAGAAGAACTCA
655074 CAAAAAATAA
Statistics
Matches: 138, Mismatches: 20, Indels: 11
0.82 0.12 0.07
Matches are distributed among these distances:
134 2 0.01
135 3 0.02
136 1 0.01
137 72 0.52
138 32 0.23
140 28 0.20
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (136 bp):
AAAGAGTTCATAATGAGAAGAACTCATCCGACGAAAGGCTCATAATGAGAAAAACTCATCCAACA
AGAGAAGAAGTTCATAATGACAAGAGCTTATTCAACCTGGAATAGTCCATTGCACAAGGAGGTGG
ATAAAG
Found at i:655181 original size:9 final size:10
Alignment explanation
Indices: 655164--655222 Score: 61
Period size: 9 Copynumber: 5.9 Consensus size: 10
655154 CTGAAATCAA
*
655164 TATTTTTATT
1 TATTATTATT
655174 TATTTTATTATT
1 TA--TTATTATT
655186 T-TTATT-TT
1 TATTATTATT
655194 TATTATTATAT
1 TATTATTAT-T
655205 TATTATTA-T
1 TATTATTATT
655214 TATTATTAT
1 TATTATTAT
655223 ATCAAAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
8 3 0.07
9 19 0.45
10 3 0.07
11 9 0.21
12 8 0.19
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TATTATTATT
Found at i:655199 original size:3 final size:3
Alignment explanation
Indices: 655173--655222 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
655163 ATATTTTTAT
* *
655173 TTA TT- TTA TTA TTT TTA TTT TTA TTA TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
655219 TTA T
1 TTA T
655223 ATCAAAAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 37 0.90
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:655223 original size:20 final size:19
Alignment explanation
Indices: 655167--655224 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
655157 AAATCAATAT
655167 TTTTATTTATT-TTATTAT-
1 TTTTA-TTATTATTATTATA
*
655185 TTTTATTTTTATTATTATA
1 TTTTATTATTATTATTATA
655204 TTATTATTATTATTATTATA
1 TT-TTATTATTATTATTATA
655224 T
1 T
655225 CAAAAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.11
18 12 0.34
19 2 0.06
20 17 0.49
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTATTATTATTATA
Found at i:659261 original size:30 final size:30
Alignment explanation
Indices: 659190--659249 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
659180 ACAATTTAAG
659190 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
659220 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
659250 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:659360 original size:21 final size:21
Alignment explanation
Indices: 659331--659384 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
659321 AGGGTGTCAA
659331 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
*
659352 AGTGTATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
659373 AGTGCATCCATG
1 AGTGCATCCATG
659385 TATCTGCACT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.33, G:0.20, T:0.26
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:659465 original size:21 final size:21
Alignment explanation
Indices: 659439--659514 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
659429 ATGTAATTAG
*
659439 TGCATCGATGCATCCTTTCCA
1 TGCATCGATGCATCCTTGCCA
*
659460 TGCATCGATGCATCATTGCCA
1 TGCATCGATGCATCCTTGCCA
659481 TGCATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
659501 TGCATCCATGCATC
1 TGCATCGATGCATC
659515 AAGGCTGCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 18 0.35
21 33 0.65
ACGTcount: A:0.21, C:0.33, G:0.17, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:659538 original size:10 final size:10
Alignment explanation
Indices: 659523--659552 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
659513 TCAAGGCTGC
659523 AACGGCTAGT
1 AACGGCTAGT
659533 AACGGCTAGT
1 AACGGCTAGT
659543 AACGGCTAGT
1 AACGGCTAGT
659553 TTATTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (10 bp):
AACGGCTAGT
Done.