Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009580.1 Hibiscus syriacus cultivar Beakdansim tig00116954_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: 1633873
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 6
Found at i:386258 original size:35 final size:35
Alignment explanation
Indices: 386203--386314 Score: 118
Period size: 35 Copynumber: 3.2 Consensus size: 35
386193 TCTAAACCTT
* * * *
386203 AAATCGAAGTATTTTAGAATTTGGGATTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGATTTAAAATA
***
386238 TGTTTGAATTATTTTGGAATTTAGGG-TTTAAAATA
1 AAATTGAATTATTTTGGAATTT-GGGATTTAAAATA
* * *
386273 AAATTGAATTACTTTGGAATTTGGGATTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGATTTAAAATA
386308 AAATTGA
1 AAATTGA
386315 GGAATGTTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
34 3 0.05
35 56 0.90
36 3 0.05
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.42
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGATTTAAAATA
Found at i:386520 original size:15 final size:15
Alignment explanation
Indices: 386500--386530 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
386490 TAAATACAAT
386500 CCCTTATATGATTTA
1 CCCTTATATGATTTA
386515 CCCTTATATGATTTA
1 CCCTTATATGATTTA
386530 C
1 C
386531 TTTTCCTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (15 bp):
CCCTTATATGATTTA
Found at i:402995 original size:84 final size:84
Alignment explanation
Indices: 402845--403018 Score: 203
Period size: 84 Copynumber: 2.1 Consensus size: 84
402835 AGTTAAAAAG
* * ** *
402845 GCTGCTGGTGTTCTCAAGAGGAGAGCCAATGAGGTGGTTGTAGCTGAGGCCAAGCCATTGATGGT
1 GCTGTTGGTGTTCTCAAGAGGAGAGCCAAGGAGGTAATTGTAGCTGAGGCCAAGCCATTGAAGGT
*
402910 TGTGGA-GATGAAAGAGGCTT
66 TGTGAAGGA-GAAAGAGG-TT
** *
402930 -CTGTTGGTGTTCTCAAGAGGAGAGCCCCGGAGGTAATT-TCGGCTGAGGTCC-AGCCATTGAAG
1 GCTGTTGGTGTTCTCAAGAGGAGAGCCAAGGAGGTAATTGT-AGCTGAGG-CCAAGCCATTGAAG
402992 GTTGTGAAGGAGAAAGAGGTT
64 GTTGTGAAGGAGAAAGAGGTT
403013 GCTGTT
1 GCTGTT
403019 TGCATGGAGA
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
83 3 0.04
84 69 0.91
85 4 0.05
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (84 bp):
GCTGTTGGTGTTCTCAAGAGGAGAGCCAAGGAGGTAATTGTAGCTGAGGCCAAGCCATTGAAGGT
TGTGAAGGAGAAAGAGGTT
Found at i:409953 original size:184 final size:187
Alignment explanation
Indices: 409643--410014 Score: 723
Period size: 184 Copynumber: 2.0 Consensus size: 187
409633 CAGGGACAGA
409643 GACTCAAGGAAACTGTGGCTATCTCAACGGGGTTATGTTGAGAAAATACTAGAAAGGTTTGCGAT
1 GACTCAAGGAAACTGTGGCTATCTCAACGGGGTTATGTTGAGAAAATACTAGAAAGGTTTGCGAT
409708 GAGCAGCGCGAAACCAGTTAGCACTCCATTGGCGAATCACTTTAAGCTCTCATCAGAACAGTG-C
66 GAGCAGCGCGAAACCAGTTAGCACTCCATTGGCGAATCACTTTAAGCTCTCATCAGAACAGTGCC
409772 CCAAGACAGATAAGGAAG-TGAAGATATGGCAAAGGTTCCGTATTCTAATGCTGTTG
131 CCAAGACAGATAAGGAAGCTGAAGATATGGCAAAGGTTCCGTATTCTAATGCTGTTG
409828 GACTCAAGGAAACTGTGGCTATCTCAACGGGGTTATGTTGAGAAAA-ACTAGAAAGGTTTGCGAT
1 GACTCAAGGAAACTGTGGCTATCTCAACGGGGTTATGTTGAGAAAATACTAGAAAGGTTTGCGAT
409892 GAGCAGCGCGAAACCAGTTAGCACTCCATTGGCGAATCACTTTAAGCTCTCATCAGAACAGTGCC
66 GAGCAGCGCGAAACCAGTTAGCACTCCATTGGCGAATCACTTTAAGCTCTCATCAGAACAGTGCC
409957 CCAAGACAGATAAGGAAGCTGAAGATATGGCAAAGGTTCCGTATTCTAATGCTGTTG
131 CCAAGACAGATAAGGAAGCTGAAGATATGGCAAAGGTTCCGTATTCTAATGCTGTTG
410014 G
1 G
410015 CTGCTTGATG
Statistics
Matches: 185, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
184 81 0.44
185 65 0.35
186 39 0.21
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (187 bp):
GACTCAAGGAAACTGTGGCTATCTCAACGGGGTTATGTTGAGAAAATACTAGAAAGGTTTGCGAT
GAGCAGCGCGAAACCAGTTAGCACTCCATTGGCGAATCACTTTAAGCTCTCATCAGAACAGTGCC
CCAAGACAGATAAGGAAGCTGAAGATATGGCAAAGGTTCCGTATTCTAATGCTGTTG
Found at i:431601 original size:2 final size:2
Alignment explanation
Indices: 431594--431622 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
431584 TTTGTATAAT
431594 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
431623 GAAATAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:434555 original size:24 final size:24
Alignment explanation
Indices: 434523--434571 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
434513 TACAGGGTAG
434523 TATTATCGGTTACACCTTATGGCA
1 TATTATCGGTTACACCTTATGGCA
434547 TATTATCGGTTACACCTTATGGCA
1 TATTATCGGTTACACCTTATGGCA
434571 T
1 T
434572 CGCAAGGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (24 bp):
TATTATCGGTTACACCTTATGGCA
Found at i:437947 original size:2 final size:2
Alignment explanation
Indices: 437940--437975 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
437930 GAGCCTACAC
437940 AT AT AT AT AT AT AT AT AT AT AT AT ACT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
437976 GTAAATAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 29 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:440871 original size:64 final size:63
Alignment explanation
Indices: 440771--440898 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 63
440761 CGAAAAATGT
* *
440771 AAAACTGAGCTCGACTTGAAAACTCACGAGCGTAAAATTGTCAAGCTCAACTCGAACTCGAAA
1 AAAACTGAGCTCGACTGGAAAACTCACGAGCGTAAAATTGTCAAGCTCAACTCGAAATCGAAA
* * * * * * **
440834 AAAATTGAGACTCTACTGGAAAACTCGCGAGCTTAAAATTTTCAAGTTTGACTCGAAATCGAAA
1 AAAACTGAG-CTCGACTGGAAAACTCACGAGCGTAAAATTGTCAAGCTCAACTCGAAATCGAAA
440898 A
1 A
440899 TTGTAGCTTG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
63 8 0.15
64 46 0.85
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (63 bp):
AAAACTGAGCTCGACTGGAAAACTCACGAGCGTAAAATTGTCAAGCTCAACTCGAAATCGAAA
Found at i:446002 original size:80 final size:80
Alignment explanation
Indices: 445895--446063 Score: 290
Period size: 80 Copynumber: 2.1 Consensus size: 80
445885 AAATTGAAAG
*
445895 ATAT-AATATACCATTATTTCGATCTTAATTTCGTATTAATACAAGTTGATCGAATCTTAATTCA
1 ATATAAATATACCATTATTTCGATCTTAATTTCGTACTAATACAAGTTGATCGAATCTTAATTCA
445959 ATTCATATTATTAAT
66 ATTCATATTATTAAT
445974 ATATAAATATACCATTATTTTTC-A-CTTAATTTCGTACTAATACAAGTTGATCGAATCTTAATT
1 ATATAAATATACCATTA--TTTCGATCTTAATTTCGTACTAATACAAGTTGATCGAATCTTAATT
446037 CAATTCATATTATTAAT
64 CAATTCATATTATTAAT
446054 ATATAAATAT
1 ATATAAATAT
446064 TAAGCATATT
Statistics
Matches: 86, Mismatches: 1, Indels: 5
0.93 0.01 0.05
Matches are distributed among these distances:
79 4 0.05
80 77 0.90
81 1 0.01
82 4 0.05
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.44
Consensus pattern (80 bp):
ATATAAATATACCATTATTTCGATCTTAATTTCGTACTAATACAAGTTGATCGAATCTTAATTCA
ATTCATATTATTAAT
Found at i:446054 original size:39 final size:39
Alignment explanation
Indices: 445928--446054 Score: 105
Period size: 39 Copynumber: 3.2 Consensus size: 39
445918 CTTAATTTCG
445928 TATTAATACAAGTTGATCGAATCTTAATTCAATTCATAT
1 TATTAATACAAGTTGATCGAATCTTAATTCAATTCATAT
* ** * * * * * * *
445967 TATTAATATATAAAT-ATACCATTATT-TTTCACTTAATTT
1 TATTAATACA-AGTTGAT-CGAATCTTAATTCAATTCATAT
*
446006 CGTACTAATACAAGTTGATCGAATCTTAATTCAATTCATAT
1 --TATTAATACAAGTTGATCGAATCTTAATTCAATTCATAT
446047 TATTAATA
1 TATTAATA
446055 TATAAATATT
Statistics
Matches: 60, Mismatches: 22, Indels: 12
0.64 0.23 0.13
Matches are distributed among these distances:
39 27 0.45
40 14 0.23
41 19 0.32
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.43
Consensus pattern (39 bp):
TATTAATACAAGTTGATCGAATCTTAATTCAATTCATAT
Found at i:452735 original size:5 final size:5
Alignment explanation
Indices: 452725--452765 Score: 55
Period size: 5 Copynumber: 7.6 Consensus size: 5
452715 CGGTTACAAT
452725 CCGAC CCGAC CCGTTAAC CCGAC CCGAC CCGAC CCGAC CCG
1 CCGAC CCGAC CCG---AC CCGAC CCGAC CCGAC CCGAC CCG
452766 TTGACCGTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 28 0.85
8 5 0.15
ACGTcount: A:0.20, C:0.56, G:0.20, T:0.05
Consensus pattern (5 bp):
CCGAC
Found at i:452839 original size:29 final size:29
Alignment explanation
Indices: 452794--452858 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
452784 CCGTTGAACG
*
452794 GGTGCTATTCTGATAATTATTTGGAAAA-
1 GGTGCTATTATGATAATTATTTGGAAAAT
* *
452822 GGATGCTATTATGGTAATTATTTTGAAAAT
1 GG-TGCTATTATGATAATTATTTGGAAAAT
452852 GGTGCTA
1 GGTGCTA
452859 ATTTCGTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 2 0.06
29 28 0.88
30 2 0.06
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.40
Consensus pattern (29 bp):
GGTGCTATTATGATAATTATTTGGAAAAT
Found at i:452867 original size:29 final size:29
Alignment explanation
Indices: 452807--452983 Score: 124
Period size: 29 Copynumber: 6.1 Consensus size: 29
452797 GCTATTCTGA
* * * *
452807 TAATTATTTGGAAAAGGATGCT-ATTATGG
1 TAATTATTTTGAAAATGATGATAATT-TCG
* *
452836 TAATTATTTTGAAAATGGTGCTAATTTCG
1 TAATTATTTTGAAAATGATGATAATTTCG
* ** *
452865 TAATT-TTTTAAAAAAAAAGATAATTTCG
1 TAATTATTTTGAAAATGATGATAATTTCG
* * ** * *
452893 TAATTTTTTTAAAAAAAATGATATTTTAG
1 TAATTATTTTGAAAATGATGATAATTTCG
* * *
452922 TAATTATTTTGAAAATGTTGATATTTTGG
1 TAATTATTTTGAAAATGATGATAATTTCG
* * *
452951 TAATTTTTTTTGAAAATGATGTTATTTTCG
1 TAA-TTATTTTGAAAATGATGATAATTTCG
452981 TAA
1 TAA
452984 AATTGTTCAT
Statistics
Matches: 122, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
28 22 0.18
29 72 0.59
30 28 0.23
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.46
Consensus pattern (29 bp):
TAATTATTTTGAAAATGATGATAATTTCG
Found at i:453889 original size:29 final size:29
Alignment explanation
Indices: 453847--453906 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
453837 GAACGAGTGG
*
453847 TATTCTTGTAATTATTTGGAAAAGGATGC
1 TATTCTGGTAATTATTTGGAAAAGGATGC
* *
453876 TATTCTGGTAATTATTTTGAAAAGGGTGC
1 TATTCTGGTAATTATTTGGAAAAGGATGC
453905 TA
1 TA
453907 ATTTTCTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.42
Consensus pattern (29 bp):
TATTCTGGTAATTATTTGGAAAAGGATGC
Found at i:454023 original size:29 final size:29
Alignment explanation
Indices: 453952--454007 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
453942 TAAAAAAAAA
453952 TGATATTTTAGTAATTATTTTGAAAATTG
1 TGATATTTTAGTAATTATTTTGAAAATTG
* *
453981 TGATATTTTGGTAATTTTTTTGAAAAT
1 TGATATTTTAGTAATTATTTTGAAAAT
454008 GATGCTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (29 bp):
TGATATTTTAGTAATTATTTTGAAAATTG
Found at i:454972 original size:42 final size:42
Alignment explanation
Indices: 454925--455044 Score: 188
Period size: 42 Copynumber: 2.9 Consensus size: 42
454915 TATTATCAGA
*
454925 TCCCTTTGCTGTGTGCGAA-GGTAAGCCTTACAGTTTCCCAGG
1 TCCCTTTGCTGTGTGC-AAGGGTAAGCCTTACAGTTTCCCAAG
*
454967 TCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAATTTCCCAAG
1 TCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAAG
* *
455009 TCCCTTTGTTGTGTGCAAGGGTAAACCTTACAGTTT
1 TCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT
455045 TCCTAGGCTC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
41 2 0.03
42 70 0.97
ACGTcount: A:0.19, C:0.24, G:0.23, T:0.33
Consensus pattern (42 bp):
TCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCAAG
Found at i:456032 original size:17 final size:18
Alignment explanation
Indices: 456001--456034 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
455991 ATTATAACAT
456001 AAATAATCATAAATTATA
1 AAATAATCATAAATTATA
*
456019 AAATAAT-ATGAATTAT
1 AAATAATCATAAATTAT
456035 TATATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
AAATAATCATAAATTATA
Found at i:458793 original size:24 final size:25
Alignment explanation
Indices: 458752--458802 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 25
458742 AACAGATAAT
* * *
458752 TATATTTATTTATTTATTTTTAAAA
1 TATATTTATTAATGTATTTTCAAAA
458777 TATA-TTATTAATGTATTTTCAAAA
1 TATATTTATTAATGTATTTTCAAAA
458801 TA
1 TA
458803 CTGAATAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
TATATTTATTAATGTATTTTCAAAA
Found at i:460507 original size:22 final size:22
Alignment explanation
Indices: 460465--460526 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
460455 TTTTATTCTT
460465 AAATTTTATAAATTTACCTCTTTTA
1 AAATTTTATAAA-TT--CTCTTTTA
460490 AAATTTTATAAATTCTCTTTTA
1 AAATTTTATAAATTCTCTTTTA
*
460512 AAATTTTACAAATTC
1 AAATTTTATAAATTC
460527 AAACTCTAGC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
22 22 0.61
24 2 0.06
25 12 0.33
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (22 bp):
AAATTTTATAAATTCTCTTTTA
Found at i:477708 original size:17 final size:17
Alignment explanation
Indices: 477686--477718 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
477676 CAATATCACT
477686 CATTTGGCTATACAAGA
1 CATTTGGCTATACAAGA
477703 CATTTGGCTATACAAG
1 CATTTGGCTATACAAG
477719 GGGTTGGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.30
Consensus pattern (17 bp):
CATTTGGCTATACAAGA
Found at i:484583 original size:21 final size:21
Alignment explanation
Indices: 484557--484601 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
484547 GATTTCTGGG
* *
484557 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
484578 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
484599 CAA
1 CAA
484602 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:485825 original size:19 final size:21
Alignment explanation
Indices: 485801--485839 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
485791 ACACGTGGCA
485801 ATTTGA-ATTT-AATATTTTC
1 ATTTGATATTTAAATATTTTC
*
485820 ATTTGATTTTTAAATATTTT
1 ATTTGATATTTAAATATTTT
485840 AAGAAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (21 bp):
ATTTGATATTTAAATATTTTC
Found at i:486311 original size:19 final size:18
Alignment explanation
Indices: 486264--486314 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
486254 ATTATACGGC
*
486264 AATTATAATTTATAAAAT
1 AATTATAATTTAAAAAAT
* *
486282 ATTTAAAAATTTAAAAAATT
1 AATT-ATAATTTAAAAAA-T
486302 AATTATAATTTAA
1 AATTATAATTTAA
486315 GGTCTGATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 3 0.12
19 19 0.73
20 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATTATAATTTAAAAAAT
Found at i:486833 original size:18 final size:18
Alignment explanation
Indices: 486802--486836 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
486792 ATACTTAACA
486802 AAATAATATCTTATAATT
1 AAATAATATCTTATAATT
* *
486820 AAATATTATTTTATAAT
1 AAATAATATCTTATAAT
486837 ATTTAATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AAATAATATCTTATAATT
Found at i:487296 original size:19 final size:19
Alignment explanation
Indices: 487272--487312 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
487262 GTACTTTAAT
487272 TTTTATTATTCATA-TTATA
1 TTTTA-TATTCATATTTATA
*
487291 TTTTATATTTATATTTATA
1 TTTTATATTCATATTTATA
487310 TTT
1 TTT
487313 ATTGTCGTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTATATTCATATTTATA
Found at i:487301 original size:6 final size:6
Alignment explanation
Indices: 487273--487314 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
487263 TACTTTAATT
*
487273 TTTATTA TTCATA -TTATA TTTTATA TTTATA TTTATA TTTAT
1 TTTA-TA TTTATA TTTATA -TTTATA TTTATA TTTATA TTTAT
487315 TGTCGTCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 4 0.13
6 19 0.61
7 8 0.26
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:488279 original size:63 final size:63
Alignment explanation
Indices: 488189--488328 Score: 147
Period size: 63 Copynumber: 2.2 Consensus size: 63
488179 ATCGCTTTGA
* * *
488189 ATGATGTGACACATATCACACAGTCATTTTGGTTGACATGATAAATGTCACATCATCACATGG
1 ATGATGTGACAAATATCACACAGTCATTTTGGGTGACATGACAAATGTCACATCATCACATGG
* * ** * * * *
488252 ATGATGTGACAAATATTATATCA-TCATTTTGGGTGATGTGACATATGTCATATCATCACTTTG
1 ATGATGTGACAAATATCACA-CAGTCATTTTGGGTGACATGACAAATGTCACATCATCACATGG
* *
488315 ATGACGTGTCAAAT
1 ATGATGTGACAAAT
488329 GTCATGTCAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
63 61 0.97
64 2 0.03
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (63 bp):
ATGATGTGACAAATATCACACAGTCATTTTGGGTGACATGACAAATGTCACATCATCACATGG
Found at i:488291 original size:32 final size:32
Alignment explanation
Indices: 488176--488340 Score: 93
Period size: 32 Copynumber: 5.2 Consensus size: 32
488166 TATATCCAAA
* ** * *
488176 ATCATCGCTTTGAATGATGTGACACATATCAC
1 ATCATCACTTTGGGTGATGTGACAAATATCAT
* * ** * * *
488208 A-CAGTCATTTTGGTTGACATGATAAATGTCAC
1 ATCA-TCACTTTGGGTGATGTGACAAATATCAT
* * *
488240 ATCATCAC-ATGGATGATGTGACAAATATTAT
1 ATCATCACTTTGGGTGATGTGACAAATATCAT
* * *
488271 ATCATCATTTTGGGTGATGTGACATATGTCAT
1 ATCATCACTTTGGGTGATGTGACAAATATCAT
* * * *
488303 ATCATCACTTT-GATGACGTGTCAAATGTCAT
1 ATCATCACTTTGGGTGATGTGACAAATATCAT
*
488334 GTCATCA
1 ATCATCA
488341 ATTAAATACA
Statistics
Matches: 100, Mismatches: 30, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
31 46 0.46
32 52 0.52
33 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (32 bp):
ATCATCACTTTGGGTGATGTGACAAATATCAT
Found at i:492259 original size:24 final size:24
Alignment explanation
Indices: 492232--492283 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
492222 CAAAACTGGG
492232 CAAATGCAAAGCCCTCTAACTCGA
1 CAAATGCAAAGCCCTCTAACTCGA
492256 CAAATGCAAAGCCCTCTAACTCGA
1 CAAATGCAAAGCCCTCTAACTCGA
492280 CAAA
1 CAAA
492284 AATAAATCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.40, C:0.33, G:0.12, T:0.15
Consensus pattern (24 bp):
CAAATGCAAAGCCCTCTAACTCGA
Found at i:492314 original size:24 final size:23
Alignment explanation
Indices: 492249--492337 Score: 79
Period size: 24 Copynumber: 3.7 Consensus size: 23
492239 AAAGCCCTCT
* * *
492249 AACTCGACAAATGCAAAGCCCTC
1 AACTCGACAAATGCAAATCACAC
***
492272 TAACTCGACAAAAATAAATCACAC
1 -AACTCGACAAATGCAAATCACAC
*
492296 AGACTCGACAAATGCAAATCAAAC
1 A-ACTCGACAAATGCAAATCACAC
*
492320 AAACTCGACCAATGCAAA
1 -AACTCGACAAATGCAAA
492338 ACCCGAGGTG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
23 1 0.02
24 50 0.96
25 1 0.02
ACGTcount: A:0.48, C:0.28, G:0.10, T:0.13
Consensus pattern (23 bp):
AACTCGACAAATGCAAATCACAC
Found at i:495201 original size:20 final size:20
Alignment explanation
Indices: 495176--495215 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
495166 CCATATTCGA
495176 CCCGGATACGAATCCGAGGT
1 CCCGGATACGAATCCGAGGT
495196 CCCGGATACGAATCCGAGGT
1 CCCGGATACGAATCCGAGGT
495216 GTCACATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.30, G:0.30, T:0.15
Consensus pattern (20 bp):
CCCGGATACGAATCCGAGGT
Found at i:495911 original size:91 final size:91
Alignment explanation
Indices: 495803--495984 Score: 346
Period size: 91 Copynumber: 2.0 Consensus size: 91
495793 AATTATACTC
495803 ATTCACATATACCTTAACATGTACTCATGTATATCATATAACATATACCATATATACTATCATAA
1 ATTCACATATACCTTAACATGTACTCATGTATATCATATAACATATACCATATATACTATCATAA
*
495868 AACACGTATACCCAGGCAACTATAAT
66 AACACGTACACCCAGGCAACTATAAT
*
495894 ATTCACATATACCTTAACCTGTACTCATGTATATCATATAACATATACCATATATACTATCATAA
1 ATTCACATATACCTTAACATGTACTCATGTATATCATATAACATATACCATATATACTATCATAA
495959 AACACGTACACCCAGGCAACTATAAT
66 AACACGTACACCCAGGCAACTATAAT
495985 CATCTCATTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 89 1.00
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.30
Consensus pattern (91 bp):
ATTCACATATACCTTAACATGTACTCATGTATATCATATAACATATACCATATATACTATCATAA
AACACGTACACCCAGGCAACTATAAT
Found at i:496118 original size:23 final size:23
Alignment explanation
Indices: 496092--496169 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
496082 CACCACAACT
496092 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
496115 CATATAATTGCACCGGAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * *
496138 CGTAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
496161 TATAATAAT
1 CAT-ATAAT
496170 GTCCATAAGG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 43 0.91
24 4 0.09
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:496347 original size:103 final size:103
Alignment explanation
Indices: 496179--496393 Score: 358
Period size: 103 Copynumber: 2.1 Consensus size: 103
496169 TGTCCATAAG
* *
496179 GACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
496244 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAA
66 TTCACACATATTCCAAAGAATACATATATGTCCCGAAA
* *
496282 GACCGCATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
* * *
496347 TTCACACATATTCCAAAGAATATATATATGTCCTGAAG
66 TTCACACATATTCCAAAGAATACATATATGTCCCGAAA
496385 GACCACATA
1 GACCACATA
496394 GACCCTCGAA
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATATTCCAAAGAATACATATATGTCCCGAAA
Found at i:511572 original size:21 final size:21
Alignment explanation
Indices: 511542--511590 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
511532 ACATAATATT
*
511542 ACAATATCAAAATTAGGTGCA
1 ACAATGTCAAAATTAGGTGCA
*
511563 ACAATGTCAAAATTAGGTGTA
1 ACAATGTCAAAATTAGGTGCA
*
511584 ATAATGT
1 ACAATGT
511591 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (21 bp):
ACAATGTCAAAATTAGGTGCA
Found at i:516167 original size:21 final size:21
Alignment explanation
Indices: 516142--516189 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
516132 ACCTAATATG
516142 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
516163 CAATGTCAAAATTAGGTGTAA
1 CAATGTCAAAATTAGGTGCAA
*
516184 TAATGT
1 CAATGT
516190 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:520892 original size:19 final size:19
Alignment explanation
Indices: 520868--520906 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
520858 TACATATTCG
520868 CATTGCGATAGTCCAAGTT
1 CATTGCGATAGTCCAAGTT
*
520887 CATTGCGATAGTCGAAGTT
1 CATTGCGATAGTCCAAGTT
520906 C
1 C
520907 GCGTTGCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (19 bp):
CATTGCGATAGTCCAAGTT
Found at i:521618 original size:21 final size:20
Alignment explanation
Indices: 521577--521634 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
521567 GTTTCGTTTC
*
521577 GGAAAATCGCAA-CGAATTT
1 GGAAAATCGCAAGCGAACTT
521596 GGAAAATCGCAACGCGAACTT
1 GGAAAATCGCAA-GCGAACTT
**
521617 GGACTATCGCAATGCGAA
1 GGAAAATCGCAA-GCGAA
521635 TATGTAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 12 0.36
21 21 0.64
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (20 bp):
GGAAAATCGCAAGCGAACTT
Found at i:521668 original size:21 final size:21
Alignment explanation
Indices: 521643--521688 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
521633 AATATGTAAA
521643 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
521664 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
521685 TCGC
1 TCGC
521689 GTTGTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:523049 original size:70 final size:70
Alignment explanation
Indices: 522936--523077 Score: 284
Period size: 70 Copynumber: 2.0 Consensus size: 70
522926 AGAATAAAGA
522936 TCATACCTGCATGAAGGGCAAAAAAATATCATAGAATAAGGCTGAAGATCCACTAAGACTAGCTG
1 TCATACCTGCATGAAGGGCAAAAAAATATCATAGAATAAGGCTGAAGATCCACTAAGACTAGCTG
523001 TGTTT
66 TGTTT
523006 TCATACCTGCATGAAGGGCAAAAAAATATCATAGAATAAGGCTGAAGATCCACTAAGACTAGCTG
1 TCATACCTGCATGAAGGGCAAAAAAATATCATAGAATAAGGCTGAAGATCCACTAAGACTAGCTG
523071 TGTTT
66 TGTTT
523076 TC
1 TC
523078 TCACATTAAT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.25
Consensus pattern (70 bp):
TCATACCTGCATGAAGGGCAAAAAAATATCATAGAATAAGGCTGAAGATCCACTAAGACTAGCTG
TGTTT
Found at i:527107 original size:45 final size:45
Alignment explanation
Indices: 527056--527146 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
527046 ATTTATTTGG
527056 ACCTTCCTGACTTTGCTTATATTCGAAGCCTTGTTCAATAGGTAC
1 ACCTTCCTGACTTTGCTTATATTCGAAGCCTTGTTCAATAGGTAC
527101 ACCTTCCTGACTTTGCTTATATTCGAAGCCTTGTTCAATAGGTAC
1 ACCTTCCTGACTTTGCTTATATTCGAAGCCTTGTTCAATAGGTAC
527146 A
1 A
527147 ATTACACTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (45 bp):
ACCTTCCTGACTTTGCTTATATTCGAAGCCTTGTTCAATAGGTAC
Found at i:528133 original size:23 final size:23
Alignment explanation
Indices: 528107--528150 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
528097 AAAACGGCTT
*
528107 CAGTGGTTTGGAACACA-GTCCTC
1 CAGTGCTTTGGAA-ACATGTCCTC
*
528130 CAGTTCTTTGGAAACATGTCC
1 CAGTGCTTTGGAAACATGTCC
528151 ACAACGGTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (23 bp):
CAGTGCTTTGGAAACATGTCCTC
Found at i:531869 original size:23 final size:23
Alignment explanation
Indices: 531843--531903 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
531833 CTCATATAAA
*
531843 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
531866 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
531889 TACACCGTAGTGCCA
1 TGCACCGTAGTGCCA
531904 TATAATAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:532034 original size:18 final size:18
Alignment explanation
Indices: 532011--532046 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
532001 GAATACATAT
*
532011 ATGTCCTGAAGGACCACA
1 ATGTCCCGAAGGACCACA
532029 ATGTCCCGAAGGACCACA
1 ATGTCCCGAAGGACCACA
532047 TATCATTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.14
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACA
Found at i:533358 original size:21 final size:21
Alignment explanation
Indices: 533332--533375 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
533322 ATTTTATTCG
* *
533332 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
533353 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
533374 CT
1 CT
533376 AGCCCAGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:537368 original size:62 final size:63
Alignment explanation
Indices: 537181--537376 Score: 153
Period size: 62 Copynumber: 3.2 Consensus size: 63
537171 ATTATTCCTT
* * *
537181 AAGAAT-CATATACATATACTAGGGATCAAGTATGCGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
* * * * * * * *
537243 AAGAATACATAT--ATGTCCCGAAGGA-CTA-CA-ATGTC-C-CGAAGGAC--CACATATCATTC
1 AAGAATACATATACATATACC-AAGGATCAAGTATGTGTCTCAC-CA-GACTTCACACAT-GTTC
*
537299 CTT
62 C-A
*
537302 AAGAAT-CATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
1 AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
537364 AAGAATACATATA
1 AAGAATACATATA
537377 TGTCCTGAAG
Statistics
Matches: 97, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
57 7 0.07
58 11 0.11
59 17 0.18
60 8 0.08
61 7 0.07
62 23 0.24
63 17 0.18
64 7 0.07
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.25
Consensus pattern (63 bp):
AAGAATACATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCCA
Found at i:537374 original size:121 final size:121
Alignment explanation
Indices: 537160--537389 Score: 406
Period size: 121 Copynumber: 1.9 Consensus size: 121
537150 TAATCTCCAT
* * *
537160 AAGGACCACATATTATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGCGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGCGTCTCACCA
537225 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACTACAATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACTACAATGTCCCG
* *
537281 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGCGTCTCACCA
*
537346 GACTTCACACATGTTCCAAAGAATACATATATGTCCTGAAGGAC
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGAC
537390 CACATAGACC
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 103 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (121 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGCGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCGAAGGACTACAATGTCCCG
Found at i:553571 original size:73 final size:73
Alignment explanation
Indices: 553450--553606 Score: 278
Period size: 73 Copynumber: 2.2 Consensus size: 73
553440 TCCGGTTTGC
* *
553450 TCTTGTTTCCTACACTGCTCAGGTTCATACTTTCTACATGATTCTCCTGTTATGATACACCATTC
1 TCTTGTTGCTTACACTGCTCAGGTTCATACTTTCTACATGATTCTCCTGTTATGATACACCATTC
553515 ATTAAACT
66 ATTAAACT
* *
553523 TCTTGTTGCTTACACTGCTCAGGTTCATACTTTCTACATGCTTGTCCTGTTATGATACACCATTC
1 TCTTGTTGCTTACACTGCTCAGGTTCATACTTTCTACATGATTCTCCTGTTATGATACACCATTC
553588 ATTAAACT
66 ATTAAACT
553596 TCTTGTTGCTT
1 TCTTGTTGCTT
553607 CCATTCTTCT
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 80 1.00
ACGTcount: A:0.21, C:0.25, G:0.11, T:0.43
Consensus pattern (73 bp):
TCTTGTTGCTTACACTGCTCAGGTTCATACTTTCTACATGATTCTCCTGTTATGATACACCATTC
ATTAAACT
Found at i:560735 original size:12 final size:11
Alignment explanation
Indices: 560706--560740 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
560696 CCTTAACCTC
560706 TTTTA-AAATA
1 TTTTATAAATA
560716 TTTTATAAATA
1 TTTTATAAATA
560727 TTTTAATAAATA
1 TTTT-ATAAATA
560739 TT
1 TT
560741 CATAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.22
11 9 0.39
12 9 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTATAAATA
Found at i:561672 original size:50 final size:51
Alignment explanation
Indices: 561600--561695 Score: 135
Period size: 50 Copynumber: 1.9 Consensus size: 51
561590 TTTAAAATAA
* *
561600 TTATTGAATTTATCAAATTATTATAA-A-AAT-ATTAAATTTCATAAATTGT
1 TTATTAAATTTATCAAACTATTATAATATAATCATTAAATTT-ATAAATTGT
561649 TTATTAAATTTTATCAAACTATTATAATATAATCATTAAATTTATAA
1 TTATTAAA-TTTATCAAACTATTATAATATAATCATTAAATTTATAA
561696 TACTTTCATA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
49 7 0.17
50 17 0.41
51 1 0.02
52 7 0.17
53 9 0.22
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (51 bp):
TTATTAAATTTATCAAACTATTATAATATAATCATTAAATTTATAAATTGT
Found at i:562413 original size:6 final size:6
Alignment explanation
Indices: 562391--562424 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
562381 TGACTTTTTT
*
562391 AAAAAG AAAAA- AGAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
562425 ACGATTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:562413 original size:17 final size:16
Alignment explanation
Indices: 562391--562422 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
562381 TGACTTTTTT
562391 AAAAAGAAAAAAGAAAG
1 AAAAAG-AAAAAGAAAG
562408 AAAAAGAAAAAGAAA
1 AAAAAGAAAAAGAAA
562423 AAACGATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAGAAAG
Found at i:564284 original size:43 final size:43
Alignment explanation
Indices: 564223--564310 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
564213 AATAGTGCAT
564223 ATGTCTGTGTGAGAGTCATATGTATTCCATTAAAGTAAAGAAC
1 ATGTCTGTGTGAGAGTCATATGTATTCCATTAAAGTAAAGAAC
564266 ATGTCTGTGTGAGAGTCATATGTATTCCATTAAAGTAAAGAAC
1 ATGTCTGTGTGAGAGTCATATGTATTCCATTAAAGTAAAGAAC
564309 AT
1 AT
564311 TTCCTTTGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (43 bp):
ATGTCTGTGTGAGAGTCATATGTATTCCATTAAAGTAAAGAAC
Found at i:567795 original size:24 final size:25
Alignment explanation
Indices: 567768--567830 Score: 74
Period size: 28 Copynumber: 2.4 Consensus size: 25
567758 AAATTGAACG
*
567768 ACCGGTTTTTTT-ACCGGATTAAAA
1 ACCGGTTTTTTTAACCGGATAAAAA
567792 ACCGGTTTTTTTTCAAACCGGATAAAAA
1 ACCGG-TTTTTTT--AACCGGATAAAAA
*
567820 ACCAGTTTTTT
1 ACCGGTTTTTT
567831 ATCCGAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
24 5 0.15
25 7 0.21
27 6 0.18
28 15 0.45
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.38
Consensus pattern (25 bp):
ACCGGTTTTTTTAACCGGATAAAAA
Found at i:567907 original size:39 final size:38
Alignment explanation
Indices: 567815--567908 Score: 118
Period size: 39 Copynumber: 2.4 Consensus size: 38
567805 CAAACCGGAT
*
567815 AAAAAACCAGTTTTTTATCCGAAAGAAATCCGGTTTTTA
1 AAAAAACCA-ATTTTTATCCGAAAGAAATCCGGTTTTTA
**
567854 AAAAAACTGGATTTTTATCCGAAA-AAATCCGGTTTTTTTA
1 AAAAAAC-CAATTTTTATCCGAAAGAAATCCGG--TTTTTA
567894 AAAAAACCAATTTTT
1 AAAAAACCAATTTTT
567909 TTGCAAACCG
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 8 0.17
39 26 0.55
40 13 0.28
ACGTcount: A:0.40, C:0.14, G:0.11, T:0.35
Consensus pattern (38 bp):
AAAAAACCAATTTTTATCCGAAAGAAATCCGGTTTTTA
Found at i:575893 original size:2 final size:2
Alignment explanation
Indices: 575886--575918 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
575876 ATTGGATCAC
575886 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
575919 TGAAGTTATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:576510 original size:65 final size:66
Alignment explanation
Indices: 576384--576518 Score: 254
Period size: 65 Copynumber: 2.1 Consensus size: 66
576374 AGTTATCTAG
576384 AATAAAAGTTACCATAATAATCGTTGATCGATATTTTTTTATGAAATAAAAATTTACTCTTAATC
1 AATAAAAGTTACCATAATAATCGTTGATCGATATTTTTTTATGAAATAAAAATTTACTCTTAATC
576449 A
66 A
*
576450 AATAAAAGTTACCATAATAATCGTTGGTC-ATATTTTTTTATGAAATAAAAATTTACTCTTAATC
1 AATAAAAGTTACCATAATAATCGTTGATCGATATTTTTTTATGAAATAAAAATTTACTCTTAATC
576514 A
66 A
576515 AATA
1 AATA
576519 GTACGAAGAT
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
65 40 0.59
66 28 0.41
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (66 bp):
AATAAAAGTTACCATAATAATCGTTGATCGATATTTTTTTATGAAATAAAAATTTACTCTTAATC
A
Found at i:577162 original size:2 final size:2
Alignment explanation
Indices: 577151--577199 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
577141 TTAAGTAATA
577151 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
577192 AT AT AT AT
1 AT AT AT AT
577200 TATTGGTGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:577408 original size:21 final size:21
Alignment explanation
Indices: 577384--577436 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
577374 ATTCTGACTA
*
577384 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
577405 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
577426 TCGCAATGCGA
1 TCGCATTGCGA
577437 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:577451 original size:20 final size:20
Alignment explanation
Indices: 577426--577471 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
577416 TTTTCCTAAT
*
577426 TCGCAATGCGAATAC-GTAAA
1 TCGCAATGCGAAT-CTATAAA
577446 TCGCAATGCGAATCTATAAA
1 TCGCAATGCGAATCTATAAA
577466 TCGCAA
1 TCGCAA
577472 CGAGATTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATCTATAAA
Found at i:578361 original size:24 final size:24
Alignment explanation
Indices: 578334--578387 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
578324 GTATTCGAAA
578334 TTTGATCTTAGTCAATACCCGGAC
1 TTTGATCTTAGTCAATACCCGGAC
* * *
578358 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTAGTCAATACCCGGAC
578382 TTTGAT
1 TTTGAT
578388 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTAGTCAATACCCGGAC
Found at i:580826 original size:20 final size:20
Alignment explanation
Indices: 580801--580892 Score: 141
Period size: 20 Copynumber: 4.6 Consensus size: 20
580791 GACATTCATT
580801 TGACTATCGCAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
580821 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* *
580841 TGACTATCGCAATGCGGAAT
1 TGACTATCGCAACGCGGAAA
580861 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
580881 TGACTATCGCAA
1 TGACTATCGCAA
580893 TGAGAGAATT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 62 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:580865 original size:40 final size:40
Alignment explanation
Indices: 580801--580903 Score: 154
Period size: 40 Copynumber: 2.5 Consensus size: 40
580791 GACATTCATT
*
580801 TGACTATCGCAACGC-GAATATGACTATCGCAACACGGAAA
1 TGACTATCGCAATGCGGAAT-TGACTATCGCAACACGGAAA
*
580841 TGACTATCGCAATGCGGAATTGACTATCGCAACGCGGAAA
1 TGACTATCGCAATGCGGAATTGACTATCGCAACACGGAAA
*
580881 TGACTATCGCAATGAGAGAATTG
1 TGACTATCGCAATGCG-GAATTG
580904 CAATGCGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
40 48 0.83
41 10 0.17
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.20
Consensus pattern (40 bp):
TGACTATCGCAATGCGGAATTGACTATCGCAACACGGAAA
Found at i:580923 original size:33 final size:33
Alignment explanation
Indices: 580866--580961 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
580856 GGAATTGACT
* ** *
580866 ATCGCAACGCGGAAATGACTATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
580900 ATTGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
580933 ATCGCAATGCGAAAATAAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
580962 CGATAGTCAT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 29 0.55
34 24 0.45
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:581106 original size:14 final size:14
Alignment explanation
Indices: 581087--581123 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
581077 CATCAATTAA
581087 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
581101 ACAAATCATCTTTT
1 ACAAATCAACATTT
581115 ACAAATCAA
1 ACAAATCAA
581124 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:582582 original size:42 final size:42
Alignment explanation
Indices: 582475--582584 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
582465 TCTAGAATGT
* * *
582475 TGGGAG-GGACCTCTTCAACGATGACAATGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAAGGGCCTCTTGAACGA
* * ** * *
582517 TGGGAGGGGGCTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAAGGGCCTCTTGAACGA
582559 TAGGG-GAGGCCTCTTGAACGATGACA
1 T-GGGAGAGGCCTCTTGAACGATGACA
582585 GGTGAGTCGG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
42 48 0.91
43 5 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAAGGGCCTCTTGAACGA
Found at i:583089 original size:20 final size:20
Alignment explanation
Indices: 583066--583152 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
583056 GAAGCTTAAA
* *
583066 ATCGCAACGTGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* *
583086 ATCGCAATGTGAAAATAACT
1 ATCGCAATGCGAAAATGACT
* *
583106 ATAGCCATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
583126 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
583146 ATCGCAA
1 ATCGCAA
583153 CGAGAGAATC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:583196 original size:33 final size:34
Alignment explanation
Indices: 583126--583199 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 34
583116 GAAAATGACT
* ** * * *
583126 ATCGCAATGCGAATTTGACTATCGCAACGAGAGA
1 ATCGCAATGCGAATATGAAAATCGCAACAACAAA
583160 ATCGCAATGCGAA-ATGAAAATCGCAACAACAAA
1 ATCGCAATGCGAATATGAAAATCGCAACAACAAA
583193 ATCGCAA
1 ATCGCAA
583200 CGTGAAAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAATATGAAAATCGCAACAACAAA
Found at i:583314 original size:20 final size:20
Alignment explanation
Indices: 583286--583335 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
583276 AATTCTTTCG
583286 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
* **
583306 TTGCAATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
583326 TTGCGATAGT
1 TTGCGATAGT
583336 AAACTATTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:585312 original size:20 final size:20
Alignment explanation
Indices: 585264--585312 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
585254 GCGATTCTCT
585264 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
585284 CATTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
585304 CGTTACGAT
1 CGTTGCGAT
585313 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:585901 original size:20 final size:20
Alignment explanation
Indices: 585876--585929 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
585866 ACGCTATGTA
585876 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
585896 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
585916 AATCGCATTGCGAT
1 AATCGCATTGCGAT
585930 TTACGTATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:585941 original size:20 final size:20
Alignment explanation
Indices: 585918--585968 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
585908 ATAGTCAGAA
585918 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
585938 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
585958 TCGCATTGCGA
1 TCGCATTGCGA
585969 ATTAGGAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:586002 original size:21 final size:22
Alignment explanation
Indices: 585965--586011 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
585955 TATTCGCATT
585965 GCGAATTAGGAAAAATCGCAAC
1 GCGAATTAGGAAAAATCGCAAC
* *
585987 GCGAATTTGG-AAAATCGCAAT
1 GCGAATTAGGAAAAATCGCAAC
586008 GCGA
1 GCGA
586012 TAGTAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (22 bp):
GCGAATTAGGAAAAATCGCAAC
Found at i:594640 original size:19 final size:20
Alignment explanation
Indices: 594616--594655 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
594606 AATTATTCTC
*
594616 ATTTTATA-ATTTTTTTTAA
1 ATTTTATATATTTTTTGTAA
594635 ATTTTATATATTTTTTGTAA
1 ATTTTATATATTTTTTGTAA
594655 A
1 A
594656 ACACACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (20 bp):
ATTTTATATATTTTTTGTAA
Found at i:595954 original size:2 final size:2
Alignment explanation
Indices: 595947--595974 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
595937 TCCCCATAAT
595947 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
595975 AACAACACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:607129 original size:24 final size:24
Alignment explanation
Indices: 607097--607157 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
607087 ACATAGGTAG
*
607097 TGTATCGATACACACGTTAAGGGA
1 TGTACCGATACACACGTTAAGGGA
607121 TGTACCGATACACACGTTAAGGGA
1 TGTACCGATACACACGTTAAGGGA
607145 TGTACCGATACAC
1 TGTACCGATACAC
607158 TATAGAGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (24 bp):
TGTACCGATACACACGTTAAGGGA
Found at i:607736 original size:18 final size:18
Alignment explanation
Indices: 607713--607763 Score: 77
Period size: 17 Copynumber: 2.8 Consensus size: 18
607703 GGATTAACAA
607713 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
607731 TGGTCCTAC-GGACATAG
1 TGGTCCTTCGGGACATAG
607748 TGGTCCTTCCGGGACA
1 TGGTCCTT-CGGGACA
607764 GGTCATTCGG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.52
18 9 0.31
19 5 0.17
ACGTcount: A:0.18, C:0.25, G:0.31, T:0.25
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:607895 original size:160 final size:158
Alignment explanation
Indices: 607629--607947 Score: 579
Period size: 160 Copynumber: 2.0 Consensus size: 158
607619 GAGATTGAAA
607629 TGAGAATGTATTCATATTTAAGCCCATGACATTAATATGAGAGTTGTAGATATAATTGGCATGCC
1 TGAGAATGTATTCATATTTAAGCCCATGACATTAATATGAGAGTTGTAGATATAATTGGCATGCC
607694 AGAGTCGAGGGATTAACAATGGTCCTTCGGGACATAGTGGTCCTAC-GGACATAGTGGTCCTTCC
66 AGAGTCGAGGGATTAACAATGGTCCTTCGGGACATAGTGGTCCTACGGGACATAGTGGTCCTTCC
607758 GGGACA-GGTCATTCGGGACAAAATATTC
131 GGGACAGGGTCATTCGGGAC-AAATATTC
607786 TGAGAAATGTATTCATATTTAAGCCCATGACATTTAATATGAGAGTTGTAGATATAATTGGCATG
1 TGAG-AATGTATTCATATTTAAGCCCATGACA-TTAATATGAGAGTTGTAGATATAATTGGCATG
607851 CCAAGAGTCGAGGGATTAACAATGGTCCTTCGGGACATAGTGGTCCTACGGGACATAGTGGTCCT
64 CC-AGAGTCGAGGGATTAACAATGGTCCTTCGGGACATAGTGGTCCTACGGGACATAGTGGTCCT
607916 TCCGGGACAGTGGTCATTCGGGACAAATATTC
128 TCCGGGACAG-GGTCATTCGGGACAAATATTC
607948 AGTGCCCCTA
Statistics
Matches: 156, Mismatches: 0, Indels: 7
0.96 0.00 0.04
Matches are distributed among these distances:
157 4 0.03
158 27 0.17
159 34 0.22
160 46 0.29
161 24 0.15
162 8 0.05
163 13 0.08
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (158 bp):
TGAGAATGTATTCATATTTAAGCCCATGACATTAATATGAGAGTTGTAGATATAATTGGCATGCC
AGAGTCGAGGGATTAACAATGGTCCTTCGGGACATAGTGGTCCTACGGGACATAGTGGTCCTTCC
GGGACAGGGTCATTCGGGACAAATATTC
Found at i:607896 original size:18 final size:18
Alignment explanation
Indices: 607873--607940 Score: 95
Period size: 18 Copynumber: 3.8 Consensus size: 18
607863 GGATTAACAA
607873 TGGTCCTTCGGGACATAG
1 TGGTCCTTCGGGACATAG
*
607891 TGGTCCTACGGGACATAG
1 TGGTCCTTCGGGACATAG
607909 TGGTCCTTCCGGGAC--AG
1 TGGTCCTT-CGGGACATAG
*
607926 TGGTCATTCGGGACA
1 TGGTCCTTCGGGACA
607941 AATATTCAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.13
17 9 0.20
18 24 0.53
19 6 0.13
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.25
Consensus pattern (18 bp):
TGGTCCTTCGGGACATAG
Found at i:607938 original size:35 final size:35
Alignment explanation
Indices: 607873--607940 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
607863 GGATTAACAA
*
607873 TGGTCCTTCGGGACATAGTGGTCCTACGGGACATAG
1 TGGTCCTTCGGGACA-AGTGGTCATACGGGACATAG
*
607909 TGGTCCTTCCGGGAC-AGTGGTCATTCGGGACA
1 TGGTCCTT-CGGGACAAGTGGTCATACGGGACA
607941 AATATTCAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
35 15 0.52
36 8 0.28
37 6 0.21
ACGTcount: A:0.18, C:0.24, G:0.34, T:0.25
Consensus pattern (35 bp):
TGGTCCTTCGGGACAAGTGGTCATACGGGACATAG
Found at i:608779 original size:18 final size:18
Alignment explanation
Indices: 608756--608829 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
608746 CATTGGATAT
*
608756 GTCCCGAAGGACTACTAC
1 GTCCCGAAGGACCACTAC
*
608774 GTCCCGAAGGACCACTGGATAT
1 GTCCCGAAGGACCAC----TAC
608796 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
*
608814 ATCCCGAAGGACCACT
1 GTCCCGAAGGACCACT
608830 GGATATGTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 31 0.65
22 17 0.35
ACGTcount: A:0.28, C:0.34, G:0.23, T:0.15
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAC
Found at i:608793 original size:40 final size:40
Alignment explanation
Indices: 608744--608852 Score: 182
Period size: 40 Copynumber: 2.7 Consensus size: 40
608734 GCCCCTAAAA
* * *
608744 ACCATTGGATATGTCCCGAAGGACTACTACGTCCCGAAGG
1 ACCACTGGATATGTCCCGAAGGACCACTACATCCCGAAGG
608784 ACCACTGGATATGTCCCGAAGGACCACTACATCCCGAAGG
1 ACCACTGGATATGTCCCGAAGGACCACTACATCCCGAAGG
*
608824 ACCACTGGATATGTCCCGAATGACCACTA
1 ACCACTGGATATGTCCCGAAGGACCACTA
608853 GATATATCCC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.18
Consensus pattern (40 bp):
ACCACTGGATATGTCCCGAAGGACCACTACATCCCGAAGG
Found at i:608802 original size:22 final size:22
Alignment explanation
Indices: 608744--608874 Score: 143
Period size: 22 Copynumber: 6.3 Consensus size: 22
608734 GCCCCTAAAA
*
608744 ACCATTGGATATGTCCCGAAGG
1 ACCACTGGATATGTCCCGAAGG
* *
608766 ACTAC----TACGTCCCGAAGG
1 ACCACTGGATATGTCCCGAAGG
608784 ACCACTGGATATGTCCCGAAGG
1 ACCACTGGATATGTCCCGAAGG
*
608806 ACCACT--ACA--TCCCGAAGG
1 ACCACTGGATATGTCCCGAAGG
*
608824 ACCACTGGATATGTCCCGAATG
1 ACCACTGGATATGTCCCGAAGG
* *
608846 ACCACTAGATATATCCCGAAGG
1 ACCACTGGATATGTCCCGAAGG
608868 ACCACTG
1 ACCACTG
608875 TAACCCTCGA
Statistics
Matches: 89, Mismatches: 12, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
18 31 0.35
20 4 0.04
22 54 0.61
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (22 bp):
ACCACTGGATATGTCCCGAAGG
Found at i:609526 original size:63 final size:63
Alignment explanation
Indices: 609408--609566 Score: 176
Period size: 63 Copynumber: 2.5 Consensus size: 63
609398 GATGCATCCC
* *
609408 TTAACGGGTGCATCGATGCACTACATGTGCATCGGTACACGAATCTCATTCGATGTTTGAATA
1 TTAACGGGTGCATCGATGCACTACATGTGCATCGATACACGAATCGCATTCGATGTTTGAATA
* * * * ** *
609471 TTAAGGGGTGCATCGATGCACTACTTGTGCATCGATACACTG-ATGGCATTTGATGTTTTTATT
1 TTAACGGGTGCATCGATGCACTACATGTGCATCGATACAC-GAATCGCATTCGATGTTTGAATA
* * * *
609534 TTAAAGGAGTGCATCAATACACTTCATGTGCAT
1 TTAACGG-GTGCATCGATGCACTACATGTGCAT
609567 TGATGCACCA
Statistics
Matches: 80, Mismatches: 14, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
63 58 0.73
64 22 0.28
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (63 bp):
TTAACGGGTGCATCGATGCACTACATGTGCATCGATACACGAATCGCATTCGATGTTTGAATA
Found at i:612031 original size:22 final size:22
Alignment explanation
Indices: 611997--612184 Score: 231
Period size: 22 Copynumber: 8.7 Consensus size: 22
611987 GACCATTACA
* *
611997 TCCCTAAGGACCACTGGATATA
1 TCCCGAAGGACCACTGGATATG
* *
612019 TCCCGAAGAACCACTGGACATG
1 TCCCGAAGGACCACTGGATATG
*
612041 TCCCGAAGGACCA-T---TACG
1 TCCCGAAGGACCACTGGATATG
* *
612059 TCCCGAAGAACCACTAGATATG
1 TCCCGAAGGACCACTGGATATG
*
612081 TCCCGAAGGACCACTGGATATA
1 TCCCGAAGGACCACTGGATATG
* *
612103 TTCCGAAAGACCACTGGATATG
1 TCCCGAAGGACCACTGGATATG
* *
612125 TCCCGAAAGACCATTGGATATG
1 TCCCGAAGGACCACTGGATATG
*
612147 TCCCGAAGGACCACTAGATATG
1 TCCCGAAGGACCACTGGATATG
612169 TCCCGAAGGACCACTG
1 TCCCGAAGGACCACTG
612185 TAACCCTCGA
Statistics
Matches: 141, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
18 14 0.10
19 1 0.01
21 1 0.01
22 125 0.89
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (22 bp):
TCCCGAAGGACCACTGGATATG
Found at i:612079 original size:62 final size:62
Alignment explanation
Indices: 611977--612181 Score: 232
Period size: 62 Copynumber: 3.2 Consensus size: 62
611967 AGTGAATATT
* * * * * *
611977 TGTCCCGAAAGACCATTACATCCCTAAGGACCACTGGATATATCCCGAAGAACCACTGGACA
1 TGTCCCGAAAGACCATTACGTCCCGAAGAACCACTGGATATGTCCCGAAGGACCACTGGATA
* *
612039 TGTCCCGAAGGACCATTACGTCCCGAAGAACCACTAGATATGTCCCGAAGGACCACTGGATA
1 TGTCCCGAAAGACCATTACGTCCCGAAGAACCACTGGATATGTCCCGAAGGACCACTGGATA
* * * * *
612101 TATTCCGAAAGACCACTGGATATGTCCCGAA-AGACCATTGGATATGTCCCGAAGGACCACTAGA
1 TGTCCCGAAAGACCA-T---TACGTCCCGAAGA-ACCACTGGATATGTCCCGAAGGACCACTGGA
612165 TA
61 TA
*
612167 TGTCCCGAAGGACCA
1 TGTCCCGAAAGACCA
612182 CTGTAACCCT
Statistics
Matches: 120, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
62 66 0.55
63 1 0.01
65 1 0.01
66 52 0.43
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (62 bp):
TGTCCCGAAAGACCATTACGTCCCGAAGAACCACTGGATATGTCCCGAAGGACCACTGGATA
Found at i:612818 original size:63 final size:64
Alignment explanation
Indices: 612711--612867 Score: 190
Period size: 63 Copynumber: 2.5 Consensus size: 64
612701 TGAACTCTAC
* * * *
612711 AGTGCATCGATGCACTACCTGTGCATCGGTACACAAATCTCATTCGATGTTTGAATATT-AAGG
1 AGTGCATCGATGCACTACATGTGCATCGATACACAAATCGCATTCAATGTTTGAATATTAAAGG
* * * * ** *
612774 GGTGCATCGATGCACTACTTGTGCATCGATACACAGATGGCATTCAATGTTTTTATTTTAAAGG
1 AGTGCATCGATGCACTACATGTGCATCGATACACAAATCGCATTCAATGTTTGAATATTAAAGG
* *
612838 AGTGCATCGATACACTTCATGTGCATCGAT
1 AGTGCATCGATGCACTACATGTGCATCGAT
612868 GCAACTTCAA
Statistics
Matches: 79, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
63 49 0.62
64 30 0.38
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
AGTGCATCGATGCACTACATGTGCATCGATACACAAATCGCATTCAATGTTTGAATATTAAAGG
Found at i:613687 original size:27 final size:27
Alignment explanation
Indices: 613640--613697 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
613630 GATATTGAGG
*
613640 ATGTTACAGTGCATATCATATTTGTAC
1 ATGTTACAGTGCATATCATATATGTAC
* * *
613667 ATGTTATAGTGTAGTAT-ATATATGTAT
1 ATGTTACAGTGCA-TATCATATATGTAC
613694 ATGT
1 ATGT
613698 ACATTGTAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.88
28 3 0.12
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (27 bp):
ATGTTACAGTGCATATCATATATGTAC
Found at i:614322 original size:14 final size:15
Alignment explanation
Indices: 614290--614322 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
614280 TGAAAAAGAA
*
614290 ATATTATTGTATTGT
1 ATATTATTGTATTGC
614305 ATATTATT-TATTGC
1 ATATTATTGTATTGC
614319 ATAT
1 ATAT
614323 ATATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.58
Consensus pattern (15 bp):
ATATTATTGTATTGC
Found at i:615447 original size:26 final size:26
Alignment explanation
Indices: 615389--615447 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 26
615379 TGAAGCTTTT
* *
615389 AACATTCGAAGACTTTGGTGAACATT
1 AACATTTGAAGACTTTGGTGAACATG
* * *
615415 AAGATTTGAATACTTTGGTGAATATG
1 AACATTTGAAGACTTTGGTGAACATG
*
615441 CACATTT
1 AACATTT
615448 TTATATTAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.36
Consensus pattern (26 bp):
AACATTTGAAGACTTTGGTGAACATG
Found at i:618985 original size:2 final size:2
Alignment explanation
Indices: 618978--619031 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
618968 TTCTATCATT
618978 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
619019 TA TA TA AA TA TA T
1 TA TA TA TA TA TA T
619032 TAAGAAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:619582 original size:14 final size:14
Alignment explanation
Indices: 619560--619592 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
619550 GTTTTTTCCC
619560 AAAAA-GGAAAAGG
1 AAAAAGGGAAAAGG
*
619573 GAAAAGGGAAAAGG
1 AAAAAGGGAAAAGG
619587 AAAAAG
1 AAAAAG
619593 CAAATCTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (14 bp):
AAAAAGGGAAAAGG
Found at i:620531 original size:16 final size:17
Alignment explanation
Indices: 620501--620538 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
620491 TCTAATTATA
620501 TATTTTTGAATTATTGT
1 TATTTTTGAATTATTGT
*
620518 TATTTTTTAA-TATTGT
1 TATTTTTGAATTATTGT
620534 T-TTTT
1 TATTTT
620539 AGCATTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 7 0.35
17 9 0.45
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.71
Consensus pattern (17 bp):
TATTTTTGAATTATTGT
Found at i:632521 original size:33 final size:33
Alignment explanation
Indices: 632484--632548 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
632474 TCTTAACTTC
632484 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACAT
1 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACAT
632517 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACA
1 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACA
632549 CCGGCTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.57
Consensus pattern (33 bp):
TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACAT
Found at i:639137 original size:4 final size:4
Alignment explanation
Indices: 639128--639161 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
639118 ATAAAAGGGT
639128 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
639162 CTGACACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:640327 original size:24 final size:22
Alignment explanation
Indices: 640287--640349 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 22
640277 AAGCGACGGT
*
640287 GGGGGTGGGCGGAGGAGCGGGCGGA
1 GGGGGT-GG-GGAGGAGAGGG-GGA
*
640312 GGGGGTGGGGATGGAGATGGGGA
1 GGGGGTGGGGA-GGAGAGGGGGA
640335 GGGGGATGGGGAGGA
1 GGGGG-TGGGGAGGA
640350 ACATTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 14 0.41
24 14 0.41
25 6 0.18
ACGTcount: A:0.16, C:0.05, G:0.71, T:0.08
Consensus pattern (22 bp):
GGGGGTGGGGAGGAGAGGGGGA
Found at i:643855 original size:2 final size:2
Alignment explanation
Indices: 643812--643838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
643802 TCGGGCCGGG
643812 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
643839 TTAAATTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:643886 original size:24 final size:25
Alignment explanation
Indices: 643821--643886 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 25
643811 GTATATATAT
643821 ATATATATATATATATATTTAAATTAA
1 ATATATAT-TATAT-TATTTAAATTAA
*
643848 ATATATATT-TTTTATTTAAATTAA
1 ATATATATTATATTATTTAAATTAA
643872 AT-T-TATTAATATTAT
1 ATATATATT-ATATTAT
643887 ATATATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
22 4 0.11
23 1 0.03
24 19 0.54
25 2 0.06
26 1 0.03
27 8 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATATATATTATATTATTTAAATTAA
Found at i:644533 original size:16 final size:16
Alignment explanation
Indices: 644501--644535 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
644491 TAACGCCTTT
* *
644501 AATCATTAAACAGAGG
1 AATCATTAAAAAAAGG
644517 AATCATTAAAAAAAGG
1 AATCATTAAAAAAAGG
644533 AAT
1 AAT
644536 AATTTCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (16 bp):
AATCATTAAAAAAAGG
Found at i:645817 original size:155 final size:155
Alignment explanation
Indices: 645535--645837 Score: 561
Period size: 155 Copynumber: 2.0 Consensus size: 155
645525 AACTTTTTGG
**
645535 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTTTGAGGCTAGTG
1 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCAGAGGCTAGTG
*
645600 ATTTAATCATGTTGCGGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
66 ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
*
645665 ACATTCACCCTTACCAATATTACAT
131 ACATTCACCCCTACCAATATTACAT
645690 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCAGAGGCTAGTG
1 TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCAGAGGCTAGTG
*
645755 ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGTTCTCACTTGTGAATGAAAGTTGT
66 ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
645820 ACATTCACCCCTACCAAT
131 ACATTCACCCCTACCAAT
645838 GTTATATTAT
Statistics
Matches: 143, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 143 1.00
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.41
Consensus pattern (155 bp):
TTTTACTATTACTTCTGATGAGTGTACAATGATGCTTCCCTCTTTCTTATTTTCAGAGGCTAGTG
ATTTAATCATGTTGCAGTTTGACATTGCCATACTTGTCGAGGTCTCACTTGTGAATGAAAGTTGT
ACATTCACCCCTACCAATATTACAT
Found at i:659602 original size:2 final size:2
Alignment explanation
Indices: 659558--659586 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
659548 CCTTGTAGTT
659558 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
659587 TGCAGCAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:669728 original size:55 final size:54
Alignment explanation
Indices: 669619--669728 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 54
669609 AAGGAAAAAG
669619 ATAATGACATGCTTTGTATGTTTGATTATGTGACAGTCAAGTTTAAGTTGTAAA
1 ATAATGACATGCTTTGTATGTTTGATTATGTGACAGTCAAGTTTAAGTTGTAAA
669673 ATAATGACATGCTTTGTATGTTTGATTAATGTGACAGTCAAGTTTAAGTTGTAAA
1 ATAATGACATGCTTTGTATGTTTGATT-ATGTGACAGTCAAGTTTAAGTTGTAAA
669728 A
1 A
669729 CTATCCACAT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
54 27 0.49
55 28 0.51
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (54 bp):
ATAATGACATGCTTTGTATGTTTGATTATGTGACAGTCAAGTTTAAGTTGTAAA
Found at i:673524 original size:15 final size:15
Alignment explanation
Indices: 673480--673530 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
673470 ATCGTTCTGA
*
673480 TATAATTGTTTTTAT
1 TATAATTGATTTTAT
* ** *
673495 TATGACGGATCTTAT
1 TATAATTGATTTTAT
673510 TATAATTGATTTTAT
1 TATAATTGATTTTAT
673525 TATAAT
1 TATAAT
673531 CGTTATGATA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.55
Consensus pattern (15 bp):
TATAATTGATTTTAT
Found at i:673563 original size:14 final size:14
Alignment explanation
Indices: 673525--673564 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
673515 TTGATTTTAT
**
673525 TATAATCGTTATGA
1 TATAATCGTTCCGA
673539 TATAATCGTTCCGA
1 TATAATCGTTCCGA
673553 TATAATCGTTCC
1 TATAATCGTTCC
673565 TATAATTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (14 bp):
TATAATCGTTCCGA
Found at i:673570 original size:12 final size:13
Alignment explanation
Indices: 673538--673570 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
673528 AATCGTTATG
673538 ATATAATCGTTCC
1 ATATAATCGTTCC
673551 GATATAATCGTTCC
1 -ATATAATCGTTCC
673565 -TATAAT
1 ATATAAT
673571 TGTTTTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
14 13 0.68
ACGTcount: A:0.33, C:0.18, G:0.09, T:0.39
Consensus pattern (13 bp):
ATATAATCGTTCC
Found at i:679217 original size:135 final size:134
Alignment explanation
Indices: 678994--679265 Score: 471
Period size: 135 Copynumber: 2.0 Consensus size: 134
678984 GGTGAGATAA
678994 TTTGAAAGTTCCTTTCTCCTTGCTAATACCATACTCGAAAATACCCTTCTGAAACAGCCACAATC
1 TTTGAAAGTTCCTTTCTCCTTGCTAATACCATACTCGAAAATACCCTTCTGAAACAGCCACAATC
679059 ATAAGATTAAGGAGTTCTCCTACTATGTT-AATAACATA-G-GAC-AAGAGAAACCTTGACGAAT
66 ATAAGATTAAGGAGTTCTCCTACTATGTTAAATAACATAGGAGACAAAGAGAAACCTTGACGAAT
679120 ACCC
131 ACCC
679124 TTTGAAAGTTCCTTTCTCCTTGCTAATAACCATACTCGAAAATAACCCTTCTGAAACAGCCCTAC
1 TTTGAAAGTTCCTTTCTCCTTGCTAAT-ACCATACTCGAAAAT-ACCCTTCTGAAACAG-CC-AC
679189 GAATCATAAGATTAAGGAGTTCTCCTACTATGTTAAATAACATAGGAGACAAAGAGAAACCTTGA
62 -AATCATAAGATTAAGGAGTTCTCCTACTATGTTAAATAACATAGGAGACAAAGAGAAACCTTGA
679254 CGAATACCC
126 CGAATACCC
679263 TTT
1 TTT
679266 CCCATTGGGA
Statistics
Matches: 133, Mismatches: 0, Indels: 9
0.94 0.00 0.06
Matches are distributed among these distances:
130 27 0.20
131 15 0.11
132 15 0.11
133 2 0.02
134 2 0.02
135 33 0.25
136 9 0.07
137 1 0.01
138 3 0.02
139 26 0.20
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (134 bp):
TTTGAAAGTTCCTTTCTCCTTGCTAATACCATACTCGAAAATACCCTTCTGAAACAGCCACAATC
ATAAGATTAAGGAGTTCTCCTACTATGTTAAATAACATAGGAGACAAAGAGAAACCTTGACGAAT
ACCC
Found at i:680540 original size:30 final size:31
Alignment explanation
Indices: 680472--680620 Score: 83
Period size: 31 Copynumber: 4.9 Consensus size: 31
680462 GAAGGACCTA
* ** *
680472 TCCAGAGGTCACAAAG-ACCCCGGT-AACTA
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * * * *
680501 TCAAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
680531 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* ** * *
680562 TCCATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTAAACTG
* * *
680593 TCCATATGTCTCGAAAG-ACATAGGTAAA
1 TCCATAGGTCAC-AAAGAACCTAGGTAAA
680621 ACCCTCGACT
Statistics
Matches: 94, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
29 14 0.15
30 31 0.33
31 44 0.47
32 5 0.05
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.22
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:680564 original size:31 final size:31
Alignment explanation
Indices: 680526--680620 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
680516 GAACCTCGGC
* *
680526 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
680557 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
680588 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
680619 AA
1 AA
680621 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:681921 original size:64 final size:63
Alignment explanation
Indices: 681788--681948 Score: 189
Period size: 64 Copynumber: 2.5 Consensus size: 63
681778 TAATGAAGGT
** * * *
681788 ATGCATCGATGCACTATACCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* * *
681853 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
681917 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTCCATATGCATCGATGCA
681949 CCTTAAACAA
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
64 58 0.70
65 22 0.27
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:682891 original size:2 final size:2
Alignment explanation
Indices: 682884--682938 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
682874 CCTTTTCCTT
682884 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
682926 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
682939 TCATATCATG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:683020 original size:20 final size:18
Alignment explanation
Indices: 682984--683024 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
682974 GTAACTTCAA
*
682984 TCCATTTTCTTTCTTTAT
1 TCCATTTTCTTTATTTAT
683002 TCCATTCTTCCTTTATTTAT
1 TCCATT-TT-CTTTATTTAT
683022 TCC
1 TCC
683025 TTATGCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 2 0.10
20 12 0.60
ACGTcount: A:0.12, C:0.27, G:0.00, T:0.61
Consensus pattern (18 bp):
TCCATTTTCTTTATTTAT
Found at i:685094 original size:30 final size:31
Alignment explanation
Indices: 685026--685174 Score: 85
Period size: 31 Copynumber: 4.9 Consensus size: 31
685016 AAAGGACCTA
* * *
685026 TCCAGAGGTCACAAAGACCCCTA--T-AACTA
1 TCCATAGGTCACAAAGA-ACCTAGGTAAACTG
* * * *
685055 TCCAGAGGTCATAAAGAACCTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
685085 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* ** * *
685116 TCCATATGTTC-CTTAGAACATAGGTATACTG
1 TCCATA-GGTCACAAAGAACCTAGGTAAACTG
* * *
685147 TCCATATGTCTCGAAAG-ACATAGGTAAA
1 TCCATAGGTCAC-AAAGAACCTAGGTAAA
685175 ACCTTCGACT
Statistics
Matches: 94, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
28 3 0.03
29 16 0.17
30 26 0.28
31 44 0.47
32 5 0.05
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:685118 original size:31 final size:31
Alignment explanation
Indices: 685080--685174 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
685070 GAACCTCGGC
* *
685080 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
685111 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
685142 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
685173 AA
1 AA
685175 ACCTTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:686357 original size:64 final size:64
Alignment explanation
Indices: 686238--686357 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 64
686228 TGAAGGTATG
*
686238 ATCGATGCACTACACATGCATCGATGCATAAATCCTATTCGAGTGTTTGTATTTAATGGGAAAC
1 ATCGATGCACTACACATGCATCGATGCATAAATCCTATTCGAGTGTTTCTATTTAATGGGAAAC
* ** *
686302 ATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGA-TGTTTTCTTTTTAA
1 ATCGATGCACTACACATGCATCGATGCATAAATCCTATTCGAGTG-TTTCTATTTAA
686358 ATAATGCATC
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
63 2 0.04
64 48 0.96
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (64 bp):
ATCGATGCACTACACATGCATCGATGCATAAATCCTATTCGAGTGTTTCTATTTAATGGGAAAC
Found at i:690683 original size:20 final size:20
Alignment explanation
Indices: 690646--690688 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
690636 ATTCCACCAT
*
690646 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
690666 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
690686 ATG
1 ATG
690689 TGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:691106 original size:15 final size:16
Alignment explanation
Indices: 691078--691107 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
691068 CGAGGAGAGT
691078 CATCCCATCACTCTAC
1 CATCCCATCACTCTAC
691094 CATCCCA-CACTCTA
1 CATCCCATCACTCTA
691108 GATGAAAGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.50, G:0.00, T:0.23
Consensus pattern (16 bp):
CATCCCATCACTCTAC
Found at i:695442 original size:20 final size:20
Alignment explanation
Indices: 695405--695447 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
695395 ATTCCACCAC
*
695405 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
695425 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
695445 ATG
1 ATG
695448 TTCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:697680 original size:2 final size:2
Alignment explanation
Indices: 697673--697703 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
697663 TCATAGTTTC
*
697673 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
697704 CTTGTTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:697789 original size:2 final size:2
Alignment explanation
Indices: 697782--697817 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
697772 TTGTAATTCG
697782 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
697818 GAATTTGATT
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:699440 original size:2 final size:2
Alignment explanation
Indices: 699433--699466 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
699423 TTTATGTCAG
699433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
699467 GACATAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.