Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008539.1 Hibiscus syriacus cultivar Beakdansim tig00111427_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: 6067759
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 18 of 31
Found at i:3248314 original size:33 final size:34
Alignment explanation
Indices: 3248257--3248328 Score: 137
Period size: 33 Copynumber: 2.1 Consensus size: 34
3248247 ACAACGAATA
3248257 TTGTTCAATCTTAGTTGGCTCCACTAGTTTCTCG
1 TTGTTCAATCTTAGTTGGCTCCACTAGTTTCTCG
3248291 TTGTTCAATCTTAG-TGGCTCCACTAGTTTCTCG
1 TTGTTCAATCTTAGTTGGCTCCACTAGTTTCTCG
3248324 TTGTT
1 TTGTT
3248329 AAAATTTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 24 0.63
34 14 0.37
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (34 bp):
TTGTTCAATCTTAGTTGGCTCCACTAGTTTCTCG
Found at i:3248529 original size:54 final size:54
Alignment explanation
Indices: 3248465--3248572 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
3248455 AGAATAACTG
* * *
3248465 GTTCGTAAAACATTTGACAACACATTCATTCTTTCATGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATATGGCTTCTGCCCAGAT
* *
3248519 GTTCGTAAAACATTTGATAACACATTCATCCTTTCTTATGGCTTCTGCCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATATGGCTTCTGCCCAGAT
3248573 TTTTCAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCATATGGCTTCTGCCCAGAT
Found at i:3249549 original size:76 final size:75
Alignment explanation
Indices: 3249451--3249700 Score: 304
Period size: 76 Copynumber: 3.3 Consensus size: 75
3249441 GATATAAGCC
* * *
3249451 TTCAGCATGCCCCAACATTTGCTAATACAGACGTTCAAAATGAGCCAACATTCCTGA-TTCTGAT
1 TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATGAGTCAACATTCCT-ATTTCTGAT
*
3249515 TAAAATGGGCT
65 TGAAATGGGCT
* ** * *
3249526 TTCAGCATACCCCCAACATTTGCTGATACAAACGTTCAAAACAAATCAACATTTCTATTTCTGAT
1 TTCAGCAT-GCCCCAACATTTGCTGATACAAACGTTCAAAATGAGTCAACATTCCTATTTCTGAT
3249591 TGAAATGGGCCT
65 TGAAATGGG-CT
* ** * * * *
3249603 TTCAGCGTGCCCCAACATTTGCTGATACAAATATTCAAAATGCGTTAATATTCATATTTCTGATT
1 TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATGAGTCAACATTCCTATTTCTGATT
3249668 GAAATGGGCT
66 GAAATGGGCT
* *
3249678 TTCAGCATTCCTCAACATTTGCT
1 TTCAGCATGCCCCAACATTTGCT
3249701 TCTTGTTGAT
Statistics
Matches: 148, Mismatches: 24, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
75 31 0.21
76 108 0.73
77 9 0.06
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (75 bp):
TTCAGCATGCCCCAACATTTGCTGATACAAACGTTCAAAATGAGTCAACATTCCTATTTCTGATT
GAAATGGGCT
Found at i:3249734 original size:40 final size:39
Alignment explanation
Indices: 3249675--3249770 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 39
3249665 ATTGAAATGG
** * * ** *
3249675 GCTTTCAGCATTCCTCAACATTTGCTTCTTGTTGATGTGA
1 GCTTTCAAAATTCCCCAACATTT-CTTCATACTGATATGA
*
3249715 GCTTTCAAAATTCCCCAACATTTTTTCATACTGATATGA
1 GCTTTCAAAATTCCCCAACATTTCTTCATACTGATATGA
*
3249754 GCCTTCAAAATTCCCCA
1 GCTTTCAAAATTCCCCA
3249771 TATGGGTATG
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 27 0.57
40 20 0.43
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (39 bp):
GCTTTCAAAATTCCCCAACATTTCTTCATACTGATATGA
Found at i:3250910 original size:64 final size:63
Alignment explanation
Indices: 3250798--3250953 Score: 217
Period size: 64 Copynumber: 2.5 Consensus size: 63
3250788 GTGCACTAAG
* *
3250798 AGTGCATCGATGCATAAAATGAATTCGATGTTTTAAACAAGCCAGAGTGCATCGATGCATGGT
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCAGAGTGCATAGATGCATGGT
* **
3250861 CTGTGCATCGATGCATAAAATGCATTCGATGTTTTCATAA-AA-CTTGAGTGCATAGATGCATGG
1 -AGTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AACAAGCCAGAGTGCATAGATGCATGG
3250924 T
63 T
*
3250925 AGTGTATCGATGCATAAAATGCATTCGAT
1 AGTGCATCGATGCATAAAATGCATTCGAT
3250954 ATGGTGAGTG
Statistics
Matches: 83, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
63 27 0.33
64 51 0.61
65 3 0.04
66 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.22, T:0.30
Consensus pattern (63 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTTAAACAAGCCAGAGTGCATAGATGCATGGT
Found at i:3250984 original size:20 final size:20
Alignment explanation
Indices: 3250959--3251015 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
3250949 TCGATATGGT
*
3250959 GAGTGCATTGATGCATCAAC
1 GAGTGCATCGATGCATCAAC
*
3250979 GAGTGCATCGATGCATCAAT
1 GAGTGCATCGATGCATCAAC
3250999 GAGTGCATCGATGCATC
1 GAGTGCATCGATGCATC
3251016 CCTTCTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.25
Consensus pattern (20 bp):
GAGTGCATCGATGCATCAAC
Found at i:3252655 original size:44 final size:45
Alignment explanation
Indices: 3252602--3252699 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 45
3252592 GGCCTTGTGC
*
3252602 ATCGATGCACATTT-AAGGCG-TGCATCGGTGCA-TCTTCAT-GATGT
1 ATCGATGCACATTTAAAGG-GATGCATCGATGCACT-TTCATAG-TGT
*
3252646 ATCGATGCACATTTAAAGGGATGCATCGATGTACTTTCATAGTGT
1 ATCGATGCACATTTAAAGGGATGCATCGATGCACTTTCATAGTGT
3252691 ATCGATGCA
1 ATCGATGCA
3252700 TTATGCACAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
44 15 0.31
45 31 0.65
46 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (45 bp):
ATCGATGCACATTTAAAGGGATGCATCGATGCACTTTCATAGTGT
Found at i:3258235 original size:20 final size:20
Alignment explanation
Indices: 3258210--3258247 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3258200 TTCGATATGG
3258210 TGAGTGAATCGATGCATCAA
1 TGAGTGAATCGATGCATCAA
* *
3258230 TGAGTGCATCGGTGCATC
1 TGAGTGAATCGATGCATC
3258248 CCTTCTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGAATCGATGCATCAA
Found at i:3260329 original size:72 final size:72
Alignment explanation
Indices: 3260170--3260370 Score: 246
Period size: 72 Copynumber: 2.7 Consensus size: 72
3260160 TAGTTGAAAC
* ** * * *
3260170 TTATCCATAAAGTCGGGG-TGATTAACCAATTGCTCTAGAGG-GACAGTTTTATTGCCTATAATA
1 TTATCCATAAAGTCGGGGCT-ATTAACCAATTGCTTTAG-GGAGACA-ACTCA-AG-C-ATAACA
3260233 GGTTAGCTGAATA
60 GGTTAGCTGAATA
3260246 TTATCCATAAAG-CTGGGGCTATTAACCAATTGCTTTAGGGAGACAACTCAAGCATAACAGGTTA
1 TTATCCATAAAGTC-GGGGCTATTAACCAATTGCTTTAGGGAGACAACTCAAGCATAACAGGTTA
3260310 GCTGAATA
65 GCTGAATA
* *
3260318 TTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGGGATAACTCAAGC
1 TTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGAGACAACTCAAGC
3260371 TTTATTGTAT
Statistics
Matches: 113, Mismatches: 8, Indels: 12
0.85 0.06 0.09
Matches are distributed among these distances:
72 67 0.59
73 2 0.02
74 1 0.01
75 5 0.04
76 37 0.33
77 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (72 bp):
TTATCCATAAAGTCGGGGCTATTAACCAATTGCTTTAGGGAGACAACTCAAGCATAACAGGTTAG
CTGAATA
Found at i:3262509 original size:42 final size:42
Alignment explanation
Indices: 3262450--3262532 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
3262440 TAGTTTTTTT
* * * * *
3262450 ATTTGCTCTTTTGAATCATCTTAGAATTTTTTTGCTTGATCC
1 ATTTGCTCATTTGAATCACCCTAGAACTTTTTTACTTGATCC
* *
3262492 ATTTGTTCATTTGAATCACCCTGGAACTTTTTTACTTGATC
1 ATTTGCTCATTTGAATCACCCTAGAACTTTTTTACTTGATC
3262533 AGTAATCTCT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.20, C:0.18, G:0.12, T:0.49
Consensus pattern (42 bp):
ATTTGCTCATTTGAATCACCCTAGAACTTTTTTACTTGATCC
Found at i:3263018 original size:43 final size:43
Alignment explanation
Indices: 3262938--3263025 Score: 117
Period size: 43 Copynumber: 2.0 Consensus size: 43
3262928 AAGTTTCGGT
* * *
3262938 ACATCAAACAAAACTTTATATATAGGGATAGATTTCACTCCTA
1 ACATCAAACAAAACTTTACATATAGGGACAGACTTCACTCCTA
3262981 ACATC-AACAAAACTTTACATATAGGGGACA-ACCTTCACTCCTA
1 ACATCAAACAAAACTTTACATATA-GGGACAGA-CTTCACTCCTA
3263024 AC
1 AC
3263026 TTCTCTAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 18 0.45
43 22 0.55
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (43 bp):
ACATCAAACAAAACTTTACATATAGGGACAGACTTCACTCCTA
Found at i:3264899 original size:3 final size:3
Alignment explanation
Indices: 3264891--3264968 Score: 93
Period size: 3 Copynumber: 25.0 Consensus size: 3
3264881 ATTTATAATT
* * *
3264891 TAA TAA TAA TAA TAA TAA TAA TAT TAA CAA TAA TAA TAG TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
*
3264937 TAAA TAAA TAA TGA TAA TAA TAA TAA TAA TAA
1 T-AA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
3264969 AAATGGGCAA
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
3 56 0.86
4 9 0.14
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3270476 original size:24 final size:25
Alignment explanation
Indices: 3270443--3270496 Score: 92
Period size: 24 Copynumber: 2.2 Consensus size: 25
3270433 AGGGCACTAA
*
3270443 GTGTATATGGTGGGCATGACCTTAT
1 GTGTATATGGTGGGCACGACCTTAT
3270468 GTGT-TATGGTGGGCACGACCTTAT
1 GTGTATATGGTGGGCACGACCTTAT
3270492 GTGTA
1 GTGTA
3270497 AGCACTGCGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (25 bp):
GTGTATATGGTGGGCACGACCTTAT
Found at i:3276978 original size:26 final size:25
Alignment explanation
Indices: 3276943--3276997 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
3276933 GGGCACTAAG
3276943 TGTATATGGTGGGCACA-ACCTTATA
1 TGTATATGGTGGGCA-AGACCTTATA
*
3276968 TGTATTATGGTGGGCAAGACCTTATG
1 TGTA-TATGGTGGGCAAGACCTTATA
3276994 TGTA
1 TGTA
3276998 AGCACTACGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (25 bp):
TGTATATGGTGGGCAAGACCTTATA
Found at i:3278314 original size:2 final size:2
Alignment explanation
Indices: 3278307--3278338 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3278297 AGATTTAATC
*
3278307 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3278339 ATCATCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3279288 original size:2 final size:2
Alignment explanation
Indices: 3279281--3279305 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3279271 ATCTTAACTC
3279281 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3279306 ATCCCTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3283328 original size:14 final size:13
Alignment explanation
Indices: 3283308--3283347 Score: 53
Period size: 14 Copynumber: 3.0 Consensus size: 13
3283298 TTTGATTTTT
3283308 CGGTCAAAGTCAA
1 CGGTCAAAGTCAA
*
3283321 CAGGTCAAAGTAAA
1 C-GGTCAAAGTCAA
*
3283335 CGATCAAAGTCAA
1 CGGTCAAAGTCAA
3283348 TGGGTCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (13 bp):
CGGTCAAAGTCAA
Found at i:3283394 original size:14 final size:14
Alignment explanation
Indices: 3283365--3283415 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
3283355 ATGTTAATGG
**
3283365 GTTGACTCGGACGA
1 GTTGACTCAAACGA
* * *
3283379 GTTAACTCATATGA
1 GTTGACTCAAACGA
3283393 GTTGACTCAAACGA
1 GTTGACTCAAACGA
3283407 GTTGACTCA
1 GTTGACTCA
3283416 GTTTGAGTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (14 bp):
GTTGACTCAAACGA
Found at i:3283406 original size:28 final size:29
Alignment explanation
Indices: 3283365--3283426 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
3283355 ATGTTAATGG
**
3283365 GTTGACTCGGACGAGTTAACTCA-TATGA
1 GTTGACTCAAACGAGTTAACTCAGTATGA
* *
3283393 GTTGACTCAAACGAGTTGACTCAGTTTGA
1 GTTGACTCAAACGAGTTAACTCAGTATGA
3283422 GTTGA
1 GTTGA
3283427 GTCGATCGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 20 0.69
29 9 0.31
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (29 bp):
GTTGACTCAAACGAGTTAACTCAGTATGA
Found at i:3288254 original size:33 final size:30
Alignment explanation
Indices: 3288212--3288271 Score: 75
Period size: 33 Copynumber: 1.9 Consensus size: 30
3288202 GAGTCGTATT
* *
3288212 TAATTATTTTTACTAAGCTTGAATTTCTTTAAA
1 TAATCATTTTAACTAA-CTT-AA-TTCTTTAAA
3288245 TAATCATTTTAACTAACTTAATTCTTT
1 TAATCATTTTAACTAACTTAATTCTTT
3288272 TTTGTCTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 2 0.08
32 3 0.12
33 14 0.56
ACGTcount: A:0.33, C:0.12, G:0.03, T:0.52
Consensus pattern (30 bp):
TAATCATTTTAACTAACTTAATTCTTTAAA
Found at i:3291829 original size:20 final size:19
Alignment explanation
Indices: 3291806--3291866 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
3291796 AATATATAGC
3291806 AAAAAGAGAGAAAGAAACAT
1 AAAAAGAGAGAAAGAAA-AT
3291826 AAAAA-AGAGAAAAGAAAGA-
1 AAAAAGAGAG-AAAGAAA-AT
* *
3291845 AAGAAGAGAGAGAGAAAAT
1 AAAAAGAGAGAAAGAAAAT
3291864 AAA
1 AAA
3291867 GAAACAGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
18 1 0.03
19 16 0.47
20 17 0.50
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.03
Consensus pattern (19 bp):
AAAAAGAGAGAAAGAAAAT
Found at i:3291846 original size:24 final size:24
Alignment explanation
Indices: 3291814--3291911 Score: 83
Period size: 24 Copynumber: 4.0 Consensus size: 24
3291804 GCAAAAAGAG
3291814 AGAAAGAAACATA-AAAAAGAGAAA
1 AGAAAGAAACA-AGAAAAAGAGAAA
* * *
3291838 AGAAAGAAAGAAGAGAGAGAGAAA
1 AGAAAGAAACAAGAAAAAGAGAAA
* * *
3291862 ATAAAGAAACAGAGAGAGAGAGAAA
1 AGAAAGAAACA-AGAAAAAGAGAAA
* *
3291887 ATAAAGCAAAAAAGAAAAA-AGAAA
1 AGAAAG-AAACAAGAAAAAGAGAAA
3291911 A
1 A
3291912 ATACTTCAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.02
24 34 0.54
25 24 0.38
26 4 0.06
ACGTcount: A:0.71, C:0.03, G:0.22, T:0.03
Consensus pattern (24 bp):
AGAAAGAAACAAGAAAAAGAGAAA
Found at i:3291883 original size:25 final size:24
Alignment explanation
Indices: 3291831--3291901 Score: 97
Period size: 25 Copynumber: 2.9 Consensus size: 24
3291821 AACATAAAAA
* *
3291831 AGAGAAAAGAAAGAAAGAAGAGAG
1 AGAGAAAATAAAGAAACAAGAGAG
3291855 AGAGAAAATAAAGAAACAGAGAGAG
1 AGAGAAAATAAAGAAACA-AGAGAG
*
3291880 AGAGAAAATAAAGCAAAAAAGA
1 AGAGAAAATAAAG-AAACAAGA
3291902 AAAAAGAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 16 0.38
25 22 0.52
26 4 0.10
ACGTcount: A:0.68, C:0.03, G:0.27, T:0.03
Consensus pattern (24 bp):
AGAGAAAATAAAGAAACAAGAGAG
Found at i:3294222 original size:54 final size:54
Alignment explanation
Indices: 3294000--3294383 Score: 309
Period size: 54 Copynumber: 7.1 Consensus size: 54
3293990 TTTTTAAAAA
* * * * * *
3294000 CTAAACCTAATTTTTA-GGGTTTCATGAT-TTTTCAAAT-AATTTTTAAAGGAG
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAG
* * ** * * *
3294051 CTAAGTCC-GATTTTTAGAAGTTTCTTGATGATTTCTTCAAATGATTTTTTAAATAAG
1 CTAAG-CCTAATTTTCAGGGGTTTCTTGATG---TCTTCAAATGAATTTTGAAAGAAG
* * * * * * * *
3294108 CTAAGCCTAATTTTTATAGGTTTTCTTGATGTTTTCAGAGGAACTTTGAATGAAG
1 CTAAGCCTAATTTTCA-GGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAG
* * *
3294163 TTAAGCCTGATTTTCAGGGGTTTCTTAATGTCTTCAAATGAATTTTGAAAGAAG
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAG
* * *
3294217 ATAAGCCTAATTTTCAGGGGTTTCTTGATTTCTTCAAATGGATTTTGAAAGAAG
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAG
* * * *
3294271 CTAAGTCTAATTTTCA-AGG---CTTGATGTTTTCAAATGAATTTTTAAAGAAG
1 CTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAG
* * *
3294321 CTAAGCCTAATATTTTAGGGGTTTCTTGATGATAATTGTAAATGAATTTTTG-AAGAAG
1 CTAAGCCTAAT-TTTCAGGGGTTTCTTGATG-T-CTT-CAAATGAA-TTTTGAAAGAAG
3294379 CTAAG
1 CTAAG
3294384 TTTGATTTTC
Statistics
Matches: 264, Mismatches: 51, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
50 37 0.14
51 15 0.06
52 13 0.05
53 2 0.01
54 93 0.35
55 36 0.14
56 11 0.04
57 25 0.09
58 28 0.11
59 4 0.02
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (54 bp):
CTAAGCCTAATTTTCAGGGGTTTCTTGATGTCTTCAAATGAATTTTGAAAGAAG
Found at i:3296074 original size:117 final size:117
Alignment explanation
Indices: 3295863--3296075 Score: 327
Period size: 117 Copynumber: 1.8 Consensus size: 117
3295853 TTCTAATGAA
*
3295863 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAACTTGTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAAATTGTT
* *
3295928 CAACCTTAGCTTGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTGG
66 CAACCTCAGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTGG
* ** * *
3295980 AGAGTTCATAATGAGAATAACTCATGTGATGAGGGAGAAGAAGTTCATAATGAGAAGAAATTTTT
1 AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAAATTGTT
* * *
3296045 CAACCTCAGCTCGTTTCCATCAGATAAGGAG
66 CAACCTCAGCTCGATTCCATCACAGAAGGAG
3296076 TTAAAGCAAC
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 85 1.00
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (117 bp):
AGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAATTCATAATGAGAAGAAATTGTT
CAACCTCAGCTCGATTCCATCACAGAAGGAGGTGGATCAACATTTTCAGTGG
Found at i:3296330 original size:158 final size:158
Alignment explanation
Indices: 3296107--3296742 Score: 618
Period size: 158 Copynumber: 4.0 Consensus size: 158
3296097 GCTCATCAGG
* * *
3296107 ATCATTACTTTGTTCGATTCCATCAACAAAAACAGTTGGATCAACATTT-CAATGGAGATTTCAT
1 ATCATTACTTTGTTCGATTCCATC-ACAGAAAGAGGTGGATCAACATTTCCAATGGAGATTTCAT
*
3296171 AATGAGAAGAACTCATCCAATGAATGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTGG
65 AATGAGAAGAACTCATCCAAT-AATGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAG
*
3296235 CTCATCCATCGCATATGGAGTTGGATGAAC
129 CTCATCCATCGCATATGGAGTTGGATCAAC
* * * * * * *
3296265 ATCATCACTTTGTTCGATCCCATCATAGAAAGATGTGGATCAACATTTCCAGTAGAGAGTTCATA
1 ATCATTACTTTGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTTCCAATGGAGATTTCATA
** * * * ** *** * * ** * **
3296330 ATGAGAAGAACTTGTTCAAT-CTCAGCTCGTTTCTATCACATAAGGTGTTGGAAC-AGCACCAAT
66 ATGAGAAGAACTCATCCAATAATGAG-AAG-AAGT-T--CATAATGAG-AAGAACTTG-TTCAA-
* * *
3296393 ACTT-GTCTCATTCATCACATAT-GAGTTGGATCAAC
123 CCTTAG-CTCATCCATCGCATATGGAGTTGGATCAAC
* * * * *
3296428 ATCATTACTTTGTTCGATTCCATTAACAGAATGAGGAGGATCAATATTTCCAATGGATATTTCAT
1 ATCATTACTTTGTTCGATTCCA-TCACAGAAAGAGGTGGATCAACATTTCCAATGGAGATTTCAT
* *
3296493 AATGAGAATAACTCATCCAATAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGC
65 AATGAGAAGAACTCATCCAATAATGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGC
* *
3296558 TCATACATCGCATATGGAGTTGGATCATC
130 TCATCCATCGCATATGGAGTTGGATCAAC
** * * *
3296587 ATCATTACTTTGTTTAATTCCATCACAGAATGAGGTGGATCAACATTTCTAGTGGAGATTTCATA
1 ATCATTACTTTGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTTCCAATGGAGATTTCATA
** * * *
3296652 ATGAGAAGAACTCATCTGATGAAAGAGAAGAAGATCATAATGAGAAGAACTTGTTCAACCTTATC
66 ATGAGAAGAACTCATCCAAT-AATGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGC
* *
3296717 TCGTTTCCATCGCATAAGGAGTTGGA
130 TC--ATCCATCGCATATGGAGTTGGA
3296743 ACAGCACCGA
Statistics
Matches: 377, Mismatches: 82, Indels: 35
0.76 0.17 0.07
Matches are distributed among these distances:
156 3 0.01
157 20 0.05
158 124 0.33
159 84 0.22
160 8 0.02
161 27 0.07
162 8 0.02
163 34 0.09
164 67 0.18
165 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (158 bp):
ATCATTACTTTGTTCGATTCCATCACAGAAAGAGGTGGATCAACATTTCCAATGGAGATTTCATA
ATGAGAAGAACTCATCCAATAATGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCT
CATCCATCGCATATGGAGTTGGATCAAC
Found at i:3296767 original size:158 final size:158
Alignment explanation
Indices: 3296444--3296786 Score: 395
Period size: 158 Copynumber: 2.2 Consensus size: 158
3296434 ACTTTGTTCG
* * * * *
3296444 ATTCCATTAACAGAATGAGGAGGATCAATATTTCCAATGGATATTTCATAATGAGAATAACTCAT
1 ATTCCA-TCACAGAATGAGGTGGATCAACATTTCCAATGGAGATTTCATAATGAGAAGAACTCAT
* * *
3296509 CCAATAAGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATACATCGCATATG
65 CCAATAAAGAGAAGAAGATCATAATGAGAAGAACTTGTTCAACCTTAGCTCATACATCGCATAAG
* * ** * **
3296574 GAGTTGGATCATCATCATTACTTTGTTTA
130 GAGTTGGAACAGCATCACGACCTTGCCTA
* *
3296603 ATTCCATCACAGAATGAGGTGGATCAACATTTCTAGTGGAGATTTCATAATGAGAAGAACTCATC
1 ATTCCATCACAGAATGAGGTGGATCAACATTTCCAATGGAGATTTCATAATGAGAAGAACTCATC
** * * *
3296668 TGATGAAAGAGAAGAAGATCATAATGAGAAGAACTTGTTCAACCTTATCTCGTTTCCATCGCATA
66 CAAT-AAAGAGAAGAAGATCATAATGAGAAGAACTTGTTCAACCTTAGCTC--ATACATCGCATA
*
3296733 AGGAGTTGGAACAGCA-C-CGACCTTGCCTC
128 AGGAGTTGGAACAGCATCACGACCTTGCCTA
* * *
3296762 A-TCCATCACATAAGGAGTTGGATCA
1 ATTCCATCACAGAATGAGGTGGATCA
3296787 GCATCATCAT
Statistics
Matches: 155, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
158 75 0.48
159 56 0.36
160 1 0.01
161 23 0.15
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (158 bp):
ATTCCATCACAGAATGAGGTGGATCAACATTTCCAATGGAGATTTCATAATGAGAAGAACTCATC
CAATAAAGAGAAGAAGATCATAATGAGAAGAACTTGTTCAACCTTAGCTCATACATCGCATAAGG
AGTTGGAACAGCATCACGACCTTGCCTA
Found at i:3296867 original size:44 final size:42
Alignment explanation
Indices: 3296763--3296876 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 42
3296753 CCTTGCCTCA
* *
3296763 TCCATCACATAAGGAGTTGGATCAGCATCATCATTTCACTCT
1 TCCATCATATAAGGAGTTGGATCAGCATAATCATTTCACTCT
* **
3296805 TCCATCATAAAAGGAGTTGGA-CAAGCATAATCATTTTTCTCGTT
1 TCCATCATATAAGGAGTTGGATC-AGCATAATCATTTCACTC--T
* *
3296849 TCCATCATATAAGAAGTTGGAACAGCAT
1 TCCATCATATAAGGAGTTGGATCAGCAT
3296877 TACCTTGGCT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
41 1 0.02
42 34 0.56
44 25 0.41
45 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (42 bp):
TCCATCATATAAGGAGTTGGATCAGCATAATCATTTCACTCT
Found at i:3297634 original size:42 final size:42
Alignment explanation
Indices: 3297575--3297727 Score: 175
Period size: 42 Copynumber: 3.7 Consensus size: 42
3297565 TAGCTTGATC
*
3297575 CCATCGCATAAGGAGTTGGATCAACATCATCATTTCGCTCGT
1 CCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCGT
* * *
3297617 CCATCACATAAGGAGTTGGATCAACATCATTATTTCACTCGC
1 CCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCGT
* * * *
3297659 CCATCATATAAGGAGTTGGATTAACATCA-C-CTTGGCTCGT
1 CCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCGT
** ** *
3297699 CCATTGCATAACAAGTTGGATCAGCATCA
1 CCATCACATAAGGAGTTGGATCAACATCA
3297728 CCTTGGGCCA
Statistics
Matches: 93, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
40 28 0.30
42 65 0.70
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (42 bp):
CCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCGT
Found at i:3301288 original size:32 final size:32
Alignment explanation
Indices: 3301238--3301309 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
3301228 TCCCACGATT
*
3301238 TACCCAAGAGAGTGTCTTGGGACCTGAGAGCC
1 TACCCAAGAAAGTGTCTTGGGACCTGAGAGCC
* * ***
3301270 TACCCAAGAAAGTTTCTTGGGGCCTTTTAGCC
1 TACCCAAGAAAGTGTCTTGGGACCTGAGAGCC
3301302 TACCCAAG
1 TACCCAAG
3301310 GGTCACCTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (32 bp):
TACCCAAGAAAGTGTCTTGGGACCTGAGAGCC
Found at i:3304862 original size:17 final size:17
Alignment explanation
Indices: 3304827--3304882 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
3304817 CATTTTTATC
*
3304827 ATTTTATTTTA-T-TTT
1 ATTTTATTTTAGTCATT
3304842 ATTTTATTTTAGTCATT
1 ATTTTATTTTAGTCATT
* *
3304859 ATTTTATTTTTGCCATTT
1 ATTTTATTTTAGTCA-TT
3304877 ATTTTA
1 ATTTTA
3304883 AATTGATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
15 11 0.31
16 1 0.03
17 15 0.43
18 8 0.23
ACGTcount: A:0.21, C:0.05, G:0.04, T:0.70
Consensus pattern (17 bp):
ATTTTATTTTAGTCATT
Found at i:3304878 original size:18 final size:18
Alignment explanation
Indices: 3304839--3304882 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
3304829 TTTATTTTAT
*
3304839 TTTATTTTATTTTAGTCA
1 TTTATTTTATTTTAGCCA
*
3304857 -TTATTTTATTTTTGCCA
1 TTTATTTTATTTTAGCCA
3304874 TTTATTTTA
1 TTTATTTTA
3304883 AATTGATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTATTTTATTTTAGCCA
Found at i:3304882 original size:5 final size:5
Alignment explanation
Indices: 3304827--3304868 Score: 57
Period size: 5 Copynumber: 8.0 Consensus size: 5
3304817 CATTTTTATC
*
3304827 ATTTT ATTTT ATTTT ATTTT ATTTT AGTCATT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT A-T-TTT ATTTT ATTTT
3304869 TGCCATTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 28 0.85
6 2 0.06
7 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:3305312 original size:14 final size:14
Alignment explanation
Indices: 3305293--3305325 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3305283 GGTCCGGACT
3305293 CTTTTAA-CTACTAA
1 CTTTTAACCT-CTAA
3305307 CTTTTAACCTCTAA
1 CTTTTAACCTCTAA
3305321 CTTTT
1 CTTTT
3305326 TATTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.27, C:0.24, G:0.00, T:0.48
Consensus pattern (14 bp):
CTTTTAACCTCTAA
Found at i:3306248 original size:15 final size:15
Alignment explanation
Indices: 3306228--3306263 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
3306218 TAATAATAAA
3306228 ATGTTTGATTGCATC
1 ATGTTTGATTGCATC
3306243 ATGTTTGATTGCATC
1 ATGTTTGATTGCATC
3306258 ATGTTT
1 ATGTTT
3306264 TAAAACTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.50
Consensus pattern (15 bp):
ATGTTTGATTGCATC
Found at i:3307942 original size:30 final size:30
Alignment explanation
Indices: 3307908--3307981 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
3307898 GAACAATAAA
3307908 TAAACGAACACGGATATAATATTAAAAATT
1 TAAACGAACACGGATATAATATTAAAAATT
**
3307938 TAAACGAACACTAATATAATATTAAAAATT
1 TAAACGAACACGGATATAATATTAAAAATT
*
3307968 TAAACAAACACGGA
1 TAAACGAACACGGA
3307982 CACCTTTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.55, C:0.12, G:0.08, T:0.24
Consensus pattern (30 bp):
TAAACGAACACGGATATAATATTAAAAATT
Found at i:3308093 original size:40 final size:40
Alignment explanation
Indices: 3308047--3308122 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
3308037 TTCATTTACA
3308047 CCCCTAACATAACAAGCATTACATGAGCTAATAATATGAT
1 CCCCTAACATAACAAGCATTACATGAGCTAATAATATGAT
3308087 CCCCTAACATAACAAGCATTACATGAGCTAATAATA
1 CCCCTAACATAACAAGCATTACATGAGCTAATAATA
3308123 AGATTGGTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.43, C:0.24, G:0.09, T:0.24
Consensus pattern (40 bp):
CCCCTAACATAACAAGCATTACATGAGCTAATAATATGAT
Found at i:3315902 original size:108 final size:108
Alignment explanation
Indices: 3315682--3315886 Score: 261
Period size: 108 Copynumber: 1.9 Consensus size: 108
3315672 AAAGAAACAT
* ** * *
3315682 AATGAGACAAGTATTTAGAATTTTACCTATGAATATAAGCACCTTTAAACATTAGAGAGCCAACA
1 AATGAGACAAGTATTTAGAATTTTACATACAAATATAAGCACCTCTAAACATGAGAGAGCCAACA
* * *
3315747 TATCCTTAGCTTCTAGGTAATGCATCCACAAGTAAAAGAGCAA
66 TAGCCTTAGCTTCTAAGTAAGGCATCCACAAGTAAAAGAGCAA
** * *
3315790 AATGAGACGAA-TATTTAGAATTTTGTATACAAATGTAAGCACCTCTAAACATGAGAGTGCCAAC
1 AATGAGAC-AAGTATTTAGAATTTTACATACAAATATAAGCACCTCTAAACATGAGAGAGCCAAC
**
3315854 ATAGCCTTATTTTC-AAGTAAGGCATCCACAAGT
65 ATAGCCTTAGCTTCTAAGTAAGGCATCCACAAGT
3315887 CATAAAAGCC
Statistics
Matches: 82, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
107 17 0.21
108 63 0.77
109 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.27
Consensus pattern (108 bp):
AATGAGACAAGTATTTAGAATTTTACATACAAATATAAGCACCTCTAAACATGAGAGAGCCAACA
TAGCCTTAGCTTCTAAGTAAGGCATCCACAAGTAAAAGAGCAA
Found at i:3326400 original size:18 final size:19
Alignment explanation
Indices: 3326366--3326401 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3326356 ATGTAATAAA
*
3326366 ACATATTTATCAAAATATC
1 ACATAATTATCAAAATATC
3326385 ACATAATTAT-AAAATAT
1 ACATAATTATCAAAATAT
3326402 AAGAACATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (19 bp):
ACATAATTATCAAAATATC
Found at i:3326957 original size:3 final size:3
Alignment explanation
Indices: 3326949--3326973 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3326939 GAATAGGGTT
3326949 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
3326974 ATATAAAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:3331117 original size:19 final size:17
Alignment explanation
Indices: 3331093--3331138 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 17
3331083 TCAAATTTAA
3331093 TTATTTATTTATTTTATC
1 TTATTT-TTTATTTTATC
3331111 TTTATTTTTTATTTTAATC
1 -TTATTTTTTATTTT-ATC
3331130 TTATTTTTT
1 TTATTTTTT
3331139 TTATTTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.65
19 9 0.35
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTTTATTTTATC
Found at i:3331123 original size:18 final size:18
Alignment explanation
Indices: 3331093--3331146 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 18
3331083 TCAAATTTAA
3331093 TTATTTATTTATTTTATCT
1 TTATTT-TTTATTTTATCT
3331112 TTATTTTTTATTTTAATCT
1 TTATTTTTTATTTT-ATCT
*
3331131 TATTTTTTTTATTTTA
1 T-TATTTTTTATTTTA
3331147 AAACAACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 8 0.25
19 12 0.38
20 12 0.38
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTTTATTTTATCT
Found at i:3331139 original size:19 final size:19
Alignment explanation
Indices: 3331093--3331147 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
3331083 TCAAATTTAA
*
3331093 TTATTTATTTATTTT-ATC
1 TTATTTTTTTATTTTAATC
3331111 TT-TATTTTTTATTTTAATC
1 TTAT-TTTTTTATTTTAATC
3331130 TTATTTTTTTTATTTTAA
1 TTA-TTTTTTTATTTTAA
3331148 AACAACTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.03
18 12 0.38
19 5 0.16
20 13 0.41
21 1 0.03
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (19 bp):
TTATTTTTTTATTTTAATC
Found at i:3339848 original size:8 final size:8
Alignment explanation
Indices: 3339835--3339864 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3339825 ATGTATGTTC
3339835 ATTATTTT
1 ATTATTTT
*
3339843 ATTATTTC
1 ATTATTTT
3339851 ATTATTTT
1 ATTATTTT
3339859 ATTATT
1 ATTATT
3339865 ATTGTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (8 bp):
ATTATTTT
Found at i:3339851 original size:16 final size:16
Alignment explanation
Indices: 3339832--3339864 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3339822 TTGATGTATG
3339832 TTCATTATTTTATTAT
1 TTCATTATTTTATTAT
3339848 TTCATTATTTTATTAT
1 TTCATTATTTTATTAT
3339864 T
1 T
3339865 ATTGTCATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCATTATTTTATTAT
Found at i:3339972 original size:20 final size:19
Alignment explanation
Indices: 3339922--3339974 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
3339912 AAAAAATAGC
*
3339922 AAGAAGAAAACAAAACAAAA
1 AAGAAGAAAA-AAAAAAAAA
* *
3339942 ATGAAAAAAAAAAAAAAAAA
1 AAG-AAGAAAAAAAAAAAAA
3339962 AAGAACGAAAAAA
1 AAGAA-GAAAAAA
3339975 TGTTTATGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 6 0.23
ACGTcount: A:0.83, C:0.06, G:0.09, T:0.02
Consensus pattern (19 bp):
AAGAAGAAAAAAAAAAAAA
Found at i:3341721 original size:18 final size:18
Alignment explanation
Indices: 3341698--3341742 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
3341688 AATTAATTGC
3341698 TTATTTTATCTT-TATATT
1 TTATTTTATCTTAT-TATT
*
3341716 TTATTTTAATCTTATTTTT
1 TTATTTT-ATCTTATTATT
3341735 TTATTTTA
1 TTATTTTA
3341743 AAACAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 15 0.62
20 1 0.04
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTTTATCTTATTATT
Found at i:3346678 original size:18 final size:19
Alignment explanation
Indices: 3346655--3346693 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3346645 ACACCTGAAG
*
3346655 AAAAGAAA-ACAAAAGAAA
1 AAAAGAAAGAAAAAAGAAA
3346673 AAAAGAAAGAAAAAAGAAA
1 AAAAGAAAGAAAAAAGAAA
3346692 AA
1 AA
3346694 TAATGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAGAAAGAAAAAAGAAA
Found at i:3346689 original size:19 final size:18
Alignment explanation
Indices: 3346655--3346713 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 18
3346645 ACACCTGAAG
*
3346655 AAAAGAAAACAAAAGAAA
1 AAAAGAAAAAAAAAGAAA
3346673 AAAAGAAAGAAAAAAGAAA
1 AAAAGAAA-AAAAAAGAAA
* *
3346692 AATAATGAAAAATAATGAAA
1 AA-AA-GAAAAAAAAAGAAA
3346712 AA
1 AA
3346714 TAATGAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.23
19 11 0.31
20 12 0.34
21 4 0.11
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAAAAAGAAA
Found at i:3346701 original size:29 final size:28
Alignment explanation
Indices: 3346655--3346751 Score: 72
Period size: 29 Copynumber: 3.3 Consensus size: 28
3346645 ACACCTGAAG
*
3346655 AAAAGAAAACA-AAAGAAAAAAAGAAAGAA
1 AAAAGAAAA-ATAATGAAAAAAAGAAA-AA
3346684 AAAAGAAAAATAATGAAAAATAATGAAAAA
1 AAAAGAAAAATAATGAAAAA-AA-GAAAAA
* * * *
3346714 TAATG-AAAATAATAAATAAAAATAAATAA
1 AAAAGAAAAATAATGAA-AAAAAGAAA-AA
*
3346743 AAAATAAAA
1 AAAAGAAAA
3346752 TGAGAAAAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
28 4 0.07
29 33 0.61
30 13 0.24
31 4 0.07
ACGTcount: A:0.78, C:0.01, G:0.08, T:0.12
Consensus pattern (28 bp):
AAAAGAAAAATAATGAAAAAAAGAAAAA
Found at i:3346702 original size:9 final size:10
Alignment explanation
Indices: 3346688--3346749 Score: 72
Period size: 10 Copynumber: 5.9 Consensus size: 10
3346678 AAAGAAAAAA
3346688 GAAAAATAAT
1 GAAAAATAAT
3346698 GAAAAATAAT
1 GAAAAATAAT
3346708 GAAAAATAAT
1 GAAAAATAAT
3346718 GAAAATAATAAAT
1 G-AAA-AAT-AAT
3346731 -AAAAATAAAT
1 GAAAAAT-AAT
*
3346741 AAAAAATAA
1 GAAAAATAA
3346750 AATGAGAAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
10 30 0.62
11 12 0.25
12 3 0.06
13 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (10 bp):
GAAAAATAAT
Found at i:3346764 original size:17 final size:18
Alignment explanation
Indices: 3346744--3346777 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3346734 AATAAATAAA
3346744 AAATAAAATG-AGAAAAG
1 AAATAAAATGAAGAAAAG
*
3346761 AAATAAATTGAAGAAAA
1 AAATAAAATGAAGAAAA
3346778 AATGAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (18 bp):
AAATAAAATGAAGAAAAG
Found at i:3349583 original size:161 final size:162
Alignment explanation
Indices: 3349292--3349763 Score: 490
Period size: 162 Copynumber: 2.9 Consensus size: 162
3349282 AATCCATTAT
* * ** * * * *
3349292 AGAATGAGGTGGATCAATATTTCCAAAAG-AGAGTTCATAACGTA-AAGAAATCATCCACAGAAG
1 AGAATGAGATGGATCAACATTTCCAATGGAAGGGTTCATAATG-AGAAGAACTCATCCAAAGAAG
* * * *
3349355 AGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGA-TTCTATCGTAGAAAAAG
65 -GAGAAGAAGTTCATAATGAGAAGAACTTGTTC-ACCTTTTGCTCGACTT-TATCGCAGAAGAAG
* *
3349419 ATAGATTAACATCATCATTTTGATCGAACCCTTCA-
127 ATAGATTAACATCATCATTTTGATAGAACCCATCAC
* ** *
3349454 AGAA-GAAGGTGGATCGTCATTTCCAATGGAAGGGTTCATAATGAGAAG-ACTCATCCAAATAAG
1 AGAATG-AGATGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCCAAAGAAG
* *
3349517 GAGAAGAAGTTCATAATGAAAAGAACTTGTTCACCCTTTTGCTCGACTTTATCACAGAAGAAGAT
65 GAGAAGAAGTTCATAATGAGAAGAACTTGTTCA-CCTTTTGCTCGACTTTATCGCAGAAGAAGAT
* * ** * **
3349582 AGATCATCATCAAAATTTTGTTAGATTCCATCAC
129 AGATTAACATCATCATTTTGATAGAACCCATCAC
* * * *
3349616 AGAATGAGATGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATACGAAGATGA
1 AGAATGAGATGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCCAAAGAAGG
* ** * * * *
3349681 AGAAGAAGTTCATAATGAGAATAACTTGTTCAAATTTTACTCGACTCTATCGCATAAGGAGATAG
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCACCTTTTGCTCGACTTTATCGCAGAAGAAGATAG
3349746 A-TAAGCATCATCATTTTG
131 ATTAA-CATCATCATTTTG
3349764 TTTGATTCCA
Statistics
Matches: 255, Mismatches: 46, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
160 1 0.00
161 80 0.31
162 118 0.46
163 56 0.22
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (162 bp):
AGAATGAGATGGATCAACATTTCCAATGGAAGGGTTCATAATGAGAAGAACTCATCCAAAGAAGG
AGAAGAAGTTCATAATGAGAAGAACTTGTTCACCTTTTGCTCGACTTTATCGCAGAAGAAGATAG
ATTAACATCATCATTTTGATAGAACCCATCAC
Found at i:3350453 original size:21 final size:21
Alignment explanation
Indices: 3350424--3350476 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
3350414 TTGCCCGAAA
*
3350424 GACCTCATATATGTCCTGAAG
1 GACCACATATATGTCCTGAAG
3350445 GACCACATATATGTCCTGAAG
1 GACCACATATATGTCCTGAAG
3350466 GACCACATATA
1 GACCACATATA
3350477 ACCCTCGACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.25
Consensus pattern (21 bp):
GACCACATATATGTCCTGAAG
Found at i:3350813 original size:26 final size:27
Alignment explanation
Indices: 3350760--3350814 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 27
3350750 ATATGTCAAT
*
3350760 TATGCATGTACTCATAAGTATCATAACA
1 TATGCATGTA-TCATAACTATCATAACA
3350788 TATGCATGT-TCATAACTATGCA-AACA
1 TATGCATGTATCATAACTAT-CATAACA
3350814 T
1 T
3350815 GAATTCAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 14 0.56
27 2 0.08
28 9 0.36
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (27 bp):
TATGCATGTATCATAACTATCATAACA
Found at i:3351178 original size:19 final size:19
Alignment explanation
Indices: 3351139--3351180 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
3351129 TCCTTTACTG
*
3351139 TGGTATCGATACTATTCCC
1 TGGTATCGATACCATTCCC
* *
3351158 TGGTATCGATACCCTTTCC
1 TGGTATCGATACCATTCCC
3351177 TGGT
1 TGGT
3351181 TCTGGAATTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (19 bp):
TGGTATCGATACCATTCCC
Found at i:3371145 original size:28 final size:28
Alignment explanation
Indices: 3371114--3371175 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
3371104 AATTCTAGGG
3371114 TTTAGAGGTA-ATTTAGGAT-ATTTTACAC
1 TTTAG-GGTATATTTAGG-TCATTTTACAC
*
3371142 TTTAGGG-ATATTTTGGTCATTTTACAC
1 TTTAGGGTATATTTAGGTCATTTTACAC
3371169 TTTAGGG
1 TTTAGGG
3371176 GTATTTCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
26 2 0.06
27 24 0.77
28 5 0.16
ACGTcount: A:0.26, C:0.08, G:0.21, T:0.45
Consensus pattern (28 bp):
TTTAGGGTATATTTAGGTCATTTTACAC
Found at i:3371154 original size:27 final size:27
Alignment explanation
Indices: 3371124--3371181 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
3371114 TTTAGAGGTA
3371124 ATTTAGGAT-ATTTTACACTTTAGGGAT
1 ATTTAGG-TCATTTTACACTTTAGGGAT
* *
3371151 ATTTTGGTCATTTTACACTTTAGGGGT
1 ATTTAGGTCATTTTACACTTTAGGGAT
3371178 ATTT
1 ATTT
3371182 CTATAATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.24, C:0.09, G:0.19, T:0.48
Consensus pattern (27 bp):
ATTTAGGTCATTTTACACTTTAGGGAT
Found at i:3372065 original size:12 final size:12
Alignment explanation
Indices: 3372048--3372078 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3372038 GATAAACGGT
3372048 CGGTCAACGCCC
1 CGGTCAACGCCC
3372060 CGGTCAACGCCC
1 CGGTCAACGCCC
3372072 CGGTCAA
1 CGGTCAA
3372079 TGAACAACAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.19, C:0.45, G:0.26, T:0.10
Consensus pattern (12 bp):
CGGTCAACGCCC
Found at i:3376787 original size:18 final size:18
Alignment explanation
Indices: 3376763--3376844 Score: 119
Period size: 18 Copynumber: 4.6 Consensus size: 18
3376753 GAGGGATTAT
*
3376763 CAGTGGTCCTTTGGGACA
1 CAGTGGTCCTTCGGGACA
*
3376781 TAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
* *
3376799 CAGTGGTCATTCAGGACA
1 CAGTGGTCCTTCGGGACA
3376817 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
3376835 TAGTGGTCCT
1 CAGTGGTCCT
3376845 ACTAGACAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 56 1.00
ACGTcount: A:0.18, C:0.23, G:0.32, T:0.27
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:3380258 original size:20 final size:20
Alignment explanation
Indices: 3380229--3380266 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3380219 TCAGTTTTTT
3380229 CTTTGAAGTATCGATACTCC
1 CTTTGAAGTATCGATACTCC
*
3380249 CTTTGTAGTATCGATACT
1 CTTTGAAGTATCGATACT
3380267 ACCCGTCAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (20 bp):
CTTTGAAGTATCGATACTCC
Found at i:3382620 original size:95 final size:93
Alignment explanation
Indices: 3382346--3382626 Score: 357
Period size: 95 Copynumber: 3.0 Consensus size: 93
3382336 CTGAGTTATG
* * *
3382346 GTACCGATACTGTCAAAACAGAATGCTAAATTGGTACTGATACCATATATGATATCAATACTACT
1 GTACCGATACTGTCAAAACAAAATGCTAAA-TGGTACCGATACCATATATGATATCGATACTACT
* * * *
3382411 TATAGTTA-TAGTACCGATAATTCTCAGGCA
65 TAGA-TTAGTAGTATCGAT-ACTCTGAGGCA
* * * *
3382441 GTACCGATACTGTCAAAACATAATGCTAAAATGGTACCGATACTATATATGATATCGATATTACA
1 GTACCGATACTGTCAAAACAAAATGCT-AAATGGTACCGATACCATATATGATATCGATACTACT
* * *
3382506 TAGAGTAGTAGTATTGATACTGCTGATGCA
65 TAGATTAGTAGTATCGATACT-CTGAGGCA
* *
3382536 GTACTGATACTGTCAAAACAAAATGATAGAATGGTACCGATACCATATATGATATCGATACTACT
1 GTACCGATACTGTCAAAACAAAATGCTA-AATGGTACCGATACCATATATGATATCGATACTACT
3382601 TAGATTAGTAGTATCGATACTCTGAG
65 TAGATTAGTAGTATCGATACTCTGAG
3382627 TAATGGTACC
Statistics
Matches: 160, Mismatches: 22, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
94 9 0.06
95 148 0.93
96 3 0.02
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (93 bp):
GTACCGATACTGTCAAAACAAAATGCTAAATGGTACCGATACCATATATGATATCGATACTACTT
AGATTAGTAGTATCGATACTCTGAGGCA
Found at i:3382993 original size:21 final size:21
Alignment explanation
Indices: 3382967--3383019 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3382957 GTTTTCAGAT
3382967 TCGCAACGCGAACATCGACTA
1 TCGCAACGCGAACATCGACTA
* *
3382988 TCGCAACACGAACTTCGACTA
1 TCGCAACGCGAACATCGACTA
*
3383009 TCGCAATGCGA
1 TCGCAACGCGA
3383020 TTTTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.32, G:0.19, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACTA
Found at i:3383057 original size:21 final size:21
Alignment explanation
Indices: 3383031--3383165 Score: 143
Period size: 21 Copynumber: 6.4 Consensus size: 21
3383021 TTTCCAAATT
3383031 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
3383052 CGTTGCGATTTATTCCAAATTCG
1 CGTTGCGA--TAGTCCAAGTTCG
3383075 CGTTGCGATAGTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
* *
3383094 CGTTGAGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
3383115 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
3383136 CATTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
3383157 CGTTGCGAT
1 CGTTGCGAT
3383166 TTATTCCAAG
Statistics
Matches: 93, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
19 26 0.28
21 39 0.42
23 28 0.30
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:3383085 original size:44 final size:40
Alignment explanation
Indices: 3383015--3383095 Score: 126
Period size: 44 Copynumber: 1.9 Consensus size: 40
3383005 ACTATCGCAA
3383015 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
3383055 TGCGATTTATTCCAAATTCGCGTTGCGATAGTCCAAGTTCG
1 TGCGA-TT-TTCCAAATT--CGTTGCGATAGTCCAAGTTCG
3383096 TTGAGATAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
40 5 0.14
41 2 0.05
42 9 0.24
44 21 0.57
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
TGCGATTTTCCAAATTCGTTGCGATAGTCCAAGTTCGCGT
Found at i:3383103 original size:19 final size:19
Alignment explanation
Indices: 3383023--3383156 Score: 106
Period size: 19 Copynumber: 6.5 Consensus size: 19
3383013 AATGCGATTT
*
3383023 TCCAAATTCGTTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
3383042 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
3383065 TCCAAATTCGCGTTGCGATAG
1 TCCAAGTT--CGTTGCGATAG
*
3383086 TCCAAGTTCGTTGAGATAG
1 TCCAAGTTCGTTGCGATAG
* *
3383105 TCGAAGTTCGCGTTGCGATTTAT
1 TCCAAGTT--CGTTGCGA--TAG
*
3383128 TCCAAGTTCATTGCGATAG
1 TCCAAGTTCGTTGCGATAG
*
3383147 TCGAAGTTCG
1 TCCAAGTTCG
3383157 CGTTGCGATT
Statistics
Matches: 93, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
19 34 0.37
21 31 0.33
23 28 0.30
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (19 bp):
TCCAAGTTCGTTGCGATAG
Found at i:3383161 original size:63 final size:62
Alignment explanation
Indices: 3383023--3383156 Score: 198
Period size: 63 Copynumber: 2.2 Consensus size: 62
3383013 AATGCGATTT
* * *
3383023 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGCGTTGCGATAG
1 TCCAAGTTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTC-CATTGCGATAG
* *
3383086 TCCAAGTTCGTTGAGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT-CATTGCGATAG
1 TCCAAGTTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCCATTGCGATAG
*
3383147 TCGAAGTTCG
1 TCCAAGTTCG
3383157 CGTTGCGATT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 19 0.29
63 46 0.71
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (62 bp):
TCCAAGTTCGTTGAGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCCATTGCGATAG
Found at i:3383166 original size:42 final size:42
Alignment explanation
Indices: 3383071--3383180 Score: 179
Period size: 42 Copynumber: 2.7 Consensus size: 42
3383061 TTATTCCAAA
* *
3383071 TTCGCGTTGCGA--TAGTCCAAGTTCGTTGAGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCATTGAGATAGTCGAAG
*
3383111 TTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATTTATTCCAAGTTCATTGAGATAGTCGAAG
3383153 TTCGCGTTGCGATTTATTCCAAGTTCAT
1 TTCGCGTTGCGATTTATTCCAAGTTCAT
3383181 CGCAACGACT
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 12 0.18
42 53 0.82
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (42 bp):
TTCGCGTTGCGATTTATTCCAAGTTCATTGAGATAGTCGAAG
Found at i:3383953 original size:6 final size:5
Alignment explanation
Indices: 3383916--3383949 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
3383906 CTGTCTCGTC
*
3383916 TCGGG CCGGG TCGGG TCGGG TCGGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG
3383950 TGGTAATACG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.00, C:0.24, G:0.56, T:0.21
Consensus pattern (5 bp):
TCGGG
Found at i:3384061 original size:21 final size:21
Alignment explanation
Indices: 3384046--3384374 Score: 172
Period size: 21 Copynumber: 15.8 Consensus size: 21
3384036 TGCGATTTTG
3384046 GACTATCGCAACGCGAACTTC
1 GACTATCGCAACGCGAACTTC
*
3384067 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
* *
3384086 GAATAAATCACAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
* * *
3384109 GACTATCGCAA--TGAATTTG
1 GACTATCGCAACGCGAACTTC
*
3384128 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
*
3384151 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
* * *
3384170 GAATAAATCGCAA--CGAATTTG
1 GACT--ATCGCAACGCGAACTTC
*
3384191 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
* *
3384214 GACTATCGCAA--CGAATTTG
1 GACTATCGCAACGCGAACTTC
*
3384233 GAATAAATCGCAACGCGAACTTC
1 GACT--ATCGCAACGCGAACTTC
*
3384256 GACTATCGCAA--CGAACTTG
1 GACTATCGCAACGCGAACTTC
* *
3384275 GACTATCGCAA--TGAA-TTT
1 GACTATCGCAACGCGAACTTC
*
3384293 GTAATAAATCGCAACGCGAACTTC
1 G-ACT--ATCGCAACGCGAACTTC
* ** **
3384317 GACTGTCGCAAATC-AGTTTCC
1 GACTATCGCAACGCGAACTT-C
3384338 AGA-T-TCGCAACGCGAACTTC
1 -GACTATCGCAACGCGAACTTC
*
3384358 GACTATCGCAATGCGAA
1 GACTATCGCAACGCGAA
3384375 TATGTAAATC
Statistics
Matches: 238, Mismatches: 43, Indels: 54
0.71 0.13 0.16
Matches are distributed among these distances:
18 3 0.01
19 62 0.26
20 12 0.05
21 115 0.48
22 2 0.01
23 41 0.17
24 3 0.01
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (21 bp):
GACTATCGCAACGCGAACTTC
Found at i:3384101 original size:42 final size:42
Alignment explanation
Indices: 3384050--3384327 Score: 252
Period size: 42 Copynumber: 6.7 Consensus size: 42
3384040 ATTTTGGACT
3384050 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* * *
3384092 ATCACAACGCGAACTTCGACTATCGCAATGAATTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
3384134 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
* * * * *
3384176 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTGGAATAA
* * * * *
3384218 ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTCGACT--
1 ATCGCAACGCGAACTTCGACT--ATCGCAA--CGAACTTGGAATAA
* * * *
3384260 ATCGCAA--CGAACTTGGACTATCGCAATGAATTTGTAATAA
1 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
*
3384300 ATCGCAACGCGAACTTCGACTGTCGCAA
1 ATCGCAACGCGAACTTCGACTATCGCAA
3384328 ATCAGTTTCC
Statistics
Matches: 208, Mismatches: 20, Indels: 16
0.85 0.08 0.07
Matches are distributed among these distances:
38 7 0.03
40 23 0.11
42 168 0.81
44 10 0.05
ACGTcount: A:0.36, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:3384163 original size:63 final size:64
Alignment explanation
Indices: 3384096--3384247 Score: 206
Period size: 63 Copynumber: 2.4 Consensus size: 64
3384086 GAATAAATCA
* *
3384096 CAACGCGAACTTCGACT-ATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGAATAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
*
3384159 CAA--CGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
1 CAACGCGAACTTCGAAT-AATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
* *
3384222 CAA--CGAATTTGGAATAAATCGCAACG
1 CAACGCGAACTTCGAAT-AATCGCAACG
3384248 CGAACTTCGA
Statistics
Matches: 83, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 10 0.12
63 73 0.88
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (64 bp):
CAACGCGAACTTCGAATAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCG
Found at i:3384230 original size:105 final size:103
Alignment explanation
Indices: 3384046--3384368 Score: 456
Period size: 105 Copynumber: 3.1 Consensus size: 103
3384036 TGCGATTTTG
* * *
3384046 GACTATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTCGA
1 GACTATCGCAA--CGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
*
3384111 CTATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTC
64 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
3384151 GACTATCGCAACGAACTTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
1 GACTATCGCAACGAACTTGGACT--ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGA
3384216 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
64 CTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
3384256 GACTATCGCAACGAACTTGGACTATCGCAATGAATTTGTAATAAATCGCAACGCGAACTTCGACT
1 GACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * **
3384321 GTCGCAAATC-AGTTTCCAGAT---TCGCAACGCGAACTTC
66 ATCGC-AA-CGAATTTGGA-ATAAATCGCAACGCGAACTTC
3384358 GACTATCGCAA
1 GACTATCGCAA
3384369 TGCGAATATG
Statistics
Matches: 201, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
102 27 0.13
103 54 0.27
104 7 0.03
105 113 0.56
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (103 bp):
GACTATCGCAACGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:3384264 original size:63 final size:63
Alignment explanation
Indices: 3384134--3384327 Score: 270
Period size: 61 Copynumber: 3.1 Consensus size: 63
3384124 TTTGGAATAA
* * * *
3384134 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAA--CGAATTTGGAAT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
3384195 AAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 --ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
* * *
3384260 ATCGCAA--CGAACTTGGACTATCGCAATGAATTTGTAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
3384321 GTCGCAA
1 ATCGCAA
3384328 ATCAGTTTCC
Statistics
Matches: 121, Mismatches: 8, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
61 57 0.47
63 55 0.45
65 9 0.07
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (63 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:3398388 original size:15 final size:15
Alignment explanation
Indices: 3398364--3398393 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3398354 TTTTTGCAGA
3398364 AAATAACCTTAAAAT
1 AAATAACCTTAAAAT
*
3398379 AAATATCCTTAAAAT
1 AAATAACCTTAAAAT
3398394 GGAGTAACTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAACCTTAAAAT
Found at i:3400590 original size:23 final size:23
Alignment explanation
Indices: 3400558--3400605 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
3400548 AAATCAGTGA
*
3400558 TTAGTGGTTAGAAGTTAGCAAAG
1 TTAGTGGTTAGAAATTAGCAAAG
* *
3400581 TTAGTTGTTAGAAATTAGTAAAG
1 TTAGTGGTTAGAAATTAGCAAAG
3400604 TT
1 TT
3400606 TAAATCATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (23 bp):
TTAGTGGTTAGAAATTAGCAAAG
Found at i:3407175 original size:2 final size:2
Alignment explanation
Indices: 3407168--3407199 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3407158 GATCATTTTA
3407168 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
3407200 TAGTTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3407605 original size:3 final size:3
Alignment explanation
Indices: 3407597--3407624 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3407587 TTCATTCATT
3407597 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3407625 GGATCTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3411210 original size:13 final size:13
Alignment explanation
Indices: 3411188--3411223 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
3411178 TTTCCGATTC
3411188 TTTC-TTTTTTCT
1 TTTCTTTTTTTCT
*
3411200 TTTCTTTTTTTTT
1 TTTCTTTTTTTCT
3411213 TTTCTTTTTTT
1 TTTCTTTTTTT
3411224 GTAATTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:3411223 original size:12 final size:12
Alignment explanation
Indices: 3411188--3411223 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
3411178 TTTCCGATTC
*
3411188 TTTCTTTTTTCT
1 TTTCTTTTTTTT
3411200 TTTCTTTTTTTTT
1 TTTC-TTTTTTTT
3411213 TTTCTTTTTTT
1 TTTCTTTTTTT
3411224 GTAATTTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:3415577 original size:16 final size:16
Alignment explanation
Indices: 3415556--3415587 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3415546 CTCTGTTCAA
3415556 TATCCTGTCTCCAAGT
1 TATCCTGTCTCCAAGT
3415572 TATCCTGTCTCCAAGT
1 TATCCTGTCTCCAAGT
3415588 AGGAATTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.31, G:0.12, T:0.38
Consensus pattern (16 bp):
TATCCTGTCTCCAAGT
Found at i:3417959 original size:65 final size:63
Alignment explanation
Indices: 3417890--3418049 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
3417880 AATTAAATTT
* *
3417890 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
3417954 A
63 A
* * * *
3417955 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
*
3418019 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
3418050 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 50 0.58
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:3418049 original size:17 final size:19
Alignment explanation
Indices: 3418021--3418069 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
3418011 TATTTTGAAA
3418021 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
3418039 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
3418058 CACCGATGCACT
1 CATCGATGCACT
3418070 AAGGGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:3421687 original size:24 final size:23
Alignment explanation
Indices: 3421655--3421735 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 23
3421645 TCTGTGCTTA
3421655 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCAT-CCTTTGAAT
* *
3421679 GTGCATCGATTCATCATGTTG-A-
1 GTGCATCGATGCATCCT-TTGAAT
3421701 -TGCA-CTGATGCATGCC-TTGAAT
1 GTGCATC-GATGCAT-CCTTTGAAT
3421723 GTGCATCGATGCA
1 GTGCATCGATGCA
3421736 CATGGTCATG
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 1 0.02
23 13 0.28
24 17 0.37
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.32
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTTGAAT
Found at i:3423283 original size:21 final size:21
Alignment explanation
Indices: 3423241--3423284 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3423231 ACTCCGGGAG
* *
3423241 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
3423262 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
3423283 CT
1 CT
3423285 CCTCCAGCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:3424452 original size:65 final size:63
Alignment explanation
Indices: 3424372--3424524 Score: 200
Period size: 65 Copynumber: 2.4 Consensus size: 63
3424362 TTGAATATCG
* *
3424372 AATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATC
1 AATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-AAACATC
3424436 A
63 A
* * * *
3424437 AATGTATTTGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCA
1 AATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGAAACATCA
*
3424501 AATGCACTTGATGCATCGATGCAC
1 AATGCATTTGATGCATCGATGCAC
3424525 TCTTAGTGCA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
63 1 0.01
64 29 0.37
65 43 0.55
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (63 bp):
AATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGAAACATCA
Found at i:3424524 original size:17 final size:19
Alignment explanation
Indices: 3424502--3424544 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3424492 GAAACATCAA
*
3424502 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
3424519 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
3424538 ATGCACT
1 ATGCACT
3424545 AAGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:3424540 original size:64 final size:63
Alignment explanation
Indices: 3424372--3424544 Score: 172
Period size: 64 Copynumber: 2.7 Consensus size: 63
3424362 TTGAATATCG
* * *
3424372 AATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGATTTTATGAAAACATCA
1 AATGCATTTGATGCATCGATGCAC-T-CAATGCACCGATGCACTCAGGATTTTATGAAAACATCA
* * * *
3424437 AATGTATTTGATGCATCGATGCAC-CAACCATGCATCGATGCACTCTGGCTATTT-TG-AAACAT
1 AATGCATTTGATGCATCGATGCACTC-A--ATGCACCGATGCACTCAGGAT-TTTATGAAAACAT
3424499 CA
62 CA
* *
3424501 AATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AATGCATTTGATGCATCGATGCACTC--AATGCACCGATGCACT
3424545 AAGGGTCCAA
Statistics
Matches: 90, Mismatches: 12, Indels: 13
0.78 0.10 0.11
Matches are distributed among these distances:
62 1 0.01
64 43 0.48
65 42 0.47
66 4 0.04
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (63 bp):
AATGCATTTGATGCATCGATGCACTCAATGCACCGATGCACTCAGGATTTTATGAAAACATCA
Found at i:3428472 original size:14 final size:14
Alignment explanation
Indices: 3428455--3428484 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3428445 AATAATTGTT
*
3428455 AAATAATAATTAAA
1 AAATAATAAATAAA
3428469 AAATAATAAATAAA
1 AAATAATAAATAAA
3428483 AA
1 AA
3428485 TATTAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAATAATAAATAAA
Found at i:3432344 original size:16 final size:17
Alignment explanation
Indices: 3432323--3432361 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
3432313 AAAGTCAAAA
3432323 AATATTT-AGAAATAAG
1 AATATTTAAGAAATAAG
*
3432339 AATATTTACAGAAATGAG
1 AATATTTA-AGAAATAAG
3432357 AATAT
1 AATAT
3432362 ATTTACTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
18 13 0.65
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (17 bp):
AATATTTAAGAAATAAG
Found at i:3437238 original size:13 final size:12
Alignment explanation
Indices: 3437210--3437238 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3437200 AAAAGTCAAT
3437210 GGGGGTTTGATC
1 GGGGGTTTGATC
3437222 GGGGGTTTGATC
1 GGGGGTTTGATC
3437234 GGGGG
1 GGGGG
3437239 CCGATGCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.07, G:0.59, T:0.28
Consensus pattern (12 bp):
GGGGGTTTGATC
Found at i:3443836 original size:20 final size:22
Alignment explanation
Indices: 3443813--3443892 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 22
3443803 TTGGTGCAGA
3443813 GGGAATCGA-TCCCCCCATGA-
1 GGGAATCGATTCCCCCCATGAG
* **
3443833 GGGAACCGATTCCCCCTTTGAAG
1 GGGAATCGATTCCCCCCATG-AG
*
3443856 GGGAA-CGATTCCCCCCA-CAG
1 GGGAATCGATTCCCCCCATGAG
*
3443876 GGGAATCGATACCCCCC
1 GGGAATCGATTCCCCCC
3443893 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 15 0.31
21 18 0.37
22 11 0.22
23 5 0.10
ACGTcount: A:0.24, C:0.36, G:0.25, T:0.15
Consensus pattern (22 bp):
GGGAATCGATTCCCCCCATGAG
Found at i:3444239 original size:24 final size:25
Alignment explanation
Indices: 3444192--3444241 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
3444182 AGAATTTTCC
3444192 AAAAAAAATTTAAATTTTCGAAATT
1 AAAAAAAATTTAAATTTTCGAAATT
3444217 AAAAAAAATGTT-AATTTTC-AAATT
1 AAAAAAAAT-TTAAATTTTCGAAATT
3444241 A
1 A
3444242 TTATGTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 16 0.67
26 2 0.08
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (25 bp):
AAAAAAAATTTAAATTTTCGAAATT
Found at i:3450059 original size:14 final size:14
Alignment explanation
Indices: 3450040--3450074 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
3450030 GAACCCGAGA
3450040 TTTTTTATTATTAT
1 TTTTTTATTATTAT
3450054 TTTTTTATTATTAT
1 TTTTTTATTATTAT
*
3450068 TATTTTA
1 TTTTTTA
3450075 AAATAAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTTTTATTATTAT
Found at i:3450066 original size:17 final size:16
Alignment explanation
Indices: 3450040--3450073 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
3450030 GAACCCGAGA
3450040 TTTTTTATTATTATTT
1 TTTTTTATTATTATTT
3450056 TTTTATTATTATTATTT
1 TTTT-TTATTATTATTT
3450073 T
1 T
3450074 AAAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTTATTATTATTT
Found at i:3452161 original size:178 final size:177
Alignment explanation
Indices: 3451843--3452166 Score: 443
Period size: 178 Copynumber: 1.8 Consensus size: 177
3451833 TTCACTATAC
* * *
3451843 CATTTTATATAAAGGTTATAACTTAAGACCTCACCTAATCAATATACTTGTTTATCATGCATGTA
1 CATTTTATATAAAGGTTATAACTTAAGACATCACCTAATCAATATAATTGTTTATCATGCATATA
* * * * * ** *
3451908 TATTTATGAACTATTTTATTTGAGACAATTTGAAAGGAAAATAGCATTAACGAGCACATGCGTGT
66 AATTTATGAACTATTTTATTGGAGACAATTTGAAACGAAAATAGAATCAACGAGCACAACCCTGT
3451973 GCACATACAAAGACAGACACTGTTTATATAGTCTCATCTCACTGGAG
131 GCACATACAAAGACAGACACTGTTTATATAGTCTCATCTCACTGGAG
* * *
3452020 CATTTTATCTAAAGGTTTTGAACTTAAGACATCACCTAATCAGTATAATTGTTTATCATGCATAT
1 CATTTTATATAAAGGTTAT-AACTTAAGACATCACCTAATCAATATAATTGTTTATCATGCATAT
* ** * *
3452085 AAATTTATGACCTATTTTATTGGAGATGATTTGAAACGAAAATATAATCAACTA-CTACAACCCT
65 AAATTTATGAACTATTTTATTGGAGACAATTTGAAACGAAAATAGAATCAACGAGC-ACAACCCT
*
3452149 GTGCATATACAAAGACAG
129 GTGCACATACAAAGACAG
3452167 GCACCGTCCA
Statistics
Matches: 125, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
177 18 0.14
178 107 0.86
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (177 bp):
CATTTTATATAAAGGTTATAACTTAAGACATCACCTAATCAATATAATTGTTTATCATGCATATA
AATTTATGAACTATTTTATTGGAGACAATTTGAAACGAAAATAGAATCAACGAGCACAACCCTGT
GCACATACAAAGACAGACACTGTTTATATAGTCTCATCTCACTGGAG
Found at i:3455814 original size:14 final size:12
Alignment explanation
Indices: 3455784--3455816 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3455774 TTCGAACTTT
3455784 TTATATATTTTG
1 TTATATATTTTG
3455796 TTATATATTTTG
1 TTATATATTTTG
3455808 TTATATATT
1 TTATATATT
3455817 ATCGATGACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (12 bp):
TTATATATTTTG
Found at i:3460203 original size:21 final size:21
Alignment explanation
Indices: 3460174--3460217 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3460164 CTTGCACTAC
3460174 CACAACAATATTGTAAATTGT
1 CACAACAATATTGTAAATTGT
* *
3460195 CACATCAATATTGTAGATTGT
1 CACAACAATATTGTAAATTGT
3460216 CA
1 CA
3460218 TGTAAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.34
Consensus pattern (21 bp):
CACAACAATATTGTAAATTGT
Found at i:3467147 original size:2 final size:2
Alignment explanation
Indices: 3467137--3467196 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
3467127 ATTTTTTTAT
3467137 TA TA T- 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
3467178 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
3467197 GGATTATTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3467213 original size:16 final size:17
Alignment explanation
Indices: 3467135--3467220 Score: 62
Period size: 16 Copynumber: 5.4 Consensus size: 17
3467125 TTATTTTTTT
3467135 ATTATATTATATATAT--
1 ATTAT-TTATATATATGG
*
3467151 A-TATATATATATAT--
1 ATTATTTATATATATGG
*
3467165 ATATATATATATATAT--
1 AT-TATTTATATATATGG
*
3467181 ATATATATATATATATGG
1 AT-TATTTATATATATGG
3467199 ATTATTTATAT-TATGG
1 ATTATTTATATATATGG
3467215 ATTATT
1 ATTATT
3467221 AGATTTTGTA
Statistics
Matches: 64, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
14 10 0.16
15 3 0.05
16 41 0.64
17 8 0.12
18 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTATTTATATATATGG
Found at i:3468212 original size:12 final size:12
Alignment explanation
Indices: 3468192--3468225 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3468182 TTCGTGCGAT
3468192 TTTTCGTTATAAA
1 TTTT-GTTATAAA
3468205 TTTTGTTATAAA
1 TTTTGTTATAAA
*
3468217 TTTTTTTAT
1 TTTTGTTAT
3468226 TATACTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (12 bp):
TTTTGTTATAAA
Found at i:3470149 original size:18 final size:18
Alignment explanation
Indices: 3470126--3470165 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
3470116 TGGAAAGGCG
*
3470126 GCGGCATCATATATGGTT
1 GCGGCATCATAAATGGTT
3470144 GCGGCATCATAAATGGTT
1 GCGGCATCATAAATGGTT
3470162 GCGG
1 GCGG
3470166 TGGCTGTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.28
Consensus pattern (18 bp):
GCGGCATCATAAATGGTT
Found at i:3471861 original size:17 final size:18
Alignment explanation
Indices: 3471839--3471879 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
3471829 AAAATATATT
3471839 AGTAAAAT-ATTAAATAA
1 AGTAAAATGATTAAATAA
*
3471856 AGTAAAATGCTTAAATAA
1 AGTAAAATGATTAAATAA
*
3471874 ATTAAA
1 AGTAAA
3471880 TACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.61, C:0.02, G:0.07, T:0.29
Consensus pattern (18 bp):
AGTAAAATGATTAAATAA
Found at i:3472088 original size:50 final size:52
Alignment explanation
Indices: 3472029--3472144 Score: 123
Period size: 51 Copynumber: 2.3 Consensus size: 52
3472019 CCTCTTGTAC
* * *
3472029 CGCGTTATACCCCACATGTCAGATA-AACAGC-TATAGCATGG-ATCAGGGGG
1 CGCGCTATACCCCACATGTAAGATATAACAGCGTATAGCACGGTA-CAGGGGG
* * ** *
3472079 CGCGCTATA-CCCACGTGTAAGCTATGTCAGCGTATAGCGCGGTACAGGGGG
1 CGCGCTATACCCCACATGTAAGATATAACAGCGTATAGCACGGTACAGGGGG
3472130 CGCGCTATACCCCAC
1 CGCGCTATACCCCAC
3472145 GTGGCGCCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
49 12 0.22
50 12 0.22
51 24 0.44
52 6 0.11
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (52 bp):
CGCGCTATACCCCACATGTAAGATATAACAGCGTATAGCACGGTACAGGGGG
Found at i:3472160 original size:51 final size:51
Alignment explanation
Indices: 3472072--3472186 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
3472062 TAGCATGGAT
* ** * *
3472072 CAGGGGGCGCGCTATACCCACGTGTAAGCTATGTCAGCGTATAGCGCGGTA
1 CAGGGGGCGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGCGCGGGA
** *
3472123 CAGGGGGCGCGCTATACCCCACGTG-GCGCCAAATCAGCATATAGCGCGGGG
1 CAGGGGGCGCGCTATA-CCCACGTGTAAGCCAAATCAGCATATAGCGCGGGA
*
3472174 CAGGGAGCGCGCT
1 CAGGGGGCGCGCT
3472187 TTACTGCTAC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
51 46 0.85
52 8 0.15
ACGTcount: A:0.21, C:0.29, G:0.36, T:0.15
Consensus pattern (51 bp):
CAGGGGGCGCGCTATACCCACGTGTAAGCCAAATCAGCATATAGCGCGGGA
Found at i:3472557 original size:23 final size:25
Alignment explanation
Indices: 3472521--3472569 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
3472511 TGTCAAAAAC
3472521 AGAAGAAAATATGTCATAAAGGCAT
1 AGAAGAAAATATGTCATAAAGGCAT
* *
3472546 AGAA-AAAA-ATGTTATACAGGCAT
1 AGAAGAAAATATGTCATAAAGGCAT
3472569 A
1 A
3472570 CTTATTGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.64
24 4 0.18
25 4 0.18
ACGTcount: A:0.53, C:0.08, G:0.18, T:0.20
Consensus pattern (25 bp):
AGAAGAAAATATGTCATAAAGGCAT
Found at i:3474142 original size:2 final size:2
Alignment explanation
Indices: 3474135--3474182 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3474125 TCTTTATTTC
3474135 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3474177 AT AT AT
1 AT AT AT
3474183 GGTTAGAATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3475059 original size:22 final size:21
Alignment explanation
Indices: 3475034--3475074 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3475024 TATGATTCTG
3475034 GATTTT-GAGGTTTAGAGTTTGA
1 GATTTTGGA-GTTTAG-GTTTGA
3475056 GATTTTGGAGTTTAGGTTT
1 GATTTTGGAGTTTAGGTTT
3475075 AAGGTGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 12 0.67
23 2 0.11
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.49
Consensus pattern (21 bp):
GATTTTGGAGTTTAGGTTTGA
Found at i:3477109 original size:31 final size:29
Alignment explanation
Indices: 3477058--3477150 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 29
3477048 AGAGTCGAGG
*
3477058 GTTACCTATATCTTTCGAGACATATGGATA
1 GTTACCTATGTCTTT-GAGACATATGGATA
*
3477088 GTCTACCTATGTCCTTTGAGACATATGGACA
1 GT-TACCTATGT-CTTTGAGACATATGGATA
*
3477119 GGTTACCTATGT-TCTTCAGAACATATGGATA
1 -GTTACCTATGTCT-TTGAG-ACATATGGATA
3477150 G
1 G
3477151 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
29 1 0.02
30 7 0.13
31 40 0.74
32 6 0.11
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.34
Consensus pattern (29 bp):
GTTACCTATGTCTTTGAGACATATGGATA
Found at i:3480060 original size:18 final size:18
Alignment explanation
Indices: 3480037--3480076 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3480027 TTGTGATTCG
3480037 AATAAGGATTT-TGCAAAT
1 AATAAGG-TTTATGCAAAT
*
3480055 AATAAGGTTTATGCAAGT
1 AATAAGGTTTATGCAAAT
3480073 AATA
1 AATA
3480077 CTAACTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.33
Consensus pattern (18 bp):
AATAAGGTTTATGCAAAT
Found at i:3481173 original size:17 final size:17
Alignment explanation
Indices: 3481134--3481167 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3481124 TAAGATGAAG
* *
3481134 AGAATAGAGGGAATTAA
1 AGAAAAGAGGGAAATAA
3481151 AGAAAAGAGGGAAATAA
1 AGAAAAGAGGGAAATAA
3481168 GTAAAATCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (17 bp):
AGAAAAGAGGGAAATAA
Found at i:3482623 original size:31 final size:30
Alignment explanation
Indices: 3482583--3482678 Score: 122
Period size: 31 Copynumber: 3.1 Consensus size: 30
3482573 AAGAGTCGAG
3482583 GGTTACCTATGTCTTTCGAGACATATGGATA
1 GGTTACCTATGTCTTTCG-GACATATGGATA
* * *
3482614 GTTTACCTATGTCCTTCGGGACATATGGACA
1 GGTTACCTATGTCTTTC-GGACATATGGATA
3482645 GGTTACCTATGT-TCTTCGGAACATATGGATA
1 GGTTACCTATGTCT-TTCGG-ACATATGGATA
3482676 GGT
1 GGT
3482679 CATTCGGGAC
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.04
31 53 0.95
32 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (30 bp):
GGTTACCTATGTCTTTCGGACATATGGATA
Found at i:3483579 original size:25 final size:25
Alignment explanation
Indices: 3483542--3483600 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
3483532 GATCTTAAAT
*
3483542 TTGTGTAAAACTAAAGAATTTTACA
1 TTGTGTAAGACTAAAGAATTTTACA
3483567 TTGTGTAAGACTAAAGAATTTTACA
1 TTGTGTAAGACTAAAGAATTTTACA
*
3483592 TTATGTAAG
1 TTGTGTAAG
3483601 TGGATCATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (25 bp):
TTGTGTAAGACTAAAGAATTTTACA
Found at i:3485296 original size:16 final size:16
Alignment explanation
Indices: 3485234--3485295 Score: 106
Period size: 16 Copynumber: 3.9 Consensus size: 16
3485224 TCTAATTTTT
*
3485234 TTTTTGAGTTCAAGCC
1 TTTTCGAGTTCAAGCC
3485250 TTTTCGAGTTCAAGCC
1 TTTTCGAGTTCAAGCC
*
3485266 TTTTCGAGTTCAAGTC
1 TTTTCGAGTTCAAGCC
3485282 TTTTCGAGTTCAAG
1 TTTTCGAGTTCAAG
3485296 TTTCAATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (16 bp):
TTTTCGAGTTCAAGCC
Found at i:3489122 original size:44 final size:44
Alignment explanation
Indices: 3489056--3489151 Score: 138
Period size: 44 Copynumber: 2.2 Consensus size: 44
3489046 TAGCAACAAA
* * *
3489056 ATATAAAACAAATACATTCATTATGAAGCATAATAAAATAAACT
1 ATATAAAACAAATACATCCATTAAGAAGCATAATAAAATAAACC
* *
3489100 ATATAAAACAAATATATCCATTAAGAAGCATAATGAAATAAACC
1 ATATAAAACAAATACATCCATTAAGAAGCATAATAAAATAAACC
3489144 ATGATAAA
1 AT-ATAAA
3489152 TTAAGTTTAT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 41 0.89
45 5 0.11
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.25
Consensus pattern (44 bp):
ATATAAAACAAATACATCCATTAAGAAGCATAATAAAATAAACC
Found at i:3489455 original size:25 final size:25
Alignment explanation
Indices: 3489421--3489473 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
3489411 TGGTGCGAAT
3489421 TCCATGAAATAGTACCCGTATGCCA
1 TCCATGAAATAGTACCCGTATGCCA
*
3489446 TCCATGAAATAGTACCCGTCTGCCA
1 TCCATGAAATAGTACCCGTATGCCA
3489471 TCC
1 TCC
3489474 CTAATTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.32, G:0.15, T:0.25
Consensus pattern (25 bp):
TCCATGAAATAGTACCCGTATGCCA
Found at i:3492227 original size:21 final size:20
Alignment explanation
Indices: 3492203--3492241 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3492193 TACAAATGTT
*
3492203 TTAAAAATATATATTAAAATA
1 TTAAAAATA-ATATAAAAATA
*
3492224 TTAACAATAATATAAAAA
1 TTAAAAATAATATAAAAA
3492242 AATAATCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
TTAAAAATAATATAAAAATA
Found at i:3492350 original size:29 final size:29
Alignment explanation
Indices: 3492304--3492370 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
3492294 TGTATTGGTT
*
3492304 GCCATGCAGTCCAAGCGAGCTTATAGGCC
1 GCCATGCAGTCCAAGCGACCTTATAGGCC
*** * *
3492333 GCCATGCAGTCGTTGCGACCTTGTAGGTC
1 GCCATGCAGTCCAAGCGACCTTATAGGCC
3492362 GCCATGCAG
1 GCCATGCAG
3492371 GTAGCTCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.19, C:0.30, G:0.30, T:0.21
Consensus pattern (29 bp):
GCCATGCAGTCCAAGCGACCTTATAGGCC
Found at i:3492437 original size:15 final size:15
Alignment explanation
Indices: 3492417--3492446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3492407 GACAAAGGTG
3492417 GCCCTGCCTCCCTCA
1 GCCCTGCCTCCCTCA
*
3492432 GCCCTGTCTCCCTCA
1 GCCCTGCCTCCCTCA
3492447 TACATACAAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.57, G:0.13, T:0.23
Consensus pattern (15 bp):
GCCCTGCCTCCCTCA
Found at i:3492605 original size:37 final size:36
Alignment explanation
Indices: 3492564--3492634 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
3492554 TCCCTCATGC
*
3492564 ATGCAATAATAATTTAACGTAAATTGAAGGCGTGAAA
1 ATGCAACAATAA-TTAACGTAAATTGAAGGCGTGAAA
* * * *
3492601 ATGCAGCAATAATTCACGTAAATTGCAGGTGTGA
1 ATGCAACAATAATTAACGTAAATTGAAGGCGTGA
3492635 TTTGCAGCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 19 0.66
37 10 0.34
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (36 bp):
ATGCAACAATAATTAACGTAAATTGAAGGCGTGAAA
Done.