Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009001.1 Hibiscus syriacus cultivar Beakdansim tig00112383_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: 4740655
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 24
Found at i:3445083 original size:3 final size:3
Alignment explanation
Indices: 3445077--3445163 Score: 140
Period size: 3 Copynumber: 29.3 Consensus size: 3
3445067 ATGTAAACAA
3445077 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
3445125 AAT AAT AAT TAT AAT AAT AA- AAT AAC GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3445164 TTATTAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
2 2 0.03
3 75 0.97
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3445649 original size:133 final size:134
Alignment explanation
Indices: 3445399--3445714 Score: 528
Period size: 133 Copynumber: 2.4 Consensus size: 134
3445389 TATGGTTGGG
*
3445399 GGGATGACACGGCTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTT
1 GGGATGACACGACTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTT
*
3445464 CCTATGCGATGAGGATAACTGGTTATCTAGGGGTGACACGACTCCTATGCGATGAAGAGATCTGA
66 CCTATGCGATGAGGATAACTGGTTATCTAGGGGTGACACGACTCCTACGCGATGAAGAGATCTGA
3445529 TC-A
131 TCGA
* *
3445532 GTGATGGCACGACTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTT
1 GGGATGACACGACTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTT
** * *
3445597 CCTATGCGATGAGGATGGCTGGTTATCTAGGGGTGACACGACTCCTACGCGATGAGGAGATCTGG
66 CCTATGCGATGAGGATAACTGGTTATCTAGGGGTGACACGACTCCTACGCGATGAAGAGATCTGA
*
3445662 TCGG
131 TCGA
3445666 GGGATGACACGGA-TCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAA
1 GGGATGACAC-GACTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAA
3445715 TTATGGTTTC
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
133 124 0.73
134 44 0.26
135 2 0.01
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (134 bp):
GGGATGACACGACTCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTT
CCTATGCGATGAGGATAACTGGTTATCTAGGGGTGACACGACTCCTACGCGATGAAGAGATCTGA
TCGA
Found at i:3445662 original size:43 final size:43
Alignment explanation
Indices: 3445463--3445662 Score: 131
Period size: 43 Copynumber: 4.6 Consensus size: 43
3445453 ATAACTCGGT
* *
3445463 TCCTATGCGATGAGGATAACTGGTTATCTAGGGGTGACACGAC
1 TCCTATGCGATGAGGAGATCTGGTTATCTAGGGGTGACACGAC
* * * *
3445506 TCCTATGCGATGAAGAGATCT-G--ATC-AGTGATGGCACGAC
1 TCCTATGCGATGAGGAGATCTGGTTATCTAGGGGTGACACGAC
* * * * * * * **
3445545 TCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGT
1 TCCTATGCGATGAGGAGATCTGGTTATC--TA-G--GGGTG---ACACGAC
*
3445596 TCCTATGCGATGAGGATG-GCTGGTTATCTAGGGGTGACACGAC
1 TCCTATGCGATGAGGA-GATCTGGTTATCTAGGGGTGACACGAC
*
3445639 TCCTACGCGATGAGGAGATCTGGT
1 TCCTATGCGATGAGGAGATCTGGT
3445663 CGGGGGATGA
Statistics
Matches: 116, Mismatches: 27, Indels: 28
0.68 0.16 0.16
Matches are distributed among these distances:
39 28 0.24
40 4 0.03
42 5 0.04
43 42 0.36
45 1 0.01
46 6 0.05
48 4 0.03
49 2 0.02
51 23 0.20
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (43 bp):
TCCTATGCGATGAGGAGATCTGGTTATCTAGGGGTGACACGAC
Found at i:3445691 original size:40 final size:39
Alignment explanation
Indices: 3445626--3445703 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
3445616 TGGTTATCTA
* *
3445626 GGGGTGACACGACTCCTACGCGATGAGGAGATCTGGTCG
1 GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
* *
3445665 GGGGATGACACGGA-TCATACGTGATGAAGAGTTCTGGTC
1 GGGG-TGACAC-GACTCATACGCGATGAAGAGATCTGGTC
3445704 ATCTTTAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 4 0.12
40 27 0.82
41 2 0.06
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (39 bp):
GGGGTGACACGACTCATACGCGATGAAGAGATCTGGTCG
Found at i:3445760 original size:28 final size:28
Alignment explanation
Indices: 3445720--3445799 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
3445710 AGGAATTATG
** *
3445720 GTTTCAAGGGAAACCGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
3445748 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACTCAAAGATTT
* *
3445776 GTTTTAAGAA-AAACAAACTCAAAG
1 GTTTCAA-AAGAAACAGACTCAAAG
3445800 GTGATGTGTT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 44 0.96
29 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACTCAAAGATTT
Found at i:3445983 original size:32 final size:33
Alignment explanation
Indices: 3445936--3446005 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
3445926 CAAAGATCGG
* *
3445936 TGTTTCGAGAGAAACAAACTCAAAGATGTT-TT
1 TGTTTCCAGAAAAACAAACTCAAAGATGTTGTT
* *
3445968 TGTTTCCAGAAAAACATACTCAAAGATTTTGTT
1 TGTTTCCAGAAAAACAAACTCAAAGATGTTGTT
3446001 TGTTT
1 TGTTT
3446006 TGTTTCAAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (33 bp):
TGTTTCCAGAAAAACAAACTCAAAGATGTTGTT
Found at i:3446010 original size:38 final size:38
Alignment explanation
Indices: 3445965--3446071 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 38
3445955 TCAAAGATGT
* **
3445965 TTTTGTTTCCAGAAAAACATACTCAAAGATTTTGTTTG
1 TTTTGTTTCCAGAAAAACAAACTCAAAGATTTTGTTAC
* ** *
3446003 TTTTGTTTCAAGGGAAACAAACTCAAAGA--TGGTTAC
1 TTTTGTTTCCAGAAAAACAAACTCAAAGATTTTGTTAC
* *
3446039 TTTTGTTTCCA-AAGAAATAGACTCAAAGATTTT
1 TTTTGTTTCCAGAA-AAACAAACTCAAAGATTTT
3446072 TCTTAAAAGA
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
36 27 0.51
38 26 0.49
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (38 bp):
TTTTGTTTCCAGAAAAACAAACTCAAAGATTTTGTTAC
Found at i:3446020 original size:70 final size:73
Alignment explanation
Indices: 3445936--3446071 Score: 190
Period size: 74 Copynumber: 1.9 Consensus size: 73
3445926 CAAAGATCGG
* *
3445936 TGTTTCGAGAGAAACAAACTCAAAGAT-G-T-TTTTGTTTCCAGAA-AAACATACTCAAAGATTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGGTTATTTTGTTTCCA-AAGAAACAGACTCAAAGATTT
3445997 TGTTTGTTT
65 TGTTTGTTT
* *
3446006 TGTTTCAAGGGAAACAAACTCAAAGATGGTTACTTTTGTTTCCAAAGAAATAGACTCAAAGATTT
1 TGTTTCAAGAGAAACAAACTCAAAGATGGTTA-TTTTGTTTCCAAAGAAACAGACTCAAAGATTT
3446071 T
65 T
3446072 TCTTAAAAGA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 25 0.44
71 1 0.02
72 1 0.02
73 2 0.04
74 28 0.49
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (73 bp):
TGTTTCAAGAGAAACAAACTCAAAGATGGTTATTTTGTTTCCAAAGAAACAGACTCAAAGATTTT
GTTTGTTT
Found at i:3446185 original size:64 final size:64
Alignment explanation
Indices: 3446041--3446197 Score: 199
Period size: 64 Copynumber: 2.4 Consensus size: 64
3446031 ATGGTTACTT
* * * **
3446041 TTGTTTCCAAAGAAATAGACTCAAAGATTTTTCTTAAAAGAAACTGTCTCAAAAGAGACGAAATT
1 TTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTTAAAAGAAACTGTCTC-AAAGAGACAAAACC
* * * *
3446106 TTGTTTCCAAAGAAACAAATTCAAAGATTTTTCTTCAAAATAAACTGTCTC-AAGGGATAAAACC
1 TTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTT-AAAAGAAACTGTCTCAAAGAGACAAAACC
*
3446170 TTGTTTCCAGAGAAACAAACTCAAAGAT
1 TTGTTTCCAAAGAAACAAACTCAAAGAT
3446198 GGGTTACGTC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 34 0.43
65 32 0.40
66 14 0.17
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (64 bp):
TTGTTTCCAAAGAAACAAACTCAAAGATTTTTCTTAAAAGAAACTGTCTCAAAGAGACAAAACC
Found at i:3446911 original size:35 final size:36
Alignment explanation
Indices: 3446827--3446956 Score: 138
Period size: 35 Copynumber: 3.6 Consensus size: 36
3446817 TATCTCAAAG
* **
3446827 GAAAAATGTCTCAAGCGAGACGCAATTTGTTTTTCA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
**
3446863 -AGAAATTGTCTCAAATGAGACAAAATTTGTTTTT-A
1 GA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
*
3446898 GAAAATTGTCTCAAGCGAGACATAATTTGTTTTTCA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
* * *
3446934 AAAGAAGTTGTCCCTAGCGAGAC
1 GAA-AA-TTGTCTCAAGCGAGAC
3446957 GATATTTTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 8
0.80 0.11 0.08
Matches are distributed among these distances:
35 31 0.40
36 31 0.40
37 2 0.03
38 14 0.18
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (36 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTCA
Found at i:3447309 original size:16 final size:17
Alignment explanation
Indices: 3447280--3447314 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
3447270 ATGCAACATG
3447280 TATGTATGTATTGATGTA
1 TATGTATG-ATTGATGTA
3447298 TATGTATG-TTGATGTA
1 TATGTATGATTGATGTA
3447314 T
1 T
3447315 TTTTTTCTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (17 bp):
TATGTATGATTGATGTA
Found at i:3454677 original size:20 final size:20
Alignment explanation
Indices: 3454652--3454690 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3454642 ACAAAATTAT
3454652 AATAACAATAATAATAATAA
1 AATAACAATAATAATAATAA
*
3454672 AATAACGATAATAATAATA
1 AATAACAATAATAATAATA
3454691 TTACCAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.67, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
AATAACAATAATAATAATAA
Found at i:3456524 original size:2 final size:2
Alignment explanation
Indices: 3456517--3456552 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3456507 AGACCCGAAA
3456517 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
3456553 ATGAAGGCTC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3461918 original size:320 final size:320
Alignment explanation
Indices: 3461330--3461966 Score: 1168
Period size: 320 Copynumber: 2.0 Consensus size: 320
3461320 TCTTCATCAT
3461330 CAAGGTATTTGGCAAATATTCGATAGATATGGCGAGGTGGTTGATTCTTTCATCCCTAACAAAAG
1 CAAGGTATTTGGCAAATATTCGATAGATATGGCGAGGTGGTTGATTCTTTCATCCCTAACAAAAG
* *
3461395 AAACAAGGGAGGAAGTAGGTTTGACTTTGTTCGTTTTACCATATTGGAGGACGCGAGGAATGCAA
66 AAACAAGGGAGGAAGTAGGTTTGACTTTGTTCGTTTTACCAGATTGGAGGACGCGAGGAAGGCAA
*
3461460 TCAACTGTGCTGATAGATCTAGGATTCAAGGTAATTAAGTTAGAGTTTTCATGAAGAGATTTCAA
131 TCAACTGTGCTGATAGATCTAGGATTCAAGGTAATAAAGTTAGAGTTTTCATGAAGAGATTTCAA
* *
3461525 CGTCGTGAAGCTTTCTGGAGAAAGAAGTTTTCTGGTCCAAAATCAGCCGAGGCCAAGAGTAGAGT
196 CCTCGTGAAGCTTTCTGGAGAAAGAAGTTTTCTAGTCCAAAATCAGCCGAGGCCAAGAGTAGAGT
* *
3461590 GAAGGATGATAGTCAATCAGAGGCTCCCGTTGTCGGTTGTGTTGACTAGGATAAGCTTCA
261 GAAGGATGATAGTCAATCAGAGGCTCCCATTGTCGGTTGTGTTGACGAGGATAAGCTTCA
3461650 CAAGGTATTTGGCAAATATTCGATAGATATGGCGAGGTGGTTGATTCTTTCATCCCTAACAAAAG
1 CAAGGTATTTGGCAAATATTCGATAGATATGGCGAGGTGGTTGATTCTTTCATCCCTAACAAAAG
*
3461715 AAGCAAGGGAGGAAGTAGGTTTGACTTTGTTCGTTTTACCAGATTGGAGGACGCGAGGAAGGCAA
66 AAACAAGGGAGGAAGTAGGTTTGACTTTGTTCGTTTTACCAGATTGGAGGACGCGAGGAAGGCAA
*
3461780 TCAACTGTGCTGATAGATCTAGGATTCAAGGTAATAAAGTTAGAGTTTTCATGGAGAGATTTCAA
131 TCAACTGTGCTGATAGATCTAGGATTCAAGGTAATAAAGTTAGAGTTTTCATGAAGAGATTTCAA
*
3461845 CCTCGTGAAGCTTTCTGGAGAAAGAAGTTTTCTAGTCCAAAATCAGCCGATGCCAAGAGTAGAGT
196 CCTCGTGAAGCTTTCTGGAGAAAGAAGTTTTCTAGTCCAAAATCAGCCGAGGCCAAGAGTAGAGT
3461910 -AGAGGATGATAGTCAATCAGAGGCTCCCATTGTCGGTTGTGTTGACGAGGATAAGCT
261 GA-AGGATGATAGTCAATCAGAGGCTCCCATTGTCGGTTGTGTTGACGAGGATAAGCT
3461967 CTTAACTCTT
Statistics
Matches: 306, Mismatches: 10, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
319 1 0.00
320 305 1.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (320 bp):
CAAGGTATTTGGCAAATATTCGATAGATATGGCGAGGTGGTTGATTCTTTCATCCCTAACAAAAG
AAACAAGGGAGGAAGTAGGTTTGACTTTGTTCGTTTTACCAGATTGGAGGACGCGAGGAAGGCAA
TCAACTGTGCTGATAGATCTAGGATTCAAGGTAATAAAGTTAGAGTTTTCATGAAGAGATTTCAA
CCTCGTGAAGCTTTCTGGAGAAAGAAGTTTTCTAGTCCAAAATCAGCCGAGGCCAAGAGTAGAGT
GAAGGATGATAGTCAATCAGAGGCTCCCATTGTCGGTTGTGTTGACGAGGATAAGCTTCA
Found at i:3463247 original size:18 final size:18
Alignment explanation
Indices: 3463224--3463258 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3463214 GCAATGATCG
3463224 ATTTTGCTGCTGTGTTTT
1 ATTTTGCTGCTGTGTTTT
*
3463242 ATTTTGCTGTTGTGTTT
1 ATTTTGCTGCTGTGTTT
3463259 AGTTGGGTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.09, G:0.23, T:0.63
Consensus pattern (18 bp):
ATTTTGCTGCTGTGTTTT
Found at i:3463672 original size:31 final size:31
Alignment explanation
Indices: 3463636--3463694 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
3463626 AACTTAAAAG
*
3463636 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
3463667 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
3463695 CCATACAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:3466257 original size:2 final size:2
Alignment explanation
Indices: 3466250--3466275 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3466240 TCGTACATGC
3466250 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
3466276 GTTTAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3467307 original size:20 final size:20
Alignment explanation
Indices: 3467278--3467316 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3467268 CGGTAAAGCG
*
3467278 TTACCTAAAATATTATTTTT
1 TTACCGAAAATATTATTTTT
*
3467298 TTACCGAAAATGTTATTTT
1 TTACCGAAAATATTATTTT
3467317 CGCTAACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.51
Consensus pattern (20 bp):
TTACCGAAAATATTATTTTT
Found at i:3467498 original size:20 final size:20
Alignment explanation
Indices: 3467473--3467515 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3467463 GGCAATGAAC
*
3467473 CGGCTGAAAACCGGTAGAAT
1 CGGCTGAAAACCGGTAAAAT
*
3467493 CGGCTGAAAATCGGTAAAAT
1 CGGCTGAAAACCGGTAAAAT
3467513 CGG
1 CGG
3467516 GGTGAACCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.30, T:0.16
Consensus pattern (20 bp):
CGGCTGAAAACCGGTAAAAT
Found at i:3468541 original size:12 final size:13
Alignment explanation
Indices: 3468516--3468549 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
3468506 ATTAAAAAAA
3468516 TAATAATATTTTT
1 TAATAATATTTTT
3468529 TAATAAT-TTTTT
1 TAATAATATTTTT
3468541 TAATAATAT
1 TAATAATAT
3468550 ATTAAGACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATAATATTTTT
Found at i:3468873 original size:19 final size:19
Alignment explanation
Indices: 3468835--3468871 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3468825 AACTATTAAA
3468835 AATTATAAAATTATTATTT
1 AATTATAAAATTATTATTT
3468854 AATTATAAAA-TATTATTT
1 AATTATAAAATTATTATTT
3468872 TATTGATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
AATTATAAAATTATTATTT
Found at i:3468892 original size:60 final size:60
Alignment explanation
Indices: 3468802--3468919 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
3468792 CATTGATTAT
* * * *
3468802 AATATTATTTTACGTATACTTTTAACTATTAAAAATTATAAAATTATTATTTAATTATAA
1 AATATTATTTTACGTATACTTTCAACTATTAAAAATTATAAAATAATAATTAAATTATAA
* * *
3468862 AATATTATTTTA-TTGATTCTTTCAATTATTAAAAATTATAAAATAATAATTAAATTAT
1 AATATTATTTTACGT-ATACTTTCAACTATTAAAAATTATAAAATAATAATTAAATTAT
3468920 TTATATATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 49 0.98
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (60 bp):
AATATTATTTTACGTATACTTTCAACTATTAAAAATTATAAAATAATAATTAAATTATAA
Found at i:3469545 original size:10 final size:10
Alignment explanation
Indices: 3469530--3469560 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
3469520 ATTATCAATT
3469530 TTATTATTTA
1 TTATTATTTA
3469540 TTATTATTTA
1 TTATTATTTA
3469550 TTATTATTTA
1 TTATTATTTA
3469560 T
1 T
3469561 CCACTAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTATTATTTA
Found at i:3472507 original size:3 final size:3
Alignment explanation
Indices: 3472494--3472565 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
3472484 TTTCTTTCAT
* *
3472494 TTA TT- TTA TTA TTA TT- TTA ATA TTA TTA TTTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
* * *
3472538 TTA ATA TTA ATA TTA TTA ATA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3472566 ATATCCAAAC
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 4 0.07
3 49 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3472535 original size:30 final size:30
Alignment explanation
Indices: 3472500--3472565 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
3472490 TCATTTATTT
*
3472500 TATTATTATT-TTAATATTATTA-T-TTAA
1 TATTATTATTATTAATATTAATATTATTAA
3472527 TATTATTATTATTAATATTAATATTATTAA
1 TATTATTATTATTAATATTAATATTATTAA
3472557 TATTATTAT
1 TATTATTAT
3472566 ATATCCAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
27 10 0.29
28 11 0.31
29 1 0.03
30 13 0.37
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (30 bp):
TATTATTATTATTAATATTAATATTATTAA
Found at i:3475093 original size:16 final size:16
Alignment explanation
Indices: 3475069--3475115 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
3475059 CATTTCCAAA
*
3475069 TCATGCATTAAAATAT
1 TCATTCATTAAAATAT
3475085 TCATTCATTAAAATAT
1 TCATTCATTAAAATAT
*
3475101 TCAGTCATTAAAATA
1 TCATTCATTAAAATA
3475116 AGGATTTCGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (16 bp):
TCATTCATTAAAATAT
Found at i:3477330 original size:10 final size:10
Alignment explanation
Indices: 3477309--3477369 Score: 51
Period size: 9 Copynumber: 6.4 Consensus size: 10
3477299 TTCAAATAGC
3477309 AAAAAGAA-A
1 AAAAAGAAGA
*
3477318 AAAAAGAGGA
1 AAAAAGAAGA
3477328 AAAAAGGATA-A
1 AAAAA-GA-AGA
3477339 AAAAAGAAGA
1 AAAAAGAAGA
3477349 AAAAA-AAG-
1 AAAAAGAAGA
*
3477357 AGAAAGAA-A
1 AAAAAGAAGA
3477366 AAAA
1 AAAA
3477370 GAGAGGTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
8 4 0.10
9 16 0.38
10 14 0.33
11 8 0.19
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (10 bp):
AAAAAGAAGA
Found at i:3477332 original size:11 final size:10
Alignment explanation
Indices: 3477309--3477366 Score: 55
Period size: 11 Copynumber: 5.5 Consensus size: 10
3477299 TTCAAATAGC
3477309 AAAAAGA-AA
1 AAAAAGAGAA
3477318 AAAAAGAGGAA
1 AAAAAGA-GAA
* *
3477329 AAAAGGATAA
1 AAAAAGAGAA
3477339 AAAAAGAAGAAA
1 AAAAAG-AG-AA
3477351 AAAAAGAGAA
1 AAAAAGAGAA
3477361 AGAAAA
1 A-AAAA
3477367 AAAGAGAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
9 7 0.17
10 10 0.25
11 15 0.38
12 8 0.20
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
AAAAAGAGAA
Found at i:3477360 original size:14 final size:14
Alignment explanation
Indices: 3477337--3477373 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
3477327 AAAAAAGGAT
3477337 AAAAAA-AG-AAGAA
1 AAAAAAGAGAAAG-A
3477350 AAAAAAGAGAAAGA
1 AAAAAAGAGAAAGA
3477364 AAAAAAGAGA
1 AAAAAAGAGA
3477374 GGTTATAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAGAGAAAGA
Found at i:3479615 original size:37 final size:36
Alignment explanation
Indices: 3479560--3479988 Score: 252
Period size: 37 Copynumber: 11.8 Consensus size: 36
3479550 AGCAACTTTG
* *
3479560 TCTCGCTTGAGAAAGTTTTACTTGAAATAACAATTTA
1 TCTCACTTGAGAAAGTTTTACTTAAAATAA-AATTTA
** * * * *
3479597 TCTCACTTGAGATTGTTTTTTCTTAAAACAAACTTTG
1 TCTCACTTGAGAAAG-TTTTACTTAAAATAAAATTTA
* * **
3479634 TCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTA
1 TCTCACTTGAGAAAGTTTTACTTAAAATAA-AATTTA
** * * * *
3479671 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
1 TCTCACTTGAGAAAGTTTTACTTAAAATAAAATTTA
* * ** *
3479707 TCTCGCTTGAGAAAGTTTCACTCGAAATAGTAATTTA
1 TCTCACTTGAGAAAGTTTTACTTAAAATA-AAATTTA
* * * * *
3479744 TCTCACTCGAGATTA-TTTTTCTTAAAATAAACTTTG
1 TCTCACTTGAGA-AAGTTTTACTTAAAATAAAATTTA
* * * **
3479780 TCTCGCTTGAGAAAGTTTCAATCGAAATAACAAATTT-
1 TCTCACTTGAGAAAGTTTTACTTAAAAT-A-AAATTTA
** * * * *
3479817 TCTCACTTGAGATTGTTTTTCTTAAAACAAACTTTG
1 TCTCACTTGAGAAAGTTTTACTTAAAATAAAATTTA
* * * *
3479853 TCTCGCTTGAGAAAGTTTCACTCAAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTTACTTAAAATA-AAATTTA
** * * * *
3479890 TCTCACTTGAG-ATTTTTTTCTTAAAACAAACTTTG
1 TCTCACTTGAGAAAGTTTTACTTAAAATAAAATTTA
* ** *
3479925 TCTCACTTGAGAAAGTTTCACTCGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTTACTTAAAATA-AAATTTA
** *
3479962 TCTCACTTGAGATTGTTTTTCTTAAAA
1 TCTCACTTGAGAAAGTTTTACTTAAAA
3479989 CAAACTTAGC
Statistics
Matches: 277, Mismatches: 104, Indels: 22
0.69 0.26 0.05
Matches are distributed among these distances:
35 21 0.08
36 101 0.36
37 137 0.49
38 18 0.06
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (36 bp):
TCTCACTTGAGAAAGTTTTACTTAAAATAAAATTTA
Found at i:3479725 original size:73 final size:73
Alignment explanation
Indices: 3479482--3479995 Score: 773
Period size: 73 Copynumber: 7.0 Consensus size: 73
3479472 GAAGCAAATA
* * * * ** **
3479482 TTTGTCTCGCTTGAGACAGGTTTCACTCGAAACAAAAAAATTATCTCACTCAAGATAATTTTTCT
1 TTTGTCTCGCTTGAGA-AAGTTTCACTCGAAA-TAACAATTTATCTCACTTGAGATTGTTTTTCT
* *
3479547 CAAAGC-AAC
64 TAAAACAAAC
* *
3479556 TTTGTCTCGCTTGAGAAAGTTTTACTTGAAATAACAATTTATCTCACTTGAGATTGTTTTTTCTT
1 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTG-TTTTTCTT
3479621 AAAACAAAC
65 AAAACAAAC
3479630 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
3479695 AAACAAAC
66 AAACAAAC
** * *
3479703 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAGTAATTTATCTCACTCGAGATTATTTTTCTTA
1 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
*
3479768 AAATAAAC
66 AAACAAAC
*
3479776 TTTGTCTCGCTTGAGAAAGTTTCAATCGAAATAACAAATTT-TCTCACTTGAGATTGTTTTTCTT
1 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAAC-AATTTATCTCACTTGAGATTGTTTTTCTT
3479840 AAAACAAAC
65 AAAACAAAC
* *
3479849 TTTGTCTCGCTTGAGAAAGTTTCACTCAAAATAGCAATTTATCTCACTTGAGATT-TTTTTCTTA
1 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
3479913 AAACAAAC
66 AAACAAAC
* *
3479921 TTTGTCTCACTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
3479986 AAACAAAC
66 AAACAAAC
3479994 TT
1 TT
3479996 AGCCTCACTT
Statistics
Matches: 405, Mismatches: 30, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
72 93 0.23
73 234 0.58
74 78 0.19
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (73 bp):
TTTGTCTCGCTTGAGAAAGTTTCACTCGAAATAACAATTTATCTCACTTGAGATTGTTTTTCTTA
AAACAAAC
Found at i:3480348 original size:14 final size:14
Alignment explanation
Indices: 3480329--3480356 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3480319 CATCCCCAGG
3480329 GGAAGAGTTCATAA
1 GGAAGAGTTCATAA
3480343 GGAAGAGTTCATAA
1 GGAAGAGTTCATAA
3480357 TGAGAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.29, T:0.21
Consensus pattern (14 bp):
GGAAGAGTTCATAA
Found at i:3480403 original size:20 final size:20
Alignment explanation
Indices: 3480348--3480413 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
3480338 CATAAGGAAG
3480348 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
3480368 AGTCCCA-AA-GAGGAAGAA-T
1 AGT-TCATAATGA-GAAGAACT
3480387 AAGTTCATAATGAGAAGAACT
1 -AGTTCATAATGAGAAGAACT
*
3480408 TGTTCA
1 AGTTCA
3480414 ACATTTCCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
19 5 0.14
20 27 0.73
21 5 0.14
ACGTcount: A:0.44, C:0.12, G:0.21, T:0.23
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:3481438 original size:2 final size:2
Alignment explanation
Indices: 3481431--3481469 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3481421 AATGAGGAGA
3481431 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3481470 GCTTAGGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3483756 original size:26 final size:26
Alignment explanation
Indices: 3483726--3483782 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
3483716 TCACCCATGA
3483726 ATTTAGTTCAATTCATGTTAACACGT
1 ATTTAGTTCAATTCATGTTAACACGT
3483752 ATTTAGTTCAATTCATGTTAACACGT
1 ATTTAGTTCAATTCATGTTAACACGT
3483778 ATTTA
1 ATTTA
3483783 CAGTACGTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.44
Consensus pattern (26 bp):
ATTTAGTTCAATTCATGTTAACACGT
Found at i:3485166 original size:5 final size:5
Alignment explanation
Indices: 3485156--3485225 Score: 61
Period size: 5 Copynumber: 13.2 Consensus size: 5
3485146 ATAGGGAAGC
*
3485156 AAATA AAAT- AAATA AAATA AAGATAA AAATG AAATAA AAATA TAAATA
1 AAATA AAATA AAATA AAATA AA-AT-A AAATA AAAT-A AAATA -AAATA
* *
3485204 ATATAA AAATA AAATA ATATA A
1 AAAT-A AAATA AAATA AAATA A
3485226 GAAAATAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
4 4 0.07
5 30 0.56
6 17 0.31
7 3 0.06
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (5 bp):
AAATA
Found at i:3485183 original size:11 final size:10
Alignment explanation
Indices: 3485156--3485225 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 10
3485146 ATAGGGAAGC
3485156 AAATAAAAT-
1 AAATAAAATA
3485165 AAATAAAATA
1 AAATAAAATA
*
3485175 AAGATAAAAATG
1 AA-AT-AAAATA
3485187 AAATAAAAATA
1 AAAT-AAAATA
*
3485198 TAAATAATATAA
1 -AAATAAAAT-A
3485210 AAATAAAATA
1 AAATAAAATA
*
3485220 ATATAA
1 AAATAA
3485226 GAAAATAATA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 9 0.18
10 8 0.16
11 22 0.43
12 12 0.24
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (10 bp):
AAATAAAATA
Found at i:3485190 original size:17 final size:16
Alignment explanation
Indices: 3485156--3485291 Score: 68
Period size: 16 Copynumber: 8.3 Consensus size: 16
3485146 ATAGGGAAGC
*
3485156 AAAT-AAAATAAATA-
1 AAATAAAAATAAAAAT
*
3485170 AAATAAAGATAAAAAT
1 AAATAAAAATAAAAAT
*
3485186 GAAATAAAAATATAAAT
1 -AAATAAAAATAAAAAT
3485203 AATATAAAAAT-AAAAT
1 AA-ATAAAAATAAAAAT
* *
3485219 AATATAAGAA-AATAAT
1 AA-ATAAAAATAAAAAT
*
3485235 -AATAATATATACCATAAAT
1 AAATAA-AAATA--A-AAAT
* *
3485254 AAATAAATAAGAACAA-
1 AAATAAA-AATAAAAAT
*
3485270 GAATAAAAAGTAAAAAT
1 AAATAAAAA-TAAAAAT
3485287 AAATA
1 AAATA
3485292 CAGTAATAAA
Statistics
Matches: 91, Mismatches: 17, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
14 8 0.09
15 12 0.13
16 30 0.33
17 28 0.31
18 2 0.02
19 4 0.04
20 7 0.08
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.22
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:3485209 original size:28 final size:28
Alignment explanation
Indices: 3485156--3485220 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
3485146 ATAGGGAAGC
3485156 AAATAAAAT--AAATAAAATAAAGATAA
1 AAATAAAATAAAAATAAAATAAAGATAA
* *
3485182 AAATGAAATAAAAATATAAAT-AATATAA
1 AAATAAAATAAAAATA-AAATAAAGATAA
3485210 AAATAAAATAA
1 AAATAAAATAA
3485221 TATAAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 8 0.24
28 21 0.64
29 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (28 bp):
AAATAAAATAAAAATAAAATAAAGATAA
Found at i:3485214 original size:8 final size:8
Alignment explanation
Indices: 3485189--3485238 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
3485179 TAAAAATGAA
3485189 ATAAAAAT
1 ATAAAAAT
3485197 ATAAATAAT
1 ATAAA-AAT
3485206 ATAAAAAT
1 ATAAAAAT
3485214 A-AAATAAT
1 ATAAA-AAT
3485222 ATAAGAAA-
1 ATAA-AAAT
*
3485230 ATAATAAT
1 ATAAAAAT
3485238 A
1 A
3485239 ATATATACCA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
7 5 0.14
8 18 0.50
9 12 0.33
10 1 0.03
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (8 bp):
ATAAAAAT
Found at i:3485230 original size:19 final size:17
Alignment explanation
Indices: 3485156--3485243 Score: 74
Period size: 17 Copynumber: 4.9 Consensus size: 17
3485146 ATAGGGAAGC
*
3485156 AAATAAAATAAATAAAATA
1 AAATAAAAT-AATATAA-A
3485175 AAGATAAAAATGAA-AT-AA
1 AA-AT-AAAAT-AATATAAA
3485193 AAATATAAATAATAT-AA
1 AAATA-AAATAATATAAA
3485210 AAATAAAATAATATAAGA
1 AAATAAAATAATATAA-A
3485228 AAATAATAATAATATA
1 AAATAA-AATAATATA
3485244 TACCATAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
16 12 0.20
17 16 0.27
18 10 0.17
19 12 0.20
20 3 0.05
21 7 0.12
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATAAAATAATATAAA
Found at i:3486891 original size:37 final size:37
Alignment explanation
Indices: 3486840--3486978 Score: 189
Period size: 37 Copynumber: 3.8 Consensus size: 37
3486830 CAAAGCTTTG
3486840 GTGTTTCAAGAGAAAC-ATGTTCAAAGGTTTTCTTTTT
1 GTGTTTCAAGAGAAACAAT-TTCAAAGGTTTTCTTTTT
*
3486877 TTGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
* *
3486914 GTGTTCCAAGAGAAACAATTTCACAGG---T-TTTTT
1 GTGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
*
3486947 GTGTTTCAAGAGAAAACGATTTCAAAGGTTTT
1 GTGTTTCAAGAG-AAACAATTTCAAAGGTTTT
3486979 TTTCAAGAGA
Statistics
Matches: 90, Mismatches: 7, Indels: 10
0.84 0.07 0.09
Matches are distributed among these distances:
33 16 0.18
34 14 0.16
37 58 0.64
38 2 0.02
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.40
Consensus pattern (37 bp):
GTGTTTCAAGAGAAACAATTTCAAAGGTTTTCTTTTT
Found at i:3487048 original size:29 final size:29
Alignment explanation
Indices: 3487006--3487085 Score: 90
Period size: 30 Copynumber: 2.7 Consensus size: 29
3486996 TCCAGGGAAG
* *
3487006 CAAATTTTTTTTTCAAGAGAAAC-ATATT
1 CAAACTTTTGTTTCAAGAGAAACTATATT
* * *
3487034 CAAAGGTTTTGTTTCAAGGGAAACTATTTT
1 CAAA-CTTTTGTTTCAAGAGAAACTATATT
3487064 CAAACTTTATGTTTCAAGAGAA
1 CAAACTTT-TGTTTCAAGAGAA
3487086 TTTGTCTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 4 0.09
29 19 0.44
30 20 0.47
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (29 bp):
CAAACTTTTGTTTCAAGAGAAACTATATT
Found at i:3487130 original size:36 final size:36
Alignment explanation
Indices: 3487090--3487158 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
3487080 AGAGAATTTG
* **
3487090 TCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACTA
3487126 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
1 TCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
3487159 TGTTTTCAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.23
Consensus pattern (36 bp):
TCTCAAGAGAGACAAAATTCATTTCAAGGGAAACTA
Found at i:3487180 original size:101 final size:105
Alignment explanation
Indices: 3487045--3487247 Score: 297
Period size: 101 Copynumber: 2.0 Consensus size: 105
3487035 AAAGGTTTTG
**
3487045 TTTCAAGGGAAACTATTTTCAAACTTTATGTTTCAAGAGAATTTGTCTCAAGGGAGACA-AA-AT
1 TTTCAAGGGAAACTATTTTCAAACTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACACAATAT
3487108 T-TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 TCTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* ** * *
3487147 TTTCAAGGGAAA-TGTTTTCAATGTTTATGTTTCAAGTGAAACTGTCTCAAGGGAGACACAATTT
1 TTTCAAGGGAAACTATTTTCAAACTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACACAATAT
* *
3487211 TCTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
66 TCTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAAT
3487248 CTTGTTTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 40 0.45
102 14 0.16
103 2 0.02
104 33 0.37
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (105 bp):
TTTCAAGGGAAACTATTTTCAAACTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACACAATAT
TCTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:3487228 original size:39 final size:40
Alignment explanation
Indices: 3487165--3487241 Score: 111
Period size: 39 Copynumber: 1.9 Consensus size: 40
3487155 GAAATGTTTT
* * *
3487165 CAATGTTTATGTTTCAAGTGAAACTGTCTCAAGGGAGACA
1 CAATGTTTATGTTTCAAGGGAAACTATCTCAAGCGAGACA
*
3487205 CAAT-TTTCTGTTTCAAGGGAAACTATCTCAAGCGAGA
1 CAATGTTTATGTTTCAAGGGAAACTATCTCAAGCGAGA
3487242 TAAAATCTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 29 0.88
40 4 0.12
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (40 bp):
CAATGTTTATGTTTCAAGGGAAACTATCTCAAGCGAGACA
Found at i:3487300 original size:36 final size:36
Alignment explanation
Indices: 3487244--3487371 Score: 123
Period size: 36 Copynumber: 3.6 Consensus size: 36
3487234 AAGCGAGATA
*
3487244 AAATCTTGTTTTAAGAAAAACAATCTTGAGGGAAAT
1 AAATCTTCTTTTAAGAAAAACAATCTTGAGGGAAAT
* * * ** * * *
3487280 AAATCTTCTTTTGAGTAAAACAGTCTCAAGTGAGAC
1 AAATCTTCTTTTAAGAAAAACAATCTTGAGGGAAAT
*
3487316 AAAGTC-TGTTTTAAGAAAAACAATCTTGAGGGAAAT
1 AAA-TCTTCTTTTAAGAAAAACAATCTTGAGGGAAAT
* * *
3487352 AAATCCTCTTTCAAGTAAAA
1 AAATCTTCTTTTAAGAAAAA
3487372 TAGTCTCAAG
Statistics
Matches: 69, Mismatches: 21, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
35 2 0.03
36 65 0.94
37 2 0.03
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (36 bp):
AAATCTTCTTTTAAGAAAAACAATCTTGAGGGAAAT
Found at i:3487334 original size:72 final size:72
Alignment explanation
Indices: 3487230--3487534 Score: 421
Period size: 72 Copynumber: 4.2 Consensus size: 72
3487220 AGGGAAACTA
* * * * **
3487230 TCTCAAGCGAGATAAAATCTTGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCTTCTTTTGAG
1 TCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAG
*
3487295 TAAAACAG
65 TAAAATAG
* *
3487303 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTGAGGGAAATAAATCCTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
3487368 AAAATAG
66 AAAATAG
* * ** * *
3487375 TCTCAAGTGAGACAAGGTCCGTTTTAAGAATGACAATCTCAAGGGAAATAAATATTCTTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
3487440 AAAATAG
66 AAAATAG
* ** *
3487447 TCTCAAGTGAGACAAGGTCTGTTTTAAGAATGACAATCTTAAGGGAAATAAATCTTATTTCAAGT
1 TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
3487512 AAAATAG
66 AAAATAG
*
3487519 TTTCAAGTGAGACAAA
1 TCTCAAGTGAGACAAA
3487535 TCATCTGTAT
Statistics
Matches: 211, Mismatches: 21, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
72 195 0.92
73 16 0.08
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.29
Consensus pattern (72 bp):
TCTCAAGTGAGACAAAGTCTGTTTTAAGAAAAACAATCTTAAGGGAAATAAATCTTCTTTCAAGT
AAAATAG
Found at i:3488869 original size:95 final size:95
Alignment explanation
Indices: 3488703--3488884 Score: 260
Period size: 95 Copynumber: 1.9 Consensus size: 95
3488693 ATATGTAAAT
* * **
3488703 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGTGTTTAACCAATCGCCTTAAAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATCGCCTTAAAGGG
*
3488768 ACAACTCAA-TCTTTATTGTATAGTATAATC
66 AAAACTCAAGT-TTTATTGTATAGTATAATC
* * *
3488798 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCTGGGGCATTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATCGCCT-TAAAGG
3488862 GAAAACTCAAGTTTTATTGTATA
65 GAAAACTCAAGTTTTATTGTATA
3488885 TAAATAATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
94 2 0.03
95 74 0.96
96 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATCGCCTTAAAGGG
AAAACTCAAGTTTTATTGTATAGTATAATC
Found at i:3489534 original size:25 final size:25
Alignment explanation
Indices: 3489500--3489559 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
3489490 TTCCTTATGG
*
3489500 ATGCCCCATTTGACTCTCGATCATA
1 ATGCCCCATTTGAATCTCGATCATA
*
3489525 ATGCTCCATTTGAATCTCGATCATA
1 ATGCCCCATTTGAATCTCGATCATA
3489550 ATGCCCCATT
1 ATGCCCCATT
3489560 ACACATTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.25, C:0.30, G:0.12, T:0.33
Consensus pattern (25 bp):
ATGCCCCATTTGAATCTCGATCATA
Found at i:3492900 original size:14 final size:13
Alignment explanation
Indices: 3492874--3492940 Score: 64
Period size: 13 Copynumber: 4.8 Consensus size: 13
3492864 ATAGGGAAGC
3492874 AAATAAAATAAAA
1 AAATAAAATAAAA
3492887 AAATAAAGAT-AAA
1 AAATAAA-ATAAAA
*
3492900 AAATGAAATAAAAA
1 AAATAAAAT-AAAA
*
3492914 AAATATAATATAACA
1 AAATA-AA-ATAAAA
3492929 AAATAATAATAA
1 AAATAA-AATAA
3492941 TATATGCCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
12 2 0.04
13 16 0.36
14 14 0.31
15 11 0.24
16 2 0.04
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.19
Consensus pattern (13 bp):
AAATAAAATAAAA
Found at i:3499814 original size:21 final size:20
Alignment explanation
Indices: 3499728--3499885 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
3499718 AAATGACCAA
**
3499728 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
3499747 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
3499767 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
3499787 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
3499808 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
3499829 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
3499849 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* *
3499870 GAAAATTGCAACGCGA
1 CAAAATCGCAACGCGA
3499886 ACACATAAAT
Statistics
Matches: 103, Mismatches: 30, Indels: 11
0.72 0.21 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 47 0.46
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:3499902 original size:40 final size:40
Alignment explanation
Indices: 3499852--3500082 Score: 126
Period size: 40 Copynumber: 5.8 Consensus size: 40
3499842 CGATTTTCCA
* *
3499852 AAATCGCAACGCGAATATGAAAATTGCAACGCG-AACACAT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAAC-CAT
* * * * *
3499892 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAACCAT
* ** * * * *
3499932 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAACCAT
* * * * * **
3499972 ATATCGCAACGCGTATCCGTAAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAA-CCAT
** * * * **
3500012 AAATCGCAACGATAATCCGTAAATCGCAACGAG-AATCTGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCGTAA-CCAT
** * *
3500052 AAATCGCAACGATAATCCGTAAATCGCAACG
1 AAATCGCAACGCGAATACGAAAATCGCAACG
3500083 AGAATCTGTA
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
39 1 0.01
40 165 0.98
41 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (40 bp):
AAATCGCAACGCGAATACGAAAATCGCAACGCGTAACCAT
Found at i:3499914 original size:20 final size:20
Alignment explanation
Indices: 3499891--3500101 Score: 246
Period size: 20 Copynumber: 10.6 Consensus size: 20
3499881 CGCGAACACA
3499891 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
3499911 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
**
3499931 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACGCGTATCCG
*
3499951 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCG
*
3499971 TATATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCG
* * *
3499991 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
3500011 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
3500031 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
3500051 TAAATCGCAACG-ATAATCCG
1 TAAATCGCAACGCGT-ATCCG
* * *
3500071 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCG
*
3500091 TAAATCACAAC
1 TAAATCGCAAC
3500102 ACTGAAATTT
Statistics
Matches: 163, Mismatches: 24, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
20 163 1.00
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (20 bp):
TAAATCGCAACGCGTATCCG
Found at i:3500083 original size:40 final size:40
Alignment explanation
Indices: 3499891--3500101 Score: 273
Period size: 40 Copynumber: 5.3 Consensus size: 40
3499881 CGCGAACACA
* * *
3499891 TAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTG
** * * * *
3499931 TAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTG
*
3499971 TATATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTG
*
3500011 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGAATCTG
*
3500051 TAAATCGCAACG-ATAATCCGTAAATCGCAACGAGAATCTG
1 TAAATCGCAACGCGT-ATCCGTAAATCGCAACGAGAATCTG
*
3500091 TAAATCACAAC
1 TAAATCGCAAC
3500102 ACTGAAATTT
Statistics
Matches: 157, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
39 1 0.01
40 156 0.99
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.21
Consensus pattern (40 bp):
TAAATCGCAACGCGTATCCGTAAATCGCAACGAGAATCTG
Found at i:3500823 original size:24 final size:24
Alignment explanation
Indices: 3500784--3500830 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3500774 AAATTTGGTC
3500784 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
3500808 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
3500831 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:3501022 original size:12 final size:12
Alignment explanation
Indices: 3501005--3501029 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3500995 ATATAATCCT
3501005 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3501017 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3501029 G
1 G
3501030 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:3503399 original size:19 final size:19
Alignment explanation
Indices: 3503357--3503454 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
3503347 GATTCTCTCG
3503357 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
3503377 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
*
3503396 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3503410 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3503429 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3503448 TTGCGAT
1 TTGCGAT
3503455 AGTCAATTTT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 6 0.09
16 6 0.09
17 7 0.10
19 35 0.51
20 15 0.22
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3503451 original size:52 final size:53
Alignment explanation
Indices: 3503338--3503454 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
3503328 GAAATGAAAA
3503338 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
3503391 TCACATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3503443 TCGCATTGCGAT
1 TCGCATTGCGAT
3503455 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:3503537 original size:19 final size:18
Alignment explanation
Indices: 3503513--3503659 Score: 120
Period size: 19 Copynumber: 8.6 Consensus size: 18
3503503 CCATTACATT
3503513 TCGCAATGCGGAAATGAAA
1 TCGCAATGC-GAAATGAAA
*
3503532 TCGCAA--CGAGA-G-AA
1 TCGCAATGCGAAATGAAA
3503546 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATG-AAA
*
3503565 TCGCAA--CGAGA-G-AA
1 TCGCAATGCGAAATGAAA
*
3503579 TCGCAATGCAAAATGAAA
1 TCGCAATGCGAAATGAAA
3503597 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATG-AAA
*
3503616 TCGCAA--CGAGAT--AA
1 TCGCAATGCGAAATGAAA
*
3503630 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAA-TGAAA
*
3503649 TCGCATTGCGA
1 TCGCAATGCGA
3503660 TTCTCCCATT
Statistics
Matches: 104, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
14 24 0.23
15 1 0.01
16 15 0.14
17 13 0.12
18 16 0.15
19 35 0.34
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (18 bp):
TCGCAATGCGAAATGAAA
Found at i:3503549 original size:14 final size:14
Alignment explanation
Indices: 3503530--3503584 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
3503520 GCGGAAATGA
3503530 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3503544 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3503563 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3503577 AATCGCAA
1 AATCGCAA
3503585 TGCAAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3503550 original size:33 final size:32
Alignment explanation
Indices: 3503513--3503602 Score: 153
Period size: 33 Copynumber: 2.8 Consensus size: 32
3503503 CCATTACATT
3503513 TCGCAATGCGGAAATGAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAATCGCAACGAGAGAA
3503546 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATG-AAATCGCAACGAGAGAA
*
3503579 TCGCAATGCAAAATGAAATCGCAA
1 TCGCAATGCGAAATGAAATCGCAA
3503603 TGCGAAATGA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
32 15 0.27
33 40 0.73
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (32 bp):
TCGCAATGCGAAATGAAATCGCAACGAGAGAA
Found at i:3503602 original size:51 final size:52
Alignment explanation
Indices: 3503544--3503659 Score: 189
Period size: 51 Copynumber: 2.2 Consensus size: 52
3503534 GCAACGAGAG
*
3503544 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC-AAAATGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATAA
* *
3503595 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATAA
*
3503647 AATCGCATTGCGA
1 AATCGCAATGCGA
3503660 TTCTCCCATT
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 43 0.72
52 17 0.28
ACGTcount: A:0.45, C:0.18, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATAA
Found at i:3503708 original size:19 final size:19
Alignment explanation
Indices: 3503666--3503765 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
3503656 GCGATTCTCC
3503666 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
3503686 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
3503705 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
3503721 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
3503738 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
3503757 CATTGCGAT
1 CATTGCGAT
3503766 AGTCAATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:3503762 original size:52 final size:53
Alignment explanation
Indices: 3503649--3503765 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
3503639 GAAATTAAAA
3503649 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
3503702 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
3503754 TCGCATTGCGAT
1 TCGCATTGCGAT
3503766 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:3503891 original size:14 final size:14
Alignment explanation
Indices: 3503872--3503908 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
3503862 CATCAATTAC
3503872 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
3503886 ACAAATCATCTTTT
1 ACAAATCAACTTTT
3503900 ACAAATCAA
1 ACAAATCAA
3503909 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:3505847 original size:20 final size:20
Alignment explanation
Indices: 3505822--3505887 Score: 91
Period size: 19 Copynumber: 3.4 Consensus size: 20
3505812 TAGTTTACTT
* *
3505822 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAACTCAAAA
3505842 TCGCAACGCGAAAC-CAAAA
1 TCGCAACGCGAAACTCAAAA
*
3505861 TCGCAACGCGAAA-TGAAAA
1 TCGCAACGCGAAACTCAAAA
3505880 TCGCAACG
1 TCGCAACG
3505888 ACATAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.45, C:0.27, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACTCAAAA
Found at i:3505905 original size:33 final size:33
Alignment explanation
Indices: 3505859--3505950 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
3505849 GCGAAACCAA
* *
3505859 AATCGCAACGCGAAATGAAAATCGCAACGACAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
3505892 AATCGCAATGCGAAATGAAAATCACAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
3505925 AATCGCAACGCG-AATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
3505951 TGCGATTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
32 13 0.25
33 40 0.75
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:3505973 original size:19 final size:19
Alignment explanation
Indices: 3505951--3506079 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
3505941 AAAATCGCAA
3505951 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3505970 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
3505984 TGCGATTATGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
3506003 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
3506017 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
3506036 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
3506055 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
3506075 TGCGA
1 TGCGA
3506080 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.54
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:3505996 original size:33 final size:33
Alignment explanation
Indices: 3505951--3506042 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
3505941 AAAATCGCAA
3505951 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
*
3505984 TGCGATTATGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
3506017 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
3506043 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:3506242 original size:93 final size:93
Alignment explanation
Indices: 3506122--3506502 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
3506112 TTGAATGGAT
3506122 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3506187 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3506215 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3506280 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3506308 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
3506373 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3506401 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
3506466 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
3506494 AAATTTACT
1 AAATTTACT
3506503 AAGCAATCTA
Statistics
Matches: 287, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 287 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:3508223 original size:14 final size:14
Alignment explanation
Indices: 3508204--3508260 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
3508194 TTGAAATGAA
3508204 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3508218 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
3508235 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
3508251 AATCGCAACG
1 AATCGCAACG
3508261 CGAAATAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3508241 original size:33 final size:33
Alignment explanation
Indices: 3508196--3508277 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
3508186 TCTTTTGGTT
3508196 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
3508229 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
3508262 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
3508278 TGCGATTTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3508326 original size:33 final size:37
Alignment explanation
Indices: 3508278--3508363 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 37
3508268 AAAATCGCAA
**
3508278 TGCGATTTTGGTTTCGCGTT-G-C-G-ATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTCGACAGCATTCTCTCGT
3508311 TGCGATTTTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT-CGACAG-CATTCTCTCGT
3508350 TGCGATTTTCATTT
1 TGCGATTTTCATTT
3508364 ATCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 18 0.40
35 1 0.02
36 1 0.02
37 1 0.02
39 24 0.53
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (37 bp):
TGCGATTTTCATTTCGCGTTCGACAGCATTCTCTCGT
Found at i:3508352 original size:20 final size:20
Alignment explanation
Indices: 3508301--3508354 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
3508291 TCGCGTTGCG
***
3508301 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
3508321 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
3508340 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
3508355 TTTTCATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:3508361 original size:20 final size:20
Alignment explanation
Indices: 3508301--3508375 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
3508291 TCGCGTTGCG
3508301 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
3508321 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
3508340 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
3508360 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
3508376 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.34
20 16 0.36
21 13 0.30
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3508497 original size:33 final size:33
Alignment explanation
Indices: 3508455--3508525 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
3508445 AATACTAACT
3508455 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
3508488 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
3508521 TGAAA
1 TGAAA
3508526 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:3508758 original size:21 final size:22
Alignment explanation
Indices: 3508707--3508760 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
3508697 TGGTTGTGAG
**
3508707 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
3508729 GGAAATCTTCGGAGAT-GGGAC
1 GGATTTCTTCGGAGATGGGGAC
3508750 GGATTTCTTCG
1 GGATTTCTTCG
3508761 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 14 0.54
22 12 0.46
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:3508929 original size:20 final size:20
Alignment explanation
Indices: 3508904--3509097 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
3508894 CTTTAAATAT
3508904 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3508924 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
3508946 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3508965 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
3508985 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
3509005 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
3509025 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
3509045 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
3509065 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
3509085 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3509098 TTGGAAAATC
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:3509091 original size:60 final size:60
Alignment explanation
Indices: 3508904--3509097 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
3508894 CTTTAAATAT
**
3508904 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
3508965 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
3509025 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
3509085 CGCGTTGCGATTT
1 CGCGTTGCGATTT
3509098 TTGGAAAATC
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:3515896 original size:15 final size:15
Alignment explanation
Indices: 3515878--3515908 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3515868 AAATTTTAAA
3515878 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
3515893 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
3515908 T
1 T
3515909 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:3517926 original size:93 final size:94
Alignment explanation
Indices: 3517765--3517954 Score: 310
Period size: 93 Copynumber: 2.0 Consensus size: 94
3517755 CTATGTTTCG
* * * *
3517765 AGTAGCAAGCACATGAACACTTGACAAACTTTTTACAGTTGCCGCTGAGACAAGAGGAAACACGA
1 AGTAGCAAACACATGAACACTAGAC-AACTTTTTACAATTGACGCTGAGACAAGAGGAAACACGA
3517830 AACAAGGAAAACCAACAGCATAAATGCATA
65 AACAAGGAAAACCAACAGCATAAATGCATA
*
3517860 AGTAGCAAACACATGAACACTAGAC-ACTTTTTACAATTGACGCTGAGACAAGCGGAAACACGAA
1 AGTAGCAAACACATGAACACTAGACAACTTTTTACAATTGACGCTGAGACAAGAGGAAACACGAA
*
3517924 ACAAGGAAAACCAACATCATAAATGCATA
66 ACAAGGAAAACCAACAGCATAAATGCATA
3517953 AG
1 AG
3517955 AAGCTTCAGA
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
93 66 0.74
95 23 0.26
ACGTcount: A:0.45, C:0.21, G:0.18, T:0.16
Consensus pattern (94 bp):
AGTAGCAAACACATGAACACTAGACAACTTTTTACAATTGACGCTGAGACAAGAGGAAACACGAA
ACAAGGAAAACCAACAGCATAAATGCATA
Found at i:3521058 original size:21 final size:21
Alignment explanation
Indices: 3521025--3521092 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
3521015 ACCACTCCTT
*
3521025 AAGGATCACATATATGTTCCA
1 AAGGACCACATATATGTTCCA
* * * *
3521046 AAGGACCAAATATGTGTCCCT
1 AAGGACCACATATATGTTCCA
* *
3521067 AAGAACCGCATATATGTTCCA
1 AAGGACCACATATATGTTCCA
3521088 AAGGA
1 AAGGA
3521093 TTAGATATAT
Statistics
Matches: 35, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (21 bp):
AAGGACCACATATATGTTCCA
Found at i:3523085 original size:24 final size:24
Alignment explanation
Indices: 3523058--3523162 Score: 126
Period size: 24 Copynumber: 4.4 Consensus size: 24
3523048 GGTTCTACGC
3523058 GGTCATTCGGGACAAATTCTATGT
1 GGTCATTCGGGACAAATTCTATGT
*
3523082 GGTCCTTCGGGACAAATTCTATGT
1 GGTCATTCGGGACAAATTCTATGT
* *
3523106 GGTCATTTGGGACAAATTCTAAT-C
1 GGTCATTCGGGACAAATTCT-ATGT
* *
3523130 GGTCCTTCGAGACAAA-TCTATGT
1 GGTCATTCGGGACAAATTCTATGT
3523153 GG-CACTTCGG
1 GGTCA-TTCGG
3523163 TGCATATTCT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
22 3 0.04
23 9 0.13
24 54 0.79
25 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (24 bp):
GGTCATTCGGGACAAATTCTATGT
Found at i:3523173 original size:47 final size:48
Alignment explanation
Indices: 3523058--3523162 Score: 144
Period size: 48 Copynumber: 2.2 Consensus size: 48
3523048 GGTTCTACGC
* *
3523058 GGTCATTCGGGACAAATTCT-ATGTGGTCCTTCGGGACAAATTCTATGT
1 GGTCATTCGGGACAAATTCTAAT-CGGTCCTTCGAGACAAATTCTATGT
*
3523106 GGTCATTTGGGACAAATTCTAATCGGTCCTTCGAGACAAA-TCTATGT
1 GGTCATTCGGGACAAATTCTAATCGGTCCTTCGAGACAAATTCTATGT
3523153 GG-CACTTCGG
1 GGTCA-TTCGG
3523163 TGCATATTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
46 2 0.04
47 13 0.25
48 34 0.67
49 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (48 bp):
GGTCATTCGGGACAAATTCTAATCGGTCCTTCGAGACAAATTCTATGT
Found at i:3527773 original size:31 final size:31
Alignment explanation
Indices: 3527738--3527798 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3527728 ACACCTTGGT
*
3527738 AAGGTATCGGTACTCAATAGACAATATCGAC
1 AAGGTATCGATACTCAATAGACAATATCGAC
*
3527769 AAGGTATTGATACTCAATAGACAATATCGA
1 AAGGTATCGATACTCAATAGACAATATCGA
3527799 TACTGTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (31 bp):
AAGGTATCGATACTCAATAGACAATATCGAC
Found at i:3534682 original size:31 final size:31
Alignment explanation
Indices: 3534636--3534706 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
3534626 ATATTTAAAA
3534636 AGTTT-GGGACCAATTTAGAACAAAGATCAT
1 AGTTTGGGGACCAATTTAGAACAAAGATCAT
* **
3534666 AGTTTGGGGACTAATTTAGAATGAAGATCAT
1 AGTTTGGGGACCAATTTAGAACAAAGATCAT
3534697 AGTTTGGGGA
1 AGTTTGGGGA
3534707 TGAAACTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 5 0.14
31 32 0.86
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.30
Consensus pattern (31 bp):
AGTTTGGGGACCAATTTAGAACAAAGATCAT
Found at i:3534737 original size:60 final size:60
Alignment explanation
Indices: 3534666--3534786 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
3534656 CAAAGATCAT
* * * *
3534666 AGTTTGGGGACTAATTTAGAATGA-AGATCATAGTTTGGGGATGAAACTGAAATGTTCAAA
1 AGTTTGAGGACTAATCTAAAATGATAG-TCATAGTTTAGGGATGAAACTGAAATGTTCAAA
* * * *
3534726 AGTTTGAGGACTAATCTAAAATGATAGTCATAGTTTAGGTATGAAATTGGAATGTTTAAA
1 AGTTTGAGGACTAATCTAAAATGATAGTCATAGTTTAGGGATGAAACTGAAATGTTCAAA
3534786 A
1 A
3534787 ATTTAGAGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
60 50 0.96
61 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (60 bp):
AGTTTGAGGACTAATCTAAAATGATAGTCATAGTTTAGGGATGAAACTGAAATGTTCAAA
Found at i:3534761 original size:31 final size:31
Alignment explanation
Indices: 3534662--3534761 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 31
3534652 AGAACAAAGA
* *
3534662 TCATAGTTTGGGGACTAATTTAGAATGA-AG
1 TCATAGTTTGGGGACTAATCTAAAATGATAG
* *
3534692 ATCATAGTTTGGGGA-TGAAACTGAAATG-T--
1 -TCATAGTTTGGGGACT-AATCTAAAATGATAG
* *
3534721 TCAAAAGTTTGAGGACTAATCTAAAATGATAG
1 TC-ATAGTTTGGGGACTAATCTAAAATGATAG
3534753 TCATAGTTT
1 TCATAGTTT
3534762 AGGTATGAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
28 2 0.04
29 19 0.36
30 3 0.06
31 27 0.51
32 2 0.04
ACGTcount: A:0.36, C:0.08, G:0.23, T:0.33
Consensus pattern (31 bp):
TCATAGTTTGGGGACTAATCTAAAATGATAG
Found at i:3534806 original size:60 final size:60
Alignment explanation
Indices: 3534668--3534811 Score: 141
Period size: 60 Copynumber: 2.4 Consensus size: 60
3534658 AAGATCATAG
* * * * *
3534668 TTTGGGGACTAATTTAGAATGAAGATCATAGTTTGGGGATGAAACTGAAATGTTCAAAAG
1 TTTGAGGACCAATTTAAAATGAAGATCATAGTTTAGGGATGAAACTGAAATGTTCAAAAA
* * * * * *
3534728 TTTGAGGACTAATCTAAAATGATAG-TCATAGTTTAGGTATGAAATTGGAATGTTTAAAAA
1 TTTGAGGACCAATTTAAAATGA-AGATCATAGTTTAGGGATGAAACTGAAATGTTCAAAAA
*
3534788 TTT-AGAGACCACTTTAAAAT-AAGA
1 TTTGAG-GACCAATTTAAAATGAAGA
3534812 ATCAGAATTG
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.03
59 3 0.04
60 62 0.90
61 2 0.03
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.32
Consensus pattern (60 bp):
TTTGAGGACCAATTTAAAATGAAGATCATAGTTTAGGGATGAAACTGAAATGTTCAAAAA
Found at i:3534957 original size:5 final size:5
Alignment explanation
Indices: 3534947--3534972 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3534937 TTGAATAATA
3534947 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
3534973 ATCGGGGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:3535052 original size:2 final size:2
Alignment explanation
Indices: 3535045--3535086 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
3535035 TCGCCTCGAT
*
3535045 TA TA TA TA TA TA TA TA TA TA TA TA TG 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
3535086 T
1 T
3535087 TTTATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3537612 original size:43 final size:43
Alignment explanation
Indices: 3537531--3537612 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
3537521 TTATAGTTTT
* **
3537531 TAATATGTTAGTTTGATATATTTGTGGATTATTATTTTTGATG
1 TAATATGTTAGTTTGATAAATTTGTGGAAAATTATTTTTGATG
* *
3537574 TAATATGTTAGTTTGGATAAATTTGT-TAAAATTTTTTTT
1 TAATATGTTAGTTT-GATAAATTTGTGGAAAATTATTTTT
3537613 AACGAGTACG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
43 23 0.70
44 10 0.30
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (43 bp):
TAATATGTTAGTTTGATAAATTTGTGGAAAATTATTTTTGATG
Found at i:3541545 original size:16 final size:16
Alignment explanation
Indices: 3541524--3541559 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3541514 ACATTTAATG
*
3541524 AAAATATATAAAATTT
1 AAAATAAATAAAATTT
*
3541540 AAAATAAATATAATTT
1 AAAATAAATAAAATTT
3541556 AAAA
1 AAAA
3541560 AATTTGATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAAATAAAATTT
Found at i:3542127 original size:22 final size:22
Alignment explanation
Indices: 3542102--3542147 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
3542092 AATCCAAAGA
3542102 AAATTACTCAAAAACGAGAAAT
1 AAATTACTCAAAAACGAGAAAT
*
3542124 AAATTACTCAAAAACGAGATAT
1 AAATTACTCAAAAACGAGAAAT
3542146 AA
1 AA
3542148 GTTTTCTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.59, C:0.13, G:0.09, T:0.20
Consensus pattern (22 bp):
AAATTACTCAAAAACGAGAAAT
Found at i:3546463 original size:23 final size:23
Alignment explanation
Indices: 3546445--3546505 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
3546435 CTCGTATAAA
3546445 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3546468 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
3546491 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
3546506 TATAAGATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:3552142 original size:3 final size:3
Alignment explanation
Indices: 3552123--3552184 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
3552113 TTGTAATATT
* **
3552123 TAA TAAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TTT
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3552170 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
3552185 ACTTAAATGA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
3 45 0.88
4 6 0.12
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:3552561 original size:76 final size:76
Alignment explanation
Indices: 3552312--3553490 Score: 2196
Period size: 76 Copynumber: 15.5 Consensus size: 76
3552302 GATGGAAATG
* * *
3552312 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
3552377 TCCCGAAGGCTT
65 TCCCGAAGGCTT
* *
3552389 TTTGGAAACATCATGCACTGAAGGACTTACAGATGATCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
3552454 TCCCGAAGGCTT
65 TCCCGAAGGCTT
3552466 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3552531 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
3552542 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGTTTTTAAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
3552607 TCCCGAAGGCTT
65 TCCCGAAGGCTT
3552619 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3552684 CCCGAAGGCTT
66 CCCGAAGGCTT
3552695 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3552760 CCCGAAGGCTT
66 CCCGAAGGCTT
3552771 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3552836 CCCGAAGGCTT
66 CCCGAAGGCTT
3552847 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3552912 CCCGAAGGCTT
66 CCCGAAGGCTT
3552923 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3552988 CCCGAAGGCTT
66 CCCGAAGGCTT
3552999 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3553064 CCCGAAGGCTT
66 CCCGAAGGCTT
3553075 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3553140 CCCGAAGGCTT
66 CCCGAAGGCTT
**
3553151 TTTGGAAACATCATGCACTGAAGGGTTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3553216 CCCGAAGGCTT
66 CCCGAAGGCTT
3553227 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
3553292 CCCAAAGGCTT
66 CCCGAAGGCTT
*
3553303 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
* *
3553368 TCGCGAAGGCCT
65 TCCCGAAGGCTT
3553380 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
3553445 CCCGAAGGCTT
66 CCCGAAGGCTT
3553456 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
3553491 TGGGAAATAG
Statistics
Matches: 1077, Mismatches: 23, Indels: 5
0.97 0.02 0.00
Matches are distributed among these distances:
76 815 0.76
77 262 0.24
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:3556917 original size:92 final size:93
Alignment explanation
Indices: 3556749--3556937 Score: 310
Period size: 92 Copynumber: 2.0 Consensus size: 93
3556739 CTTATTTCTA
* * *
3556749 CTATGAGCAAAATTCATCTTTCAAATCCAATGATTGATTTTGGAGTTCATACCAAATCATATCAG
1 CTATGAGCAAAATTCATCTTCCAAATCCAATGATTGATTCTGGAGTTCATACCAAATCAGATCAG
3556814 ATAACTCAAAGAACACTTCCAGAAGATG
66 ATAACTCAAAGAACACTTCCAGAAGATG
* *
3556842 CTATGAGC-ACATTCATCTTCCAAATTCAATGATTGATTCTGTG-GTTCATACCAAATCAGATCA
1 CTATGAGCAAAATTCATCTTCCAAATCCAATGATTGATTCTG-GAGTTCATACCAAATCAGATCA
3556905 GATAACTCAAAGAACACTTCCAGAAGATG
65 GATAACTCAAAGAACACTTCCAGAAGATG
3556934 CTAT
1 CTAT
3556938 TGGGTCTCCT
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
92 81 0.90
93 9 0.10
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (93 bp):
CTATGAGCAAAATTCATCTTCCAAATCCAATGATTGATTCTGGAGTTCATACCAAATCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATG
Found at i:3565805 original size:3 final size:3
Alignment explanation
Indices: 3565786--3565850 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
3565776 TTGTAATATT
* *
3565786 TAA TAAA TAA TATA TAA TAA TAA TTA TAA TAA TAA TAA TAA TAG TAA
1 TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
3565833 TTT TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
3565851 ACTTAAATGA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
3 46 0.88
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:3565806 original size:24 final size:23
Alignment explanation
Indices: 3565779--3565850 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
3565769 ATGGGCTTTG
3565779 TAAT-ATTTAATAAATAATATATAA
1 TAATAATTTAAT-AATAATA-ATAA
3565803 TAATAATTATAATAATAATAATAA
1 TAATAATT-TAATAATAATAATAA
*
3565827 TAGTAATTTTAATAATAATAATAA
1 TAATAA-TTTAATAATAATAATAA
3565851 ACTTAAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
24 28 0.64
25 12 0.27
26 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (23 bp):
TAATAATTTAATAATAATAATAA
Found at i:3569460 original size:16 final size:16
Alignment explanation
Indices: 3569403--3569449 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
3569393 GTGTGTTTTT
3569403 GGTGGAAGAGACAACC
1 GGTGGAAGAGACAACC
3569419 GGTGGAAGAGACAACC
1 GGTGGAAGAGACAACC
3569435 GGTGGAAGAGACAAC
1 GGTGGAAGAGACAAC
3569450 TAGTGAAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.38, T:0.06
Consensus pattern (16 bp):
GGTGGAAGAGACAACC
Found at i:3570080 original size:2 final size:2
Alignment explanation
Indices: 3570075--3570108 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3570065 ATATGAAGAA
3570075 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
3570109 GATTATAAAA
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
Found at i:3575369 original size:22 final size:22
Alignment explanation
Indices: 3575344--3575417 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
3575334 AGTACCTCAA
*
3575344 CACTGATACGAAAGTGTATTTG
1 CACTGATACGAAAGTGTATTAG
* **
3575366 CACTGATACGGAAGTCCATTAG
1 CACTGATACGAAAGTGTATTAG
*
3575388 CACTGAATACTAAAGTGCT-TTAG
1 CACTG-ATACGAAAGTG-TATTAG
3575411 CACTGAT
1 CACTGAT
3575418 TAGAGAATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
22 25 0.60
23 17 0.40
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (22 bp):
CACTGATACGAAAGTGTATTAG
Found at i:3576176 original size:14 final size:14
Alignment explanation
Indices: 3576159--3576192 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3576149 AAACCAGGCA
3576159 AGAAATACCATTTT
1 AGAAATACCATTTT
*
3576173 AGAAATATCATTTT
1 AGAAATACCATTTT
3576187 AGAAAT
1 AGAAAT
3576193 CACGAGAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (14 bp):
AGAAATACCATTTT
Found at i:3578783 original size:23 final size:22
Alignment explanation
Indices: 3578714--3578790 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 22
3578704 TAAAATGCCG
*
3578714 TAGCACTAATACAAAAGTGCAT
1 TAGCACTAATACTAAAGTGCAT
* **
3578736 TAGCACTAATACGAAAGAACAT
1 TAGCACTAATACTAAAGTGCAT
*
3578758 TAGCACTAAATACTAAAGTGCCT
1 TAGCACT-AATACTAAAGTGCAT
*
3578781 TAGCATTAAT
1 TAGCACTAAT
3578791 TAGAGTGTAC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 29 0.63
23 17 0.37
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (22 bp):
TAGCACTAATACTAAAGTGCAT
Found at i:3582655 original size:23 final size:23
Alignment explanation
Indices: 3582629--3582695 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
3582619 AGTGTTTTCG
* * *
3582629 AACATGTTCGTTTATTGTTCATC
1 AACATGTTCATTTAGTATTCATC
*
3582652 AACATGTTTATTTAGTATTCATC
1 AACATGTTCATTTAGTATTCATC
* *
3582675 AACATATTCATTTAGCATTCA
1 AACATGTTCATTTAGTATTCA
3582696 CAAATATGTT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (23 bp):
AACATGTTCATTTAGTATTCATC
Found at i:3582711 original size:23 final size:23
Alignment explanation
Indices: 3582691--3582734 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3582681 TTCATTTAGC
3582691 ATTCACAAATATGTTCGTTTAAA
1 ATTCACAAATATGTTCGTTTAAA
* *
3582714 ATTCCCAAATATGTTTGTTTA
1 ATTCACAAATATGTTCGTTTA
3582735 TATGGTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (23 bp):
ATTCACAAATATGTTCGTTTAAA
Found at i:3601995 original size:37 final size:36
Alignment explanation
Indices: 3601920--3601995 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
3601910 TTTTTATATT
*
3601920 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* * *
3601956 TTTATTTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
3601993 TTT
1 TTT
3601996 GTAATATTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
36 25 0.74
37 9 0.26
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:3602177 original size:20 final size:20
Alignment explanation
Indices: 3602141--3602178 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3602131 ATCCTATTCC
**
3602141 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3602161 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3602179 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3609386 original size:2 final size:2
Alignment explanation
Indices: 3609379--3609415 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3609369 TTGCATCTAT
*
3609379 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3609416 CGTAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3609707 original size:38 final size:38
Alignment explanation
Indices: 3609665--3609779 Score: 101
Period size: 38 Copynumber: 3.3 Consensus size: 38
3609655 TGATTTTGAA
3609665 ATAATTTAAAGTTTAAGTACTAAAATAGATCAAAATTG
1 ATAATTTAAAGTTTAAGTACTAAAATAGATCAAAATTG
*
3609703 ATAATTTAAA---T-A-T--T-AAATATGAT----TTTG
1 ATAATTTAAAGTTTAAGTACTAAAATA-GATCAAAATTG
*
3609730 AAATAATTTAAAGTTTAAGTACTAAAATAGATCAAAACTG
1 --ATAATTTAAAGTTTAAGTACTAAAATAGATCAAAATTG
3609770 ATAATTTAAA
1 ATAATTTAAA
3609780 TATTAAATGC
Statistics
Matches: 59, Mismatches: 3, Indels: 30
0.64 0.03 0.33
Matches are distributed among these distances:
27 3 0.05
29 10 0.17
30 5 0.08
31 4 0.07
32 1 0.02
33 2 0.03
34 2 0.03
35 1 0.02
36 4 0.07
37 5 0.08
38 20 0.34
40 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (38 bp):
ATAATTTAAAGTTTAAGTACTAAAATAGATCAAAATTG
Found at i:3609722 original size:67 final size:67
Alignment explanation
Indices: 3609642--3609787 Score: 274
Period size: 67 Copynumber: 2.2 Consensus size: 67
3609632 AAACAAAAAC
* *
3609642 TAAATGTTAAATATGATTTTGAAATAATTTAAAGTTTAAGTACTAAAATAGATCAAAATTGATAA
1 TAAATATTAAATATGATTTTGAAATAATTTAAAGTTTAAGTACTAAAATAGATCAAAACTGATAA
3609707 TT
66 TT
3609709 TAAATATTAAATATGATTTTGAAATAATTTAAAGTTTAAGTACTAAAATAGATCAAAACTGATAA
1 TAAATATTAAATATGATTTTGAAATAATTTAAAGTTTAAGTACTAAAATAGATCAAAACTGATAA
3609774 TT
66 TT
3609776 TAAATATTAAAT
1 TAAATATTAAAT
3609788 GCGTACTCTC
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 77 1.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.38
Consensus pattern (67 bp):
TAAATATTAAATATGATTTTGAAATAATTTAAAGTTTAAGTACTAAAATAGATCAAAACTGATAA
TT
Found at i:3612281 original size:14 final size:16
Alignment explanation
Indices: 3612252--3612284 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
3612242 CTCTCGTCAG
3612252 TATTTTACTCTTAAAA
1 TATTTTACTCTTAAAA
3612268 TATTTT-CT-TTAAAA
1 TATTTTACTCTTAAAA
3612282 TAT
1 TAT
3612285 AATATTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 2 0.12
16 6 0.35
ACGTcount: A:0.36, C:0.09, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTACTCTTAAAA
Found at i:3612519 original size:19 final size:20
Alignment explanation
Indices: 3612470--3612530 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 20
3612460 AAATAACACA
3612470 AATTTTTTTTAACTCAACTC
1 AATTTTTTTTAACTCAACTC
*** *
3612490 AATTCAATTTAACTCGA-TC
1 AATTTTTTTTAACTCAACTC
*
3612509 AATTTTTTTTAACTCATCTC
1 AATTTTTTTTAACTCAACTC
3612529 AA
1 AA
3612531 CTCAACCCGA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.33, C:0.20, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTTTTTTTAACTCAACTC
Found at i:3619600 original size:28 final size:30
Alignment explanation
Indices: 3619543--3619602 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
3619533 TTATCCGACA
*
3619543 TCTGATTTACCGTATATTATTGATTTGATT
1 TCTGATTTACCGTATATTATTGATATGATT
3619573 TCTGA-TTACCGTAT-TTA-TGTATATGATT
1 TCTGATTTACCGTATATTATTG-ATATGATT
3619601 TC
1 TC
3619603 CAAGCATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 2 0.07
28 12 0.43
29 9 0.32
30 5 0.18
ACGTcount: A:0.23, C:0.12, G:0.13, T:0.52
Consensus pattern (30 bp):
TCTGATTTACCGTATATTATTGATATGATT
Found at i:3619810 original size:44 final size:44
Alignment explanation
Indices: 3619729--3619847 Score: 141
Period size: 44 Copynumber: 2.7 Consensus size: 44
3619719 CTATTGCAAG
* *
3619729 GGTAAGACATTACCATTT-TTAAGGCTCCTCTACTATGTGAAAA
1 GGTAAGACATTACCATTTCTGAAGGCTCCTCCACTATGTGAAAA
* * *
3619772 GGTAAGACCTTACCATTTCTGAAGGCTCCTCCACTATGTGCAAG
1 GGTAAGACATTACCATTTCTGAAGGCTCCTCCACTATGTGAAAA
* * * *
3619816 GGTAAGACTTTACCGTTTTCCGCAGGCTCCTC
1 GGTAAGACATTACC-ATTTCTGAAGGCTCCTC
3619848 GGCTTTGTCC
Statistics
Matches: 65, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
43 17 0.26
44 34 0.52
45 14 0.22
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.30
Consensus pattern (44 bp):
GGTAAGACATTACCATTTCTGAAGGCTCCTCCACTATGTGAAAA
Found at i:3620274 original size:38 final size:38
Alignment explanation
Indices: 3620231--3620303 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
3620221 CTATTACCAA
* * * *
3620231 TATTTTGTTATGTAAATGTTTTTTACGGTTTTCTGCGG
1 TATTTTGATATGTAAATATTTTATACAGTTTTCTGCGG
*
3620269 TATTTTGATATGTATATATTTTATACAGTTTTCTG
1 TATTTTGATATGTAAATATTTTATACAGTTTTCTG
3620304 ACATATGTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.56
Consensus pattern (38 bp):
TATTTTGATATGTAAATATTTTATACAGTTTTCTGCGG
Found at i:3626111 original size:44 final size:44
Alignment explanation
Indices: 3626046--3626139 Score: 161
Period size: 44 Copynumber: 2.1 Consensus size: 44
3626036 GTTGGAGGAA
*
3626046 GTTTCTGAAGGCTCATTTGCTATGTGCAAGGGTAAGACCTTACC
1 GTTTCTGAAGGCTCATATGCTATGTGCAAGGGTAAGACCTTACC
*
3626090 GTTTCTGAAGGCTCCTATGCTATGTGCAAGGGTAAGACCTTACC
1 GTTTCTGAAGGCTCATATGCTATGTGCAAGGGTAAGACCTTACC
3626134 GCTTTC
1 G-TTTC
3626140 CACAAGCTCC
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 43 0.91
45 4 0.09
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.32
Consensus pattern (44 bp):
GTTTCTGAAGGCTCATATGCTATGTGCAAGGGTAAGACCTTACC
Found at i:3635279 original size:15 final size:15
Alignment explanation
Indices: 3635254--3635341 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 15
3635244 AGCCCGACTA
3635254 ATTTATATTTTTATTT
1 ATTT-TATTTTTATTT
3635270 ATTTTATTTTTATTT
1 ATTTTATTTTTATTT
*
3635285 CACTTTATTTTATATTAT
1 -ATTTTATTTT-TATT-T
3635303 ATATATATATTTTATATTT
1 AT-T-T-TATTTT-TATTT
* *
3635322 -TATTAGTTTTAATTT
1 ATTTTA-TTTTTATTT
3635337 ATTTT
1 ATTTT
3635342 CTTTCTAAGT
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
15 17 0.29
16 21 0.36
17 5 0.08
18 3 0.05
19 2 0.03
20 11 0.19
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.69
Consensus pattern (15 bp):
ATTTTATTTTTATTT
Done.