Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
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: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 160 of 163
Found at i:53863511 original size:11 final size:11
Alignment explanation
Indices: 53863489--53863534 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
53863479 ACAAATCCTA
53863489 TCTCATATTTCC
1 TCTCA-ATTTCC
53863501 TCTCAATTTCC
1 TCTCAATTTCC
*
53863512 TCTCAATTTTC
1 TCTCAATTTCC
53863523 TCTCAATTTCC
1 TCTCAATTTCC
53863534 T
1 T
53863535 TCCAAAATTC
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 27 0.84
12 5 0.16
ACGTcount: A:0.17, C:0.33, G:0.00, T:0.50
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:53863545 original size:22 final size:22
Alignment explanation
Indices: 53863500--53863546 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
53863490 CTCATATTTC
**
53863500 CTCTCAATTTCCTCTCAATTTT
1 CTCTCAATTTCCTCTCAAAATT
53863522 CTCTCAATTTCCT-TCCAAAATT
1 CTCTCAATTTCCTCT-CAAAATT
53863544 CTC
1 CTC
53863547 ATAAATCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (22 bp):
CTCTCAATTTCCTCTCAAAATT
Found at i:53863577 original size:51 final size:51
Alignment explanation
Indices: 53863522--53863634 Score: 165
Period size: 51 Copynumber: 2.2 Consensus size: 51
53863512 TCTCAATTTT
* * *
53863522 CTCTCAATTTCCTTCCAAAATTCTCAT-AAATCCATATTTAATTTCAATCTC
1 CTCTCAATTTCATTCCAAAAATCTC-TCAAACCCATATTTAATTTCAATCTC
* *
53863573 CTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATTTCAATTTG
1 CTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATTTCAATCTC
53863624 CTCTCAATTTC
1 CTCTCAATTTC
53863635 TTTTTTTAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
50 1 0.02
51 55 0.98
ACGTcount: A:0.31, C:0.27, G:0.01, T:0.41
Consensus pattern (51 bp):
CTCTCAATTTCATTCCAAAAATCTCTCAAACCCATATTTAATTTCAATCTC
Found at i:53865924 original size:25 final size:26
Alignment explanation
Indices: 53865895--53866030 Score: 130
Period size: 25 Copynumber: 5.6 Consensus size: 26
53865885 TTAAACTTTG
53865895 TTTGATGTAATAAAATAGAAGTTTTA
1 TTTGATGTAATAAAATAGAAGTTTTA
* *
53865921 -TTGATGTAATAAAAATTGAAATTTT-
1 TTTGATGTAAT-AAAATAGAAGTTTTA
** * *
53865946 TTTGA-GT--T-ATTTTG-A-TATTA
1 TTTGATGTAATAAAATAGAAGTTTTA
53865966 TTTGATGTAATAAAATAGAAG-TTTA
1 TTTGATGTAATAAAATAGAAGTTTTA
53865991 TTTGATGTAATAAAATAGAAG-TTTA
1 TTTGATGTAATAAAATAGAAGTTTTA
*
53866016 TTTGATGTGATAAAA
1 TTTGATGTAATAAAA
53866031 ATTGAAAACC
Statistics
Matches: 91, Mismatches: 10, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
19 3 0.03
20 6 0.07
21 6 0.07
23 2 0.02
24 3 0.03
25 55 0.60
26 16 0.18
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.44
Consensus pattern (26 bp):
TTTGATGTAATAAAATAGAAGTTTTA
Found at i:53866062 original size:23 final size:23
Alignment explanation
Indices: 53866032--53866139 Score: 109
Period size: 21 Copynumber: 4.9 Consensus size: 23
53866022 GTGATAAAAA
*
53866032 TTGAAAACCCTAACCTAATTAAG
1 TTGAAAACCCTAACCTAATTAAC
*
53866055 TTGAAAACCCTAACCT--TAAAC
1 TTGAAAACCCTAACCTAATTAAC
* * * *
53866076 TTAAAAACCATAACATAATTAAG
1 TTGAAAACCCTAACCTAATTAAC
53866099 TTGAAAACCCTAACCCT-A--AAC
1 TTGAAAACCCTAA-CCTAATTAAC
*
53866120 TTAAAAACCCTAACCTAATT
1 TTGAAAACCCTAACCTAATT
53866140 CTTTTACGAA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
20 3 0.04
21 31 0.46
23 31 0.46
24 2 0.03
ACGTcount: A:0.46, C:0.24, G:0.05, T:0.25
Consensus pattern (23 bp):
TTGAAAACCCTAACCTAATTAAC
Found at i:53866095 original size:44 final size:44
Alignment explanation
Indices: 53866035--53866139 Score: 183
Period size: 44 Copynumber: 2.4 Consensus size: 44
53866025 ATAAAAATTG
*
53866035 AAAACCCTAACCTAATTAAGTTGAAAACCCTAACCTTAAACTTA
1 AAAACCCTAACCTAATTAAGTTGAAAACCCTAACCCTAAACTTA
* *
53866079 AAAACCATAACATAATTAAGTTGAAAACCCTAACCCTAAACTTA
1 AAAACCCTAACCTAATTAAGTTGAAAACCCTAACCCTAAACTTA
53866123 AAAACCCTAACCTAATT
1 AAAACCCTAACCTAATT
53866140 CTTTTACGAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.48, C:0.25, G:0.04, T:0.24
Consensus pattern (44 bp):
AAAACCCTAACCTAATTAAGTTGAAAACCCTAACCCTAAACTTA
Found at i:53866601 original size:123 final size:123
Alignment explanation
Indices: 53866392--53866739 Score: 457
Period size: 125 Copynumber: 2.8 Consensus size: 123
53866382 TAGCAAAAGT
* * * *
53866392 GCGTCCCCGAGGGCGCGATTTTCACAAAATATTCTCAAATAGCATCCTGCTAGAAGCGATTTTAT
1 GCGTCCACGAGGGCGCGATTTT-ACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGAATTTAT
* **
53866457 ATTATTTGCTCAGAAAGGTCAAAAAAATTATTTCATCCACGACCTACTGTAGCAATTCC
65 ACTATTTGCTCAGAAAGGTCAAAAAAATTATTTCATCCACGACCTACTGTAGCAAGACC
* *
53866516 GCGTCCACGAGGGCGGGATTTTACAAATTCTTTTCAAATAGCATCCTGCTAGAAGCGAATTTATA
1 GCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGAATTTATA
* * *
53866581 CTATTTGCTCAGAAACGTCAAAAAAAATTTATTTCATCCATGACCTACTGTAGCAAGAGC
66 CTATTTGCTCAGAAAGGTC-AAAAAAA-TTATTTCATCCACGACCTACTGTAGCAAGACC
* * * * * * *
53866641 GCATCCATGAGGGCGCAATTTCA-AAATTTCTTCTCAAATAGCATCCTGCTATATG-TAATTTTA
1 GCGTCCACGAGGGCGCGATTTTACAAA-TTCTTCTCAAATAGCATCCTGCTAGAAGCGAA-TTTA
53866704 TACTATTTGCTCAGAAAGGTCAAATAAAATTATTTC
64 TACTATTTGCTCAGAAAGGTCAAA-AAAATTATTTC
53866740 TTCTCGGACC
Statistics
Matches: 197, Mismatches: 22, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
123 56 0.28
124 42 0.21
125 99 0.50
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (123 bp):
GCGTCCACGAGGGCGCGATTTTACAAATTCTTCTCAAATAGCATCCTGCTAGAAGCGAATTTATA
CTATTTGCTCAGAAAGGTCAAAAAAATTATTTCATCCACGACCTACTGTAGCAAGACC
Found at i:53867372 original size:23 final size:23
Alignment explanation
Indices: 53867345--53867408 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
53867335 TGAATTGAAA
*
53867345 TAATTTTTTATTTAAGTTATAAT
1 TAATTTTTTATTTAAGTTAAAAT
*
53867368 TAATTATTTT-TTATAATTTAAAAT
1 TAATT-TTTTATT-TAAGTTAAAAT
*
53867392 AAATATTTTATATTTAA
1 TAAT-TTTT-TATTTAA
53867409 AGTATGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
23 7 0.21
24 19 0.58
25 5 0.15
26 2 0.06
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TAATTTTTTATTTAAGTTAAAAT
Found at i:53873037 original size:19 final size:19
Alignment explanation
Indices: 53873013--53873049 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
53873003 CATTACAAGT
53873013 AAAATGGTATTATTAAAAA
1 AAAATGGTATTATTAAAAA
53873032 AAAATGGTATTATTAAAA
1 AAAATGGTATTATTAAAA
53873050 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAATGGTATTATTAAAAA
Found at i:53874274 original size:29 final size:26
Alignment explanation
Indices: 53874241--53874295 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 26
53874231 TTAAAAATAT
*
53874241 TTTTAAAATACATTTTTTATTATTTTTAA
1 TTTTAAAACAC-TTTTTTA--ATTTTTAA
53874270 TTTTAAAACACTTTTTTAATTTTTAA
1 TTTTAAAACACTTTTTTAATTTTTAA
53874296 AATAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 8 0.32
28 7 0.28
29 10 0.40
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTTAAAACACTTTTTTAATTTTTAA
Found at i:53874305 original size:20 final size:19
Alignment explanation
Indices: 53874262--53874306 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
53874252 ATTTTTTATT
*
53874262 ATTTTTAATTTTAAAACAC
1 ATTTTTAATTTTAAAACAA
* *
53874281 TTTTTTAATTTTTAAAATAA
1 ATTTTTAA-TTTTAAAACAA
53874301 ATTTTT
1 ATTTTT
53874307 GGTATTTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTAATTTTAAAACAA
Found at i:53881108 original size:3 final size:3
Alignment explanation
Indices: 53881100--53881137 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
53881090 GTTGTCATTA
*
53881100 TTG TTG TTG TTG TTG TTG TTG TTG CTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
53881138 TTATGTGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.03, G:0.32, T:0.66
Consensus pattern (3 bp):
TTG
Found at i:53884425 original size:15 final size:15
Alignment explanation
Indices: 53884405--53884455 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
53884395 CTTCAATTTT
53884405 GGTGGTGACCCCTTC
1 GGTGGTGACCCCTTC
*
53884420 GGTGGTGACCTCTTC
1 GGTGGTGACCCCTTC
53884435 GGTGGTGACCCCTTC
1 GGTGGTGACCCCTTC
53884450 GGTGGT
1 GGTGGT
53884456 TCTGGGGGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.06, C:0.27, G:0.37, T:0.29
Consensus pattern (15 bp):
GGTGGTGACCCCTTC
Found at i:53887343 original size:122 final size:123
Alignment explanation
Indices: 53887115--53887360 Score: 485
Period size: 123 Copynumber: 2.0 Consensus size: 123
53887105 TAAAACATTG
53887115 AACTTTATTTTTTTTTTGAATACAACCCAGGTGGAAGGCAAACAAGGTCTTCATAGATTACAACT
1 AACTTTATTTTTTTTTTGAATACAACCCAGGTGGAAGGCAAACAAGGTCTTCATAGATTACAACT
53887180 CCCGAAAGAGCTCTATCTCATAAGTACTTCTTTGAGCCCAAATTAAGACACAGTAACA
66 CCCGAAAGAGCTCTATCTCATAAGTACTTCTTTGAGCCCAAATTAAGACACAGTAACA
53887238 AACTTTATTTTTTTTTTGAATACAACCCAGGTGGAAGGCAAACAAGGTCTTCATAGATTACAACT
1 AACTTTATTTTTTTTTTGAATACAACCCAGGTGGAAGGCAAACAAGGTCTTCATAGATTACAACT
53887303 -CCGAAAGAGCTCTATCTCATAAGTACTTCTTTGAGCCCAAATTAAGACACAGTAACA
66 CCCGAAAGAGCTCTATCTCATAAGTACTTCTTTGAGCCCAAATTAAGACACAGTAACA
53887360 A
1 A
53887361 CTGTTTGACA
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 58 0.47
123 65 0.53
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (123 bp):
AACTTTATTTTTTTTTTGAATACAACCCAGGTGGAAGGCAAACAAGGTCTTCATAGATTACAACT
CCCGAAAGAGCTCTATCTCATAAGTACTTCTTTGAGCCCAAATTAAGACACAGTAACA
Found at i:53889340 original size:33 final size:33
Alignment explanation
Indices: 53889291--53889358 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
53889281 CGCCCAATGC
* *
53889291 TACTTGGTCAAGAGTTAGAATTCGAGAACTTCG
1 TACTAGGTCAACAGTTAGAATTCGAGAACTTCG
*
53889324 TACTAGGTCAACAGTTAGGATTCGAGAACTTCG
1 TACTAGGTCAACAGTTAGAATTCGAGAACTTCG
53889357 TA
1 TA
53889359 TATGTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (33 bp):
TACTAGGTCAACAGTTAGAATTCGAGAACTTCG
Found at i:53893023 original size:60 final size:59
Alignment explanation
Indices: 53892901--53893015 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 59
53892891 TTTTGGAGCT
*
53892901 TGAAATTGGCAATTACTCCCACATAGGGGCCTAATCCTTTTTTTGGTCCAAATTAATCCC
1 TGAAATTGGCAATTACTCCCACATAGGGGCCTAA-CCTTTTTTTGGTCCAAAGTAATCCC
* ** *
53892961 TGAACTTGGCAATTGTTCCCACATTGGGGCCTCAA-CTTTTCTTTGGTCC-AAGTAA
1 TGAAATTGGCAATTACTCCCACATAGGGGCCT-AACCTTTT-TTTGGTCCAAAGTAA
53893016 GTGCCTGATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
59 10 0.21
60 36 0.75
61 2 0.04
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (59 bp):
TGAAATTGGCAATTACTCCCACATAGGGGCCTAACCTTTTTTTGGTCCAAAGTAATCCC
Found at i:53893116 original size:62 final size:61
Alignment explanation
Indices: 53893043--53893166 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 61
53893033 GAAAACCTTT
* * *
53893043 AAGTTAAAGCCCTAA-CGTGGGAATAGTTACCAAGTTCAGAGACTTACTTGA-ACAGAAAAAAA
1 AAGTTAAAGCCCTAATC-TGGGAACAATTACCAAGTTCAGAGACTAACTT-ATACA-AAAAAAA
* *
53893105 AAGTTCAAGCCCTAATCTGGGAACAATTACCAAGTTCAGGGACTAACTTATACAAAAAAAA
1 AAGTTAAAGCCCTAATCTGGGAACAATTACCAAGTTCAGAGACTAACTTATACAAAAAAAA
53893166 A
1 A
53893167 TTCAAACCCC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
61 9 0.16
62 45 0.82
63 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.17, T:0.21
Consensus pattern (61 bp):
AAGTTAAAGCCCTAATCTGGGAACAATTACCAAGTTCAGAGACTAACTTATACAAAAAAAA
Found at i:53903793 original size:17 final size:16
Alignment explanation
Indices: 53903768--53903801 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
53903758 GGCCCCAAAA
53903768 TAAAATAAAAACTAAAT
1 TAAAATAAAAA-TAAAT
*
53903785 TAAAGTAAAAATAAAT
1 TAAAATAAAAATAAAT
53903801 T
1 T
53903802 TTTAGTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (16 bp):
TAAAATAAAAATAAAT
Found at i:53915188 original size:11 final size:10
Alignment explanation
Indices: 53915137--53915213 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
53915127 AAAATTATTA
53915137 TTTTAGAATTT
1 TTTTA-AATTT
53915148 TTTTAAA---
1 TTTTAAATTT
*
53915155 TTTTAACTTT
1 TTTTAAATTT
* *
53915165 CTTTATATATT
1 TTTTAAAT-TT
53915176 TTTTAGAA-TT
1 TTTTA-AATTT
*
53915186 TTTTAATTTT
1 TTTTAAATTT
*
53915196 TTTTTAATTT
1 TTTTAAATTT
53915206 TTTTAAAT
1 TTTTAAAT
53915214 ATAAATTTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
7 6 0.12
9 1 0.02
10 31 0.62
11 11 0.22
12 1 0.02
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:53923257 original size:22 final size:22
Alignment explanation
Indices: 53923217--53923258 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
53923207 ATCTAAACAC
* *
53923217 TAATAATAAAATAATAGTAATA
1 TAATAACAAAATAACAGTAATA
*
53923239 TAATAACAAAATGACAGTAA
1 TAATAACAAAATAACAGTAA
53923259 AACATAAGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (22 bp):
TAATAACAAAATAACAGTAATA
Found at i:53926585 original size:413 final size:413
Alignment explanation
Indices: 53925818--53926643 Score: 1589
Period size: 413 Copynumber: 2.0 Consensus size: 413
53925808 AGCAAGGATA
53925818 ACAAGGCTCTTGGGAAGCTTAGGAGGGAAGCTGAGCGTGCCAAGAGAGCTCTCAGCAGCCAGCAC
1 ACAAGGCTCTTGGGAAGCTTAGGAGGGAAGCTGAGCGTGCCAAGAGAGCTCTCAGCAGCCAGCAC
*
53925883 CAGGTCCGAGTAGAGATTGAATCACTTTTTGATGGTATCGATTTCTCTGAGCCACTGACCAGGGC
66 CAGGTCCGAGTAGAGATTGAATCACTTTTTGATGGTATCGATTTCTCCGAGCCACTGACCAGGGC
53925948 TCGCTTTGAGGAGTTGAACAATGATCTGTTCAGAAAGACCATGGGACCTGTGAAGAAAGCAATGG
131 TCGCTTTGAGGAGTTGAACAATGATCTGTTCAGAAAGACCATGGGACCTGTGAAGAAAGCAATGG
*
53926013 AAGATGCTGGTTTGGAGAAGCGCCAAATCGATGAGATTGTTCTAGTAGGTGGAAGCACTAGAATT
196 AAGATGCTGGTTTGGAGAAGCGACAAATCGATGAGATTGTTCTAGTAGGTGGAAGCACTAGAATT
* *
53926078 CCCAAGGTTCAACAGCTCCTCAAGGACTATTTTGATGGAAAGGAGCCCAACAAGGGTGTTAACCC
261 CCCAAGGTTCAACAGCTCCTCAAGGACTACTTCGATGGAAAGGAGCCCAACAAGGGTGTTAACCC
53926143 GGATGAAGCAGTTGCTTATGGTGCTGCAGTACAAGGAGGCATCTTGAGTGGAGAGGGTGGTGATG
326 GGATGAAGCAGTTGCTTATGGTGCTGCAGTACAAGGAGGCATCTTGAGTGGAGAGGGTGGTGATG
53926208 AAACCAAAGGTACGTTTTCATCT
391 AAACCAAAGGTACGTTTTCATCT
53926231 ACAAGGCTCTTGGGAAGCTTAGGAGGGAAGCTGAGCGTGCCAAGAGAGCTCTCAGCAGCCAGCAC
1 ACAAGGCTCTTGGGAAGCTTAGGAGGGAAGCTGAGCGTGCCAAGAGAGCTCTCAGCAGCCAGCAC
53926296 CAGGTCCGAGTAGAGATTGAATCACTTTTTGATGGTATCGATTTCTCCGAGCCACTGACCAGGGC
66 CAGGTCCGAGTAGAGATTGAATCACTTTTTGATGGTATCGATTTCTCCGAGCCACTGACCAGGGC
53926361 TCGCTTTGAGGAGTTGAACAATGATCTGTTCAGAAAGACCATGGGACCTGTGAAGAAAGCAATGG
131 TCGCTTTGAGGAGTTGAACAATGATCTGTTCAGAAAGACCATGGGACCTGTGAAGAAAGCAATGG
* *
53926426 AAGATGCTGGTTTGGAGAAGCGACAAATTGATGAGATTGTTCTGGTAGGTGGAAGCACTAGAATT
196 AAGATGCTGGTTTGGAGAAGCGACAAATCGATGAGATTGTTCTAGTAGGTGGAAGCACTAGAATT
53926491 CCCAAGGTTCAACAGCTCCTCAAGGACTACTTCGATGGAAAGGAGCCCAACAAGGGTGTTAACCC
261 CCCAAGGTTCAACAGCTCCTCAAGGACTACTTCGATGGAAAGGAGCCCAACAAGGGTGTTAACCC
53926556 GGATGAAGCAGTTGCTTATGGTGCTGCAGTACAAGGAGGCATCTTGAGTGGAGAGGGTGGTGATG
326 GGATGAAGCAGTTGCTTATGGTGCTGCAGTACAAGGAGGCATCTTGAGTGGAGAGGGTGGTGATG
*
53926621 AAACCAAAGGTGCGTTTTCATCT
391 AAACCAAAGGTACGTTTTCATCT
53926644 CCTGCAACTT
Statistics
Matches: 406, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
413 406 1.00
ACGTcount: A:0.28, C:0.19, G:0.30, T:0.23
Consensus pattern (413 bp):
ACAAGGCTCTTGGGAAGCTTAGGAGGGAAGCTGAGCGTGCCAAGAGAGCTCTCAGCAGCCAGCAC
CAGGTCCGAGTAGAGATTGAATCACTTTTTGATGGTATCGATTTCTCCGAGCCACTGACCAGGGC
TCGCTTTGAGGAGTTGAACAATGATCTGTTCAGAAAGACCATGGGACCTGTGAAGAAAGCAATGG
AAGATGCTGGTTTGGAGAAGCGACAAATCGATGAGATTGTTCTAGTAGGTGGAAGCACTAGAATT
CCCAAGGTTCAACAGCTCCTCAAGGACTACTTCGATGGAAAGGAGCCCAACAAGGGTGTTAACCC
GGATGAAGCAGTTGCTTATGGTGCTGCAGTACAAGGAGGCATCTTGAGTGGAGAGGGTGGTGATG
AAACCAAAGGTACGTTTTCATCT
Found at i:53928462 original size:33 final size:33
Alignment explanation
Indices: 53928420--53928485 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
53928410 CAGTCATCTA
*
53928420 TCACCTACTTTAACTACTATCGGAGAGACCTCC
1 TCACCTACTTTAACTACTATCAGAGAGACCTCC
*
53928453 TCACCTACTTTCACTACTATCAGAGAGACCTCC
1 TCACCTACTTTAACTACTATCAGAGAGACCTCC
53928486 AATGGCTGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (33 bp):
TCACCTACTTTAACTACTATCAGAGAGACCTCC
Found at i:53933714 original size:22 final size:22
Alignment explanation
Indices: 53933673--53933726 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
53933663 AAAATTCAAC
*
53933673 AAAACAGT-GGAAAAATAACAA
1 AAAACAGTAGGAAAAACAACAA
53933694 GAAAACAGTAGG-AAAACAACAA
1 -AAAACAGTAGGAAAAACAACAA
*
53933716 AAAAAAGTAGG
1 AAAACAGTAGG
53933727 CTTTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 10 0.34
22 17 0.59
23 2 0.07
ACGTcount: A:0.65, C:0.09, G:0.19, T:0.07
Consensus pattern (22 bp):
AAAACAGTAGGAAAAACAACAA
Found at i:53933724 original size:21 final size:22
Alignment explanation
Indices: 53933684--53933726 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
53933674 AAACAGTGGA
* *
53933684 AAAATAACAAGAAAACAGTAGG
1 AAAACAACAAGAAAAAAGTAGG
53933706 AAAACAACAA-AAAAAAGTAGG
1 AAAACAACAAGAAAAAAGTAGG
53933727 CTTTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.67, C:0.09, G:0.16, T:0.07
Consensus pattern (22 bp):
AAAACAACAAGAAAAAAGTAGG
Found at i:53934436 original size:17 final size:18
Alignment explanation
Indices: 53934408--53934441 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
53934398 GAAAAGTTAA
*
53934408 ATTATTATAAAATACTTC
1 ATTATTATAAAAAACTTC
53934426 ATTATTA-AAAAAACTT
1 ATTATTATAAAAAACTT
53934442 GTACAAATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (18 bp):
ATTATTATAAAAAACTTC
Found at i:53948655 original size:162 final size:162
Alignment explanation
Indices: 53948388--53948712 Score: 616
Period size: 162 Copynumber: 2.0 Consensus size: 162
53948378 GAATTCGAAA
*
53948388 ATGAGTGTTCAAAGACATTCATGTGCTTAAAACCAGACGGCACAGTTATACCTATATTCGTATAT
1 ATGAGTGTTCAAAGACATTCATGTGCTTAAAACCAGACCGCACAGTTATACCTATATTCGTATAT
53948453 GTGTTGTGTTGCTGTATCTTTAGGGATGGAGAGGTTCTTATACTCGAATTGGTAACCCGTAATTG
66 GTGTTGTGTTGCTGTATCTTTAGGGATGGAGAGGTTCTTATACTCGAATTGGTAACCCGTAATTG
53948518 AGGTAGGTTCGAATGCGTCCATCAAAGCTTGC
131 AGGTAGGTTCGAATGCGTCCATCAAAGCTTGC
*
53948550 ATGAGTGTTCAAAGACATGT-ATGTGTTTAAAACCAGACCGCACAGTTATACCTATATTCGTATA
1 ATGAGTGTTCAAAGACAT-TCATGTGCTTAAAACCAGACCGCACAGTTATACCTATATTCGTATA
53948614 TGTGTTGTGTTGCTGTATCTTTAGGGATGGAGAGGTTCTTATACTCGAATTGGTAACCCGTAATT
65 TGTGTTGTGTTGCTGTATCTTTAGGGATGGAGAGGTTCTTATACTCGAATTGGTAACCCGTAATT
53948679 GAGGTAGGTTCGAATGCGTCCATCAAAGCTTGC
130 GAGGTAGGTTCGAATGCGTCCATCAAAGCTTGC
53948712 A
1 A
53948713 GTGACAATCA
Statistics
Matches: 160, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
162 159 0.99
163 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (162 bp):
ATGAGTGTTCAAAGACATTCATGTGCTTAAAACCAGACCGCACAGTTATACCTATATTCGTATAT
GTGTTGTGTTGCTGTATCTTTAGGGATGGAGAGGTTCTTATACTCGAATTGGTAACCCGTAATTG
AGGTAGGTTCGAATGCGTCCATCAAAGCTTGC
Found at i:53956667 original size:21 final size:21
Alignment explanation
Indices: 53956635--53956675 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
53956625 TTAACATGTT
*
53956635 CCACTACCAGATG-GATGAAG
1 CCACTACAAGATGAGATGAAG
53956655 CCACATACAAGATGAGATGAA
1 CCAC-TACAAGATGAGATGAA
53956676 TTTATATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (21 bp):
CCACTACAAGATGAGATGAAG
Found at i:53960023 original size:10 final size:10
Alignment explanation
Indices: 53960010--53960034 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
53960000 ATGAAAATTT
53960010 AAAAAAATAA
1 AAAAAAATAA
53960020 AAAAAAATAA
1 AAAAAAATAA
53960030 AAAAA
1 AAAAA
53960035 TAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:53966421 original size:150 final size:150
Alignment explanation
Indices: 53966150--53966452 Score: 579
Period size: 150 Copynumber: 2.0 Consensus size: 150
53966140 CGGAGGGCGA
*
53966150 TCAGAATCATCAACCATGGGACTTTCTCCCTTAGTTGACCTTCTACCACTAACCACATCCTCTAA
1 TCAGAATCATCAACCATGGGACTTTCTCCCTCAGTTGACCTTCTACCACTAACCACATCCTCTAA
*
53966215 GCCTGAAGAATCAACAACTTGACTTAAATCCTCACTGTCTTCATTGCAGTTGTTTCCAGCAGTTT
66 GCCTGAAGAATCAACAACTTGACTTAAATCCTCACTGTCTTCATTGCAGTAGTTTCCAGCAGTTT
*
53966280 CCTTAACCTTAGAGCTATTC
131 CCTTAACCGTAGAGCTATTC
53966300 TCAGAATCATCAACCATGGGACTTTCTCCCTCAGTTGACCTTCTACCACTAACCACATCCTCTAA
1 TCAGAATCATCAACCATGGGACTTTCTCCCTCAGTTGACCTTCTACCACTAACCACATCCTCTAA
53966365 GCCTGAAGAATCAACAACTTGACTTAAATCCTCACTGTCTTCATTGCAGTAGTTTCCAGCAGTTT
66 GCCTGAAGAATCAACAACTTGACTTAAATCCTCACTGTCTTCATTGCAGTAGTTTCCAGCAGTTT
53966430 CCTTAACCGTAGAGCTATTC
131 CCTTAACCGTAGAGCTATTC
53966450 TCA
1 TCA
53966453 ATACGTTTAA
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.27, C:0.30, G:0.12, T:0.31
Consensus pattern (150 bp):
TCAGAATCATCAACCATGGGACTTTCTCCCTCAGTTGACCTTCTACCACTAACCACATCCTCTAA
GCCTGAAGAATCAACAACTTGACTTAAATCCTCACTGTCTTCATTGCAGTAGTTTCCAGCAGTTT
CCTTAACCGTAGAGCTATTC
Found at i:53970699 original size:31 final size:31
Alignment explanation
Indices: 53970644--53970710 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
53970634 TTTATCGTTA
*
53970644 AATATTTTAGTTTAATTTTAATATTTAATTT
1 AATATTTTAGTTTAATTTCAATATTTAATTT
* * * *
53970675 GATATTTTAGTTTAGTTTCGATATTTATTTT
1 AATATTTTAGTTTAATTTCAATATTTAATTT
53970706 AATAT
1 AATAT
53970711 CCAAAACAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.01, G:0.07, T:0.60
Consensus pattern (31 bp):
AATATTTTAGTTTAATTTCAATATTTAATTT
Found at i:53971881 original size:19 final size:19
Alignment explanation
Indices: 53971859--53971937 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
53971849 TAATTAATTT
53971859 TTAAAAT-TTTTAAAAATCA
1 TTAAAATATTTTAAAAAT-A
53971878 TTAAAATCATTTTAAAAGA-A
1 TTAAAAT-ATTTTAAAA-ATA
* * *
53971898 TAAAAATATTTTGAATATA
1 TTAAAATATTTTAAAAATA
*
53971917 TTTAAAT-TTTTAAAAAT-
1 TTAAAATATTTTAAAAATA
53971934 TTAA
1 TTAA
53971938 TTAAAGGATG
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
17 3 0.06
18 9 0.19
19 20 0.42
20 7 0.15
21 8 0.17
22 1 0.02
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (19 bp):
TTAAAATATTTTAAAAATA
Found at i:53972499 original size:20 final size:21
Alignment explanation
Indices: 53972457--53972501 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
53972447 TAGTTTATAA
*
53972457 TTTTTATAATATCATTAGGTTT
1 TTTTTATAATATCACTA-GTTT
*
53972479 TTTTTATAATATTACTA-TTT
1 TTTTTATAATATCACTAGTTT
53972499 TTT
1 TTT
53972502 AAAGTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
22 15 0.71
ACGTcount: A:0.27, C:0.04, G:0.04, T:0.64
Consensus pattern (21 bp):
TTTTTATAATATCACTAGTTT
Found at i:53975908 original size:167 final size:167
Alignment explanation
Indices: 53975621--53976102 Score: 919
Period size: 167 Copynumber: 2.9 Consensus size: 167
53975611 GTAGCTACTT
* *
53975621 GCCAAGGGGATGTGAGCATCTCACCCTGGTGGAATTCGAACGGCTGATCTATGGCATATAAGTTA
1 GCCAAGGGGATGTGAGCATCTCACCCTGGTGGAATTCGAACGCCTGATCTATGGCATATAAGTCA
53975686 CTTGTTGAGGAAGATGGTTCACTTGGGCTACACCCACGTACGCTTGAGGCACTTCCATCTTTGTG
66 CTTGTTGAGGAAGATGGTTCACTTGGGCTACACCCACGTACGCTTGAGGCACTTCCATCTTTGTG
53975751 AACTAGACCTTCAGGGCACTTCCATCTTTGTGAACTC
131 AACTAGACCTTCAGGGCACTTCCATCTTTGTGAACTC
*
53975788 GCCAAGTGGATGTGAGCATCTCACCCTGGTGGAATTCGAACGCCTGATCTATGGCATATAAGTCA
1 GCCAAGGGGATGTGAGCATCTCACCCTGGTGGAATTCGAACGCCTGATCTATGGCATATAAGTCA
*
53975853 CTTGTTGAGGAAGATGGTTCACTTGGGCTACACCCACGTACGCTTGAGACACTTCCATCTTTGTG
66 CTTGTTGAGGAAGATGGTTCACTTGGGCTACACCCACGTACGCTTGAGGCACTTCCATCTTTGTG
53975918 AACTAGACCTTCAGGGCACTTCCATCTTTGTGAACTC
131 AACTAGACCTTCAGGGCACTTCCATCTTTGTGAACTC
53975955 GCCAAGGGGATGTGAGCATCTCACCCTGGTGGAATTCGAACGCCTGATCTATGGCATATAAGTCA
1 GCCAAGGGGATGTGAGCATCTCACCCTGGTGGAATTCGAACGCCTGATCTATGGCATATAAGTCA
*
53976020 CTTGTTGAGGAAGATGGTTCACTTGGGCTACACCCACGTGCGCTTGAGGCACTTCCATCTTTGTG
66 CTTGTTGAGGAAGATGGTTCACTTGGGCTACACCCACGTACGCTTGAGGCACTTCCATCTTTGTG
53976085 AACTAGACCTTCAGGGCA
131 AACTAGACCTTCAGGGCA
53976103 GCCGCTCACG
Statistics
Matches: 308, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 308 1.00
ACGTcount: A:0.23, C:0.24, G:0.25, T:0.27
Consensus pattern (167 bp):
GCCAAGGGGATGTGAGCATCTCACCCTGGTGGAATTCGAACGCCTGATCTATGGCATATAAGTCA
CTTGTTGAGGAAGATGGTTCACTTGGGCTACACCCACGTACGCTTGAGGCACTTCCATCTTTGTG
AACTAGACCTTCAGGGCACTTCCATCTTTGTGAACTC
Found at i:53980318 original size:25 final size:23
Alignment explanation
Indices: 53980273--53980331 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 23
53980263 TAACTCTTTT
*
53980273 TAAAAAAATTAAAAGTCAAATTTAA
1 TAAAAAAA-TAAAACTCAAA-TTAA
*
53980298 CTAAAAAAATAAAGACT-AAATTGA
1 -TAAAAAAATAAA-ACTCAAATTAA
53980322 TAAAAAAATA
1 TAAAAAAATA
53980332 TAAATATTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 10 0.33
24 3 0.10
25 7 0.23
26 10 0.33
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (23 bp):
TAAAAAAATAAAACTCAAATTAA
Found at i:53982258 original size:2 final size:2
Alignment explanation
Indices: 53982247--53982280 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
53982237 AAAACAAAGA
53982247 AT AT -T 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 A
53982281 GTTACATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53983527 original size:21 final size:21
Alignment explanation
Indices: 53983489--53983528 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
53983479 CATGGGAGAA
*
53983489 AAAAAGACAAAGAAAAAGACC
1 AAAAAGACAAACAAAAAGACC
53983510 AAAAAGA-AAACAAGAAAGA
1 AAAAAGACAAACAA-AAAGA
53983529 TGAACAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.75, C:0.10, G:0.15, T:0.00
Consensus pattern (21 bp):
AAAAAGACAAACAAAAAGACC
Found at i:53984135 original size:16 final size:15
Alignment explanation
Indices: 53984104--53984143 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
53984094 TATAATTACG
53984104 TAATTTTATTATTTTA
1 TAATTTT-TTATTTTA
*
53984120 TTATTTTTTATATTTA
1 TAATTTTTTAT-TTTA
53984136 TAATTTTT
1 TAATTTTT
53984144 AAAGGTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TAATTTTTTATTTTA
Found at i:53996204 original size:20 final size:22
Alignment explanation
Indices: 53996181--53996220 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
53996171 AAGAACTTTT
53996181 AATTTT-TA-ATAAAATATTTA
1 AATTTTATATATAAAATATTTA
53996201 AATTTTATATATAAAATATT
1 AATTTTATATATAAAATATT
53996221 ACTTATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTTTATATATAAAATATTTA
Found at i:53997483 original size:236 final size:237
Alignment explanation
Indices: 53997059--53997531 Score: 939
Period size: 236 Copynumber: 2.0 Consensus size: 237
53997049 TAGTGGCATA
53997059 GTGTGTCATATGTACTTCAATAAAAATAAATAAAATAAATATATAAAAATTAATTTACTTACTTT
1 GTGTGTCATATGTACTTCAATAAAAATAAATAAAATAAATATATAAAAATTAATTTACTTACTTT
53997124 TAATAGAAGAAGCAAAATTCAAACCAACTTCTAATATAACAAAAACTTCCGTCATATTTTTACCT
66 TAATAGAAGAAGCAAAATTCAAACCAACTTCTAATATAACAAAAACTTCCGTCATATTTTTACCT
53997189 CAATCAGTCCCTCATAGCTGCCTCTCCTTAAAATTTATCTTTTCAGTAACCGTTGACTTGCTACA
131 CAATCAGTCCCTCATAGCTGCCTCTCCTTAAAATTTATCTTTTCAGTAACCGTTGACTTGCTACA
53997254 CTGTGTGTCGCCGTATAAAAAGAGACCGTTTTGAGATGGTGG
196 CTGTGTGTCGCCGTATAAAAAGAGACCGTTTTGAGATGGTGG
53997296 GTGTGTCATA-GTACTTCAATAAAAATAAATAAAATAAATATATAAAAATTAATTTACTTACTTT
1 GTGTGTCATATGTACTTCAATAAAAATAAATAAAATAAATATATAAAAATTAATTTACTTACTTT
53997360 TAATAGAAGAAGCAAAATTCAAACCAACTTCTAATATAACAAAAACTTCCGTCATATTTTTACCT
66 TAATAGAAGAAGCAAAATTCAAACCAACTTCTAATATAACAAAAACTTCCGTCATATTTTTACCT
53997425 CAATCAGTCCCTCATAGCTGCCTCTCCTTAAAATTTATCTTTTCAGTAACCGTTGACTTGCTACA
131 CAATCAGTCCCTCATAGCTGCCTCTCCTTAAAATTTATCTTTTCAGTAACCGTTGACTTGCTACA
53997490 CTGTGTGTCGCCGTATAAAAAGAGACCGTTTTGAGATGGTGG
196 CTGTGTGTCGCCGTATAAAAAGAGACCGTTTTGAGATGGTGG
53997532 TTTTACTGTG
Statistics
Matches: 236, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
236 226 0.96
237 10 0.04
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.33
Consensus pattern (237 bp):
GTGTGTCATATGTACTTCAATAAAAATAAATAAAATAAATATATAAAAATTAATTTACTTACTTT
TAATAGAAGAAGCAAAATTCAAACCAACTTCTAATATAACAAAAACTTCCGTCATATTTTTACCT
CAATCAGTCCCTCATAGCTGCCTCTCCTTAAAATTTATCTTTTCAGTAACCGTTGACTTGCTACA
CTGTGTGTCGCCGTATAAAAAGAGACCGTTTTGAGATGGTGG
Found at i:53999219 original size:16 final size:16
Alignment explanation
Indices: 53999183--53999213 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53999173 TTAATATTAT
*
53999183 TTTAATATTAAATAAA
1 TTTAAAATTAAATAAA
53999199 TTTAAAATTAAATAA
1 TTTAAAATTAAATAA
53999214 CATTAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAAATTAAATAAA
Found at i:54003549 original size:32 final size:33
Alignment explanation
Indices: 54003503--54003571 Score: 131
Period size: 32 Copynumber: 2.1 Consensus size: 33
54003493 TGTAATAAAT
54003503 AACATGTGCAAATATATTATTTCTTAAGAACTA
1 AACATGTGCAAATATATTATTTCTTAAGAACTA
54003536 AACA-GTGCAAATATATTATTTCTTAAGAACTA
1 AACATGTGCAAATATATTATTTCTTAAGAACTA
54003568 AACA
1 AACA
54003572 ATCGGCTCAC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (33 bp):
AACATGTGCAAATATATTATTTCTTAAGAACTA
Found at i:54012929 original size:57 final size:56
Alignment explanation
Indices: 54012845--54012954 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 56
54012835 AATTAATTTT
* *
54012845 TTAAAATTTTAAAATTAAAAAAGTTATAAAGATTA-ATTTTAAAAATTTAAAATCA
1 TTAAAATTTTAAAATTAAAAAAGTTATAAAAAATATATTTTAAAAATTTAAAATCA
* * * * *
54012900 TTAAAATTATTTAAATGTATAAAATTTATAAAAAATATTTTTTTAAAATTTAAAA
1 TTAAAATT-TTAAAAT-TAAAAAAGTTATAAAAAATATATTTTAAAAATTTAAAA
54012955 AAATAGTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
55 8 0.18
56 6 0.13
57 16 0.36
58 15 0.33
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (56 bp):
TTAAAATTTTAAAATTAAAAAAGTTATAAAAAATATATTTTAAAAATTTAAAATCA
Found at i:54017558 original size:3 final size:3
Alignment explanation
Indices: 54017537--54017576 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
54017527 GAAGAGAAGG
* * *
54017537 TGA TGG TGA TGG TGG TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
54017577 TATCATCATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:54022975 original size:18 final size:18
Alignment explanation
Indices: 54022933--54022978 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
54022923 TTTTTAGAAT
* *
54022933 ATTTATAATTTTTTAAAA
1 ATTTATAAATTTTGAAAA
*
54022951 ATATATAAATTTTGAAAA
1 ATTTATAAATTTTGAAAA
*
54022969 TTTTATAAAT
1 ATTTATAAAT
54022979 ATGTTGAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTATAAATTTTGAAAA
Found at i:54030009 original size:30 final size:30
Alignment explanation
Indices: 54029973--54030033 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
54029963 TTCTTTTAAA
54029973 TTATAATTAATATTATTATGTCACTTTTGT
1 TTATAATTAATATTATTATGTCACTTTTGT
54030003 TTATAATTAATATTATTATGTCACTTTTGT
1 TTATAATTAATATTATTATGTCACTTTTGT
54030033 T
1 T
54030034 GTTTCATACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (30 bp):
TTATAATTAATATTATTATGTCACTTTTGT
Found at i:54032979 original size:23 final size:22
Alignment explanation
Indices: 54032952--54032995 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
54032942 AAATTTGTAT
*
54032952 TAGATATTATAATTATTTATACA
1 TAGATATTACAATTA-TTATACA
54032975 TAGATATTACAATTATTATAC
1 TAGATATTACAATTATTATAC
54032996 TTTATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.45
Consensus pattern (22 bp):
TAGATATTACAATTATTATACA
Found at i:54037969 original size:25 final size:27
Alignment explanation
Indices: 54037919--54037985 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 27
54037909 TAATTTAATG
*
54037919 AAAAAAATATTTAAAATTAAATAATAT
1 AAAAAAAAATTTAAAATTAAATAATAT
*
54037946 -AAATAAAATTTAAAA-TAAATAATAT
1 AAAAAAAAATTTAAAATTAAATAATAT
54037971 AAAAAAAAATTTAAA
1 AAAAAAAAATTTAAA
54037986 GGATAGGAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 10 0.28
26 26 0.72
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAAAAAATTTAAAATTAAATAATAT
Found at i:54039015 original size:35 final size:36
Alignment explanation
Indices: 54038953--54039036 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 36
54038943 TGAAAACACG
*
54038953 GAAAATTTTTTTAGAAATACAAGAATCT-TAGAAATAC
1 GAAAA-TTTTTTAGAAACACAAGAATCTGTA-AAATAC
54038990 GAAAATTTTTTA-AAACACGAA-AATCTGTAAAATAC
1 GAAAATTTTTTAGAAACAC-AAGAATCTGTAAAATAC
54039025 GAGAAATTTTTT
1 GA-AAATTTTTT
54039037 TTTGAAAACA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
35 18 0.42
36 20 0.47
37 5 0.12
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (36 bp):
GAAAATTTTTTAGAAACACAAGAATCTGTAAAATAC
Found at i:54039058 original size:21 final size:20
Alignment explanation
Indices: 54038938--54039095 Score: 81
Period size: 18 Copynumber: 8.2 Consensus size: 20
54038928 AACACGGGAA
54038938 TTTTTTGAAAACACGGAAAAT
1 TTTTTTGAAAACAC-GAAAAT
*
54038959 TTTTTTAGAAATACA--AGAA-
1 TTTTTT-GAAA-ACACGAAAAT
* * *
54038978 -TCTTAG-AAATACGAAAA-
1 TTTTTTGAAAACACGAAAAT
54038995 TTTTTT-AAAACACGAAAA-
1 TTTTTTGAAAACACGAAAAT
* * *
54039013 -TCTGT-AAAATACGAGAAATTT
1 TTTTTTGAAAACACGA-AAA--T
54039034 TTTTTTGAAAACACGAAAAT
1 TTTTTTGAAAACACGAAAAT
*
54039054 ATTTTTTGAAAACATGAAAA-
1 -TTTTTTGAAAACACGAAAAT
*
54039074 -TTTTTG-AAACACGAGAAT
1 TTTTTTGAAAACACGAAAAT
54039092 TTTT
1 TTTT
54039096 ATTTTTTTTA
Statistics
Matches: 105, Mismatches: 17, Indels: 32
0.68 0.11 0.21
Matches are distributed among these distances:
15 2 0.02
16 2 0.02
17 24 0.23
18 25 0.24
19 3 0.03
20 4 0.04
21 24 0.23
22 10 0.10
23 11 0.10
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (20 bp):
TTTTTTGAAAACACGAAAAT
Found at i:54039076 original size:19 final size:19
Alignment explanation
Indices: 54038936--54039095 Score: 93
Period size: 17 Copynumber: 8.4 Consensus size: 19
54038926 GAAACACGGG
54038936 AATTTTTTGAAAACACGGAA
1 AATTTTTTGAAAACAC-GAA
* *
54038956 AATTTTTTTAGAAATAC-AA
1 AATTTTTTGA-AAACACGAA
* * *
54038975 GAA-TCTTAG-AAATACGAA
1 -AATTTTTTGAAAACACGAA
54038993 AATTTTTT-AAAACACGAA
1 AATTTTTTGAAAACACGAA
* * *
54039011 AA-TCTGT-AAAATACGAGA
1 AATTTTTTGAAAACACGA-A
54039029 AATTTTTTTTTGAAAACACGAAA
1 AA---TTTTTTGAAAACACG-AA
*
54039052 ATATTTTTTGAAAACATGAA
1 A-ATTTTTTGAAAACACGAA
*
54039072 AA-TTTTTG-AAACACGAG
1 AATTTTTTGAAAACACGAA
54039089 AATTTTT
1 AATTTTT
54039096 ATTTTTTTTA
Statistics
Matches: 109, Mismatches: 17, Indels: 30
0.70 0.11 0.19
Matches are distributed among these distances:
17 28 0.26
18 28 0.26
19 6 0.06
20 14 0.13
21 19 0.17
22 3 0.03
23 9 0.08
24 2 0.02
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (19 bp):
AATTTTTTGAAAACACGAA
Found at i:54039119 original size:61 final size:59
Alignment explanation
Indices: 54038988--54039124 Score: 143
Period size: 61 Copynumber: 2.3 Consensus size: 59
54038978 TCTTAGAAAT
*
54038988 ACGAAAATTTTTT-AAAACACGAAAATCTGTAAAATACGAGAAATTTTTTTTTGAAAAC
1 ACGAAAATTTTTTGAAAACACGAAAATCTGTAAAACACGAGAAATTTTTTTTTGAAAAC
* * * * * **
54039046 ACGAAAATATTTTTTGAAAACATGAAAATTTTTGAAACACGAGAATTTTTATTTTTTTTAAAC
1 ACG-AAA-ATTTTTTGAAAACACGAAAATCTGTAAAACACGAGAA-ATTT-TTTTTTGAAAAC
*
54039109 ACGAAGA-TTTTTGAAA
1 ACGAAAATTTTTTGAAA
54039125 CAATTATTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
58 3 0.05
59 3 0.05
60 16 0.25
61 25 0.38
62 5 0.08
63 13 0.20
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (59 bp):
ACGAAAATTTTTTGAAAACACGAAAATCTGTAAAACACGAGAAATTTTTTTTTGAAAAC
Found at i:54039510 original size:7 final size:7
Alignment explanation
Indices: 54039498--54039551 Score: 56
Period size: 7 Copynumber: 7.3 Consensus size: 7
54039488 TAATTCGGGC
54039498 TTCTTTT
1 TTCTTTT
54039505 TTCTTTTT
1 TTC-TTTT
54039513 TTCCTTTT
1 TT-CTTTT
54039521 CTT-TTTT
1 -TTCTTTT
*
54039528 CTCTTTT
1 TTCTTTT
54039535 TTCTTTT
1 TTCTTTT
54039542 TTCTCTTT
1 TTCT-TTT
54039550 TT
1 TT
54039552 TTCTGGACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
6 1 0.03
7 21 0.52
8 15 0.38
9 3 0.08
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (7 bp):
TTCTTTT
Found at i:54039519 original size:9 final size:8
Alignment explanation
Indices: 54039501--54039555 Score: 62
Period size: 9 Copynumber: 7.0 Consensus size: 8
54039491 TTCGGGCTTC
54039501 TTTTTTCT
1 TTTTTTCT
54039509 TTTTTTC-
1 TTTTTTCT
*
54039516 -CTTTTC-
1 TTTTTTCT
54039522 TTTTTTCT
1 TTTTTTCT
54039530 CTTTTTTCT
1 -TTTTTTCT
54039539 TTTTTCTCT
1 TTTTT-TCT
54039548 TTTTTTCT
1 TTTTTTCT
54039556 GGACTGGGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.12
7 5 0.12
8 15 0.37
9 16 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTTCT
Found at i:54039536 original size:16 final size:16
Alignment explanation
Indices: 54039499--54039552 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
54039489 AATTCGGGCT
54039499 TCTTTTTTCTTTTTT-
1 TCTTTTTTCTTTTTTC
*
54039514 TC-CTTTTCTTTTTTC
1 TCTTTTTTCTTTTTTC
54039529 TCTTTTTTCTTTTTTC
1 TCTTTTTTCTTTTTTC
54039545 TCTTTTTT
1 TCTTTTTT
54039553 TCTGGACTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
14 11 0.31
15 4 0.11
16 20 0.57
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTTTTCTTTTTTC
Found at i:54039675 original size:23 final size:25
Alignment explanation
Indices: 54039637--54039696 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
54039627 GCTGCTGTGA
*
54039637 TGGGCCTGCTGGCCTGCCAAGCTGT
1 TGGGCCTGTTGGCCTGCCAAGCTGT
* *
54039662 T-GG-CTGTTGGCCTGCTAGGCTGT
1 TGGGCCTGTTGGCCTGCCAAGCTGT
54039685 TGGGCCTGTTGG
1 TGGGCCTGTTGG
54039697 TTTTTTTTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 18 0.60
24 4 0.13
25 8 0.27
ACGTcount: A:0.05, C:0.25, G:0.40, T:0.30
Consensus pattern (25 bp):
TGGGCCTGTTGGCCTGCCAAGCTGT
Found at i:54040044 original size:29 final size:29
Alignment explanation
Indices: 54039999--54040059 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
54039989 AATTTTGAGA
* * * *
54039999 AAATTTAAGGGTTAAAATATAGTTTTAGG
1 AAATTTAAGGGTCAAAACATAATTTCAGG
54040028 AAATTT-AGGTGTCAAAACATAATTTCAGG
1 AAATTTAAGG-GTCAAAACATAATTTCAGG
54040057 AAA
1 AAA
54040060 CTTCAGAGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 3 0.11
29 24 0.89
ACGTcount: A:0.44, C:0.05, G:0.18, T:0.33
Consensus pattern (29 bp):
AAATTTAAGGGTCAAAACATAATTTCAGG
Found at i:54040356 original size:11 final size:11
Alignment explanation
Indices: 54040316--54040356 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
54040306 AATGTAACAC
54040316 ATAGAAGGAAA
1 ATAGAAGGAAA
*
54040327 AAAGATA-GAAA
1 ATAGA-AGGAAA
54040338 ATAG-AGGAAA
1 ATAGAAGGAAA
54040348 ATAGAAGGA
1 ATAGAAGGA
54040357 GAAACAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 1 0.04
10 8 0.32
11 15 0.60
12 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.27, T:0.10
Consensus pattern (11 bp):
ATAGAAGGAAA
Found at i:54040387 original size:22 final size:20
Alignment explanation
Indices: 54040362--54040406 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 20
54040352 AAGGAGAAAC
54040362 AAAAGAAAATGAAAAAAAAGTT
1 AAAAGAAAAT-AAAAAAAA-TT
*
54040384 AAAAGAACATAAAAAAAATT
1 AAAAGAAAATAAAAAAAATT
54040404 AAA
1 AAA
54040407 TTGTTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.23
21 8 0.36
22 9 0.41
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (20 bp):
AAAAGAAAATAAAAAAAATT
Found at i:54040597 original size:13 final size:13
Alignment explanation
Indices: 54040579--54040604 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
54040569 AAACTATTTC
54040579 CTTATGTTAAGAT
1 CTTATGTTAAGAT
54040592 CTTATGTTAAGAT
1 CTTATGTTAAGAT
54040605 TTTAAGTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
CTTATGTTAAGAT
Found at i:54042967 original size:2 final size:2
Alignment explanation
Indices: 54042960--54042992 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
54042950 CATAAATTGA
54042960 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 A
54042993 CCTCAAGATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54047838 original size:15 final size:14
Alignment explanation
Indices: 54047812--54047846 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
54047802 TATATAACCG
54047812 AAAATAAAAATAAT
1 AAAATAAAAATAAT
54047826 AAAATACAAAATAAT
1 AAAATA-AAAATAAT
54047841 AAAATA
1 AAAATA
54047847 TTTTCTGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAATAAAAATAAT
Found at i:54050407 original size:2 final size:2
Alignment explanation
Indices: 54050395--54050425 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
54050385 TTCTTTTAAC
*
54050395 AT AT TT 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 A
54050426 CCGACCACCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:54053608 original size:13 final size:12
Alignment explanation
Indices: 54053592--54053643 Score: 61
Period size: 12 Copynumber: 4.3 Consensus size: 12
54053582 TTTTTCTTTA
54053592 TTTTTTTATTAAT
1 TTTTTTTATT-AT
54053605 TTTTTTTATTAT
1 TTTTTTTATTAT
* *
54053617 TCTTTTTATTCT
1 TTTTTTTATTAT
*
54053629 TTTTTATA-TAT
1 TTTTTTTATTAT
54053640 TTTT
1 TTTT
54053644 CGTATTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
11 6 0.18
12 18 0.53
13 10 0.29
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTATTAT
Found at i:54053649 original size:23 final size:22
Alignment explanation
Indices: 54053606--54053649 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
54053596 TTTATTAATT
*
54053606 TTTTTTATTATTCTTTTTATTC
1 TTTTTTATTATTCTTTGTATTC
54053628 TTTTTTATATATT-TTTCGTATT
1 TTTTTTAT-TATTCTTT-GTATT
54053650 TATTTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (22 bp):
TTTTTTATTATTCTTTGTATTC
Found at i:54055556 original size:2 final size:2
Alignment explanation
Indices: 54055549--54055573 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54055539 AACAACAAAA
54055549 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
54055574 AATAAGATAT
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:54059847 original size:16 final size:17
Alignment explanation
Indices: 54059826--54059903 Score: 83
Period size: 16 Copynumber: 4.8 Consensus size: 17
54059816 GTGATGTAAG
*
54059826 ATTATTTATAGATCA-A
1 ATTATTTATAAATCATA
54059842 ATTATTTATAAATCGATA
1 ATTATTTATAAATC-ATA
* *
54059860 A-AATTGA-AAATCA-A
1 ATTATTTATAAATCATA
*
54059874 ATTATTTATAAATTATA
1 ATTATTTATAAATCATA
54059891 ATTATTTATAAAT
1 ATTATTTATAAAT
54059904 TTATTTAATC
Statistics
Matches: 51, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
14 2 0.04
15 5 0.10
16 23 0.45
17 19 0.37
18 2 0.04
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
ATTATTTATAAATCATA
Found at i:54062283 original size:24 final size:24
Alignment explanation
Indices: 54062249--54062458 Score: 231
Period size: 24 Copynumber: 8.8 Consensus size: 24
54062239 TTTTGGTTCC
* * *
54062249 AGTACTCCTGCCTTCGGTGCCACG
1 AGTACCCCTGCTTTTGGTGCCACG
* * *
54062273 AGCACCTCTGCTTTTGGTGCCACA
1 AGTACCCCTGCTTTTGGTGCCACG
*
54062297 AGTACCCCTGCCTTTGGTGCCACG
1 AGTACCCCTGCTTTTGGTGCCACG
*
54062321 AGTGCCCCTGCTTTTGGTGCCACG
1 AGTACCCCTGCTTTTGGTGCCACG
*
54062345 AGTACCCCTTCTTTTGGTGCCACG
1 AGTACCCCTGCTTTTGGTGCCACG
* * *
54062369 AGTGCCCCTGCTTTTGGTGGCACA
1 AGTACCCCTGCTTTTGGTGCCACG
* * *
54062393 AGTACCCCTGCCTTTGGTTCCATG
1 AGTACCCCTGCTTTTGGTGCCACG
* * * *
54062417 AGTACTCCAGCCTTTGGTGCCACA
1 AGTACCCCTGCTTTTGGTGCCACG
* *
54062441 AGCACCCCTGCCTTTGGT
1 AGTACCCCTGCTTTTGGT
54062459 TCAACTGGAA
Statistics
Matches: 154, Mismatches: 32, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 154 1.00
ACGTcount: A:0.13, C:0.34, G:0.24, T:0.29
Consensus pattern (24 bp):
AGTACCCCTGCTTTTGGTGCCACG
Found at i:54062377 original size:72 final size:72
Alignment explanation
Indices: 54062249--54062458 Score: 258
Period size: 72 Copynumber: 2.9 Consensus size: 72
54062239 TTTTGGTTCC
* * * *
54062249 AGTACTCCTGCCTTCGGTGCCACGAGCACCTCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
1 AGTACCCCTGCCTTTGGTGCCACGAGTACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
*
54062314 TGCCACG
66 TGCCACA
* * * * * *
54062321 AGTGCCCCTGCTTTTGGTGCCACGAGTACCCCTTCTTTTGGTGCCACGAGTGCCCCTGCTTTTGG
1 AGTACCCCTGCCTTTGGTGCCACGAGTACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
*
54062386 TGGCACA
66 TGCCACA
* * * * * *
54062393 AGTACCCCTGCCTTTGGTTCCATGAGTACTCCAGCCTTTGGTGCCACAAGCACCCCTGCCTTTGG
1 AGTACCCCTGCCTTTGGTGCCACGAGTACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
54062458 T
66 T
54062459 TCAACTGGAA
Statistics
Matches: 114, Mismatches: 24, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 114 1.00
ACGTcount: A:0.13, C:0.34, G:0.24, T:0.29
Consensus pattern (72 bp):
AGTACCCCTGCCTTTGGTGCCACGAGTACCCCTGCTTTTGGTGCCACAAGTACCCCTGCCTTTGG
TGCCACA
Found at i:54062460 original size:48 final size:48
Alignment explanation
Indices: 54062249--54062458 Score: 276
Period size: 48 Copynumber: 4.4 Consensus size: 48
54062239 TTTTGGTTCC
* * ** *
54062249 AGTACTCCTGCCTTCGGTGCCACGAGCACCTCTGCTTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGCCACA
*
54062297 AGTACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGCCACG
1 AGTACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGCCACA
* * *
54062345 AGTACCCCTTCTTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGGCACA
1 AGTACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGCCACA
* * * * * *
54062393 AGTACCCCTGCCTTTGGTTCCATGAGTACTCCAGCCTTTGGTGCCACA
1 AGTACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGCCACA
*
54062441 AGCACCCCTGCCTTTGGT
1 AGTACCCCTGCCTTTGGT
54062459 TCAACTGGAA
Statistics
Matches: 142, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 142 1.00
ACGTcount: A:0.13, C:0.34, G:0.24, T:0.29
Consensus pattern (48 bp):
AGTACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCTTTTGGTGCCACA
Found at i:54062474 original size:48 final size:48
Alignment explanation
Indices: 54062285--54062481 Score: 135
Period size: 48 Copynumber: 4.1 Consensus size: 48
54062275 CACCTCTGCT
* * * * ** * * *
54062285 TTTGGTGCCACAAGTACCCCTGCCTTTGGTGCCACGAGTGCCCCTGCT
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
* * * * * * * ** * * *
54062333 TTTGGTGCCACGAGTACCCCTTCTTTTGGTGCCACGAGTGCCCCTGCT
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
* * * * *
54062381 TTTGGTGGCACAAGTACCCCTGCCTTTGGTTCCATGAGTACTCCAGCC
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
*
54062429 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAACTG-GAAGTCCAGCA
1 TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAA-TGAGAACTCCAGCA
54062477 TTTGG
1 TTTGG
54062482 GAGCACTGGA
Statistics
Matches: 129, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
48 127 0.98
49 2 0.02
ACGTcount: A:0.15, C:0.32, G:0.24, T:0.29
Consensus pattern (48 bp):
TTTGGTGCCACAAGCACCCCTGCCTTTGGTTCAATGAGAACTCCAGCA
Found at i:54062579 original size:24 final size:24
Alignment explanation
Indices: 54062552--54062616 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
54062542 TGGAGCATCA
*
54062552 AGCACACCTGCTTTTGGCACTTCC
1 AGCACTCCTGCTTTTGGCACTTCC
* *** *
54062576 AGCACTCCTGCATTTGGGGGTTCG
1 AGCACTCCTGCTTTTGGCACTTCC
54062600 AGCACTCCTGCTTTTGG
1 AGCACTCCTGCTTTTGG
54062617 AGCATCTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.14, C:0.31, G:0.25, T:0.31
Consensus pattern (24 bp):
AGCACTCCTGCTTTTGGCACTTCC
Found at i:54062710 original size:24 final size:24
Alignment explanation
Indices: 54062683--54062809 Score: 139
Period size: 24 Copynumber: 5.3 Consensus size: 24
54062673 CATTTGGTAG
*
54062683 CTTTGGTGCCACGAGCACTCCTGC
1 CTTTGGTGCCACAAGCACTCCTGC
* *
54062707 CTTTGGTTCCACAAGCACCCCTGC
1 CTTTGGTGCCACAAGCACTCCTGC
* * * *
54062731 CTTTGGTGCTACCAGCACCCCGGC
1 CTTTGGTGCCACAAGCACTCCTGC
*
54062755 CTTTGGTTCCACAAGCA-TCCCTGC
1 CTTTGGTGCCACAAGCACT-CCTGC
* * *
54062779 CTTTGGTGCTACCAGCACTCCGGC
1 CTTTGGTGCCACAAGCACTCCTGC
54062803 CTTTGGT
1 CTTTGGT
54062810 TCAACTGGAA
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
24 84 0.99
25 1 0.01
ACGTcount: A:0.13, C:0.38, G:0.22, T:0.27
Consensus pattern (24 bp):
CTTTGGTGCCACAAGCACTCCTGC
Found at i:54062757 original size:48 final size:48
Alignment explanation
Indices: 54062683--54062811 Score: 213
Period size: 48 Copynumber: 2.7 Consensus size: 48
54062673 CATTTGGTAG
* * *
54062683 CTTTGGTGCCACGAGCACTCCTGCCTTTGGTTCCACAAGCACCCCTGC
1 CTTTGGTGCTACCAGCACTCCGGCCTTTGGTTCCACAAGCACCCCTGC
* *
54062731 CTTTGGTGCTACCAGCACCCCGGCCTTTGGTTCCACAAGCATCCCTGC
1 CTTTGGTGCTACCAGCACTCCGGCCTTTGGTTCCACAAGCACCCCTGC
54062779 CTTTGGTGCTACCAGCACTCCGGCCTTTGGTTC
1 CTTTGGTGCTACCAGCACTCCGGCCTTTGGTTC
54062812 AACTGGAAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 75 1.00
ACGTcount: A:0.13, C:0.38, G:0.22, T:0.27
Consensus pattern (48 bp):
CTTTGGTGCTACCAGCACTCCGGCCTTTGGTTCCACAAGCACCCCTGC
Found at i:54062919 original size:24 final size:24
Alignment explanation
Indices: 54062891--54062949 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
54062881 AGAAGGCACA
54062891 TTTGGAGCATCAAGCACACCTGCT
1 TTTGGAGCATCAAGCACACCTGCT
* **
54062915 TTTGGCA-CTTCAAGCAGTCCTGCT
1 TTTGG-AGCATCAAGCACACCTGCT
54062939 TTTGGAGCATC
1 TTTGGAGCATC
54062950 TTCTACTCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (24 bp):
TTTGGAGCATCAAGCACACCTGCT
Found at i:54067923 original size:22 final size:22
Alignment explanation
Indices: 54067879--54067923 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
54067869 TGAGACAAAT
**
54067879 AAAAACTTAAGTATCAATTTAA
1 AAAAACTTAAGTATCAAACTAA
*
54067901 AAAAACTTAGGTATCAAACTAA
1 AAAAACTTAAGTATCAAACTAA
54067923 A
1 A
54067924 CATTGAAGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.56, C:0.11, G:0.07, T:0.27
Consensus pattern (22 bp):
AAAAACTTAAGTATCAAACTAA
Found at i:54076460 original size:18 final size:17
Alignment explanation
Indices: 54076439--54076488 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
54076429 AAAAATATTA
54076439 AATTTGAAAAATAGACTT
1 AATTT-AAAAATAGACTT
*
54076457 AATTAAAAAATTAGACTT
1 AATTTAAAAA-TAGACTT
*
54076475 AGTTTAAAATATAG
1 AATTTAAAA-ATAG
54076489 GTCGAGCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 5 0.19
18 21 0.78
19 1 0.04
ACGTcount: A:0.52, C:0.04, G:0.10, T:0.34
Consensus pattern (17 bp):
AATTTAAAAATAGACTT
Found at i:54082218 original size:44 final size:44
Alignment explanation
Indices: 54082155--54082335 Score: 355
Period size: 44 Copynumber: 4.1 Consensus size: 44
54082145 TTTACTTAAG
54082155 GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
1 GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
54082199 GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
1 GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
54082243 GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
1 GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
54082287 GACACGTAGATAGTAACATATTATGCTACTTCC-AAAAAAAAAA
1 GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
54082330 GACACG
1 GACACG
54082336 CAGACAGGGT
Statistics
Matches: 137, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
43 16 0.12
44 121 0.88
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.22
Consensus pattern (44 bp):
GACACGTAGATAGTAACATATTATGCTACTTCCAAAAAAAAAAA
Found at i:54086146 original size:163 final size:164
Alignment explanation
Indices: 54085961--54086287 Score: 647
Period size: 163 Copynumber: 2.0 Consensus size: 164
54085951 TTTTTATATA
54085961 TTGGATTATAGGTTAATTAATTTAAATTTATTATATTTTTATAATTATTAATTTTATAATAAATT
1 TTGGATTATAGGTTAATTAATTTAAATTTATTATATTTTTATAATTATTAATTTTATAATAAATT
54086026 TAAACCAATTAATAATTCATGTACTTCTATTTTTAAAATATAGATACAAATAACTTGAATTTAAA
66 TAAACCAATTAATAATTCATGTACTTCTATTTTTAAAATATAGATACAAATAACTTGAATTTAAA
54086091 ATAATCGGATTCAAAATAATCCGAGTATCAAATT
131 ATAATCGGATTCAAAATAATCCGAGTATCAAATT
54086125 TTGGATTATA-GTTAATTAATTTAAATTTATTATATTTTTATAATTATTAATTTTATAATAAATT
1 TTGGATTATAGGTTAATTAATTTAAATTTATTATATTTTTATAATTATTAATTTTATAATAAATT
54086189 TAAACCAATTAATAATTCATGTACTTCTATTTTTAAAATATAGATACAAATAACTTGAATTTAAA
66 TAAACCAATTAATAATTCATGTACTTCTATTTTTAAAATATAGATACAAATAACTTGAATTTAAA
54086254 ATAATCGGATTCAAAATAATCCGAGTATCAAATT
131 ATAATCGGATTCAAAATAATCCGAGTATCAAATT
54086288 AAACCCAAAT
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
163 153 0.94
164 10 0.06
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (164 bp):
TTGGATTATAGGTTAATTAATTTAAATTTATTATATTTTTATAATTATTAATTTTATAATAAATT
TAAACCAATTAATAATTCATGTACTTCTATTTTTAAAATATAGATACAAATAACTTGAATTTAAA
ATAATCGGATTCAAAATAATCCGAGTATCAAATT
Found at i:54092168 original size:15 final size:15
Alignment explanation
Indices: 54092150--54092192 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
54092140 TTTTTTATAT
54092150 AATATTTTTATTTAG
1 AATATTTTTATTTAG
*
54092165 AATATTTTTATTTAT
1 AATATTTTTATTTAG
*
54092180 TATATTTTATATT
1 AATATTTT-TATT
54092193 GATAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 21 0.84
16 4 0.16
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (15 bp):
AATATTTTTATTTAG
Found at i:54106010 original size:22 final size:22
Alignment explanation
Indices: 54105982--54106031 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
54105972 AAAATGGTAA
*
54105982 GTTAACAGCTGAAGTTTACTCT
1 GTTAACAGCTGAAGTTTACCCT
*
54106004 GTTAACAGCTTAAGTTTACCCT
1 GTTAACAGCTGAAGTTTACCCT
54106026 GTTAAC
1 GTTAAC
54106032 TTACCAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (22 bp):
GTTAACAGCTGAAGTTTACCCT
Found at i:54109717 original size:9 final size:9
Alignment explanation
Indices: 54109685--54109717 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
54109675 TTTGGTTAAA
54109685 AATTAACCG
1 AATTAACCG
54109694 AATT-ACCTG
1 AATTAACC-G
54109703 AATTAACCG
1 AATTAACCG
54109712 AATTAA
1 AATTAA
54109718 ATCACTACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 3 0.14
9 16 0.73
10 3 0.14
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:54109806 original size:18 final size:17
Alignment explanation
Indices: 54109779--54109817 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
54109769 ATAAGTATTG
54109779 AAATTAACACATAATTA
1 AAATTAACACATAATTA
54109796 AAATGTAACACATAATTA
1 AAAT-TAACACATAATTA
54109814 AAAT
1 AAAT
54109818 ATAAGTCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (17 bp):
AAATTAACACATAATTA
Found at i:54110505 original size:14 final size:14
Alignment explanation
Indices: 54110488--54110537 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
54110478 TACTGTTTTT
54110488 TTGTTATTTTCTTG
1 TTGTTATTTTCTTG
54110502 TTGTT-TTTTCATTG
1 TTGTTATTTTC-TTG
* *
54110516 TTGCTACTATT-TTG
1 TTGTTA-TTTTCTTG
54110530 TTGTTATT
1 TTGTTATT
54110538 GTTTGGATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
13 6 0.21
14 20 0.69
16 3 0.10
ACGTcount: A:0.10, C:0.08, G:0.14, T:0.68
Consensus pattern (14 bp):
TTGTTATTTTCTTG
Found at i:54115746 original size:121 final size:121
Alignment explanation
Indices: 54115590--54115819 Score: 460
Period size: 121 Copynumber: 1.9 Consensus size: 121
54115580 ACAATGACCC
54115590 AGAAATACAGTTCTACTCTTTCTTCTAGGAGCCTGTTTTATAGCTCGGTGGAGAGACGTTTAGAC
1 AGAAATACAGTTCTACTCTTTCTTCTAGGAGCCTGTTTTATAGCTCGGTGGAGAGACGTTTAGAC
54115655 GAGAACGTTGGCAGAAACATCACTAAAACTGGGCTTTTGTACATGGTGAGAGCTTG
66 GAGAACGTTGGCAGAAACATCACTAAAACTGGGCTTTTGTACATGGTGAGAGCTTG
54115711 AGAAATACAGTTCTACTCTTTCTTCTAGGAGCCTGTTTTATAGCTCGGTGGAGAGACGTTTAGAC
1 AGAAATACAGTTCTACTCTTTCTTCTAGGAGCCTGTTTTATAGCTCGGTGGAGAGACGTTTAGAC
54115776 GAGAACGTTGGCAGAAACATCACTAAAACTGGGCTTTTGTACAT
66 GAGAACGTTGGCAGAAACATCACTAAAACTGGGCTTTTGTACAT
54115820 CTTTATAGCT
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
121 109 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (121 bp):
AGAAATACAGTTCTACTCTTTCTTCTAGGAGCCTGTTTTATAGCTCGGTGGAGAGACGTTTAGAC
GAGAACGTTGGCAGAAACATCACTAAAACTGGGCTTTTGTACATGGTGAGAGCTTG
Found at i:54118024 original size:25 final size:24
Alignment explanation
Indices: 54117982--54118035 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
54117972 TCCACTCTTA
54117982 TATTAAAATTAAACATAAATATTAT
1 TATTAAAATTAAACATAAAT-TTAT
* **
54118007 TATTTAAATTAATTATAAATTTA-
1 TATTAAAATTAAACATAAATTTAT
54118030 TATTAA
1 TATTAA
54118036 TATTGAAGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 5 0.20
24 3 0.12
25 17 0.68
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
TATTAAAATTAAACATAAATTTAT
Found at i:54118031 original size:158 final size:159
Alignment explanation
Indices: 54117846--54118163 Score: 629
Period size: 158 Copynumber: 2.0 Consensus size: 159
54117836 AAAAATAATA
54117846 ATTATTTAAATTTAATTATAAATTTATATTAATATTGAAGATAGAATTATTTTTATTAATTGAGC
1 ATTATTTAAATTTAATTATAAATTTATATTAATATTGAAGATAGAATTATTTTTATTAATTGAGC
54117911 CAATAAATATTGAAATTATAAATGCAAGTTCAACCCAGAGTCTCACAAGCTCATCATCACCTCCA
66 CAATAAATATTGAAATTATAAATGCAAGTTCAACCCAGAGTCTCACAAGCTCATCATCACCTCCA
54117976 CTCTTATATTAAAATTAAACATAAATATT
131 CTCTTATATTAAAATTAAACATAAATATT
54118005 ATTATTTAAA-TTAATTATAAATTTATATTAATATTGAAGATAGAATTATTTTTATTAATTGAGC
1 ATTATTTAAATTTAATTATAAATTTATATTAATATTGAAGATAGAATTATTTTTATTAATTGAGC
54118069 CAATAAATATTGAAATTATAAATGCAAGTTCAACCCAGAGTCTCACAAGCTCATCATCACCTCCA
66 CAATAAATATTGAAATTATAAATGCAAGTTCAACCCAGAGTCTCACAAGCTCATCATCACCTCCA
54118134 CTCTTATATTAAAATTAAACATAAATATT
131 CTCTTATATTAAAATTAAACATAAATATT
54118163 A
1 A
54118164 AACTTATTTT
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 149 0.94
159 10 0.06
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.37
Consensus pattern (159 bp):
ATTATTTAAATTTAATTATAAATTTATATTAATATTGAAGATAGAATTATTTTTATTAATTGAGC
CAATAAATATTGAAATTATAAATGCAAGTTCAACCCAGAGTCTCACAAGCTCATCATCACCTCCA
CTCTTATATTAAAATTAAACATAAATATT
Found at i:54129427 original size:12 final size:12
Alignment explanation
Indices: 54129410--54129435 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
54129400 CTTGATTTTC
54129410 TTCGTTTTCCCA
1 TTCGTTTTCCCA
54129422 TTCGTTTTCCCA
1 TTCGTTTTCCCA
54129434 TT
1 TT
54129436 GATCCTTGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.08, T:0.54
Consensus pattern (12 bp):
TTCGTTTTCCCA
Found at i:54142588 original size:151 final size:151
Alignment explanation
Indices: 54142309--54142615 Score: 587
Period size: 151 Copynumber: 2.0 Consensus size: 151
54142299 AGGATTTGGC
*
54142309 TTTTGAGGCTGTCGTTTAATCTTTGCATATAAAATAATAAAAAATTTAATTATTTGATTTAATTA
1 TTTTTAGGCTGTCGTTTAATCTTTGCATATAAAATAATAAAAAATTTAATTATTTGATTTAATTA
54142374 ATTAATTAATTAAGGGTCAAGTGTCAATAAAATAATGCGGACCTTAAGCTTCGGTCTCTTTTTTT
66 ATTAATTAATTAAGGGTCAAGTGTCAATAAAATAATGCGGACCTTAAGCTTCGGTCTCTTTTTTT
* *
54142439 TTTTTTTTTAGTTTTGAGATT
131 TTTTTTTTTAGATTTGAGATA
54142460 TTTTTAGGCTGTCGTTTAATCTTTGCATATAAAATAATAAAAAATTTAATTATTTGATTTAATTA
1 TTTTTAGGCTGTCGTTTAATCTTTGCATATAAAATAATAAAAAATTTAATTATTTGATTTAATTA
54142525 ATTAATTAATTAAGGGTCAAGTGTCAATAAAATAATGCGGACCTTAAGCTTCGGTCTCTTTTTTT
66 ATTAATTAATTAAGGGTCAAGTGTCAATAAAATAATGCGGACCTTAAGCTTCGGTCTCTTTTTTT
54142590 TTTTTTTTTAGATTTGAGATA
131 TTTTTTTTTAGATTTGAGATA
54142611 TTTTT
1 TTTTT
54142616 GTGTGTATGG
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
151 153 1.00
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.47
Consensus pattern (151 bp):
TTTTTAGGCTGTCGTTTAATCTTTGCATATAAAATAATAAAAAATTTAATTATTTGATTTAATTA
ATTAATTAATTAAGGGTCAAGTGTCAATAAAATAATGCGGACCTTAAGCTTCGGTCTCTTTTTTT
TTTTTTTTTAGATTTGAGATA
Found at i:54149299 original size:19 final size:20
Alignment explanation
Indices: 54149264--54149315 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
54149254 AAGATCATAA
54149264 ATTTAGAATAAAAATATG-T
1 ATTTAGAATAAAAATATGAT
*
54149283 ATTTAGAA-ATAACATATGAT
1 ATTTAGAATA-AAAATATGAT
*
54149303 A-TTAAAATAAAAA
1 ATTTAGAATAAAAA
54149316 ATTTAGATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.04
19 23 0.85
20 3 0.11
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.33
Consensus pattern (20 bp):
ATTTAGAATAAAAATATGAT
Found at i:54153028 original size:91 final size:90
Alignment explanation
Indices: 54152925--54153190 Score: 299
Period size: 91 Copynumber: 2.9 Consensus size: 90
54152915 TAAAAAGTCT
*
54152925 TCAAACTTAAAAAAAGAAATAAAGCAATTAAGCCCCTTTTTTTTTGCACTCAATTGAGCACTTGA
1 TCAAACTTAAAAAAAGAAAT-AAGCAATTAAGCCCCTTTTTTTTTACACTCAATTGAGCACTTGA
*
54152990 ACTTTTAAAATACATCAAAAAGGCCC
65 ACTTTCAAAATACATCAAAAAGGCCC
* * * *
54153016 TCAAACTTAAAAAAAG-AAGAAGCAATTAAGCCCCTCATTTTTTTTATACTCAATTAAGCACTTA
1 TCAAACTTAAAAAAAGAAATAAGCAATTAAGCCCCT--TTTTTTTTACACTCAATTGAGCACTTG
*
54153080 AACTTTCAAAATCCATCAAAAAGGCCC
64 AACTTTCAAAATACATCAAAAAGGCCC
*** * * * * *
54153107 TCAAACTTCTTAAAA-AAAT-A--AATTAAGCCTCTTCTTTATTTTTCCACCCAATTGGGTACTT
1 TCAAACTTAAAAAAAGAAATAAGCAATTAAGCC-C--CTTTTTTTTTACACTCAATTGAGCACTT
*
54153168 GAACTTTCAAAATGCATCAAAAA
63 GAACTTTCAAAATACATCAAAAA
54153191 AATCCTCAAA
Statistics
Matches: 149, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
88 9 0.06
89 57 0.38
90 3 0.02
91 80 0.54
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (90 bp):
TCAAACTTAAAAAAAGAAATAAGCAATTAAGCCCCTTTTTTTTTACACTCAATTGAGCACTTGAA
CTTTCAAAATACATCAAAAAGGCCC
Found at i:54153302 original size:29 final size:27
Alignment explanation
Indices: 54153269--54153575 Score: 170
Period size: 29 Copynumber: 10.9 Consensus size: 27
54153259 AAATAATAAA
54153269 TAATAAAATTTAGAATAATTATTAAATTT
1 TAATAAAATTTA-AA-AATTATTAAATTT
* *
54153298 TAATAAAAATTTAAAAATTTATTAAAAAATA
1 TAAT-AAAATTTAAAAA-TTATT--AAATTT
* * *
54153329 GAAAAAAATTATAAAAA-TAATAAA---
1 TAATAAAATT-TAAAAATTATTAAATTT
54153353 TAATAAAATTTAGAATAATTATTAAATTT
1 TAATAAAATTTA-AA-AATTATTAAATTT
* *
54153382 TAATAAAAATTTAAAAATTTATTAAAAAATA
1 TAAT-AAAATTTAAAAA-TTATT--AAATTT
* * *
54153413 GAAAAAAATTATAAAAA-TAATAAA---
1 TAATAAAATT-TAAAAATTATTAAATTT
54153437 TAATAAAATTTAGAATAATTATTAAATTT
1 TAATAAAATTTA-AA-AATTATTAAATTT
* *
54153466 TAATAAAAATTTAAAAATTTATTAAAAAATA
1 TAAT-AAAATTTAAAAA-TTATT--AAATTT
* * *
54153497 GAAAAAAATTATAAAAA-TAATAAA---
1 TAATAAAATT-TAAAAATTATTAAATTT
54153521 TAATAAAATTTAGAATAATTATTAAATTT
1 TAATAAAATTTA-AA-AATTATTAAATTT
54153550 TAATAAAAATTTAAAAATTTATTAAA
1 TAAT-AAAATTTAAAAA-TTATTAAA
54153576 AAATAGATTT
Statistics
Matches: 219, Mismatches: 24, Indels: 70
0.70 0.08 0.22
Matches are distributed among these distances:
23 6 0.03
24 30 0.14
25 6 0.03
26 18 0.08
27 9 0.04
28 8 0.04
29 56 0.26
30 50 0.23
31 36 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
TAATAAAATTTAAAAATTATTAAATTT
Found at i:54153612 original size:84 final size:84
Alignment explanation
Indices: 54153232--54153582 Score: 702
Period size: 84 Copynumber: 4.2 Consensus size: 84
54153222 GCCCATGCTC
54153232 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
1 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
54153297 TTAATAAAAATTTAAAAAT
66 TTAATAAAAATTTAAAAAT
54153316 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
1 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
54153381 TTAATAAAAATTTAAAAAT
66 TTAATAAAAATTTAAAAAT
54153400 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
1 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
54153465 TTAATAAAAATTTAAAAAT
66 TTAATAAAAATTTAAAAAT
54153484 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
1 TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
54153549 TTAATAAAAATTTAAAAAT
66 TTAATAAAAATTTAAAAAT
54153568 TTATTAAAAAATAGA
1 TTATTAAAAAATAGA
54153583 TTTTTTTTAT
Statistics
Matches: 267, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
84 267 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (84 bp):
TTATTAAAAAATAGAAAAAAATTATAAAAATAATAAATAATAAAATTTAGAATAATTATTAAATT
TTAATAAAAATTTAAAAAT
Found at i:54169985 original size:16 final size:16
Alignment explanation
Indices: 54169964--54169999 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
54169954 TTTAAAAAGC
54169964 TTTAAAATTATAATTA
1 TTTAAAATTATAATTA
54169980 TTTAAAATTATAATTA
1 TTTAAAATTATAATTA
54169996 TTTA
1 TTTA
54170000 GGGAATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAAAATTATAATTA
Found at i:54190854 original size:31 final size:32
Alignment explanation
Indices: 54190819--54190889 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 32
54190809 ATTGTTTAAG
54190819 ATTTTTTTA-ATTATTTAACGATAT-T-TTAATA
1 ATTTTTTTATATTA-TTAA-GATATATGTTAATA
*
54190850 A-TTTTTTATATTATTAATATATAATGTTAATA
1 ATTTTTTTATATTATTAAGATAT-ATGTTAATA
54190882 ATTTTTTT
1 ATTTTTTT
54190890 TTCTTAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
29 4 0.12
30 11 0.32
31 6 0.18
32 7 0.21
33 6 0.18
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (32 bp):
ATTTTTTTATATTATTAAGATATATGTTAATA
Found at i:54197749 original size:19 final size:19
Alignment explanation
Indices: 54197714--54197756 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
54197704 AATAATACTT
54197714 GAAAATATTAGAAAAATGA
1 GAAAATATTAGAAAAATGA
54197733 -AAAATTATTA-AATAAATGA
1 GAAAA-TATTAGAA-AAATGA
54197752 GAAAA
1 GAAAA
54197757 CGGAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 6 0.29
19 11 0.52
20 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.12, T:0.23
Consensus pattern (19 bp):
GAAAATATTAGAAAAATGA
Found at i:54237217 original size:41 final size:40
Alignment explanation
Indices: 54237116--54237218 Score: 100
Period size: 42 Copynumber: 2.5 Consensus size: 40
54237106 GTTTAGTTAT
* * **
54237116 TAATAATTATTGTTACTTAG-TATTATTATTAGTAAAAAAC
1 TAATTATTATT-TTAGTTAGTTATTAGGATTAGTAAAAAAC
* * *
54237156 TAATATTATTATCTTGGTTAGTTATTAGGATTAGTAAAAATCC
1 T-A-ATTATTATTTTAGTTAGTTATTAGGATTAGTAAAAA-AC
54237199 TAATTATTATTTTAGTTAGT
1 TAATTATTATTTTAGTTAGT
54237219 ATGATTGTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
40 1 0.02
41 23 0.46
42 24 0.48
43 2 0.04
ACGTcount: A:0.37, C:0.05, G:0.11, T:0.48
Consensus pattern (40 bp):
TAATTATTATTTTAGTTAGTTATTAGGATTAGTAAAAAAC
Found at i:54237290 original size:96 final size:96
Alignment explanation
Indices: 54237177--54237359 Score: 330
Period size: 96 Copynumber: 1.9 Consensus size: 96
54237167 TCTTGGTTAG
* * *
54237177 TTATTAGGATTAGTAAAAATCCTAATTATTATTTTAGTTAGTATGATTGTTAGTTTTTACATTAT
1 TTATTAGGATTAATAAAAACCCTAATTATTATTTTAGTTAGTATGACTGTTAGTTTTTACATTAT
54237242 ATTATTGTTAGTTATTATTTTTAGTAAAACC
66 ATTATTGTTAGTTATTATTTTTAGTAAAACC
*
54237273 TTATTAGGATTAATAAAAACCCTAATTATTATTTTAGTTGGTATGACTGTTAGTTTTTACATTAT
1 TTATTAGGATTAATAAAAACCCTAATTATTATTTTAGTTAGTATGACTGTTAGTTTTTACATTAT
54237338 ATTATTGTTAGTTATTATTTTT
66 ATTATTGTTAGTTATTATTTTT
54237360 TTCTCCGGAT
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
96 83 1.00
ACGTcount: A:0.31, C:0.05, G:0.11, T:0.52
Consensus pattern (96 bp):
TTATTAGGATTAATAAAAACCCTAATTATTATTTTAGTTAGTATGACTGTTAGTTTTTACATTAT
ATTATTGTTAGTTATTATTTTTAGTAAAACC
Found at i:54237946 original size:24 final size:24
Alignment explanation
Indices: 54237919--54237964 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
54237909 TTTCTTTCTT
54237919 TTTCCTTCCCTCTTCTTCTTCTCC
1 TTTCCTTCCCTCTTCTTCTTCTCC
* * *
54237943 TTTCCTTTCCTTTTCTTTTTCT
1 TTTCCTTCCCTCTTCTTCTTCT
54237965 TTCTTTCTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCCTTCCCTCTTCTTCTTCTCC
Found at i:54245694 original size:29 final size:27
Alignment explanation
Indices: 54245643--54245708 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
54245633 TTTTTTCCTG
54245643 AAAATTTTAATTAAGCTCACAAAATTTT
1 AAAATTTTAATTAAGCTCAC-AAATTTT
*
54245671 AAAAGTTTTAATT-AGACTCTCAAATTTT
1 AAAA-TTTTAATTAAG-CTCACAAATTTT
54245699 ATTAAATTTT
1 A--AAATTTT
54245709 TTTTCATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
28 14 0.42
29 16 0.48
30 3 0.09
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (27 bp):
AAAATTTTAATTAAGCTCACAAATTTT
Found at i:54252240 original size:17 final size:18
Alignment explanation
Indices: 54252218--54252255 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
54252208 ATTTGTGGGG
54252218 TTTTCTT-TTCTTT-CTCT
1 TTTTCTTCTT-TTTACTCT
54252235 TTTTCTTCTTTTTACTCT
1 TTTTCTTCTTTTTACTCT
54252253 TTT
1 TTT
54252256 AAATGGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTCTTCTTTTTACTCT
Found at i:54256988 original size:9 final size:9
Alignment explanation
Indices: 54256974--54257040 Score: 55
Period size: 10 Copynumber: 7.0 Consensus size: 9
54256964 ATTATTAATC
54256974 TAATTTTTT
1 TAATTTTTT
54256983 TAA-TTTTT
1 TAATTTTTT
54256991 TAATTTTCTT
1 TAATTTT-TT
54257001 TATATATTTTT
1 TA-AT-TTTTT
*
54257012 TAGTTTTTTT
1 TA-ATTTTTT
* *
54257022 TGAAATTTTA
1 T-AATTTTTT
54257032 TAATTTTTT
1 TAATTTTTT
54257041 AAAANNNNNN
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
8 8 0.17
9 12 0.26
10 15 0.33
11 8 0.17
12 3 0.07
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.72
Consensus pattern (9 bp):
TAATTTTTT
Found at i:54257029 original size:20 final size:20
Alignment explanation
Indices: 54256984--54257040 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
54256974 TAATTTTTTT
54256984 AATTTTTTAATTTTCTTTATA
1 AATTTTTTAATTTT-TTTATA
* *
54257005 TATTTTTTAGTTTTTTT-TGA
1 AATTTTTTAATTTTTTTAT-A
*
54257025 AATTTTATAATTTTTT
1 AATTTTTTAATTTTTT
54257041 AAAANNNNNN
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 1 0.03
20 17 0.57
21 12 0.40
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (20 bp):
AATTTTTTAATTTTTTTATA
Found at i:54257381 original size:19 final size:18
Alignment explanation
Indices: 54257339--54257381 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
54257329 AGATTTTGGA
* *
54257339 ATTTTTATAAATATTTTT
1 ATTTTTAAAAATATTTTG
*
54257357 AATTTTAAAAATTATTTTG
1 ATTTTTAAAAA-TATTTTG
54257376 ATTTTT
1 ATTTTT
54257382 TTTTTTGTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
ATTTTTAAAAATATTTTG
Found at i:54262047 original size:31 final size:32
Alignment explanation
Indices: 54262001--54262062 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
54261991 AAATCATCAC
*
54262001 TAAACTATTCGAAAG-TTTTTATTTAAGTCGG
1 TAAACTATTCAAAAGTTTTTTATTTAAGTCGG
*
54262032 TAAATTATTCAAAAGTTTTTTTATTTAAGTC
1 TAAACTATTCAAAAG-TTTTTTATTTAAGTC
54262063 ATTGGGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 13 0.48
33 14 0.52
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (32 bp):
TAAACTATTCAAAAGTTTTTTATTTAAGTCGG
Found at i:54267025 original size:16 final size:16
Alignment explanation
Indices: 54267004--54267036 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54266994 ATATTACTGA
*
54267004 AATGGAGTAGAAATGT
1 AATGGAATAGAAATGT
54267020 AATGGAATAGAAATGT
1 AATGGAATAGAAATGT
54267036 A
1 A
54267037 CATACATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.27, T:0.24
Consensus pattern (16 bp):
AATGGAATAGAAATGT
Found at i:54268685 original size:16 final size:16
Alignment explanation
Indices: 54268666--54268702 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
54268656 CTCGGCCCTG
54268666 AAGCTCCTCTCATACA
1 AAGCTCCTCTCATACA
54268682 AAGCTCCTCTCATACA
1 AAGCTCCTCTCATACA
54268698 AAGCT
1 AAGCT
54268703 TTCAATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.35, G:0.08, T:0.24
Consensus pattern (16 bp):
AAGCTCCTCTCATACA
Found at i:54271440 original size:2 final size:2
Alignment explanation
Indices: 54271435--54271472 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
54271425 TTTCATCACA
54271435 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
54271473 CAATTTCTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54273235 original size:2 final size:2
Alignment explanation
Indices: 54273230--54273256 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
54273220 TTACAAGTTT
54273230 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
54273257 TGTTAGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:54277797 original size:4 final size:4
Alignment explanation
Indices: 54277790--54277829 Score: 55
Period size: 4 Copynumber: 10.0 Consensus size: 4
54277780 GAATAAATAA
*
54277790 AAAG AAAG AAAG AAAG AAAG AAAAG AAA- AAGG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG AAAG AAAG
54277830 GAAGGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 2 0.06
4 26 0.81
5 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:54277840 original size:20 final size:20
Alignment explanation
Indices: 54277796--54277840 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
54277786 ATAAAAAGAA
54277796 AGAAA-GAAAGAAAGAAAAG
1 AGAAAGGAAAGAAAGAAAAG
* * *
54277815 AAAAAGGAAAGAAAGGAAGG
1 AGAAAGGAAAGAAAGAAAAG
54277835 AGAAAG
1 AGAAAG
54277841 CCACGACCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AGAAAGGAAAGAAAGAAAAG
Found at i:54279743 original size:17 final size:17
Alignment explanation
Indices: 54279721--54279754 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54279711 TTAAATATTC
*
54279721 AATTGTGCCTATTATAT
1 AATTGTGCCGATTATAT
*
54279738 AATTGTTCCGATTATAT
1 AATTGTGCCGATTATAT
54279755 TATTTTGTCT
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:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (17 bp):
AATTGTGCCGATTATAT
Found at i:54280547 original size:151 final size:152
Alignment explanation
Indices: 54280287--54280591 Score: 578
Period size: 151 Copynumber: 2.0 Consensus size: 152
54280277 ACATGGGAAG
54280287 ACAAAATAGACACAAAAATCACATCACCAATTGCTTGTTCTCTCCCTCTTTGCAGTCAATATATT
1 ACAAAATAGA-ACAAAAATCACATCACCAATTGCTTGTTCTCTCCCTCTTTGCAGTCAATATATT
54280352 GCATGTACTTTTATGTATTTATTTTTTAAATATTAAAAATATTAATTATTTTAATAATTTAAATA
65 GCATGTACTTTTATGTATTTATTTTTTAAATATTAAAAATATTAATTATTTTAATAATTTAAATA
54280417 ATTTAAATATTACAATAATAAAA
130 ATTTAAATATTACAATAATAAAA
54280440 ACAAAATAG-ACAAAAATCACATCACCAATTGCTTGTTCTCTCCCTCTTTGCAGTCAATATATTG
1 ACAAAATAGAACAAAAATCACATCACCAATTGCTTGTTCTCTCCCTCTTTGCAGTCAATATATTG
54280504 CATGTACTTTTATGTATTTATTTTTTATAA-ATTAAAAATATTAATTATTTTAATAATTTAAATA
66 CATGTACTTTTATGTATTTATTTTTTA-AATATTAAAAATATTAATTATTTTAATAATTTAAATA
54280568 ATTTAAATATTACAATAATAAAA
130 ATTTAAATATTACAATAATAAAA
54280591 A
1 A
54280592 TTCNNNNNNN
Statistics
Matches: 151, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
151 140 0.93
152 2 0.01
153 9 0.06
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (152 bp):
ACAAAATAGAACAAAAATCACATCACCAATTGCTTGTTCTCTCCCTCTTTGCAGTCAATATATTG
CATGTACTTTTATGTATTTATTTTTTAAATATTAAAAATATTAATTATTTTAATAATTTAAATAA
TTTAAATATTACAATAATAAAA
Found at i:54280559 original size:26 final size:26
Alignment explanation
Indices: 54280525--54280578 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
54280515 ATGTATTTAT
* *
54280525 TTTTTATAAATTAAA-AATATTAATTA
1 TTTTAATAAATTAAATAAT-TTAAATA
*
54280551 TTTTAATAATTTAAATAATTTAAATA
1 TTTTAATAAATTAAATAATTTAAATA
54280577 TT
1 TT
54280579 ACAATAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TTTTAATAAATTAAATAATTTAAATA
Found at i:54290183 original size:18 final size:18
Alignment explanation
Indices: 54290110--54290175 Score: 62
Period size: 18 Copynumber: 3.7 Consensus size: 18
54290100 TCCAATATCC
* * *
54290110 CGCTCTCGATCACGCTCC
1 CGCTCTCTATCACGATCA
* *
54290128 CGCTCCCTAT-AGCGCTCA
1 CGCTCTCTATCA-CGATCA
*
54290146 CGGTCTCTATCACGATCA
1 CGCTCTCTATCACGATCA
54290164 CGCTCTCTATCA
1 CGCTCTCTATCA
54290176 TGGTCACGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 1 0.03
18 37 0.95
19 1 0.03
ACGTcount: A:0.17, C:0.42, G:0.15, T:0.26
Consensus pattern (18 bp):
CGCTCTCTATCACGATCA
Found at i:54293438 original size:4 final size:4
Alignment explanation
Indices: 54293429--54293458 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
54293419 AATAATGAGC
54293429 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
54293459 AGGAATCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:54298566 original size:24 final size:24
Alignment explanation
Indices: 54298506--54298600 Score: 64
Period size: 24 Copynumber: 4.0 Consensus size: 24
54298496 ACGGTTGCGG
* * * *
54298506 TCACGTTCTCGATAATGGTCACGA
1 TCACGCTCTCGATAACGCTCACGC
* * *
54298530 TCAGGATCACGATAACGCTCACGC
1 TCACGCTCTCGATAACGCTCACGC
** *
54298554 TCACGCTCTCGATCCCGCTCCCGC
1 TCACGCTCTCGATAACGCTCACGC
* * * *
54298578 TCCCTCTCCCTATAACGCTCACG
1 TCACGCTCTCGATAACGCTCACG
54298601 GTCTCTATCA
Statistics
Matches: 52, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 52 1.00
ACGTcount: A:0.20, C:0.40, G:0.17, T:0.23
Consensus pattern (24 bp):
TCACGCTCTCGATAACGCTCACGC
Found at i:54298608 original size:18 final size:18
Alignment explanation
Indices: 54298587--54298626 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
54298577 CTCCCTCTCC
*
54298587 CTATAACGCTCACGGTCT
1 CTATAACGATCACGGTCT
*
54298605 CTATCACGATCACGGTCT
1 CTATAACGATCACGGTCT
54298623 CTAT
1 CTAT
54298627 CATGGTCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.30
Consensus pattern (18 bp):
CTATAACGATCACGGTCT
Found at i:54302438 original size:31 final size:32
Alignment explanation
Indices: 54302400--54302464 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
54302390 GGTAAGACAT
54302400 TTTCCACAGCTCATC-TCCACTCTCTTCACCC
1 TTTCCACAGCTCATCTTCCACTCTCTTCACCC
* *
54302431 TTTCCACAGCTCCTCTTTTCACTCTCTTCACCC
1 TTTCCACAGCTCATC-TTCCACTCTCTTCACCC
54302464 T
1 T
54302465 AACGATTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 14 0.47
33 16 0.53
ACGTcount: A:0.14, C:0.46, G:0.03, T:0.37
Consensus pattern (32 bp):
TTTCCACAGCTCATCTTCCACTCTCTTCACCC
Found at i:54303431 original size:20 final size:20
Alignment explanation
Indices: 54303406--54303445 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
54303396 AATATTTTCC
*
54303406 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
54303426 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
54303446 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:54303464 original size:14 final size:15
Alignment explanation
Indices: 54303426--54303468 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
54303416 TTTACAGAAA
*
54303426 AGTAAAACATTTTCC
1 AGTAAAACATTTTAC
*
54303441 AG-AAATCATTTTAC
1 AGTAAAACATTTTAC
54303455 -GTAAAACATTTTAC
1 AGTAAAACATTTTAC
54303469 TGGCAATCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 1 0.04
14 21 0.88
15 2 0.08
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.35
Consensus pattern (15 bp):
AGTAAAACATTTTAC
Done.