Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 138 of 204
Found at i:41861880 original size:22 final size:22
Alignment explanation
Indices: 41861853--41861955 Score: 76
Period size: 22 Copynumber: 4.7 Consensus size: 22
41861843 ATTAACAAAG
41861853 TTATGTAATTTATGTA-TAATA
1 TTATGTAATTTATGTATTAATA
41861874 TTAATGTAA-TTA-GTTATGTAAT-
1 TT-ATGTAATTTATG-TAT-TAATA
* *
41861896 TTATGTATATTAAT-TAATTAA-G
1 TTATGTA-ATTTATGT-ATTAATA
41861918 TTATGTAATTTATGTA-TAATA
1 TTATGTAATTTATGTATTAATA
*
41861939 TTAATGTAAGTTATGTA
1 TT-ATGTAATTTATGTA
41861956 ATTTATGAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 23
0.71 0.04 0.25
Matches are distributed among these distances:
20 4 0.06
21 20 0.30
22 34 0.52
23 8 0.12
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (22 bp):
TTATGTAATTTATGTATTAATA
Found at i:41861961 original size:62 final size:62
Alignment explanation
Indices: 41861837--41862233 Score: 434
Period size: 62 Copynumber: 6.2 Consensus size: 62
41861827 GTTATGTATA
**
41861837 ATATTAATTAACAAAGTTATGTAATTTATGTATAATATTAATGTAATTAGTTATGTAATTTATGT
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGT-A--AGTTATGTAATTTATGT
*
41861902 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGA
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGT
** *
41861964 ATAATTATAAAAATGTAAGTTATGTAAGTTGTAAGTTATGTATAATATTAATTAATTAAGTTATG
1 AT-ATTA-ATTAAT-TAAGTTATGTAA----T---TTATGTATAATATTAA-T--GTAAGTTATG
41862029 TAATTTATGT
53 TAATTTATGT
* ** *
41862039 ATAAT-ATTAATGTAAGCAATGTAATTTATGTGTAATACTTAAT-TAAGTTATGTAATTTATGT
1 ATATTAATTAAT-TAAGTTATGTAATTTATGTATAATA-TTAATGTAAGTTATGTAATTTATGT
* * *
41862101 ATAAT-ACTAATGTAAGTTATGTAATTTATGTATAATATTAATGCAAGTTATGT-A--TA---
1 ATATTAATTAAT-TAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGT
*
41862157 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAACTTATGTAATTTATGT
1 ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGT
41862219 ATATTAATTAATTAA
1 ATATTAATTAATTAA
41862234 ATGATATGTA
Statistics
Matches: 288, Mismatches: 22, Indels: 47
0.81 0.06 0.13
Matches are distributed among these distances:
56 43 0.15
57 6 0.02
59 4 0.01
61 6 0.02
62 94 0.33
63 4 0.01
64 5 0.02
65 66 0.23
66 4 0.01
68 1 0.00
69 1 0.00
72 31 0.11
73 1 0.00
74 2 0.01
75 20 0.07
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.47
Consensus pattern (62 bp):
ATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAATGTAAGTTATGTAATTTATGT
Found at i:41862003 original size:41 final size:43
Alignment explanation
Indices: 41861942--41862039 Score: 114
Period size: 41 Copynumber: 2.3 Consensus size: 43
41861932 TATAATATTA
*
41861942 ATGTAAGTTATGTAATTTATGAATAAT-TATAA-AAATGTAAGTT
1 ATGTAAGTTATGTAAGTTATGAATAATAT-TAATAAAT-TAAGTT
* *
41861985 ATGTAAG-T-TGTAAGTTATGTATAATATTAATTAATTAAGTT
1 ATGTAAGTTATGTAAGTTATGAATAATATTAATAAATTAAGTT
*
41862026 ATGTAATTTATGTA
1 ATGTAAGTTATGTA
41862040 TAATATTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
41 30 0.64
42 6 0.13
43 11 0.23
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (43 bp):
ATGTAAGTTATGTAAGTTATGAATAATATTAATAAATTAAGTT
Found at i:41863494 original size:84 final size:83
Alignment explanation
Indices: 41863346--41863603 Score: 239
Period size: 76 Copynumber: 3.2 Consensus size: 83
41863336 TCGTAAAGGC
* * *
41863346 AAAACGGCACCGTTTTGTTTAAAAAACCCGAAACTTTGCGGCGTTTTCACCATAGCGCCACTAAT
1 AAAACGACACCGTTTGGTTTAAAAAACCCGAAACTTTGCGGCGTTTTCACCATAGCACCACTAAT
* *
41863411 GTCGTTAATGTGCCAGGG
66 GCCCTTAATGTGCCAGGG
*
41863429 AAAACGACACCGTTTGGTTTAAAAAACCCGAAAACTTTGCGGCGCTTTT-ACCATTGCACCACTA
1 AAAACGACACCGTTTGGTTTAAAAAACCCG-AAACTTTGCGGCG-TTTTCACCATAGCACCACTA
41863493 ATGCCCTTAA--TG-C----
64 ATGCCCTTAATGTGCCAGGG
** * * ** * ***
41863506 -AAACGACACCGTTTCATTAAAAAAACCCCGGCAA-TTTGCGGCGTTTTCGGCGTAATGCCACTA
1 AAAACGACACCGTTTGGTTTAAAAAA-CCC-GAAACTTTGCGGCGTTTTCACCATAGCACCACTA
* * *
41863569 ATGCCGTTAATATGCCAGGC
64 ATGCCCTTAATGTGCCAGGG
41863589 AAAACGACACCGTTT
1 AAAACGACACCGTTT
41863604 TGTTCACAAA
Statistics
Matches: 144, Mismatches: 18, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
75 4 0.03
76 48 0.33
77 5 0.03
78 3 0.02
79 1 0.01
81 1 0.01
82 2 0.01
83 28 0.19
84 48 0.33
85 4 0.03
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (83 bp):
AAAACGACACCGTTTGGTTTAAAAAACCCGAAACTTTGCGGCGTTTTCACCATAGCACCACTAAT
GCCCTTAATGTGCCAGGG
Found at i:41864018 original size:20 final size:20
Alignment explanation
Indices: 41863973--41864025 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
41863963 AAAAATTAAA
*
41863973 AATTTTAGAGTTTTTATATTT
1 AATTTT-GATTTTTTATATTT
*
41863994 CATTTTGATTTTTGTAT-TTT
1 AATTTTGATTTTT-TATATTT
*
41864014 AATTTTAATTTT
1 AATTTTGATTTT
41864026 AATTTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 19 0.70
21 8 0.30
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.66
Consensus pattern (20 bp):
AATTTTGATTTTTTATATTT
Found at i:41864405 original size:15 final size:17
Alignment explanation
Indices: 41864366--41864398 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41864356 CTAACCCGAC
41864366 CCTCTTAAAACCCTAAA
1 CCTCTTAAAACCCTAAA
*
41864383 CCTCTTAAATCCCTAA
1 CCTCTTAAAACCCTAA
41864399 CTCTTAACCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.27
Consensus pattern (17 bp):
CCTCTTAAAACCCTAAA
Found at i:41864487 original size:14 final size:15
Alignment explanation
Indices: 41864468--41864498 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
41864458 GACCAACCCT
41864468 TAATCCCT-AATCCA
1 TAATCCCTAAATCCA
41864482 TAATCCCTAAATCCA
1 TAATCCCTAAATCCA
41864497 TA
1 TA
41864499 TATATATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (15 bp):
TAATCCCTAAATCCA
Found at i:41865290 original size:41 final size:42
Alignment explanation
Indices: 41865204--41865293 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 42
41865194 AATGTTTTTA
* *
41865204 GCGGCGC-TTAAGCAGAAACGCCGTGAAAACCTAGAACATTT
1 GCGGCGCTTTAAGCAAAAACGCCGTGAAAACCTAGAACATTC
* **
41865245 GCGGCGCTTTAA-CAAAAACGCCGCT-AAAACCTATATTATTC
1 GCGGCGCTTTAAGCAAAAACGCCG-TGAAAACCTAGAACATTC
41865286 GCGGCGCT
1 GCGGCGCT
41865294 AATCTAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
41 37 0.88
42 5 0.12
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (42 bp):
GCGGCGCTTTAAGCAAAAACGCCGTGAAAACCTAGAACATTC
Found at i:41865781 original size:32 final size:31
Alignment explanation
Indices: 41865736--41865831 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
41865726 CTTAGATAAT
41865736 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41865767 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
41865799 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41865830 TT
1 TT
41865832 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:41872106 original size:32 final size:31
Alignment explanation
Indices: 41872061--41872156 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
41872051 CTTAGATAAT
41872061 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41872092 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
41872124 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
41872155 TT
1 TT
41872157 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:41872810 original size:114 final size:113
Alignment explanation
Indices: 41872605--41872962 Score: 610
Period size: 114 Copynumber: 3.1 Consensus size: 113
41872595 NNNNNNNNNN
*
41872605 ACGCCGCTAATACTCATATTATTAGCGGCGCTATT-AGAAAAACGCCACTAAAGTCACCGAAGTG
1 ACGCCGCTAATACTCATATTATTAGCGGCGCTATTCA-AAAAACGCCACTAATGTCACCGAAGTG
41872669 TCTCCAAACGACGTCGTCTGGGGTTTAGTTTTTGCGGCATTTTTATAGAA
65 TCTCCAAACGACGTCGTCT-GGGTTTAGTTTTTGCGGCATTTTTATAGAA
* *
41872719 ACGTCGCTAATACTCATATTATTAGCGGTGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGT
1 ACGCCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGT
*
41872784 CTCCAAACGACGTCGTCTGGGTTTTAGTTTTTGCGGCATTTTTACAGAA
66 CTCCAAACGACGTCGTCTGGG-TTTAGTTTTTGCGGCATTTTTATAGAA
* *
41872833 ACGCCGCTAATACTCATATTATTAGCGGCGCTATTCGAAAAACGCCACTAATGTCACCGAAGTTT
1 ACGCCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGT
*
41872898 CTCCAAACGACGTCGTCTGGGTTTAGTTTTTTGCGGCGTTTTTATAGAA
66 CTCCAAACGACGTCGTCTGGGTTTAG-TTTTTGCGGCATTTTTATAGAA
41872947 ACGCCGCTAATACTCA
1 ACGCCGCTAATACTCA
41872963 ATCGGTTGCG
Statistics
Matches: 231, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
113 8 0.03
114 222 0.96
115 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (113 bp):
ACGCCGCTAATACTCATATTATTAGCGGCGCTATTCAAAAAACGCCACTAATGTCACCGAAGTGT
CTCCAAACGACGTCGTCTGGGTTTAGTTTTTGCGGCATTTTTATAGAA
Found at i:41874330 original size:2 final size:2
Alignment explanation
Indices: 41874323--41874349 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41874313 TTTGTTCTTT
41874323 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
41874350 TCTAATTTTG
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:41875077 original size:26 final size:27
Alignment explanation
Indices: 41875044--41875095 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
41875034 TGAGTTGAGA
41875044 AGTTTATTTAATT-AAGAAATTAATTT
1 AGTTTATTTAATTAAAGAAATTAATTT
*
41875070 AGTTTATTTAATTAAATAAATTAATT
1 AGTTTATTTAATTAAAGAAATTAATT
41875096 GATTAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (27 bp):
AGTTTATTTAATTAAAGAAATTAATTT
Found at i:41878545 original size:43 final size:43
Alignment explanation
Indices: 41878492--41878722 Score: 345
Period size: 43 Copynumber: 5.3 Consensus size: 43
41878482 TTATAGAAAA
* *
41878492 AAACGCCGCTAAAGAGCAAGACCTTTAGCGGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
41878535 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
*
41878578 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCCCTTCTCTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* *
41878621 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
* * * * * * *
41878664 AAACGCCGTTAAAAACTAGGACCTTTAGCGGCGTTTCTATTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
41878707 AAACGCCGCTATAAGA
1 AAACGCCGCTA-AAGA
41878723 TTGACTTTTA
Statistics
Matches: 172, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
43 169 0.98
44 3 0.02
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCTCAC
Found at i:41878745 original size:86 final size:83
Alignment explanation
Indices: 41878492--41878761 Score: 281
Period size: 86 Copynumber: 3.2 Consensus size: 83
41878482 TTATAGAAAA
* * * **
41878492 AAACGCCGCTAAAGAGCAAGACCTTTAGCGGCGCTTCTCCCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAAACCAAGACCTTTAGCGGCCCTTCTATCACAAACGCCGCTAAAGA-CAAGAC
*
41878557 CTTTAGCGGCGCTTCTCTCAC
65 CTTTAGCGACGCTT-T-TCAC
* *
41878578 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCCCTTCTCTCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAAACCAAGACCTTTAGCGGCCCTTCTATCACAAACGCCGCTAAAGA-CAAGAC
*
41878643 CTTTAGCGGCGCTTTTCTTAC
65 CTTTAGCGACGCTTTTC--AC
* * * ** * **
41878664 AAACGCCGTTAAAAACTAGGACCTTTAGCGGCGTTTCTATTACAAACGCCGCTATAAGA-TTGAC
1 AAACGCCGCTAAAAACCAAGACCTTTAGCGGCCCTTCTATCACAAACGCCGCTA-AAGACAAGAC
* *
41878728 TTTTAGTGACGCTTTTTCAC
65 CTTTAGCGACGC-TTTTCAC
*
41878748 AAATGCCGCTAAAA
1 AAACGCCGCTAAAA
41878762 GCATAACTTT
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
84 16 0.10
85 13 0.08
86 129 0.80
87 4 0.02
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.23
Consensus pattern (83 bp):
AAACGCCGCTAAAAACCAAGACCTTTAGCGGCCCTTCTATCACAAACGCCGCTAAAGACAAGACC
TTTAGCGACGCTTTTCAC
Found at i:41883086 original size:21 final size:21
Alignment explanation
Indices: 41883060--41883105 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41883050 TGTGGGATGT
41883060 GGGAAA-TTAGGGATTTTAGGG
1 GGGAAAGTTAGGGA-TTTAGGG
* *
41883081 GGGAAAGTTGGGGATTTCGGG
1 GGGAAAGTTAGGGATTTAGGG
41883102 GGGA
1 GGGA
41883106 GGGGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.24, C:0.02, G:0.50, T:0.24
Consensus pattern (21 bp):
GGGAAAGTTAGGGATTTAGGG
Found at i:41883403 original size:148 final size:147
Alignment explanation
Indices: 41883130--41883396 Score: 396
Period size: 148 Copynumber: 1.8 Consensus size: 147
41883120 ATGGCGCGTG
* *
41883130 AAATTTTTATTTGTGGCTTTTTTATAAAAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTACA
1 AAATTATTATTTGTGGCTTTTTTATAAAAACGCCGCTATTGCTTACCTATTGCGGCGTTTTTACA
* ** *
41883195 AAAAACGCCGTAAAAAAATTATTTTGTTTGGAATAAAACGACACTGTGTTGTTATATAAAATGTC
66 AAAAACGCCGCAAAAAAATTATTTCATTTGGAATAAAACGACACTGTGTTGCTATATAAAATGTC
41883260 GTTATTTTTTTAAAGTA
131 GTTATTTTTTTAAAGTA
* * *
41883277 AAATTATT-TTTGTGGCGTTTTTTTATAAAAACGCTGCTATTGCTTACCTTTTGTGGCGTTTTT-
1 AAATTATTATTTGTGGC--TTTTTTATAAAAACGCCGCTATTGCTTACCTATTGCGGCGTTTTTA
*
41883340 CACAAAAACGCCGCAAAAAAA-TATTTCATTTGGAATAAAACGACACTGTTTTGCTAT
64 CA-AAAAACGCCGCAAAAAAATTATTTCATTTGGAATAAAACGACACTGTGTTGCTAT
41883397 GCTAAAAATC
Statistics
Matches: 107, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
146 8 0.07
147 41 0.38
148 58 0.54
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (147 bp):
AAATTATTATTTGTGGCTTTTTTATAAAAACGCCGCTATTGCTTACCTATTGCGGCGTTTTTACA
AAAAACGCCGCAAAAAAATTATTTCATTTGGAATAAAACGACACTGTGTTGCTATATAAAATGTC
GTTATTTTTTTAAAGTA
Found at i:41884324 original size:7 final size:7
Alignment explanation
Indices: 41884308--41884385 Score: 58
Period size: 7 Copynumber: 11.9 Consensus size: 7
41884298 ACTAATTAAT
*
41884308 CTAAATC
1 CTAAACC
41884315 CTAAACC
1 CTAAACC
41884322 CTAAACC
1 CTAAACC
41884329 CT-AACC
1 CTAAACC
41884335 CT-AACC
1 CTAAACC
41884341 CT-AACC
1 CTAAACC
41884347 CT-AACC
1 CTAAACC
* *
41884353 C-GACCC
1 CTAAACC
* *
41884359 CGAATCC
1 CTAAACC
*
41884366 CTAACCC
1 CTAAACC
*
41884373 CTAACCC
1 CTAAACC
41884380 CTAAAC
1 CTAAAC
41884386 GTTATTTAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
6 27 0.44
7 35 0.56
ACGTcount: A:0.35, C:0.47, G:0.03, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:41884336 original size:6 final size:6
Alignment explanation
Indices: 41884318--41884379 Score: 70
Period size: 6 Copynumber: 9.8 Consensus size: 6
41884308 CTAAATCCTA
* * *
41884318 AACCCT AAACCCT AACCCT AACCCT AACCCT AACCCG ACCCCG AATCCCT
1 AACCCT -AACCCT AACCCT AACCCT AACCCT AACCCT AACCCT AA-CCCT
41884368 AACCCCT AACCC
1 AA-CCCT AACCC
41884380 CTAAACGTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
6 32 0.65
7 17 0.35
ACGTcount: A:0.32, C:0.52, G:0.03, T:0.13
Consensus pattern (6 bp):
AACCCT
Found at i:41884538 original size:14 final size:15
Alignment explanation
Indices: 41884521--41884553 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
41884511 CTTAAATCAG
41884521 AATCCCT-ACTCCAT
1 AATCCCTAACTCCAT
*
41884535 AATCCCTAATTCCAT
1 AATCCCTAACTCCAT
41884550 AATC
1 AATC
41884554 TATAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (15 bp):
AATCCCTAACTCCAT
Found at i:41885125 original size:40 final size:40
Alignment explanation
Indices: 41885081--41885206 Score: 119
Period size: 40 Copynumber: 3.1 Consensus size: 40
41885071 TTTTTGAGGT
*
41885081 GTTTTTCCAAAAAACGCTGCTAATGCTC-ATTTTTAGCGGC
1 GTTTTT-CAAAAAGCGCTGCTAATGCTCAATTTTTAGCGGC
* * * * * * *
41885121 GTTTTTGAAAATGCGCCGCTAATGCTCGATCTTTACCAGC
1 GTTTTTCAAAAAGCGCTGCTAATGCTCAATTTTTAGCGGC
* ** * *
41885161 GTTTTACGTAAAGCGCTGGTAATGCTCAATTTTTGGCGGC
1 GTTTTTCAAAAAGCGCTGCTAATGCTCAATTTTTAGCGGC
41885201 GTTTTT
1 GTTTTT
41885207 TTCCAAACGC
Statistics
Matches: 65, Mismatches: 20, Indels: 2
0.75 0.23 0.02
Matches are distributed among these distances:
39 17 0.26
40 48 0.74
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
GTTTTTCAAAAAGCGCTGCTAATGCTCAATTTTTAGCGGC
Found at i:41907329 original size:19 final size:19
Alignment explanation
Indices: 41907305--41907352 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
41907295 TTCTTTTATC
41907305 TTTCTTCTTATCGTTT-CTT
1 TTTCTTCTTAT-GTTTACTT
41907324 TTTCTTCTT-TGTTTACCTT
1 TTTCTTCTTATGTTTA-CTT
41907343 TTTCTT-TTAT
1 TTTCTTCTTAT
41907353 TTCCTACCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.15
18 3 0.12
19 19 0.73
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (19 bp):
TTTCTTCTTATGTTTACTT
Found at i:41908056 original size:54 final size:54
Alignment explanation
Indices: 41907945--41908085 Score: 133
Period size: 54 Copynumber: 2.6 Consensus size: 54
41907935 TGTAACTCTC
* * * ** * *
41907945 TGACTTGAGTCACACGGGCGTGTG-TCAGGCCATGTGTCTGACCATGTAACTCTT
1 TGACTTGAGTCACACGGTCGTGTGCT-AGGCCATATGACAAACCATGTAACGCAT
*
41907999 TGACTTGAGTCACACGGTCGTGTGCTAGGCCATATGACAAACCGTGT-ACGGCAT
1 TGACTTGAGTCACACGGTCGTGTGCTAGGCCATATGACAAACCATGTAAC-GCAT
* * * * *
41908053 TGACATGAGCCACACAGTCATGTTCTAGGCCAT
1 TGACTTGAGTCACACGGTCGTGTGCTAGGCCAT
41908086 GTGAGCCGCA
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
53 2 0.03
54 69 0.96
55 1 0.01
ACGTcount: A:0.23, C:0.25, G:0.26, T:0.26
Consensus pattern (54 bp):
TGACTTGAGTCACACGGTCGTGTGCTAGGCCATATGACAAACCATGTAACGCAT
Found at i:41908702 original size:28 final size:28
Alignment explanation
Indices: 41908640--41908696 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
41908630 GTAGGACTTT
* *
41908640 GAATCTGTATCTGATATGCTCTGCATCT
1 GAATCTGTATCTGATATACTCTGCATCC
* *
41908668 GAATCTGTATCTGATATACTTTGCTTCC
1 GAATCTGTATCTGATATACTCTGCATCC
41908696 G
1 G
41908697 TTTCTGATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.18, T:0.40
Consensus pattern (28 bp):
GAATCTGTATCTGATATACTCTGCATCC
Found at i:41917664 original size:3 final size:3
Alignment explanation
Indices: 41917656--41917696 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
41917646 CAGAGAAGTG
*
41917656 GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA -AA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
41917697 CCTCACTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41918213 original size:129 final size:130
Alignment explanation
Indices: 41917950--41918230 Score: 350
Period size: 129 Copynumber: 2.2 Consensus size: 130
41917940 TTTGAATTTA
* * *
41917950 AGAAGAAATTGTTCATGATCATAAATCAATGAACTTAGGCTATGATCGTAAATCAACGAACCTTA
1 AGAAGAAAATGTTCATGATCATAAATCAATGAACATAGGCTATGATCCTAAATCAACGAACCTTA
* ** * *
41918015 ATAATAGCACTCATGATCGTAAATTAACAAGCTGGTTGGAGTTGCGATCGTAAATCAACTAACTT
66 ATAATAGCAATCATGATCGTAAACCAACAAGCTGGTTGAAGTTGCGATCGTAAATCAACTAACTC
* * * * * *
41918080 AGAAGAAAATGTTCATGATCGTAAATCAATGAACATAGGTTGTGATCCTAAAT-AGCGAGCCTTG
1 AGAAGAAAATGTTCATGATCATAAATCAATGAACATAGGCTATGATCCTAAATCAACGAACCTTA
* * ** * * *
41918144 ATAATATCAATCATGATTGTAAACCAATGAGTTGTTTGAAGTTGTGATCGTAAAT-AAGCTAACT
66 ATAATAGCAATCATGATCGTAAACCAACAAGCTGGTTGAAGTTGCGATCGTAAATCAA-CTAACT
41918208 C
130 C
41918209 AGAAGAAAATGTTCATGATCAT
1 AGAAGAAAATGTTCATGATCAT
41918231 TAATAAGCTT
Statistics
Matches: 128, Mismatches: 22, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
128 2 0.02
129 79 0.62
130 47 0.37
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.29
Consensus pattern (130 bp):
AGAAGAAAATGTTCATGATCATAAATCAATGAACATAGGCTATGATCCTAAATCAACGAACCTTA
ATAATAGCAATCATGATCGTAAACCAACAAGCTGGTTGAAGTTGCGATCGTAAATCAACTAACTC
Found at i:41920680 original size:13 final size:13
Alignment explanation
Indices: 41920662--41920686 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41920652 TAACTAAAAC
41920662 AACACATAAATAA
1 AACACATAAATAA
41920675 AACACATAAATA
1 AACACATAAATA
41920687 TCATATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (13 bp):
AACACATAAATAA
Found at i:41921430 original size:41 final size:41
Alignment explanation
Indices: 41921396--41921539 Score: 207
Period size: 41 Copynumber: 3.5 Consensus size: 41
41921386 ACCGGCACTT
* * *
41921396 AGCCTTCTAGACATAAAGTCTGATATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
*
41921437 AGCCTGCTAGACGTAAAGTTTGGTATGTTTCACCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
* * * *
41921478 AGCCTACTAGACGTAATGACTGGTATGTTTCATCGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
*
41921519 AGCCTGCTAGACGTAATGTCT
1 AGCCTGCTAGACGTAAAGTCT
41921540 AGATTACTTT
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGGTATGTTTCACCGGCATCA
Found at i:41926765 original size:28 final size:28
Alignment explanation
Indices: 41926732--41926870 Score: 172
Period size: 28 Copynumber: 5.0 Consensus size: 28
41926722 AAAATAAGAT
* *
41926732 AAAACTATAAAATCTAAAAAATAGTGTC
1 AAAACTGTAAAATCTAAAAAATAGTGGC
**
41926760 AAAACTGTAAAATCTAAAAACCAGTGGC
1 AAAACTGTAAAATCTAAAAAATAGTGGC
*
41926788 AAAACTGTAAAATCTAAAAAATAATGGC
1 AAAACTGTAAAATCTAAAAAATAGTGGC
* *
41926816 AAAATTGTAAAATTTGAAAAAA-AGTGGC
1 AAAACTGTAAAATCT-AAAAAATAGTGGC
* * *
41926844 AAAACTATAAAATCTGAAAAGTAGTGG
1 AAAACTGTAAAATCTAAAAAATAGTGG
41926871 ACACACGGTT
Statistics
Matches: 94, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
27 4 0.04
28 84 0.89
29 6 0.06
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (28 bp):
AAAACTGTAAAATCTAAAAAATAGTGGC
Found at i:41926799 original size:56 final size:56
Alignment explanation
Indices: 41926732--41926870 Score: 190
Period size: 56 Copynumber: 2.5 Consensus size: 56
41926722 AAAATAAGAT
* *
41926732 AAAACTATAAAATCTAAAAAATAGTGTCAAAACTGTAAAATCT-AAAAACCAGTGGC
1 AAAACTATAAAATCTAAAAAATAGTGGCAAAACTGTAAAATCTGAAAAA-AAGTGGC
* * * *
41926788 AAAACTGTAAAATCTAAAAAATAATGGCAAAATTGTAAAATTTGAAAAAAAGTGGC
1 AAAACTATAAAATCTAAAAAATAGTGGCAAAACTGTAAAATCTGAAAAAAAGTGGC
* *
41926844 AAAACTATAAAATCTGAAAAGTAGTGG
1 AAAACTATAAAATCTAAAAAATAGTGG
41926871 ACACACGGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
56 67 0.93
57 5 0.07
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (56 bp):
AAAACTATAAAATCTAAAAAATAGTGGCAAAACTGTAAAATCTGAAAAAAAGTGGC
Found at i:41930401 original size:18 final size:18
Alignment explanation
Indices: 41930374--41930409 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
41930364 TTTCAAAAAT
*
41930374 GCCGCGAAAGACCTGAGC
1 GCCGCGAAAGACCCGAGC
*
41930392 GCCGCTAAAGACCCGAGC
1 GCCGCGAAAGACCCGAGC
41930410 ATTAGTGGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.36, G:0.31, T:0.06
Consensus pattern (18 bp):
GCCGCGAAAGACCCGAGC
Found at i:41930523 original size:39 final size:40
Alignment explanation
Indices: 41930479--41930614 Score: 130
Period size: 40 Copynumber: 3.4 Consensus size: 40
41930469 TGGGCTTAGG
* *
41930479 TTTTTTGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTC-A
1 TTTTTAGCGGCG-TTTTCCAAAAAGCGCCGCTAATGCTCGA
** * ***
41930519 TTTTTCTCGGCGCTTTCCTGGAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
* * * **
41930559 TCTTTAGCAGCGTTTTACGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
*
41930599 TTTTTAGCGGCATTTT
1 TTTTTAGCGGCGTTTT
41930615 TTATCCAAAC
Statistics
Matches: 76, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
39 21 0.28
40 55 0.72
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.35
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCGA
Found at i:41933422 original size:3 final size:3
Alignment explanation
Indices: 41933416--41933466 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
41933406 AATATCATCA
41933416 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
41933464 TCT
1 TCT
41933467 GTTGTTAAAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:41934507 original size:13 final size:15
Alignment explanation
Indices: 41934479--41934510 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
41934469 AAGATTATAA
41934479 AAAGAGAGAGAGGGG
1 AAAGAGAGAGAGGGG
41934494 AAAGAGA-AGA-GGG
1 AAAGAGAGAGAGGGG
41934507 AAAG
1 AAAG
41934511 GAAATAAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 3 0.18
15 7 0.41
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (15 bp):
AAAGAGAGAGAGGGG
Found at i:41941082 original size:13 final size:13
Alignment explanation
Indices: 41941066--41941114 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
41941056 TTTCTGTAAT
41941066 TATTTTTTATTTA
1 TATTTTTTATTTA
*
41941079 TATTTTTTGTTT-
1 TATTTTTTATTTA
41941091 TCATTTATTTATTTA
1 T-ATTT-TTTATTTA
41941106 TATTTTTTA
1 TATTTTTTA
41941115 AAAACAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
12 1 0.03
13 19 0.61
14 10 0.32
15 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (13 bp):
TATTTTTTATTTA
Found at i:41941084 original size:27 final size:27
Alignment explanation
Indices: 41941054--41941113 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
41941044 ATTATTCCTT
41941054 TTTTTCTGTAATT-ATTT-TTTATTTATA
1 TTTTT-TGT-ATTCATTTATTTATTTATA
*
41941081 TTTTTTGTTTTCATTTATTTATTTATA
1 TTTTTTGTATTCATTTATTTATTTATA
41941108 TTTTTT
1 TTTTTT
41941114 AAAAACAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 2 0.07
26 7 0.23
27 21 0.70
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (27 bp):
TTTTTTGTATTCATTTATTTATTTATA
Found at i:41941186 original size:21 final size:20
Alignment explanation
Indices: 41941123--41941186 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 20
41941113 TAAAAACAAA
* *
41941123 TATTTTTATATGTATGTATATC
1 TATTTTTA-ATAT-TGTATATT
41941145 TATTTTTAATATTGTA-A-T
1 TATTTTTAATATTGTATATT
*
41941163 TATTATTTAATATTTTATATT
1 TATT-TTTAATATTGTATATT
41941184 TAT
1 TAT
41941187 ATACTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.11
19 12 0.33
20 5 0.14
21 7 0.19
22 8 0.22
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (20 bp):
TATTTTTAATATTGTATATT
Found at i:41945387 original size:20 final size:20
Alignment explanation
Indices: 41945309--41945392 Score: 75
Period size: 20 Copynumber: 4.2 Consensus size: 20
41945299 AATTCAACAT
*
41945309 GTATCGATACCTATATTGAA
1 GTATCGATACCTTTATTGAA
*
41945329 GTATCGATACCTTGACTAT-AA
1 GTATCGATACCTTTA-T-TGAA
*
41945350 -TATTGATA-CTTTGATTGAA
1 GTATCGATACCTTT-ATTGAA
* *
41945369 GTATCGATACCTTTCTTGAG
1 GTATCGATACCTTTATTGAA
41945389 GTAT
1 GTAT
41945393 AAATATTTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.02
19 6 0.12
20 36 0.71
21 7 0.14
22 1 0.02
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (20 bp):
GTATCGATACCTTTATTGAA
Found at i:41961574 original size:20 final size:20
Alignment explanation
Indices: 41961551--41961595 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41961541 TACAATGTTG
41961551 TAAGAAATTTAACAATCTTA
1 TAAGAAATTTAACAATCTTA
* * *
41961571 TAAGAAGTTTAATAATTTTA
1 TAAGAAATTTAACAATCTTA
41961591 TAAGA
1 TAAGA
41961596 TATCCAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (20 bp):
TAAGAAATTTAACAATCTTA
Found at i:41961660 original size:20 final size:20
Alignment explanation
Indices: 41961635--41961695 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
41961625 ATAATAAAGC
41961635 TGTAAGAAATTTTGTAATTT
1 TGTAAGAAATTTTGTAATTT
* **
41961655 TGTAAGAGATTTAATAATTT
1 TGTAAGAAATTTTGTAATTT
*
41961675 TGTCA-AAATTTTAGTAATTT
1 TGTAAGAAATTTT-GTAATTT
41961695 T
1 T
41961696 TGTTGTAATG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
19 5 0.15
20 28 0.85
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (20 bp):
TGTAAGAAATTTTGTAATTT
Found at i:41966266 original size:2 final size:2
Alignment explanation
Indices: 41966259--41966315 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
41966249 TTGAATACTA
*
41966259 TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
41966301 TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG T
41966316 ATTTGTATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:41968994 original size:23 final size:23
Alignment explanation
Indices: 41968968--41969041 Score: 94
Period size: 23 Copynumber: 3.1 Consensus size: 23
41968958 CAGCCATATG
41968968 TACCCTTCGAACACAACCAAATA
1 TACCCTTCGAACACAACCAAATA
*
41968991 TACCCTTCAAACACAACCATATATA
1 TACCCTTCGAACACAACCA-A-ATA
* * *
41969016 TAACCTCCGAACACAACCAAGTA
1 TACCCTTCGAACACAACCAAATA
41969039 TAC
1 TAC
41969042 TAAGCCAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
23 22 0.51
24 2 0.05
25 19 0.44
ACGTcount: A:0.43, C:0.34, G:0.04, T:0.19
Consensus pattern (23 bp):
TACCCTTCGAACACAACCAAATA
Found at i:41969028 original size:25 final size:23
Alignment explanation
Indices: 41968975--41969040 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 23
41968965 ATGTACCCTT
* *
41968975 CGAACACAACCAAATATACCCTT
1 CGAACACAACCAAATATAACCTC
*
41968998 CAAACACAACCATATATATAACCTC
1 CGAACACAACCA-A-ATATAACCTC
*
41969023 CGAACACAACCAAGTATA
1 CGAACACAACCAAATATA
41969041 CTAAGCCAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 15 0.42
24 2 0.06
25 19 0.53
ACGTcount: A:0.47, C:0.32, G:0.05, T:0.17
Consensus pattern (23 bp):
CGAACACAACCAAATATAACCTC
Found at i:41970505 original size:15 final size:14
Alignment explanation
Indices: 41970484--41970519 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
41970474 ATAATCCTTA
*
41970484 ATAATTATCTTAAT
1 ATAATTATCCTAAT
41970498 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
41970513 ATAATTA
1 ATAATTA
41970520 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:41971930 original size:36 final size:33
Alignment explanation
Indices: 41971882--41972022 Score: 102
Period size: 30 Copynumber: 4.4 Consensus size: 33
41971872 AATATTGAAA
*
41971882 ATATCTTAGATTTCTTATGCCAATATCTTGATACCC
1 ATATCTTTGATTTCTT-T-CCAATAT-TTGATACCC
41971918 ATATCTTTGA--T-TTTCCAATATTTGATACCC
1 ATATCTTTGATTTCTTTCCAATATTTGATACCC
* * *
41971948 ATATCTTTGA---CTTTCCATTATTTGACAACC
1 ATATCTTTGATTTCTTTCCAATATTTGATACCC
* * * *
41971978 ATATATTTGA---CTTTCCATTATTTGACAACC
1 ATATCTTTGATTTCTTTCCAATATTTGATACCC
*
41972008 ATATATTTGACTTTC
1 ATATCTTTGA-TTTC
41972023 CATAAATACG
Statistics
Matches: 95, Mismatches: 5, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
30 74 0.78
31 7 0.07
32 1 0.01
33 2 0.02
34 2 0.02
36 9 0.09
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (33 bp):
ATATCTTTGATTTCTTTCCAATATTTGATACCC
Found at i:41971945 original size:30 final size:30
Alignment explanation
Indices: 41971901--41972024 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
41971891 ATTTCTTATG
* * * *
41971901 CCAATATCTTGATACCCATATCTTTGATTTT
1 CCAATAT-TTGACAACCATATATTTGACTTT
* * *
41971932 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGACAACCATATATTTGACTTT
*
41971962 CCATTATTTGACAACCATATATTTGACTTT
1 CCAATATTTGACAACCATATATTTGACTTT
*
41971992 CCATTATTTGACAACCATATATTTGACTTT
1 CCAATATTTGACAACCATATATTTGACTTT
41972022 CCA
1 CCA
41972025 TAAATACGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGACAACCATATATTTGACTTT
Found at i:41971956 original size:15 final size:15
Alignment explanation
Indices: 41971904--41971957 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
41971894 TCTTATGCCA
41971904 ATATC-TTGATACCC
1 ATATCTTTGATACCC
**
41971918 ATATCTTTGATTTTCC
1 ATATCTTTGA-TACCC
*
41971934 A-ATATTTGATACCC
1 ATATCTTTGATACCC
41971948 ATATCTTTGA
1 ATATCTTTGA
41971958 CTTTCCATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
14 9 0.29
15 18 0.58
16 4 0.13
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.44
Consensus pattern (15 bp):
ATATCTTTGATACCC
Found at i:41971971 original size:15 final size:16
Alignment explanation
Indices: 41971916--41972026 Score: 99
Period size: 15 Copynumber: 7.3 Consensus size: 16
41971906 ATCTTGATAC
* *
41971916 CCATATCTTTGATTTT
1 CCATATATTTGACTTT
**
41971932 CCA-ATATTTGA-TAC
1 CCATATATTTGACTTT
*
41971946 CCATATCTTTGACTTT
1 CCATATATTTGACTTT
**
41971962 CCAT-TATTTGAC-AA
1 CCATATATTTGACTTT
41971976 CCATATATTTGACTTT
1 CCATATATTTGACTTT
**
41971992 CCAT-TATTTGAC-AA
1 CCATATATTTGACTTT
41972006 CCATATATTTGACTTT
1 CCATATATTTGACTTT
41972022 CCATA
1 CCATA
41972027 AATACGGATG
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
14 12 0.16
15 45 0.61
16 17 0.23
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (16 bp):
CCATATATTTGACTTT
Found at i:41972025 original size:30 final size:30
Alignment explanation
Indices: 41971916--41972025 Score: 166
Period size: 30 Copynumber: 3.7 Consensus size: 30
41971906 ATCTTGATAC
* * * * *
41971916 CCATATCTTTGATTTTCCAATATTTGATAC
1 CCATATATTTGACTTTCCATTATTTGACAA
*
41971946 CCATATCTTTGACTTTCCATTATTTGACAA
1 CCATATATTTGACTTTCCATTATTTGACAA
41971976 CCATATATTTGACTTTCCATTATTTGACAA
1 CCATATATTTGACTTTCCATTATTTGACAA
41972006 CCATATATTTGACTTTCCAT
1 CCATATATTTGACTTTCCAT
41972026 AAATACGGAT
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.27, C:0.22, G:0.06, T:0.45
Consensus pattern (30 bp):
CCATATATTTGACTTTCCATTATTTGACAA
Found at i:41976648 original size:30 final size:30
Alignment explanation
Indices: 41976602--41976695 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
41976592 ATTTCTTATG
* *
41976602 CCAATATCTCGATACCCATATCTTTGATTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
41976633 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
41976663 CCATTATTTGATAACCATATATTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
41976693 CCA
1 CCA
41976696 TAAATACGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:41976657 original size:15 final size:15
Alignment explanation
Indices: 41976612--41976658 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
41976602 CCAATATCTC
41976612 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
41976627 GATTTTCCA-ATATTT
1 GA-TACCCATATCTTT
41976642 GATACCCATATCTTT
1 GATACCCATATCTTT
41976657 GA
1 GA
41976659 CTTTCCATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.28, C:0.21, G:0.09, T:0.43
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:41976672 original size:15 final size:16
Alignment explanation
Indices: 41976617--41976697 Score: 71
Period size: 15 Copynumber: 5.3 Consensus size: 16
41976607 ATCTCGATAC
* *
41976617 CCATATCTTTGATTTT
1 CCATATATTTGACTTT
**
41976633 CCA-ATATTTGA-TAC
1 CCATATATTTGACTTT
*
41976647 CCATATCTTTGACTTT
1 CCATATATTTGACTTT
**
41976663 CCAT-TATTTGA-TAA
1 CCATATATTTGACTTT
41976677 CCATATATTTGACTTT
1 CCATATATTTGACTTT
41976693 CCATA
1 CCATA
41976698 AATACGGATG
Statistics
Matches: 50, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
14 9 0.18
15 27 0.54
16 14 0.28
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.46
Consensus pattern (16 bp):
CCATATATTTGACTTT
Found at i:41983902 original size:15 final size:16
Alignment explanation
Indices: 41983873--41983902 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41983863 TTTTTCTTTT
41983873 AAATAAATGTATGTCA
1 AAATAAATGTATGTCA
41983889 AAATAAAT-TATGTC
1 AAATAAATGTATGTC
41983903 TAGGAGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (16 bp):
AAATAAATGTATGTCA
Found at i:41984241 original size:15 final size:16
Alignment explanation
Indices: 41984223--41984252 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41984213 TAATAACTAA
41984223 TATATAAT-TATATTT
1 TATATAATATATATTT
41984238 TATATAATATATATT
1 TATATAATATATATT
41984253 AATTGTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:41991193 original size:123 final size:123
Alignment explanation
Indices: 41990972--41991243 Score: 402
Period size: 123 Copynumber: 2.2 Consensus size: 123
41990962 TGGGTTTTTG
* * *
41990972 GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTCGGGCATTTAGCGGCGTTTTTGAAA
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCACTAATGCTCGGGCATTTAGCAGCGTTTTTGAAA
* * * *
41991037 ATGCGCCGCTAATGCTTGGTCCTTTAGCGGCGTTTTTATAGAAACACCACTAATGCTC
66 ATGCGCCGCTAATGCTCGGGCCTTTAGCAGCGTTTTTAAAGAAACACCACTAATGCTC
* * *
41991095 GGGCCTTTAGCGGCGTTTTTGACGAAGCGCCACTAATGCTCGGGCCTTTAGCAGTGTTTTTGAAG
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCACTAATGCTCGGGCATTTAGCAGCGTTTTTGAA-
* ** *
41991160 AA-GCGCCGCTAATGCTCGGGCCTTTAGCAGCGTTTTTAAAGAATCACCGTTAATGCTG
65 AATGCGCCGCTAATGCTCGGGCCTTTAGCAGCGTTTTTAAAGAAACACCACTAATGCTC
41991218 GGGCCTTTAGCGGCGTTTTTGAAGAA
1 GGGCCTTTAGCGGCGTTTTTGAAGAA
41991244 ACACCGCAAA
Statistics
Matches: 133, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
123 131 0.98
124 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (123 bp):
GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCACTAATGCTCGGGCATTTAGCAGCGTTTTTGAAA
ATGCGCCGCTAATGCTCGGGCCTTTAGCAGCGTTTTTAAAGAAACACCACTAATGCTC
Found at i:41991249 original size:41 final size:41
Alignment explanation
Indices: 41990972--41991243 Score: 359
Period size: 41 Copynumber: 6.6 Consensus size: 41
41990962 TGGGTTTTTG
*
41990972 GGGCCTTTAGCGGCGTTTTTAAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
41991013 GGGCATTTAGCGGCGTTTTTGAA-AATGCGCCGCTAATGCTT
1 GGGCCTTTAGCGGCGTTTTTGAAGAA-GCGCCGCTAATGCTC
* * * *
41991054 GGTCCTTTAGCGGCGTTTTT-ATAGAAACACCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGA-AGAAGCGCCGCTAATGCTC
* *
41991095 GGGCCTTTAGCGGCGTTTTTGACGAAGCGCCACTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
41991136 GGGCCTTTAGCAGTGTTTTTGAAGAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* * * * * *
41991177 GGGCCTTTAGCAGCGTTTTTAAAGAATCACCGTTAATGCTG
1 GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
41991218 GGGCCTTTAGCGGCGTTTTTGAAGAA
1 GGGCCTTTAGCGGCGTTTTTGAAGAA
41991244 ACACCGCAAA
Statistics
Matches: 202, Mismatches: 25, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
40 3 0.01
41 196 0.97
42 3 0.01
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:41991662 original size:14 final size:15
Alignment explanation
Indices: 41991629--41991666 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
41991619 ATTTTAAGGT
41991629 TTAGGGATTATGGAA
1 TTAGGGATTATGGAA
41991644 TTAGGGATTATGG-A
1 TTAGGGATTATGGAA
41991658 TTAGGGATT
1 TTAGGGATT
41991667 CTGATTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.29, C:0.00, G:0.34, T:0.37
Consensus pattern (15 bp):
TTAGGGATTATGGAA
Found at i:41991789 original size:15 final size:15
Alignment explanation
Indices: 41991747--41991817 Score: 83
Period size: 15 Copynumber: 4.8 Consensus size: 15
41991737 AAGGTTTATT
41991747 GGTTTAGGGG-TTAGG
1 GGTTT-GGGGTTTAGG
* * *
41991762 TGTTAGGGATTTAGG
1 GGTTTGGGGTTTAGG
41991777 GGTTTGGGGTTTA-G
1 GGTTTGGGGTTTAGG
*
41991791 GGTTTGGGATTTAGG
1 GGTTTGGGGTTTAGG
41991806 GGTTTGGGGTTT
1 GGTTTGGGGTTT
41991818 GGTGTTTAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
14 16 0.35
15 30 0.65
ACGTcount: A:0.11, C:0.00, G:0.48, T:0.41
Consensus pattern (15 bp):
GGTTTGGGGTTTAGG
Found at i:41991799 original size:29 final size:30
Alignment explanation
Indices: 41991748--41991828 Score: 114
Period size: 29 Copynumber: 2.7 Consensus size: 30
41991738 AGGTTTATTG
41991748 GTTTAGGGG-TTAGGTGTTAGGGATTTAGGG
1 GTTT-GGGGTTTAGGTGTTAGGGATTTAGGG
*
41991778 GTTTGGGGTTTAGG-GTTTGGGATTTAGGG
1 GTTTGGGGTTTAGGTGTTAGGGATTTAGGG
41991807 GTTTGGGGTTT-GGTGTTTAGGG
1 GTTTGGGGTTTAGGTG-TTAGGG
41991829 TGTCAAGGGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
28 2 0.04
29 30 0.65
30 14 0.30
ACGTcount: A:0.11, C:0.00, G:0.48, T:0.41
Consensus pattern (30 bp):
GTTTGGGGTTTAGGTGTTAGGGATTTAGGG
Found at i:41991809 original size:22 final size:22
Alignment explanation
Indices: 41991782--41991828 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
41991772 TTAGGGGTTT
41991782 GGGGTTTAGGGTTTGG-GATTTA
1 GGGGTTTAGGGTTTGGTG-TTTA
*
41991804 GGGGTTTGGGGTTTGGTGTTTA
1 GGGGTTTAGGGTTTGGTGTTTA
41991826 GGG
1 GGG
41991829 TGTCAAGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.09, C:0.00, G:0.51, T:0.40
Consensus pattern (22 bp):
GGGGTTTAGGGTTTGGTGTTTA
Found at i:41991817 original size:7 final size:7
Alignment explanation
Indices: 41991747--41991829 Score: 67
Period size: 7 Copynumber: 11.4 Consensus size: 7
41991737 AAGGTTTATT
41991747 GGTTTAGG
1 GGTTT-GG
*
41991755 GGTTAGG
1 GGTTTGG
* *
41991762 TGTTAGG
1 GGTTTGG
*
41991769 GATTTAGG
1 GGTTT-GG
41991777 GGTTTGG
1 GGTTTGG
*
41991784 GGTTTAG
1 GGTTTGG
41991791 GGTTTGG
1 GGTTTGG
*
41991798 GATTTAGG
1 GGTTT-GG
41991806 GGTTTGG
1 GGTTTGG
41991813 GGTTTGG
1 GGTTTGG
* *
41991820 TGTTTAG
1 GGTTTGG
41991827 GGT
1 GGT
41991830 GTCAAGGGTA
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
7 44 0.73
8 16 0.27
ACGTcount: A:0.11, C:0.00, G:0.48, T:0.41
Consensus pattern (7 bp):
GGTTTGG
Found at i:41992523 original size:16 final size:16
Alignment explanation
Indices: 41992502--41992534 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
41992492 ACTTAGTAAT
41992502 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
41992518 TAAAAGATACAATTAA
1 TAAAAGATACAATTAA
41992534 T
1 T
41992535 TGTATTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (16 bp):
TAAAAGATACAATTAA
Found at i:41992632 original size:15 final size:16
Alignment explanation
Indices: 41992612--41992647 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
41992602 GATATTTTAG
*
41992612 AATATAAATGTAAA-T
1 AATATAAATATAAATT
41992627 AATATAAATATAAATT
1 AATATAAATATAAATT
41992643 AATAT
1 AATAT
41992648 TTAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (16 bp):
AATATAAATATAAATT
Found at i:42000561 original size:15 final size:15
Alignment explanation
Indices: 42000541--42000571 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42000531 TGAACGACGG
42000541 AATTCAAAGTTATTT
1 AATTCAAAGTTATTT
42000556 AATTCAAAGTTATTT
1 AATTCAAAGTTATTT
42000571 A
1 A
42000572 GTTTACGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (15 bp):
AATTCAAAGTTATTT
Found at i:42000980 original size:66 final size:66
Alignment explanation
Indices: 42000874--42001027 Score: 299
Period size: 66 Copynumber: 2.3 Consensus size: 66
42000864 AGGACACTTC
42000874 ATAACTTTTATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAA
1 ATAACTTTTATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAA
42000939 G
66 G
42000940 ATAACTTTTATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAA
1 ATAACTTTTATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAA
42001005 G
66 G
*
42001006 ATAACTTATATAATATTAAGAT
1 ATAACTTTTATAATATTAAGAT
42001028 TACTTATATA
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 87 1.00
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.37
Consensus pattern (66 bp):
ATAACTTTTATAATATTAAGATAAAATTTCTAACCACACATCAATTTCTAATTACATAAAATTAA
G
Found at i:42001023 original size:20 final size:20
Alignment explanation
Indices: 42000995--42001105 Score: 115
Period size: 20 Copynumber: 5.8 Consensus size: 20
42000985 TTCTAATTAC
*
42000995 ATAAAATTAAGATAACTTAT
1 ATAATATTAAGATAACTTAT
*
42001015 ATAATATTAAGATTACTTAT
1 ATAATATTAAGATAACTTAT
* *
42001035 ATAGTATTAAGACAA-TT-T
1 ATAATATTAAGATAACTTAT
* *
42001053 CT-AT-TT-ACATAACTTAT
1 ATAATATTAAGATAACTTAT
42001070 ATAATTATTAAGATAACTTAT
1 ATAA-TATTAAGATAACTTAT
*
42001091 ATAATATTAATATAA
1 ATAATATTAAGATAA
42001106 AATTTCTAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
15 4 0.05
16 4 0.05
17 3 0.04
18 3 0.04
19 3 0.04
20 42 0.58
21 14 0.19
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (20 bp):
ATAATATTAAGATAACTTAT
Found at i:42001078 original size:21 final size:21
Alignment explanation
Indices: 42001054--42001105 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
42001044 AGACAATTTC
*
42001054 TATTTACATAACTTATATAAT
1 TATTAACATAACTTATATAAT
*
42001075 TATTAAGATAACTTATATAA-
1 TATTAACATAACTTATATAAT
*
42001095 TATTAATATAA
1 TATTAACATAA
42001106 AATTTCTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (21 bp):
TATTAACATAACTTATATAAT
Found at i:42001166 original size:25 final size:25
Alignment explanation
Indices: 42001138--42001191 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
42001128 GGTTACATTC
42001138 TACACAACTTA-CATAAC-ATACATAA
1 TACACAAC-TAGCATAACTA-ACATAA
*
42001163 TACATAACTAGCATAACTAACATAA
1 TACACAACTAGCATAACTAACATAA
42001188 TACA
1 TACA
42001192 TAGCTTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 2 0.08
25 23 0.88
26 1 0.04
ACGTcount: A:0.52, C:0.22, G:0.02, T:0.24
Consensus pattern (25 bp):
TACACAACTAGCATAACTAACATAA
Found at i:42001180 original size:9 final size:8
Alignment explanation
Indices: 42001137--42001360 Score: 72
Period size: 9 Copynumber: 27.0 Consensus size: 8
42001127 AGGTTACATT
*
42001137 CTACACAA
1 CTACATAA
42001145 CTTACATAA
1 C-TACATAA
42001154 CATACATAA
1 C-TACATAA
42001163 -TACATAA
1 CTACATAA
42001170 CTAGCATAA
1 CTA-CATAA
42001179 CTAACATAA
1 CT-ACATAA
*
42001188 -TACATAG
1 CTACATAA
*
42001195 CTTATATAA
1 C-TACATAA
* *
42001204 TTA-TTAA
1 CTACATAA
* *
42001211 GATA-ACTTA
1 -CTACA-TAA
*
42001220 -TATATAA
1 CTACATAA
42001227 CTCACATAA
1 CT-ACATAA
*
42001236 CTTACATAG
1 C-TACATAA
*
42001245 CTTACAT-T
1 C-TACATAA
*
42001253 CTACACAA
1 CTACATAA
*
42001261 CTTACATGA
1 C-TACATAA
42001270 CATACATAA
1 C-TACATAA
42001279 -TACATAA
1 CTACATAA
42001286 CTGACATAA
1 CT-ACATAA
42001295 CTAACATAA
1 CT-ACATAA
*
42001304 -TACATAG
1 CTACATAA
42001311 CTTACATAA
1 C-TACATAA
*
42001320 -TACACAA
1 CTACATAA
*
42001327 CTTACATAG
1 C-TACATAA
42001336 CTTACATAA
1 C-TACATAA
*
42001345 -TAAATAA
1 CTACATAA
42001352 CTAACATAA
1 CT-ACATAA
42001361 AATACAACTT
Statistics
Matches: 165, Mismatches: 29, Indels: 43
0.70 0.12 0.18
Matches are distributed among these distances:
7 47 0.28
8 15 0.09
9 101 0.61
10 2 0.01
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (8 bp):
CTACATAA
Found at i:42001192 original size:41 final size:41
Alignment explanation
Indices: 42001147--42001360 Score: 89
Period size: 41 Copynumber: 5.0 Consensus size: 41
42001137 CTACACAACT
*
42001147 TACATAACATACATAATACATAACTAGCATAACTAACATAA
1 TACATAACTTACATAATACATAACTAGCATAACTAACATAA
* * * ** *
42001188 TACATAGCTTATATAATTATTAAGATAACTTATATATAACTCACATAA
1 TACATAACTTACAT-A--A-T-ACATAAC-TA-GCATAACTAACATAA
* ** * *
42001236 CTTACATAGCTTACATTCTACACAACTTA-CATGAC-ATACATAA
1 --TACATAACTTACATAATACATAAC-TAGCATAACTA-ACATAA
* * *
42001279 TACATAACTGACATAACTAACATAA-TA-CATAGCTTACATAA
1 TACATAACTTACATAA-T-ACATAACTAGCATAACTAACATAA
* * *
42001320 TACACAACTTACATAGCTTACATAA-TA-AATAACTAACATAA
1 TACATAACTTACATA--ATACATAACTAGCATAACTAACATAA
42001361 AATACAACTT
Statistics
Matches: 129, Mismatches: 29, Indels: 30
0.69 0.15 0.16
Matches are distributed among these distances:
41 67 0.52
42 3 0.02
43 15 0.12
44 1 0.01
45 9 0.07
46 7 0.05
47 2 0.02
48 12 0.09
50 13 0.10
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (41 bp):
TACATAACTTACATAATACATAACTAGCATAACTAACATAA
Found at i:42001193 original size:16 final size:16
Alignment explanation
Indices: 42001138--42001334 Score: 91
Period size: 16 Copynumber: 11.9 Consensus size: 16
42001128 GGTTACATTC
*
42001138 TACACAACTTACATAACA
1 TACATAACTTACAT-A-A
42001156 TACATAA--TACATAA
1 TACATAACTTACATAA
*
42001170 CTAGCATAACTAACATAA
1 -TA-CATAACTTACATAA
* *
42001188 TACATAGCTTATATAA
1 TACATAACTTACATAA
* ** *
42001204 TTA-TTAAGATA-ACTTA
1 -TACATAACTTACA-TAA
* *
42001220 TATATAACTCACATAA
1 TACATAACTTACATAA
* **
42001236 CTTACATAGCTTACATTC
1 --TACATAACTTACATAA
*
42001254 TACACAACTTACATGACA
1 TACATAACTTACAT-A-A
42001272 TACATAA--TACATAA
1 TACATAACTTACATAA
*
42001286 CTGACATAACTAACATAA
1 -T-ACATAACTTACATAA
*
42001304 TACATAGCTTACATAA
1 TACATAACTTACATAA
*
42001320 TACACAACTTACATA
1 TACATAACTTACATA
42001335 GCTTACATAA
Statistics
Matches: 133, Mismatches: 30, Indels: 34
0.68 0.15 0.17
Matches are distributed among these distances:
14 2 0.02
15 8 0.06
16 82 0.62
17 6 0.05
18 35 0.26
ACGTcount: A:0.47, C:0.20, G:0.04, T:0.29
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:42001282 original size:25 final size:25
Alignment explanation
Indices: 42001230--42001360 Score: 92
Period size: 25 Copynumber: 5.2 Consensus size: 25
42001220 TATATAACTC
* * **
42001230 ACATAACTTACATAGCTTACATTCT
1 ACATAACTTACATAACTAACATAAT
* *
42001255 ACACAACTTACATGAC-ATACATAAT
1 ACATAACTTACATAACTA-ACATAAT
*
42001280 ACATAACTGACATAACTAACATAAT
1 ACATAACTTACATAACTAACATAAT
* *
42001305 ACATAGCTTACATAA-TACACA-ACTT
1 ACATAACTTACATAACTA-ACATA-AT
*
42001330 ACATAGCTTACATAA-TAA-ATAACT
1 ACATAACTTACATAACTAACATAA-T
42001354 AACATAA
1 -ACATAA
42001361 AATACAACTT
Statistics
Matches: 85, Mismatches: 14, Indels: 14
0.75 0.12 0.12
Matches are distributed among these distances:
23 1 0.01
24 6 0.07
25 77 0.91
26 1 0.01
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.27
Consensus pattern (25 bp):
ACATAACTTACATAACTAACATAAT
Found at i:42001324 original size:66 final size:65
Alignment explanation
Indices: 42001223--42001417 Score: 196
Period size: 66 Copynumber: 2.9 Consensus size: 65
42001213 TAACTTATAT
* ** *
42001223 ATAACTCACATAACTTACATAGCTTACATTCTACACAACTTACATGACATACATAATACATAACT
1 ATAACTAACATAA--TACATAGCTTACATAATACACAACTTACAT-ACTTACATAATACATAACT
*
42001288 GAC
63 AAC
*
42001291 ATAACTAACATAATACATAGCTTACATAATACACAACTTACATAGCTTACATAATAAATAACTAA
1 ATAACTAACATAATACATAGCTTACATAATACACAACTTACATA-CTTACATAATACATAACTAA
42001356 C
65 C
* * * ** * *
42001357 ATAA-AATACA-ACTTCCATAGCTTACATAATACGTAACTTACATAATTTATATAATACATAA
1 ATAACTA-ACATA-ATACATAGCTTACATAATACACAACTTACAT-ACTTACATAATACATAA
42001418 ATTTTTAGGC
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
65 3 0.03
66 93 0.85
67 1 0.01
68 12 0.11
ACGTcount: A:0.47, C:0.21, G:0.04, T:0.29
Consensus pattern (65 bp):
ATAACTAACATAATACATAGCTTACATAATACACAACTTACATACTTACATAATACATAACTAAC
Found at i:42001359 original size:116 final size:116
Alignment explanation
Indices: 42001123--42001359 Score: 297
Period size: 116 Copynumber: 2.0 Consensus size: 116
42001113 AACATAACCT
*
42001123 ACATAGGTTACATTCTACACAACTTACATAACATACATAATACATAACTAGCATAACTAACATAA
1 ACATAGCTTACATTCTACACAACTTACATAACATACATAATACATAACTAGCATAACTAACATAA
** * * * *
42001188 TACATAGCTTATATAATTATTAAGATAACTTATATATAACTCACATAACTT
66 TACATAGCTTATATAACAATTAACATAACTTATACATAACTCAAATAACTA
*
42001239 ACATAGCTTACATTCTACACAACTTACATGACATACATAATACATAACT-GACATAACTAACATA
1 ACATAGCTTACATTCTACACAACTTACATAACATACATAATACATAACTAG-CATAACTAACATA
*
42001303 ATACATAGCTTACATAATACACAACTT-ACATAGC-T-TACATAA-T-AAATAACTA
65 ATACATAGCTT--AT-ATA-ACAA-TTAACATAACTTATACATAACTCAAATAACTA
42001355 ACATA
1 ACATA
42001360 AAATACAACT
Statistics
Matches: 106, Mismatches: 9, Indels: 12
0.83 0.07 0.09
Matches are distributed among these distances:
115 1 0.01
116 83 0.78
117 1 0.01
118 8 0.08
119 4 0.04
120 7 0.07
121 2 0.02
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (116 bp):
ACATAGCTTACATTCTACACAACTTACATAACATACATAATACATAACTAGCATAACTAACATAA
TACATAGCTTATATAACAATTAACATAACTTATACATAACTCAAATAACTA
Found at i:42006744 original size:66 final size:66
Alignment explanation
Indices: 42006638--42006794 Score: 190
Period size: 66 Copynumber: 2.4 Consensus size: 66
42006628 CAAATTACAC
* * *
42006638 AACTTAAAGCGGAGGCAGCATCGAGAGAAGCTGAGGTTCAA-AAAAGATATAAAGAACTCCAGCT
1 AACTTAAAGCAGAGGCAGCAGCGAGAAAAGCTGAGGTTCAACAAAAG-TATAAAGAACTCCAGCT
42006702 AA
65 AA
* * * ** *
42006704 AACTTAAAGCAGATGCAGCAGCGAGAAAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAATTG
1 AACTTAAAGCAGAGGCAGCAGCGAGAAAAGCTGAGGTTCAACAAAAGTATAAAGAACTCCAGCTA
*
42006769 T
66 A
* *
42006770 AGCTTAAAGCAGAGGCTGCAGCGAG
1 AACTTAAAGCAGAGGCAGCAGCGAG
42006795 GGAAGCAGAG
Statistics
Matches: 77, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
66 73 0.95
67 4 0.05
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.16
Consensus pattern (66 bp):
AACTTAAAGCAGAGGCAGCAGCGAGAAAAGCTGAGGTTCAACAAAAGTATAAAGAACTCCAGCTA
A
Found at i:42007177 original size:43 final size:43
Alignment explanation
Indices: 42007142--42007378 Score: 314
Period size: 43 Copynumber: 5.5 Consensus size: 43
42007132 CGTTTTTAAA
* * *
42007142 AAAAACGCCACTAAAGGTCATGGTC-TTATGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTA-GCGGCGTTTGTCGG
** * * **
42007185 AAAAGCGCCGCTAAAGACCAGGGTCTTTAGCGGCATTTGTTTG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
* *
42007228 AAAAACGCTGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
* * *
42007271 ATAAGCGCCGCTAAAGGTCATGGTCTTCAGCGGCATTTGTCGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
*
42007314 ATAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
*
42007357 GAAAGCGCCGCTAAAGGTCATG
1 AAAAGCGCCGCTAAAGGTCATG
42007379 CGGCGTTTTT
Statistics
Matches: 168, Mismatches: 25, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
43 165 0.98
44 3 0.02
ACGTcount: A:0.24, C:0.21, G:0.30, T:0.25
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCGG
Found at i:42007459 original size:22 final size:22
Alignment explanation
Indices: 42007431--42007473 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
42007421 TAGTGGCGCT
*
42007431 AAAAAGCGCCACTAAAGGCCTA
1 AAAAAGCGCCACTAAAAGCCTA
42007453 AAAAAGCGCCACTAAAAGCCT
1 AAAAAGCGCCACTAAAAGCCT
42007474 GTTTTGGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCACTAAAAGCCTA
Found at i:42008648 original size:16 final size:15
Alignment explanation
Indices: 42008627--42008656 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42008617 TAAAACTATA
42008627 TTAATTATATTTATTT
1 TTAATTAT-TTTATTT
42008643 TTAATTATTTTATT
1 TTAATTATTTTATT
42008657 GATGGTGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTAATTATTTTATTT
Found at i:42011109 original size:18 final size:20
Alignment explanation
Indices: 42011058--42011098 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42011048 CAATTTCTCA
*
42011058 AAATTTATATATATATATAT
1 AAATATATATATATATATAT
42011078 AAATATATA-ATATAT-TAT
1 AAATATATATATATATATAT
42011096 AAA
1 AAA
42011099 ATTACTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 6 0.30
20 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATATATATATATATATAT
Found at i:42011768 original size:7 final size:7
Alignment explanation
Indices: 42011758--42011807 Score: 50
Period size: 7 Copynumber: 7.1 Consensus size: 7
42011748 CAATCCCCAT
42011758 TTTTCAA
1 TTTTCAA
42011765 TTTT-ATA
1 TTTTCA-A
42011772 TTTTCAA
1 TTTTCAA
*
42011779 TCTTCAA
1 TTTTCAA
*
42011786 TCTTCAAA
1 TTTTC-AA
42011794 TTTT-AA
1 TTTTCAA
42011800 TTTTCAA
1 TTTTCAA
42011807 T
1 T
42011808 ATTTATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 7 0.19
7 24 0.65
8 6 0.16
ACGTcount: A:0.30, C:0.14, G:0.00, T:0.56
Consensus pattern (7 bp):
TTTTCAA
Found at i:42011778 original size:28 final size:28
Alignment explanation
Indices: 42011746--42011807 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
42011736 ATTCTCAATC
* *
42011746 TTCAATCCCCATTTTTC-AATTTTATATT
1 TTCAATCCCCAATCTTCAAATTTTA-ATT
**
42011774 TTCAATCTTCAATCTTCAAATTTTAATT
1 TTCAATCCCCAATCTTCAAATTTTAATT
42011802 TTCAAT
1 TTCAAT
42011808 ATTTATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 22 0.76
29 7 0.24
ACGTcount: A:0.29, C:0.19, G:0.00, T:0.52
Consensus pattern (28 bp):
TTCAATCCCCAATCTTCAAATTTTAATT
Found at i:42012249 original size:5 final size:5
Alignment explanation
Indices: 42012239--42012263 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
42012229 CCCATGTTAA
42012239 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
42012264 CCTATTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:42012372 original size:26 final size:26
Alignment explanation
Indices: 42012324--42012373 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
42012314 ATCGCACGTG
* *
42012324 TTTAATTTTTAATTTTGTGTTGTTGA
1 TTTAATTTTTAATTTTATATTGTTGA
42012350 TTTAATTATTTAA-TTTATATTGTT
1 TTTAATT-TTTAATTTTATATTGTT
42012374 TCATGACTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (26 bp):
TTTAATTTTTAATTTTATATTGTTGA
Found at i:42012842 original size:21 final size:21
Alignment explanation
Indices: 42012813--42012867 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
42012803 AACAGTGGTG
*
42012813 GCAGTGAGATTAGTTACTGTA
1 GCAGTGAGATTAGGTACTGTA
** *
42012834 GTGGTGAGATTGGGTACTGTA
1 GCAGTGAGATTAGGTACTGTA
42012855 GCAGTGAGATTAG
1 GCAGTGAGATTAG
42012868 AAACAGTGGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.36, T:0.31
Consensus pattern (21 bp):
GCAGTGAGATTAGGTACTGTA
Found at i:42016496 original size:6 final size:6
Alignment explanation
Indices: 42016485--42016522 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
42016475 TTTGCAACCC
*
42016485 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
42016523 GAAGAAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:42016508 original size:18 final size:18
Alignment explanation
Indices: 42016485--42016520 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
42016475 TTTGCAACCC
42016485 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
42016503 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
42016521 GAGAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGG
Found at i:42016529 original size:18 final size:18
Alignment explanation
Indices: 42016490--42016531 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
42016480 AACCCAAGGG
**
42016490 GAAGGGGAAAGGGAAGGG
1 GAAGGGGAAAGGGAAGAA
*
42016508 GAAGGGGAAAGGGGAGAA
1 GAAGGGGAAAGGGAAGAA
42016526 GAAGGG
1 GAAGGG
42016532 TAACCATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAAGGGAAGAA
Found at i:42017615 original size:23 final size:23
Alignment explanation
Indices: 42017581--42017639 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
42017571 GCACTAAACT
42017581 AAAT-AACTTAATTCAACTCAAAA
1 AAATAAAC-TAATTCAACTCAAAA
*
42017604 AAATAAACTAATTCAACTCAACA
1 AAATAAACTAATTCAACTCAAAA
* *
42017627 AACTAATCTAATT
1 AAATAAACTAATT
42017640 AGCCCGTACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 29 0.91
24 3 0.09
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (23 bp):
AAATAAACTAATTCAACTCAAAA
Found at i:42023269 original size:5 final size:5
Alignment explanation
Indices: 42023255--42023288 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
42023245 GATACCTCTA
*
42023255 ATATG TTATG ATATG ATATG ATATG ATATG ATAT
1 ATATG ATATG ATATG ATATG ATATG ATATG ATAT
42023289 ATGTGTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (5 bp):
ATATG
Found at i:42024468 original size:19 final size:20
Alignment explanation
Indices: 42024446--42024490 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
42024436 AATAAAAATG
*
42024446 ATTGAAC-CGCTAAAAACTA
1 ATTGAACACACTAAAAACTA
*
42024465 ATTGAACATACTAAAAACTA
1 ATTGAACACACTAAAAACTA
*
42024485 GTTGAA
1 ATTGAA
42024491 TTGGGTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (20 bp):
ATTGAACACACTAAAAACTA
Found at i:42026145 original size:6 final size:6
Alignment explanation
Indices: 42026134--42026163 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
42026124 AATATTATAA
42026134 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
42026164 GAAATTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:42027150 original size:13 final size:13
Alignment explanation
Indices: 42027132--42027159 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42027122 GGACCCCAAT
42027132 GTCTCTAAAGAGA
1 GTCTCTAAAGAGA
42027145 GTCTCTAAAGAGA
1 GTCTCTAAAGAGA
42027158 GT
1 GT
42027160 GTTCGCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (13 bp):
GTCTCTAAAGAGA
Found at i:42037603 original size:63 final size:63
Alignment explanation
Indices: 42037474--42037636 Score: 184
Period size: 63 Copynumber: 2.6 Consensus size: 63
42037464 TAGGGTTGAA
* * * *
42037474 ACACATGGGCATGTGTCTAGGCCGTGTAACTCACTGACTTCGTATTAGAGTCACATAGGCATG
1 ACACACGGGCATGTGTCCAGGCCGTGTAACTCACTGACTTCGTATTAGAGTCACAGAGGCAAG
* * * *
42037537 ACACACGGGCATGTTTCCAGGCCGTGTAACTCATTGGCTTCGTATTATAGTCACACGA-GCAAG
1 ACACACGGGCATGTGTCCAGGCCGTGTAACTCACTGACTTCGTATTAGAGTCACA-GAGGCAAG
* * * * * *
42037600 ACACACGAGCGTATGTCCAAGCCATATAACTCACTGA
1 ACACACGGGCATGTGTCCAGGCCGTGTAACTCACTGA
42037637 TTTTAGATTT
Statistics
Matches: 82, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
63 81 0.99
64 1 0.01
ACGTcount: A:0.28, C:0.25, G:0.23, T:0.25
Consensus pattern (63 bp):
ACACACGGGCATGTGTCCAGGCCGTGTAACTCACTGACTTCGTATTAGAGTCACAGAGGCAAG
Found at i:42044619 original size:63 final size:63
Alignment explanation
Indices: 42044538--42044726 Score: 202
Period size: 63 Copynumber: 3.0 Consensus size: 63
42044528 AGACCGTGTT
* * *
42044538 ACTCATTGACTTTGTATTAGAGTCGCACAAGCATGACACATGGGCGTGTGTCTAAGCCATGTA
1 ACTCACTGACTTAGTATTAGAGTCACACAAGCATGACACATGGGCGTGTGTCTAAGCCATGTA
* * * * * * *
42044601 ACTCACTGACTTCGTATTAGAGTCACACAAGCAAGAGACACGGGTGTGTGTCCAAGCCGTGTA
1 ACTCACTGACTTAGTATTAGAGTCACACAAGCATGACACATGGGCGTGTGTCTAAGCCATGTA
* * * * * * *
42044664 ACTCACTGATTTTAG-ATTTGAGACACACATGCATGGCACATGGGCATGTG-CTAGGCCATGTA
1 ACTCACTGA-CTTAGTATTAGAGTCACACAAGCATGACACATGGGCGTGTGTCTAAGCCATGTA
42044726 A
1 A
42044727 AGCTACATTG
Statistics
Matches: 102, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
62 10 0.10
63 89 0.87
64 3 0.03
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (63 bp):
ACTCACTGACTTAGTATTAGAGTCACACAAGCATGACACATGGGCGTGTGTCTAAGCCATGTA
Found at i:42048028 original size:30 final size:28
Alignment explanation
Indices: 42047987--42048050 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 28
42047977 AGTTACAAAA
*
42047987 TGGTCATCCAACTATTCA-ACTTTTTCCTTT
1 TGGTCACCCAACTATTCATA-TTTTT--TTT
42048017 TGGTCACCCAACTATTCATATTTTTTTT
1 TGGTCACCCAACTATTCATATTTTTTTT
42048045 TGGTCA
1 TGGTCA
42048051 TCAACCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 9 0.28
30 22 0.69
31 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.09, T:0.47
Consensus pattern (28 bp):
TGGTCACCCAACTATTCATATTTTTTTT
Found at i:42048717 original size:23 final size:23
Alignment explanation
Indices: 42048692--42048735 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
42048682 TCTCTTTCTT
*
42048692 TTTTA-TTTAAAAATTTTGATCA
1 TTTTACTTTAAAAATGTTGATCA
42048714 TTTTACCTTTAAAAATGTTGAT
1 TTTTA-CTTTAAAAATGTTGAT
42048736 GTGACTATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
24 14 0.74
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTACTTTAAAAATGTTGATCA
Found at i:42048832 original size:19 final size:19
Alignment explanation
Indices: 42048800--42048892 Score: 61
Period size: 19 Copynumber: 4.8 Consensus size: 19
42048790 TAAAAGTACC
42048800 TAAACAATT-AAAAATATTT
1 TAAA-AATTAAAAAATATTT
42048819 TAAAAATTAAAAAATCAATTT
1 TAAAAATTAAAAAAT--ATTT
*
42048840 T-TAAA-TAAAAAATATTTTT
1 TAAAAATTAAAAAATA--TTT
* * *
42048859 TGAAATATTAAAAACT-CTT
1 T-AAAAATTAAAAAATATTT
42048878 T-AAAATTAAAAAATA
1 TAAAAATTAAAAAATA
42048893 AATAATTTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
17 12 0.21
18 4 0.07
19 25 0.43
20 3 0.05
21 7 0.12
22 7 0.12
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (19 bp):
TAAAAATTAAAAAATATTT
Found at i:42048903 original size:22 final size:23
Alignment explanation
Indices: 42048876--42048924 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 23
42048866 TTAAAAACTC
42048876 TTTAAAATTA-AAAA-ATAAATAA
1 TTTAAAATTAGAAAATATAAA-AA
42048898 TTTAAAATTATGAAAATATAAAAA
1 TTTAAAATTA-GAAAATATAAAAA
42048922 TTT
1 TTT
42048925 TCAAACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.42
24 9 0.38
25 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TTTAAAATTAGAAAATATAAAAA
Found at i:42052186 original size:28 final size:29
Alignment explanation
Indices: 42052126--42052246 Score: 235
Period size: 29 Copynumber: 4.2 Consensus size: 29
42052116 TAGATTAAAT
42052126 TTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTATTTTTAAAATACACTACATATA
42052155 TTTTTTATTTTTAAAATACACTACATAT-
1 TTTTTTATTTTTAAAATACACTACATATA
42052183 TTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTATTTTTAAAATACACTACATATA
42052212 TTTTTTATTTTTAAAATACACTACATATA
1 TTTTTTATTTTTAAAATACACTACATATA
42052241 TTTTTT
1 TTTTTT
42052247 TATTGAAGCA
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
28 28 0.31
29 63 0.69
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (29 bp):
TTTTTTATTTTTAAAATACACTACATATA
Found at i:42052212 original size:57 final size:57
Alignment explanation
Indices: 42052124--42052246 Score: 237
Period size: 57 Copynumber: 2.1 Consensus size: 57
42052114 ATTAGATTAA
42052124 ATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACAT
1 ATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACAT
42052181 ATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACAT
1 ATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACAT
42052238 ATATTTTTT
1 AT-TTTTTT
42052247 TATTGAAGCA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
57 59 0.91
58 6 0.09
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.54
Consensus pattern (57 bp):
ATTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAAATACACTACAT
Found at i:42058778 original size:43 final size:42
Alignment explanation
Indices: 42058695--42058798 Score: 127
Period size: 43 Copynumber: 2.4 Consensus size: 42
42058685 AAATGCCACC
** *
42058695 AAAGAACATGACCTTAGTGGCACTTTTCCCACAAACGCTGCT
1 AAAGAACATGACCTTAGCAGCACTTTTCACACAAACGCTGCT
* * * *
42058737 AAAGAACATGATCTTTAGCAGCGCTTTTCACATAAATGCTGCT
1 AAAGAACATGA-CCTTAGCAGCACTTTTCACACAAACGCTGCT
42058780 AAAGAACATGACCTGTAGC
1 AAAGAACATGACCT-TAGC
42058799 GACATTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
42 13 0.25
43 39 0.75
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (42 bp):
AAAGAACATGACCTTAGCAGCACTTTTCACACAAACGCTGCT
Found at i:42061892 original size:11 final size:11
Alignment explanation
Indices: 42061874--42061922 Score: 80
Period size: 11 Copynumber: 4.5 Consensus size: 11
42061864 TGAATGAGAA
42061874 ATGATTGAGGG
1 ATGATTGAGGG
*
42061885 ATGCTTGAGGG
1 ATGATTGAGGG
*
42061896 ATGATGGAGGG
1 ATGATTGAGGG
42061907 ATGATTGAGGG
1 ATGATTGAGGG
42061918 ATGAT
1 ATGAT
42061923 GAATGAAGGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.27, C:0.02, G:0.45, T:0.27
Consensus pattern (11 bp):
ATGATTGAGGG
Found at i:42066898 original size:35 final size:35
Alignment explanation
Indices: 42066854--42066920 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
42066844 TTTTTATATT
*
42066854 CTTTAAATGTTTATGTAAGTTATGATAATCATAAA
1 CTTTAAATGTTTATGTAAGTCATGATAATCATAAA
*
42066889 CTTTAAATGTTTATGTAAGTCATGATTATCAT
1 CTTTAAATGTTTATGTAAGTCATGATAATCAT
42066921 CTTTAAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (35 bp):
CTTTAAATGTTTATGTAAGTCATGATAATCATAAA
Found at i:42067276 original size:13 final size:13
Alignment explanation
Indices: 42067253--42067294 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
42067243 TTTCAACCTA
*
42067253 ATTAATTACAAA-
1 ATTAGTTACAAAT
42067265 AGTTAGTTACAAAT
1 A-TTAGTTACAAAT
*
42067279 ATTAGTTATAAAT
1 ATTAGTTACAAAT
42067292 ATT
1 ATT
42067295 TGGTCAAGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 1 0.04
13 24 0.92
14 1 0.04
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.40
Consensus pattern (13 bp):
ATTAGTTACAAAT
Found at i:42068277 original size:154 final size:154
Alignment explanation
Indices: 42067997--42068296 Score: 582
Period size: 154 Copynumber: 1.9 Consensus size: 154
42067987 TTGTTTGCTT
* *
42067997 TAATGGCTAAATGATTTGGGTTTGTATGTGAGTGTTTGAGAAGCCTGGGTTTAAGTCTTGGCTTT
1 TAATGGCTAAATGATTTGGGTTTGTATGGGAGTGTTTGAGAAGCCTGGGTTCAAGTCTTGGCTTT
42068062 TGCAGAATTTTTAGTTTTGCTCTTAAATGAATCTGGACACTGGCATATAGACCTTTTAAATAATA
66 TGCAGAATTTTTAGTTTTGCTCTTAAATGAATCTGGACACTGGCATATAGACCTTTTAAATAATA
42068127 GTGTTTGTTTTATGACCTTTTAAA
131 GTGTTTGTTTTATGACCTTTTAAA
42068151 TAATGGCTAAATGATTTGGGTTTGTATGGGAGTGTTTGAGAAGCCTGGGTTCAAGTCTTGGCTTT
1 TAATGGCTAAATGATTTGGGTTTGTATGGGAGTGTTTGAGAAGCCTGGGTTCAAGTCTTGGCTTT
42068216 TGCAGAATTTTTAGTTTTGCTCTTAAATGAATCTGGACACTGGCATATAGACCTTTTAAATAATA
66 TGCAGAATTTTTAGTTTTGCTCTTAAATGAATCTGGACACTGGCATATAGACCTTTTAAATAATA
42068281 GTGTTTGTTTTATGAC
131 GTGTTTGTTTTATGAC
42068297 ACAAAAATAG
Statistics
Matches: 144, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
154 144 1.00
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (154 bp):
TAATGGCTAAATGATTTGGGTTTGTATGGGAGTGTTTGAGAAGCCTGGGTTCAAGTCTTGGCTTT
TGCAGAATTTTTAGTTTTGCTCTTAAATGAATCTGGACACTGGCATATAGACCTTTTAAATAATA
GTGTTTGTTTTATGACCTTTTAAA
Found at i:42069873 original size:27 final size:25
Alignment explanation
Indices: 42069843--42069920 Score: 93
Period size: 27 Copynumber: 3.0 Consensus size: 25
42069833 AAGAAGTCAA
42069843 TAAAATGACCGAAATACCCTTATAGGG
1 TAAAATGACCGAAATACCC--ATAGGG
* *
42069870 TAAAATGACTGAAATATGCCCATAGTG
1 TAAAATGACCGAAATA--CCCATAGGG
*
42069897 TAAAATGACCGAAATACCCCTAGG
1 TAAAATGACCGAAATACCCATAGG
42069921 AGATGAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 6 0.14
27 35 0.80
29 3 0.07
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (25 bp):
TAAAATGACCGAAATACCCATAGGG
Found at i:42070107 original size:26 final size:26
Alignment explanation
Indices: 42070078--42070132 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
42070068 TCTGCCACAT
*
42070078 ATACTGTTACTAGCAGCTTTGCTACG
1 ATACTATTACTAGCAGCTTTGCTACG
* *
42070104 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTAGCAGCTTTGCTACG
42070130 ATA
1 ATA
42070133 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (26 bp):
ATACTATTACTAGCAGCTTTGCTACG
Found at i:42070275 original size:28 final size:28
Alignment explanation
Indices: 42070235--42070291 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
42070225 ATTGGACTGT
42070235 ACTGATACTGTATTGGGCTATAG-CCCAC
1 ACTGATACTGTATTGGGCTA-AGACCCAC
*
42070263 ACTGTTACTGTATTGGGCTAAGACCCAC
1 ACTGATACTGTATTGGGCTAAGACCCAC
42070291 A
1 A
42070292 TTGTACTATC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (28 bp):
ACTGATACTGTATTGGGCTAAGACCCAC
Found at i:42073534 original size:82 final size:82
Alignment explanation
Indices: 42073292--42073543 Score: 337
Period size: 82 Copynumber: 3.1 Consensus size: 82
42073282 AATTCGTGGC
* * * ** * * *
42073292 GTTTATGGGAAAAACAATACTATTGCCTTACCTTTTGTTGTATTTATGGG-GAAAACGCCACTAT
1 GTTTATGGGGAAAACACTGCTATTGCCTTACCTTTTGCAGTGTTTATGGGAG-AAACACCGCTAT
* * *
42073356 TGCCTTACGTTTTGTGGCA
65 TGCTTTACCTTTTGCGG-A
* *
42073375 -TTTATGGGGAAAACACTGCTATTGCTTTACCTTTTGCAGTGTTTATGGGAGAAACACCGTTATT
1 GTTTATGGGGAAAACACTGCTATTGCCTTACCTTTTGCAGTGTTTATGGGAGAAACACCGCTATT
*
42073439 ACTTTACCTTTTGCGGA
66 GCTTTACCTTTTGCGGA
42073456 GTTTATGGGGAAAACACTGCTATTGCCTTACCTTTTGCAGTGTTTATGGGAGAAACACCGCTATT
1 GTTTATGGGGAAAACACTGCTATTGCCTTACCTTTTGCAGTGTTTATGGGAGAAACACCGCTATT
*
42073521 GCTTTACCTTTTGCAGA
66 GCTTTACCTTTTGCGGA
42073538 GTTTAT
1 GTTTAT
42073544 AAGAAAAAGC
Statistics
Matches: 149, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
81 1 0.01
82 147 0.99
83 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (82 bp):
GTTTATGGGGAAAACACTGCTATTGCCTTACCTTTTGCAGTGTTTATGGGAGAAACACCGCTATT
GCTTTACCTTTTGCGGA
Found at i:42073542 original size:41 final size:41
Alignment explanation
Indices: 42073292--42073543 Score: 251
Period size: 41 Copynumber: 6.1 Consensus size: 41
42073282 AATTCGTGGC
* *** **
42073292 GTTTATGGGAAAAACAATACTATTGCCTTACCTTTTGTTGTA
1 GTTTATGGGGAAAACACCGCTATTGCCTTACCTTTTGCAG-A
* * * **
42073334 -TTTATGGGGAAAACGCCACTATTGCCTTACGTTTTGTGGCA
1 GTTTATGGGGAAAACACCGCTATTGCCTTACCTTTTGCAG-A
* * *
42073375 -TTTATGGGGAAAACACTGCTATTGCTTTACCTTTTGCAGT
1 GTTTATGGGGAAAACACCGCTATTGCCTTACCTTTTGCAGA
* * * *
42073415 GTTTAT-GGGAGAAACACCGTTATTACTTTACCTTTTGCGGA
1 GTTTATGGGGA-AAACACCGCTATTGCCTTACCTTTTGCAGA
* *
42073456 GTTTATGGGGAAAACACTGCTATTGCCTTACCTTTTGCAGT
1 GTTTATGGGGAAAACACCGCTATTGCCTTACCTTTTGCAGA
*
42073497 GTTTAT-GGGAGAAACACCGCTATTGCTTTACCTTTTGCAGA
1 GTTTATGGGGA-AAACACCGCTATTGCCTTACCTTTTGCAGA
42073538 GTTTAT
1 GTTTAT
42073544 AAGAAAAAGC
Statistics
Matches: 177, Mismatches: 29, Indels: 9
0.82 0.13 0.04
Matches are distributed among these distances:
40 8 0.05
41 165 0.93
42 4 0.02
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (41 bp):
GTTTATGGGGAAAACACCGCTATTGCCTTACCTTTTGCAGA
Found at i:42078337 original size:40 final size:40
Alignment explanation
Indices: 42078290--42078577 Score: 321
Period size: 40 Copynumber: 7.2 Consensus size: 40
42078280 GACATTATAA
* * *
42078290 TGCATTCAGGAGTACCGAAGGACAAATAGAGGC-CTGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGAGGCAC-GTATG
* *
42078330 TGCATTCAGGGGTACTGAACTACAAACA-AGGGCACGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGA-GGCACGTATG
* * * *
42078370 AGCATTCAGGTGTATCGAAGTACAAACAGGGGCACGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGAGGCACGTATG
* * * * * *
42078410 TGCATTTAGGGGTATCAAAGTGCAAACAGGGGCATGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGAGGCACGTATG
42078450 TGCATTCAGGGGTACCGAAGTACAAACA-AGGCCACGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGAGG-CACGTATG
* * * * *
42078490 TGCATTTAGTGGTATCGAAGTACAAATAGGGGCACGTATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGAGGCACGTATG
* * *
42078530 TGCATTCAGGGGTACCGAAGTATAAACAGGGGCACGCATG
1 TGCATTCAGGGGTACCGAAGTACAAACAGAGGCACGTATG
42078570 TGCATTCA
1 TGCATTCA
42078578 TGATACCAAA
Statistics
Matches: 209, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.01
40 203 0.97
41 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.22
Consensus pattern (40 bp):
TGCATTCAGGGGTACCGAAGTACAAACAGAGGCACGTATG
Found at i:42078436 original size:80 final size:80
Alignment explanation
Indices: 42078290--42078575 Score: 369
Period size: 80 Copynumber: 3.6 Consensus size: 80
42078280 GACATTATAA
* * * * * *
42078290 TGCATTCAGGAGTACCGAAGGACAAATAGAGGC-CTGTATGTGCATTCAGGGGTA-CTGAACTAC
1 TGCATTCAGGGGTACCGAAGTACAAACAGGGGCAC-GTATGTGCATTTAGGGGTATC-GAAGTAC
*
42078353 AAACAAGGGCACGTATG
64 AAACAGGGGCACGTATG
* * * * *
42078370 AGCATTCAGGTGTATCGAAGTACAAACAGGGGCACGTATGTGCATTTAGGGGTATCAAAGTGCAA
1 TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTTAGGGGTATCGAAGTACAA
*
42078435 ACAGGGGCATGTATG
66 ACAGGGGCACGTATG
* * *
42078450 TGCATTCAGGGGTACCGAAGTACAAACAAGGCCACGTATGTGCATTTAGTGGTATCGAAGTACAA
1 TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTTAGGGGTATCGAAGTACAA
*
42078515 ATAGGGGCACGTATG
66 ACAGGGGCACGTATG
* *
42078530 TGCATTCAGGGGTACCGAAGTATAAACAGGGGCACGCATGTGCATT
1 TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATT
42078576 CATGATACCA
Statistics
Matches: 178, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
80 176 0.99
81 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (80 bp):
TGCATTCAGGGGTACCGAAGTACAAACAGGGGCACGTATGTGCATTTAGGGGTATCGAAGTACAA
ACAGGGGCACGTATG
Found at i:42078459 original size:20 final size:20
Alignment explanation
Indices: 42078396--42078461 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 20
42078386 GAAGTACAAA
*
42078396 CAGGGGCACGTATGTGCATT
1 CAGGGGCATGTATGTGCATT
* * ** * **
42078416 TAGGGGTATCAAAGTGCAAA
1 CAGGGGCATGTATGTGCATT
42078436 CAGGGGCATGTATGTGCATT
1 CAGGGGCATGTATGTGCATT
42078456 CAGGGG
1 CAGGGG
42078462 TACCGAAGTA
Statistics
Matches: 31, Mismatches: 15, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (20 bp):
CAGGGGCATGTATGTGCATT
Found at i:42078505 original size:120 final size:120
Alignment explanation
Indices: 42078290--42078577 Score: 389
Period size: 120 Copynumber: 2.4 Consensus size: 120
42078280 GACATTATAA
* * * * * * *
42078290 TGCATTCAGGAGTACCGAAGGACAAATAGAGGCCTGTATGTGCATTCAGGGGTACTGAACTACAA
1 TGCATTCAGGGGTACCAAAGTACAAACAGGGGCATGTATGTGCATTCAGGGGTACCGAACTACAA
*
42078355 ACAAGGGCACGTATGAGCATTCAGGTGTATCGAAGTACAAACAGGGGCACGTATG
66 ACAAGGCCACGTATGAGCATTCAGGTGTATCGAAGTACAAACAGGGGCACGTATG
* * * *
42078410 TGCATTTAGGGGTATCAAAGTGCAAACAGGGGCATGTATGTGCATTCAGGGGTACCGAAGTACAA
1 TGCATTCAGGGGTACCAAAGTACAAACAGGGGCATGTATGTGCATTCAGGGGTACCGAACTACAA
* * *
42078475 ACAAGGCCACGTATGTGCATTTA-GTGGTATCGAAGTACAAATAGGGGCACGTATG
66 ACAAGGCCACGTATGAGCATTCAGGT-GTATCGAAGTACAAACAGGGGCACGTATG
* * * *
42078530 TGCATTCAGGGGTACCGAAGTATAAACAGGGGCACGCATGTGCATTCA
1 TGCATTCAGGGGTACCAAAGTACAAACAGGGGCATGTATGTGCATTCA
42078578 TGATACCAAA
Statistics
Matches: 145, Mismatches: 22, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
119 2 0.01
120 143 0.99
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.22
Consensus pattern (120 bp):
TGCATTCAGGGGTACCAAAGTACAAACAGGGGCATGTATGTGCATTCAGGGGTACCGAACTACAA
ACAAGGCCACGTATGAGCATTCAGGTGTATCGAAGTACAAACAGGGGCACGTATG
Found at i:42081410 original size:10 final size:10
Alignment explanation
Indices: 42081397--42081435 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
42081387 AAGAAAACAA
42081397 TTTTGAAATTT
1 TTTTGAAA-TT
*
42081408 TTTTGAAAAT
1 TTTTGAAATT
42081418 TTTTGAAATT
1 TTTTGAAATT
42081428 TTTTGAAA
1 TTTTGAAA
42081436 AATGACGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 18 0.69
11 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (10 bp):
TTTTGAAATT
Found at i:42081438 original size:21 final size:21
Alignment explanation
Indices: 42081397--42081436 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
42081387 AAGAAAACAA
42081397 TTTTGAAATTTTTTTGAAAAT
1 TTTTGAAATTTTTTTGAAAAT
42081418 TTTTGAAA-TTTTTTGAAAA
1 TTTTGAAATTTTTTTGAAAA
42081437 ATGACGTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (21 bp):
TTTTGAAATTTTTTTGAAAAT
Found at i:42081742 original size:39 final size:39
Alignment explanation
Indices: 42081699--42081817 Score: 97
Period size: 39 Copynumber: 3.1 Consensus size: 39
42081689 TGCAACAAAT
42081699 TCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACC
1 TCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACC
* ** * * * **
42081738 TC-AAA--TAAG-TTAACTAAATTTAAACATGCA-AC-AAAT
1 TCAAAACCTAAGCTAAAC-AAAAGTAAATA-G-AGTCTTACC
42081774 TCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACC
1 TCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACC
42081813 TCAAA
1 TCAAA
42081818 CAAGTTAATT
Statistics
Matches: 55, Mismatches: 16, Indels: 18
0.62 0.18 0.20
Matches are distributed among these distances:
35 4 0.07
36 15 0.27
37 6 0.11
38 6 0.11
39 20 0.36
40 4 0.07
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.23
Consensus pattern (39 bp):
TCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACC
Found at i:42081799 original size:75 final size:75
Alignment explanation
Indices: 42081676--42081825 Score: 291
Period size: 75 Copynumber: 2.0 Consensus size: 75
42081666 ATACAAAGTC
42081676 CTAAATTTAAACATGCAACAAATTCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACCTCA
1 CTAAATTTAAACATGCAACAAATTCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACCTCA
*
42081741 AATAAGTTAA
66 AACAAGTTAA
42081751 CTAAATTTAAACATGCAACAAATTCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACCTCA
1 CTAAATTTAAACATGCAACAAATTCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACCTCA
42081816 AACAAGTTAA
66 AACAAGTTAA
42081826 TTATTTACAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.51, C:0.18, G:0.08, T:0.23
Consensus pattern (75 bp):
CTAAATTTAAACATGCAACAAATTCAAAACCTAAGCTAAACAAAAGTAAATAGAGTCTTACCTCA
AACAAGTTAA
Found at i:42085612 original size:13 final size:14
Alignment explanation
Indices: 42085595--42085626 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42085585 AGTCATTTTT
42085595 ATTTTTA-ATT-TA
1 ATTTTTATATTCTA
42085607 ATTTTTATATTCTA
1 ATTTTTATATTCTA
42085621 ATTTTT
1 ATTTTT
42085627 TGTTTGTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 3 0.17
14 8 0.44
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
ATTTTTATATTCTA
Found at i:42085622 original size:19 final size:18
Alignment explanation
Indices: 42085589--42085624 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
42085579 TAATTTAGTC
*
42085589 ATTTTTATTTTTAATTTA
1 ATTTTTATTTCTAATTTA
42085607 ATTTTTATATTCTAATTT
1 ATTTTTAT-TTCTAATTT
42085625 TTTGTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTATTTCTAATTTA
Done.