Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold176
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: 918983
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.33
Warning! 19517 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:308234 original size:3 final size:3
Alignment explanation
Indices: 308226--308271 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
308216 GGATTTTAAG
308226 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
308272 AGAGCTGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:328736 original size:88 final size:88
Alignment explanation
Indices: 328587--328764 Score: 320
Period size: 88 Copynumber: 2.0 Consensus size: 88
328577 TTGTTTCTTT
*
328587 ATTTTCTTCCATTTATTTCCACAAACATCTTTGGTTCTTGAACCCTTCCTAATTAGCCTTTAAGC
1 ATTTTCTTCCATTTAATTCCACAAACATCTTTGGTTCTTGAACCCTTCCTAATTAGCCTTTAAGC
328652 ATGTATAATTAGGGAAAAAAACA
66 ATGTATAATTAGGGAAAAAAACA
* *
328675 ATTTTCTTCCATTTAATTCCACTAACGTCTTTGGTTCTTGAACCCTTCCTAATTAGCCTTTAAGC
1 ATTTTCTTCCATTTAATTCCACAAACATCTTTGGTTCTTGAACCCTTCCTAATTAGCCTTTAAGC
*
328740 ATGTATAATTAGGGAAAAAATCA
66 ATGTATAATTAGGGAAAAAAACA
328763 AT
1 AT
328765 CTTGATCAAT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (88 bp):
ATTTTCTTCCATTTAATTCCACAAACATCTTTGGTTCTTGAACCCTTCCTAATTAGCCTTTAAGC
ATGTATAATTAGGGAAAAAAACA
Found at i:332954 original size:90 final size:90
Alignment explanation
Indices: 332693--332961 Score: 294
Period size: 90 Copynumber: 3.0 Consensus size: 90
332683 TTTAATAATA
* * *
332693 TGCAAC-TCTGGTGGTTCATCCA-CAAATATTCTGGCAGCTCTTATCTGCAAATACGTTATGCAT
1 TGCAACAT-TGGTGGTTCATCCACCCATTA-TCTGGCAGCTCTTATCTGCAAATATGTTATGCAT
* *
332756 TCACAACCTTCTGGCAGCATATTAACT
64 TCACAACCTTCTGGCAACGTATTAACT
* * * * ** * * *
332783 TGCAACACTCGTGGCTCATCCACCCACTT-TTTGGCAGCTCTTAGATGCAAAAATGTTGTGTATT
1 TGCAACATTGGTGGTTCATCCACCCA-TTATCTGGCAGCTCTTATCTGCAAATATGTTATGCATT
* **
332847 CACAACCATCTAACAACGTATTAACT
65 CACAACCTTCTGGCAACGTATTAACT
* * *
332873 TGCAACATTGGTGGTTCATCCACCCATTATCTGGAAACTCTTATCTGCATATATGTTATGCATTC
1 TGCAACATTGGTGGTTCATCCACCCATTATCTGGCAGCTCTTATCTGCAAATATGTTATGCATTC
332938 ACAACCTT-TCGGCAACGTATTAAC
66 ACAACCTTCT-GGCAACGTATTAAC
332962 CTATAATTTT
Statistics
Matches: 142, Mismatches: 32, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
89 3 0.02
90 136 0.96
91 2 0.01
92 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.32
Consensus pattern (90 bp):
TGCAACATTGGTGGTTCATCCACCCATTATCTGGCAGCTCTTATCTGCAAATATGTTATGCATTC
ACAACCTTCTGGCAACGTATTAACT
Found at i:334340 original size:19 final size:19
Alignment explanation
Indices: 334315--334371 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
334305 CAAGATTTTC
334315 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
334334 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
334353 AAAAATTCAAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
334371 A
1 A
334372 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
18 11 0.31
19 24 0.69
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:334389 original size:9 final size:9
Alignment explanation
Indices: 334375--334441 Score: 55
Period size: 10 Copynumber: 6.9 Consensus size: 9
334365 ATTTATATTT
334375 TTAAAAAAA
1 TTAAAAAAA
334384 TTAAAAAAAA
1 TT-AAAAAAA
334394 TTCAAAAAATA
1 TT-AAAAAA-A
*
334405 TCTAAAAATA
1 T-TAAAAAAA
*
334415 TATAAAGAAAG
1 T-TAAA-AAAA
334426 TT-AAAAAA
1 TTAAAAAAA
334434 TTAAAAAA
1 TTAAAAAA
334442 TTTTCTAGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
8 5 0.11
9 9 0.19
10 22 0.47
11 10 0.21
12 1 0.02
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:336671 original size:34 final size:34
Alignment explanation
Indices: 336563--336671 Score: 112
Period size: 34 Copynumber: 3.1 Consensus size: 34
336553 AGGCTAGTTC
* *
336563 GATAACCGACGATGGTTGTGCCCAGCACTAGTCA
1 GATAATCGACGATGGTTATGCCCAGCACTAGTCA
* * * * * *
336597 AATGAGTCGACGAT-GTTTTGCACCCAACGCTAGTCC
1 GAT-AATCGACGATGGTTATG--CCCAGCACTAGTCA
336633 GATAATCGACGATGGTTATGCCCAGCACTAGTCA
1 GATAATCGACGATGGTTATGCCCAGCACTAGTCA
336667 GATAA
1 GATAA
336672 ACTAATAGAA
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
34 23 0.40
35 17 0.29
36 18 0.31
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.23
Consensus pattern (34 bp):
GATAATCGACGATGGTTATGCCCAGCACTAGTCA
Found at i:338602 original size:27 final size:27
Alignment explanation
Indices: 338563--338634 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
338553 GAGAGGTCAA
*
338563 TAAATGACCGAAATACCCTCGTAAGGT
1 TAAATGACCGAAATACCCTCATAAGGT
* *
338590 TAAATGACTGAAATACCCTCATATGGT
1 TAAATGACCGAAATACCCTCATAAGGT
* *
338617 AAAATGACCGAAACACCC
1 TAAATGACCGAAATACCC
338635 ACGTTGGGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (27 bp):
TAAATGACCGAAATACCCTCATAAGGT
Found at i:338644 original size:27 final size:26
Alignment explanation
Indices: 338564--338650 Score: 93
Period size: 27 Copynumber: 3.2 Consensus size: 26
338554 AGAGGTCAAT
* *
338564 AAATGACCGAAATACCCTCGTAAGGTT
1 AAATGACCGAAATACCCTCGT-TGGTA
* *
338591 AAATGACTGAAATACCCTCATATGGTA
1 AAATGACCGAAATACCCTCGT-TGGTA
* *
338618 AAATGACCGAAACACCCACGTTGGGTA
1 AAATGACCGAAATACCCTCGTT-GGTA
338645 AAATGA
1 AAATGA
338651 TTGTTATACC
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
26 1 0.02
27 50 0.98
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (26 bp):
AAATGACCGAAATACCCTCGTTGGTA
Found at i:338872 original size:26 final size:26
Alignment explanation
Indices: 338843--338897 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
338833 TTTGCCATAT
* *
338843 ATACTGTTACTGGCAGCTTCGTTGCG
1 ATACTATTACTGGCAGCTTCGGTGCG
*
338869 ATACTATTACTGGCAGCTTTGGTGCG
1 ATACTATTACTGGCAGCTTCGGTGCG
338895 ATA
1 ATA
338898 TTAGTGTGTT
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:0.20, C:0.20, G:0.25, T:0.35
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTCGGTGCG
Found at i:339030 original size:28 final size:28
Alignment explanation
Indices: 338994--339088 Score: 122
Period size: 28 Copynumber: 3.4 Consensus size: 28
338984 TGCATTATTG
338994 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
339022 CACTATTACTGTATTGGG-TTAGAGCCCA
1 CACTGTTACTGTATTGGGCTAAG-GCCCA
* * *
339050 CACTGTTATTGTATCGGGCTAAAGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
339078 CACTG-TACTGT
1 CACTGTTACTGT
339089 TACTGAATAG
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
27 8 0.14
28 47 0.82
29 2 0.04
ACGTcount: A:0.23, C:0.24, G:0.22, T:0.31
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:344259 original size:27 final size:27
Alignment explanation
Indices: 344190--344334 Score: 137
Period size: 27 Copynumber: 5.3 Consensus size: 27
344180 AGAGGTCAAT
* *
344190 AAATGACTGAAATACCCTCATAGGGTCAA
1 AAATGACCGAAATACCCCCATAGGGT--A
*
344219 TAAATGACCAAAATACCCCCATAGGGTA
1 -AAATGACCGAAATACCCCCATAGGGTA
* * * *
344247 AAATGACCGAAATATCCCCGTAAGGTT
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
344274 AAATGACCAAAATACCCTCATATGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* ** *
344301 AAATTACCGAAATACGTCCGTAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
344328 AAATGAC
1 AAATGAC
344335 TGTTATACTT
Statistics
Matches: 93, Mismatches: 22, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
27 69 0.74
28 1 0.01
30 23 0.25
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:344332 original size:54 final size:54
Alignment explanation
Indices: 344220--344334 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 54
344210 TAGGGTCAAT
*
344220 AAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATATCCCCGTAAGGTT
1 AAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATATCCCCGTAAGGTA
* * * * *
344274 AAATGACCAAAATACCCTCATATGGTAAAATTACCGAAATA-CGTCCGTAGGGTA
1 AAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATATC-CCCGTAAGGTA
344328 AAATGAC
1 AAATGAC
344335 TGTTATACTT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 1 0.02
54 53 0.98
ACGTcount: A:0.42, C:0.22, G:0.17, T:0.20
Consensus pattern (54 bp):
AAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATATCCCCGTAAGGTA
Found at i:344555 original size:26 final size:26
Alignment explanation
Indices: 344526--344580 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
344516 TTTGCCACAT
* * *
344526 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTACTACG
* *
344552 ATACTATTATTGGCATCTTTACTACG
1 ATACTATTACTGGCAGCTTTACTACG
344578 ATA
1 ATA
344581 TTGGTGTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTACTACG
Found at i:344709 original size:28 final size:28
Alignment explanation
Indices: 344677--344771 Score: 138
Period size: 28 Copynumber: 3.4 Consensus size: 28
344667 TGCATTATTG
344677 CACTGTTACTGTATTGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
344705 CACTGTTACTATATTTGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
* *
344733 CACTGATACTGTATCGGGCTAAGGCCCA
1 CACTGTTACTGTATTGGGCTAAGGCCCA
*
344761 TACTG-TACTGT
1 CACTGTTACTGT
344772 TACTGAATAG
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
27 6 0.10
28 54 0.90
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.29
Consensus pattern (28 bp):
CACTGTTACTGTATTGGGCTAAGGCCCA
Found at i:354772 original size:5 final size:5
Alignment explanation
Indices: 354762--354788 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
354752 TCACCATTTA
354762 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
354789 CTTTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:355980 original size:75 final size:75
Alignment explanation
Indices: 355857--355995 Score: 210
Period size: 75 Copynumber: 1.9 Consensus size: 75
355847 AAATCAGGAC
* *
355857 TATTCCCTTATTAATAAAGAAGGCAGATGTAAAGTTAGAAAAACGAATTATATT-TTGTCCAAAA
1 TATTCCCTTATTAATAAAGAAGGCAAATGTAAAGTTACAAAAACGAATTATATTCTT-TCCAAAA
355921 GAATATAGCAT
65 GAATATAGCAT
* *
355932 TATTCCCTTATTAATATAGAAGGCAAAT-TGAAAGTTACAAAAAGGAATTATATTCTTTCCAAAA
1 TATTCCCTTATTAATAAAGAAGGCAAATGT-AAAGTTACAAAAACGAATTATATTCTTTCCAAAA
355996 AACATTAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
74 1 0.02
75 55 0.95
76 2 0.03
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.32
Consensus pattern (75 bp):
TATTCCCTTATTAATAAAGAAGGCAAATGTAAAGTTACAAAAACGAATTATATTCTTTCCAAAAG
AATATAGCAT
Found at i:356157 original size:137 final size:138
Alignment explanation
Indices: 355977--356395 Score: 648
Period size: 138 Copynumber: 3.1 Consensus size: 138
355967 TACAAAAAGG
* *
355977 AATTATATTCTTTCCAAAA-AACATTAA-TTCCATGTCTTTTATATTTTGACCGAAACTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * * * **
356040 TATAATTTTTTAGATTAATAAATTCGGTAATATATATATAATTAATATTTT-TATGAATCAAATT
66 TATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAATTAATATTTTGTATGAATCAAATT
*
356104 TATATATT
131 CATATATT
*
356112 AATTATA-TCTTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTA
1 AATTATATTC-TTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTA
356176 ATATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAATTAATATTTTGTATGAATCAAAT
65 ATATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAATTAATATTTTGTATGAATCAAAT
356241 TCATATATT
130 TCATATATT
* * * *
356250 AATTATATTCTTTCCAAAAGAATATTAATTACCATGCCTTTTATATTTAGACCAAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
*
356315 TATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAATTAATATTTTGTATGAATCGAATT
66 TATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAATTAATATTTTGTATGAATCAAATT
356380 CATATATT
131 CATATATT
356388 AATTATAT
1 AATTATAT
356396 CTATGTTCTC
Statistics
Matches: 261, Mismatches: 18, Indels: 7
0.91 0.06 0.02
Matches are distributed among these distances:
134 2 0.01
135 16 0.06
136 7 0.03
137 77 0.30
138 157 0.60
139 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:356225 original size:67 final size:67
Alignment explanation
Indices: 356154--356366 Score: 162
Period size: 67 Copynumber: 3.1 Consensus size: 67
356144 CATGTCTTTT
356154 ATATTTTGACTGAAATTAATTAATATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAAT
1 ATATTTTGACTGAAATTAATTAATATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAAT
356219 TA
66 TA
* * * ** ** ** *** * *
356221 ATATTTTGTA-TG-AATCAAATTCATAT-ATTAATTATATTCTTTCCAAAAGAATATTAATTACC
1 ATATTTTG-ACTGAAAT-TAATTAATATAACTGTTTATATTAATAACTTCAG--TA--AAATA-T
** *
356283 ATGCCTTTT
59 ATGCAATTA
* **
356292 ATATTTAGACCAAAATTAATTAATATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAAT
1 ATATTTTGACTGAAATTAATTAATATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAAT
356357 TA
66 TA
356359 ATATTTTG
1 ATATTTTG
356367 TATGAATCGA
Statistics
Matches: 98, Mismatches: 38, Indels: 20
0.63 0.24 0.13
Matches are distributed among these distances:
66 16 0.16
67 31 0.32
68 7 0.07
70 7 0.07
71 21 0.21
72 16 0.16
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (67 bp):
ATATTTTGACTGAAATTAATTAATATAACTGTTTATATTAATAACTTCAGTAAAATATATGCAAT
TA
Found at i:362698 original size:74 final size:75
Alignment explanation
Indices: 362564--362710 Score: 226
Period size: 74 Copynumber: 2.0 Consensus size: 75
362554 GAAAAATCAA
* * *
362564 GATTATTCTCTTACTAAGAGAGAATGCAAATGGAAAGTTATAAAAAGGAATTATATTATTTCCAA
1 GATTATTCCCTTACTAAGAGAGAAGGCAAATGGAAAATTATAAAAAGGAATTATATTATTTCCAA
362629 AAGAATATAG
66 AAGAATATAG
* *
362639 GATTATTCCCTTA-TTAGTAGAGAAGGCAAATTGAAAATTA-AAAAAGGAATTATATTATTTCCA
1 GATTATTCCCTTACTAAG-AGAGAAGGCAAATGGAAAATTATAAAAAGGAATTATATTATTTCCA
362702 AAAGAATAT
65 AAAGAATAT
362711 TAATTTCCAT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
74 35 0.53
75 31 0.47
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (75 bp):
GATTATTCCCTTACTAAGAGAGAAGGCAAATGGAAAATTATAAAAAGGAATTATATTATTTCCAA
AAGAATATAG
Found at i:362932 original size:138 final size:138
Alignment explanation
Indices: 362686--363611 Score: 1773
Period size: 138 Copynumber: 6.7 Consensus size: 138
362676 TTAAAAAAGG
* *
362686 AATTATATTATTTCCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGATTTAGACCGAAA-T
1 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTAC------ATTTAGACCGAAATT
362750 AATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAAT
60 AATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAAT
362815 CAAATTCACATATT
125 CAAATTCACATATT
362829 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
362894 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
362959 CACATATT
131 CACATATT
362967 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
363032 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
363097 CACATATT
131 CACATATT
363105 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
363170 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
363235 CACATATT
131 CACATATT
363243 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
363308 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
363373 CACATATT
131 CACATATT
363381 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
363446 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
363511 CACATATT
131 CACATATT
363519 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
1 AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
363584 TATAATTGTTTATATTAATAAATTCGGT
66 TATAATTGTTTATATTAATAAATTCGGT
363612 TTTGTATGAA
Statistics
Matches: 780, Mismatches: 2, Indels: 7
0.99 0.00 0.01
Matches are distributed among these distances:
137 13 0.02
138 725 0.93
143 42 0.05
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (138 bp):
AATTATATTCTTTTCAAAAGAATATTAATTTCCATGTCTTTTACATTTAGACCGAAATTAATTAA
TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATAATTTTTATGAATCAAATT
CACATATT
Found at i:364375 original size:31 final size:31
Alignment explanation
Indices: 364339--364401 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
364329 TAATATTATG
364339 ACTATTACATAATAATCCAAGAAACATACTC
1 ACTATTACATAATAATCCAAGAAACATACTC
364370 ACTATTACATAATAATCCAAGAAACATACTC
1 ACTATTACATAATAATCCAAGAAACATACTC
364401 A
1 A
364402 TAGTGTGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.49, C:0.22, G:0.03, T:0.25
Consensus pattern (31 bp):
ACTATTACATAATAATCCAAGAAACATACTC
Found at i:367595 original size:23 final size:22
Alignment explanation
Indices: 367563--367605 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
367553 TCGACTCTTC
*
367563 CAAAAGTTTTCAATTTAATCCTA
1 CAAAAATTTT-AATTTAATCCTA
*
367586 CAAAAATTTTAGTTTAATCC
1 CAAAAATTTTAATTTAATCC
367606 AATAAATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.16, G:0.05, T:0.40
Consensus pattern (22 bp):
CAAAAATTTTAATTTAATCCTA
Found at i:367862 original size:17 final size:17
Alignment explanation
Indices: 367814--367862 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
367804 TGTTATGTTT
367814 TTATATTATAATATTAAA
1 TTATATTATAAT-TTAAA
**
367832 AAATATTCAT-ATTTAAA
1 TTATATT-ATAATTTAAA
367849 TTATATTATAATTT
1 TTATATTATAATTT
367863 CTTAAAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
16 2 0.08
17 14 0.56
18 7 0.28
19 2 0.08
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TTATATTATAATTTAAA
Found at i:378289 original size:24 final size:25
Alignment explanation
Indices: 378243--378292 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
378233 GTTATTTTAA
378243 TTTATTTAGTTATGTTTGTAATTTT
1 TTTATTTAGTTATGTTTGTAATTTT
*
378268 TTTATGTTATTTAT-TTT-TAATTTT
1 TTTAT-TTAGTTATGTTTGTAATTTT
378292 T
1 T
378293 GAAAACCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 8 0.35
25 8 0.35
26 7 0.30
ACGTcount: A:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (25 bp):
TTTATTTAGTTATGTTTGTAATTTT
Found at i:390310 original size:18 final size:18
Alignment explanation
Indices: 390284--390318 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
390274 AGATGTGTTT
* *
390284 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
390302 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
390319 TCCTTTTTCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:392963 original size:72 final size:72
Alignment explanation
Indices: 392841--392984 Score: 261
Period size: 72 Copynumber: 2.0 Consensus size: 72
392831 AACTCGAAAT
*
392841 AATTTATTCCGAGACCTAAAAACCCTAAAAAGCTTGAACCCTAAACCCTAAAAGCCAAAAAAACC
1 AATTTATTCCGAGACCTAAAAACCCTAAAAAGCCTGAACCCTAAACCCTAAAAGCCAAAAAAACC
392906 AAACGTG
66 AAACGTG
* *
392913 AATTTATTCCGTGACCTAAAAACCCTAAAAAGCCTGAACCCTAAATCCTAAAAGCCAAAAAAACC
1 AATTTATTCCGAGACCTAAAAACCCTAAAAAGCCTGAACCCTAAACCCTAAAAGCCAAAAAAACC
392978 AAACGTG
66 AAACGTG
392985 CGCTTACGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 69 1.00
ACGTcount: A:0.47, C:0.26, G:0.10, T:0.17
Consensus pattern (72 bp):
AATTTATTCCGAGACCTAAAAACCCTAAAAAGCCTGAACCCTAAACCCTAAAAGCCAAAAAAACC
AAACGTG
Found at i:419000 original size:11 final size:11
Alignment explanation
Indices: 418981--419010 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
418971 ACTATTTATT
*
418981 TATTAATAAAA
1 TATTTATAAAA
418992 TATTTATAAAA
1 TATTTATAAAA
419003 TATTTATA
1 TATTTATA
419011 TTTATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTTATAAAA
Found at i:419404 original size:23 final size:24
Alignment explanation
Indices: 419372--419418 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
419362 TGATATTATT
419372 ATTTATTTTAAAAAATAAAAAATA
1 ATTTATTTTAAAAAATAAAAAATA
* *
419396 ATTT-TTTTAAAAATTTAAAAATA
1 ATTTATTTTAAAAAATAAAAAATA
419419 TAGTAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTTATTTTAAAAAATAAAAAATA
Found at i:424193 original size:30 final size:29
Alignment explanation
Indices: 424154--424216 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 29
424144 ATGGATTTAA
424154 ATTACTTATTATTTAAGTAAATAGATATTT
1 ATTACTTATTATTTAAGTAAA-AGATATTT
* *
424184 ATTATTTATTTTTTAAGTAAAAGATATTT
1 ATTACTTATTATTTAAGTAAAAGATATTT
424213 ATTA
1 ATTA
424217 ATTAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 12 0.39
30 19 0.61
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (29 bp):
ATTACTTATTATTTAAGTAAAAGATATTT
Found at i:424881 original size:17 final size:18
Alignment explanation
Indices: 424859--424894 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
424849 TAAATGAGTT
424859 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
424876 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
424894 A
1 A
424895 TAAAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:425204 original size:21 final size:21
Alignment explanation
Indices: 425178--425236 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
425168 GCTTTCCTGA
425178 TCAGGCACTATATGTGTCATAT
1 TCAGGCACTATATGTGTCAT-T
* *
425200 T-AGGCACCACT-TGTGTCGTT
1 TCAGGCACTA-TATGTGTCATT
*
425220 TCAGGCACTTTATGTGT
1 TCAGGCACTATATGTGT
425237 TGTATACTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
20 3 0.10
21 25 0.83
22 2 0.07
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.37
Consensus pattern (21 bp):
TCAGGCACTATATGTGTCATT
Found at i:429451 original size:4 final size:4
Alignment explanation
Indices: 429442--429470 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
429432 GTGATATTTT
429442 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
429471 ATTTTCGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:435269 original size:14 final size:13
Alignment explanation
Indices: 435244--435281 Score: 60
Period size: 14 Copynumber: 2.9 Consensus size: 13
435234 TCAGATCCTT
435244 TCAAAA-AAAAAA
1 TCAAAATAAAAAA
435256 TCAAAATCAAAAAA
1 TCAAAAT-AAAAAA
435270 TCAAAATAAAAA
1 TCAAAATAAAAA
435282 GAAAGAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 5 0.21
14 13 0.54
ACGTcount: A:0.76, C:0.11, G:0.00, T:0.13
Consensus pattern (13 bp):
TCAAAATAAAAAA
Found at i:435293 original size:12 final size:13
Alignment explanation
Indices: 435278--435306 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
435268 AATCAAAATA
435278 AAAAGAAAG-AAG
1 AAAAGAAAGAAAG
435290 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
435303 AAAA
1 AAAA
435307 ATCTAGATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:435418 original size:14 final size:14
Alignment explanation
Indices: 435401--435444 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
435391 AAAAAAAAGT
435401 GAAAAATAAAAATG
1 GAAAAATAAAAATG
435415 G-AAAATGAAAAA-G
1 GAAAAAT-AAAAATG
435428 GAAAAAGTAAAAATG
1 GAAAAA-TAAAAATG
435443 GA
1 GA
435445 GAGGCTAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
13 7 0.27
14 15 0.58
15 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.20, T:0.11
Consensus pattern (14 bp):
GAAAAATAAAAATG
Found at i:436804 original size:50 final size:49
Alignment explanation
Indices: 436740--437398 Score: 410
Period size: 50 Copynumber: 13.2 Consensus size: 49
436730 GCAGTGGAGC
* *
436740 AGATTAAAGCCACAACGGTGAATCTTGCCTTCCCGACATTGCAGTTAAA
1 AGATTAAAGCCACAACGGCGAATCTTGACTTCCCGACATTGCAGTTAAA
* * * * *
436789 ATGATTAAAGTCACAACGACGAATCTT-ACTCCCCAGGCGA-TGCAGTGAAA
1 A-GATTAAAGCCACAACGGCGAATCTTGACTTCCC-GAC-ATTGCAGTTAAA
* *
436839 CAGATTAAAGCCACATCGGTGAATCTTG-CTTCCCCGACATTGCAGTTAAAA
1 -AGATTAAAGCCACAACGGCGAATCTTGACTT-CCCGACATTGCAGTT-AAA
* * * * * * *
436890 AGATTAAAGCTAGAACAGCGAATCTT-ACTTCCCTGGCAGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTGACTTCCC-GACATTGCAGT-TAAA
* * *
436940 AGATTAAAGCCACATCGGTGAATCTTG-CTCCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTGACT-TCCCGACATTGCAGTT-AAA
* * * * * *
436990 AGATTAAAGCTACAACAGCGAATCTT-ACTCCCCAGGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTGACTTCCC-GAC-ATTGCAGT-TAAA
* *
437040 AGATTAAAGCCACAATGGCGAACCTTG-CTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTGACTT-CCCGACATTGCAGTT-AAA
* * ** * ** * *
437090 AGATTAAAGCTACAACAGCGAATCTT-ACTTATCAAGCGGTGCAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTGACTTCCCGA-CATTGCAGT-TAAA
* * **
437140 AGATTAAAACCACATCGATGAATCTTG-CTTTCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGCGAATCTTGAC-TTCCCGACATTGCAGTT-AAA
* * * * ** * *
437190 AGATTAAAGCTACAACAGCGAATCTT-ATTTCCCTGGCGGTGCAATGAAA
1 AGATTAAAGCCACAACGGCGAATCTTGACTTCCC-GACATTGCAGTTAAA
**
437239 CAGATTAAAGCCACAACGGTTAATCTTG-CTTCCCCGACATTGCAGTTAAAA
1 -AGATTAAAGCCACAACGGCGAATCTTGACTT-CCCGACATTGCAGTT-AAA
* * * * * * *
437290 AGATTAAAGCTACAACAGCGAATCTT-ACTTCCCAGGCAGTGTAGTGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTGACTTCCC-GACATTGCAGT-TAAA
* * * * **
437340 AGATTGAAGCTACAACAGCGAGTCTTG-CTTCCTCGACATCACAGTTAAA
1 AGATTAAAGCCACAACGGCGAATCTTGACTTCC-CGACATTGCAGTTAAA
437389 CAGATTAAAG
1 -AGATTAAAG
437399 TTACGAGTTA
Statistics
Matches: 457, Mismatches: 113, Indels: 79
0.70 0.17 0.12
Matches are distributed among these distances:
49 30 0.07
50 401 0.88
51 26 0.06
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (49 bp):
AGATTAAAGCCACAACGGCGAATCTTGACTTCCCGACATTGCAGTTAAA
Found at i:436895 original size:100 final size:100
Alignment explanation
Indices: 436729--437398 Score: 920
Period size: 100 Copynumber: 6.7 Consensus size: 100
436719 TCCCAGGTAG
* * *
436729 TGCAGTGGAGCAGATTAAAGCCACAACGGTGAATCTTGCCTT-CCCGACATTGCAGTTAAAATGA
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTG-CTTCCCCGACATTGCAGTTAAAAAGA
*
436793 TTAAAG-TCACAAC-GACGAATCTTACTCCCCAGGCGA
65 TTAAAGCT-ACAACAG-CGAATCTTACTTCCCAGGCGA
*
436829 TGCAGTGAAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* *
436894 TAAAGCTAGAACAGCGAATCTTACTTCCCTGGC-A
66 TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
*
436928 GTGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTCCCCCGACATTGCAGTTAAAAAGA
1 -TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
*
436993 TTAAAGCTACAACAGCGAATCTTACTCCCCAGGCGA
65 TTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
* *
437029 TGCAGTGGAACAGATTAAAGCCACAAT-GGCGAACCTTGCTTCCCCGACATTGCAGTTAAAAAGA
1 TGCAGTGGAACAGATTAAAGCCAC-ATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
** * *
437093 TTAAAGCTACAACAGCGAATCTTACTTATCAAGCGG
65 TTAAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
* * *
437129 TGCAGTGGAACAGATTAAAACCACATCGATGAATCTTGCTTTCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
* * *
437194 TAAAGCTACAACAGCGAATCTTATTTCCCTGGCGG
66 TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
* * * *
437229 TGCAATGAAACAGATTAAAGCCACAACGGTTAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
1 TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
437294 TAAAGCTACAACAGCGAATCTTACTTCCCAGGC-A
66 TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
* * * * * * * * ** *
437328 GTGTAGTGGAACAGATTGAAGCTACAACAGCGAGTCTTGCTTCCTCGACATCACAGTTAAACAGA
1 -TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGA
437393 TTAAAG
65 TTAAAG
437399 TTACGAGTTA
Statistics
Matches: 509, Mismatches: 53, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
99 6 0.01
100 498 0.98
101 5 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (100 bp):
TGCAGTGGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGAT
TAAAGCTACAACAGCGAATCTTACTTCCCAGGCGA
Found at i:437951 original size:24 final size:25
Alignment explanation
Indices: 437912--437961 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
437902 GGTCGTACCT
*
437912 GCAACAAACAAAAACA-AACACACA
1 GCAACAAACAAAAACAGAAAACACA
* *
437936 GCAACAAAGAATAACAGAAAACACA
1 GCAACAAACAAAAACAGAAAACACA
437961 G
1 G
437962 GAGAAAAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.64, C:0.24, G:0.10, T:0.02
Consensus pattern (25 bp):
GCAACAAACAAAAACAGAAAACACA
Found at i:438929 original size:22 final size:22
Alignment explanation
Indices: 438885--438943 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
438875 ATGAATGTTG
*
438885 TTTAAATTTATCACATATTATTAT
1 TTTAAATTTAT--CATATAATTAT
438909 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATATAATTAT
*
438931 TTTAAGTTT-TCAT
1 TTTAAATTTATCAT
438944 GTATCATTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 4 0.12
22 18 0.55
24 11 0.33
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (22 bp):
TTTAAATTTATCATATAATTAT
Found at i:440883 original size:19 final size:21
Alignment explanation
Indices: 440832--440886 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
440822 GGTGGATCAA
*
440832 CTCTTATGAGCTTCTGTTAAG
1 CTCTTACGAGCTTCTGTTAAG
*
440853 CTCTTACGAGCTTCTGTTCAG
1 CTCTTACGAGCTTCTGTTAAG
440874 CT-TT-CGAGCTTCT
1 CTCTTACGAGCTTCT
440887 ATTGGCGTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 9 0.28
20 2 0.06
21 21 0.66
ACGTcount: A:0.15, C:0.25, G:0.18, T:0.42
Consensus pattern (21 bp):
CTCTTACGAGCTTCTGTTAAG
Found at i:444824 original size:14 final size:14
Alignment explanation
Indices: 444805--444842 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
444795 CTCTTGAGAG
444805 AATTTTCTCTCTAC
1 AATTTTCTCTCTAC
444819 AATTTTCTCTCTAC
1 AATTTTCTCTCTAC
*
444833 AACTTTCTCT
1 AATTTTCTCT
444843 TGAATTCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (14 bp):
AATTTTCTCTCTAC
Found at i:445069 original size:37 final size:34
Alignment explanation
Indices: 445025--445134 Score: 96
Period size: 37 Copynumber: 3.0 Consensus size: 34
445015 TACAATATAA
445025 AAATTAAATTAAATTTAATATTAAGATAATTACTTT
1 AAATTAAATTAAATTTAATATTAAGATAATTA--TT
** * *
445061 AATATTAAATTAATAGAATACTATTAAGATAAGTATT
1 AA-ATTAAATTAA-A-TTTAATATTAAGATAATTATT
*
445098 AAATTAAATTAAATATTAAACTATTAAAATAA-TATT
1 AAATTAAATTAAAT-TT-AA-TATTAAGATAATTATT
445134 A
1 A
445135 TTTTTTGAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
35 2 0.03
36 18 0.30
37 24 0.40
38 1 0.02
39 15 0.25
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.40
Consensus pattern (34 bp):
AAATTAAATTAAATTTAATATTAAGATAATTATT
Found at i:445074 original size:20 final size:18
Alignment explanation
Indices: 445027--445133 Score: 62
Period size: 20 Copynumber: 5.8 Consensus size: 18
445017 CAATATAAAA
445027 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
445044 ATTAAGA-TAATTACTTTAAT
1 ATTAA-ATTAA-TA-TTTAAT
** *
445064 ATTAAATTAATAGAATACT
1 ATTAAATTAATA-TTTAAT
445083 ATTAAGA-TAAGTA-TTAA-
1 ATTAA-ATTAA-TATTTAAT
*
445100 ATTAAATTAAATATTAAACT
1 ATTAAATT-AATATTTAA-T
*
445120 ATTAAAATAATATT
1 ATTAAATTAATATT
445134 ATTTTTTGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
16 1 0.01
17 16 0.23
18 8 0.11
19 21 0.30
20 24 0.34
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:448590 original size:30 final size:30
Alignment explanation
Indices: 448530--448590 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
448520 GGTGGTGTCA
* *
448530 CTTCATGAATATCTTTCCAGGTTGATGTGT
1 CTTCATGAATATCCTTCCAGGTTGACGTGT
* * *
448560 CTTCATGTATATCCTTCCATGTTGGCGTGT
1 CTTCATGAATATCCTTCCAGGTTGACGTGT
448590 C
1 C
448591 CTGAGCTGCT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (30 bp):
CTTCATGAATATCCTTCCAGGTTGACGTGT
Found at i:458733 original size:29 final size:28
Alignment explanation
Indices: 458701--458756 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
458691 GAAAATTATT
458701 TTAAAAATACA-AAAAATTATTTTAAAAAA
1 TTAAAAAT-CATAAAAATTA-TTTAAAAAA
*
458730 TTAAAAATCATTAAAATTATTTAAAAA
1 TTAAAAATCATAAAAATTATTTAAAAA
458757 TAAAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 10 0.40
29 15 0.60
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (28 bp):
TTAAAAATCATAAAAATTATTTAAAAAA
Found at i:458807 original size:20 final size:20
Alignment explanation
Indices: 458770--458808 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
458760 AAAAAAATAC
*
458770 TTTTAAAAATATTTTTAAAA
1 TTTTAAAAATATTATTAAAA
458790 TTTTAAAAA-ATTAATTAAA
1 TTTTAAAAATATT-ATTAAA
458809 TGTTATGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTTAAAAATATTATTAAAA
Found at i:459409 original size:26 final size:27
Alignment explanation
Indices: 459356--459418 Score: 101
Period size: 26 Copynumber: 2.3 Consensus size: 27
459346 ATAAAAAATA
*
459356 ACCAAAATATTATAACTTTTTTTTATTT
1 ACCAAAATAATATAAC-TTTTTTTATTT
459384 ACCAAAATAATATAA-TTTTTTTATTT
1 ACCAAAATAATATAACTTTTTTTATTT
459410 ACCAAAATA
1 ACCAAAATA
459419 TACCAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 20 0.59
28 14 0.41
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (27 bp):
ACCAAAATAATATAACTTTTTTTATTT
Found at i:459541 original size:27 final size:27
Alignment explanation
Indices: 459472--459529 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
459462 CCTTGGTTAG
*
459472 GCCAAAGCCATTGGCGGCACCAATGGT
1 GCCAAAGCCATTGGCGACACCAATGGT
459499 GCCAAAGCCATTGGCGACACCAATGGT
1 GCCAAAGCCATTGGCGACACCAATGGT
459526 GCCA
1 GCCA
459530 TATTGATTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (27 bp):
GCCAAAGCCATTGGCGACACCAATGGT
Found at i:459797 original size:3 final size:3
Alignment explanation
Indices: 459791--459819 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
459781 ATTATTATTA
459791 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
459820 NNNNNNNNNN
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:460815 original size:18 final size:18
Alignment explanation
Indices: 460792--460829 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
460782 GGTTGGTGGT
460792 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
460810 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
460828 GA
1 GA
460830 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.47, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:465144 original size:24 final size:24
Alignment explanation
Indices: 465117--465230 Score: 63
Period size: 25 Copynumber: 4.5 Consensus size: 24
465107 TTACCTTTTT
465117 TTCTTTTTTTTCCTTCCTTCCCTC
1 TTCTTTTTTTTCCTTCCTTCCCTC
*
465141 TTCTTCTTTTTT-TTTCTCTTCTCCT-
1 TTCTT-TTTTTTCCTTC-CTTC-CCTC
* * * *
465166 TTCCTTTTCTTTTTC-TCCTTTCTTT
1 TT-CTTTT-TTTTCCTTCCTTCCCTC
* *
465191 TTCTTTCTTTTTTCTTCTCCTTTCCTC
1 TTC-TT-TTTTTTCCT-TCCTTCCCTC
465218 TTCTTTTTCTTTC
1 TTCTTTTT-TTTC
465231 TTTTTTTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 22
0.70 0.08 0.22
Matches are distributed among these distances:
24 11 0.16
25 28 0.40
26 20 0.29
27 11 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (24 bp):
TTCTTTTTTTTCCTTCCTTCCCTC
Found at i:465181 original size:19 final size:19
Alignment explanation
Indices: 465159--465196 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
465149 TTTTTTTCTC
465159 TTCTCCTTTCCTTTTCTTT
1 TTCTCCTTTCCTTTTCTTT
*
465178 TTCTCCTTTCTTTTTCTTT
1 TTCTCCTTTCCTTTTCTTT
465197 CTTTTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTCTCCTTTCCTTTTCTTT
Found at i:465186 original size:14 final size:14
Alignment explanation
Indices: 465167--465213 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
465157 TCTTCTCCTT
465167 TCCTTTTCTTTTTC
1 TCCTTTTCTTTTTC
465181 TCC-TTTCTTTTTC
1 TCCTTTTCTTTTTC
* *
465194 TTTCTTTT-TTCTTC
1 -TCCTTTTCTTTTTC
465208 TCCTTT
1 TCCTTT
465214 CCTCTTCTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 15 0.54
14 10 0.36
15 3 0.11
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TCCTTTTCTTTTTC
Found at i:465197 original size:4 final size:4
Alignment explanation
Indices: 465190--465361 Score: 80
Period size: 4 Copynumber: 43.0 Consensus size: 4
465180 CTCCTTTCTT
465190 TTTC TTTC TTT- TTTC TTCTCC TTTCC TCTTC -TT- TTTC TTTC TTT-
1 TTTC TTTC TTTC TTTC TT-T-C TTT-C T-TTC TTTC TTTC TTTC TTTC
* * *
465234 TTTT TTTC TCTTC -TCC TTTC GTTTTC TTTC CTTC -TT- TTTC TTTC TTT-
1 TTTC TTTC T-TTC TTTC TTTC --TTTC TTTC TTTC TTTC TTTC TTTC TTTC
* *
465281 TTT- TTTC TCTTC -TCC TTTCC TTTAC TTTC CTTC -TT- TTTC TTTC TTTCC
1 TTTC TTTC T-TTC TTTC TTT-C TTT-C TTTC TTTC TTTC TTTC TTTC TTT-C
* * *
465329 TCTCC TTCC TTCC TTTC TTTC TTTC TTTC TTTC
1 T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
465362 CCTCTCCTTC
Statistics
Matches: 137, Mismatches: 10, Indels: 42
0.72 0.05 0.22
Matches are distributed among these distances:
3 28 0.20
4 75 0.55
5 24 0.18
6 10 0.07
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.69
Consensus pattern (4 bp):
TTTC
Found at i:465210 original size:46 final size:43
Alignment explanation
Indices: 465134--465326 Score: 184
Period size: 46 Copynumber: 4.5 Consensus size: 43
465124 TTTTCCTTCC
* * *
465134 TTCCCTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTT
1 TTCCTTCTTTTTCTTTCTTTTT-TCTTCTCCTTTCCTTTTC-TTT
*
465179 TCTCCTTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTT
1 T-TCC-TTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTT
* * *
465224 TT-CTT-TCTTT-TTT-TTTTCTCTTCTCCTTTCGTTTTC--T
1 TTCCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTT
* *
465261 TTCCTTCTTTTTCTTTCTTTTTTTTTCT-CTTCTCCTTTCCTTTACT
1 TTCCTTCTTTTTCTTTCTTTTTTCTTCTCCTT-TCCTTTTC-TT--T
465307 TTCCTTCTTTTTCTTTCTTT
1 TTCCTTCTTTTTCTTTCTTT
465327 CCTCTCCTTC
Statistics
Matches: 123, Mismatches: 13, Indels: 23
0.77 0.08 0.14
Matches are distributed among these distances:
37 3 0.02
38 3 0.02
39 24 0.20
40 9 0.07
41 19 0.15
42 2 0.02
43 1 0.01
44 1 0.01
45 5 0.04
46 41 0.33
47 15 0.12
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (43 bp):
TTCCTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTT
Found at i:465277 original size:80 final size:83
Alignment explanation
Indices: 465147--465324 Score: 231
Period size: 80 Copynumber: 2.1 Consensus size: 83
465137 CCTCTTCTTC
465147 TTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTTTCTCCTTTCTTTTTCTTTCTTTTTTCTTCTCCT
1 TTTTTTTTTCTCTTCTCCTTTCCTTTTC--TTTCTCCTTTCTTTTTCTTTCTTTTTTCTTCT-CT
* *
465212 T-TCCTCTTCTTTTTCTTT-CT
63 TCTCCT-TTCCTTTACTTTCCT
* *
465232 TTTTTTTTTCTCTTCTCCTTTCGTTTTC-TT-TCC-TTCTTTTTCTTTCTTTTTTTTTCTCTTCT
1 TTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCTCCTTTCTTTTTCTTTCTTTTTTCTTCTCTTCT
465294 CCTTTCCTTTACTTTCCT
66 CCTTTCCTTTACTTTCCT
465312 TCTTTTTCTTTCT
1 T-TTTTT-TTTCT
465325 TTCCTCTCCT
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
79 13 0.15
80 30 0.35
81 8 0.09
82 7 0.08
85 27 0.32
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.71
Consensus pattern (83 bp):
TTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCTCCTTTCTTTTTCTTTCTTTTTTCTTCTCTTCT
CCTTTCCTTTACTTTCCT
Found at i:465299 original size:36 final size:36
Alignment explanation
Indices: 465259--465370 Score: 106
Period size: 36 Copynumber: 3.1 Consensus size: 36
465249 CTTTCGTTTT
*
465259 CTTTCCTTCTTTTTCTTTCTTTTTTTTTCTCTTCTC
1 CTTTCCTTCTCTTTCTTTCTTTTTTTTTCTCTTCTC
* *
465295 CTTTCCTT-TACTTTCCTTCTTTTTCTTTCT-TTCCTC
1 CTTTCCTTCT-CTTTCTTTCTTTTTTTTTCTCTT-CTC
* *
465331 TCCTTCCTTC-CTTTCTTTCTTTCTTTCTTTC-CCTCTC
1 -CTTTCCTTCTCTTTCTTTCTTT-TTT-TTTCTCTTCTC
465368 CTT
1 CTT
465371 CTCCCCCCAC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
35 3 0.05
36 41 0.67
37 12 0.20
38 5 0.08
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (36 bp):
CTTTCCTTCTCTTTCTTTCTTTTTTTTTCTCTTCTC
Found at i:465343 original size:46 final size:45
Alignment explanation
Indices: 465217--465360 Score: 150
Period size: 46 Copynumber: 3.2 Consensus size: 45
465207 CTCCTTTCCT
** * *
465217 CTTCTTTTTCTTTCTTTTTTTTTTCTCTTCTCCTTTCGTTTTCTTTC
1 CTTCTTTTTCTTTC-TTTTCCTCTCTCTTCTCCTTTC-CTTTCTTTC
** *
465264 CTTCTTTTTCTTTCTTTTTTTTTCTCTTCTCCTTTCCTTTACTTTC
1 CTTCTTTTTCTTTCTTTTCCTCTCTCTTCTCCTTTCCTTT-CTTTC
465310 CTTCTTTTTCTTTC-TTTCCTCTC-CTTCCTTCCTTT-CTTTCTTTC
1 CTTCTTTTTCTTTCTTTTCCTCTCTCTT-C-TCCTTTCCTTTCTTTC
*
465354 TTTCTTT
1 CTTCTTT
465361 CCCTCTCCTT
Statistics
Matches: 89, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
44 14 0.16
45 14 0.16
46 47 0.53
47 14 0.16
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (45 bp):
CTTCTTTTTCTTTCTTTTCCTCTCTCTTCTCCTTTCCTTTCTTTC
Found at i:465518 original size:22 final size:22
Alignment explanation
Indices: 465493--465536 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
465483 TTTTTTTTGG
465493 TATATTTTGGTAAATAAAAAAA
1 TATATTTTGGTAAATAAAAAAA
465515 TATATTTTGGTAAATAAAAAAA
1 TATATTTTGGTAAATAAAAAAA
465537 GTTATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (22 bp):
TATATTTTGGTAAATAAAAAAA
Found at i:467048 original size:151 final size:152
Alignment explanation
Indices: 466882--467185 Score: 601
Period size: 151 Copynumber: 2.0 Consensus size: 152
466872 TGGTAAAAAT
466882 TTTTTTATTATATTTAATGTAATTTAATTTAAATATTTTTTTAATTATATTAAAATTTAATATTT
1 TTTTTTATTATATTTAATGTAATTTAATTTAAATATTTTTTTAATTATATTAAAATTTAATATTT
466947 GTAATCTACTCATTCCTCCATCACCCTTAATCGAACCCTACTTGCGAGATGTTGGATTTTTGCAC
66 GTAATCTACTCATTCCTCCATCACCCTTAATCGAACCCTACTTGCGAGATGTTGGATTTTTGCAC
467012 GTGGCTCTTATTGGTTGGGGTG
131 GTGGCTCTTATTGGTTGGGGTG
467034 TTTTTTATTA-ATTTAATGTAATTTAATTTAAATATTTTTTTAATTATATTAAAATTTAATATTT
1 TTTTTTATTATATTTAATGTAATTTAATTTAAATATTTTTTTAATTATATTAAAATTTAATATTT
467098 GTAATCTACTCATTCCTCCATCACCCTTAATCGAACCCTACTTGCGAGATGTTGGATTTTTGCAC
66 GTAATCTACTCATTCCTCCATCACCCTTAATCGAACCCTACTTGCGAGATGTTGGATTTTTGCAC
467163 GTGGCTCTTATTGGTTGGGGTG
131 GTGGCTCTTATTGGTTGGGGTG
467185 T
1 T
467186 AAATTGGGCC
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
151 142 0.93
152 10 0.07
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (152 bp):
TTTTTTATTATATTTAATGTAATTTAATTTAAATATTTTTTTAATTATATTAAAATTTAATATTT
GTAATCTACTCATTCCTCCATCACCCTTAATCGAACCCTACTTGCGAGATGTTGGATTTTTGCAC
GTGGCTCTTATTGGTTGGGGTG
Found at i:470137 original size:50 final size:46
Alignment explanation
Indices: 470028--470153 Score: 144
Period size: 50 Copynumber: 2.7 Consensus size: 46
470018 GGGAAAGAGA
* * **
470028 TCCCATGTAAGACCATGTCTAGGACATGGCGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTTTGGGACATGGCGCACCGAGATGAGAAC
** * *
470074 TCCCCCGTAAGACCATGTTTGGGACATGGCATGGACACTGATATGAGAAC
1 TCCCATGTAAGACCATGTTTGGGACATGGC---G-CACCGAGATGAGAAC
470124 TCCCATGTAAGACCATGTTTGGGACATGGC
1 TCCCATGTAAGACCATGTTTGGGACATGGC
470154 TTTGGCATGT
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
46 26 0.39
49 1 0.02
50 39 0.59
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (46 bp):
TCCCATGTAAGACCATGTTTGGGACATGGCGCACCGAGATGAGAAC
Found at i:474679 original size:35 final size:35
Alignment explanation
Indices: 474615--474696 Score: 98
Period size: 36 Copynumber: 2.4 Consensus size: 35
474605 AAAACTTTAA
* * *
474615 AAAATATA-AAAAAATCCCCTAAACTTTAAAC-TT
1 AAAATATATAAAAAATCCACAAAACCTTAAACATT
474648 AAAATATATAAAAAATCCTACAAAACCTTAAACATT
1 AAAATATATAAAAAATCC-ACAAAACCTTAAACATT
474684 AAAAT-TCATAAAA
1 AAAATAT-ATAAAA
474697 CCCTATCCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
33 8 0.19
34 9 0.21
35 12 0.29
36 13 0.31
ACGTcount: A:0.59, C:0.16, G:0.00, T:0.26
Consensus pattern (35 bp):
AAAATATATAAAAAATCCACAAAACCTTAAACATT
Found at i:484520 original size:41 final size:41
Alignment explanation
Indices: 484463--484627 Score: 330
Period size: 41 Copynumber: 4.0 Consensus size: 41
484453 TGAAAAAGAA
484463 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
1 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
484504 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
1 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
484545 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
1 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
484586 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
1 AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
484627 A
1 A
484628 TGTTACTATG
Statistics
Matches: 124, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 124 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (41 bp):
AGATCCCAGTGATGGGCATATATAGTTTATATATCACTTGC
Found at i:485242 original size:14 final size:15
Alignment explanation
Indices: 485223--485251 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
485213 GTGGCACTTC
485223 TTCATTG-GATTATA
1 TTCATTGTGATTATA
485237 TTCATTGTGATTATA
1 TTCATTGTGATTATA
485252 ACGGTGCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (15 bp):
TTCATTGTGATTATA
Found at i:487461 original size:22 final size:20
Alignment explanation
Indices: 487424--487463 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
487414 AAAAAAATTA
*
487424 AGATTTTAAAATTTTTTAAT
1 AGATTTTAAAAATTTTTAAT
487444 AGATTTTCCAAAAATTTTTA
1 AGATTTT--AAAAATTTTTA
487464 GTGTAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
22 10 0.59
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
AGATTTTAAAAATTTTTAAT
Found at i:492263 original size:50 final size:50
Alignment explanation
Indices: 492151--492448 Score: 283
Period size: 50 Copynumber: 5.8 Consensus size: 50
492141 ATTTGGGTAA
* * * *
492151 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATG
1 AGAGGTCCCAAGTAAGACCATGTCTGGGACATGGCGTTGGCA-C--CGAG---ATG
* * * *
492207 AGAGGTCCCAAGTCAGACCATGTTTGGGGCATGGCGTTGGCACTGAGATG
1 AGAGGTCCCAAGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
492257 AGAGGTCCTATGTAAGACCACGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCAAGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * *
492307 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGCTG
1 AGAGGTCCCAAGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
* * * * * *
492357 AGAGGTCCCCCA-TAAGACCATGTCTGGGACATGGCATGGGCACCTATATA
1 AGAGGT-CCCAAGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
** * * * * *
492407 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 AGAGGTCCCAAGTAAGACCATGTCTGGGACATGGCGTTGGCA
492449 GTNNNNNNNN
Statistics
Matches: 207, Mismatches: 33, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
49 2 0.01
50 161 0.78
51 3 0.01
53 4 0.02
55 1 0.00
56 36 0.17
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCAAGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
Found at i:492344 original size:100 final size:100
Alignment explanation
Indices: 492151--492448 Score: 317
Period size: 100 Copynumber: 2.9 Consensus size: 100
492141 ATTTGGGTAA
* *
492151 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGTCCC
* * * * **
492216 AAGTCAGACCATGTTTGGGGCATGGCGTTGGCACTGAGATG
60 ATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
* * *
492257 AGAGGTCCTATGTAAGACCACGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
*
492322 GACCATGTCTGGGACATGGCGTTGGCACCAAGCTG
66 GACCATGTCTGGGACATGGCGTTGGCACCAAGATG
*** * * * * ** *
492357 AGAGGTCCCCCATAAGACCATGTCTGGGACATGGCATGGGCACCTATATAAGAACTCTCATGTAA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
* * *
492422 GACCATATCTGGGATATGGCATTGGCA
66 GACCATGTCTGGGACATGGCGTTGGCA
492449 GTNNNNNNNN
Statistics
Matches: 164, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
100 122 0.74
103 3 0.02
105 1 0.01
106 38 0.23
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (100 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCCCATGTAA
GACCATGTCTGGGACATGGCGTTGGCACCAAGATG
Found at i:492433 original size:150 final size:152
Alignment explanation
Indices: 492151--492448 Score: 336
Period size: 150 Copynumber: 1.9 Consensus size: 152
492141 ATTTGGGTAA
*
492151 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AG--TATGAGAGGTCCC
* * * * * * ** *
492216 AAGTCAGACCATGTTTGGGGCATGGCGTTGGCACTGAGATGAGAGGTCCTATGTAAGACCACGTC
62 AAGTAAGACCATGTCTGGGACATGGCATGGGCACTGAGATAAGAACTCCTATGTAAGACCACATC
*
492281 TGGGACATGGCGTTGGCACCGAGATG
127 TGGGACATGGCATTGGCACCGAGATG
* * * *
492307 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCA-AG-CTGAGAGGTCCCCCA-
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGT-CCCAAG
* *
492369 TAAGACCATGTCTGGGACATGGCATGGGCACCT-ATATAAGAACT-CTCATGTAAGACCATATCT
65 TAAGACCATGTCTGGGACATGGCATGGGCA-CTGAGATAAGAACTCCT-ATGTAAGACCACATCT
*
492432 GGGATATGGCATTGGCA
128 GGGACATGGCATTGGCA
492449 GTNNNNNNNN
Statistics
Matches: 121, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
149 2 0.02
150 69 0.57
151 6 0.05
153 2 0.02
156 42 0.35
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.22
Consensus pattern (152 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGTATGAGAGGTCCCAAGT
AAGACCATGTCTGGGACATGGCATGGGCACTGAGATAAGAACTCCTATGTAAGACCACATCTGGG
ACATGGCATTGGCACCGAGATG
Found at i:492607 original size:29 final size:29
Alignment explanation
Indices: 492565--492622 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
492555 TTATAGGAGT
492565 TAAGAACATATTATGTTATCAATTGAGAA
1 TAAGAACATATTATGTTATCAATTGAGAA
492594 TAAGAACATATTATGTTATCAATTGAGAA
1 TAAGAACATATTATGTTATCAATTGAGAA
492623 CCAACATTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAGAACATATTATGTTATCAATTGAGAA
Found at i:495229 original size:16 final size:16
Alignment explanation
Indices: 495202--495248 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
495192 TAGAATTTGG
495202 TTGAGAAAATTATTTAA
1 TTGAG-AAATTATTTAA
*
495219 TTGAGAAATTAATTAA
1 TTGAGAAATTATTTAA
495235 TT-A-AAATTAATTTA
1 TTGAGAAATT-ATTTA
495249 TGATATTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 12 0.44
17 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (16 bp):
TTGAGAAATTATTTAA
Found at i:498924 original size:40 final size:40
Alignment explanation
Indices: 498828--498986 Score: 185
Period size: 41 Copynumber: 3.9 Consensus size: 40
498818 TTATCCCTTG
* *
498828 TTTGTACTTCGGTACGCC-TGAATTGTACATACGTGCCCATG
1 TTTGTACTTCGGTAC-CCTTGAATTGCACATACGTGCCC-TA
* * *
498869 TTTGTACTTTGGTACCATTGAATTACACATACGTGCCCTA
1 TTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCTA
* *
498909 TTTGTACTTCGGTACCCTTAAATTGCACATACGTGCCTTTA
1 TTTGTACTTCGGTACCCTTGAATTGCACATACGTGCC-CTA
* * * *
498950 TTTGTACTTTGGTACCCTTGAATAGCATATACATGCC
1 TTTGTACTTCGGTACCCTTGAATTGCACATACGTGCC
498987 TCATTTTACA
Statistics
Matches: 101, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
40 35 0.35
41 66 0.65
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (40 bp):
TTTGTACTTCGGTACCCTTGAATTGCACATACGTGCCCTA
Found at i:505803 original size:20 final size:19
Alignment explanation
Indices: 505778--505953 Score: 57
Period size: 20 Copynumber: 8.7 Consensus size: 19
505768 GGGTACCGAA
505778 GTGCAAACAGGGGCACATAT
1 GTGCAAACAGGGGCAC-TAT
** * *
505798 GTGCAATTTA-GGGTACTGAA
1 GTGCAA-ACAGGGGCACT-AT
*
505818 GTACAAACAGGGGCACATAT
1 GTGCAAACAGGGGCAC-TAT
* * *
505838 GTGCAATTCAGGGGTACCGAT
1 GTGCAA-ACAGGGGCA-CTAT
* *
505859 GTACAAACATGGGCACGTAT
1 GTGCAAACAGGGGCAC-TAT
* * * *
505879 GTGTAATTCAGGGGTACTAAA
1 GTGCAA-ACAGGGGCACT-AT
* *
505900 GTACAAATAGGGGCACGTAT
1 GTGCAAACAGGGGCAC-TAT
* * *
505920 GTGCAATTCAGGGGTACCTAA
1 GTGCAA-ACAGGGGCA-CTAT
*
505941 GTACAAACAGGGG
1 GTGCAAACAGGGG
505954 ATAATTCAGT
Statistics
Matches: 107, Mismatches: 37, Indels: 24
0.64 0.22 0.14
Matches are distributed among these distances:
19 3 0.03
20 60 0.56
21 42 0.39
22 2 0.02
ACGTcount: A:0.33, C:0.16, G:0.30, T:0.21
Consensus pattern (19 bp):
GTGCAAACAGGGGCACTAT
Found at i:505865 original size:41 final size:41
Alignment explanation
Indices: 505756--505953 Score: 263
Period size: 41 Copynumber: 4.9 Consensus size: 41
505746 GTTACCGGAG
* * *
505756 TGTGCTATTCAAGGGTACCGAAGTGCAAACAGGGGCACATA
1 TGTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACATA
* *
505797 TGTGCAATTTA-GGGTACTGAAGTACAAACAGGGGCACATA
1 TGTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACATA
* * *
505837 TGTGCAATTCAGGGGTACCGATGTACAAACATGGGCACGTA
1 TGTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACATA
* ** * *
505878 TGTGTAATTCAGGGGTACTAAAGTACAAATAGGGGCACGTA
1 TGTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACATA
*
505919 TGTGCAATTCAGGGGTACCTAAGTACAAACAGGGG
1 TGTGCAATTCAGGGGTACCGAAGTACAAACAGGGG
505954 ATAATTCAGT
Statistics
Matches: 137, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
40 37 0.27
41 100 0.73
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (41 bp):
TGTGCAATTCAGGGGTACCGAAGTACAAACAGGGGCACATA
Found at i:506129 original size:53 final size:53
Alignment explanation
Indices: 506040--506143 Score: 163
Period size: 53 Copynumber: 2.0 Consensus size: 53
506030 CTATGAACTT
* *
506040 AGCTTGACAACTAGAGCGTAAAAGTACAATCGAGCTAATTCATGATTTTCACC
1 AGCTTGACAACTAAAGCGTAAAAGTACAATCAAGCTAATTCATGATTTTCACC
** *
506093 AGCTTGACAACTAAAGCGTAAAAGTATGATCAAGCTAATTCATGGTTTTCA
1 AGCTTGACAACTAAAGCGTAAAAGTACAATCAAGCTAATTCATGATTTTCA
506144 TCTTTCCTCG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (53 bp):
AGCTTGACAACTAAAGCGTAAAAGTACAATCAAGCTAATTCATGATTTTCACC
Found at i:507821 original size:48 final size:47
Alignment explanation
Indices: 507716--507849 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 47
507706 GGAAGAATGG
* * * ** *
507716 GGCAGTTTATCTGCAAATGTGGTGGCTTCTCCATGA-TTTGATTATGT
1 GGCAGTTTATCTGC-ATTTTGGTGGCTTGTCCACAATTTTGATCATGT
*
507763 GGTAGTTTATCTGCGATTTTGGTGGCTTGTCCACAATTTTGATCATGT
1 GGCAGTTTATCTGC-ATTTTGGTGGCTTGTCCACAATTTTGATCATGT
* * *
507811 GGCAGTTTATCTGCATTTTTGTGACATTGTTCACAATTT
1 GGCAGTTTATCTGCATTTTGGTGGC-TTGTCCACAATTT
507850 GGTGTGTTGG
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
47 38 0.52
48 35 0.48
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.43
Consensus pattern (47 bp):
GGCAGTTTATCTGCATTTTGGTGGCTTGTCCACAATTTTGATCATGT
Found at i:512427 original size:27 final size:26
Alignment explanation
Indices: 512373--512429 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
512363 TAAAATGATA
* *
512373 ATTTTACCTCTAGGGGTATTTTGGTC
1 ATTTTACCTCTAGGGGTATTTCGATC
* *
512399 ATTTTACCTTTTGAGGGTATTTCGATC
1 ATTTTACCTCTAG-GGGTATTTCGATC
512426 ATTT
1 ATTT
512430 AACAACCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 11 0.42
27 15 0.58
ACGTcount: A:0.18, C:0.14, G:0.19, T:0.49
Consensus pattern (26 bp):
ATTTTACCTCTAGGGGTATTTCGATC
Found at i:525691 original size:12 final size:12
Alignment explanation
Indices: 525676--525718 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
525666 TTCACTCGTT
* *
525676 TCTTTTGCAAAC
1 TCTTTTTCAATC
*
525688 TCTTTTTCAATT
1 TCTTTTTCAATC
525700 TCTTTTTCAATC
1 TCTTTTTCAATC
525712 TCTTTTT
1 TCTTTTT
525719 GCTTTTCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.16, C:0.21, G:0.02, T:0.60
Consensus pattern (12 bp):
TCTTTTTCAATC
Found at i:525725 original size:24 final size:24
Alignment explanation
Indices: 525674--525750 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
525664 TCTTCACTCG
* * **
525674 TTTCTTTTGCAAACTCTTTTTCAA
1 TTTCTTTTTCAATCTCTTTTTCTT
525698 TTTCTTTTTCAATCTCTTTTTGCTTT
1 TTTCTTTTTCAATCTCTTTTT-C-TT
525724 TCTTCTTTTTC-ATCTCTTTTTTCTT
1 T-TTCTTTTTCAATCTC-TTTTTCTT
525749 TT
1 TT
525751 CACTCTCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
24 20 0.44
25 4 0.09
26 7 0.16
27 14 0.31
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.66
Consensus pattern (24 bp):
TTTCTTTTTCAATCTCTTTTTCTT
Found at i:525739 original size:26 final size:27
Alignment explanation
Indices: 525699--525751 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
525689 CTTTTTCAAT
525699 TTCTTTTTCAATCTCTTTTTGCTTTTC
1 TTCTTTTTCAATCTCTTTTTGCTTTTC
*
525726 TTCTTTTTC-ATCTCTTTTTTCTTTTC
1 TTCTTTTTCAATCTCTTTTTGCTTTTC
525752 ACTCTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.70
Consensus pattern (27 bp):
TTCTTTTTCAATCTCTTTTTGCTTTTC
Found at i:525744 original size:27 final size:26
Alignment explanation
Indices: 525699--525751 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
525689 CTTTTTCAAT
525699 TTCTTTTTCAATCTCTTTTTGCTTTTC
1 TTCTTTTTCAATCTCTTTTT-CTTTTC
525726 TTCTTTTTC-ATCTCTTTTTTCTTTTC
1 TTCTTTTTCAATCTC-TTTTTCTTTTC
525752 ACTCTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.06, C:0.23, G:0.02, T:0.70
Consensus pattern (26 bp):
TTCTTTTTCAATCTCTTTTTCTTTTC
Found at i:525752 original size:17 final size:20
Alignment explanation
Indices: 525720--525761 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
525710 TCTCTTTTTG
525720 CTTTTCTTCTTTTTCA-TCT
1 CTTTTCTTCTTTTTCACTCT
525739 CTTTT-TTC-TTTTCACTCT
1 CTTTTCTTCTTTTTCACTCT
525757 CTTTT
1 CTTTT
525762 GTTTTTGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.27
18 11 0.50
19 5 0.23
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (20 bp):
CTTTTCTTCTTTTTCACTCT
Found at i:525767 original size:17 final size:16
Alignment explanation
Indices: 525729--525767 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
525719 GCTTTTCTTC
*
525729 TTTTTCATCTCTTTTT
1 TTTTTCATCTCTTTTG
525745 TCTTTTCACTCTCTTTTG
1 T-TTTTCA-TCTCTTTTG
525763 TTTTT
1 TTTTT
525768 GAAATCTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.05, C:0.21, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTCATCTCTTTTG
Found at i:525829 original size:12 final size:12
Alignment explanation
Indices: 525787--525828 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
525777 TTTTCATCTT
525787 TTTCTTTTTC-A
1 TTTCTTTTTCAA
525798 TTTC--TTTCAA
1 TTTCTTTTTCAA
525808 TTTCTTTTTCAA
1 TTTCTTTTTCAA
525820 TGTTCTTTT
1 T-TTCTTTT
525829 CTCGCTCACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 4 0.15
12 7 0.26
13 7 0.26
ACGTcount: A:0.12, C:0.17, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:531709 original size:36 final size:36
Alignment explanation
Indices: 531661--531732 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
531651 TGAGTTATAA
531661 AAGTTGGATTGTAGTCCTTGCGTCCCTCAGTTTTGG
1 AAGTTGGATTGTAGTCCTTGCGTCCCTCAGTTTTGG
*
531697 AAGTTGGGTTGTAGTCCTTGCGTCCCTCAGTTTTGG
1 AAGTTGGATTGTAGTCCTTGCGTCCCTCAGTTTTGG
531733 TTGGTTACCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.39
Consensus pattern (36 bp):
AAGTTGGATTGTAGTCCTTGCGTCCCTCAGTTTTGG
Found at i:534638 original size:50 final size:50
Alignment explanation
Indices: 534522--534692 Score: 207
Period size: 50 Copynumber: 3.3 Consensus size: 50
534512 NNNNNNNNNN
*
534522 TTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTC
1 TTACATGGGAGCTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTC
** *
534572 TTACGGGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTC
1 TTACATGGGAGCTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTC
* * * *
534622 TTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCAAGACATGGTC
1 TTACATGGGAGCTCTCAT-A--TC---GGTGCCCATGCCATGTCCCAGACATGGTC
*
534678 TTACATGGGATCTCT
1 TTACATGGGAGCTCT
534693 TTACCCAAAA
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
50 62 0.59
51 1 0.01
53 2 0.02
56 40 0.38
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (50 bp):
TTACATGGGAGCTCTCATATCGGTGCCCATGCCATGTCCCAGACATGGTC
Found at i:537062 original size:25 final size:25
Alignment explanation
Indices: 537008--537056 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
536998 AATTAAAGTG
537008 GGAATAAATTAAAACTAATTATATT
1 GGAATAAATTAAAACTAATTATATT
*
537033 GGAATAAA-TAAAATTAATTATATT
1 GGAATAAATTAAAACTAATTATATT
537057 ATGAATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.65
25 8 0.35
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (25 bp):
GGAATAAATTAAAACTAATTATATT
Found at i:537272 original size:20 final size:19
Alignment explanation
Indices: 537243--537292 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
537233 ATTCATCATG
537243 TTAA-TATTTTTA-ACATAAT
1 TTAATTATTTTTATA-AT-AT
537262 TTAATTATTTTTATAATAT
1 TTAATTATTTTTATAATAT
537281 TTAATTATTTTT
1 TTAATTATTTTT
537293 CGACAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 18 0.62
20 10 0.34
21 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTAATTATTTTTATAATAT
Found at i:551384 original size:35 final size:36
Alignment explanation
Indices: 551333--551513 Score: 183
Period size: 35 Copynumber: 5.1 Consensus size: 36
551323 CTATTTGGCA
* * *
551333 TGTTTCGGTTGAACTAGCTCTTTTGAGCATTGA-TG
1 TGTTTTGGTTGGACTAGCTCTTATGAGCATTGAGTG
* *
551368 TGTTTTAGTTGGACTAGCTCTTATGAGCATT-AGCG
1 TGTTTTGGTTGGACTAGCTCTTATGAGCATTGAGTG
* * * *
551403 TGTTTTGGTTGGAATAGCTCTTATTAGCA-TCAGCG
1 TGTTTTGGTTGGACTAGCTCTTATGAGCATTGAGTG
* ** *
551438 TGTTTCGGTTGGACTAGCTCTTATGAGCATCAACT-
1 TGTTTTGGTTGGACTAGCTCTTATGAGCATTGAGTG
* *
551473 TGTTTTGGTTGGATTGGCTCTTATGAGCATCTG-GTG
1 TGTTTTGGTTGGACTAGCTCTTATGAGCAT-TGAGTG
551509 TGTTT
1 TGTTT
551514 GAGTGGTTTG
Statistics
Matches: 120, Mismatches: 21, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
34 2 0.02
35 112 0.93
36 6 0.05
ACGTcount: A:0.17, C:0.14, G:0.27, T:0.42
Consensus pattern (36 bp):
TGTTTTGGTTGGACTAGCTCTTATGAGCATTGAGTG
Found at i:559524 original size:22 final size:21
Alignment explanation
Indices: 559469--559528 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 21
559459 TAATTTTATT
559469 TTTATTTTTATTTTTTATTCAA
1 TTTA-TTTTATTTTTTATTCAA
**
559491 TTT-TGTGTTATTTTTTATTTTA
1 TTTAT-T-TTATTTTTTATTCAA
559513 TTTATTTCTATTTTTT
1 TTTATTT-TATTTTTT
559529 GCAAAATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
20 1 0.03
21 2 0.06
22 28 0.88
23 1 0.03
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (21 bp):
TTTATTTTATTTTTTATTCAA
Found at i:560116 original size:20 final size:20
Alignment explanation
Indices: 560073--560114 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
560063 ACAAAATCTT
560073 AAAGCAAAAATTCCACCTAG
1 AAAGCAAAAATTCCACCTAG
*
560093 AAAGCAAAACTTCCACC-AG
1 AAAGCAAAAATTCCACCTAG
560112 AAA
1 AAA
560115 AGGACATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.12
Consensus pattern (20 bp):
AAAGCAAAAATTCCACCTAG
Found at i:563815 original size:32 final size:32
Alignment explanation
Indices: 563748--563951 Score: 286
Period size: 32 Copynumber: 6.4 Consensus size: 32
563738 GAATGGCTAC
* * *
563748 AAGCCATAAGT-ACAGTAATAT-ATTGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*** *
563778 AAGCCATCAGTAGTAGTGATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
563810 CAGCCATCAGTAACGGTAATATGATCGGTACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
*
563842 AAGCCATCAGTAACGGTAATATGATCGACACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
* *
563874 ACGCCATCAGTAACGGTAATATGATCAGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
563906 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACGGTAATATGATCGGCACA
563938 AAGCCATCAGTAAC
1 AAGCCATCAGTAAC
563952 CATCAGTAAC
Statistics
Matches: 153, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
30 10 0.07
31 7 0.05
32 136 0.89
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (32 bp):
AAGCCATCAGTAACGGTAATATGATCGGCACA
Found at i:563960 original size:42 final size:42
Alignment explanation
Indices: 563909--564035 Score: 254
Period size: 42 Copynumber: 3.0 Consensus size: 42
563899 CAGCACAAAG
563909 CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
1 CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
563951 CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
1 CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
563993 CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
1 CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
564035 C
1 C
564036 ATCGCAGCAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 85 1.00
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (42 bp):
CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAA
Found at i:564029 original size:74 final size:74
Alignment explanation
Indices: 563845--564035 Score: 203
Period size: 74 Copynumber: 2.6 Consensus size: 74
563835 CGGTACAAAG
*
563845 CCATCAGTAACGGTAATATGATCGACACAACGCCATCAGTAACGGTAATATGATCAGCACAAAGC
1 CCATCAGTAACGGTAATATGATCGACACAAAGCCATCAGTAACGGTAATATGATCAGCACAAAGC
563910 CATCAGTAA
66 CATCAGTAA
** * * * * ** *
563919 CGGT-AATATGATCGGCACA-A--AGCCATCAGTAA-CCATCAGTAACGGTAATATGATCGGCAC
1 CCATCAGTA--A-CGGTA-ATATGATCGA-CACAAAGCCATCAGTAACGGTAATATGATCAGCAC
563979 AAAGCCATCAGTAA
61 AAAGCCATCAGTAA
*
563993 CCATCAGTAACGGTAATATGATCGGCACAAAGCCATCAGTAAC
1 CCATCAGTAACGGTAATATGATCGACACAAAGCCATCAGTAAC
564036 ATCGCAGCAA
Statistics
Matches: 88, Mismatches: 19, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
71 1 0.01
72 5 0.06
73 8 0.09
74 61 0.69
75 7 0.08
76 5 0.06
77 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (74 bp):
CCATCAGTAACGGTAATATGATCGACACAAAGCCATCAGTAACGGTAATATGATCAGCACAAAGC
CATCAGTAA
Found at i:564277 original size:23 final size:23
Alignment explanation
Indices: 564219--564285 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
564209 TCGTTCAAAT
* *
564219 CACAGCCAAATCAGTCATACTAAA
1 CACAGACAAATCAGTCAT-TTAAA
* *
564243 CACTGACAAATCAGTCATTTAAC
1 CACAGACAAATCAGTCATTTAAA
*
564266 CACAGACAAATCAATCATTT
1 CACAGACAAATCAGTCATTT
564286 GACCTCGAGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 21 0.57
24 16 0.43
ACGTcount: A:0.43, C:0.27, G:0.07, T:0.22
Consensus pattern (23 bp):
CACAGACAAATCAGTCATTTAAA
Found at i:564365 original size:27 final size:27
Alignment explanation
Indices: 564324--564553 Score: 320
Period size: 27 Copynumber: 8.6 Consensus size: 27
564314 CCACTAGGGC
564324 ATTACGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * *
564351 ATTACGATCAGTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
564378 ATTACGGTCA-TTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * *
564404 ATTACGGTTATTTTACCTTACTGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
564431 ATTACGGTCATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
564458 ATTACGGTCATTTTACCCTATA-GGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
564484 ATTACGGTTATTTTACCCTACATGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
564511 ATTACAGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
564538 ATTACGATCATTTTAC
1 ATTACGGTCATTTTAC
564554 AACCTTTCCG
Statistics
Matches: 177, Mismatches: 24, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
26 47 0.27
27 130 0.73
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:564367 original size:53 final size:54
Alignment explanation
Indices: 564309--564553 Score: 313
Period size: 53 Copynumber: 4.6 Consensus size: 54
564299 AAAATAGTCA
*
564309 TTTACCC-ACTAGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCAG
1 TTTACCCTACTAGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCAT
* *
564362 TTTACCCTA-TAGGGGCATTACGGTCA-TTTACCCTACAGGGGTATTACGGTTAT
1 TTTACCCTACTA-GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCAT
* * * *
564415 TTTACCTTACTGGGGCATTACGGTCATTTTACCCTACAAGGGTATTACGGTCAT
1 TTTACCCTACTAGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCAT
* * *
564469 TTTACCCTA-TAGGGTATTACGGTTATTTTACCCTACATGGGTATTAC-AGTCAT
1 TTTACCCTACTAGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGA-TCAT
* *
564522 TTTACCCTAC-AGGGGTATTACGATCATTTTAC
1 TTTACCCTACTA-GGGCATTACGGTCATTTTAC
564554 AACCTTTCCG
Statistics
Matches: 170, Mismatches: 15, Indels: 13
0.86 0.08 0.07
Matches are distributed among these distances:
53 103 0.61
54 67 0.39
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (54 bp):
TTTACCCTACTAGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCAT
Found at i:564435 original size:80 final size:79
Alignment explanation
Indices: 564305--564550 Score: 318
Period size: 80 Copynumber: 3.1 Consensus size: 79
564295 GGGCAAAATA
* * * *
564305 GTCATTTACCC-ACTAGGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCAGTTTACCC
1 GTCATTTACCCTAC-AGGGTATTACGGTTATTTTACCCTACTGGGGTATTACGATCATTTTACCC
* *
564369 TATAGGGGCATTACG
65 TACAGGGGTATTACG
* * *
564384 GTCATTTACCCTACAGGGGTATTACGGTTATTTTACCTTACTGGGGCATTACGGTCATTTTACCC
1 GTCATTTACCCTACA-GGGTATTACGGTTATTTTACCCTACTGGGGTATTACGATCATTTTACCC
*
564449 TACAAGGGTATTACG
65 TACAGGGGTATTACG
*
564464 GTCATTTTACCCTATAGGGTATTACGGTTATTTTACCCTACAT-GGGTATTAC-AGTCATTTTAC
1 GTCA-TTTACCCTACAGGGTATTACGGTTATTTTACCCTAC-TGGGGTATTACGA-TCATTTTAC
564527 CCTACAGGGGTATTACG
63 CCTACAGGGGTATTACG
*
564544 ATCATTT
1 GTCATTT
564551 TACAACCTTT
Statistics
Matches: 146, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
79 15 0.10
80 120 0.82
81 11 0.08
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (79 bp):
GTCATTTACCCTACAGGGTATTACGGTTATTTTACCCTACTGGGGTATTACGATCATTTTACCCT
ACAGGGGTATTACG
Found at i:564445 original size:107 final size:107
Alignment explanation
Indices: 564304--564553 Score: 346
Period size: 107 Copynumber: 2.4 Consensus size: 107
564294 GGGGCAAAAT
*
564304 AGTCA-TTTACCC-ACTA-GGGCATTACGGTCATTTTACCCTACAGGGGTATTACGATCAGTTTA
1 AGTCATTTTACCCTAC-AGGGGCATTACGGTCATTTTACCCTACAAGGGTATTACGATCAGTTTA
564366 CCCTATAGGGGCATTACGGTCA-TTTACCCTACAGGGGTATTAC
65 CCCTATA-GGGCATTACGGTCATTTTACCCTACAGGGGTATTAC
* * * * * *
564409 GGTTATTTTACCTTACTGGGGCATTACGGTCATTTTACCCTACAAGGGTATTACGGTCATTTTAC
1 AGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAAGGGTATTACGATCAGTTTAC
* * *
564474 CCTATAGGGTATTACGGTTATTTTACCCTACATGGGTATTAC
66 CCTATAGGGCATTACGGTCATTTTACCCTACAGGGGTATTAC
* *
564516 AGTCATTTTACCCTACAGGGGTATTACGATCATTTTAC
1 AGTCATTTTACCCTACAGGGGCATTACGGTCATTTTAC
564554 AACCTTTCCG
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
105 3 0.02
106 18 0.14
107 104 0.83
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (107 bp):
AGTCATTTTACCCTACAGGGGCATTACGGTCATTTTACCCTACAAGGGTATTACGATCAGTTTAC
CCTATAGGGCATTACGGTCATTTTACCCTACAGGGGTATTAC
Found at i:573704 original size:16 final size:16
Alignment explanation
Indices: 573683--573715 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
573673 AGATGTAATT
573683 TGACCACTATTTAAAC
1 TGACCACTATTTAAAC
573699 TGACCACTATTTAAAC
1 TGACCACTATTTAAAC
573715 T
1 T
573716 AAGCAGAATT
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:0.36, C:0.24, G:0.06, T:0.33
Consensus pattern (16 bp):
TGACCACTATTTAAAC
Found at i:582280 original size:226 final size:224
Alignment explanation
Indices: 581879--582336 Score: 794
Period size: 226 Copynumber: 2.0 Consensus size: 224
581869 CATCATCCAT
* * *
581879 GACTATAAACATTAGCAAACTCATAACAAAACCTATATACATGCCACAACCCAAAAAGAGATACA
1 GACTATAAACATTAACAAACTCATAACAAAACCTATATACATGCCACAACCCAAAAAAAGATAAA
*
581944 AAAGCTACCAAAATAGTTGGATAGTGTGAGCTTTATGGCTGATCCTTCCGATCAGTCCACAACTA
66 AAAGCTACCAAAATAGTTGGATAGTGTGAGCTTTATGGCTGATCCTTCCGATCAGGCCACAACTA
* *
582009 TTATCTACAAAATAACGTGAGAAAAATAATAAGCTCAAGTAGCTTAGTAAGATCATAGTGTAATA
131 TTATCTACAAAATAACATGAGAAAAATAATAAGCTCAAATAGCTTAGTAAGATCATAGTGTAATA
582074 TCTACTTGACTTATTTTAGTTAACATAAG
196 TCTACTTGACTTATTTTAGTTAACATAAG
582103 GACTATAAACATTAACAAACTCATAACAAAACCTATATACATGCCACAACCCAAAAAAAGATAAA
1 GACTATAAACATTAACAAACTCATAACAAAACCTATATACATGCCACAACCCAAAAAAAGAT--A
582168 AAAAAGCTACCAAAATAGTTGGATAGTGTGAGCTTTATGGCCT-ATCCTTCCGATCAGGCCACAA
64 AAAAAGCTACCAAAATAGTTGGATAGTGTGAGCTTTATGG-CTGATCCTTCCGATCAGGCCACAA
* * *
582232 CTGTTATCTACTAAATAACATGAGAAAAATAATAAGCTGAAATAGCTTAGTAAGATCATAGTGTA
128 CTATTATCTACAAAATAACATGAGAAAAATAATAAGCTCAAATAGCTTAGTAAGATCATAGTGTA
582297 ATATCTACTTGACTTATTTTAGTTAACATAAG
193 ATATCTACTTGACTTATTTTAGTTAACATAAG
582329 GACT-TAAA
1 GACTATAAA
582337 AAGTATAACA
Statistics
Matches: 222, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
224 60 0.27
225 4 0.02
226 156 0.70
227 2 0.01
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (224 bp):
GACTATAAACATTAACAAACTCATAACAAAACCTATATACATGCCACAACCCAAAAAAAGATAAA
AAAGCTACCAAAATAGTTGGATAGTGTGAGCTTTATGGCTGATCCTTCCGATCAGGCCACAACTA
TTATCTACAAAATAACATGAGAAAAATAATAAGCTCAAATAGCTTAGTAAGATCATAGTGTAATA
TCTACTTGACTTATTTTAGTTAACATAAG
Found at i:582630 original size:20 final size:20
Alignment explanation
Indices: 582569--582630 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
582559 GTATAGTTAA
* *
582569 GGGCACCGAACTGCAAACAG
1 GGGCACCGAAGTGTAAACAG
582589 GGGCA-CG-AGTGTGAGAACAG
1 GGGCACCGAAGTGT-A-AACAG
*
582609 GGGCACCGAAGTGTAAATAG
1 GGGCACCGAAGTGTAAACAG
582629 GG
1 GG
582631 ACATTGAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
18 3 0.09
19 3 0.09
20 21 0.60
21 3 0.09
22 5 0.14
ACGTcount: A:0.32, C:0.19, G:0.39, T:0.10
Consensus pattern (20 bp):
GGGCACCGAAGTGTAAACAG
Found at i:582667 original size:40 final size:39
Alignment explanation
Indices: 582623--582745 Score: 122
Period size: 40 Copynumber: 3.1 Consensus size: 39
582613 ACCGAAGTGT
*
582623 AAATAGGGACATTGAAGTGTATTCAGTGGCACAGTTGTGC
1 AAATAGGGACATCGAAGTGTATTCAG-GGCACAGTTGTGC
* * * *
582663 AAATAGGCACACCGAAGTGTATTAAGGGCCACAATTGTGC
1 AAATAGGGACATCGAAGTGTATTCAGGG-CACAGTTGTGC
* * * *
582703 AAACAGGGACATCG-AGTTATATTCTGGGGCACAGTTCTGC
1 AAATAGGGACATCGAAG-TGTATTC-AGGGCACAGTTGTGC
582743 AAA
1 AAA
582746 CAAGAGCACT
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
39 4 0.06
40 60 0.90
41 3 0.04
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.24
Consensus pattern (39 bp):
AAATAGGGACATCGAAGTGTATTCAGGGCACAGTTGTGC
Found at i:583916 original size:47 final size:46
Alignment explanation
Indices: 583809--583990 Score: 166
Period size: 47 Copynumber: 3.8 Consensus size: 46
583799 ATGTGATTTC
* * * * *
583809 TGTATAAGACCATAGCTGGGCTATGGTATCAGTGTGATGTGATTATGAGTTT
1 TGTATAAGACCATATCTGGGATATGGCATCGGTGTGA--T-A-TATGA--TA
*
583861 TCGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGCTA
1 T-GTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGATA
* * * *
583908 CTGTATAAGGCTATATCTGGGATATGGCATCAGTGTGATATGTGATA
1 -TGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGATA
** * *
583955 TGTATAAGACCATGGCTGGGCTATGGCTTCGGTGTG
1 TGTATAAGACCATATCTGGGATATGGCATCGGTGTG
583991 TGATATGTGA
Statistics
Matches: 110, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
46 29 0.26
47 41 0.37
48 1 0.01
49 4 0.04
50 1 0.01
51 1 0.01
52 1 0.01
53 32 0.29
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.34
Consensus pattern (46 bp):
TGTATAAGACCATATCTGGGATATGGCATCGGTGTGATATATGATA
Found at i:585510 original size:18 final size:18
Alignment explanation
Indices: 585487--585524 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
585477 ATTACTGATC
585487 TGAACTGAGTTGAAAGTT
1 TGAACTGAGTTGAAAGTT
585505 TGAACTGAGTTGAAAGTT
1 TGAACTGAGTTGAAAGTT
585523 TG
1 TG
585525 GTAATGCCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (18 bp):
TGAACTGAGTTGAAAGTT
Found at i:601994 original size:50 final size:50
Alignment explanation
Indices: 601940--602116 Score: 239
Period size: 50 Copynumber: 3.5 Consensus size: 50
601930 GGTGGTCACG
601940 TGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCA
1 TGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCA
* * * * * * * * *
601990 TGTGTAGTACTATGTGCAGGCTACTATGCGCACCAG-ATAGCTTCGATCACG
1 TGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAAT-G-ATAGGTCGCA
602041 TGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCA
1 TGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCA
*
602091 TGTGTAGTACTATGTGTAGGCTACTA
1 TGTGTAGTACTATGTGGAGGCTACTA
602117 TGTGAACCTG
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
49 2 0.02
50 63 0.60
51 38 0.36
52 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (50 bp):
TGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCA
Found at i:602056 original size:101 final size:101
Alignment explanation
Indices: 601935--602118 Score: 359
Period size: 101 Copynumber: 1.8 Consensus size: 101
601925 AAAGTGGTGG
601935 TCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
602000 TATGTGCAGGCTACTATGCGCACCAGATAGCTTCGA
66 TATGTGCAGGCTACTATGCGCACCAGATAGCTTCGA
602036 TCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
1 TCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
*
602101 TATGTGTAGGCTACTATG
66 TATGTGCAGGCTACTATG
602119 TGAACCTGTA
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 82 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTAC
TATGTGCAGGCTACTATGCGCACCAGATAGCTTCGA
Found at i:604270 original size:22 final size:23
Alignment explanation
Indices: 604245--604296 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
604235 GATTACCCAA
604245 TTAAATT-AATTCTATAATTAAT
1 TTAAATTCAATTCTATAATTAAT
* *
604267 TT-AATTCATTTGTATAATTAAT
1 TTAAATTCAATTCTATAATTAAT
604289 TT-AATTCA
1 TTAAATTCA
604297 TGTGGCAACC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 4 0.15
22 23 0.85
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAATTCAATTCTATAATTAAT
Found at i:618567 original size:38 final size:38
Alignment explanation
Indices: 618513--618664 Score: 232
Period size: 38 Copynumber: 4.0 Consensus size: 38
618503 TATATAATTA
* *
618513 TACCCCTGATCGCACTTATGTGCCCTGTTGTACTTCGG
1 TACCCCTGATCGCACTTACGTGCCCTATTGTACTTCGG
*
618551 TACCCCTGATCACACTTACGTGCCCTATTGTACTTCGG
1 TACCCCTGATCGCACTTACGTGCCCTATTGTACTTCGG
* * *
618589 TACCCTTGATCGCACTTACGTGCCCTATTATACTTTGG
1 TACCCCTGATCGCACTTACGTGCCCTATTGTACTTCGG
*
618627 TACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCG
1 TACCCCTGATCGCACTTACGTG-CCCTATTGTACTTCG
618665 ATACTCTCGA
Statistics
Matches: 102, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 90 0.88
39 12 0.12
ACGTcount: A:0.16, C:0.33, G:0.18, T:0.34
Consensus pattern (38 bp):
TACCCCTGATCGCACTTACGTGCCCTATTGTACTTCGG
Found at i:618614 original size:20 final size:19
Alignment explanation
Indices: 618516--618651 Score: 66
Period size: 18 Copynumber: 7.2 Consensus size: 19
618506 ATAATTATAC
*
618516 CCCTGATCGCACTTATGTG
1 CCCTGATCGCACTTACGTG
* * *
618535 CCCTG-TTGTACTT-CGGTAC
1 CCCTGATCGCACTTAC-GT-G
*
618554 CCCTGATCACACTTACGTG
1 CCCTGATCGCACTTACGTG
* * *
618573 CCCT-ATTGTACTT-CGGTA
1 CCCTGATCGCACTTAC-GTG
618591 CCCTTGATCGCACTTACGTG
1 CCC-TGATCGCACTTACGTG
*** ** *
618611 CCCT-ATTATACTTTGGTAC
1 CCCTGATCGCACTTACGT-G
618630 CCCTGATCGCACTTACGTG
1 CCCTGATCGCACTTACGTG
618649 CCC
1 CCC
618652 CTGTTGTACT
Statistics
Matches: 80, Mismatches: 27, Indels: 20
0.63 0.21 0.16
Matches are distributed among these distances:
17 1 0.01
18 27 0.34
19 23 0.29
20 27 0.34
21 2 0.03
ACGTcount: A:0.16, C:0.34, G:0.18, T:0.32
Consensus pattern (19 bp):
CCCTGATCGCACTTACGTG
Found at i:618643 original size:76 final size:77
Alignment explanation
Indices: 618512--618682 Score: 236
Period size: 76 Copynumber: 2.2 Consensus size: 77
618502 TTATATAATT
* * * *
618512 ATACCCCTGATCGCACTTATGTGCCCTGTTGTACTTCGGTACCCCTGATCACACTTACGTG-CCC
1 ATACCCTTGATCGCACTTACGTGCCCTATTATACTTCGGTACCCCTGATCACACTTACGTGCCCC
618576 TATTGTACTTCG
66 TATTGTACTTCG
* * *
618588 GTACCCTTGATCGCACTTACGTGCCCTATTATACTTTGGTACCCCTGATCGCACTTACGTGCCCC
1 ATACCCTTGATCGCACTTACGTGCCCTATTATACTTCGGTACCCCTGATCACACTTACGTGCCCC
*
618653 TGTTGTACTTCG
66 TATTGTACTTCG
* * *
618665 ATACTCTCGATAGCACTT
1 ATACCCTTGATCGCACTT
618683 TTGTGTCGTG
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
76 54 0.66
77 28 0.34
ACGTcount: A:0.18, C:0.32, G:0.17, T:0.33
Consensus pattern (77 bp):
ATACCCTTGATCGCACTTACGTGCCCTATTATACTTCGGTACCCCTGATCACACTTACGTGCCCC
TATTGTACTTCG
Found at i:618652 original size:20 final size:20
Alignment explanation
Indices: 618515--618654 Score: 71
Period size: 20 Copynumber: 7.3 Consensus size: 20
618505 TATAATTATA
*
618515 CCCCTGATCGCACTTATGTG
1 CCCCTGATCGCACTTACGTG
* * *
618535 -CCCTG-TTGTACTT-CGGTA
1 CCCCTGATCGCACTTAC-GTG
*
618553 CCCCTGATCACACTTACGTG
1 CCCCTGATCGCACTTACGTG
* * *
618573 -CCCT-ATTGTACTT-CGGTA
1 CCCCTGATCGCACTTAC-GTG
*
618591 CCCTTGATCGCACTTACGTG
1 CCCCTGATCGCACTTACGTG
*** ** *
618611 -CCCT-ATTATACTTTGGTA
1 CCCCTGATCGCACTTACGTG
618629 CCCCTGATCGCACTTACGTG
1 CCCCTGATCGCACTTACGTG
618649 CCCCTG
1 CCCCTG
618655 TTGTACTTCG
Statistics
Matches: 81, Mismatches: 29, Indels: 20
0.62 0.22 0.15
Matches are distributed among these distances:
17 1 0.01
18 24 0.30
19 24 0.30
20 30 0.37
21 2 0.02
ACGTcount: A:0.16, C:0.34, G:0.18, T:0.32
Consensus pattern (20 bp):
CCCCTGATCGCACTTACGTG
Found at i:621141 original size:49 final size:49
Alignment explanation
Indices: 621083--621176 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
621073 ACAGAAAAAG
*
621083 AAAATACATGTTGAATTTACTGAATATACTATTAAGGTTACAAATCTTA
1 AAAATACATGTTGAATTTACTAAATATACTATTAAGGTTACAAATCTTA
621132 AAAATACATGTTGAATTTACTAAATATACTATTAAGGTTACAAAT
1 AAAATACATGTTGAATTTACTAAATATACTATTAAGGTTACAAAT
621177 TTTATAGGTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.36
Consensus pattern (49 bp):
AAAATACATGTTGAATTTACTAAATATACTATTAAGGTTACAAATCTTA
Found at i:625202 original size:39 final size:38
Alignment explanation
Indices: 625119--625229 Score: 134
Period size: 39 Copynumber: 2.9 Consensus size: 38
625109 ATAATTATAC
* * *
625119 CCCTGATTGCACCTACGTG-CCCTATTGTACTTCGGTA
1 CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTA
625156 CCTCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTA
1 CC-CTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTA
* * *
625195 TCCCTGATCACACTTACGTACCCCTGATCGTACTT
1 -CCCTGATCGCACTTACGTGCCCCTG-TTGTACTT
625230 ATGTGTCCCT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
37 2 0.03
38 15 0.23
39 38 0.59
40 9 0.14
ACGTcount: A:0.16, C:0.34, G:0.17, T:0.32
Consensus pattern (38 bp):
CCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTA
Found at i:625229 original size:20 final size:20
Alignment explanation
Indices: 625153--625270 Score: 73
Period size: 20 Copynumber: 6.0 Consensus size: 20
625143 TTGTACTTCG
*
625153 GTACCTCTGATCGCACTTAC
1 GTACCCCTGATCGCACTTAC
* * *
625173 GTGCCCCTG-TTGTACTT-C
1 GTACCCCTGATCGCACTTAC
* *
625191 GGTATCCCTGATCACACTTAC
1 -GTACCCCTGATCGCACTTAC
* *
625212 GTACCCCTGATCGTACTTAT
1 GTACCCCTGATCGCACTTAC
** * *
625232 GTGTCCCTG-TTGTACTT-C
1 GTACCCCTGATCGCACTTAC
*
625250 GGTCCCCCTGATCGCACTTAC
1 -GTACCCCTGATCGCACTTAC
625271 ATGCCCTGTT
Statistics
Matches: 71, Mismatches: 21, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
18 1 0.01
19 27 0.38
20 41 0.58
21 2 0.03
ACGTcount: A:0.15, C:0.34, G:0.18, T:0.33
Consensus pattern (20 bp):
GTACCCCTGATCGCACTTAC
Found at i:625230 original size:59 final size:59
Alignment explanation
Indices: 625153--625270 Score: 173
Period size: 59 Copynumber: 2.0 Consensus size: 59
625143 TTGTACTTCG
* *
625153 GTACCTCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTATCCCTGATCACACTTAC
1 GTACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTGATCACACTTAC
* * * * *
625212 GTACCCCTGATCGTACTTATGTGTCCCTGTTGTACTTCGGTCCCCCTGATCGCACTTAC
1 GTACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTGATCACACTTAC
625271 ATGCCCTGTT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.15, C:0.34, G:0.18, T:0.33
Consensus pattern (59 bp):
GTACCCCTGATCGCACTTACGTGCCCCTGTTGTACTTCGGTACCCCTGATCACACTTAC
Found at i:625289 original size:38 final size:38
Alignment explanation
Indices: 625212--625407 Score: 230
Period size: 38 Copynumber: 5.1 Consensus size: 38
625202 TCACACTTAC
* **
625212 GTACCCCTGATCGTACTTATGTGTCCCTGTTGTACTTCG
1 GTACCCCTGATCGCACTTACATG-CCCTGTTGTACTTCG
* *
625251 GTCCCCCTGATCGCACTTACATGCCCTGTTGTAATTCG
1 GTACCCCTGATCGCACTTACATGCCCTGTTGTACTTCG
* * * *
625289 GTACCGCTGATCGCATTTACGTGCCCTGTTGTACTTTG
1 GTACCCCTGATCGCACTTACATGCCCTGTTGTACTTCG
* * *
625327 GTACCCTTGATTGCACTTACATGCACCTATTGTACTTCG
1 GTACCCCTGATCGCACTTACATGC-CCTGTTGTACTTCG
* * **
625366 GTACCCCTGACCGAACTTTTATGCCCTGTTGTACTTCG
1 GTACCCCTGATCGCACTTACATGCCCTGTTGTACTTCG
625404 GTAC
1 GTAC
625408 TCCCAATAGC
Statistics
Matches: 131, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
38 82 0.63
39 49 0.37
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.35
Consensus pattern (38 bp):
GTACCCCTGATCGCACTTACATGCCCTGTTGTACTTCG
Found at i:625300 original size:77 final size:77
Alignment explanation
Indices: 625212--625407 Score: 250
Period size: 77 Copynumber: 2.5 Consensus size: 77
625202 TCACACTTAC
* *
625212 GTACCCCTGATCGTACTTATGTGTCCCTGTTGTACTTCGGTCCCCCTGATCGCACTTACATGC-C
1 GTACCCCTGATCGAACTTATGTG-CCCTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCAC
*
625276 CTGTTGTAATTCG
65 CTATTGTAATTCG
* * * * * * *
625289 GTACCGCTGATCGCATTTACGTGCCCTGTTGTACTTTGGTACCCTTGATTGCACTTACATGCACC
1 GTACCCCTGATCGAACTTATGTGCCCTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCACC
*
625354 TATTGTACTTCG
66 TATTGTAATTCG
* * *
625366 GTACCCCTGACCGAACTTTTATGCCCTGTTGTACTTCGGTAC
1 GTACCCCTGATCGAACTTATGTGCCCTGTTGTACTTCGGTAC
625408 TCCCAATAGC
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
76 35 0.35
77 65 0.65
ACGTcount: A:0.16, C:0.30, G:0.19, T:0.35
Consensus pattern (77 bp):
GTACCCCTGATCGAACTTATGTGCCCTGTTGTACTTCGGTACCCCTGATCGCACTTACATGCACC
TATTGTAATTCG
Found at i:633921 original size:45 final size:45
Alignment explanation
Indices: 633810--633993 Score: 212
Period size: 45 Copynumber: 4.1 Consensus size: 45
633800 AATAATAACA
* * *
633810 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
* * * * *
633853 GATACTCGGTTGAATCAGTACATAGCAACCAGCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
*
633898 -AGTACCCGGTGGAATTAGCACATAGCAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
* * * *
633943 GATATCTGGTGGAATCAGCATACAGCAACCACCTTTATAATCAAT
1 GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
*
633988 GGTACC
1 GATACC
633994 TGGTACACGT
Statistics
Matches: 117, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
43 10 0.09
44 13 0.11
45 93 0.79
46 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACATAGCAACCACCTTTATAATCAAT
Found at i:641906 original size:43 final size:43
Alignment explanation
Indices: 641743--641907 Score: 172
Period size: 43 Copynumber: 3.8 Consensus size: 43
641733 ACGTCACTAA
* * * *
641743 CTTTAGCGGCGTTTTTTTCTAAAAACGCCACTAAAGACTAAGAC
1 CTTTAGCGGCGCTTTTCTC-ACAAACGCCACTAAAGACCAAGAC
* * *
641787 CTTTAGCGGCGCTTTTCCCACAAACGCCGA-TAAAGAGCACGAC
1 CTTTAGCGGCGCTTTTCTCACAAACGCC-ACTAAAGACCAAGAC
* * * * *
641830 CTTTAGCGGCACATTTT-ACACAAATGCCGCTAAAGACCATGAC
1 CTTTAGCGGCGC-TTTTCTCACAAACGCCACTAAAGACCAAGAC
*
641873 CTTTAGCGGGGCTTTTCTCACAAACGCCACTAAAG
1 CTTTAGCGGCGCTTTTCTCACAAACGCCACTAAAG
641908 GTCATGAAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
42 4 0.04
43 74 0.75
44 21 0.21
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.24
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCTCACAAACGCCACTAAAGACCAAGAC
Found at i:642832 original size:23 final size:22
Alignment explanation
Indices: 642814--643309 Score: 285
Period size: 23 Copynumber: 21.7 Consensus size: 22
642804 GTAGCACTTT
642814 AACACTTCAATTTACAGCATTTA
1 AACACTTCAATTTACAGCA-TTA
*
642837 AACACTTCAATTTGA-AGCACTTT
1 AACACTTCAATTT-ACAGCA-TTA
* *
642860 AACA-TATCAATTAACAACATTTA
1 AACACT-TCAATTTACAGCA-TTA
* * *
642883 TACACATCAA-TTACAGCGATAA
1 AACACTTCAATTTACAGC-ATTA
* * *
642905 AACA-TCTCAATTTCCAACAACTA
1 AACACT-TCAATTTACAGC-ATTA
*
642928 AACACTTCAATTTGCAGCACTTA
1 AACACTTCAATTTACAGCA-TTA
642951 AACACTTCAATTTACAGCACTTA
1 AACACTTCAATTTACAGCA-TTA
*
642974 AACACTTCAATTTATAGCATTTA
1 AACACTTCAATTTACAGCA-TTA
* * *
642997 AAAACTTAAATTTGCAGCAGTTTA
1 AACACTTCAATTTACAGCA--TTA
* *
643021 AACA-TATC-ATTAACAACATTTA
1 AACACT-TCAATTTACAGCA-TTA
* * * *
643043 TACACCTCAA-TTACAACGATAA
1 AACACTTCAATTTACAGC-ATTA
* *
643065 AACATCTT-AATTTCCAGCAACTA
1 AACA-CTTCAATTTACAGC-ATTA
* *
643088 AACAATTCAATTTGCAGCACTTA
1 AACACTTCAATTTACAGCA-TTA
* **
643111 AACACTTCAATTTATAATATTTA
1 AACACTTCAATTTACAGCA-TTA
643134 AACACTTCAATTTACAGCATTTA
1 AACACTTCAATTTACAGCA-TTA
* *
643157 AACACTTAAATTTGCAGCACTTA
1 AACACTTCAATTTACAGCA-TTA
* *
643180 AACA-TATCAATTAACAACATTTA
1 AACACT-TCAATTTACAGCA-TTA
* * *
643203 TACACCTCAA-TTACAGCGATAA
1 AACACTTCAATTTACAGC-ATTA
* *
643225 AACA-TCTCAATTTCCAGCAACTA
1 AACACT-TCAATTTACAGC-ATTA
* *
643248 AATACTTCAATTTGCAGCACTTA
1 AACACTTCAATTTACAGCA-TTA
* **
643271 AACACTTCAATTTATAATATTTA
1 AACACTTCAATTTACAGCA-TTA
643294 AACACTTCAATTTACA
1 AACACTTCAATTTACA
643310 AACCCACCAT
Statistics
Matches: 363, Mismatches: 85, Indels: 50
0.73 0.17 0.10
Matches are distributed among these distances:
22 58 0.16
23 294 0.81
24 11 0.03
ACGTcount: A:0.42, C:0.22, G:0.05, T:0.32
Consensus pattern (22 bp):
AACACTTCAATTTACAGCATTA
Done.