Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A10
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: 110302803
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1825971 characters in sequence are not A, C, G, or T
File 9 of 343
Found at i:3271633 original size:23 final size:24
Alignment explanation
Indices: 3271588--3271636 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
3271578 AATTTTATAG
* * *
3271588 TTTTAATAATTTATATTTTAATAT
1 TTTTAAAAATTTATAATTAAATAT
3271612 TTTTAAAAATTTA-AATTAAATAT
1 TTTTAAAAATTTATAATTAAATAT
3271635 TT
1 TT
3271637 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 10 0.45
24 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAAAAATTTATAATTAAATAT
Found at i:3271654 original size:29 final size:29
Alignment explanation
Indices: 3271602--3271676 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
3271592 AATAATTTAT
* * *
3271602 ATTTTAATATTTTTAAAAATTTAAAT-TAA
1 ATTTTATTATTTTTAAAAGTTAAAATAT-A
3271631 ATATTTATTATTTTTAAAAGTTAAAATATA
1 AT-TTTATTATTTTTAAAAGTTAAAATATA
3271661 ATTTTATT-TTTATTAA
1 ATTTTATTATTT-TTAA
3271677 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
28 3 0.08
29 12 0.30
30 24 0.60
31 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
ATTTTATTATTTTTAAAAGTTAAAATATA
Found at i:3273069 original size:15 final size:15
Alignment explanation
Indices: 3273049--3273105 Score: 71
Period size: 15 Copynumber: 3.8 Consensus size: 15
3273039 TTGGCCAAAA
3273049 ACCGCTGGTTCTGCT
1 ACCGCTGGTTCTGCT
*
3273064 ACCGCTGGTTTTGCT
1 ACCGCTGGTTCTGCT
*
3273079 ATCGCTGGTT-TAGCT
1 ACCGCTGGTTCT-GCT
*
3273094 ACAGCTGGTTCT
1 ACCGCTGGTTCT
3273106 TCTAATGACC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
14 1 0.03
15 34 0.94
16 1 0.03
ACGTcount: A:0.11, C:0.26, G:0.26, T:0.37
Consensus pattern (15 bp):
ACCGCTGGTTCTGCT
Found at i:3280606 original size:42 final size:43
Alignment explanation
Indices: 3280547--3280641 Score: 147
Period size: 42 Copynumber: 2.2 Consensus size: 43
3280537 AATGATGATA
* *
3280547 TAAAATTATACAAATATAAATTATTTTA-TTTTATATATCTTT
1 TAAAATTAAAAAAATATAAATTATTTTATTTTTATATATCTTT
* *
3280589 TAAAATTAAAAAAATATAAATTATTTTATTTTTGTATGTCTTT
1 TAAAATTAAAAAAATATAAATTATTTTATTTTTATATATCTTT
3280632 TAAAATTAAA
1 TAAAATTAAA
3280642 GGAAACAATC
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
42 26 0.54
43 22 0.46
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.49
Consensus pattern (43 bp):
TAAAATTAAAAAAATATAAATTATTTTATTTTTATATATCTTT
Found at i:3284889 original size:10 final size:11
Alignment explanation
Indices: 3284874--3284902 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
3284864 CTGTGTGTTC
3284874 TTTATTTTA-T
1 TTTATTTTATT
3284884 TTTATTTTATT
1 TTTATTTTATT
3284895 TTTATTTT
1 TTTATTTT
3284903 TCACAACTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:3291317 original size:7 final size:6
Alignment explanation
Indices: 3291301--3291348 Score: 69
Period size: 6 Copynumber: 7.8 Consensus size: 6
3291291 AAAATTCCAA
* *
3291301 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTTC TTTTTA TTTTTA TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTT
3291349 TGCGGTGGCC
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
6 34 0.85
7 6 0.15
ACGTcount: A:0.04, C:0.10, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTC
Found at i:3291323 original size:13 final size:13
Alignment explanation
Indices: 3291301--3291342 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
3291291 AAAATTCCAA
3291301 TTTTTCTTTTTC-
1 TTTTTCTTTTTCT
3291313 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
*
3291326 TTTTTCTTTTTAT
1 TTTTTCTTTTTCT
3291339 TTTT
1 TTTT
3291343 ATTTTTTGCG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 12 0.43
13 16 0.57
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:3291329 original size:19 final size:19
Alignment explanation
Indices: 3291300--3291349 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
3291290 CAAAATTCCA
3291300 ATTTTTC-TTTTTCTTTTT
1 ATTTTTCTTTTTTCTTTTT
*
3291318 CTTTTTCTTTTTTCTTTTT
1 ATTTTTCTTTTTTCTTTTT
*
3291337 ATTTTTATTTTTT
1 ATTTTTCTTTTTT
3291350 GCGGTGGCCA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 6 0.21
19 22 0.79
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (19 bp):
ATTTTTCTTTTTTCTTTTT
Found at i:3298395 original size:18 final size:19
Alignment explanation
Indices: 3298379--3298420 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
3298369 CTTAATTATT
3298379 AAAATGTAAAAAATTATAA
1 AAAATGTAAAAAATTATAA
* *
3298398 AAAATTTAAAAAAAT-TAA
1 AAAATGTAAAAAATTATAA
3298416 AAAAT
1 AAAAT
3298421 ATATAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATGTAAAAAATTATAA
Found at i:3298400 original size:10 final size:9
Alignment explanation
Indices: 3298379--3298420 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
3298369 CTTAATTATT
*
3298379 AAAATGTAA
1 AAAATTTAA
3298388 AAAATTATAA
1 AAAATT-TAA
3298398 AAAATTTAA
1 AAAATTTAA
*
3298407 AAAAATTAA
1 AAAATTTAA
3298416 AAAAT
1 AAAAT
3298421 ATATAAAGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 20 0.69
10 9 0.31
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAATTTAA
Found at i:3298427 original size:20 final size:20
Alignment explanation
Indices: 3298386--3298427 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3298376 ATTAAAATGT
*
3298386 AAAAAATTATAAAAAATTTA
1 AAAAAATTATAAAAAATATA
3298406 AAAAAATTA-AAAAATATATA
1 AAAAAATTATAAAAA-ATATA
3298426 AA
1 AA
3298428 GTTTCGCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATTATAAAAAATATA
Found at i:3302171 original size:42 final size:41
Alignment explanation
Indices: 3302123--3302228 Score: 169
Period size: 42 Copynumber: 2.5 Consensus size: 41
3302113 ACGTCAGAAT
*
3302123 TCGGTTTGTCCCTT-GAGAGCCTGGGGGATTGAAATGCAGTA
1 TCGGTTTGT-CCTTGGAGAGCCTGGGCGATTGAAATGCAGTA
3302164 TCTGGTTTGTCCTTGGAGAGCCTGGGCGATTGAAATGCAGTA
1 TC-GGTTTGTCCTTGGAGAGCCTGGGCGATTGAAATGCAGTA
3302206 TCGGATTTGTCCTTGGAGAGCCT
1 TCGG-TTTGTCCTTGGAGAGCCT
3302229 AGGTGGTTCA
Statistics
Matches: 61, Mismatches: 1, Indels: 5
0.91 0.01 0.07
Matches are distributed among these distances:
41 8 0.13
42 53 0.87
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (41 bp):
TCGGTTTGTCCTTGGAGAGCCTGGGCGATTGAAATGCAGTA
Found at i:3302242 original size:42 final size:40
Alignment explanation
Indices: 3302123--3302244 Score: 147
Period size: 42 Copynumber: 2.9 Consensus size: 40
3302113 ACGTCAGAAT
*
3302123 TCGGTTTGTCCCTT-GAGAGCCTGGGGGATTGAAATGCAGTA
1 TCGGTTTGT-CCTTGGAGAGCCTGGCGG-TTGAAATGCAGTA
*
3302164 TCTGGTTTGTCCTTGGAGAGCCTGGGCGATTGAAATGCAGTA
1 TC-GGTTTGTCCTTGGAGAGCCT-GGCGGTTGAAATGCAGTA
* *
3302206 TCGGATTTGTCCTTGGAGAGCCTAGGTGGTTCAAATGCA
1 TCGG-TTTGTCCTTGGAGAGCCT-GGCGGTTGAAATGCA
3302245 CCATCAGATT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
41 8 0.11
42 60 0.85
43 3 0.04
ACGTcount: A:0.20, C:0.17, G:0.33, T:0.30
Consensus pattern (40 bp):
TCGGTTTGTCCTTGGAGAGCCTGGCGGTTGAAATGCAGTA
Found at i:3309572 original size:22 final size:22
Alignment explanation
Indices: 3309541--3309590 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
3309531 TTTATGTTAT
* *
3309541 TTTTTATAAACTTTATATATAGA
1 TTTTTATAAAATATATATATA-A
*
3309564 TTTTT-TAAAATATATTTATAA
1 TTTTTATAAAATATATATATAA
3309585 TTTTTA
1 TTTTTA
3309591 AATTATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.26
22 12 0.52
23 5 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTTTATAAAATATATATATAA
Found at i:3310835 original size:13 final size:14
Alignment explanation
Indices: 3310817--3310850 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3310807 AATTTGATTG
3310817 AAAAAAATACAAA-
1 AAAAAAATACAAAC
*
3310830 AAAAAAATAGAAAC
1 AAAAAAATACAAAC
3310844 AAAAAAA
1 AAAAAAA
3310851 ATCCAAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (14 bp):
AAAAAAATACAAAC
Found at i:3315460 original size:84 final size:84
Alignment explanation
Indices: 3315369--3315537 Score: 266
Period size: 84 Copynumber: 2.0 Consensus size: 84
3315359 CTATCTTTTT
* * * * *
3315369 TTCCCTTATTCGCCTCATAAGTTAACAATTATCATTTTTTTAAAAGTTTTTCAGTAAAATATCTT
1 TTCCCTTATTCACCTCACAAGTTAACAAATATCATTTTTCTAAAAGATTTTCAGTAAAATATCTT
*
3315434 TGATTCTGTATGTAAGTGA
66 TGATTCTATATGTAAGTGA
* *
3315453 TTCCCTTATTTACCTCACAGGTTAACAAATATCATTTTTCTAAAAGATTTTCAGTAAAATATCTT
1 TTCCCTTATTCACCTCACAAGTTAACAAATATCATTTTTCTAAAAGATTTTCAGTAAAATATCTT
3315518 TGATTCTATATGTAAGTGA
66 TGATTCTATATGTAAGTGA
3315537 T
1 T
3315538 GGTTAGAATT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 77 1.00
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (84 bp):
TTCCCTTATTCACCTCACAAGTTAACAAATATCATTTTTCTAAAAGATTTTCAGTAAAATATCTT
TGATTCTATATGTAAGTGA
Found at i:3327968 original size:15 final size:15
Alignment explanation
Indices: 3327948--3327980 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3327938 AGTAATTAAG
3327948 AAAACTTAGTTCATT
1 AAAACTTAGTTCATT
3327963 AAAACTTAGTTCATT
1 AAAACTTAGTTCATT
3327978 AAA
1 AAA
3327981 TGTAATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (15 bp):
AAAACTTAGTTCATT
Found at i:3329358 original size:24 final size:22
Alignment explanation
Indices: 3329331--3329383 Score: 52
Period size: 24 Copynumber: 2.3 Consensus size: 22
3329321 CCTGCAAAAA
3329331 AGAAAAAAAACAGAAACATAAAGT
1 AGAAAAAAAACA-AAACA-AAAGT
** *
3329355 AGAACAAAGGACAAAACAGAAGT
1 AGAA-AAAAAACAAAACAAAAGT
3329378 AGAAAA
1 AGAAAA
3329384 TAGAACATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 2 0.08
23 8 0.32
24 9 0.36
25 6 0.24
ACGTcount: A:0.68, C:0.09, G:0.17, T:0.06
Consensus pattern (22 bp):
AGAAAAAAAACAAAACAAAAGT
Found at i:3333100 original size:15 final size:15
Alignment explanation
Indices: 3333075--3333112 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
3333065 CATGACAAAA
3333075 ATAAAAA-AGAACATT
1 ATAAAAATAGAA-ATT
3333090 -TAAAAATAGAAATT
1 ATAAAAATAGAAATT
3333104 ATAAAAATA
1 ATAAAAATA
3333113 TATATATGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (15 bp):
ATAAAAATAGAAATT
Found at i:3335299 original size:48 final size:48
Alignment explanation
Indices: 3335244--3335340 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
3335234 AGACTATGAG
3335244 CCCAAGTATTATAAGGTCGATGTTAATTATGCAAATAGAAAAAATTTT
1 CCCAAGTATTATAAGGTCGATGTTAATTATGCAAATAGAAAAAATTTT
3335292 CCCAAGTATTATAAGGTCGATGTTAATTATGCAAATAGAAAAAATTTT
1 CCCAAGTATTATAAGGTCGATGTTAATTATGCAAATAGAAAAAATTTT
3335340 C
1 C
3335341 TTACACATAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (48 bp):
CCCAAGTATTATAAGGTCGATGTTAATTATGCAAATAGAAAAAATTTT
Found at i:3340290 original size:26 final size:25
Alignment explanation
Indices: 3340248--3340297 Score: 82
Period size: 26 Copynumber: 2.0 Consensus size: 25
3340238 TGCAGTTTGG
*
3340248 TACATAAAGTTTGATTTTGGTTCAT
1 TACATAAACTTTGATTTTGGTTCAT
3340273 TACATAAAACTTTGATTTTGGTTCA
1 TACAT-AAACTTTGATTTTGGTTCA
3340298 ATTTTATACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (25 bp):
TACATAAACTTTGATTTTGGTTCAT
Found at i:3343556 original size:20 final size:21
Alignment explanation
Indices: 3343517--3343556 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3343507 AATTAATTAT
*
3343517 GATATTATTGATTTAGTGTATA
1 GATATTATTGA-TCAGTGTATA
3343539 GATATTATTG-TCAGTGTA
1 GATATTATTGATCAGTGTA
3343557 GGAGATCGTA
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:0.30, C:0.03, G:0.20, T:0.47
Consensus pattern (21 bp):
GATATTATTGATCAGTGTATA
Found at i:3344164 original size:21 final size:23
Alignment explanation
Indices: 3344133--3344184 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
3344123 GCTTCGCCTC
3344133 TGATTCTTTTA-TA-ATATGATAT
1 TGATT-TTTTATTACATATGATAT
3344155 TGATTTTTTATTACATATGATAT
1 TGATTTTTTATTACATATGATAT
3344178 TG-TTTTT
1 TGATTTTT
3344185 ATGAGAGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.18
22 12 0.43
23 11 0.39
ACGTcount: A:0.27, C:0.04, G:0.10, T:0.60
Consensus pattern (23 bp):
TGATTTTTTATTACATATGATAT
Found at i:3344185 original size:21 final size:21
Alignment explanation
Indices: 3344139--3344186 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
3344129 CCTCTGATTC
3344139 TTTTA-TAATATGATATTGATT
1 TTTTATTAATATGATATTGA-T
3344160 TTTTATTACATATGATATTG-T
1 TTTTATTA-ATATGATATTGAT
3344181 TTTTAT
1 TTTTAT
3344187 GAGAGTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 11 0.44
ACGTcount: A:0.29, C:0.02, G:0.08, T:0.60
Consensus pattern (21 bp):
TTTTATTAATATGATATTGAT
Found at i:3344323 original size:22 final size:20
Alignment explanation
Indices: 3344285--3344326 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 20
3344275 TAATATTCTG
*
3344285 TAAATTAATTATTTTTAAAT
1 TAAATTAATTAATTTTAAAT
3344305 TAAATATAACTTAATTTTAAAT
1 TAAAT-TAA-TTAATTTTAAAT
3344327 ACTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 3 0.16
22 11 0.58
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TAAATTAATTAATTTTAAAT
Found at i:3344983 original size:22 final size:21
Alignment explanation
Indices: 3344958--3344998 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
3344948 AATTACCTAA
3344958 ATCTATTGTTAAAGTACCAACT
1 ATCTATTGTTAAAGT-CCAACT
3344980 ATCTATTGTTAAAGTCCAA
1 ATCTATTGTTAAAGTCCAA
3344999 GCATAAAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (21 bp):
ATCTATTGTTAAAGTCCAACT
Found at i:3346372 original size:16 final size:17
Alignment explanation
Indices: 3346342--3346374 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3346332 TCAAGTTTTT
*
3346342 TTTTATAATTTATAATA
1 TTTTATAATTAATAATA
3346359 TTTTA-AATTAATAATA
1 TTTTATAATTAATAATA
3346375 AAATTACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTTATAATTAATAATA
Found at i:3347390 original size:20 final size:20
Alignment explanation
Indices: 3347358--3347414 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
3347348 ATGTTTTCAA
3347358 TCTCATATCTCAATTCCAATT
1 TCTCAT-TCTCAATTCCAATT
3347379 T-TCAATTCTCAATT-CAATT
1 TCTC-ATTCTCAATTCCAATT
3347398 TCTCATT-TC-ATTCCAAT
1 TCTCATTCTCAATTCCAAT
3347415 AGCTCAATCA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.09
18 6 0.18
19 9 0.27
20 12 0.36
21 3 0.09
ACGTcount: A:0.28, C:0.26, G:0.00, T:0.46
Consensus pattern (20 bp):
TCTCATTCTCAATTCCAATT
Found at i:3349231 original size:5 final size:5
Alignment explanation
Indices: 3349221--3349277 Score: 62
Period size: 5 Copynumber: 11.0 Consensus size: 5
3349211 TTACTTATTT
* *
3349221 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
3349269 ATAT- ATATA
1 ATATA ATATA
3349278 TTTTAACACA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
4 4 0.09
5 29 0.66
6 7 0.16
7 4 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:3349237 original size:12 final size:12
Alignment explanation
Indices: 3349220--3349275 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
3349210 TTTACTTATT
3349220 TATATAATATAA
1 TATATAATATAA
3349232 TATATAATATAATA
1 TATATAATAT-A-A
3349246 TACTATAATATAA
1 TA-TATAATATAA
*
3349259 TA-ATAATTTAA
1 TATATAATATAA
3349270 TATATA
1 TATATA
3349276 TATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:3349290 original size:26 final size:26
Alignment explanation
Indices: 3349222--3349277 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
3349212 TACTTATTTA
*
3349222 TATAATATAATATATAATATAATATAC
1 TATAATATAACA-ATAATATAATATAC
* *
3349249 TATAATATAATAATAATTTAATATA-
1 TATAATATAACAATAATATAATATAC
3349274 TATA
1 TATA
3349278 TTTTAACACA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 4 0.14
26 12 0.43
27 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (26 bp):
TATAATATAACAATAATATAATATAC
Found at i:3352790 original size:13 final size:13
Alignment explanation
Indices: 3352772--3352796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3352762 TATTTTAATA
3352772 TTATTTTGTGTGT
1 TTATTTTGTGTGT
3352785 TTATTTTGTGTG
1 TTATTTTGTGTG
3352797 CATTTGATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:3354364 original size:41 final size:41
Alignment explanation
Indices: 3354319--3354588 Score: 370
Period size: 41 Copynumber: 6.6 Consensus size: 41
3354309 CGGACGTTAC
3354319 GTCTAGCAGGCTTAATGCCGGTGAAGTA-A-TTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTG-A-TACATTTCAGACTTTAA
3354360 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
*
3354401 GTCTAGCAGGCTTAATGCCGGTGATATATTTCAGACTTTAA
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
* *
3354442 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
* *
3354483 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATAT
1 GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
* *
3354524 GTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAA
1 GTCTAGCAGGCTTAA-TGCCGGTGATACAT--TTCAGACTTTAA
* **
3354565 GCCTAGCAGGCAAAATGCCGGTGA
1 GTCTAGCAGGCTTAATGCCGGTGA
3354589 ATCTGTTTAA
Statistics
Matches: 212, Mismatches: 10, Indels: 13
0.90 0.04 0.06
Matches are distributed among these distances:
39 3 0.01
40 8 0.04
41 199 0.94
42 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (41 bp):
GTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTTTAA
Found at i:3356538 original size:13 final size:14
Alignment explanation
Indices: 3356522--3356557 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3356512 CAATCTTATA
3356522 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
3356535 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
3356548 TCTC-ATTTCA
1 TCTCAATTTCA
3356558 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:3356739 original size:39 final size:40
Alignment explanation
Indices: 3356696--3356807 Score: 102
Period size: 38 Copynumber: 2.8 Consensus size: 40
3356686 TCAGATAGTT
* *
3356696 CGAAGCAATATTTGACACCCAGTGTCTCATCG-GCCTAGC
1 CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCTAGC
* * ** ** * *
3356735 CGAAGTAA-AGTTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCTAGC
*
3356774 CGAAGAAATATAGTGACACCCAGTGTCTCATCGA
1 CGAAGAAATAT-TTGACACCCAGTGTCTCATCGA
3356808 CTCGAGGTCG
Statistics
Matches: 54, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
38 18 0.33
39 18 0.33
40 1 0.02
41 17 0.31
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (40 bp):
CGAAGAAATATTTGACACCCAGTGTCTCATCGAACCTAGC
Found at i:3358386 original size:5 final size:5
Alignment explanation
Indices: 3358376--3358437 Score: 72
Period size: 5 Copynumber: 12.0 Consensus size: 5
3358366 TTACTTATTT
*
3358376 ATATA ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA
1 ATATA ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA
*
3358424 ATTTA ATAT- ATATA
1 ATATA ATATA ATATA
3358438 TTTTAACACG
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
4 4 0.08
5 34 0.69
6 7 0.14
7 4 0.08
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:3358396 original size:12 final size:12
Alignment explanation
Indices: 3358381--3358435 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
3358371 TATTTATATA
3358381 ATATAATATAAT
1 ATATAATATAAT
3358393 ATATAATATAATAT
1 ATATAATAT-A-AT
3358407 ACTATAATATAAT
1 A-TATAATATAAT
*
3358420 A-ATAATTTAAT
1 ATATAATATAAT
3358431 ATATA
1 ATATA
3358436 TATTTTAACA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 12 0.32
13 4 0.11
14 4 0.11
15 8 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATAATATAAT
Found at i:3358401 original size:22 final size:21
Alignment explanation
Indices: 3358376--3358438 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 21
3358366 TTACTTATTT
3358376 ATATAATATAATATAATATATA
1 ATATAATATAATAT-ATATATA
*
3358398 ATATAATATACTATA-ATATA
1 ATATAATATAATATATATATA
*
3358418 ATAATAATTTAATATATATAT
1 AT-ATAATATAATATATATAT
3358439 TTTAACACGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 7 0.19
21 12 0.33
22 17 0.47
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAATATAATATATATATA
Found at i:3361692 original size:3 final size:3
Alignment explanation
Indices: 3361677--3361710 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
3361667 AGGAACTATT
* *
3361677 CTG CTG TTG CTG CTG CTG CGG CTG CTG CTG CTG C
1 CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG CTG C
3361711 GGAAAGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32
Consensus pattern (3 bp):
CTG
Found at i:3361711 original size:15 final size:15
Alignment explanation
Indices: 3361684--3361712 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3361674 ATTCTGCTGT
3361684 TGCTGCTGCTGCGGC
1 TGCTGCTGCTGCGGC
3361699 TGCTGCTGCTGCGG
1 TGCTGCTGCTGCGG
3361713 AAAGTGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.31, G:0.41, T:0.28
Consensus pattern (15 bp):
TGCTGCTGCTGCGGC
Found at i:3361745 original size:15 final size:15
Alignment explanation
Indices: 3361727--3361766 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
3361717 TGATGAGGAG
*
3361727 GAGGGTGAGGAAAGC
1 GAGGGAGAGGAAAGC
*
3361742 GAGGGAGAGGAAAGT
1 GAGGGAGAGGAAAGC
*
3361757 GAAGGAGAGG
1 GAGGGAGAGG
3361767 GAGAGGAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.38, C:0.03, G:0.55, T:0.05
Consensus pattern (15 bp):
GAGGGAGAGGAAAGC
Found at i:3361766 original size:21 final size:21
Alignment explanation
Indices: 3361742--3361782 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3361732 TGAGGAAAGC
*
3361742 GAGGGAGAGGAAAGTGAAGGA
1 GAGGGAGAGGAAAGGGAAGGA
*
3361763 GAGGGAGAGGAGAGGGAAGG
1 GAGGGAGAGGAAAGGGAAGG
3361783 GATGAAGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.59, T:0.02
Consensus pattern (21 bp):
GAGGGAGAGGAAAGGGAAGGA
Found at i:3364500 original size:24 final size:24
Alignment explanation
Indices: 3364452--3364500 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3364442 TTTATGGGGT
* **
3364452 TAGAGTCCAAGCTTTCTTTGGCCC
1 TAGAGTCCAAGCTTTATTTCCCCC
3364476 TAGAGTCCAAGCTTTATTTCCCCC
1 TAGAGTCCAAGCTTTATTTCCCCC
3364500 T
1 T
3364501 GTGGAGACGG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (24 bp):
TAGAGTCCAAGCTTTATTTCCCCC
Found at i:3365250 original size:60 final size:61
Alignment explanation
Indices: 3365143--3365264 Score: 237
Period size: 61 Copynumber: 2.0 Consensus size: 61
3365133 GTTCGAGGGT
3365143 GTTCTTTTTTCTGTTTCTTTTTGTTCACTGCCCAAATTGGGCGTTCATATGTCCATGCTTG
1 GTTCTTTTTTCTGTTTCTTTTTGTTCACTGCCCAAATTGGGCGTTCATATGTCCATGCTTG
3365204 GTTCTTTTTTCTGTTTCTTTTTGTTCACTGCCC-AATTGGGCGTTCATATGTCCATGCTTG
1 GTTCTTTTTTCTGTTTCTTTTTGTTCACTGCCCAAATTGGGCGTTCATATGTCCATGCTTG
3365264 G
1 G
3365265 ACCTTTGTTT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 28 0.46
61 33 0.54
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (61 bp):
GTTCTTTTTTCTGTTTCTTTTTGTTCACTGCCCAAATTGGGCGTTCATATGTCCATGCTTG
Found at i:3368234 original size:3 final size:3
Alignment explanation
Indices: 3368228--3368261 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
3368218 AAAAACAAAA
*
3368228 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3368262 TTGCATGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:3369662 original size:6 final size:6
Alignment explanation
Indices: 3369626--3369661 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3369616 CAATTATTGT
* *
3369626 ATGCCA ATGCCA ATGCCA ATGCCA CTGCCA TTGCCA
1 ATGCCA ATGCCA ATGCCA ATGCCA ATGCCA ATGCCA
3369662 TCATCTCTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (6 bp):
ATGCCA
Found at i:3373447 original size:14 final size:15
Alignment explanation
Indices: 3373428--3373459 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
3373418 ATATTTATCT
3373428 AATAAAATA-TTAAA
1 AATAAAATATTTAAA
3373442 AAT-AAATATTTAAA
1 AATAAAATATTTAAA
3373456 AATA
1 AATA
3373460 CATAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATAAAATATTTAAA
Found at i:3382584 original size:64 final size:64
Alignment explanation
Indices: 3382500--3382676 Score: 240
Period size: 64 Copynumber: 2.8 Consensus size: 64
3382490 ATATATATTT
*
3382500 AAAGTTCTTGAGCTGTATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
* *
3382564 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTACT-TACACATGTGGTTCGAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTA-TATACATATGTGGTTCAAATATAGGTTAC
*
3382628 AAA-TTCTTTGAGCTGAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTC-TTGAGCTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
3382677 GAATGTTTGT
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
61 1 0.01
62 13 0.13
63 4 0.04
64 74 0.72
65 11 0.11
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.42
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:3382852 original size:41 final size:41
Alignment explanation
Indices: 3382795--3383691 Score: 1213
Period size: 41 Copynumber: 21.9 Consensus size: 41
3382785 TATATGAGAT
* * *
3382795 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3382836 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * *
3382877 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGATGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3382918 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3382959 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3383000 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383041 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3383082 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383123 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3383164 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383205 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383246 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3383287 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383328 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3383369 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383410 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3383451 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383492 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3383533 TTTCAGGCTTAATGCCTAGCAGGCTTTATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* *
3383574 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * *
3383615 ATTCCGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGA
1 TTTCAGACTTTATGCCTAGCAGGC-TTGATGCCGGTG-AATTA
* * * * *
3383657 -ATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTG
3383692 TTTTATATAG
Statistics
Matches: 754, Mismatches: 99, Indels: 6
0.88 0.12 0.01
Matches are distributed among these distances:
40 2 0.00
41 745 0.99
42 7 0.01
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (41 bp):
TTTCAGACTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:3384382 original size:14 final size:15
Alignment explanation
Indices: 3384358--3384392 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3384348 TACTTTAATC
3384358 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
3384373 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
3384388 ATGGT
1 ATGGT
3384393 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:3389735 original size:63 final size:64
Alignment explanation
Indices: 3389652--3389825 Score: 222
Period size: 61 Copynumber: 2.8 Consensus size: 64
3389642 ATATATATTT
*
3389652 AAAGTTCTTGAGCTGTATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
*
3389716 AAAGTTCTTGAGCT-AATTTAATGTATGAATTTTACT-TAC--ATGTGGTTCGAATATAGGTTAC
1 AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTA-TATACATATGTGGTTCAAATATAGGTTAC
*
3389777 AAA-TTCTTTGAGCTGAATTTTAATGT-TGTAA--AT-TATACATATGTGGTTC
1 AAAGTTC-TTGAGCTGAA-TTTAATGTATG-AATTTTATATACATATGTGGTTC
3389826 GAATGTTTGT
Statistics
Matches: 99, Mismatches: 3, Indels: 18
0.82 0.03 0.15
Matches are distributed among these distances:
59 1 0.01
60 6 0.06
61 32 0.32
62 13 0.13
63 32 0.32
64 15 0.15
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (64 bp):
AAAGTTCTTGAGCTGAATTTAATGTATGAATTTTATATACATATGTGGTTCAAATATAGGTTAC
Found at i:3390001 original size:41 final size:41
Alignment explanation
Indices: 3389944--3390471 Score: 691
Period size: 41 Copynumber: 12.9 Consensus size: 41
3389934 TATATGAGAT
* *
3389944 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
*
3389985 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * *
3390026 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
*
3390067 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * * *
3390108 TTTTAGACTTTATGTCTAGCAAGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
*
3390149 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * *
3390190 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
*
3390231 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * * *
3390272 TTTTAGACTTTATGTCTAGCATGCTTGATGCCGGTGGATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
*
3390313 TTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * *
3390354 TTTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTA
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
* * * * *
3390395 ATTCTGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGA
1 TTTCAGGCTTTATGCCTAGCAGGC-TTGATGCCGGTG-AATTA
* * * *
3390437 -ATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTG
3390472 TTTTATATAG
Statistics
Matches: 425, Mismatches: 59, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
40 2 0.00
41 416 0.98
42 7 0.02
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (41 bp):
TTTCAGGCTTTATGCCTAGCAGGCTTGATGCCGGTGAATTA
Found at i:3390471 original size:82 final size:82
Alignment explanation
Indices: 3389959--3390432 Score: 860
Period size: 82 Copynumber: 5.8 Consensus size: 82
3389949 GGCTTAATGC
3389959 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
1 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
3390024 TATTTTAGACTTTATGT
66 TATTTTAGACTTTATGT
3390041 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
1 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
3390106 TATTTTAGACTTTATGT
66 TATTTTAGACTTTATGT
*
3390123 CTAGCAAGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
1 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
3390188 TATTTTAGACTTTATGT
66 TATTTTAGACTTTATGT
3390205 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
1 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
3390270 TATTTTAGACTTTATGT
66 TATTTTAGACTTTATGT
*
3390287 CTAGCATGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
1 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
3390352 TATTTTAGACTTTATGT
66 TATTTTAGACTTTATGT
* * * * * *
3390369 CTAGCAGGCTTGATGCCGGTGAATTAATTCTGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGC-TTGATGCCGGTGAA
3390433 ATGAATCGGG
Statistics
Matches: 381, Mismatches: 10, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
82 378 0.99
83 3 0.01
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (82 bp):
CTAGCAGGCTTGATGCCGGTGGATTATTTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAAT
TATTTTAGACTTTATGT
Found at i:3391163 original size:14 final size:15
Alignment explanation
Indices: 3391139--3391173 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
3391129 TACTTTAATC
3391139 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
3391154 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
3391169 ATGGT
1 ATGGT
3391174 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:3392550 original size:15 final size:15
Alignment explanation
Indices: 3392530--3392637 Score: 87
Period size: 15 Copynumber: 7.2 Consensus size: 15
3392520 TTTATGGAAA
3392530 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
3392545 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
3392559 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
3392575 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3392589 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
3392605 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3392619 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
3392635 ATC
1 ATC
3392638 GAGATATTGG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
14 13 0.19
15 43 0.62
16 13 0.19
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:3392559 original size:30 final size:30
Alignment explanation
Indices: 3392523--3392637 Score: 203
Period size: 30 Copynumber: 3.8 Consensus size: 30
3392513 ATCCATATTT
*
3392523 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
3392553 ATGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3392583 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3392613 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
3392638 GAGATATTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 83 1.00
ACGTcount: A:0.44, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:3397230 original size:15 final size:15
Alignment explanation
Indices: 3397210--3397317 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
3397200 TTTATGGAAA
3397210 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* **
3397225 ATCAAATA-ATGGAA
1 ATCAAAGATATGGGT
*
3397239 AGTCAAAGATATAGGT
1 A-TCAAAGATATGGGT
* **
3397255 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3397269 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
3397285 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
3397299 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
3397315 ATC
1 ATC
3397318 GAGATATTGG
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:3397239 original size:30 final size:30
Alignment explanation
Indices: 3397203--3397317 Score: 194
Period size: 30 Copynumber: 3.8 Consensus size: 30
3397193 ATCCATATTT
*
3397203 ATGGAAAATCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3397233 ATGGAAAGTCAAAGATATAGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3397263 TTGGAAAGTCAAAGATATGGGTATCAAATA
1 ATGGAAAGTCAAAGATATGGGTATCAAATA
*
3397293 TTGGAAAGTCAAAGATATGGGTATC
1 ATGGAAAGTCAAAGATATGGGTATC
3397318 GAGATATTGG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 81 1.00
ACGTcount: A:0.45, C:0.07, G:0.23, T:0.25
Consensus pattern (30 bp):
ATGGAAAGTCAAAGATATGGGTATCAAATA
Found at i:3398844 original size:31 final size:30
Alignment explanation
Indices: 3398801--3398879 Score: 113
Period size: 31 Copynumber: 2.6 Consensus size: 30
3398791 TGGACCCACT
*
3398801 ATTAACTTAATTTAATTATATTATATAACA
1 ATTAATTTAATTTAATTATATTATATAACA
* * *
3398831 TTTTAATTTAATTTAATCATATTATATAATA
1 -ATTAATTTAATTTAATTATATTATATAACA
3398862 ATTAATTTAATTTAATTA
1 ATTAATTTAATTTAATTA
3398880 CCATATTACA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
30 16 0.38
31 26 0.62
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (30 bp):
ATTAATTTAATTTAATTATATTATATAACA
Found at i:3399474 original size:28 final size:28
Alignment explanation
Indices: 3399439--3399496 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
3399429 TAATTGATAC
3399439 ATATTTAATAAAATAAGAGTTATATAAT
1 ATATTTAATAAAATAAGAGTTATATAAT
3399467 ATATTTAATAAAATAAGAGTTATATAAT
1 ATATTTAATAAAATAAGAGTTATATAAT
3399495 AT
1 AT
3399497 TCAAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (28 bp):
ATATTTAATAAAATAAGAGTTATATAAT
Found at i:3402274 original size:1 final size:1
Alignment explanation
Indices: 3402268--3402297 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
3402258 TCTTTCTTTC
3402268 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3402298 GTAGTTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3404572 original size:210 final size:210
Alignment explanation
Indices: 3404208--3405047 Score: 1229
Period size: 210 Copynumber: 4.0 Consensus size: 210
3404198 CAATCTATAA
*
3404208 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCATGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA
* * *
3404273 GTTCCCTCAGC-GAATTTTGCCAGTGAGCAGATGTTGCAAATCTTAGGGAAATCTTCTGATCCTG
66 GTTTCCTCA-CAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG
* *
3404337 ACAATTTATCCCAT-T-CTGGTTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGTAT
130 ACAATTTA-CCC-TGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAAT
*
3404400 CTGTCATCAGTAATCCAT
193 CTGTCATCAGTGATCCAT
* * **
3404418 TTGAATCCTCTGCCTCATCCGATATCATTTTAAGTGATGAGATCTCCACGAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA
* ** *
3404483 GTTTCCTCGCAGAATTTTGCCAGTGAACTTATGTTGCAAATCTCAGGGAAATCTTCTGATACTGA
66 GTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
3404548 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCAAAAAAATTCTCAAGTGGAATCTG
131 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3404613 TCATCAATGATCCAT
196 TCATCAGTGATCCAT
* * *
3404628 TTGAATCCTCTGCCTCATCCAATATCATTGCAAGCAATGGGATCTCCACAAGTTTACCTGATCCA
1 TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA
* * * *
3404693 ATTTCCTCACAGAATTTTGCCAGTGAGCAGATGTTGCAAATCTCTGGGAAATCTTCTGATCCTGT
66 GTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
* *
3404758 CAATTTACCCTGTACTGATTTATACATGAGTGGTGAAATTCATAAAAATTTACAAGTGGAATCTG
131 CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
*
3404823 TCATTAGTGATCCAT
196 TCATCAGTGATCCAT
* * * *
3404838 TTGTATCCTCTGCCTCATCCAATATCATCTCTAA-CAATGGGATCTCCATGAGTTTACCTGATCC
1 TTGAATCCTCTGCCTCATCCAATATCATTTC-AAGCAATGAGATCTCCACGAGTTTACCTGATCC
* * * * *
3404902 AGTTTCCTCACAGAATTTTGCCGGTGAACATATGTTGCAAAACTCGGGGGAATCTTCTGATCCTG
65 AGTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTG
* * ** *
3404967 ACAATTTACCATGTACTGATTTATGCACAAGTGATGAAATTCATAAAATTTCACAAGTGGAATCT
130 ACAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCT
*
3405032 GTCATCAGTCATCCAT
195 GTCATCAGTGATCCAT
3405048 CATCATCCTC
Statistics
Matches: 565, Mismatches: 61, Indels: 8
0.89 0.10 0.01
Matches are distributed among these distances:
208 1 0.00
209 5 0.01
210 557 0.99
211 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (210 bp):
TTGAATCCTCTGCCTCATCCAATATCATTTCAAGCAATGAGATCTCCACGAGTTTACCTGATCCA
GTTTCCTCACAGAATTTTGCCAGTGAACAGATGTTGCAAATCTCAGGGAAATCTTCTGATCCTGA
CAATTTACCCTGTACTGATTTATACATGAGTGATGAAATTCATAAAAATTCACAAGTGGAATCTG
TCATCAGTGATCCAT
Found at i:3407856 original size:55 final size:55
Alignment explanation
Indices: 3407773--3407905 Score: 241
Period size: 55 Copynumber: 2.4 Consensus size: 55
3407763 CCAGTCTATA
*
3407773 ACATA-TTTTGTCCATTACTTTTCATTTGTTTCAATACACCCATCATTATCATTT
1 ACATATTTTTGTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT
3407827 ACATATTTTTGTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT
1 ACATATTTTTGTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT
*
3407882 ACATTTTTTTGTCCATTACTTTTC
1 ACATATTTTTGTCCATTACTTTTC
3407906 TTGCAATTGT
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
54 5 0.07
55 71 0.93
ACGTcount: A:0.24, C:0.23, G:0.04, T:0.50
Consensus pattern (55 bp):
ACATATTTTTGTCCATTACTTTTCATTTGTTCCAATACACCCATCATTATCATTT
Found at i:3415928 original size:3 final size:3
Alignment explanation
Indices: 3415922--3415968 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
3415912 ACAACAAGAA
3415922 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3415969 GAGTAATACA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:3416221 original size:17 final size:18
Alignment explanation
Indices: 3416195--3416232 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3416185 TTTTAATTCA
*
3416195 TTTCATTCCA-AATTTAT
1 TTTCAATCCAGAATTTAT
*
3416212 TTTCAATCCAGAATTTCT
1 TTTCAATCCAGAATTTAT
3416230 TTT
1 TTT
3416233 AGGGTTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.26, C:0.18, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCAATCCAGAATTTAT
Found at i:3420557 original size:48 final size:48
Alignment explanation
Indices: 3420486--3420580 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 48
3420476 CCCAACTGAG
*
3420486 CTGTTAAAGCAATGAATTAAAAAATGAATGTAGTTTCAAAGTTTCAAC
1 CTGTTAAAGCAATGAATTAAAAAATGAATGGAGTTTCAAAGTTTCAAC
3420534 CTGTTAAAGCAATGAATTAAAAAATGAATGGAGTTTCAAAGTTTCAA
1 CTGTTAAAGCAATGAATTAAAAAATGAATGGAGTTTCAAAGTTTCAA
3420581 ACTTCTCTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.31
Consensus pattern (48 bp):
CTGTTAAAGCAATGAATTAAAAAATGAATGGAGTTTCAAAGTTTCAAC
Found at i:3423133 original size:53 final size:53
Alignment explanation
Indices: 3423052--3423202 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
3423042 CTTACACGGT
* *
3423052 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
3423107 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
3423160 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
3423203 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:3430637 original size:53 final size:53
Alignment explanation
Indices: 3430556--3430706 Score: 178
Period size: 53 Copynumber: 2.8 Consensus size: 53
3430546 CTTACACGGT
** *
3430556 TCACATATCATACCGAAACCATATCCCAGAC-ATGATCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGATCTTATACGGAATCACATTA
* * *
3430611 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCATATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGATCTTATACGGAATCACATTA
** * *
3430664 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGATCTTATACGG
3430707 GCACACTTAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
52 1 0.01
53 78 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGATCTTATACGGAATCACATTA
Found at i:3438039 original size:20 final size:22
Alignment explanation
Indices: 3438000--3438040 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3437990 ATATTACATA
*
3438000 TATATATATTTTATAGTTGTTT
1 TATATATATTATATAGTTGTTT
3438022 TATATATATTAT-TA-TTGTT
1 TATATATATTATATAGTTGTT
3438041 CCTAATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (22 bp):
TATATATATTATATAGTTGTTT
Found at i:3439922 original size:24 final size:24
Alignment explanation
Indices: 3439890--3439939 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
3439880 GTTTACAACC
3439890 CGATCACACCTTGTCAAAAAGGAT
1 CGATCACACCTTGTCAAAAAGGAT
3439914 CGATCACACCTTGTCAAAAAGGAT
1 CGATCACACCTTGTCAAAAAGGAT
3439938 CG
1 CG
3439940 GTGGCGACTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (24 bp):
CGATCACACCTTGTCAAAAAGGAT
Found at i:3445334 original size:42 final size:42
Alignment explanation
Indices: 3445274--3445359 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
3445264 GGATACCATA
*
3445274 AGAGTTGCGTTAAGAGTTACCAACCTGCATGTAGCATTTCGG
1 AGAGTTGCGTTAAAAGTTACCAACCTGCATGTAGCATTTCGG
3445316 AGAGTTGCGTTAAAAGTTACCAACCTGCATGTAGCATTTCGG
1 AGAGTTGCGTTAAAAGTTACCAACCTGCATGTAGCATTTCGG
3445358 AG
1 AG
3445360 TTTTGATTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.28
Consensus pattern (42 bp):
AGAGTTGCGTTAAAAGTTACCAACCTGCATGTAGCATTTCGG
Found at i:3445916 original size:32 final size:32
Alignment explanation
Indices: 3445875--3445939 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
3445865 TGCAAAAAAG
3445875 ATCAAAACTAGGTATCAGAAAGCTGTAAAACA
1 ATCAAAACTAGGTATCAGAAAGCTGTAAAACA
3445907 ATCAAAACTAGGTATCAGAAAGCTGTAAAACA
1 ATCAAAACTAGGTATCAGAAAGCTGTAAAACA
3445939 A
1 A
3445940 AGATCATTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.18
Consensus pattern (32 bp):
ATCAAAACTAGGTATCAGAAAGCTGTAAAACA
Found at i:3451532 original size:12 final size:11
Alignment explanation
Indices: 3451511--3451547 Score: 65
Period size: 11 Copynumber: 3.3 Consensus size: 11
3451501 AATTCATAGT
3451511 TAAATTAAAAA
1 TAAATTAAAAA
3451522 TAAATTAAAAA
1 TAAATTAAAAA
3451533 TAAATTTAAAAA
1 TAAA-TTAAAAA
3451545 TAA
1 TAA
3451548 TATATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
TAAATTAAAAA
Found at i:3457311 original size:19 final size:20
Alignment explanation
Indices: 3457262--3457311 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
3457252 ATATAAATTA
*
3457262 TTTTTGTAAAAAAATTACTT
1 TTTTTATAAAAAAATTACTT
*
3457282 TTGTTATTAAAAATAA-TA-TT
1 TTTTTA-TAAAAA-AATTACTT
3457302 TTTTTATAAA
1 TTTTTATAAA
3457312 CGAAAATACT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 8 0.32
22 2 0.08
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
TTTTTATAAAAAAATTACTT
Found at i:3459589 original size:30 final size:30
Alignment explanation
Indices: 3459550--3459606 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3459540 GAATTTGATT
* * *
3459550 AAATTAAAATTTTATTTATAAAATTACTCA
1 AAATCAAAATTATATATATAAAATTACTCA
*
3459580 AAATCAAAATTATATATATATAATTAC
1 AAATCAAAATTATATATATAAAATTAC
3459607 ACATTAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (30 bp):
AAATCAAAATTATATATATAAAATTACTCA
Found at i:3460542 original size:20 final size:20
Alignment explanation
Indices: 3460507--3460549 Score: 61
Period size: 19 Copynumber: 2.1 Consensus size: 20
3460497 CCTAAAAGCT
*
3460507 AAACCTTGAACTCGAATC-C
1 AAACCTCGAACTCGAATCTC
3460526 AAACCTCGAATCTCGAATCTC
1 AAACCTCGAA-CTCGAATCTC
3460547 AAA
1 AAA
3460550 TCCTAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
20 8 0.38
21 4 0.19
ACGTcount: A:0.40, C:0.30, G:0.09, T:0.21
Consensus pattern (20 bp):
AAACCTCGAACTCGAATCTC
Found at i:3473502 original size:23 final size:22
Alignment explanation
Indices: 3473453--3473510 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
3473443 AAAAATTGAC
3473453 AAATATTTTATAAAAATATAATA
1 AAATATTTTA-AAAAATATAATA
3473476 AAATATTTTAAAAAATATACGAT-
1 AAATATTTTAAAAAATATA--ATA
3473499 AAAT-TTTTAAAA
1 AAATATTTTAAAA
3473511 TTATTTATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
22 17 0.52
23 14 0.42
24 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAATATTTTAAAAAATATAATA
Found at i:3484473 original size:5 final size:5
Alignment explanation
Indices: 3484463--3484487 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
3484453 AGAGAGATAA
3484463 AAGAG AAGAG AAGAG AAGAG AAGAG
1 AAGAG AAGAG AAGAG AAGAG AAGAG
3484488 GGGGGGTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (5 bp):
AAGAG
Found at i:3494119 original size:17 final size:18
Alignment explanation
Indices: 3494093--3494127 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
3494083 CATGTTTTTA
*
3494093 TTTAATAATTTGATTAAT
1 TTTAATAATTAGATTAAT
3494111 TTTAA-AATTAGATTAAT
1 TTTAATAATTAGATTAAT
3494128 ATAATTCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTAATAATTAGATTAAT
Found at i:3494976 original size:16 final size:15
Alignment explanation
Indices: 3494937--3494979 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 15
3494927 CCCTAAAATA
3494937 ATAAAATTTTAATTT
1 ATAAAATTTTAATTT
**
3494952 ATATCATTTATAATTT
1 ATAAAATTT-TAATTT
3494968 ATAAAATTTTAA
1 ATAAAATTTTAA
3494980 ATTAATAATG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAAAATTTTAATTT
Found at i:3494982 original size:16 final size:16
Alignment explanation
Indices: 3494937--3494987 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
3494927 CCCTAAAATA
3494937 ATAAAATTTT-AATTT
1 ATAAAATTTTAAATTT
**
3494952 ATATCA-TTTATAATTT
1 ATAAAATTTTA-AATTT
*
3494968 ATAAAATTTTAAATTA
1 ATAAAATTTTAAATTT
3494984 ATAA
1 ATAA
3494988 TGATAAAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
14 3 0.11
15 4 0.14
16 17 0.61
17 4 0.14
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAAATTTTAAATTT
Found at i:3495022 original size:27 final size:25
Alignment explanation
Indices: 3494983--3495059 Score: 70
Period size: 25 Copynumber: 2.9 Consensus size: 25
3494973 ATTTTAAATT
3494983 AATAATGATAAAATTACATTTTATCTAAA
1 AATAAT-A-AAAATTA-ATTTTAT-TAAA
3495012 AATAATAAAAATTTAA-TTTATTAAA
1 AATAATAAAAA-TTAATTTTATTAAA
3495037 AA-AAT-AAAATTATATTTTTATTA
1 AATAATAAAAATTA-A-TTTTATTA
3495060 TAATAAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
22 3 0.07
23 5 0.11
24 3 0.07
25 13 0.30
26 5 0.11
27 5 0.11
28 4 0.09
29 6 0.14
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (25 bp):
AATAATAAAAATTAATTTTATTAAA
Found at i:3495079 original size:23 final size:23
Alignment explanation
Indices: 3495013--3495079 Score: 59
Period size: 25 Copynumber: 2.9 Consensus size: 23
3495003 TTATCTAAAA
3495013 ATAATAAAAAT-T-TAATTTATT
1 ATAATAAAAATATATAATTTATT
* * *
3495034 A-AAAAAATAAAATTATATTTTTATT
1 ATAATAAA-AATA-TATA-ATTTATT
3495059 ATAATAAAAATATATAATTTA
1 ATAATAAAAATATATAATTTA
3495080 ATTTCGATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
20 5 0.15
21 3 0.09
23 5 0.15
24 6 0.18
25 10 0.29
26 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAATAAAAATATATAATTTATT
Found at i:3499285 original size:25 final size:26
Alignment explanation
Indices: 3499229--3499278 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
3499219 CTTGGGCAAC
* *
3499229 AATTTTTTATTAAATTTATTTATTTT
1 AATTTTTTATTAAAGTTATTCATTTT
3499255 AATTTTTT-TTAAAGTT-TTCATTTT
1 AATTTTTTATTAAAGTTATTCATTTT
3499279 CCATTTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 7 0.32
26 8 0.36
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (26 bp):
AATTTTTTATTAAAGTTATTCATTTT
Found at i:3499318 original size:28 final size:28
Alignment explanation
Indices: 3499260--3499315 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
3499250 ATTTTAATTT
*
3499260 TTTTTAAAGTTTTCATTTTCCATTTTAA
1 TTTTTAAAGTTTTCATTTTCCATATTAA
* *
3499288 TTTTTAAAGTCTTTTATTTTTCATATTA
1 TTTTTAAAGT-TTTCATTTTCCATATTA
3499316 TTTATTATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.25, C:0.09, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTTTAAAGTTTTCATTTTCCATATTAA
Found at i:3503287 original size:2 final size:2
Alignment explanation
Indices: 3503280--3503313 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
3503270 AGACCATGTG
3503280 TA TA TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3503314 GGGTAATTGC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3504918 original size:18 final size:17
Alignment explanation
Indices: 3504871--3504926 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 17
3504861 ATTTTTATTT
3504871 GTTTATTAAAAAATAAAA
1 GTTT-TTAAAAAATAAAA
* *
3504889 ATAATTTTAAAAGATAAAA
1 GT--TTTTAAAAAATAAAA
3504908 GTTTTTAAAAAAATAAAA
1 GTTTTT-AAAAAATAAAA
3504926 G
1 G
3504927 AATAAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
17 4 0.13
18 12 0.39
19 13 0.42
20 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (17 bp):
GTTTTTAAAAAATAAAA
Found at i:3508708 original size:18 final size:17
Alignment explanation
Indices: 3508667--3508704 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
3508657 TTACACCGCC
*
3508667 AAAAT-ATTTTTTTGAT
1 AAAATAATTTTTTTGAA
*
3508683 AAAATAATTTTTTTTAA
1 AAAATAATTTTTTTGAA
3508700 AAAAT
1 AAAAT
3508705 TAATAAGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AAAATAATTTTTTTGAA
Found at i:3513655 original size:14 final size:14
Alignment explanation
Indices: 3513621--3513665 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
3513611 ATCTGGAATG
* *
3513621 CTAGCTCGCCACACG
1 CTAGCTCACCAC-CT
3513636 CTAGCTCACCACCT
1 CTAGCTCACCACCT
3513650 CTAGCTCACCACCT
1 CTAGCTCACCACCT
3513664 CT
1 CT
3513666 GCTAGCTCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.20, C:0.49, G:0.11, T:0.20
Consensus pattern (14 bp):
CTAGCTCACCACCT
Found at i:3513670 original size:17 final size:15
Alignment explanation
Indices: 3513619--3513673 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
3513609 AAATCTGGAA
*
3513619 TGCTAGCTCGCCACAC
1 TGCTAGCTCACCAC-C
3513635 -GCTAGCTCACCACC
1 TGCTAGCTCACCACC
3513649 T-CTAGCTCACCACCTC
1 TGCTAGCTCACCA-C-C
3513665 TGCTAGCTC
1 TGCTAGCTC
3513674 GGGGGATCGC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 12 0.35
15 13 0.38
16 2 0.06
17 7 0.21
ACGTcount: A:0.18, C:0.45, G:0.15, T:0.22
Consensus pattern (15 bp):
TGCTAGCTCACCACC
Found at i:3514690 original size:21 final size:22
Alignment explanation
Indices: 3514644--3514692 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
3514634 TTTCTTAATA
3514644 AATTTGAATAATATTGTACACT
1 AATTTGAATAATATTGTACACT
* * *
3514666 -ATTTTAATAATTTTGTATA-T
1 AATTTGAATAATATTGTACACT
3514686 AATTTGA
1 AATTTGA
3514693 CAACATTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (22 bp):
AATTTGAATAATATTGTACACT
Found at i:3517243 original size:13 final size:13
Alignment explanation
Indices: 3517225--3517249 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3517215 TTTCTTGCAT
3517225 ATATATAATATAA
1 ATATATAATATAA
3517238 ATATATAATATA
1 ATATATAATATA
3517250 TTAATGTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATAATATAA
Found at i:3529666 original size:15 final size:15
Alignment explanation
Indices: 3529643--3529696 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3529633 AATTCATTAG
* *
3529643 TTAAATTTTTAATAT
1 TTAATTTTTTAACAT
*
3529658 TTAATTTTTTAACAC
1 TTAATTTTTTAACAT
*
3529673 TT-ATTTTGTCAACAT
1 TTAATTTT-TTAACAT
3529688 TTAATTTTT
1 TTAATTTTT
3529697 ATCAAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 5 0.16
15 22 0.69
16 5 0.16
ACGTcount: A:0.31, C:0.07, G:0.02, T:0.59
Consensus pattern (15 bp):
TTAATTTTTTAACAT
Found at i:3543681 original size:22 final size:23
Alignment explanation
Indices: 3543648--3543696 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
3543638 AAACATGGAT
* *
3543648 TGTA-AAATGTAAATTGTCTA-G
1 TGTATAAACGTAAATTGTCAATG
3543669 TGTATAAACGTAAATTGTCAATG
1 TGTATAAACGTAAATTGTCAATG
3543692 TGTAT
1 TGTAT
3543697 GAGCATGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (23 bp):
TGTATAAACGTAAATTGTCAATG
Found at i:3553994 original size:15 final size:15
Alignment explanation
Indices: 3553974--3554002 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3553964 GATAAAATTT
3553974 CTACTTTTTAATGGG
1 CTACTTTTTAATGGG
3553989 CTACTTTTTAATGG
1 CTACTTTTTAATGG
3554003 ACTATTCACG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (15 bp):
CTACTTTTTAATGGG
Found at i:3558767 original size:25 final size:26
Alignment explanation
Indices: 3558733--3558781 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
3558723 TTGAGATTTA
*
3558733 TTAGTAAAAATAACATTTTTATTTTT
1 TTAGTAAAAATAACATTTTAATTTTT
*
3558759 TTAGT-AAAATAATATTTTAATTT
1 TTAGTAAAAATAACATTTTAATTT
3558782 CCTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (26 bp):
TTAGTAAAAATAACATTTTAATTTTT
Found at i:3558833 original size:35 final size:34
Alignment explanation
Indices: 3558767--3558831 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
3558757 TTTTAGTAAA
*
3558767 ATAATATTTTAATTTCCTATTATTTTATTTTAGG
1 ATAATATTTTAATTTCCTAGTATTTTATTTTAGG
3558801 ATAATACTTTTAATTT-CTAGTATTTTATTTT
1 ATAATA-TTTTAATTTCCTAGTATTTTATTTT
3558832 TATTTTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 20 0.69
35 9 0.31
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (34 bp):
ATAATATTTTAATTTCCTAGTATTTTATTTTAGG
Found at i:3560345 original size:51 final size:50
Alignment explanation
Indices: 3560274--3560433 Score: 248
Period size: 51 Copynumber: 3.2 Consensus size: 50
3560264 CTGATCACAT
3560274 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
* *
3560325 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCACTTATCAT
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
* * *
3560375 TTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCAC
*
3560426 TTGTCACT
1 TTATCACT
3560434 GATCAGAAGT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
50 46 0.46
51 55 0.54
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (50 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCACTTATCAC
Found at i:3567058 original size:44 final size:43
Alignment explanation
Indices: 3566995--3567154 Score: 212
Period size: 44 Copynumber: 3.5 Consensus size: 43
3566985 CTGATCACAT
3566995 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCAC
*
3567039 TTATCACTTGTCACTGATCAGATAAGAGTAGCTAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCAC
* *
3567082 TTATCATTTGTCACTTATCACTGATCAGATAAGTGTAGCTGAGGCTACCAC
1 -T-T-A----TCACTTGTCACTGATCAGATAAGTGTAGCT-AAGCTACCAC
3567133 TTATCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTGATCAGA
3567155 AGTACTCAAA
Statistics
Matches: 103, Mismatches: 5, Indels: 16
0.83 0.04 0.13
Matches are distributed among these distances:
43 10 0.10
44 51 0.50
45 1 0.01
46 1 0.01
48 1 0.01
49 1 0.01
50 29 0.28
51 9 0.09
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.31
Consensus pattern (43 bp):
TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAGCTACCAC
Found at i:3569557 original size:10 final size:10
Alignment explanation
Indices: 3569542--3569571 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3569532 CAAAAAAATG
*
3569542 TTATTTTAAC
1 TTATTTTAAA
3569552 TTATTTTAAA
1 TTATTTTAAA
3569562 TTATTTTAAA
1 TTATTTTAAA
3569572 GTTTCGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATTTTAAA
Found at i:3581718 original size:420 final size:420
Alignment explanation
Indices: 3580934--3584441 Score: 6858
Period size: 420 Copynumber: 8.4 Consensus size: 420
3580924 ATCAATTATG
*
3580934 AGTTAGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3580999 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
3581064 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
131 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
*
3581129 AATACGAAAATATTAAAATTAGATAAAATAAACTTTTGGATTAAATTTACAAAACAAAAAAGCGG
196 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
3581194 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
261 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
3581259 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
326 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
3581324 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
391 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
3581354 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3581419 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
3581484 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
131 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
3581549 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
196 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
*
3581614 TTGTCCGTTTAGGGAAAGACCCAATGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
261 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
3581679 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
326 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
3581744 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
391 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
3581774 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3581839 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
3581904 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
131 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
3581969 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
196 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
*
3582034 TTGTCCGTTTAGGGAATGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
261 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
*
3582099 CCATTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
326 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
*
3582164 CAGGAGCAAGGAGACCCAAAGCTTTCGCTC
391 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
*
3582194 AGTTAGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
*
3582259 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAATTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
3582324 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
131 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
3582389 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
196 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
*
3582454 TTGTCCGTTTAGGGAATGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
261 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
3582519 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
326 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
3582584 TAGGAGCAAGGAGA-CCAAAGCTTTCGCTC
391 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
3582613 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3582678 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
3582743 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
131 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
*
3582808 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTAGATTAAATTTACAAAACAAAAAAGCGG
196 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
3582873 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
261 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
3582938 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
326 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
3583003 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
391 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
3583033 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3583098 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
* *
3583163 AATGAAACATATGATTTGAAACTAATTATACAAGTAACTTTTTGGAGAAAATCACTTTTTGGATT
131 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
3583228 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
196 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
*
3583293 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGTCCGTTATCCTT
261 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
*
3583358 CCATTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
326 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
3583423 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
391 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
3583453 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3583518 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
3583583 AATGAAACATATGATTTGAAACTAAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGAT
131 AATGAAACATATGATTTGAAACT-AATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGAT
3583648 TAATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCG
195 TAATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCG
3583713 GTTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCT
260 GTTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCT
3583778 TCCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACT
325 TCCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACT
3583843 CTAGGAGCAAGGAGACCCAAAGCTTTCGCTC
390 CTAGGAGCAAGGAGACCCAAAGCTTTCGCTC
3583874 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3583939 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAAT-AAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
*
3584003 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGAGAAAATCACTTTTTGGATT
131 AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
3584068 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
196 AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
3584133 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
261 TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
3584198 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
326 CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
3584263 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
391 TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
3584293 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
1 AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
3584358 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
66 TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
3584423 AATGAAACATATGATTTGA
131 AATGAAACATATGATTTGA
3584442 TATAGCTTGT
Statistics
Matches: 3060, Mismatches: 25, Indels: 6
0.99 0.01 0.00
Matches are distributed among these distances:
419 784 0.26
420 1910 0.62
421 366 0.12
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (420 bp):
AGTTGGTGTTGAGTTGACTTATAACACCAACTTAATGAATAATATTATTAATATTAAAAATTCTA
TCACTTATGTATGCACGTAGAAACCATAGATTTAAAATAAAAAAATTTGTTTAAAAGTAATAAAT
AATGAAACATATGATTTGAAACTAATTATACAAGTAACGTTTTGGATAAAATCACTTTTTGGATT
AATACGAAAATATTAAAATTAGATAAAATAACCTTTTGGATTAAATTTACAAAACAAAAAAGCGG
TTGTCCGTTTAGGGAAAGACCCAAGGAACCATGAAGGATCCAAGTGACACCGGCCCGTTATCCTT
CCACTGCAAAGAGAGGGAAGTTTTCGCTGCTCTGTGAAACCAGCCTTACGCTTTGCCTTCCACTC
TAGGAGCAAGGAGACCCAAAGCTTTCGCTC
Found at i:3585483 original size:53 final size:55
Alignment explanation
Indices: 3585389--3585495 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
3585379 ATATATTTTC
* * *
3585389 TAAAATTTATATAAAATATAAAAAGACAAAAAAAATTAAAATTTAATATTATTTA
1 TAAAATTTATATAAAACATAAAAAGACAAAAAAAATCAAAATTAAATATTATTTA
3585444 TAAAATTTATATAAAACAT-AAAAGACAAAAAAAA-CAAAATTAAATATTATTT
1 TAAAATTTATATAAAACATAAAAAGACAAAAAAAATCAAAATTAAATATTATTT
3585496 TCTATAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
53 16 0.33
54 15 0.31
55 18 0.37
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.32
Consensus pattern (55 bp):
TAAAATTTATATAAAACATAAAAAGACAAAAAAAATCAAAATTAAATATTATTTA
Found at i:3591274 original size:60 final size:60
Alignment explanation
Indices: 3591201--3591323 Score: 246
Period size: 60 Copynumber: 2.0 Consensus size: 60
3591191 GCTGCAATAT
3591201 CTTCTCTAGAAGAAACCTCGATGACCTCTTTAACTTTTCTCCCCAACGATCATCAACTAA
1 CTTCTCTAGAAGAAACCTCGATGACCTCTTTAACTTTTCTCCCCAACGATCATCAACTAA
3591261 CTTCTCTAGAAGAAACCTCGATGACCTCTTTAACTTTTCTCCCCAACGATCATCAACTAA
1 CTTCTCTAGAAGAAACCTCGATGACCTCTTTAACTTTTCTCCCCAACGATCATCAACTAA
3591321 CTT
1 CTT
3591324 ATCCAGGGCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.29, C:0.32, G:0.08, T:0.31
Consensus pattern (60 bp):
CTTCTCTAGAAGAAACCTCGATGACCTCTTTAACTTTTCTCCCCAACGATCATCAACTAA
Found at i:3594417 original size:3 final size:3
Alignment explanation
Indices: 3594405--3594451 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
3594395 AAAAATCTAA
*
3594405 TAT T-T TAT TAT TAT TAT TAAT TAT TAT TAT TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT
3594450 TA
1 TA
3594452 AGTTAAAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3599356 original size:6 final size:6
Alignment explanation
Indices: 3599342--3599381 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
3599332 GTGGTGGTGG
* * *
3599342 TGGTGA TGGTCA TGGTCA TGGTCA TGGTGA TGGCCA TGGT
1 TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGGTCA TGGT
3599382 GATCATTGGA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.15, C:0.12, G:0.40, T:0.33
Consensus pattern (6 bp):
TGGTCA
Found at i:3599357 original size:12 final size:12
Alignment explanation
Indices: 3599342--3599384 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
3599332 GTGGTGGTGG
3599342 TGGTGATGGTCA
1 TGGTGATGGTCA
*
3599354 TGGTCATGGTCA
1 TGGTGATGGTCA
*
3599366 TGGTGATGGCCA
1 TGGTGATGGTCA
3599378 TGGTGAT
1 TGGTGAT
3599385 CATTGGAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.33
Consensus pattern (12 bp):
TGGTGATGGTCA
Found at i:3599363 original size:18 final size:18
Alignment explanation
Indices: 3599342--3599384 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3599332 GTGGTGGTGG
*
3599342 TGGTGATGGTCATGGTCA
1 TGGTGATGGTCATGGCCA
* *
3599360 TGGTCATGGTGATGGCCA
1 TGGTGATGGTCATGGCCA
3599378 TGGTGAT
1 TGGTGAT
3599385 CATTGGAAGC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.12, G:0.40, T:0.33
Consensus pattern (18 bp):
TGGTGATGGTCATGGCCA
Found at i:3606952 original size:12 final size:11
Alignment explanation
Indices: 3606929--3606963 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3606919 ATATTATATA
3606929 ATTATTATTTT
1 ATTATTATTTT
*
3606940 ATTGTTAATTTT
1 ATTATT-ATTTT
3606952 ATTATTATTTT
1 ATTATTATTTT
3606963 A
1 A
3606964 AAGGTATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (11 bp):
ATTATTATTTT
Found at i:3607118 original size:16 final size:16
Alignment explanation
Indices: 3607094--3607124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3607084 AATTTATTTT
*
3607094 TATATAAAATTAATAA
1 TATAAAAAATTAATAA
3607110 TATAAAAAATTAATA
1 TATAAAAAATTAATA
3607125 TAAACAAGCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAAAATTAATAA
Found at i:3618896 original size:22 final size:21
Alignment explanation
Indices: 3618871--3618925 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 21
3618861 CCATTCAAGA
**
3618871 TAAAATAATATATAAAACTCTT
1 TAAAATAATATAT-AAACAATT
3618893 TAAAAATAATATATAAACAATT
1 T-AAAATAATATATAAACAATT
3618915 TAAAAT-ATATA
1 TAAAATAATATA
3618926 ATGTGTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 5 0.17
22 8 0.27
23 12 0.40
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATAATATATAAACAATT
Found at i:3618926 original size:25 final size:25
Alignment explanation
Indices: 3618896--3619066 Score: 89
Period size: 25 Copynumber: 6.7 Consensus size: 25
3618886 AACTCTTTAA
*
3618896 AAATAATATATAAACAATTTAAAAT
1 AAATAATATATAAAAAATTTAAAAT
* * * *
3618921 ATATAATGTGTAAAAAAAAGTTTGAAAT
1 AAATAA--TATATAAAAAA-TTTAAAAT
* *
3618949 ACATAATATAT-AAAAATATTAAAGT
1 AAATAATATATAAAAAAT-TTAAAAT
* *
3618974 AAATAATGTATAAAAAA-TTGAAAT
1 AAATAATATATAAAAAATTTAAAAT
* *** *
3618998 GAACGTTATAT-AAAAAGTTAAAAT
1 AAATAATATATAAAAAATTTAAAAT
* * *
3619022 AGATAATA-ACAAAAAAATGTAAAAT
1 AAATAATATA-TAAAAAATTTAAAAT
*
3619047 AAATAAATAAATAAATAAAT
1 AAAT-AATATATAAA-AAAT
3619067 AGAATGTTAA
Statistics
Matches: 105, Mismatches: 30, Indels: 20
0.68 0.19 0.13
Matches are distributed among these distances:
23 6 0.06
24 21 0.20
25 38 0.36
26 15 0.14
27 13 0.12
28 12 0.11
ACGTcount: A:0.62, C:0.02, G:0.07, T:0.29
Consensus pattern (25 bp):
AAATAATATATAAAAAATTTAAAAT
Found at i:3619052 original size:4 final size:4
Alignment explanation
Indices: 3619043--3619067 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3619033 AAAAAATGTA
3619043 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
3619068 GAATGTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:3619165 original size:15 final size:15
Alignment explanation
Indices: 3619141--3619186 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
3619131 ATATAAATAG
*
3619141 AAATAAAAATATAAT
1 AAATAGAAATATAAT
3619156 AAATAGAAATATAAT
1 AAATAGAAATATAAT
3619171 AATAGTAGAAATATAA
1 AA-A-TAGAAATATAA
3619187 ATAGATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 16 0.57
16 1 0.04
17 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
AAATAGAAATATAAT
Found at i:3619189 original size:44 final size:44
Alignment explanation
Indices: 3619135--3619221 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
3619125 ATTAGTATAT
3619135 AAATAGAAATA-A-AAATATAATAAATAGA-AATATAATAATAGTAG
1 AAATAGAAATAGATAAATA-AA-AAATAGATAA-ATAATAATAGTAG
* *
3619179 AAATATAAATAGATAAATAAAAATTAGATAAATAATAATAGTA
1 AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTA
3619222 TTAGAATAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 28 0.74
45 5 0.13
46 5 0.13
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (44 bp):
AAATAGAAATAGATAAATAAAAAATAGATAAATAATAATAGTAG
Found at i:3619206 original size:15 final size:14
Alignment explanation
Indices: 3619133--3619219 Score: 61
Period size: 15 Copynumber: 6.0 Consensus size: 14
3619123 ATATTAGTAT
*
3619133 ATAAATAGAAATA-
1 ATAAATAAAAATAG
*
3619146 AAAATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
3619162 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
3619176 TAGAAATATAAATAG
1 -ATAAATAAAAATAG
3619191 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
*
3619206 ATAAATAATAATAG
1 ATAAATAAAAATAG
3619220 TATTAGAATA
Statistics
Matches: 60, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
13 3 0.05
14 20 0.33
15 34 0.57
16 3 0.05
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:3625048 original size:10 final size:10
Alignment explanation
Indices: 3625033--3625065 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
3625023 TAATTAATTT
3625033 TTTAAAAATA
1 TTTAAAAATA
3625043 TTTAAAAATA
1 TTTAAAAATA
3625053 TTTAAAAATA
1 TTTAAAAATA
3625063 TTT
1 TTT
3625066 TTATACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:3627105 original size:39 final size:39
Alignment explanation
Indices: 3627060--3627219 Score: 266
Period size: 39 Copynumber: 4.1 Consensus size: 39
3627050 AAGCAAGACA
3627060 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
*
3627099 CTGGAAATGTATCCGGGCTAAAGACCCGCAAGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* *
3627138 ATGGAAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
* * *
3627177 CTGGAAATGTATCCGAGCTAAAGTCCCGCAGGCTTTGTG
1 CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
3627216 CTGG
1 CTGG
3627220 TAATATAATT
Statistics
Matches: 114, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 114 1.00
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (39 bp):
CTGGAAATGTATCCGGGCTAAAGACCCGCAGGCTTCGTG
Found at i:3629306 original size:33 final size:33
Alignment explanation
Indices: 3629268--3629333 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3629258 TCTAAAATAG
* *
3629268 TAAATATTTATTTTAGTCTTTTAAATTTTTTTA
1 TAAATATTTATTTTAATCTTTTAAAATTTTTTA
*
3629301 TAAATATTTATTTTAATTTTTTAAAATTTTTTA
1 TAAATATTTATTTTAATCTTTTAAAATTTTTTA
3629334 AATTATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (33 bp):
TAAATATTTATTTTAATCTTTTAAAATTTTTTA
Found at i:3631837 original size:48 final size:48
Alignment explanation
Indices: 3631785--3631883 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
3631775 GCCATTTTTT
3631785 CAATTAATGTTCCGTAAATTCGCATTTAATACACAAAATGACATATCC
1 CAATTAATGTTCCGTAAATTCGCATTTAATACACAAAATGACATATCC
3631833 CAATTAATGTTCCGTAAATTCGCATTTAATACACAAAATGACATATCC
1 CAATTAATGTTCCGTAAATTCGCATTTAATACACAAAATGACATATCC
3631881 CAA
1 CAA
3631884 AAGGAAGCTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.30
Consensus pattern (48 bp):
CAATTAATGTTCCGTAAATTCGCATTTAATACACAAAATGACATATCC
Found at i:3632936 original size:23 final size:23
Alignment explanation
Indices: 3632906--3632950 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
3632896 TTATTATCAG
3632906 TATAAAAGAAAGGTAAATTTGAA
1 TATAAAAGAAAGGTAAATTTGAA
3632929 TATAAAAGAAAGGTAAATTTGA
1 TATAAAAGAAAGGTAAATTTGA
3632951 GCATAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.18, T:0.27
Consensus pattern (23 bp):
TATAAAAGAAAGGTAAATTTGAA
Done.