Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 10 of 230
Found at i:2969697 original size:14 final size:14
Alignment explanation
Indices: 2969648--2969781 Score: 84
Period size: 14 Copynumber: 9.4 Consensus size: 14
2969638 CTTCCCACTT
2969648 TTCTTCTTTCTTT-C
1 TTCTT-TTTCTTTCC
2969662 TT-TTTTT-TTCTCC
1 TTCTTTTTCTT-TCC
*
2969675 GTTCCTTTTCTTTCC
1 -TTCTTTTTCTTTCC
2969690 TTCTTTTTC-TT-C
1 TTCTTTTTCTTTCC
2969702 -T-TTTTTCTTCTCC
1 TTCTTTTTCTT-TCC
*
2969715 TTTCCTTTTCTTTCC
1 -TTCTTTTTCTTTCC
*
2969730 TTCTTTTTCTTTCT
1 TTCTTTTTCTTTCC
*
2969744 TTCCTCTCATTTCCTTTCT
1 TT-CT-T--TTT-CTTTCC
*
2969763 TTCTTTTTCTTTCT
1 TTCTTTTTCTTTCC
2969777 TTCTT
1 TTCTT
2969782 CTCTTTTCCC
Statistics
Matches: 99, Mismatches: 5, Indels: 32
0.73 0.04 0.24
Matches are distributed among these distances:
10 6 0.06
11 4 0.04
12 6 0.06
13 6 0.06
14 37 0.37
15 16 0.16
16 10 0.10
17 1 0.01
18 5 0.05
19 8 0.08
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (14 bp):
TTCTTTTTCTTTCC
Found at i:2969714 original size:40 final size:41
Alignment explanation
Indices: 2969648--2969745 Score: 162
Period size: 40 Copynumber: 2.4 Consensus size: 41
2969638 CTTCCCACTT
*
2969648 TTCTTCTTTCTTTCTTTTTTTTTCTCCGTTCCTTTTCTTTCC
1 TTCTT-TTTCTTTCTTTTTTCTTCTCCGTTCCTTTTCTTTCC
*
2969690 TTCTTTTTC-TTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
1 TTCTTTTTCTTTCTTTTTTCTTCTCCGTTCCTTTTCTTTCC
2969730 TTCTTTTTCTTTCTTT
1 TTCTTTTTCTTTCTTT
2969746 CCTCTCATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
40 38 0.72
41 10 0.19
42 5 0.09
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (41 bp):
TTCTTTTTCTTTCTTTTTTCTTCTCCGTTCCTTTTCTTTCC
Found at i:2969718 original size:30 final size:28
Alignment explanation
Indices: 2969681--2969787 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 28
2969671 CTCCGTTCCT
2969681 TTTCTTTCCTTCTT-TTT-CTTCTTTTTTC
1 TTTCTTTCCTT-TTCTTTCCTTC-TTTTTC
2969709 TTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TT-T-CTTTCCTTTTCTTTCCTTCTTTTTC
*
2969739 TTTCTTTCCTCTCATTTCCTTTCTTTCTTTTTC
1 TTTCTTT-C-CT--TTT-CTTTCCTTCTTTTTC
*
2969772 TTTCTTT-CTTCTCTTT
1 TTTCTTTCCTTTTCTTT
2969788 TCCCTCTCAT
Statistics
Matches: 68, Mismatches: 2, Indels: 19
0.76 0.02 0.21
Matches are distributed among these distances:
27 4 0.06
28 8 0.12
29 5 0.07
30 23 0.34
31 4 0.06
32 3 0.04
33 21 0.31
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTCTTTCCTTTTCTTTCCTTCTTTTTC
Found at i:2969776 original size:10 final size:10
Alignment explanation
Indices: 2969647--2969783 Score: 66
Period size: 10 Copynumber: 13.1 Consensus size: 10
2969637 CCTTCCCACT
2969647 TTTCTTCTTTC
1 TTTCTT-TTTC
*
2969658 TTTCTTTTTT
1 TTTCTTTTTC
* *
2969668 TTTCTCCGTTCC
1 TTTCT--TTTTC
*
2969680 TTT-TCTTTC
1 TTTCTTTTTC
*
2969689 CTTCTTTTTC
1 TTTCTTTTTC
2969699 -TTCTTTTTTC
1 TTTC-TTTTTC
* *
2969709 TTCTCCTTTCC
1 TT-TCTTTTTC
*
2969720 TTT-TCTTTC
1 TTTCTTTTTC
*
2969729 CTTCTTTTTC
1 TTTCTTTTTC
2969739 TTTCTTTCCTCTC
1 TTTCTTT--T-TC
*
2969752 ATTTC-CTTTC
1 -TTTCTTTTTC
2969762 TTTCTTTTTC
1 TTTCTTTTTC
2969772 TTTCTTTCTTC
1 TTTCTTT-TTC
2969783 T
1 T
2969784 CTTTTCCCTC
Statistics
Matches: 95, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
9 17 0.18
10 44 0.46
11 19 0.20
12 8 0.08
13 3 0.03
14 4 0.04
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:2972815 original size:281 final size:289
Alignment explanation
Indices: 2972384--2973034 Score: 903
Period size: 302 Copynumber: 2.2 Consensus size: 289
2972374 ATTACTTTCG
* * * * * *
2972384 TTTT-TTATTTTACATTGTTTTATTATATTATGTTTGAAGTGTATTAATTTAGTGTGTATTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
2972448 ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
66 ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
* *
2972513 TTTAATAAAAATATATTA-TT-TTA-TA-A-TATTTCAGTAC-AT-TTTGTATTAATTATTTCTG
131 TTCAATAAAAATATATTATTTATTATTATATTATTTCAGTACTATATTTGTATTAATTATTTCTA
* *
2972571 AATTTTTAAAAAATTTAGTAAAACACTCTTACTTC-AGCCATTTGTTCGTA-TTTTTT-TCAGCA
196 AATTTTTAAAAAATGTAGTAAAA-AATCTTACTTCGA-CC-TTTGTTCGTATTTTTTTCTCAGCA
* *
2972633 TTTTATTACTTTAAAAATATCATATTTTCTAA
258 TTTTATTACTTAAAAAAAATCATATTTTCTAA
*
2972665 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGAGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
* *
2972730 ATAAA-TTTAAAAAAAACCCTTATTCCTGCCCTTTGCTTGTATTATTTTCCCGAATTTTATTACT
66 ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
*
2972794 TTCAATAACAATATATTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGT
131 TTCAATAAAAATATATTA-TTTATTA--TTATATTATTTCAGTAC--------T---ATATTTGT
2972859 ATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGTATTT
182 ATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGTATTT
*
2972924 TTTTCTCCGCATTTTATTACTTAAAAAAAATCATATTTTCTAA
247 TTTTCTCAGCATTTTATTACTTAAAAAAAATCATATTTTCTAA
*
2972967 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTACTGTGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
2973032 ATA
66 ATA
2973035 TACCATATTT
Statistics
Matches: 326, Mismatches: 19, Indels: 29
0.87 0.05 0.08
Matches are distributed among these distances:
281 77 0.24
282 58 0.18
283 2 0.01
284 3 0.01
287 2 0.01
288 1 0.00
289 11 0.03
300 10 0.03
301 20 0.06
302 142 0.44
ACGTcount: A:0.32, C:0.10, G:0.07, T:0.51
Consensus pattern (289 bp):
TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
ATAAATTTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACT
TTCAATAAAAATATATTATTTATTATTATATTATTTCAGTACTATATTTGTATTAATTATTTCTA
AATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGTATTTTTTTCTCAGCATTT
TATTACTTAAAAAAAATCATATTTTCTAA
Found at i:2972993 original size:155 final size:155
Alignment explanation
Indices: 2972552--2973007 Score: 500
Period size: 151 Copynumber: 3.0 Consensus size: 155
2972542 TTCAGTACAT
* *
2972552 TTTGTATTAATTATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTC-AGCCATTTGT
1 TTTGTATTAATTATTTCTAAATTTTTAAAAAATTTAGTAAAA-AATCTTACTTCGA-CC-TTTGT
* * *
2972616 TCGTA-TTTTTT-TCAGCATTTTATTACTTTAAAAATATCATATTTTCTAATTTTATTATTTTAC
63 TCGTATTTTTTTCTCCGCATTTTATTACTTAAAAAAAATCATATTTTCTAATTTTATTATTTTAC
2972679 ATTATTTTAGTACATTATGTTTG-AA-A
128 ATTATTTTAGTACATTATGTTTGAAATA
* * ** * * *
2972705 -TT-TATTAATT-TAGT-GAGTTTTTTAAATAAATTTA-AAAAAAACCCTTA-TTCCTGCCCTTT
1 TTTGTATTAATTAT-TTCTAAATTTTTAAA-AAATTTAGTAAAAAA-TCTTACTT-C-GACCTTT
* * * *
2972764 GCTT-GTATTATTTTC-CCGAATTTTATTACTTTCAATAACAAT-ATA---T-T-ATTTTATTAT
61 G-TTCGTATTTTTTTCTCCGCATTTTATTAC-TT-AAAAAAAATCATATTTTCTAATTTTATTAT
* * *
2972821 TTTATATTATTTCAGTACATTTTGTTTGAAATA
123 TTTACATTATTTTAGTACATTATGTTTGAAATA
*
2972854 TTTGTATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCG
1 TTTGTATTAATTATTTCTAAATTTTTAAAAAATTTAGTAAAAAATCTTACTTCGACCTTTGTTCG
2972919 TATTTTTTTCTCCGCATTTTATTACTTAAAAAAAATCATATTTTCTAATTTTATTATTTTACATT
66 TATTTTTTTCTCCGCATTTTATTACTTAAAAAAAATCATATTTTCTAATTTTATTATTTTACATT
2972984 ATTTTAGTACATTATGTTTGAAAT
131 ATTTTAGTACATTATGTTTGAAAT
2973008 TTATTAATTT
Statistics
Matches: 242, Mismatches: 34, Indels: 52
0.74 0.10 0.16
Matches are distributed among these distances:
147 35 0.14
148 3 0.01
149 14 0.06
150 49 0.20
151 70 0.29
152 25 0.10
153 6 0.02
154 1 0.00
155 39 0.16
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.51
Consensus pattern (155 bp):
TTTGTATTAATTATTTCTAAATTTTTAAAAAATTTAGTAAAAAATCTTACTTCGACCTTTGTTCG
TATTTTTTTCTCCGCATTTTATTACTTAAAAAAAATCATATTTTCTAATTTTATTATTTTACATT
ATTTTAGTACATTATGTTTGAAATA
Found at i:2973359 original size:20 final size:20
Alignment explanation
Indices: 2973321--2973359 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2973311 ATTCCCACCA
* *
2973321 CTTCTTCTACTTTCTTTTTT
1 CTTCTTCTACGTTCCTTTTT
*
2973341 CTTCTTCTCCGTTCCTTTT
1 CTTCTTCTACGTTCCTTTT
2973360 CTTTCCTTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.31, G:0.03, T:0.64
Consensus pattern (20 bp):
CTTCTTCTACGTTCCTTTTT
Found at i:2973365 original size:10 final size:10
Alignment explanation
Indices: 2973352--2973459 Score: 52
Period size: 10 Copynumber: 11.3 Consensus size: 10
2973342 TTCTTCTCCG
2973352 TTCCTTTTCT
1 TTCCTTTTCT
*
2973362 TTCCTTTTTT
1 TTCCTTTTCT
* **
2973372 TTTCAGTT-T
1 TTCCTTTTCT
*
2973381 TT-CTTCTCCT
1 TTCCTT-TTCT
2973391 TTCCTTTTCT
1 TTCCTTTTCT
*
2973401 TTCATTCTT-T
1 TTCCTT-TTCT
2973411 TT-C-TTTCT
1 TTCCTTTTCT
*
2973419 TTCC-TCTCAT
1 TTCCTTTTC-T
2973429 TTCCTTTTCT
1 TTCCTTTTCT
* *
2973439 TTCTTTTTAT
1 TTCCTTTTCT
2973449 TT-C-TTTCT
1 TTCCTTTTCT
2973457 TTC
1 TTC
2973460 TTCTCCTTTC
Statistics
Matches: 73, Mismatches: 16, Indels: 19
0.68 0.15 0.18
Matches are distributed among these distances:
7 2 0.03
8 11 0.15
9 8 0.11
10 44 0.60
11 8 0.11
ACGTcount: A:0.04, C:0.26, G:0.01, T:0.69
Consensus pattern (10 bp):
TTCCTTTTCT
Found at i:2973395 original size:39 final size:38
Alignment explanation
Indices: 2973338--2973470 Score: 171
Period size: 38 Copynumber: 3.5 Consensus size: 38
2973328 TACTTTCTTT
*
2973338 TTTC-TTCTTCTCCGTTCCTTTTCTTTCCTTTTTTTTTC
1 TTTCTTTCTTCTCCTTTCCTTTTCTTT-CTTTTTTTTTC
* * *
2973376 AGTT-TTTCTTCTCCTTTCCTTTTCTTTCATTCTTTTTC
1 -TTTCTTTCTTCTCCTTTCCTTTTCTTTCTTTTTTTTTC
* * *
2973414 TTTCTTTCCTCTCATTTCCTTTTCTTTCTTTTTATTTC
1 TTTCTTTCTTCTCCTTTCCTTTTCTTTCTTTTTTTTTC
2973452 TTTCTTTCTTCTCCTTTCC
1 TTTCTTTCTTCTCCTTTCC
2973471 CTCTCCTTCT
Statistics
Matches: 80, Mismatches: 12, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
37 2 0.03
38 55 0.69
39 23 0.29
ACGTcount: A:0.03, C:0.29, G:0.02, T:0.67
Consensus pattern (38 bp):
TTTCTTTCTTCTCCTTTCCTTTTCTTTCTTTTTTTTTC
Found at i:2973416 original size:24 final size:25
Alignment explanation
Indices: 2973342--2973451 Score: 71
Period size: 24 Copynumber: 4.3 Consensus size: 25
2973332 TTCTTTTTTC
* *
2973342 TTCTTCTCCGTTCCTTTTCTTTCCTTT
1 TTCTT-TCAGTTCTTTTTCTTTCC-TT
* *
2973369 TTTTTTCAGTTTTTCTTCTCCTTTCCTT
1 TTCTTTCAGTTCTT-TT-T-CTTTCCTT
2973397 TTCTTTCA-TTCTTTTTCTTT-CTT
1 TTCTTTCAGTTCTTTTTCTTTCCTT
* * * * *
2973420 TCCTCTCATTTCCTTTTCTTTCTTT
1 TTCTTTCAGTTCTTTTTCTTTCCTT
*
2973445 TTATTTC
1 TTCTTTC
2973452 TTTCTTTCTT
Statistics
Matches: 65, Mismatches: 13, Indels: 12
0.72 0.14 0.13
Matches are distributed among these distances:
23 9 0.14
24 15 0.23
25 7 0.11
26 8 0.12
27 10 0.15
28 10 0.15
29 6 0.09
ACGTcount: A:0.04, C:0.27, G:0.02, T:0.67
Consensus pattern (25 bp):
TTCTTTCAGTTCTTTTTCTTTCCTT
Found at i:2973468 original size:14 final size:13
Alignment explanation
Indices: 2973389--2973469 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 13
2973379 TTTTCTTCTC
2973389 CTTTCCTTTTCTTT
1 CTTTCC-TTTCTTT
* *
2973403 CATTCTTTTTCTTT
1 CTTTC-CTTTCTTT
*
2973417 CTTTCCTCTCATTT
1 CTTTCCTTTC-TTT
*
2973431 CCTTTTCTTTCTTT
1 -CTTTCCTTTCTTT
* *
2973445 TTATTTCTTTCTTT
1 CT-TTCCTTTCTTT
2973459 CTTCTCCTTTC
1 CTT-TCCTTTC
2973470 CCTCTCCTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
13 5 0.10
14 39 0.75
15 8 0.15
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTCCTTTCTTT
Found at i:2976243 original size:10 final size:10
Alignment explanation
Indices: 2976226--2976326 Score: 59
Period size: 10 Copynumber: 10.0 Consensus size: 10
2976216 TTCCTTCCCA
2976226 CTTC-TTCTT
1 CTTCTTTCTT
2976235 CTTCTTTCTT
1 CTTCTTTCTT
* *
2976245 TTTTTTTCTT
1 CTTCTTTCTT
* *
2976255 CTCCGTTCCTT
1 CTTC-TTTCTT
2976266 -TTCTTTCCTT
1 CTTCTTT-CTT
2976276 CTT-TTTCTTT
1 CTTCTTTC-TT
*
2976286 CTGTTTTTCTT
1 CT-TCTTTCTT
*
2976297 CTCCTTTCCTT
1 CTTCTTT-CTT
2976308 -TTCTTTCCTT
1 CTTCTTT-CTT
2976318 CTT-TTTCTT
1 CTTCTTTCTT
2976327 TTTTTCCTCT
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
9 10 0.14
10 41 0.57
11 17 0.24
12 4 0.06
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:2976264 original size:44 final size:40
Alignment explanation
Indices: 2976198--2976331 Score: 126
Period size: 42 Copynumber: 3.2 Consensus size: 40
2976188 AAAAATTACC
* *
2976198 CTTTTTCTTTT-TTTTCCCTTCCTTCCCACTTCTTCTTCTTCTTT
1 CTTTTT-TTTTCTTCTCCCTTCCTT--CACTT-TCCTTCTT-TTT
* **
2976242 CTTTTTTTTTCTTCTCCGTTCCTTTTCTTTCCTTCTTTTT
1 CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
* **
2976282 CTTTCTGTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTT
1 CTTT-T-TTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
2976324 CTTTTTTT
1 CTTTTTTT
2976332 CCTCTCTGTT
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
40 10 0.12
41 9 0.11
42 41 0.51
43 4 0.05
44 17 0.21
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (40 bp):
CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
Found at i:2976286 original size:18 final size:18
Alignment explanation
Indices: 2976265--2976334 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 18
2976255 CTCCGTTCCT
2976265 TTTCTTTCCTTCTTTTTC
1 TTTCTTTCCTTCTTTTTC
* *
2976283 TTTCTGTTTTTCTTCTCCTTTCC
1 TTTC---TTTCCTTCT--TTTTC
2976306 TTTTCTTTCCTTCTTTTTC
1 -TTTCTTTCCTTCTTTTTC
*
2976325 TTTTTTTCCT
1 TTTCTTTCCT
2976335 CTCTGTTGAC
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
18 13 0.32
19 4 0.10
21 16 0.39
23 4 0.10
24 4 0.10
ACGTcount: A:0.00, C:0.27, G:0.01, T:0.71
Consensus pattern (18 bp):
TTTCTTTCCTTCTTTTTC
Found at i:2976306 original size:42 final size:40
Alignment explanation
Indices: 2976232--2976331 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 40
2976222 CCCACTTCTT
2976232 CTTCTTCTTTCTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
*
2976273 CTTCTTTTTCTTTCTGTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTT-T-TTTTTCTTCTCCGTTCCTTTTCTTTC
2976315 CTTCTTTTTCTTTTTTT
1 CTTCTTTTTCTTTTTTT
2976332 CCTCTCTGTT
Statistics
Matches: 56, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
40 10 0.18
41 8 0.14
42 38 0.68
ACGTcount: A:0.00, C:0.27, G:0.02, T:0.71
Consensus pattern (40 bp):
CTTCTTTTTCTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
Found at i:2977461 original size:107 final size:106
Alignment explanation
Indices: 2977276--2977495 Score: 291
Period size: 107 Copynumber: 2.1 Consensus size: 106
2977266 AAACCCATAC
* * * * *
2977276 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACCAGCACATTAGG
1 TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
* *
2977341 GCACGTTTTCTCGAATTTT-CAAATGCAAAATATCGCTTTAT
66 GCACGTTTTCTCG-ATTTTCCAAACGCAAAATATCGCCTTAT
* * *
2977382 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCTAACGAAAAATCGAAACCCAGCACGTTA
1 TTTGAAATTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
*
2977446 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
*
2977489 TTAGAAA
1 TTTGAAA
2977496 AATTTTCCTT
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
106 25 0.25
107 74 0.75
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (106 bp):
TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
Found at i:2979139 original size:19 final size:19
Alignment explanation
Indices: 2979115--2979165 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
2979105 TTTCCTCTAT
2979115 TTTGTTTGCTTGTGATTTG
1 TTTGTTTGCTTGTGATTTG
2979134 TTTGTTTGCTTGTGATTTG
1 TTTGTTTGCTTGTGATTTG
2979153 TTTGTTTGCTTGT
1 TTTGTTTGCTTGT
2979166 TGTCTGCGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.04, C:0.06, G:0.25, T:0.65
Consensus pattern (19 bp):
TTTGTTTGCTTGTGATTTG
Found at i:2980148 original size:21 final size:22
Alignment explanation
Indices: 2980119--2980164 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2980109 ATGTATATTG
2980119 ATATATATATATATTA-AAAAT
1 ATATATATATATATTATAAAAT
* * *
2980140 ATATTTATATGTGTTATAAAAT
1 ATATATATATATATTATAAAAT
2980162 ATA
1 ATA
2980165 GCAAATACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (22 bp):
ATATATATATATATTATAAAAT
Found at i:2980279 original size:3 final size:3
Alignment explanation
Indices: 2980271--2980344 Score: 57
Period size: 3 Copynumber: 24.7 Consensus size: 3
2980261 TAAATGAGTA
* * *
2980271 AAT AAT AAT AAT GAT TAT AAT AAT ACAA AACT AAT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
2980316 AAT -AT AAT AAT -AT AAT AAT GAAT AGAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA
2980345 ATATAAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
2 8 0.14
3 40 0.69
4 10 0.17
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2980374 original size:14 final size:15
Alignment explanation
Indices: 2980317--2980374 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 15
2980307 ATATAATATA
* *
2980317 ATATAATAATATAAT
1 ATATAAAAAGATAAT
* *
2980332 A-ATGAATAGATAA-
1 ATATAAAAAGATAAT
*
2980345 ATATAAAAAGAAAAT
1 ATATAAAAAGATAAT
2980360 ATA-AAAAAGATAAT
1 ATATAAAAAGATAAT
2980374 A
1 A
2980375 AGTAGATTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
13 1 0.03
14 28 0.85
15 4 0.12
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (15 bp):
ATATAAAAAGATAAT
Found at i:2981138 original size:7 final size:7
Alignment explanation
Indices: 2981121--2981150 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2981111 AAGAAAAATG
2981121 AAGAGAAA
1 AAGA-AAA
2981129 AAGAAAA
1 AAGAAAA
2981136 AAGAAAA
1 AAGAAAA
2981143 AAGAAAA
1 AAGAAAA
2981150 A
1 A
2981151 TAGATCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 18 0.82
8 4 0.18
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAGAAAA
Found at i:2982539 original size:15 final size:15
Alignment explanation
Indices: 2982519--2982567 Score: 91
Period size: 15 Copynumber: 3.3 Consensus size: 15
2982509 TATGTCTAAG
2982519 TTTTATTGTATTTAT
1 TTTTATTGTATTTAT
2982534 TTTTATTGTATTTAT
1 TTTTATTGTATTTAT
2982549 TTTTATT-TATTTAT
1 TTTTATTGTATTTAT
2982563 TTTTA
1 TTTTA
2982568 AGGTCATATT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 12 0.35
15 22 0.65
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (15 bp):
TTTTATTGTATTTAT
Found at i:2982683 original size:21 final size:21
Alignment explanation
Indices: 2982655--2982702 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
2982645 TTAATTTTAA
*
2982655 AATG-AAAATATTTAAAT-TT
1 AATGTAAAATATATAAATATT
2982674 AACTGTAAAATATATAAATATT
1 AA-TGTAAAATATATAAATATT
2982696 AATGTAA
1 AATGTAA
2982703 TTTTTTAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 17 0.68
22 4 0.16
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (21 bp):
AATGTAAAATATATAAATATT
Found at i:2983870 original size:4 final size:4
Alignment explanation
Indices: 2983861--2983995 Score: 64
Period size: 4 Copynumber: 31.5 Consensus size: 4
2983851 CCACTTCTTC
* * *
2983861 TTCT TTCT TTCTT TTTT TTCT TCTCCGT TCCTT TTCT TTCC TTC- TT-T
1 TTCT TTCT TTC-T TTCT TTCT T-T-C-T TTC-T TTCT TTCT TTCT TTCT
*
2983908 TTCT TTCT TT-T TTCT TCTCCT TTCCTT TTCT TTCC TTC- TT-T TTCT
1 TTCT TTCT TTCT TTCT T-T-CT TT-C-T TTCT TTCT TTCT TTCT TTCT
*
2983953 TTCT TTCCT CTCAT TTCCTT TTCT TTCT TTCT TTCT TCTCT TT
1 TTCT TT-CT TTC-T TT-C-T TTCT TTCT TTCT TTCT T-TCT TT
2983996 TCCCTCTCAT
Statistics
Matches: 105, Mismatches: 10, Indels: 32
0.71 0.07 0.22
Matches are distributed among these distances:
3 11 0.10
4 58 0.55
5 23 0.22
6 11 0.10
7 2 0.02
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:2983903 original size:10 final size:10
Alignment explanation
Indices: 2983888--2983987 Score: 63
Period size: 10 Copynumber: 10.3 Consensus size: 10
2983878 TTCTTCTCCG
2983888 TTCCTTTTCT
1 TTCCTTTTCT
2983898 TTCCTTCTT-T
1 TTCCTT-TTCT
*
2983908 TT-CTTTCTTT
1 TTCCTTT-TCT
* *
2983918 TTTCTTCTCCT
1 TTCCTT-TTCT
2983929 TTCCTTTTCT
1 TTCCTTTTCT
2983939 TTCCTTCTT-T
1 TTCCTT-TTCT
2983949 TT-C-TTTCT
1 TTCCTTTTCT
*
2983957 TTCC-TCTCAT
1 TTCCTTTTC-T
2983967 TTCCTTTTCT
1 TTCCTTTTCT
2983977 TT-C-TTTCT
1 TTCCTTTTCT
2983985 TTC
1 TTC
2983988 TTCTCTTTTC
Statistics
Matches: 73, Mismatches: 6, Indels: 23
0.72 0.06 0.23
Matches are distributed among these distances:
7 2 0.03
8 12 0.16
9 10 0.14
10 32 0.44
11 16 0.22
12 1 0.01
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (10 bp):
TTCCTTTTCT
Found at i:2983905 original size:41 final size:39
Alignment explanation
Indices: 2983827--2983996 Score: 170
Period size: 38 Copynumber: 4.3 Consensus size: 39
2983817 AAATGACCTA
**
2983827 TTTTTCATTTTTTTTC--CTCCTTTCCCACTTC-TT-CTTC
1 TTTTTC-TTTTTTTTCTTCTCCTTT-CCTTTTCTTTCCTTC
*
2983864 TTTCTTTCTTTTTTTTCTTCTCCGTTCCTTTTCTTTCCTTC
1 -TT-TTTCTTTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC
2983905 TTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC
1 TTTTTC-TT-TTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC
* * * *
2983946 TTTTTC-TTTCTTTCCTCTCATTTCCTTTTCTTTCTTTC
1 TTTTTCTTTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC
*
2983984 TTTCTTCTCTTTT
1 TTT-TTCTTTTTT
2983997 CCCTCTCATT
Statistics
Matches: 113, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
38 41 0.36
39 17 0.15
40 15 0.13
41 40 0.35
ACGTcount: A:0.02, C:0.29, G:0.01, T:0.68
Consensus pattern (39 bp):
TTTTTCTTTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTC
Found at i:2983998 original size:28 final size:28
Alignment explanation
Indices: 2983906--2983986 Score: 62
Period size: 27 Copynumber: 2.9 Consensus size: 28
2983896 CTTTCCTTCT
*
2983906 TTTTCTTTCTTT-TTTCTTCTCCTTTCC
1 TTTTCTTTCTTTCTTTCTTCTCTTTTCC
* *
2983933 TTTTCTTTCCTTCTTT-TTCTTTCTTTCC
1 TTTTCTTTCTTTCTTTCTTCTCT-TTTCC
*
2983961 -TCTCATTTCCTTTTCTTTCTT-TCTTT
1 TTTTC-TTT-C-TTTCTTTCTTCTCTTT
2983987 CTTCTCTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
27 18 0.43
28 11 0.26
29 3 0.07
30 8 0.19
31 2 0.05
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTCTTTCTTTCTTTCTTCTCTTTTCC
Found at i:2984008 original size:28 final size:28
Alignment explanation
Indices: 2983949--2984008 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2983939 TTCCTTCTTT
* * *
2983949 TTCTTTCTTTCCTCTCATTTCCTTTTCT
1 TTCTTTCTTTCCTCTCATTTCCCTCTCA
* *
2983977 TTCTTTCTTTCTTCTCTTTTCCCTCTCA
1 TTCTTTCTTTCCTCTCATTTCCCTCTCA
2984005 TTCT
1 TTCT
2984009 CTTCCCCCAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (28 bp):
TTCTTTCTTTCCTCTCATTTCCCTCTCA
Found at i:2986861 original size:147 final size:146
Alignment explanation
Indices: 2986520--2987236 Score: 535
Period size: 153 Copynumber: 4.8 Consensus size: 146
2986510 GCAAGTTCAA
* * * *
2986520 AAAAAAATTAGTAAAAACCCTTATTTCGGCCATTTGTTCGTACTATTTTCCCGAATTATATTACT
1 AAAAAATTTAGTAAAAACCCTTA-TTCTGCCATTTGTTCGTATTATTTTCCCGAATTTTATTACT
* * ** * * *
2986585 TTCAATAAAAATAAATTACTTTCGT-TTTT-TTATTTTACATTATTTTATTATATTATGT-TTGA
65 TTTAATAAAAATATATTA-TTTTTTATTTTATTATTTTACATTATTTTAGTACATTTTGTATT--
* **
2986647 AGTGTATTAATTTAGTGTGTGTTTT
127 A----ATTAATTTACTGAAT-TTTT
** *
2986672 AAATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTAC
1 AAA-AAATTTAGTAAAAACCCTTATT-CTGCCATTTGTTCGTATTATTTTCCCGAATTTTATTAC
* *
2986737 TTTTAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTA
64 TTTTAATAAAAATATATTATTTTT-TATTTTATTATTTTACATTATTTTAGTACATTTTGTATTA
2986802 ATT-ATTT-CTGAATTTTT
128 ATTAATTTACTGAATTTTT
* * * * *
2986819 AAAAAATTTAGTAAAACACTCTTACTTCAGCCATTTGTTCGTATT-TTTTTCAGCATTTTATTAC
1 AAAAAATTTAGTAAAA-ACCCTTA-TTCTGCCATTTGTTCGTATTATTTTCCCGAATTTTATTAC
2986883 --TT--TAAAAATATCA-TATTTTTTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
64 TTTTAATAAAAATAT-ATTATTTTTT-ATTTTATTATTTTACATTATTTTAGTAC---AT-TTTG
* * * *
2986943 AAATTTATTAATTTAGTGAGTTTTTT
123 -TATTAATTAATTTACTGA-ATTTTT
* * *
2986969 AAATAAATTTTA-AAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTA
1 AAA-AAA-TTTAGTAAAAACCCTTATT-CTGCCATTTGTTCGTATTATTTTCCCGAATTTTATTA
* * * *
2987033 CTTTCAATAACAATATATTATTTTATTATTTTATATTATTTCAGTACATT-TTGTTTG-AAATAT
63 CTTTTAATAAAAATATATTATTTT-TTA-TTT-TATTATTT---TACATTATT-TTAGTACAT-T
* *
2987096 TTGTAATAATT-ATTT-CTAAATTTTT
120 TTGTATTAATTAATTTACTGAATTTTT
* ** * *
2987121 AAAAAATGTAGTAAAAAATCTTACTTC-GACC-TTTGTTCGTATTTTTTTCTCCGCATTTTATTA
1 AAAAAATTTAGTAAAAACCCTTA-TTCTG-CCATTTGTTCGTATTATTTTC-CCGAATTTTATTA
* * *
2987184 C--TTAA-AAAAATCATA-T-TTTCTAATTTTATTATTTTCCATTATTTTAGTACATT
63 CTTTTAATAAAAAT-ATATTATTTTTTATTTTATTATTTTACATTATTTTAGTACATT
2987237 ATGTTTGAAA
Statistics
Matches: 458, Mismatches: 66, Indels: 93
0.74 0.11 0.15
Matches are distributed among these distances:
141 10 0.02
142 47 0.10
143 1 0.00
144 10 0.02
145 5 0.01
146 33 0.07
147 38 0.08
148 15 0.03
149 15 0.03
150 52 0.11
151 51 0.11
152 22 0.05
153 72 0.16
154 10 0.02
155 44 0.10
156 13 0.03
157 8 0.02
159 3 0.01
160 9 0.02
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (146 bp):
AAAAAATTTAGTAAAAACCCTTATTCTGCCATTTGTTCGTATTATTTTCCCGAATTTTATTACTT
TTAATAAAAATATATTATTTTTTATTTTATTATTTTACATTATTTTAGTACATTTTGTATTAATT
AATTTACTGAATTTTT
Found at i:2987273 original size:301 final size:297
Alignment explanation
Indices: 2986609--2987274 Score: 968
Period size: 297 Copynumber: 2.2 Consensus size: 297
2986599 ATTACTTTCG
* * * * * *
2986609 TTTTTTTATTTTACATTATTTTATTATATTATGTTTGAAGTGTATTAATTTAGTGTGTGTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
2986674 ATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
66 ATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
* * * *
2986739 TTAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAAT
131 TCAATAAAAATATATTATTTTTGTATTTTATTATTTTACATTATTTCAGTAAATTTTGTAATAAT
* * *
2986804 TATTTCTGAATTTTTAAAAAATTTAGTAAAACACTCTTACTTCAGCCATTTGTTCGTATTTTTTT
196 TATTTCTAAATTTTTAAAAAATGTAGTAAAACAATCTTACTTCAGCCATTTGTTCGTATTTTTTT
* *
2986869 CAGCATTTTATTACTTTAAAAATATCATATTTTTTAA
261 CAGCATTTTATTACTTTAAAAAAATCATATTTTCTAA
*
2986906 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGAGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
* *
2986971 ATAAATTTTAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTT
66 ATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
* **
2987036 TCAATAACAATATATTATTTTAT-TATTTTATATTATTTCAGTACATT-TTGTTTG-AAATATTT
131 TCAATAAAAATATATTATTTT-TGTA-TTT-TATTATTT---TACATTATT-TCAGTAAAT-TTT
2987098 GTAATAATTATTTCTAAATTTTTAAAAAATGTAGTAAAA-AATCTTACTTC-GACC-TTTGTTCG
188 GTAATAATTATTTCTAAATTTTTAAAAAATGTAGTAAAACAATCTTACTTCAG-CCATTTGTTCG
*
2987160 TATTTTTTTCTCCGCATTTTATTAC-TTAAAAAAATCATATTTTCTAA
252 TA-TTTTTT-TCAGCATTTTATTACTTTAAAAAAATCATATTTTCTAA
* *
2987207 TTTTATTATTTTCCATTATTTTAGTACATTATGTTTGAAATTTATTAATTTACTGTGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
2987272 ATA
66 ATA
2987275 TACCATTTTT
Statistics
Matches: 333, Mismatches: 25, Indels: 18
0.89 0.07 0.05
Matches are distributed among these distances:
297 142 0.43
298 4 0.01
299 8 0.02
300 11 0.03
301 108 0.32
302 60 0.18
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (297 bp):
TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
ATAAATTTAAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
TCAATAAAAATATATTATTTTTGTATTTTATTATTTTACATTATTTCAGTAAATTTTGTAATAAT
TATTTCTAAATTTTTAAAAAATGTAGTAAAACAATCTTACTTCAGCCATTTGTTCGTATTTTTTT
CAGCATTTTATTACTTTAAAAAAATCATATTTTCTAA
Found at i:2987607 original size:45 final size:43
Alignment explanation
Indices: 2987558--2987660 Score: 156
Period size: 41 Copynumber: 2.4 Consensus size: 43
2987548 CTTCCCACTT
* *
2987558 CTTCTTCTTCTTTCTTTTTTTTTCCTTCTCCGTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTGTTTTT-CTTCTCC-TTCCTTTTCTTTC
2987603 CTTCTTTTTCTTTC--TGTTTTTCTTCTCCTTCCTTTTCTTTC
1 CTTCTTTTTCTTTCTTTGTTTTTCTTCTCCTTCCTTTTCTTTC
2987644 CTTCTTTTTCTTTCTTT
1 CTTCTTTTTCTTTCTTT
2987661 CCTCTCTGTT
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
41 27 0.50
42 7 0.13
43 7 0.13
45 13 0.24
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (43 bp):
CTTCTTTTTCTTTCTTTGTTTTTCTTCTCCTTCCTTTTCTTTC
Found at i:2987772 original size:24 final size:24
Alignment explanation
Indices: 2987740--2987788 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2987730 AGTGGGAGTC
*
2987740 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTCTATTTAGGT
2987764 GCCACCAATCCTTTCTATTTAGGT
1 GCCACCAATCCTTTCTATTTAGGT
2987788 G
1 G
2987789 TGATCGGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.14, T:0.39
Consensus pattern (24 bp):
GCCACCAATCCTTTCTATTTAGGT
Found at i:2988790 original size:107 final size:106
Alignment explanation
Indices: 2988605--2988824 Score: 284
Period size: 107 Copynumber: 2.1 Consensus size: 106
2988595 AAACCCATAC
* * * * *
2988605 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACCAGCACATTAGG
1 TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
*
2988670 GCACGTTTTCTCGAATTTTC-AAACGCAAAATATCGCTTTAT
66 GCACGTTTTCTCG-ATTTTCTAAACGCAAAATATCGCCTTAT
* *
2988711 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCG-AAACCTAGCACGTT
1 TTTGAAATTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACC-AGCACATT
* *
2988774 AGGGCACGTTTTCTCGATTTTCTAAATGCAAAATATTGCCTTAT
63 AGGGCACGTTTTCTCGATTTTCTAAACGCAAAATATCGCCTTAT
*
2988818 TTAGAAA
1 TTTGAAA
2988825 AATTTTCCTT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
106 31 0.31
107 68 0.69
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (106 bp):
TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCGATTTTCTAAACGCAAAATATCGCCTTAT
Found at i:2991649 original size:3 final size:3
Alignment explanation
Indices: 2991641--2991714 Score: 57
Period size: 3 Copynumber: 24.7 Consensus size: 3
2991631 TAAATGAGTA
* * *
2991641 AAT AAT AAT AAT GAT TAT AAT AAT ACAA AACT AAT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
2991686 AAT -AT AAT AAT -AT AAT AAT GAAT AGAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA
2991715 ATATAAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
2 8 0.14
3 40 0.69
4 10 0.17
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2992536 original size:7 final size:7
Alignment explanation
Indices: 2992517--2992550 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
2992507 AAAGGAAGAA
2992517 AAAAAAG
1 AAAAAAG
2992524 AGAAAAAG
1 A-AAAAAG
2992532 AAAAAAG
1 AAAAAAG
2992539 AAAAAAG
1 AAAAAAG
2992546 AAAAA
1 AAAAA
2992551 TAGATCTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2994877 original size:21 final size:23
Alignment explanation
Indices: 2994851--2994905 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
2994841 TACAATATAG
*
2994851 TATTTAAAAATATAT-ACAT-AA
1 TATTTAAAAATATATAAAATAAA
* *
2994872 TATTTACATATATATAAAATAAA
1 TATTTAAAAATATATAAAATAAA
*
2994895 TATTGAAAAAT
1 TATTTAAAAAT
2994906 GTATGCGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 13 0.50
22 3 0.12
23 10 0.38
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (23 bp):
TATTTAAAAATATATAAAATAAA
Found at i:2994885 original size:36 final size:35
Alignment explanation
Indices: 2994790--2994885 Score: 104
Period size: 36 Copynumber: 2.7 Consensus size: 35
2994780 AAATAAATAA
* *
2994790 ATATACATAATATATACGTAATATAGTACTAAGAAT
1 ATATACATAATATATACAT-ATATAGTACTAAAAAT
* * *
2994826 ATATATATACACATATACA-ATATAGTATTTAAAAAT
1 ATATACATA-ATATATACATATATAGTA-CTAAAAAT
*
2994862 ATATACATAATATTTACATATATA
1 ATATACATAATATATACATATATA
2994886 TAAAATAAAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
35 15 0.31
36 27 0.55
37 7 0.14
ACGTcount: A:0.51, C:0.08, G:0.04, T:0.36
Consensus pattern (35 bp):
ATATACATAATATATACATATATAGTACTAAAAAT
Found at i:2995826 original size:17 final size:18
Alignment explanation
Indices: 2995804--2995841 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
2995794 AAATCAAGAG
*
2995804 AAAAAAAT-TAAAAAAAT
1 AAAAAAATAAAAAAAAAT
2995821 -AAAAAATAAAAAAAAAT
1 AAAAAAATAAAAAAAAAT
2995838 AAAA
1 AAAA
2995842 GACGAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
16 7 0.39
17 8 0.44
18 3 0.17
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (18 bp):
AAAAAAATAAAAAAAAAT
Found at i:2997122 original size:88 final size:88
Alignment explanation
Indices: 2997001--2997211 Score: 259
Period size: 89 Copynumber: 2.4 Consensus size: 88
2996991 CAACGTGTCT
* *
2997001 TGAGGCTCAACTCATTTCTCGCAATATGAGTTGA-TTCTTTCAAAAACATAATAATGAAAA-CAG
1 TGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTCTTTCAAAAA-A-AA-AATCAAAAGC-G
2997064 AAATGGAAAATACCTC-G-GTGTGACC
62 AAATGGAAAATACCTCGGCGTGTGACC
* * * * **
2997089 TGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAAAGAAATCAAAAGGCTTAA
1 TGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTCTTTCAAAAAAAAAATCAAAA-GCGAAA
* *
2997154 TTGAAAATACCTCGGCGTGTGTCC
65 TGGAAAATACCTCGGCGTGTGACC
2997178 TGAGGCTCAACTCACTTCTCGCAATATGAGTTGA
1 TGAGGCTCAACTCACTTCTCGCAATATGAGTTGA
2997212 AATTAAAACA
Statistics
Matches: 107, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
86 7 0.07
87 15 0.14
88 35 0.33
89 50 0.47
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (88 bp):
TGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTCTTTCAAAAAAAAAATCAAAAGCGAAAT
GGAAAATACCTCGGCGTGTGACC
Found at i:2997190 original size:89 final size:88
Alignment explanation
Indices: 2996968--2997211 Score: 262
Period size: 88 Copynumber: 2.8 Consensus size: 88
2996958 TTGAATTTTG
* * *** * *
2996968 AAAAGCAGAAATTGAAAATACTTCAACGTGTCTTGAGGCTCAACTCATTTCTCGCAATATGAGTT
1 AAAA-CAGAAATGGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTT
*
2997033 GATTCTTTCAAAAACATAATAATG
65 GATTCTTTCAAAAACATAATAATC
* *
2997057 AAAACAGAAATGGAAAATACCTCGGTGTGACCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAAACAGAAATGGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTG
* * *
2997122 ATTTTTTTGAAAAA-A-GA-AATC
66 A-TTCTTTCAAAAACATAATAATC
** *
2997143 AAAAGGC-TTAATTGAAAATACCTCGGCGTGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGA
1 AAAA--CAGAAATGGAAAATACCTC-G-GTGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGA
2997207 GTTGA
62 GTTGA
2997212 AATTAAAACA
Statistics
Matches: 132, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
86 7 0.05
87 15 0.11
88 56 0.42
89 54 0.41
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (88 bp):
AAAACAGAAATGGAAAATACCTCGGTGTGTCCTGAGGCTCAACTCACTTCTCGCAATATGAGTTG
ATTCTTTCAAAAACATAATAATC
Found at i:2997439 original size:72 final size:71
Alignment explanation
Indices: 2997320--2997575 Score: 377
Period size: 72 Copynumber: 3.5 Consensus size: 71
2997310 TCAACCCACC
*
2997320 TCTCGCAATATGAGTTGATTCTTGACAAACAGAAATTGAAATTACCTCATCGTGTCCTGAGGCTC
1 TCTCGCAATATGAGTTGATT-TTGA-AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTC
2997385 AACTCATT
64 AACTCATT
*
2997393 TCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
1 TCTCGCAATATGAGTTG-ATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
2997458 ACTCATT
65 ACTCATT
*
2997465 TCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
1 TCTCGCAATATGAGTTGA---TTTTGAA-AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGC
**
2997530 TCAACTCACC
62 TCAACTCATT
* *
2997540 TCTAGCAATATGAGTTGATTTTGAAAAACAAAAATT
1 TCTCGCAATATGAGTTGATTTTG-AAAACAGAAATT
2997576 AAAAGGCTTA
Statistics
Matches: 168, Mismatches: 9, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
71 1 0.01
72 75 0.45
73 22 0.13
74 9 0.05
75 61 0.36
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (71 bp):
TCTCGCAATATGAGTTGATTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAA
CTCATT
Found at i:2997667 original size:197 final size:193
Alignment explanation
Indices: 2997379--2997751 Score: 491
Period size: 197 Copynumber: 1.9 Consensus size: 193
2997369 TCGTGTCCTG
** * * * *
2997379 AGGCTCAACTCATTTCTCGCAATATAAGTTGAATTTTGAAAACAGAAATTGAAATTACCTCAGCG
1 AGGCTCAACTCACCTCTCGCAATATAAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAGCG
* * * * *
2997444 TGTCCTGAGGCTCAACTCATTTCTCGCAATATGAGTTGATTTTTTTTAACAACAGAAATTGAAAT
66 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGA---TTTTT-A-AA-A-AAATTAAAAA
*
2997509 TACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAA
124 TACCTCAACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAA
2997574 TTAAA
189 TTAAA
* * * *
2997579 AGGCTTAACTCACCTCTCGCAATATGAG-TCAA-TTT-AAAACATAAACTAAAAATACCTCGGCG
1 AGGCTCAACTCACCTCTCGCAATATAAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAGCG
2997641 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAAAATTAAAAATACCTCA
66 TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAAAATTAAAAATACCTCA
* * *
2997706 ACGTGTCTTGAGGCTCAACTCATCTCTCGCAATATGAGTTGATTTT
131 ACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTT
2997752 CCTTGGAAAG
Statistics
Matches: 154, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
190 57 0.37
191 1 0.01
192 2 0.01
193 1 0.01
194 5 0.03
197 58 0.38
198 3 0.02
199 3 0.02
200 24 0.16
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (193 bp):
AGGCTCAACTCACCTCTCGCAATATAAGTTCAATTTTGAAAACAGAAACTAAAAATACCTCAGCG
TGCCCCGAGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAAAAAATTAAAAATACCTCA
ACGTGTCCTGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTGAAAAACAAAAATTAAA
Found at i:2997724 original size:68 final size:70
Alignment explanation
Indices: 2997579--2997751 Score: 210
Period size: 68 Copynumber: 2.5 Consensus size: 70
2997569 AAAAATTAAA
* * * * **
2997579 AGGCTTAACTCACCTCTCGCAATATGAG-TCAATTTAAAACATAAACTAAAAATACCTCGGCGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
2997643 CCCCG
66 CCCCG
* *
2997648 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTTAAA-A-AAATTAAAAATACCTCAACGTG
1 AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
* **
2997711 TCTTG
66 CCCCG
2997716 AGGCTCAACTCA-TCTCTCGCAATATGAGTTGATTTT
1 AGGCTCAACTCACT-TCTCGCAATATGAGTTGATTTT
2997752 CCTTGGAAAG
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
67 1 0.01
68 55 0.60
69 27 0.30
70 8 0.09
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.29
Consensus pattern (70 bp):
AGGCTCAACTCACTTCTCGCAATATGAGTTGATTTTAAAACATAAACTAAAAATACCTCAACGTG
CCCCG
Found at i:2998587 original size:45 final size:42
Alignment explanation
Indices: 2998526--2998635 Score: 107
Period size: 43 Copynumber: 2.5 Consensus size: 42
2998516 GTTTCATTAG
*
2998526 GACGCCC-TCTCGGGTTTTCATCCTAAT-CTTTTTGTACTAATCAA
1 GACGCCCTTTTCGGGTTTTCATCCTAATCCTTTTT-T--T-ATCAA
* * * *
2998570 GACGCCCTTTTCGGGTTTTCGTCCTGATCCCTTTTTTTTTTAA
1 GACGCCCTTTTCGGGTTTTCATCCTAAT-CCTTTTTTTATCAA
*
2998613 GATGCCCTTTTCGGGTTTTCATC
1 GACGCCCTTTTCGGGTTTTCATC
2998636 TTAAGCATAA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
43 24 0.43
44 8 0.14
45 17 0.30
46 1 0.02
47 6 0.11
ACGTcount: A:0.14, C:0.26, G:0.16, T:0.44
Consensus pattern (42 bp):
GACGCCCTTTTCGGGTTTTCATCCTAATCCTTTTTTTATCAA
Found at i:3005950 original size:12 final size:12
Alignment explanation
Indices: 3005933--3005963 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3005923 TATGCAATGA
*
3005933 ATGAATTGATGC
1 ATGAATGGATGC
3005945 ATGAATGGATGC
1 ATGAATGGATGC
3005957 ATGAATG
1 ATGAATG
3005964 TCAAATGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (12 bp):
ATGAATGGATGC
Found at i:3009872 original size:38 final size:36
Alignment explanation
Indices: 3009829--3009932 Score: 113
Period size: 38 Copynumber: 2.8 Consensus size: 36
3009819 GGGTAAAAAT
3009829 AAATATATATACATAATATATACGTAATATAGTA-CTA
1 AAATATATATACATAATATATAC--AATATAGTATCTA
* * *
3009866 AGAATATATATATATACACATATACAATATAGTATTTA
1 A-AATATATATACATA-ATATATACAATATAGTATCTA
*
3009904 AAA-ATATATACATAATATTTACATATATA
1 AAATATATATACATAATATATACA-ATATA
3009933 TAAAATAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
35 7 0.12
36 15 0.26
37 12 0.21
38 16 0.28
39 7 0.12
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (36 bp):
AAATATATATACATAATATATACAATATAGTATCTA
Found at i:3009924 original size:21 final size:23
Alignment explanation
Indices: 3009898--3009952 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 23
3009888 TACAATATAG
*
3009898 TATTTAAAAATATAT-ACAT-AA
1 TATTTAAAAATATATAAAATAAA
* *
3009919 TATTTACATATATATAAAATAAA
1 TATTTAAAAATATATAAAATAAA
*
3009942 TATTGAAAAAT
1 TATTTAAAAAT
3009953 GTATGCGTTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 13 0.50
22 3 0.12
23 10 0.38
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (23 bp):
TATTTAAAAATATATAAAATAAA
Found at i:3010879 original size:12 final size:12
Alignment explanation
Indices: 3010856--3010887 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3010846 AAATCAAGAG
3010856 AAAAAAAT--TA
1 AAAAAAATAATA
3010866 AAAAAAATAATA
1 AAAAAAATAATA
3010878 AAAAAAATAA
1 AAAAAAATAA
3010888 AAGACGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 8 0.40
12 12 0.60
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAATAATA
Found at i:3011543 original size:21 final size:21
Alignment explanation
Indices: 3011519--3011562 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
3011509 TTTTAAAATG
*
3011519 AAAATATTTAAAT-TTAACTAT
1 AAAATATATAAATATTAA-TAT
3011540 AAAATATATAAATATTAATAT
1 AAAATATATAAATATTAATAT
3011561 AA
1 AA
3011563 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATATATAAATATTAATAT
Found at i:3012495 original size:10 final size:10
Alignment explanation
Indices: 3012480--3012589 Score: 74
Period size: 10 Copynumber: 11.3 Consensus size: 10
3012470 ACAATCTCCG
3012480 TTCCTTTTCT
1 TTCCTTTTCT
3012490 TTCCTTCTT-T
1 TTCCTT-TTCT
*
3012500 TT-CTTTCTTT
1 TTCCTTT-TCT
* *
3012510 TTTCTTCTCCT
1 TTCCTT-TTCT
3012521 TTCCTTTTCT
1 TTCCTTTTCT
3012531 TTCCTTCTT-T
1 TTCCTT-TTCT
3012541 TT-C-TTTCT
1 TTCCTTTTCT
*
3012549 TTCC-TCTCAT
1 TTCCTTTTC-T
3012559 TTCCTTTTCT
1 TTCCTTTTCT
*
3012569 TTCTTTTTCT
1 TTCCTTTTCT
3012579 TT-C-TTTCT
1 TTCCTTTTCT
3012587 TTC
1 TTC
3012590 TTCTCTTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
7 2 0.02
8 12 0.15
9 9 0.11
10 41 0.51
11 16 0.20
12 1 0.01
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (10 bp):
TTCCTTTTCT
Found at i:3012506 original size:4 final size:4
Alignment explanation
Indices: 3012485--3012597 Score: 69
Period size: 4 Copynumber: 27.8 Consensus size: 4
3012475 CTCCGTTCCT
*
3012485 TTTC TTTC CTTC -TT- TTTC TTTC TTT- TTTC TTCTCC TTTCC TTTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C -TTTC
* *
3012530 TTTC CTTC -TT- TTTC TTTC TTTCC TCTC ATTTCC TTTTC TTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC TTT-C TTTC -TTT-C -TTTC TTTC TTTC
3012574 TTTC TTTC TTTC TTTC TTCTC TTT
1 TTTC TTTC TTTC TTTC TT-TC TTT
3012598 TCCCTCTCAT
Statistics
Matches: 90, Mismatches: 5, Indels: 28
0.73 0.04 0.23
Matches are distributed among these distances:
3 15 0.17
4 50 0.56
5 15 0.17
6 10 0.11
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:3012519 original size:41 final size:41
Alignment explanation
Indices: 3012474--3012600 Score: 160
Period size: 41 Copynumber: 3.2 Consensus size: 41
3012464 GAATATACAA
*
3012474 TCTCCGTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCT
1 TCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCT
*
3012515 TCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC---TTTCC
1 TCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCT
*
3012553 TCTCATTTCCTTTTC--T--TTCTTTTTCTTTCTTTCTTTCT
1 TCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTT-TTTCT
*
3012591 TCTCTTTTCC
1 TCTCCTTTCC
3012601 CTCTCATTCT
Statistics
Matches: 77, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
34 13 0.17
36 1 0.01
38 31 0.40
41 32 0.42
ACGTcount: A:0.01, C:0.31, G:0.01, T:0.68
Consensus pattern (41 bp):
TCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCT
Found at i:3012523 original size:31 final size:28
Alignment explanation
Indices: 3012485--3012599 Score: 89
Period size: 28 Copynumber: 4.0 Consensus size: 28
3012475 CTCCGTTCCT
*
3012485 TTTCTTTCCTTCTT-TTTCTTTCTTTTTTC
1 TTTCTTTCCTT-TTCTTTCCTTC-TTTTTC
3012514 TTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TT-T-CTTTCCTTTTCTTTCCTTCTTTTTC
*
3012544 TTTCTTTCC-TCTCATTTCCTT-TTCTTTC
1 TTTCTTTCCTTTTC-TTTCCTTCTT-TTTC
3012572 TTTTTCTTT-C-TTTCTTT-CTTCTCTTTTC
1 --TTTCTTTCCTTTTCTTTCCTTCT-TTTTC
3012600 CCTCTCATTC
Statistics
Matches: 74, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
27 8 0.11
28 25 0.34
29 8 0.11
30 18 0.24
31 15 0.20
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTCTTTCCTTTTCTTTCCTTCTTTTTC
Found at i:3012571 original size:38 final size:38
Alignment explanation
Indices: 3012480--3012600 Score: 163
Period size: 38 Copynumber: 3.1 Consensus size: 38
3012470 ACAATCTCCG
*
3012480 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTCTCCT
1 TTCCTTTTCTTTCCTTCTTTTTCTTTC---TTTCTTCTCAT
*
3012521 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCAT
1 TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCTCAT
* *
3012559 TTCCTTTTCTTT-CTTTTTCTTTCTTTCTTTCTTCTCTT
1 TTCCTTTTCTTTCCTTCTT-TTTCTTTCTTTCTTCTCAT
3012597 TTCC
1 TTCC
3012601 CTCTCATTCT
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
37 5 0.07
38 42 0.57
41 27 0.36
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (38 bp):
TTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCTTCTCAT
Found at i:3012599 original size:14 final size:15
Alignment explanation
Indices: 3012483--3012599 Score: 71
Period size: 14 Copynumber: 8.4 Consensus size: 15
3012473 ATCTCCGTTC
3012483 CTTTTCTTTCCTTCT
1 CTTTTCTTTCCTTCT
3012498 -TTTTCTTT-C-T-T
1 CTTTTCTTTCCTTCT
3012509 -TTTTCTTCTCCTT-T
1 CTTTTCTT-TCCTTCT
3012523 CCTTTTCTTTCCTTCT
1 -CTTTTCTTTCCTTCT
3012539 -TTTTCTTT-CTT-T
1 CTTTTCTTTCCTTCT
* * *
3012551 CCTCTCATTTCCTTTT
1 CTTTTC-TTTCCTTCT
3012567 C-TTTCTTT--TTCT
1 CTTTTCTTTCCTTCT
*
3012579 TTCTTTCTTT-CTTCT
1 CT-TTTCTTTCCTTCT
3012594 CTTTTC
1 CTTTTC
3012600 CCTCTCATTC
Statistics
Matches: 83, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
11 8 0.10
12 6 0.07
13 8 0.10
14 35 0.42
15 16 0.19
16 10 0.12
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (15 bp):
CTTTTCTTTCCTTCT
Found at i:3015676 original size:8 final size:8
Alignment explanation
Indices: 3015663--3015696 Score: 50
Period size: 8 Copynumber: 4.0 Consensus size: 8
3015653 AATAACAATA
3015663 TATTATTT
1 TATTATTT
3015671 TATTATTT
1 TATTATTT
3015679 TATTATGTT
1 TATTAT-TT
3015688 ATATTATTT
1 -TATTATTT
3015697 CAGTACATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 14 0.58
9 4 0.17
10 6 0.25
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (8 bp):
TATTATTT
Found at i:3015680 original size:298 final size:299
Alignment explanation
Indices: 3015228--3015898 Score: 949
Period size: 311 Copynumber: 2.2 Consensus size: 299
3015218 TTTCATTTTT
* * * * * *
3015228 TTATTTTATATTATTTTATTATATTATGTTTGAAGTGTATTAATTTAGTGTGTGTTTTAAATAAA
1 TTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAA
*
3015293 TTTAAAAAAAAACCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTTAAT
66 TTTAAAAAAAAACCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
*
3015358 AAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTAC-AT-TTTGTATTAATTAT
131 AAAAATATATTATTTTTGTATTTTATTATGTTATATTATTTCAGTACTATATTTGTATTAATTAT
* * * *
3015421 TTCTGAATTTTTAAAATATTTAGTAAAACACTCTTACTTC-AGCCATTTGTTCGTA-TTTTTT-T
196 TTCTAAATTTTTAAAAAATGTAGTAAAA-AATCTTACTTCGA-CC-TTTGTTCGTATTTTTTTCT
* *
3015483 CAGCATTTTATTACTTTAAAAATATCATATTTTCTAACTTTA
258 CAGCATTTTATTACTTAAAAAAAATCATATTTTCTAACTTTA
* *
3015525 TTATTTTACATTATTTTAGTGCATTATGTTTGAAATTTATTAATTTAGTGAGTTTTTTAAATAAA
1 TTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAA
* *
3015590 TTTTTAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAA
66 -TTTAAAAAAAAACCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAA
*
3015655 TAACAATATATTATTTTAT-TATTTTATTATGTTATATTATTTCAGTACATTTTGTTTGAAATAT
130 TAAAAATATATTATTTT-TGTATTTTATTATGTTATATTATTTCAGTAC--------T---ATAT
3015719 TTGTATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGT
183 TTGTATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGT
* *
3015784 ATTTTTTTCTCTGCATTTTATTACTTAAAAAAAATCATATTTTCTAATTTTA
248 ATTTTTTTCTCAGCATTTTATTACTTAAAAAAAATCATATTTTCTAACTTTA
* *
3015836 TTATTTTACATTATTTTAGTACATTATGTTTGAAATTTTTTAATTTACTGTGTTTTTTAAATA
1 TTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATA
3015899 TACAATTTTT
Statistics
Matches: 331, Mismatches: 25, Indels: 22
0.88 0.07 0.06
Matches are distributed among these distances:
297 57 0.17
298 105 0.32
299 1 0.00
309 10 0.03
310 20 0.06
311 138 0.42
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (299 bp):
TTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAA
TTTAAAAAAAAACCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAAT
AAAAATATATTATTTTTGTATTTTATTATGTTATATTATTTCAGTACTATATTTGTATTAATTAT
TTCTAAATTTTTAAAAAATGTAGTAAAAAATCTTACTTCGACCTTTGTTCGTATTTTTTTCTCAG
CATTTTATTACTTAAAAAAAATCATATTTTCTAACTTTA
Found at i:3016202 original size:10 final size:10
Alignment explanation
Indices: 3016184--3016296 Score: 66
Period size: 10 Copynumber: 11.9 Consensus size: 10
3016174 CTTGCTTCCC
3016184 TCTTC-TTCT
1 TCTTCTTTCT
3016193 TCTTCTTTCT
1 TCTTCTTTCT
*
3016203 T-TTTTTTCT
1 TCTTCTTTCT
*
3016212 TCTCCTTTCCT
1 TCTTCTTT-CT
3016223 T-TTCTTTCAT
1 TCTTCTTTC-T
3016233 TCTT-TTTC-
1 TCTTCTTTCT
*
3016241 T-TTCTTTCC
1 TCTTCTTTCT
3016250 TC-TCATTTCCT
1 TCTTC-TTT-CT
3016261 T-TTCTTTCT
1 TCTTCTTTCT
* *
3016270 TTTTATTTC-
1 TCTTCTTTCT
3016279 T-TTCTTTCT
1 TCTTCTTTCT
*
3016288 TCTCCTTTC
1 TCTTCTTTC
3016297 CCTCTCCTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 27
0.70 0.07 0.23
Matches are distributed among these distances:
7 2 0.02
8 11 0.13
9 22 0.27
10 38 0.46
11 9 0.11
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (10 bp):
TCTTCTTTCT
Found at i:3016228 original size:38 final size:37
Alignment explanation
Indices: 3016189--3016297 Score: 146
Period size: 38 Copynumber: 2.8 Consensus size: 37
3016179 TTCCCTCTTC
*
3016189 TTCTTCTTCTTTCTTTTTTTTCTTCTCCTTTCCTTTTCT
1 TTCTTCTT-TTTC-TTTCTTTCTTCTCCTTTCCTTTTCT
* *
3016228 TTCATTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCT
1 TTC-TTCTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCT
*
3016266 TTCTTTTTATTTCTTTCTTTCTTCTCCTTTCC
1 TTCTTCTT-TTTCTTTCTTTCTTCTCCTTTCC
3016298 CTCTCCTTCT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
37 4 0.06
38 46 0.74
39 7 0.11
40 5 0.08
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (37 bp):
TTCTTCTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCT
Found at i:3016295 original size:14 final size:13
Alignment explanation
Indices: 3016195--3016296 Score: 60
Period size: 14 Copynumber: 7.2 Consensus size: 13
3016185 CTTCTTCTTC
**
3016195 TTCTTTCTTTTTT
1 TTCTTTCTTTCCT
3016208 TTCTTCTCCTTTCCTT
1 TTCTT-T-CTTTCC-T
* *
3016224 TTCTTTCATTCTTT
1 TTCTTTCTTTC-CT
3016238 TTCTTTCTTTCCT
1 TTCTTTCTTTCCT
* *
3016251 CTCATTTCCTTTTCT
1 TTC-TTT-CTTTCCT
* *
3016266 TTCTTTTTATTTCT
1 TTCTTTCT-TTCCT
3016280 TTCTTTCTTCTCCT
1 TTCTTTCTT-TCCT
3016294 TTC
1 TTC
3016297 CCTCTCCTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
13 10 0.14
14 40 0.58
15 13 0.19
16 6 0.09
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (13 bp):
TTCTTTCTTTCCT
Found at i:3016310 original size:38 final size:37
Alignment explanation
Indices: 3016179--3016308 Score: 125
Period size: 38 Copynumber: 3.4 Consensus size: 37
3016169 TTTTCCTTGC
* *
3016179 TTCCCTCTTCTTCTTCTTCTTTCTTTTTTTTCTTCTCCT
1 TTCCCTCTCCTTCTTCTT-TTTC-TTTCTTTCTTCTCCT
* * * * *
3016218 TTCCTTTTCTTTCATTCTTTTTCTTTCTTTCCTCTCAT
1 TTCCCTCTCCTTC-TTCTTTTTCTTTCTTTCTTCTCCT
* * * *
3016256 TTCCTTTTCTTTCTTTTTATTTCTTTCTTTCTTCTCCT
1 TTCCCTCTCCTTCTTCTT-TTTCTTTCTTTCTTCTCCT
3016294 TTCCCTCTCCTTCTT
1 TTCCCTCTCCTTCTT
3016309 TTCTCGCCAC
Statistics
Matches: 76, Mismatches: 13, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
37 4 0.05
38 54 0.71
39 13 0.17
40 5 0.07
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (37 bp):
TTCCCTCTCCTTCTTCTTTTTCTTTCTTTCTTCTCCT
Found at i:3018229 original size:156 final size:155
Alignment explanation
Indices: 3018063--3018794 Score: 716
Period size: 156 Copynumber: 4.8 Consensus size: 155
3018053 GGCCATTTAT
* * * * *
3018063 TCGTACTATTTTCTCGAATTTTATTACTTTCAATAAAAATAAATTACTTTCGTTTTTTATTATTT
1 TCGTATTATTTTCCCGAATTTTATTACTTT-AATAAAAATATATTATTTTCGTATTTTATTATTT
* *
3018128 TACATTATTTTATTACATTATGTTTGAAGTGTATTAATTTATGTGTTTTTTAAATAAATTTTTAA
65 TACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTTT-A
3018193 AAAAAACCCTTA-TTCCT-ACCCTTTGC
129 AAAAAACCCTTACTT-CTGACCCTTTGC
*
3018219 TCGTATTATTTTCCCGAATTTTATTACTTTTAATAAAAATATATTATTTTTGTATTTTATTATTT
1 TCGTATTATTTTCCCGAATTTTATTAC-TTTAATAAAAATATATTATTTTCGTATTTTATTATTT
* * * * **
3018284 TATATTATTTCAGTAC---AT-TTTG-TAT-TAATT-ATTTCTG-AATTTTTAAA-AAATTTTGT
65 TACATTATTTTAGTACATTATGTTTGAAATGT-ATTAATTTATGTGTTTTTTAAATAAATTTT-T
* * * *
3018340 -AAAACACTCTTACTT-TGGCCCTTTGT
128 AAAAAAACCCTTACTTCTGACCCTTTGC
* * *
3018366 TCGTATT-TTTTTCCGCATTTTATTA-TTT--TAAAAATATCA-TATTTT-ATAATTTTATTATT
1 TCGTATTATTTTCCCGAATTTTATTACTTTAATAAAAATAT-ATTATTTTCGT-ATTTTATTATT
*
3018425 TTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTTT
64 TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTTT
3018490 AAAAAAACCCTTA-TTCTTGA-CCTTTGC
128 AAAAAAACCCTTACTTC-TGACCCTTTGC
* *
3018517 TCGTATTATTTTCCCGAATTTTTTTACTTTCAATAACAATATATTATTTTCGTATTTTATTATTT
1 TCGTATTATTTTCCCGAATTTTATTACTTT-AATAAAAATATATTATTTTCGTATTTTATTATTT
* * * * *
3018582 TATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAA-TTATTTCTAAATTTTTAAA-AAA
65 TACATTATTTTAGTACATTATGTTTG-AA-A--TGTATTAATTTATGTGT---TTTTTAAATAAA
* * * *
3018645 TTTAGT-AAAAAA-TCTTACTTC-G-GCCTTTGT
123 TTT-TTAAAAAAACCCTTACTTCTGACCCTTTGC
* *
3018675 TCGTATT-TATTTCTCCGCATTTTATTACTTTAAAAAAAAT-TA-TATTTTC-TAATTTTATTAT
1 TCGTATTAT-TTTC-CCGAATTTTATTACTTTAATAAAAATATATTATTTTCGT-ATTTTATTAT
*
3018736 TTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTACTGTGTTTTTTAAATA
63 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATA
3018795 TACCATTTTT
Statistics
Matches: 478, Mismatches: 55, Indels: 90
0.77 0.09 0.14
Matches are distributed among these distances:
141 1 0.00
142 41 0.09
143 1 0.00
144 3 0.01
145 2 0.00
146 21 0.04
147 29 0.06
148 14 0.03
149 11 0.02
150 18 0.04
151 42 0.09
152 29 0.06
153 8 0.02
154 4 0.01
155 4 0.01
156 159 0.33
157 9 0.02
158 29 0.06
159 22 0.05
160 22 0.05
161 9 0.02
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (155 bp):
TCGTATTATTTTCCCGAATTTTATTACTTTAATAAAAATATATTATTTTCGTATTTTATTATTTT
ACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTTTAAA
AAAACCCTTACTTCTGACCCTTTGC
Found at i:3018694 original size:311 final size:299
Alignment explanation
Indices: 3018117--3018794 Score: 1015
Period size: 298 Copynumber: 2.2 Consensus size: 299
3018107 TACTTTCGTT
* * *
3018117 TTTTATTATTTTACATTATTTTATTACATTATGTTTGAAGTGTATTAATTTATGTGTTTTTTAAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTATGTGTTTTTTAAA
3018182 TAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGTATTATTTTCCCGAATTTTATTACT
66 TAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGTATTATTTTCCCGAATTTTATTACT
* *
3018247 TTTAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAA
131 TTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAA
* * * *
3018312 TTATTTCTGAATTTTTAAAAAATTTTGTAAAACACTCTTACTTTGGCCCTTTGTTCGTATTTTTT
196 TTATTTCTAAATTTTTAAAAAATTTAGTAAAACAATCTTACTTCGGCCCTTTGTTCGTATTTTTT
* *
3018377 TCCGCATTTTATTA-TTTTAAAAATATCATATTTTATAA
261 TCCGCATTTTATTACTTTAAAAAAAATCATATTTTATAA
3018415 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTA-TGTGTTTTTTAA
* *
3018480 ATAAATTTTT-AAAAAAACCCTTATTCTTGA-CCTTTGCTCGTATTATTTTCCCGAATTTTTTTA
65 ATAAATTTTTAAAAAAAACCCTTATTCCT-ACCCTTTGCTCGTATTATTTTCCCGAATTTTATTA
*
3018543 CTTTCAATAACAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTG
129 CTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTAC----------
3018608 AAATATTTGTATTAATTATTTCTAAATTTTTAAAAAATTTAGTAAAA-AATCTTACTTCGG-CCT
184 --AT-TTTGTATTAATTATTTCTAAATTTTTAAAAAATTTAGTAAAACAATCTTACTTCGGCCCT
* *
3018671 TTGTTCGTATTTATTTCTCCGCATTTTATTACTTTAAAAAAAATTATATTTTCTAA
246 TTGTTCGTATTT-TTT-TCCGCATTTTATTACTTTAAAAAAAATCATATTTTATAA
3018727 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTACTGTGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTA-TGTGTTTTTTAA
3018792 ATA
65 ATA
3018795 TACCATTTTT
Statistics
Matches: 345, Mismatches: 17, Indels: 22
0.90 0.04 0.06
Matches are distributed among these distances:
298 150 0.43
299 23 0.07
309 15 0.04
310 16 0.05
311 54 0.16
312 87 0.25
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (299 bp):
TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTATGTGTTTTTTAAA
TAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGTATTATTTTCCCGAATTTTATTACT
TTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAA
TTATTTCTAAATTTTTAAAAAATTTAGTAAAACAATCTTACTTCGGCCCTTTGTTCGTATTTTTT
TCCGCATTTTATTACTTTAAAAAAAATCATATTTTATAA
Found at i:3019108 original size:21 final size:21
Alignment explanation
Indices: 3019084--3019140 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
3019074 TTCCCACTTC
*
3019084 TTCTTCTTCTTTCTTTTTTTT
1 TTCTTCTTCTTTCTTTTTCTT
* *
3019105 TTCTTCTCCTTTCCTTTTCTT
1 TTCTTCTTCTTTCTTTTTCTT
*
3019126 TCCTTCTT-TTTCTTT
1 TTCTTCTTCTTTCTTT
3019141 CTTTCCTCTC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 6 0.20
21 24 0.80
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (21 bp):
TTCTTCTTCTTTCTTTTTCTT
Found at i:3019125 original size:40 final size:41
Alignment explanation
Indices: 3019050--3019140 Score: 107
Period size: 40 Copynumber: 2.2 Consensus size: 41
3019040 AAAAATTACC
3019050 CTTTTTCTTTTTTTTTTCCCTTCCTTCCCACTTC-TT-CTT
1 CTTTTTCTTTTTTTTTTCCCTTCCTTCCCACTTCTTTCCTT
* * **
3019089 CTTCTTTCTTTTTTTTTT-CTTCTCCTTTCCTTTTCTTTCCTT
1 CTT-TTTCTTTTTTTTTTCCCT-TCCTTCCCACTTCTTTCCTT
3019131 CTTTTTCTTT
1 CTTTTTCTTT
3019141 CTTTCCTCTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
39 5 0.11
40 24 0.55
41 9 0.20
42 6 0.14
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.69
Consensus pattern (41 bp):
CTTTTTCTTTTTTTTTTCCCTTCCTTCCCACTTCTTTCCTT
Found at i:3019256 original size:24 final size:24
Alignment explanation
Indices: 3019224--3019272 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3019214 AGTGGGAGTC
3019224 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
3019248 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
3019272 G
1 G
3019273 TGATCGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (24 bp):
GCCACCAATCCTTTTTATTTAGGT
Found at i:3020274 original size:107 final size:106
Alignment explanation
Indices: 3020089--3020308 Score: 291
Period size: 107 Copynumber: 2.1 Consensus size: 106
3020079 AAACCCATAC
* * * * *
3020089 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACCAGCACATTAGG
1 TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
*
3020154 GCACGTTTACTCGAATTTT-CAAACGCAAAATATCGCTTTAT
66 GCACGTTTACTCG-ATTTTCCAAACGCAAAATATCGCCTTAT
* * *
3020195 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACTTTA
1 TTTGAAATTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
* *
3020259 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTACTCGATTTTCCAAACGCAAAATATCGCCTTAT
*
3020302 TTAGAAA
1 TTTGAAA
3020309 AATTTTCCTT
Statistics
Matches: 99, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
106 25 0.25
107 74 0.75
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Consensus pattern (106 bp):
TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTACTCGATTTTCCAAACGCAAAATATCGCCTTAT
Found at i:3023130 original size:3 final size:3
Alignment explanation
Indices: 3023122--3023195 Score: 57
Period size: 3 Copynumber: 24.7 Consensus size: 3
3023112 TAAATGAGTA
* * *
3023122 AAT AAT AAT AAT GAT TAT AAT AAT ACAA AACT AAT AAT -AT AAT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
3023167 AAT -AT AAT AAT -AT AAT AAT GAAT AGAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT A-AT AA
3023196 ATATAAAAAG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
2 8 0.14
3 40 0.69
4 10 0.17
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3024540 original size:14 final size:15
Alignment explanation
Indices: 3024521--3024551 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3024511 CTACACTCTC
3024521 CTTTCTTTCTTT-TT
1 CTTTCTTTCTTTCTT
3024535 CTTTCTTTCTTTCTT
1 CTTTCTTTCTTTCTT
3024550 CT
1 CT
3024552 CCTTTCCCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (15 bp):
CTTTCTTTCTTTCTT
Found at i:3024556 original size:18 final size:18
Alignment explanation
Indices: 3024521--3024557 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3024511 CTACACTCTC
* *
3024521 CTTTCTTTCTTTTTCTTT
1 CTTTCTTTCTTCTCCTTT
3024539 CTTTCTTTCTTCTCCTTT
1 CTTTCTTTCTTCTCCTTT
3024557 C
1 C
3024558 CCTCTCCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
CTTTCTTTCTTCTCCTTT
Found at i:3025410 original size:14 final size:14
Alignment explanation
Indices: 3025393--3025426 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
3025383 TATGTCTAAG
3025393 TTTTATTGTATTTAT
1 TTTTATT-TATTTAT
3025408 TTTTATTTATTTAT
1 TTTTATTTATTTAT
3025422 TTTTA
1 TTTTA
3025427 AGGTCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTTATTTATTTAT
Found at i:3025528 original size:21 final size:22
Alignment explanation
Indices: 3025504--3025556 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3025494 AAACTTTAAC
3025504 TTAATTTTAAAATG-AAAATAT
1 TTAATTTTAAAATGTAAAATAT
* *
3025525 TTAAATTT-AACTGTAAAATAT
1 TTAATTTTAAAATGTAAAATAT
*
3025546 ATAATTATTAA
1 TTAATT-TTAA
3025557 TATAATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 4 0.16
21 18 0.72
22 2 0.08
23 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (22 bp):
TTAATTTTAAAATGTAAAATAT
Found at i:3026210 original size:156 final size:149
Alignment explanation
Indices: 3026016--3026428 Score: 417
Period size: 154 Copynumber: 2.7 Consensus size: 149
3026006 TACGTTTTCT
3026016 AATTTTATTACTTTAAAACATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATT
1 AATTTTATTACTTTAAAA-ATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATT
3026081 ATGTTTGAAATTTATTAATTTAGCGTGTTTTTTAAATAAATTTAAAAAAAAACCCTTA-TTCCTG
65 ATGTTTGAAATTTATTAATTTA-CGTGTTTTTTAAATAAATTT--AAAAAAACCCTTACTT-C-G
*
3026145 -CCCTTTACTCATTTTGTTTTCT-CG
125 ACCCTTTACTCATATT-TTTTCTCCG
* * *
3026169 AATTTTATTATTTTCAATAAAAATAT-ATTATTTTCGT-ATTTTATTATTTTATATTATTTCAGT
1 AATTTTATTA-CTT---TAAAAATATCA-TATTTTC-TAATTTTATTATTTTACATTATTTTAGT
* * ** ** *
3026232 ACATTTTGTTTGAAATATTTATATTAATTATTTC-TAAATTTTTAAA-AAATTTAGTAAAACTCT
60 ACATTATGTTTG-AA-A-TT-TATTAA-T-TTACGT-GTTTTTTAAATAAATTTAAAAAAACCCT
** *
3026295 TACTTCGACCCTTTGTTCGTATTTTTTCTCCG
118 TACTTCGACCCTTTACTCATATTTTTTCTCCG
* * * * *
3026327 CATTTTATTACTTTAAAAATATCATATTTTCTAATTTTCTAATTTTACATTATTTTAATAGATTA
1 AATTTTATTACTTTAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTA
3026392 TGTTTGAAATTTATTAATTTACTGTGTTTTTTAAATA
66 TGTTTGAAATTTATTAATTTAC-GTGTTTTTTAAATA
3026429 TACCATTTTT
Statistics
Matches: 213, Mismatches: 26, Indels: 45
0.75 0.09 0.16
Matches are distributed among these distances:
148 3 0.01
149 9 0.04
150 8 0.04
151 2 0.01
152 1 0.00
153 13 0.06
154 49 0.23
155 2 0.01
156 46 0.22
157 17 0.08
158 34 0.16
159 4 0.02
160 13 0.06
161 10 0.05
162 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.53
Consensus pattern (149 bp):
AATTTTATTACTTTAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTA
TGTTTGAAATTTATTAATTTACGTGTTTTTTAAATAAATTTAAAAAAACCCTTACTTCGACCCTT
TACTCATATTTTTTCTCCG
Found at i:3026731 original size:10 final size:10
Alignment explanation
Indices: 3026717--3026868 Score: 78
Period size: 10 Copynumber: 15.7 Consensus size: 10
3026707 TCCCTTCCCA
3026717 CTTC-TTCTT
1 CTTCTTTCTT
3026726 CTTTCTTTCTT
1 C-TTCTTTCTT
*
3026737 -TTTTTTCTT
1 CTTCTTTCTT
* *
3026746 CTCCGTTCCTT
1 CTTC-TTTCTT
3026757 -TTCTTTCCTT
1 CTTCTTT-CTT
3026767 CTT-TTTCTTT
1 CTTCTTTC-TT
*
3026777 CTTTTTTCTT
1 CTTCTTTCTT
*
3026787 CTCCTTTCCTT
1 CTTCTTT-CTT
3026798 -TTCTTTC--
1 CTTCTTTCTT
3026805 CTTCTTT-TT
1 CTTCTTTCTT
*
3026814 CTTTCTTTCCT
1 C-TTCTTTCTT
3026825 C-TCATTTCCTT
1 CTTC-TTT-CTT
3026836 -TTCTTTCTT
1 CTTCTTTCTT
*
3026845 TTTCTTTC-T
1 CTTCTTTCTT
3026854 -TTCTTTCTT
1 CTTCTTTCTT
3026863 C-TCTTT
1 CTTCTTT
3026869 TCCCTCTCAT
Statistics
Matches: 112, Mismatches: 11, Indels: 40
0.69 0.07 0.25
Matches are distributed among these distances:
8 13 0.12
9 26 0.23
10 48 0.43
11 25 0.22
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:3026782 original size:41 final size:42
Alignment explanation
Indices: 3026720--3026864 Score: 185
Period size: 41 Copynumber: 3.5 Consensus size: 42
3026710 CTTCCCACTT
*
3026720 CTTCTTCTTTCTTTCTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
1 CTTCTTCTTTCTTTC--TTTTTTCTTCTCCTTTCCTTTTCTTTC
3026764 CTTCTT-TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
* *
3026805 CTTCTT-TTTCTTTC---TTTCCTCTCATTTCCTTTTCTTT-
1 CTTCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
* *
3026842 CTTTTTCTTTCTTTCTTTCTTCT
1 CTTCTTCTTTCTTTCTTTTTTCT
3026865 CTTTTCCCTC
Statistics
Matches: 91, Mismatches: 6, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
37 5 0.05
38 29 0.32
41 43 0.47
43 8 0.09
44 6 0.07
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (42 bp):
CTTCTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTC
Found at i:3026794 original size:31 final size:28
Alignment explanation
Indices: 3026756--3026870 Score: 89
Period size: 28 Copynumber: 4.0 Consensus size: 28
3026746 CTCCGTTCCT
*
3026756 TTTCTTTCCTTCTT-TTTCTTTCTTTTTTC
1 TTTCTTTCCTT-TTCTTTCCTTC-TTTTTC
3026785 TTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TT-T-CTTTCCTTTTCTTTCCTTCTTTTTC
*
3026815 TTTCTTTCC-TCTCATTTCCTT-TTCTTTC
1 TTTCTTTCCTTTTC-TTTCCTTCTT-TTTC
3026843 TTTTTCTTT-C-TTTCTTT-CTTCTCTTTTC
1 --TTTCTTTCCTTTTCTTTCCTTCT-TTTTC
3026871 CCTCTCATTC
Statistics
Matches: 74, Mismatches: 3, Indels: 19
0.77 0.03 0.20
Matches are distributed among these distances:
27 8 0.11
28 25 0.34
29 8 0.11
30 18 0.24
31 15 0.20
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTCTTTCCTTTTCTTTCCTTCTTTTTC
Found at i:3026871 original size:38 final size:38
Alignment explanation
Indices: 3026721--3026871 Score: 171
Period size: 38 Copynumber: 3.8 Consensus size: 38
3026711 TTCCCACTTC
* *
3026721 TTCTTCTTTCTTTCTTTTTTTTCTTCTCCGTTCCTTTTCTTT
1 TTCTT-TTTCTTTC-TTTCTTTCTTCTCCTTTCCTTTTC--T
3026763 CCTTCTTTTTCTTTCTTT-TTTCTTCTCCTTTCCTTTTCT
1 --TTCTTTTTCTTTCTTTCTTTCTTCTCCTTTCCTTTTCT
* * *
3026802 TTCCTTCTT-TTTCTTTCTTTCCTCTCATTTCCTTTTCT
1 TT-CTTTTTCTTTCTTTCTTTCTTCTCCTTTCCTTTTCT
*
3026840 TTCTTTTTCTTTCTTTCTTTCTTCTCTTTTCC
1 TTCTTTTTCTTTCTTTCTTTCTTCTCCTTTCC
3026872 CTCTCATTCT
Statistics
Matches: 97, Mismatches: 7, Indels: 12
0.84 0.06 0.10
Matches are distributed among these distances:
37 14 0.14
38 47 0.48
39 1 0.01
41 19 0.20
42 3 0.03
43 8 0.08
44 5 0.05
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (38 bp):
TTCTTTTTCTTTCTTTCTTTCTTCTCCTTTCCTTTTCT
Found at i:3029945 original size:8 final size:8
Alignment explanation
Indices: 3029932--3029958 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3029922 AATAACAATA
3029932 TATTATTT
1 TATTATTT
3029940 TATTATTT
1 TATTATTT
3029948 TATTATTT
1 TATTATTT
3029956 TAT
1 TAT
3029959 ATTATTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTATTT
Found at i:3030092 original size:309 final size:297
Alignment explanation
Indices: 3029494--3030167 Score: 971
Period size: 309 Copynumber: 2.2 Consensus size: 297
3029484 ATTACTTTCG
* * * * * * *
3029494 TTTTTTTAATTTACATTATTTTATTATATTATGTTTGAAGTGTATTAATTTAGTGTGTGTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
3029559 ATAAATTTTAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
66 ATAAATTTTAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
*
3029624 TTAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAAT
131 TCAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAAT
* * * *
3029689 TATTTCTGAATTTTTAAAATATTTAGTAAAACACTCTTACTTCAGCCATTTGTTCGTATTTTTTT
196 TATTTCTAAATTTTTAAAAAATGTAGTAAAACAATCTTACTTCAGCCATTTGTTCGTATTTTTTT
* *
3029754 CAGCATTTTATTACTTTAAAAATATCATATTTTCTAA
261 CAGCATTTTATTACTTAAAAAAAATCATATTTTCTAA
*
3029791 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGAGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
*
3029856 ATAAA-TTTAAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTT
66 ATAAATTTTAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
*
3029920 TCAATAACAATATATTATTTTAT-TATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAA
131 TCAATAAAAATATATTATTTT-TGTATTTTATTATTTTATATTATTTCAGTACA---T-TTTG--
*
3029984 ATATTTGCATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAA-AATCTTACTTC-GATC-TT
189 -----T--ATTAATTATTTCTAAATTTTTAAAAAATGTAGTAAAACAATCTTACTTCAG-CCATT
*
3030046 TGTTCGTATTTTTTTCTCCGCATTTTATTACTTAAAAAAAATCATATTTTCTAA
246 TGTTCGTA-TTTTTT-TCAGCATTTTATTACTTAAAAAAAATCATATTTTCTAA
* *
3030100 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTTTTAATTTACTGTGTTTTTTAA
1 TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
3030165 ATA
66 ATA
3030168 TACAATTTTT
Statistics
Matches: 338, Mismatches: 22, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
296 107 0.32
297 63 0.19
299 1 0.00
300 4 0.01
307 12 0.04
308 17 0.05
309 134 0.40
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.53
Consensus pattern (297 bp):
TTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAA
ATAAATTTTAAAAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTT
TCAATAAAAATATATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAAT
TATTTCTAAATTTTTAAAAAATGTAGTAAAACAATCTTACTTCAGCCATTTGTTCGTATTTTTTT
CAGCATTTTATTACTTAAAAAAAATCATATTTTCTAA
Found at i:3030193 original size:155 final size:149
Alignment explanation
Indices: 3029737--3030167 Score: 446
Period size: 154 Copynumber: 2.8 Consensus size: 149
3029727 ACTTCAGCCA
* *
3029737 TTTGTTCGTA-TTTTTT-TCAGCATTTTATTACTTTAAAAATATCATATTTTCTAATTTTATTAT
1 TTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTAAAAAATATCATATTTTCTAATTTTATTAT
* *
3029800 TTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGAGTTTTTTAAATAAATTTA
66 TTTACATTATTTTAGTACATTATGTTTGAAATTTTTTAATTTA-TGTGTTTTTTAAATAAATTTA
* *
3029865 A-AAAAACCCTTATT-CCTGCCC
130 ATAAAAA---TTATTACTTGACC
* * * * *
3029886 TTTGCTCGTATTATTTTC-CCGAATTTTATTACTTTCAATAACAATAT-ATTATTTTATTATTTT
1 TTTGTTCGTATTTTTTTCTCCGCATTTTATTAC-TT-AA-AA-AATATCA-TATTTTCTAATTTT
* * * * *
3029949 ATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGCATTAA-TTATTTCTAAATTTTT
61 ATTATTTTACATTATTTTAGTACATTATGTTTGAAAT-TTT---TTAATTTATGTGT---TTTTT
* * * * *
3030013 AAA-AAATGTAGTAAAAAATCTTACTTCGATC
119 AAATAAATTTAATAAAAATTATTACTT-GACC
*
3030044 TTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTAAAAAAAATCATATTTTCTAATTTTATTAT
1 TTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTAAAAAATATCATATTTTCTAATTTTATTAT
3030109 TTTACATTATTTTAGTACATTATGTTTGAAATTTTTTAATTTACTGTGTTTTTTAAATA
66 TTTACATTATTTTAGTACATTATGTTTGAAATTTTTTAATTTA-TGTGTTTTTTAAATA
3030168 TACAATTTTT
Statistics
Matches: 228, Mismatches: 32, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
149 9 0.04
150 25 0.11
151 7 0.03
152 4 0.02
153 6 0.03
154 54 0.24
155 52 0.23
156 8 0.04
157 7 0.03
158 30 0.13
159 26 0.11
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.53
Consensus pattern (149 bp):
TTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTAAAAAATATCATATTTTCTAATTTTATTAT
TTTACATTATTTTAGTACATTATGTTTGAAATTTTTTAATTTATGTGTTTTTTAAATAAATTTAA
TAAAAATTATTACTTGACC
Found at i:3030236 original size:16 final size:17
Alignment explanation
Indices: 3030215--3030253 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3030205 ACAATTTCCG
*
3030215 TTTTTTCTTT-TCATAT
1 TTTTTTCTTTAACATAT
3030231 TTTTTTCTTTAACATAT
1 TTTTTTCTTTAACATAT
3030248 TTTTTT
1 TTTTTT
3030254 ATCATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTCTTTAACATAT
Found at i:3030475 original size:10 final size:10
Alignment explanation
Indices: 3030458--3030609 Score: 60
Period size: 10 Copynumber: 15.8 Consensus size: 10
3030448 TTCCTTCCCA
3030458 CTTC-TTCTT
1 CTTCTTTCTT
3030467 CTTCTTTCTT
1 CTTCTTTCTT
* *
3030477 TTTTTTTCTT
1 CTTCTTTCTT
* *
3030487 CTCCGTTCCTT
1 CTTC-TTTCTT
3030498 -TTCTTTC-T
1 CTTCTTTCTT
*
3030506 -TTCTTTTTT
1 CTTCTTTCTT
3030515 CAGTT-TTTCTT
1 C--TTCTTTCTT
*
3030526 CTCCTTTCCTT
1 CTTCTTT-CTT
3030537 -TTCTTTCATT
1 CTTCTTTC-TT
3030547 CTT-TTTC-T
1 CTTCTTTCTT
*
3030555 -TTCTTTCCT
1 CTTCTTTCTT
3030564 C-TCATTTCCTT
1 CTTC-TTT-CTT
3030575 -TTCTTTCTT
1 CTTCTTTCTT
* *
3030584 TTTATTTC-T
1 CTTCTTTCTT
3030593 -TTCTTTCTT
1 CTTCTTTCTT
*
3030602 CTCCTTTC
1 CTTCTTTC
3030610 CCTCTCCTTT
Statistics
Matches: 108, Mismatches: 16, Indels: 37
0.67 0.10 0.23
Matches are distributed among these distances:
7 2 0.02
8 18 0.17
9 18 0.17
10 48 0.44
11 20 0.19
12 2 0.02
ACGTcount: A:0.03, C:0.28, G:0.01, T:0.68
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:3030477 original size:4 final size:4
Alignment explanation
Indices: 3030468--3030601 Score: 50
Period size: 4 Copynumber: 32.2 Consensus size: 4
3030458 CTTCTTCTTC
*
3030468 TTCT TTCT TT-T TT-T TTCT TCTCCGT TCCT TTTCT TTCT TTCT TT-T
1 TTCT TTCT TTCT TTCT TTCT T-T-C-T TTCT -TTCT TTCT TTCT TTCT
* *
3030513 TTCAG TT-T TTCT TCTCCT TTCCTT TTCT TTCA TTC- TT-T TTCT TTCT
1 TTC-T TTCT TTCT T-T-CT TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT
* *
3030559 TTCCT CTCAT TTCCTT TTCT TTC- TT-T TTAT TTCT TTCT TTCT T
1 TT-CT TTC-T TT-C-T TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
3030602 CTCCTTTCCC
Statistics
Matches: 103, Mismatches: 9, Indels: 36
0.70 0.06 0.24
Matches are distributed among these distances:
3 19 0.18
4 53 0.51
5 18 0.17
6 11 0.11
7 2 0.02
ACGTcount: A:0.03, C:0.25, G:0.01, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:3030510 original size:38 final size:38
Alignment explanation
Indices: 3030468--3030610 Score: 175
Period size: 38 Copynumber: 3.7 Consensus size: 38
3030458 CTTCTTCTTC
* *
3030468 TTCTTTCTT-TTTTTTTCTTCTCCGTTCCTTTTCTTTCT
1 TTCTTT-TTCTTTCTTTCTTCTCCTTTCCTTTTCTTTCT
* *
3030506 TTCTTTTTTCAGTT-TTTCTTCTCCTTTCCTTTTCTTTCA
1 TTC-TTTTTC-TTTCTTTCTTCTCCTTTCCTTTTCTTTCT
* *
3030545 TTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCTTTCT
1 TTCTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTCT
3030583 TT-TTATTTCTTTCTTTCTTCTCCTTTCC
1 TTCTT-TTTCTTTCTTTCTTCTCCTTTCC
3030611 CTCTCCTTTT
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
37 4 0.04
38 56 0.62
39 29 0.32
40 2 0.02
ACGTcount: A:0.03, C:0.27, G:0.01, T:0.69
Consensus pattern (38 bp):
TTCTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTCT
Found at i:3030511 original size:34 final size:33
Alignment explanation
Indices: 3030468--3030593 Score: 119
Period size: 34 Copynumber: 3.6 Consensus size: 33
3030458 CTTCTTCTTC
3030468 TTCTTTCTTTTTTTTTCTTCTCCGTTCCTTTTCT
1 TTCTTTCTTTTTTTTTCTTCTCC-TTCCTTTTCT
3030502 TTCTTTCTTTTTTCAGTTTTTCTTCTCCTTTCCTTTTCT
1 TTCTTTC--TTTT---TTTTTCTTCTCC-TTCCTTTTCT
* * * *
3030541 TTCATTCTTTTTCTTTCTT-TCCTCTCATTTCCTT
1 TTCTTTCTTTTTTTTTCTTCTCCT-TCCTTTTC-T
*
3030575 TTCTTTCTTTTTATTTCTT
1 TTCTTTCTTTTTTTTTCTT
3030594 TCTTTCTTCT
Statistics
Matches: 78, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
32 1 0.01
33 9 0.12
34 32 0.41
36 4 0.05
37 4 0.05
39 28 0.36
ACGTcount: A:0.03, C:0.25, G:0.02, T:0.70
Consensus pattern (33 bp):
TTCTTTCTTTTTTTTTCTTCTCCTTCCTTTTCT
Found at i:3030608 original size:14 final size:13
Alignment explanation
Indices: 3030492--3030609 Score: 55
Period size: 14 Copynumber: 8.6 Consensus size: 13
3030482 TTCTTCTCCG
3030492 TTCCTTTTCTTTCT
1 TTCC-TTTCTTTCT
*
3030506 TT-CTTT-TTTCAG
1 TTCCTTTCTTTC-T
3030518 TT--TTTCTTCTCCT
1 TTCCTTTCTT-T-CT
*
3030531 TTCCTTTTCTTTCA
1 TTCC-TTTCTTTCT
*
3030545 TTCTTTTTCTTTCT
1 TTC-CTTTCTTTCT
*
3030559 TTCCTCTCATTTCCT
1 TTCCTTTC-TTT-CT
* *
3030574 TTTCTTTCTTTTT
1 TTCCTTTCTTTCT
*
3030587 ATTTCTTTCTTTCT
1 -TTCCTTTCTTTCT
3030601 TCTCCTTTC
1 T-TCCTTTC
3030610 CCTCTCCTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
11 7 0.09
12 7 0.09
13 9 0.11
14 42 0.52
15 9 0.11
16 6 0.08
ACGTcount: A:0.03, C:0.27, G:0.01, T:0.69
Consensus pattern (13 bp):
TTCCTTTCTTTCT
Found at i:3032456 original size:13 final size:13
Alignment explanation
Indices: 3032440--3032464 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3032430 TTTTATTATT
3032440 TTACATTATTTTA
1 TTACATTATTTTA
3032453 TTACATTATTTT
1 TTACATTATTTT
3032465 TGAAGTGTAT
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:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (13 bp):
TTACATTATTTTA
Found at i:3033018 original size:310 final size:297
Alignment explanation
Indices: 3032337--3033107 Score: 973
Period size: 310 Copynumber: 2.5 Consensus size: 297
3032327 GTGCAAGTTC
* * * * *
3032337 AAAAAAATTTTAGTAAAAACCCTTATTTCGGCCATTTATTCGTACTATTTTCT-CGAATTTTATT
1 AAAAAAA-TTTAGTAAAAACTCTTACTTCGGCC-TTTGTTCGTA-TTTTTTCTCCGCATTTTATT
* * * * *
3032401 ACTTTCAATAAAAATAAATTACTTTC-ATTTTTTATTATTTTACATTATTTTATTACATTATTTT
63 ACTTTC-A-AAAAAT-CA-TATTTTCTA-ATTTTATTATTTTACATTATTTTAGTACATTATGTT
* * *
3032465 TGAAGTGTATTAATTTATGTGTTTTTTAAAT-AATTTTTAAAAAAAAAAACCCTTATTCCTACCC
123 TGAAATTTATTAATTTATGTATTTTTTAAATAAATTTTT---AAAAAAAACCCTTATTCCTACCC
* *
3032529 TTTGCTCGTATTATTTTCCCGAATTTTAATACTTTTAATAAAAATATATTATTTTTGTATTTTAT
185 TTTGCTCGTATTATTTTCCCGAATTTTAATACTTTCAATAAAAATATATTATTTTCGTATTTTAT
* *
3032594 TATTTTATATTATTTCAGTACATTTTGTATTAATTATTTCTGAATTTT
250 TATTTTATATTATTTCAGTAAATTTTGTATTAATTATTTCTAAATTTT
* *
3032642 TAAAAAATTTAGTAAAACACTCTTACTTTGGCCCTTTGTTCGTATTTTTT-TCCGCATTTTATTA
1 AAAAAAATTTAGTAAAA-ACTCTTACTTCGG-CCTTTGTTCGTATTTTTTCTCCGCATTTTATTA
3032706 CTTT-AAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
64 CTTTCAAAAA-ATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
* *
3032770 TTTATTAATTTAGTGT-TTTTTTAAATAAATTTTT-AAAAGAACCCTTATTCCTGCCCTTTGCTC
128 TTTATTAATTTA-TGTATTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTC
** *
3032833 GTATTATTTTCCCGAATTTTTTTTACTTTCAATAACAATATATTATTTTCGTATTTT-TTATTTT
192 GTATTATTTTCCCGAA-TTTTAATACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTT
3032897 ATATTATTTTAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTT
256 ATATTA--TT--T-CA----G--T-AAAT-TTTGTATTAATTATTTCTAAATTTT
*
3032952 AAAAAAATTTAGTAAAAAATCTTACTTCGGCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTAC
1 AAAAAAATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTA-TTTTTTCTCCGCATTTTATTAC
*
3033017 TTTGAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
65 TTTCAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
3033082 TATTAATTTACTGTATTTTTTAAATA
130 TATTAATTTA-TGTATTTTTTAAATA
3033108 TACCATTTTT
Statistics
Matches: 414, Mismatches: 27, Indels: 44
0.85 0.06 0.09
Matches are distributed among these distances:
297 56 0.14
298 35 0.08
299 2 0.00
300 64 0.15
301 17 0.04
302 5 0.01
303 1 0.00
304 30 0.07
305 25 0.06
306 3 0.01
308 13 0.03
309 20 0.05
310 127 0.31
311 16 0.04
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (297 bp):
AAAAAAATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTATTTTTTCTCCGCATTTTATTACT
TTCAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
ATTAATTTATGTATTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGTAT
TATTTTCCCGAATTTTAATACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATT
ATTTCAGTAAATTTTGTATTAATTATTTCTAAATTTT
Found at i:3033406 original size:10 final size:10
Alignment explanation
Indices: 3033389--3033489 Score: 59
Period size: 10 Copynumber: 10.0 Consensus size: 10
3033379 TTCCTTCCCA
3033389 CTTC-TTCTT
1 CTTCTTTCTT
3033398 CTTCTTTCTT
1 CTTCTTTCTT
* *
3033408 TTTTTTTCTT
1 CTTCTTTCTT
* *
3033418 CTCCGTTCCTT
1 CTTC-TTTCTT
3033429 -TTCTTTCCTT
1 CTTCTTT-CTT
3033439 CTT-TTTCTT
1 CTTCTTTCTT
*
3033448 TTTCTTTTTCTT
1 CTTC--TTTCTT
*
3033460 CTCCTTTCCTT
1 CTTCTTT-CTT
3033471 -TTCTTTCCTT
1 CTTCTTT-CTT
3033481 CTT-TTTCTT
1 CTTCTTTCTT
3033490 TCTTTCCTCT
Statistics
Matches: 71, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
9 14 0.20
10 37 0.52
11 12 0.17
12 8 0.11
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:3033427 original size:44 final size:40
Alignment explanation
Indices: 3033361--3033490 Score: 118
Period size: 42 Copynumber: 3.1 Consensus size: 40
3033351 AAAAATTACC
* *
3033361 CTTTTTCTTTT-TTTTCCCTTCCTTCCCACTTCTTCTTCTTCTTT
1 CTTTTT-TTTTCTTCTCCCTTCCTT--CACTT-TCCTTCTT-TTT
* **
3033405 CTTTTTTTTTCTTCTCCGTTCCTTTTCTTTCCTTCTTTTT
1 CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
* **
3033445 CTTTTTCTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTT
1 C-TTTT-TTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
3033487 CTTT
1 CTTT
3033491 CTTTCCTCTC
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
40 4 0.05
41 14 0.18
42 38 0.49
43 4 0.05
44 17 0.22
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.68
Consensus pattern (40 bp):
CTTTTTTTTTCTTCTCCCTTCCTTCACTTTCCTTCTTTTT
Found at i:3033439 original size:21 final size:21
Alignment explanation
Indices: 3033395--3033497 Score: 90
Period size: 21 Copynumber: 5.1 Consensus size: 21
3033385 CCCACTTCTT
* * *
3033395 CTTCTTCTTT-CTTTTTTTTT
1 CTTCTCCTTTCCTTTTCTTTC
*
3033415 CTTCTCCGTTCCTTTTCTTTC
1 CTTCTCCTTTCCTTTTCTTTC
* * *
3033436 CTTCT-TTTTCTTTTTCTTTTT
1 CTTCTCCTTTCCTTTTC-TTTC
3033457 CTTCTCCTTTCCTTTTCTTTC
1 CTTCTCCTTTCCTTTTCTTTC
*
3033478 CTTCT--TTTTC-TTTCTTTC
1 CTTCTCCTTTCCTTTTCTTTC
3033496 CT
1 CT
3033498 CTCTGTTGAC
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
18 10 0.15
19 4 0.06
20 16 0.24
21 29 0.43
22 9 0.13
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (21 bp):
CTTCTCCTTTCCTTTTCTTTC
Found at i:3033469 original size:42 final size:41
Alignment explanation
Indices: 3033395--3033490 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 41
3033385 CCCACTTCTT
3033395 CTTCTTCTTTC-TTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
*
3033436 CTTCTTTTTCTTTTTCTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTTT-TTTTTCTTCTCCGTTCCTTTTCTTTC
3033478 CTTCTTTTTCTTT
1 CTTCTTTTTCTTT
3033491 CTTTCCTCTC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
40 4 0.08
41 10 0.19
42 38 0.73
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (41 bp):
CTTCTTTTTCTTTTTTTTTTCTTCTCCGTTCCTTTTCTTTC
Found at i:3033488 original size:6 final size:6
Alignment explanation
Indices: 3033390--3033490 Score: 53
Period size: 6 Copynumber: 16.0 Consensus size: 6
3033380 TCCTTCCCAC
* * ** *
3033390 TTCTTC TTCTTCT TTCTTT TTTTTT CTTCTCCG TTCCTT TTCTTT CCTTCTTT
1 TTCTTT TTCTT-T TTCTTT TTCTTT -TTCT-TT TTCTTT TTCTTT --TTCTTT
* * *
3033443 TTCTTT TTCTTT TTC-TT CTC-CT TTCCTT TTCTTT CCTTCTTT TTCTTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT --TTCTTT TTCTTT
3033491 CTTTCCTCTC
Statistics
Matches: 73, Mismatches: 14, Indels: 16
0.71 0.14 0.16
Matches are distributed among these distances:
5 7 0.10
6 43 0.59
7 11 0.15
8 12 0.16
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (6 bp):
TTCTTT
Found at i:3033606 original size:24 final size:24
Alignment explanation
Indices: 3033574--3033622 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
3033564 AGTGGGAGTC
3033574 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
3033598 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
3033622 G
1 G
3033623 TGATCGGATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.41
Consensus pattern (24 bp):
GCCACCAATCCTTTTTATTTAGGT
Found at i:3034624 original size:107 final size:106
Alignment explanation
Indices: 3034439--3034658 Score: 300
Period size: 107 Copynumber: 2.1 Consensus size: 106
3034429 AAACCCATAC
* * * * *
3034439 TTTGAAGTTTTAAGAGGATATTTGGCCATTTGGTTCAACGAGAAATTGAAAACCAGCACATTAGG
1 TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
*
3034504 GCACGTTTTCTCGAATTTT-CAAACGCAAAATATCGCTTTAT
66 GCACGTTTTCTCG-ATTTTCCAAACGCAAAATATCGCCTTAT
* * *
3034545 TTTGAAATTTTAAAAGGATATTTTAGCTATTTGG-TCGAACGAAAAATCGAAACCCAGCACGTTA
1 TTTGAAATTTTAAAAGGATA-TTTAGCCATTTGGTTC-AACGAAAAATCGAAAACCAGCACATTA
*
3034609 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATTGCCTTAT
64 GGGCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
*
3034652 TTAGAAA
1 TTTGAAA
3034659 AATTTTCCTT
Statistics
Matches: 100, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
106 25 0.25
107 75 0.75
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (106 bp):
TTTGAAATTTTAAAAGGATATTTAGCCATTTGGTTCAACGAAAAATCGAAAACCAGCACATTAGG
GCACGTTTTCTCGATTTTCCAAACGCAAAATATCGCCTTAT
Found at i:3035195 original size:20 final size:19
Alignment explanation
Indices: 3035143--3035198 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
3035133 AGTGTACCCA
*
3035143 TATATGTATATATATAAGG
1 TATATATATATATATAAGG
*
3035162 TATATAAATAATATATAA-G
1 TATATATAT-ATATATAAGG
3035181 TATGAATATATATATATA
1 TAT--ATATATATATATA
3035199 CAAATAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 11 0.35
20 15 0.48
21 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
TATATATATATATATAAGG
Found at i:3037321 original size:23 final size:23
Alignment explanation
Indices: 3037290--3037348 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
3037280 AGGCATATAT
*
3037290 ATGTGTATTTATAAAAATTAAAA
1 ATGTATATTTATAAAAATTAAAA
* *
3037313 ATGTATATTGATATATATATTAAAA
1 ATGTATATT--TATAAAAATTAAAA
3037338 A--TATATTTATA
1 ATGTATATTTATA
3037349 TGTGTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 4 0.13
23 14 0.45
25 13 0.42
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (23 bp):
ATGTATATTTATAAAAATTAAAA
Found at i:3037481 original size:3 final size:3
Alignment explanation
Indices: 3037473--3037543 Score: 60
Period size: 3 Copynumber: 23.7 Consensus size: 3
3037463 TAAATGAGTA
* *
3037473 AAT AAT AAT AAT GAT TAT AAT AAT ACACT AAT AAT -AT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT
3037518 AAT -AT AAT -AT AAT AAT GAAT AGAT AA
1 AAT AAT AAT AAT AAT AAT -AAT A-AT AA
3037544 ATATAAAAAG
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
2 8 0.14
3 39 0.68
4 8 0.14
5 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3037519 original size:13 final size:13
Alignment explanation
Indices: 3037501--3037533 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
3037491 AATAATACAC
3037501 TAATAATATAATA
1 TAATAATATAATA
3037514 TAATAATATAATA
1 TAATAATATAATA
3037527 TAATAAT
1 TAATAAT
3037534 GAATAGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATAATATAATA
Found at i:3037562 original size:19 final size:20
Alignment explanation
Indices: 3037505--3037565 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 20
3037495 ATACACTAAT
* *
3037505 AATATAATATA-ATAATAT-
1 AATATAATAAAGAAAATATA
* * *
3037523 AATATAATAATGAATAGATA
1 AATATAATAAAGAAAATATA
3037543 AATATAA-AAAGAAAATATA
1 AATATAATAAAGAAAATATA
3037562 AATA
1 AATA
3037566 AGATAATAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 3
0.75 0.18 0.07
Matches are distributed among these distances:
18 9 0.27
19 17 0.52
20 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AATATAATAAAGAAAATATA
Found at i:3039771 original size:15 final size:15
Alignment explanation
Indices: 3039751--3039785 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
3039741 TATGTCTAAG
3039751 TTTTATTGTATTTAT
1 TTTTATTGTATTTAT
3039766 TTTTATTGTATTTAT
1 TTTTATTGTATTTAT
3039781 TTTTA
1 TTTTA
3039786 AGGTCATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (15 bp):
TTTTATTGTATTTAT
Found at i:3040904 original size:10 final size:10
Alignment explanation
Indices: 3040890--3041043 Score: 80
Period size: 10 Copynumber: 15.8 Consensus size: 10
3040880 TCCCTTCCCA
3040890 CTTC-TTCTT
1 CTTCTTTCTT
3040899 CTTTCTTTCTT
1 C-TTCTTTCTT
* *
3040910 TTTTTTTCTT
1 CTTCTTTCTT
* *
3040920 CTCCGTTCCTT
1 CTTC-TTTCTT
3040931 -TTCTTTCCTT
1 CTTCTTT-CTT
3040941 CTT-TTTCTTT
1 CTTCTTTC-TT
*
3040951 CTTTTTTCTT
1 CTTCTTTCTT
*
3040961 CTCCTTTCCTT
1 CTTCTTT-CTT
3040972 -TTCTTTC--
1 CTTCTTTCTT
3040979 CTTCTTT-TT
1 CTTCTTTCTT
*
3040988 CTTTCTTTCCT
1 C-TTCTTTCTT
3040999 C-TCATTTCCTT
1 CTTC-TTT-CTT
3041010 -TTCTTTCTT
1 CTTCTTTCTT
*
3041019 TTTCTTTC-T
1 CTTCTTTCTT
3041028 -TTCTTTCTT
1 CTTCTTTCTT
3041037 C-TCTTTC
1 CTTCTTTC
3041044 CCTCTTATTC
Statistics
Matches: 113, Mismatches: 13, Indels: 38
0.69 0.08 0.23
Matches are distributed among these distances:
8 13 0.12
9 19 0.17
10 56 0.50
11 25 0.22
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:3040943 original size:38 final size:39
Alignment explanation
Indices: 3040901--3041044 Score: 183
Period size: 38 Copynumber: 3.7 Consensus size: 39
3040891 TTCTTCTTCT
*
3040901 TTCTTTCTTT-TTTTTTCTTCTCCGTTCCTTTTCTTTCC
1 TTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
3040939 TTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
1 TTC--TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
* *
3040980 TTC-TT-TTTCTTTCTTTCCTCTCATTTCCTTTTCTTT-C
1 TTCTTTCTTTCTTT-TTTCTTCTCCTTTCCTTTTCTTTCC
3041017 TT-TTTCTTTCTTTCTTTCTTCT-CTTTCC
1 TTCTTTCTTTCTTT-TTTCTTCTCCTTTCC
3041045 CTCTTATTCT
Statistics
Matches: 95, Mismatches: 5, Indels: 13
0.84 0.04 0.12
Matches are distributed among these distances:
37 17 0.18
38 41 0.43
40 7 0.07
41 30 0.32
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (39 bp):
TTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCC
Found at i:3040956 original size:41 final size:41
Alignment explanation
Indices: 3040904--3041044 Score: 183
Period size: 41 Copynumber: 3.6 Consensus size: 41
3040894 TTCTTCTTTC
*
3040904 TTTCTTT-TTTTTTCTTCTCCGTTCCTTTTCTTTCCTTCTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTT
3040944 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTT
* *
3040985 TTTCTTTC---TTTCCTCTCATTTCCTTTTC--T--TTCTT
1 TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTT
3041019 TTTCTTTCTTTCTTTCTTCT-CTTTCC
1 TTTCTTTCTTT-TTTCTTCTCCTTTCC
3041045 CTCTTATTCT
Statistics
Matches: 91, Mismatches: 5, Indels: 13
0.83 0.05 0.12
Matches are distributed among these distances:
34 13 0.14
36 1 0.01
37 5 0.05
38 25 0.27
40 7 0.08
41 40 0.44
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (41 bp):
TTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTT
Found at i:3040968 original size:31 final size:28
Alignment explanation
Indices: 3040930--3041043 Score: 87
Period size: 28 Copynumber: 4.0 Consensus size: 28
3040920 CTCCGTTCCT
*
3040930 TTTCTTTCCTTCTT-TTTCTTTCTTTTTTC
1 TTTCTTTCCTT-TTCTTTCCTTC-TTTTTC
3040959 TTCTCCTTTCCTTTTCTTTCCTTCTTTTTC
1 TT-T-CTTTCCTTTTCTTTCCTTCTTTTTC
*
3040989 TTTCTTTCC-TCTCATTTCCTT-TTCTTTC
1 TTTCTTTCCTTTTC-TTTCCTTCTT-TTTC
*
3041017 TTTTTCTTT-C-TTTCTTT-CTTCTCTTTC
1 --TTTCTTTCCTTTTCTTTCCTTCTTTTTC
3041044 CCTCTTATTC
Statistics
Matches: 73, Mismatches: 4, Indels: 18
0.77 0.04 0.19
Matches are distributed among these distances:
27 12 0.16
28 21 0.29
29 7 0.10
30 18 0.25
31 15 0.21
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTCTTTCCTTTTCTTTCCTTCTTTTTC
Found at i:3040994 original size:75 final size:75
Alignment explanation
Indices: 3040897--3041044 Score: 203
Period size: 75 Copynumber: 2.0 Consensus size: 75
3040887 CCACTTCTTC
* * * *
3040897 TTCTTTCTTTCTTTTTTTTTCTTCTCCGT-TCCTTTTC-TTTCCTTCTTTTTCTTTCTTT-TTTC
1 TTCTTTCCTTCTTTTTCTTTCTT-TCC-TCTCATTTCCTTTTCCTTCTTTTTCTTTCTTTCTTTC
3040959 TTCTCCTTTCCTT
64 TTCT-CTTTCCTT
*
3040972 TTCTTTCCTTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCTTTCTTTTTCTTTCTTTCTTTCTT
1 TTCTTTCCTTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCCTTCTTTTTCTTTCTTTCTTTCTT
3041037 CTCTTTCC
66 CTCTTTCC
3041045 CTCTTATTCT
Statistics
Matches: 65, Mismatches: 5, Indels: 6
0.86 0.07 0.08
Matches are distributed among these distances:
73 1 0.02
74 9 0.14
75 47 0.72
76 8 0.12
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (75 bp):
TTCTTTCCTTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCCTTCTTTTTCTTTCTTTCTTTCTT
CTCTTTCCTT
Found at i:3043777 original size:154 final size:149
Alignment explanation
Indices: 3043594--3044343 Score: 592
Period size: 154 Copynumber: 4.9 Consensus size: 149
3043584 AAAAATTAGT
* * * * *
3043594 AAAAACCCTTATTTCGGCCATTTGTTCGTACTATTTTCCCGAATTATATTACTTTCAATAAAAAT
1 AAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
* * * * * *
3043659 AAATTACTTTCATTTTTTTATTTTACATTATTTTATTATATTATGTTTGAAGTGTATTAATTTAG
66 ATATTA-TTTTATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAA-T-TATTAATTTAG
*
3043724 TGTGTGTTTTAAATAAATTTAAAA
128 TGAGT-TTTTAAATAAATTT-AAA
*
3043748 AAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTTAATAAAAAT
1 AAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
* *
3043813 ATATTATTTTTTTATTTTATTATTTTATATTATTTCAGTAC---AT-TTTGTATTAATT-ATTT-
66 ATATTA---TTTTATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAATT-ATTAATTTA
* * *
3043872 CTGAATTTTTAAA-AAATTTAGTA
127 GTGAGTTTTTAAATAAATTTA-AA
* * * * * * * *
3043895 AAACACTCTTACTT-CAGCCATTTGTTCGTATT-TTTTTCAGCATTTTATTACTTT-AA-AAATA
1 AAAAACCCTTA-TTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAA
* *
3043956 TCATATT-TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTT
65 T-ATATTATT-TTATTTTATTATTTTACATTATTTCAGTACATTATGTTTG-AA-TTATTAATTT
3044020 AGTGAGTTTTTTAAATAAATTT-AA
126 AGTGAG-TTTTTAAATAAATTTAAA
* *
3044044 AAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAACAAT
1 AAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
* *
3044109 ATATTATTTTATTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGTATTA
66 ATATTA--TT-TTATTTTATTATTTTACATTATTTCAGTACATTATGTTTG--A-A--T-TATTA
** * * * *
3044174 ATTATTTCTAAATTTTT-AA-AAATGTAGTA
122 A-T-TTAGTGAGTTTTTAAATAAATTTA-AA
* * * *
3044203 AAAAA-TCTTACTT-C-GACC-TTTGTTCGTATTTTTTTCTCCGCATTTTATTAC-TT-AA-AAA
1 AAAAACCCTTA-TTCCTG-CCATTTGCTCGTATTATTTTC-CCGAATTTTATTACTTTCAATAAA
* * *
3044261 AATCATATT-TTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTTTTAAT
63 AAT-ATATTATT-TTATTTTATTATTTTACATTATTTCAGTACATTATGTTTG-AA-TTATTAAT
* *
3044325 TTACTGTGTTTTTTAAATA
124 TTAGTGAG-TTTTTAAATA
3044344 TACAATTTTT
Statistics
Matches: 487, Mismatches: 70, Indels: 82
0.76 0.11 0.13
Matches are distributed among these distances:
141 2 0.00
142 27 0.06
144 5 0.01
145 9 0.02
146 24 0.05
147 40 0.08
148 23 0.05
149 38 0.08
150 35 0.07
151 18 0.04
152 11 0.02
153 40 0.08
154 102 0.21
155 7 0.01
156 34 0.07
157 26 0.05
158 28 0.06
159 14 0.03
160 4 0.01
ACGTcount: A:0.31, C:0.11, G:0.07, T:0.51
Consensus pattern (149 bp):
AAAAACCCTTATTCCTGCCATTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAAT
ATATTATTTTATTTTATTATTTTACATTATTTCAGTACATTATGTTTGAATTATTAATTTAGTGA
GTTTTTAAATAAATTTAAA
Found at i:3043838 original size:13 final size:13
Alignment explanation
Indices: 3043812--3043846 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3043802 TTAATAAAAA
*
3043812 TATATTATTTTTT
1 TATATTATTATTT
*
3043825 TATTTTATTATTT
1 TATATTATTATTT
3043838 TATATTATT
1 TATATTATT
3043847 TCAGTACATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (13 bp):
TATATTATTATTT
Found at i:3044123 original size:8 final size:8
Alignment explanation
Indices: 3044110--3044136 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
3044100 AATAACAATA
3044110 TATTATTT
1 TATTATTT
3044118 TATTATTT
1 TATTATTT
3044126 TATTATTT
1 TATTATTT
3044134 TAT
1 TAT
3044137 ATTATTTCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (8 bp):
TATTATTT
Found at i:3044427 original size:16 final size:16
Alignment explanation
Indices: 3044391--3044429 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3044381 AGAATTTCCG
*
3044391 TTTTTTTCTTTTCACA
1 TTTTTTTCTTTTAACA
3044407 TTTTTTTC-TTTAACA
1 TTTTTTTCTTTTAACA
3044422 TATTTTTT
1 T-TTTTTT
3044430 TATCATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTTCTTTTAACA
Found at i:3044647 original size:10 final size:10
Alignment explanation
Indices: 3044630--3044779 Score: 53
Period size: 10 Copynumber: 15.8 Consensus size: 10
3044620 TTCCTTCCCA
3044630 CTTC-TTCTT
1 CTTCTTTCTT
3044639 CTTCTTTCTT
1 CTTCTTTCTT
3044649 -TT-TTTCTT
1 CTTCTTTCTT
* *
3044657 CTCCGTTCCTT
1 CTTC-TTTCTT
3044668 -TTCTTTCCTT
1 CTTCTTT-CTT
3044678 -TT-TTT-TT
1 CTTCTTTCTT
3044685 CAGTT-TTTCTT
1 C--TTCTTTCTT
*
3044696 CTCCTTTCCTT
1 CTTCTTT-CTT
3044707 -TTCTTTCATT
1 CTTCTTTC-TT
3044717 CTT-TTTC-T
1 CTTCTTTCTT
*
3044725 -TTCTTTCCT
1 CTTCTTTCTT
3044734 C-TCATTTCCTT
1 CTTC-TTT-CTT
3044745 -TTCTTTCTT
1 CTTCTTTCTT
* *
3044754 TTTATTTC-T
1 CTTCTTTCTT
3044763 -TTCTTTCTT
1 CTTCTTTCTT
*
3044772 CTCCTTTC
1 CTTCTTTC
3044780 CCTCTCCTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 43
0.67 0.06 0.27
Matches are distributed among these distances:
7 4 0.04
8 17 0.16
9 22 0.20
10 49 0.45
11 17 0.16
ACGTcount: A:0.03, C:0.28, G:0.01, T:0.68
Consensus pattern (10 bp):
CTTCTTTCTT
Found at i:3044693 original size:39 final size:38
Alignment explanation
Indices: 3044601--3044780 Score: 179
Period size: 38 Copynumber: 4.7 Consensus size: 38
3044591 AAAAATTACC
* **
3044601 TTTTTTTTCTTT-TTT-TTCCTTCCTTCCCACTTC-TTCT
1 TTTTTTTTCTTTCTTTCTT-C-TCCTTTCCTTTTCTTTCT
* * * *
3044638 TCTTCTTTCTTTTTTTCTTCTCCGTTCCTTTTCTTTCCT
1 TTTTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCTTT-CT
* *
3044677 TTTTTTTTCAGTT-TTTCTTCTCCTTTCCTTTTCTTTCA
1 TTTTTTTTC-TTTCTTTCTTCTCCTTTCCTTTTCTTTCT
* * *
3044715 TTCTTTTTCTTTCTTTCCTCTCATTTCCTTTTCTTTCT
1 TTTTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTCT
*
3044753 TTTTATTTCTTTCTTTCTTCTCCTTTCC
1 TTTTTTTTCTTTCTTTCTTCTCCTTTCC
3044781 CTCTCCTTCT
Statistics
Matches: 117, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
37 21 0.18
38 61 0.52
39 33 0.28
40 2 0.02
ACGTcount: A:0.03, C:0.28, G:0.01, T:0.68
Consensus pattern (38 bp):
TTTTTTTTCTTTCTTTCTTCTCCTTTCCTTTTCTTTCT
Found at i:3044726 original size:24 final size:25
Alignment explanation
Indices: 3044637--3044761 Score: 78
Period size: 24 Copynumber: 4.9 Consensus size: 25
3044627 CCACTTCTTC
*
3044637 TTCTTCTTTCTTT--TTTTCTTCTCCG
1 TTCTT-TTTCTTTCCTTTTCTT-TCAG
* *
3044662 TTCCTTTTCTTTCCTTTTTTTTTCAG
1 TTCTTTTTCTTTCC-TTTTCTTTCAG
*
3044688 TTTTTCTTCTCCTTTCCTTTTCTTTCA-
1 TTCTT-TT-T-CTTTCCTTTTCTTTCAG
* * *
3044715 TTCTTTTTCTTT-CTTTCCTCTCAT
1 TTCTTTTTCTTTCCTTTTCTTTCAG
* * *
3044739 TTCCTTTTCTTTCTTTTTATTTC
1 TTCTTTTTCTTTCCTTTTCTTTC
3044762 TTTCTTTCTT
Statistics
Matches: 78, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
23 9 0.12
24 22 0.28
25 11 0.14
26 8 0.10
27 12 0.15
28 10 0.13
29 6 0.08
ACGTcount: A:0.03, C:0.26, G:0.02, T:0.69
Consensus pattern (25 bp):
TTCTTTTTCTTTCCTTTTCTTTCAG
Found at i:3044778 original size:14 final size:13
Alignment explanation
Indices: 3044699--3044779 Score: 54
Period size: 14 Copynumber: 5.8 Consensus size: 13
3044689 TTTTCTTCTC
3044699 CTTTCCTTTTCTTT
1 CTTTCC-TTTCTTT
* *
3044713 CATTCTTTTTCTTT
1 CTTTC-CTTTCTTT
*
3044727 CTTTCCTCTCATTT
1 CTTTCCTTTC-TTT
*
3044741 CCTTTTCTTTCTTT
1 -CTTTCCTTTCTTT
* *
3044755 TTATTTCTTTCTTT
1 CT-TTCCTTTCTTT
3044769 CTTCTCCTTTC
1 CTT-TCCTTTC
3044780 CCTCTCCTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
13 5 0.10
14 39 0.75
15 8 0.15
ACGTcount: A:0.04, C:0.28, G:0.00, T:0.68
Consensus pattern (13 bp):
CTTTCCTTTCTTT
Found at i:3047177 original size:312 final size:297
Alignment explanation
Indices: 3046508--3047276 Score: 1096
Period size: 312 Copynumber: 2.5 Consensus size: 297
3046498 GCAAGTTCAA
* * * * *
3046508 AAAAAATTTAGTAAAAACCCTTATTTCGGCCATTTATTCGTACTATTTTCT-CGAATTTTATTAC
1 AAAAAATTTAGTAAAAACTCTTACTTCGGCC-TTTGTTCGTA-TTTTTTCTCCGCATTTTATTAC
* * * *
3046572 TTTCAATAAAAATAAATTACTTTTGT-TTTTTATTATTTTACATTATTTTATTACATTATGTTTG
64 TTT-AA-AAAAAT-CA-TA-TTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTG
* *
3046636 AAGTGTATTAATTTATGTGTTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGC
124 AAATTTATTAATTTATGTGTTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGC
* *
3046701 TCGTATTATTTTCCCGAATTTTATTACTTTTAATAAAAATATATTATTTTTGTATTTTATTATTT
189 TCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTT
*
3046766 TATATTATTTCAGTACATTTTGTATTAATTATTTCTGAATTTTT
254 TATATTATTTCAGTACATTTTGTATTAATTATTTCTAAATTTTT
*
3046810 AAAAAATTTAGTAAAACACTCTTACTTTGGCCCTTTGTTCGTATTTTTT-TCCGCATTTTATTAC
1 AAAAAATTTAGTAAAA-ACTCTTACTTCGG-CCTTTGTTCGTATTTTTTCTCCGCATTTTATTAC
*
3046874 TTTAAAAATATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
64 TTTAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
*
3046939 TATTAATTTAGTGTGTTTTTTAAATAAATTTTT-AAAAAAACCCTTATTCCTGCCCTTTGCTCGT
129 TATTAATTTA-TGTGTTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGT
* *
3047003 ATTATTTTCCCGAATTTTTTTTACTTTCAATAACAATATATTATTTTCGTATTTTATTATTTTAT
193 ATTATTTTCCCGAA-TTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTAT
3047068 ATTATTTCAGTACATTTTGTTTGAAATATTTGTATTAATTATTTCTAAATTTTT
257 ATTATTTCAGTAC------------AT-TTTGTATTAATTATTTCTAAATTTTT
*
3047122 AAAAAATTTAGTAAAAAATCTTACTTCGGCCTTTGTTCGTATTTTTTTCTCCGCATTTTATTACT
1 AAAAAATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTA-TTTTTTCTCCGCATTTTATTACT
3047187 TTAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
65 TTAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
3047252 ATTAATTTACTGTGTTTTTTAAATA
130 ATTAATTTA-TGTGTTTTTTAAATA
3047277 TACCATTTTT
Statistics
Matches: 423, Mismatches: 23, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
297 5 0.01
298 95 0.22
299 82 0.19
300 5 0.01
301 3 0.01
302 36 0.09
303 19 0.04
304 2 0.00
310 12 0.03
311 19 0.04
312 145 0.34
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (297 bp):
AAAAAATTTAGTAAAAACTCTTACTTCGGCCTTTGTTCGTATTTTTTCTCCGCATTTTATTACTT
TAAAAAAATCATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
TTAATTTATGTGTTTTTTAAATAAATTTTTAAAAAAAACCCTTATTCCTACCCTTTGCTCGTATT
ATTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATTATTTTATATTA
TTTCAGTACATTTTGTATTAATTATTTCTAAATTTTT
Found at i:3047226 original size:299 final size:287
Alignment explanation
Indices: 3046614--3047227 Score: 826
Period size: 299 Copynumber: 2.1 Consensus size: 287
3046604 TTATTTTACA
*
3046614 TTATT-TTATTACATTATGTTTGAAGTGTATTAATTTATGTGTTTTTTAAATAAATTTTTAAAAA
1 TTATTATT-TTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTTTAAAAA
*
3046678 AAACCCTTATTCCTACCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTTAATAAAAATAT
65 AAACCCTTATTCCTACCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAATAT
* *
3046743 ATTATTTTTGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAATTATTTCTGAATTT
130 ATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAATTATTTCTAAATTT
* *
3046808 TTAAAAAATTTAGTAAAACACTCTTACTTTGGCCCTTTGTTCGTATTTTTTTCCGCATTTTATTA
195 TTAAAAAATTTAGTAAAACAATCTTACTTCGGCCCTTTGTTCGTATTTTTTTCCGCATTTTATTA
*
3046873 CTTTAAAAATATCATATTTTCTAATTTTATTATT
260 CTTTAAAAAAATCATATTTTC-----TTA-TATT
*
3046907 TTACATTATTTTAGTACATTATGTTTGAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTTTT
1 TT--ATTA-TTT--TACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTTT
* *
3046972 -AAAAAAACCCTTATTCCTGCCCTTTGCTCGTATTATTTTCCCGAATTTTTTTTACTTTCAATAA
60 AAAAAAAACCCTTATTCCTACCCTTTGCTCGTATTATTTTCCCGAA-TTTTATTACTTTCAATAA
*
3047036 CAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTTTGAAATATTTGT
124 AAATATATTATTTTCGTATTTTATTATTTTATATTATTTCAGTAC------------AT-TTTGT
3047101 ATTAATTATTTCTAAATTTTTAAAAAATTTAGTAAAA-AATCTTACTTCGG-CCTTTGTTCGTAT
176 ATTAATTATTTCTAAATTTTTAAAAAATTTAGTAAAACAATCTTACTTCGGCCCTTTGTTCGTA-
3047164 TTTTTTCTCCGCATTTTATTACTTTAAAAAAATCATATTTTC-TA-ATT
240 TTTTTT-TCCGCATTTTATTACTTTAAAAAAATCATATTTTCTTATATT
3047211 TTATTATTTTACATTAT
1 TTATTATTTTACATTAT
3047228 TTTAGTACAT
Statistics
Matches: 287, Mismatches: 11, Indels: 40
0.85 0.03 0.12
Matches are distributed among these distances:
293 2 0.01
295 3 0.01
296 1 0.00
297 2 0.01
298 70 0.24
299 89 0.31
301 3 0.01
302 4 0.01
304 5 0.02
306 2 0.01
310 12 0.04
311 19 0.07
312 75 0.26
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.53
Consensus pattern (287 bp):
TTATTATTTTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTTTAAAAAA
AACCCTTATTCCTACCCTTTGCTCGTATTATTTTCCCGAATTTTATTACTTTCAATAAAAATATA
TTATTTTCGTATTTTATTATTTTATATTATTTCAGTACATTTTGTATTAATTATTTCTAAATTTT
TAAAAAATTTAGTAAAACAATCTTACTTCGGCCCTTTGTTCGTATTTTTTTCCGCATTTTATTAC
TTTAAAAAAATCATATTTTCTTATATT
Found at i:3047611 original size:42 final size:43
Alignment explanation
Indices: 3047565--3047668 Score: 122
Period size: 47 Copynumber: 2.4 Consensus size: 43
3047555 TTCCCACTTC
3047565 TTCTTCTTCTTTCTTTTT-TTTTTCTTCTCCGTTCCGTTCCTT
1 TTCTTCTTCTTTCTTTTTGTTTTTCTTCTCCGTTCCGTTCCTT
* * *
3047607 TTCTTTCCTTCTTTTTCTTTTTGTTTTTCTTCTCCTTTCCTTTTCTT
1 TTC-TT-CTTC--TTTCTTTTTGTTTTTCTTCTCCGTTCCGTTCCTT
*
3047654 TCCTTCTT-TTTCTTT
1 TTCTTCTTCTTTCTTT
3047669 CTTTCCTCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
42 10 0.19
43 2 0.04
44 4 0.08
45 3 0.06
46 11 0.21
47 23 0.43
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (43 bp):
TTCTTCTTCTTTCTTTTTGTTTTTCTTCTCCGTTCCGTTCCTT
Found at i:3047616 original size:10 final size:10
Alignment explanation
Indices: 3047601--3047675 Score: 50
Period size: 10 Copynumber: 7.5 Consensus size: 10
3047591 CTCCGTTCCG
3047601 TTCCTTTTCT
1 TTCCTTTTCT
3047611 TTCCTTCTT-T
1 TTCCTT-TTCT
* *
3047621 TTCTTTTTGTT
1 TTCCTTTT-CT
* *
3047632 TTTCTTCTCCT
1 TTCCTT-TTCT
3047643 TTCCTTTTCT
1 TTCCTTTTCT
3047653 TTCCTTCTT-T
1 TTCCTT-TTCT
3047663 TT-C-TTTCT
1 TTCCTTTTCT
3047671 TTCCT
1 TTCCT
3047676 CTCTGTTGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
7 2 0.04
8 4 0.08
9 4 0.08
10 24 0.48
11 15 0.30
12 1 0.02
ACGTcount: A:0.00, C:0.28, G:0.01, T:0.71
Consensus pattern (10 bp):
TTCCTTTTCT
Found at i:3047636 original size:47 final size:41
Alignment explanation
Indices: 3047567--3047668 Score: 141
Period size: 42 Copynumber: 2.3 Consensus size: 41
3047557 CCCACTTCTT
3047567 CTTCTTCTTTCTTTTTTTTTTCTTCTCCGTTCCGTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTTTTTTTTCTTCTCC--T---TTCCTTTTCTTTC
3047614 CTTCTTTTTCTTTTTGTTTTTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTTTCTTTTT-TTTTTCTTCTCCTTTCCTTTTCTTTC
3047656 CTTCTTTTTCTTT
1 CTTCTTTTTCTTT
3047669 CTTTCCTCTC
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
42 26 0.48
45 1 0.02
46 9 0.17
47 18 0.33
ACGTcount: A:0.00, C:0.27, G:0.03, T:0.70
Consensus pattern (41 bp):
CTTCTTTTTCTTTTTTTTTTCTTCTCCTTTCCTTTTCTTTC
Found at i:3047785 original size:24 final size:24
Alignment explanation
Indices: 3047752--3047800 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3047742 AGTGAGAGTC
*
3047752 GCCACGAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
3047776 GCCACCAATCCTTTTTATTTAGGT
1 GCCACCAATCCTTTTTATTTAGGT
3047800 G
1 G
3047801 TGATCGGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (24 bp):
GCCACCAATCCTTTTTATTTAGGT
Done.