Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 42 of 187
Found at i:12318530 original size:22 final size:21
Alignment explanation
Indices: 12318500--12318546 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
12318490 ATAGTTTGGC
12318500 AGAAAAATCCAAAAGAATGAA
1 AGAAAAATCCAAAAGAATGAA
**
12318521 AGAAGAAATCGTAAAGAATGAA
1 AGAA-AAATCCAAAAGAATGAA
12318543 AGAA
1 AGAA
12318547 CATTTGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.17
22 19 0.83
ACGTcount: A:0.64, C:0.06, G:0.19, T:0.11
Consensus pattern (21 bp):
AGAAAAATCCAAAAGAATGAA
Found at i:12322830 original size:3 final size:3
Alignment explanation
Indices: 12322822--12322857 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
12322812 GATGGTATTT
12322822 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
12322858 CAAAAATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12324139 original size:33 final size:33
Alignment explanation
Indices: 12324019--12324143 Score: 103
Period size: 33 Copynumber: 3.8 Consensus size: 33
12324009 CCAGTCATCC
* * *
12324019 CGGCTCGTATCCACC-TCAATACTCCACTCCT-T
1 CGGCCCGTATCCACCGTC-GTACTCCACTTCTCT
* * *
12324051 CTAGCCTGTATCCACTGTCGTACTCCACTTCTCT
1 C-GGCCCGTATCCACCGTCGTACTCCACTTCTCT
** *
12324085 CGGCCCGTATGTACCATCGTACTCCACTTCTC-
1 CGGCCCGTATCCACCGTCGTACTCCACTTCTCT
* *
12324117 CAGGCCCTTATCCACCGCCGTACTCCA
1 C-GGCCCGTATCCACCGTCGTACTCCA
12324144 TTACTTCCGG
Statistics
Matches: 72, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
32 2 0.03
33 66 0.92
34 4 0.06
ACGTcount: A:0.17, C:0.42, G:0.13, T:0.28
Consensus pattern (33 bp):
CGGCCCGTATCCACCGTCGTACTCCACTTCTCT
Found at i:12327348 original size:19 final size:19
Alignment explanation
Indices: 12327294--12327348 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 19
12327284 ATTCAAAAGC
* *
12327294 TAACAAAATTAATAAC--C
1 TAACAAAATTACTAACAAA
* **
12327311 TAACAAAATAACTTTCAAA
1 TAACAAAATTACTAACAAA
12327330 TAACAAAATTACTAACAAA
1 TAACAAAATTACTAACAAA
12327349 AGTCTCCATT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
17 12 0.43
19 16 0.57
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (19 bp):
TAACAAAATTACTAACAAA
Found at i:12328964 original size:16 final size:16
Alignment explanation
Indices: 12328945--12328977 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12328935 TAGTTTATGT
12328945 TTTTTTTTAACTTCAA
1 TTTTTTTTAACTTCAA
*
12328961 TTTTTTTTTACTTCAA
1 TTTTTTTTAACTTCAA
12328977 T
1 T
12328978 GAATGCAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTTTTAACTTCAA
Found at i:12328964 original size:17 final size:16
Alignment explanation
Indices: 12328944--12328977 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
12328934 TTAGTTTATG
12328944 TTTTTTTTTAACTTCAA
1 TTTTTTTTT-ACTTCAA
12328961 TTTTTTTTTACTTCAA
1 TTTTTTTTTACTTCAA
12328977 T
1 T
12328978 GAATGCAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTTTTTTACTTCAA
Found at i:12331240 original size:22 final size:22
Alignment explanation
Indices: 12331197--12331242 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
12331187 GTTTTTTTTT
* *
12331197 ATTTTTTTAAATTCGACCTTTA
1 ATTTTTTTAAATTCCACATTTA
12331219 ATTTATTTTAAATTCCA-ATTTA
1 ATTT-TTTTAAATTCCACATTTA
12331241 AT
1 AT
12331243 CCTTTTGAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.33, C:0.11, G:0.02, T:0.54
Consensus pattern (22 bp):
ATTTTTTTAAATTCCACATTTA
Found at i:12332205 original size:98 final size:98
Alignment explanation
Indices: 12332085--12332281 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
12332075 AAAAAAATCA
* * * *
12332085 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCGAGTTTGGAATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
12332150 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
12332183 TAAAAGAAATATTCCGAGTTTGGAATTCTAAAGGGATCGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCGAGTTTGGAATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
12332248 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
12332281 T
1 T
12332282 TTTTATTGTA
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (98 bp):
TAAAAGAAATATTCCGAGTTTGGAATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:12333472 original size:14 final size:14
Alignment explanation
Indices: 12333453--12333504 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
12333443 AGTTATGCCC
*
12333453 ATAAATTTTTATAA
1 ATAAATTATTATAA
12333467 ATAAATATATTATAA
1 ATAAAT-TATTATAA
* *
12333482 A-AAATTATAATAT
1 ATAAATTATTATAA
*
12333495 GTAAATTATT
1 ATAAATTATT
12333505 TTTTGTAAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 6 0.19
14 17 0.55
15 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (14 bp):
ATAAATTATTATAA
Found at i:12340384 original size:11 final size:12
Alignment explanation
Indices: 12340362--12340405 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
12340352 AACAAATCTT
12340362 CTCTCAAATTTC
1 CTCTCAAATTTC
12340374 CTCTC-AATTTC
1 CTCTCAAATTTC
12340385 CT-TCCAAATTT-
1 CTCT-CAAATTTC
12340396 CTCTCAAATT
1 CTCTCAAATT
12340406 CATATTTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 17 0.59
12 11 0.38
ACGTcount: A:0.25, C:0.32, G:0.00, T:0.43
Consensus pattern (12 bp):
CTCTCAAATTTC
Found at i:12342336 original size:18 final size:18
Alignment explanation
Indices: 12342309--12342348 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
12342299 CAGGTGCGTT
* *
12342309 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
12342327 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
12342345 TCCT
1 TCCT
12342349 TTTTCGAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.07, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:12342938 original size:21 final size:21
Alignment explanation
Indices: 12342914--12343263 Score: 223
Period size: 22 Copynumber: 16.4 Consensus size: 21
12342904 TAACCCTAAT
*
12342914 CCTAACACTTAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* *
12342935 CCTAACCCTTAAATTAAAAAT
1 CCTAACCCTTAACTTAAAAAC
* *
12342956 GCTAACCCTTAATTTAAAAACC
1 CCTAACCCTTAACTTAAAAA-C
* * *
12342978 CCAAACCCTAAACCTAAAAACC
1 CCTAACCCTTAACTTAAAAA-C
12343000 CACTAACCCTTAACTT-AAAAC
1 C-CTAACCCTTAACTTAAAAAC
* *
12343021 CCTCAAACCCTAAACCTAAAAAC
1 CCT--AACCCTTAACTTAAAAAC
*
12343044 CAC-AAACCTTAAACTTAAAAAC
1 C-CTAACCCTT-AACTTAAAAAC
* * *
12343066 CCCAAACCTTAAACCTAAAAAC
1 CCTAACCCTT-AACTTAAAAAC
* *
12343088 CATAAACCCTAAAC-TAAAAAC
1 CCT-AACCCTTAACTTAAAAAC
*
12343109 CCT-A-----AACCTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
12343124 CCTAACCCTTAACTTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* * * *
12343145 CTCAAACCGTAAACCTAAAAAC
1 C-CTAACCCTTAACTTAAAAAC
*
12343167 CATAACCCTTAACTTAAAAAAC
1 CCTAACCCTTAACTT-AAAAAC
* * * *
12343189 ACAAACCCTAAACCTAAAAAC
1 CCTAACCCTTAACTTAAAAAC
* * *
12343210 CATAAACACTAAACTTAAAAAC
1 CCT-AACCCTTAACTTAAAAAC
* * *
12343232 ACTAAACCCTAAACTTTAAAAC
1 CCT-AACCCTTAACTTAAAAAC
12343254 CCTAAACCCT
1 CCT-AACCCT
12343264 AAAACCTTAA
Statistics
Matches: 260, Mismatches: 50, Indels: 37
0.75 0.14 0.11
Matches are distributed among these distances:
14 3 0.01
15 10 0.04
16 1 0.00
19 1 0.00
20 2 0.01
21 79 0.30
22 141 0.54
23 22 0.08
24 1 0.00
ACGTcount: A:0.49, C:0.31, G:0.01, T:0.19
Consensus pattern (21 bp):
CCTAACCCTTAACTTAAAAAC
Found at i:12342967 original size:42 final size:43
Alignment explanation
Indices: 12342915--12343263 Score: 298
Period size: 43 Copynumber: 8.2 Consensus size: 43
12342905 AACCCTAATC
* * **
12342915 CTAACACTTAACTTAAAAACCCTAACCCTTAAA-TTAAAAA-TG
1 CTAACCCTTAACTTAAAAACCCTAACCC-TAAACCTAAAAACCA
* *
12342957 CTAACCCTTAATTTAAAAACCCCAAACCCTAAACCTAAAAACCCA
1 CTAACCCTTAACTTAAAAA-CCCTAACCCTAAACCTAAAAA-CCA
12343002 CTAACCCTTAACTT-AAAACCCTCAAACCCTAAACCTAAAAACCA
1 CTAACCCTTAACTTAAAAACCCT--AACCCTAAACCTAAAAACCA
* * *
12343046 C-AAACCTTAAACTTAAAAACCCCAAACCTTAAACCTAAAAACCA
1 CTAACCCTT-AACTTAAAAA-CCCTAACCCTAAACCTAAAAACCA
*
12343090 -TAAACCCTAAAC-T--AAA----AACCCTAAACCTAAAAACC-
1 CT-AACCCTTAACTTAAAAACCCTAACCCTAAACCTAAAAACCA
* *
12343125 CTAACCCTTAACTTAAAAACCTCAAACCGTAAACCTAAAAACCA
1 CTAACCCTTAACTTAAAAACC-CTAACCCTAAACCTAAAAACCA
* *
12343169 -TAACCCTTAACTTAAAAAACACAAACCCTAAACCTAAAAACCA
1 CTAACCCTTAACTT-AAAAACCCTAACCCTAAACCTAAAAACCA
* * * * *
12343212 -TAAACACTAAACTTAAAAACACTAAACCCTAAACTTTAAAACC-
1 CT-AACCCTTAACTTAAAAACCCT-AACCCTAAACCTAAAAACCA
12343255 CTAAACCCT
1 CT-AACCCT
12343264 AAAACCTTAA
Statistics
Matches: 258, Mismatches: 24, Indels: 48
0.78 0.07 0.15
Matches are distributed among these distances:
35 9 0.03
36 20 0.08
38 3 0.01
41 3 0.01
42 21 0.08
43 85 0.33
44 75 0.29
45 39 0.15
46 3 0.01
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.19
Consensus pattern (43 bp):
CTAACCCTTAACTTAAAAACCCTAACCCTAAACCTAAAAACCA
Found at i:12343059 original size:44 final size:42
Alignment explanation
Indices: 12342962--12343254 Score: 260
Period size: 44 Copynumber: 6.9 Consensus size: 42
12342952 AAATGCTAAC
* *
12342962 CCTTAATTTAAAAACCCCAAACCCTAAACCTAAAAACCCACTAAC
1 CCTTAACTT-AAAACCCCAAACCCTAAACCTAAAAA-CCAC-AAA
12343007 CCTTAACTTAAAACCCTCAAACCCTAAACCTAAAAACCACAAA
1 CCTTAACTTAAAACCC-CAAACCCTAAACCTAAAAACCACAAA
* *
12343050 CCTTAAACTTAAAAACCCCAAACCTTAAACCTAAAAACCATAAA
1 CCTT-AACTT-AAAACCCCAAACCCTAAACCTAAAAACCACAAA
* *
12343094 CCCTAAAC-T--AA----AAACCCTAAACCTAAAAACC-CTAAC
1 -CCTTAACTTAAAACCCCAAACCCTAAACCTAAAAACCAC-AAA
* * * *
12343130 CCTTAACTTAAAAACCTCAAACCGTAAACCTAAAAACCATAAC
1 CCTTAACTT-AAAACCCCAAACCCTAAACCTAAAAACCACAAA
* * *
12343173 CCTTAACTTAAAAAACACAAACCCTAAACCTAAAAACCATAAA
1 CCTTAACTT-AAAACCCCAAACCCTAAACCTAAAAACCACAAA
* * * * *
12343216 CACTAAACTTAAAAACACTAAACCCTAAACTTTAAAACC
1 C-CTTAACTT-AAAACCCCAAACCCTAAACCTAAAAACC
12343255 CTAAACCCTA
Statistics
Matches: 211, Mismatches: 22, Indels: 31
0.80 0.08 0.12
Matches are distributed among these distances:
35 6 0.03
36 22 0.10
39 2 0.01
40 2 0.01
43 69 0.33
44 73 0.35
45 37 0.18
ACGTcount: A:0.51, C:0.32, G:0.00, T:0.17
Consensus pattern (42 bp):
CCTTAACTTAAAACCCCAAACCCTAAACCTAAAAACCACAAA
Found at i:12343121 original size:15 final size:15
Alignment explanation
Indices: 12343047--12343128 Score: 73
Period size: 15 Copynumber: 5.6 Consensus size: 15
12343037 TAAAAACCAC
* *
12343047 AAACCTTAAACTTAA
1 AAACCCTAAACCTAA
* *
12343062 AAACCCCAAACCT-T
1 AAACCCTAAACCTAA
*
12343076 AAA-CCTAAAAACC-AT
1 AAACCCT--AAACCTAA
12343091 AAACCCTAAA-CTAA
1 AAACCCTAAACCTAA
12343105 AAACCCTAAACCTAA
1 AAACCCTAAACCTAA
12343120 AAACCCTAA
1 AAACCCTAA
12343129 CCCTTAACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
13 3 0.05
14 17 0.31
15 32 0.58
16 3 0.05
ACGTcount: A:0.54, C:0.30, G:0.00, T:0.16
Consensus pattern (15 bp):
AAACCCTAAACCTAA
Found at i:12343253 original size:15 final size:15
Alignment explanation
Indices: 12343235--12343287 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
12343225 TAAAAACACT
12343235 AAACCCTAAACTTTA
1 AAACCCTAAACTTTA
**
12343250 AAACCCTAAACCCTA
1 AAACCCTAAACTTTA
*
12343265 AAA-CCTTAACTTTA
1 AAACCCTAAACTTTA
12343279 AAACCCTAA
1 AAACCCTAA
12343288 CCCTTAAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (15 bp):
AAACCCTAAACTTTA
Found at i:12343260 original size:29 final size:29
Alignment explanation
Indices: 12343228--12343287 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
12343218 CTAAACTTAA
*
12343228 AAACACTAAACCCTAAACTTTAAAACCCT
1 AAACACTAAAACCTAAACTTTAAAACCCT
* *
12343257 AAACCCTAAAACCTTAACTTTAAAACCCT
1 AAACACTAAAACCTAAACTTTAAAACCCT
12343286 AA
1 AA
12343288 CCCTTAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (29 bp):
AAACACTAAAACCTAAACTTTAAAACCCT
Found at i:12346544 original size:126 final size:124
Alignment explanation
Indices: 12346260--12346823 Score: 718
Period size: 125 Copynumber: 4.5 Consensus size: 124
12346250 AAACATGCTC
* * *
12346260 CTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTTTTCTCATAAAACATCCTGGTAG
1 CTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAG
*
12346325 AAGCGATTTTATACTATTTGCTCAAAAACGTCAACTCGAAATTATTTCTTCCAGGACCAA
66 AAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCAA
* * * *
12346385 CTGTAGCAAAAGCGCGTCCACGAGGACGCGATTTCAGAAATTCTTCTCA-AATAGCATCCTGCTT
1 CTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCTA
** * * * * *
12346449 GAAGCTTTTTTTTATGCTATTTGCTCAGAAACGTCTACTCGAAATAATTTTTTCAGGACCTA
65 GAAGC--GATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAA
*
12346511 CTGCAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTAG-TA
1 CTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCT-GCTA
* * *
12346575 GAAGCGATTTTATACTATTTGCTTAGAAACGTCAACTCAAAATTATTTCTTCTAGGACCAA
65 GAAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCAA
* * * * * * *
12346636 CTGTAGCAAAAGCGCGTCCAGGAGGGCACGATTTCACAAATTCTTCACATATAGTATCCTGCTTG
1 CTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAG
* *
12346701 AAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTA
66 AAGCG-ATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAA
* * * * * * * * *
12346761 CTATAGCAAAAGCGCGTACACGTGGGCGTGACTGCAAAAATCCTTCTGATAAATCATCCTGCT
1 CTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCT
12346824 TTGATTTTAT
Statistics
Matches: 373, Mismatches: 58, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
124 39 0.10
125 186 0.50
126 108 0.29
127 40 0.11
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (124 bp):
CTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTAG
AAGCGATTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCAA
Found at i:12351716 original size:31 final size:30
Alignment explanation
Indices: 12351663--12351909 Score: 142
Period size: 31 Copynumber: 8.0 Consensus size: 30
12351653 ATGTCATTAG
* * *
12351663 GTTT-TAATTATAGCAGGCACTATATGCCGGA
1 GTTTATAATT-TATCAGGTACTATGTGCC-GA
* *
12351694 GTTTATAATTTATCAGATACTATGTACCGA
1 GTTTATAATTTATCAGGTACTATGTGCCGA
* * *
12351724 TGTTTAT-ATTGTATCAGGCACTATGTGTCAGT
1 -GTTTATAATT-TATCAGGTACTATGTG-CCGA
* *
12351756 GTTTATAATTTATCAGGTACTATGTACCAA
1 GTTTATAATTTATCAGGTACTATGTGCCGA
* * * * ***
12351786 TATTTAT-ATTGTATTAAGCACTATGTGGTAA
1 -GTTTATAATT-TATCAGGTACTATGTGCCGA
* * * *
12351817 TGTTTATAGTTTATCACGTACTATGTACCAGT
1 -GTTTATAATTTATCAGGTACTATGTGCC-GA
* * *
12351849 GTTTAT-ATTGTATCAGGCACTATATGCCAGT
1 GTTTATAATT-TATCAGGTACTATGTGCC-GA
*
12351880 GTTTATAATTTATCAGGTACTATGTACCGA
1 GTTTATAATTTATCAGGTACTATGTGCCGA
12351910 TGATGGATAC
Statistics
Matches: 164, Mismatches: 41, Indels: 23
0.72 0.18 0.10
Matches are distributed among these distances:
30 12 0.07
31 137 0.84
32 15 0.09
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (30 bp):
GTTTATAATTTATCAGGTACTATGTGCCGA
Found at i:12351762 original size:62 final size:62
Alignment explanation
Indices: 12351676--12351911 Score: 321
Period size: 62 Copynumber: 3.8 Consensus size: 62
12351666 TTAATTATAG
* * *
12351676 CAGGCACTATATGCCGGAGTTTATAATTTATCAGATACTATGTACCGATGTTTATATTGTAT
1 CAGGCACTATATGCCAGTGTTTATAATTTATCAGGTACTATGTACCGATGTTTATATTGTAT
* * * *
12351738 CAGGCACTATGTGTCAGTGTTTATAATTTATCAGGTACTATGTACCAATATTTATATTGTAT
1 CAGGCACTATATGCCAGTGTTTATAATTTATCAGGTACTATGTACCGATGTTTATATTGTAT
* * * ** * * *
12351800 TAAGCACTATGTGGTAATGTTTATAGTTTATCACGTACTATGTACC-AGTGTTTATATTGTAT
1 CAGGCACTATATGCCAGTGTTTATAATTTATCAGGTACTATGTACCGA-TGTTTATATTGTAT
12351862 CAGGCACTATATGCCAGTGTTTATAATTTATCAGGTACTATGTACCGATG
1 CAGGCACTATATGCCAGTGTTTATAATTTATCAGGTACTATGTACCGATG
12351912 ATGGATACCT
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
61 1 0.01
62 147 0.99
63 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (62 bp):
CAGGCACTATATGCCAGTGTTTATAATTTATCAGGTACTATGTACCGATGTTTATATTGTAT
Found at i:12352680 original size:10 final size:10
Alignment explanation
Indices: 12352657--12352694 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
12352647 TCTTGGTTTA
12352657 ATGATGTT-G
1 ATGATGTTGG
12352666 ATGATGTTGG
1 ATGATGTTGG
12352676 ATGATGTTGG
1 ATGATGTTGG
12352686 ATGAT-TTGG
1 ATGATGTTGG
12352695 TATTATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (10 bp):
ATGATGTTGG
Found at i:12352681 original size:19 final size:19
Alignment explanation
Indices: 12352657--12352694 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
12352647 TCTTGGTTTA
12352657 ATGATGTT-GATGATGTTGG
1 ATGATGTTGGATGAT-TTGG
12352676 ATGATGTTGGATGATTTGG
1 ATGATGTTGGATGATTTGG
12352695 TATTATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (19 bp):
ATGATGTTGGATGATTTGG
Found at i:12356312 original size:19 final size:19
Alignment explanation
Indices: 12356290--12356329 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
12356280 GAACCCCAAC
12356290 TTGTACAAAGAAGAAATCT
1 TTGTACAAAGAAGAAATCT
12356309 TTGTACAAAGAAGAAATCT
1 TTGTACAAAGAAGAAATCT
12356328 TT
1 TT
12356330 CTTGCAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (19 bp):
TTGTACAAAGAAGAAATCT
Found at i:12370374 original size:39 final size:39
Alignment explanation
Indices: 12370317--12370407 Score: 146
Period size: 39 Copynumber: 2.3 Consensus size: 39
12370307 ATTATTCTAC
* * *
12370317 AAGTTTTGTATTAGCAAAGCTCCCCCGAGAGCTAAGGAT
1 AAGTTGTGTATCAACAAAGCTCCCCCGAGAGCTAAGGAT
*
12370356 AAGTTGTGTATCAACAAAGCTCCCCCGAGAGCTAAGGGT
1 AAGTTGTGTATCAACAAAGCTCCCCCGAGAGCTAAGGAT
12370395 AAGTTGTGTATCA
1 AAGTTGTGTATCA
12370408 GTGAAGTTCC
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 48 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (39 bp):
AAGTTGTGTATCAACAAAGCTCCCCCGAGAGCTAAGGAT
Found at i:12370995 original size:22 final size:23
Alignment explanation
Indices: 12370964--12371007 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
12370954 CCAGGTTAGA
12370964 TAAGACAATTAAAATA-AATAAG
1 TAAGACAATTAAAATAGAATAAG
* *
12370986 TAAGATAATTAAATTAGAATAA
1 TAAGACAATTAAAATAGAATAA
12371008 TAAATCTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.27
Consensus pattern (23 bp):
TAAGACAATTAAAATAGAATAAG
Found at i:12374695 original size:20 final size:20
Alignment explanation
Indices: 12374666--12374706 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12374656 ACTCACAGGA
*
12374666 TTTTTTTATTTT-TTCTTTTC
1 TTTTTGTATTTTCTT-TTTTC
12374686 TTTTTGTATTTTCTTTTTTC
1 TTTTTGTATTTTCTTTTTTC
12374706 T
1 T
12374707 GTACCTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.05, C:0.10, G:0.02, T:0.83
Consensus pattern (20 bp):
TTTTTGTATTTTCTTTTTTC
Found at i:12374794 original size:20 final size:20
Alignment explanation
Indices: 12374769--12374837 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 20
12374759 AATTCCATAA
12374769 ATCAATATATAAAATTTCAG
1 ATCAATATATAAAATTTCAG
**
12374789 ATCAAT-TGA-AAAGCATTTACCC
1 ATCAATAT-ATAAA--ATTT-CAG
12374811 ACTCAATATATAAAATTTCAG
1 A-TCAATATATAAAATTTCAG
12374832 ATCAAT
1 ATCAAT
12374838 TCCAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 4 0.11
20 12 0.32
21 6 0.16
22 6 0.16
23 6 0.16
24 4 0.11
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (20 bp):
ATCAATATATAAAATTTCAG
Found at i:12383102 original size:48 final size:48
Alignment explanation
Indices: 12383044--12383138 Score: 145
Period size: 48 Copynumber: 2.0 Consensus size: 48
12383034 TTCTTTGCTC
* * **
12383044 AAAAATGCCTAAGTCAGCCTAACTTGCAGTAATAAAGGATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAGT
*
12383092 AAAAACGCCTAAGTCAGCTTAACTCGCAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAG
12383139 AATTCCCTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.43, C:0.21, G:0.16, T:0.20
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGGATTCAACAGT
Found at i:12383476 original size:35 final size:36
Alignment explanation
Indices: 12383436--12383507 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
12383426 TCTAGGATCA
12383436 CATATC-TCAAAAGATCACCTTCCATATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
* *
12383471 CATATCTTCAAAAGATCACTTTCCTTATTTGCCAAG
1 CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
12383507 C
1 C
12383508 TCCGGAGATG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 6 0.18
36 28 0.82
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (36 bp):
CATATCTTCAAAAGATCACCTTCCATATTTGCCAAG
Found at i:12388288 original size:48 final size:48
Alignment explanation
Indices: 12388230--12388324 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
12388220 TTCTTTGCTC
* **
12388230 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGAATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGAATTCAACAGT
* * *
12388278 AAAAATGCCTAAGTCAGCTTAACTCGCAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGAATTCAACAG
12388325 AATTCCCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGAATTCAACAGT
Found at i:12388570 original size:48 final size:48
Alignment explanation
Indices: 12388512--12388606 Score: 136
Period size: 48 Copynumber: 2.0 Consensus size: 48
12388502 TTCTTTGCTC
* **
12388512 AAAAACGCCTAAGTCAGCCTAACTTGCAGTAATAAAGAATTCAACAGT
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGAATTCAACAGT
* * *
12388560 AAAAATGCCTAAGTCAGCTTAACTCGCAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGAATTCAACAG
12388607 AATTCCCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.44, C:0.21, G:0.15, T:0.20
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTCGCAACAATAAAGAATTCAACAGT
Found at i:12388683 original size:282 final size:282
Alignment explanation
Indices: 12388172--12388730 Score: 1109
Period size: 282 Copynumber: 2.0 Consensus size: 282
12388162 GGATACCAAC
12388172 TGTCACAGACTTAGAGTTTTCTCACGGATCCGTGCAGCCTTAGGCAGTTTCTTTGCTCAAAAACG
1 TGTCACAGACTTAGAGTTTTCTCACGGATCCGTGCAGCCTTAGGCAGTTTCTTTGCTCAAAAACG
12388237 CCTAAGTCAGCCTAACTTGCAGTAATAAAGAATTCAACAGTAAAAATGCCTAAGTCAGCTTAACT
66 CCTAAGTCAGCCTAACTTGCAGTAATAAAGAATTCAACAGTAAAAATGCCTAAGTCAGCTTAACT
12388302 CGCAACAATAAAGGATTCAACAGAATTCCCTTAAGGTTTCCACGAAGAACAACAGAAGAACAAAG
131 CGCAACAATAAAGGATTCAACAGAATTCCCTTAAGGTTTCCACGAAGAACAACAGAAGAACAAAG
12388367 TAAGAACGAGCCTTGAAATATGAACAAAAGCAATAACACTTGAGAGAAAAGTTTGAGTGAATACT
196 TAAGAACGAGCCTTGAAATATGAACAAAAGCAATAACACTTGAGAGAAAAGTTTGAGTGAATACT
12388432 CTCAAAATTCTTATTAACATAG
261 CTCAAAATTCTTATTAACATAG
*
12388454 TGTCACGGACTTAGAGTTTTCTCACGGATCCGTGCAGCCTTAGGCAGTTTCTTTGCTCAAAAACG
1 TGTCACAGACTTAGAGTTTTCTCACGGATCCGTGCAGCCTTAGGCAGTTTCTTTGCTCAAAAACG
12388519 CCTAAGTCAGCCTAACTTGCAGTAATAAAGAATTCAACAGTAAAAATGCCTAAGTCAGCTTAACT
66 CCTAAGTCAGCCTAACTTGCAGTAATAAAGAATTCAACAGTAAAAATGCCTAAGTCAGCTTAACT
12388584 CGCAACAATAAAGGATTCAACAGAATTCCCTTAAGGTTTCCACGAAGAACAACAGAAGAACAAAG
131 CGCAACAATAAAGGATTCAACAGAATTCCCTTAAGGTTTCCACGAAGAACAACAGAAGAACAAAG
12388649 TAAGAACGAGCCTTGAAATATGAACAAAAGCAATAACACTTGAGAGAAAAGTTTGAGTGAATACT
196 TAAGAACGAGCCTTGAAATATGAACAAAAGCAATAACACTTGAGAGAAAAGTTTGAGTGAATACT
12388714 CTCAAAATTCTTATTAA
261 CTCAAAATTCTTATTAA
12388731 TAACTGAATG
Statistics
Matches: 276, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
282 276 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (282 bp):
TGTCACAGACTTAGAGTTTTCTCACGGATCCGTGCAGCCTTAGGCAGTTTCTTTGCTCAAAAACG
CCTAAGTCAGCCTAACTTGCAGTAATAAAGAATTCAACAGTAAAAATGCCTAAGTCAGCTTAACT
CGCAACAATAAAGGATTCAACAGAATTCCCTTAAGGTTTCCACGAAGAACAACAGAAGAACAAAG
TAAGAACGAGCCTTGAAATATGAACAAAAGCAATAACACTTGAGAGAAAAGTTTGAGTGAATACT
CTCAAAATTCTTATTAACATAG
Found at i:12391163 original size:37 final size:37
Alignment explanation
Indices: 12391094--12391164 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 37
12391084 TTTAAGTTAC
* **
12391094 AAGTATATGGTTATTTGATATGTGAATGAAAATGAGT
1 AAGTATATGGTTATTTGATATATGAACAAAAATGAGT
* *
12391131 AAGTGTATGGTTATTTGATATATGTACAAAAATG
1 AAGTATATGGTTATTTGATATATGAACAAAAATG
12391165 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.38, C:0.01, G:0.23, T:0.38
Consensus pattern (37 bp):
AAGTATATGGTTATTTGATATATGAACAAAAATGAGT
Found at i:12399481 original size:43 final size:42
Alignment explanation
Indices: 12399378--12399573 Score: 211
Period size: 43 Copynumber: 4.6 Consensus size: 42
12399368 ATCCGTTACT
* **
12399378 CGGTGGATTCAGCACTTAGCAACCACC-TTA-AATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTACAA-TCAAAGATA
12399420 CGG-GGAATCAGCACTTAGCAACCCCTTTCACAATCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAAGATA
* * **
12399462 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTACAATCAAAGATA
* * *
12399505 CAG-GGAATCAACACATAGCAACCCCTTTCACAATCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTT-ACAATCAAAGATA
* *
12399547 TGGTGGACTCAGCACTTAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCCCT
12399574 CGGGGAATCT
Statistics
Matches: 128, Mismatches: 19, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
40 2 0.02
41 26 0.20
42 42 0.33
43 53 0.41
44 5 0.04
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.22
Consensus pattern (42 bp):
CGGTGGAATCAGCACTTAGCAACCCCTTTACAATCAAAGATA
Found at i:12399527 original size:85 final size:84
Alignment explanation
Indices: 12399378--12399570 Score: 314
Period size: 85 Copynumber: 2.3 Consensus size: 84
12399368 ATCCGTTACT
* * * *
12399378 CGGTGGATTCAGCACTTAGCAACCACCTTAAATTCAGTGATACGGGGAATCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACAGGGAATCAACACATAGCAACC
12399443 CCTTTCACAATCAAAGATA
66 CCTTTCACAATCAAAGATA
*
12399462 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACAGGGAATCAACACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACC-TTAAATTCAGTGATACAGGGAATCAACACATAGCAAC
12399527 CCCTTTCACAATCAAAGATA
65 CCCTTTCACAATCAAAGATA
* *
12399547 TGGTGGACTCAGCACTTAGCAACC
1 CGGTGGAATCAGCACTTAGCAACC
12399571 CCTCGGGGAA
Statistics
Matches: 101, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
84 26 0.26
85 75 0.74
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTAAATTCAGTGATACAGGGAATCAACACATAGCAACC
CCTTTCACAATCAAAGATA
Found at i:12403241 original size:16 final size:16
Alignment explanation
Indices: 12403201--12403245 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
12403191 ATTTTGAATC
*
12403201 TTTCTTTTGCTTCTGT
1 TTTCTTTTTCTTCTGT
* *
12403217 TTTCTTTTTCTTGTTT
1 TTTCTTTTTCTTCTGT
12403233 TTTCTTTTT-TTCT
1 TTTCTTTTTCTTCT
12403246 TTCAGTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.00, C:0.16, G:0.07, T:0.78
Consensus pattern (16 bp):
TTTCTTTTTCTTCTGT
Found at i:12403893 original size:3 final size:3
Alignment explanation
Indices: 12403875--12404001 Score: 57
Period size: 3 Copynumber: 42.3 Consensus size: 3
12403865 TTTTTTTAAT
* * * * * *
12403875 TTA TTA ATA CTA TTA TTA TTA TTA TTA CTA TTA TTA TAA GTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
12403923 TCGTA TTA GT- TTA TTT TTT TTA -CA TTA TT- TTA TT- TTA TTA TGTA
1 T--TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* * *
12403967 TTA TTA TT- TTAA TTC TTT TTA TCA TGTA TTA TTA T
1 TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA TTA T
12404002 CTAATTACAT
Statistics
Matches: 92, Mismatches: 22, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
2 8 0.09
3 74 0.80
4 7 0.08
5 3 0.03
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:12410122 original size:10 final size:10
Alignment explanation
Indices: 12410107--12410131 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
12410097 GGGTATTGGT
12410107 TGATCCAATC
1 TGATCCAATC
12410117 TGATCCAATC
1 TGATCCAATC
12410127 TGATC
1 TGATC
12410132 AGAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (10 bp):
TGATCCAATC
Found at i:12411994 original size:88 final size:88
Alignment explanation
Indices: 12411836--12413137 Score: 1496
Period size: 88 Copynumber: 14.8 Consensus size: 88
12411826 AATCACTTGT
* ** * * *
12411836 CTTGCCTCCCTAGGTTATAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACT-GACA
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAG-CA
*
12411900 GCGAAGCAGATCGAAGACACCAGT
65 GCGAAGCAGATCGAAGACACCAGC
* * * * * *
12411924 CTTGCCTCCCTAGGTTGTAGCGGAGCAGGTTGAAAATAGCAGATCTTGTCTTCTTGTACCAGCAG
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
* *
12411989 TGAAGCAGATCGAAGACACAAGC
66 CGAAGCAGATCGAAGACACCAGC
* * * * * * *
12412012 CTTGCCTCCCTGGGTTGTAGTGGAGCAGACT-AAAGATAGCAGATCTTGTCATCCTATAC-CGAC
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAA-ATAGCAGATCTTGCCTTCCTGTACTAG-C
**
12412075 AATGAAGCAGATCGAAGACACCAGC
64 AGCGAAGCAGATCGAAGACACCAGC
** * * ** * * * *
12412100 CTTGCCTCCCT-GACTGTAGTGGAGCAAACTGAAGATAACAGATCTTGCCTTCTTGT-GTAGGCA
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTA-GCA
**
12412163 GCGAAGCATTTCGAAGACACCAGC
65 GCGAAGCAGATCGAAGACACCAGC
* * * * * *
12412187 CTTGCCTCCCTAGGTTGCAGCGGAACAGGTTGAGAATAGCAGATCTTGTCTTCCTGTAC-CGACA
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAG-CA
12412251 GCGAAGCAGATCGAAGACACCAGC
65 GCGAAGCAGATCGAAGACACCAGC
* * * * * * * * * * *
12412275 CTTGTCTCTCTGGGTTGCAGTGGAGTAGACTGAAGATAGAAGATCTTGTCTTCCAGTACAAACAG
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
*
12412340 CGAAGCAGATCGAAGACACAAGC
66 CGAAGCAGATCGAAGACACCAGC
* ** * * *
12412363 CTTGCCTCCCTGGGTTACAGTAGAGCAGCCT-AAAGATAGCAGATTTTGCCTTCCTGTACCAGCA
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAA-ATAGCAGATCTTGCCTTCCTGTACTAGCA
* *
12412427 GTGAAGCAGATCGAAGACACCGGC
65 GCGAAGCAGATCGAAGACACCAGC
* * *
12412451 CTTGCCTCCCTGGGTTGC-GACGGAACAGGTTGAAAATAGCAGATCTTGTCTTCCTGTACTAGCA
1 CTTGCCTCCCTGGGTTGCAG-CGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCA
12412515 GCGAAGCAGATCGAAGACACCAGC
65 GCGAAGCAGATCGAAGACACCAGC
* * * *
12412539 CTTG----CCTGGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTATACTGGCAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
*
12412600 CGAAGCAGATCAAAGACACCAGC
66 CGAAGCAGATCGAAGACACCAGC
* * * * *
12412623 CTTGCCTCCCTGGGTCGCAGTGGAGCAGACTGAAAATAGTAGATCTTTCCTTCCTGTACTAGCAG
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
*
12412688 CGAAGCAAATCGAAGACACCAGC
66 CGAAGCAGATCGAAGACACCAGC
* * *
12412711 CTTGCCTCCCTGGGTTGCAGCGGAACAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAA
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
*
12412776 CGAAGCAAATCGAAGACACCAGC
66 CGAAGCAGATCGAAGACACCAGC
* * * * *
12412799 CTTGCCTCCCTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCTTGTACTGGCAT
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
12412864 CGAAGCAGATCGAAGACACCAGC
66 CGAAGCAGATCGAAGACACCAGC
* * * * *
12412887 CTTGCCTCCCTGGGTTGCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGGCAG
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
*
12412952 CGAAGCAGATCAAAGACACCAGC
66 CGAAGCAGATCGAAGACACCAGC
* * *
12412975 CTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTGAAAATAGCAGATCTTGCCTTCTTGTACT-GACA
1 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAG-CA
*
12413039 GCGAAGCAGGTCGAAGACACCAGC
65 GCGAAGCAGATCGAAGACACCAGC
* * * * * * * *
12413063 CTTGCCTCTCTAGGTTTGCAGCGAAGCAGACTAAAAACAGCAAATCTTGCCTTCCTGTACTGGCA
1 CTTGCCTCCCT-GGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCA
*
12413128 GCGCAGCAGA
65 GCGAAGCAGA
12413138 ATGAAATAAC
Statistics
Matches: 1037, Mismatches: 156, Indels: 41
0.84 0.13 0.03
Matches are distributed among these distances:
84 76 0.07
85 1 0.00
87 75 0.07
88 830 0.80
89 54 0.05
90 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (88 bp):
CTTGCCTCCCTGGGTTGCAGCGGAGCAGGCTGAAAATAGCAGATCTTGCCTTCCTGTACTAGCAG
CGAAGCAGATCGAAGACACCAGC
Found at i:12412532 original size:264 final size:264
Alignment explanation
Indices: 12411836--12413124 Score: 1679
Period size: 264 Copynumber: 4.9 Consensus size: 264
12411826 AATCACTTGT
* *
12411836 CTTGCCTCCCTAGGTTATAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACT-GACA
1 CTTGCCTCCCTGGGTTACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAG-CA
* * * *
12411900 GCGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTAGGTTGTAGCGGAGCAGGTTGAAAATAGCA
65 GCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAACAGGTTGAAAATAGCA
* * * * *
12411965 GATCTTGTCTTCTTGTACCAGCAGTGAAGCAGATCGAAGACACAAGCCTTGCCTCCCTGGGTTGT
130 GATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGC
* * * *
12412030 AGTGGAGCAGACT-AAAGATAGCAGATCTTGTCATCCTATACCGACAAT-GAAGCAGATCGAAGA
195 AGCGGAGCAGACTGAAA-ATAGCAGATCTTGCCTTCCTATACTGAC-ATCGAAGCAGATCGAAGA
12412093 CACCAGC
258 CACCAGC
** * * * *
12412100 CTTGCCTCCCTGACTGT--AGTGGAGCAAACTGAAGATAACAGATCTTGCCTTCTTGT-GTAGGC
1 CTTGCCTCCCTGGGT-TACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTA-GC
** * *
12412162 AGCGAAGCATTTCGAAGACACCAGCCTTGCCTCCCTAGGTTGCAGCGGAACAGGTTGAGAATAGC
64 AGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAACAGGTTGAAAATAGC
* * *
12412227 AGATCTTGTCTTCCTGTAC-CGACAGCGAAGCAGATCGAAGACACCAGCCTTGTCTCTCTGGGTT
129 AGATCTTGTCTTCCTGTACTAG-CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * * * * ** *
12412291 GCAGTGGAGTAGACTGAAGATAGAAGATCTTGTCTTCC-AGTACAAACAGCGAAGCAGATCGAAG
193 GCAGCGGAGCAGACTGAAAATAGCAGATCTTGCCTTCCTA-TACTGACATCGAAGCAGATCGAAG
*
12412355 ACACAAGC
257 ACACCAGC
* * * * *
12412363 CTTGCCTCCCTGGGTTACAGTAGAGCAGCCTAAAGATAGCAGATTTTGCCTTCCTGTACCAGCAG
1 CTTGCCTCCCTGGGTTACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAGCAG
* *
12412428 TGAAGCAGATCGAAGACACCGGCCTTGCCTCCCTGGGTTGC-GACGGAACAGGTTGAAAATAGCA
66 CGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAG-CGGAACAGGTTGAAAATAGCA
12412492 GATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACCAGCCTTG----CCTGGGTTGC
130 GATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGC
** * *
12412553 AGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTATACTGGCATCGAAGCAGATCAAAGACA
195 AGCGGAGCAGACTGAAAATAGCAGATCTTGCCTTCCTATACTGACATCGAAGCAGATCGAAGACA
12412618 CCAGC
260 CCAGC
** * * *
12412623 CTTGCCTCCCTGGGTCGCAGTGGAGCAGACTGAAAATAGTAGATCTTTCCTTCCTGTACTAGCAG
1 CTTGCCTCCCTGGGTTACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAGCAG
*
12412688 CGAAGCAAATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAACAGGTTGAAAATAGCAG
66 CGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAACAGGTTGAAAATAGCAG
* * * *
12412753 ATCTTGCCTTCCTGTACTAGCAACGAAGCAAATCGAAGACACCAGCCTTGCCTCCCTAGGTTGCA
131 ATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
** * * *
12412818 GCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCTTGTACTGGCATCGAAGCAGATCGAAGACAC
196 GCGGAGCAGACTGAAAATAGCAGATCTTGCCTTCCTATACTGACATCGAAGCAGATCGAAGACAC
12412883 CAGC
261 CAGC
* * *
12412887 CTTGCCTCCCTGGGTTGCAGTGGAGTAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTGGCAG
1 CTTGCCTCCCTGGGTTACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAGCAG
* * *
12412952 CGAAGCAGATCAAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTGAAAATAGCAG
66 CGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAACAGGTTGAAAATAGCAG
* * * * *
12413017 ATCTTGCCTTCTTGTACT-GACAGCGAAGCAGGTCGAAGACACCAGCCTTGCCTCTCTAGGTTTG
131 ATCTTGTCTTCCTGTACTAG-CAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCT-GGGTTG
* * * * *
12413081 CAGCGAAGCAGACTAAAAACAGCAAATCTTGCCTTCCTGTACTG
194 CAGCGGAGCAGACTGAAAATAGCAGATCTTGCCTTCCTATACTG
12413125 GCAGCGCAGC
Statistics
Matches: 901, Mismatches: 104, Indels: 39
0.86 0.10 0.04
Matches are distributed among these distances:
260 226 0.25
261 2 0.00
262 5 0.01
263 223 0.25
264 401 0.45
265 44 0.05
ACGTcount: A:0.27, C:0.26, G:0.25, T:0.22
Consensus pattern (264 bp):
CTTGCCTCCCTGGGTTACAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACTAGCAG
CGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCGGAACAGGTTGAAAATAGCAG
ATCTTGTCTTCCTGTACTAGCAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
GCGGAGCAGACTGAAAATAGCAGATCTTGCCTTCCTATACTGACATCGAAGCAGATCGAAGACAC
CAGC
Found at i:12413271 original size:50 final size:50
Alignment explanation
Indices: 12413179--12413273 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
12413169 GTATTGGAAT
*
12413179 AGATTGAAGCTACAACAGCGAATCTCACTCCCACGACATTGCAGTTAAAC
1 AGATTGAAGCTACAACAGCAAATCTCACTCCCACGACATTGCAGTTAAAC
*
12413229 AGATTGAAGCTACAACAGCAAATC-CTATCTCCC-CGACCTTGCAGT
1 AGATTGAAGCTACAACAGCAAATCTC-A-CTCCCACGACATTGCAGT
12413274 GGAATGGATC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
49 1 0.02
50 35 0.85
51 5 0.12
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (50 bp):
AGATTGAAGCTACAACAGCAAATCTCACTCCCACGACATTGCAGTTAAAC
Found at i:12416133 original size:43 final size:42
Alignment explanation
Indices: 12416076--12416236 Score: 173
Period size: 43 Copynumber: 3.8 Consensus size: 42
12416066 TAAATTCAGT
12416076 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATTAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATTAAA
* * ** **
12416118 GATACGGTGGAATCAGCACCTAGCAACAACCTTT-A-TGTTCAGT
1 GATACGG-GGAATCAGCACATAGCAAC-CCCTTTCACAATT-AAA
*
12416161 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATCAAA
1 GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATTAAA
* * *
12416203 GAAACGGTGGAATCAACACTTAGCAACCACCTTT
1 GATACGG-GGAATCAGCACATAGCAACC-CCTTT
12416237 AGAGTTAATA
Statistics
Matches: 96, Mismatches: 16, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
41 5 0.05
42 35 0.36
43 46 0.48
44 10 0.10
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.20
Consensus pattern (42 bp):
GATACGGGGAATCAGCACATAGCAACCCCTTTCACAATTAAA
Found at i:12416181 original size:85 final size:85
Alignment explanation
Indices: 12416039--12416237 Score: 319
Period size: 85 Copynumber: 2.4 Consensus size: 85
12416029 TCCGTTACTT
*
12416039 GGTGGATTCAACACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
1 GGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
* *
12416103 CCTTTCACAATTAAAGATAC
66 CCTTTCACAATCAAAGAAAC
* * * **
12416123 GGTGGAATCAGCACCTAGCAACAACCTTTATGTTCAGTGATACGGGGAATCAGCACATAGCAACC
1 GGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
12416188 CCTTTCACAATCAAAGAAAC
66 CCTTTCACAATCAAAGAAAC
12416208 GGTGGAATCAACACTTAGCAACCACCTTTA
1 GGTGGAATCAACACTTAGCAACCACCTTTA
12416238 GAGTTAATAA
Statistics
Matches: 103, Mismatches: 11, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
84 22 0.21
85 81 0.79
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (85 bp):
GGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
CCTTTCACAATCAAAGAAAC
Found at i:12416258 original size:85 final size:85
Alignment explanation
Indices: 12416039--12416275 Score: 253
Period size: 85 Copynumber: 2.8 Consensus size: 85
12416029 TCCGTTACTT
* * * * * * ***
12416039 GGTGGATTCAACACTTAGCAACCACC-TTAAATTCAGTGATACGGGGAATCAGCACATAGCAACC
1 GGTGGAATCAACACCTAGCAACAACCTTTAAGTTCAATAATACAAAGAATCAGCACATAGCAACC
* *
12416103 CCTTTCACAATTAAAGATAC
66 CCTTTCACAATCAAAGAAAC
* * * * ***
12416123 GGTGGAATCAGCACCTAGCAACAACCTTTATGTTCAGTGATACGGGGAATCAGCACATAGCAACC
1 GGTGGAATCAACACCTAGCAACAACCTTTAAGTTCAATAATACAAAGAATCAGCACATAGCAACC
12416188 CCTTTCACAATCAAAGAAAC
66 CCTTTCACAATCAAAGAAAC
* * * *
12416208 GGTGGAATCAACACTTAGCAACCACCTTTAGAGTT-AATAATTCAAAGAATCAGCACTTAGCAAC
1 GGTGGAATCAACACCTAGCAACAACCTTTA-AGTTCAATAATACAAAGAATCAGCACATAGCAAC
12416272 CCCT
65 CCCT
12416276 CGGGGAATCT
Statistics
Matches: 132, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 22 0.17
85 107 0.81
86 3 0.02
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (85 bp):
GGTGGAATCAACACCTAGCAACAACCTTTAAGTTCAATAATACAAAGAATCAGCACATAGCAACC
CCTTTCACAATCAAAGAAAC
Found at i:12418272 original size:5 final size:5
Alignment explanation
Indices: 12418264--12418291 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12418254 CCCAAAATAA
12418264 AAACT AAACT AAACT AAACT AAACT AAA
1 AAACT AAACT AAACT AAACT AAACT AAA
12418292 ACTGAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (5 bp):
AAACT
Found at i:12421170 original size:23 final size:24
Alignment explanation
Indices: 12421144--12421188 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
12421134 ATGCAATTAA
12421144 AAGGAAAATTAAAA-AA-TAAAAGC
1 AAGGAAAA-TAAAATAACTAAAAGC
12421167 AAGGAAAATAAAATAACTAAAA
1 AAGGAAAATAAAATAACTAAAA
12421189 AGAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 5 0.25
23 10 0.50
24 5 0.25
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (24 bp):
AAGGAAAATAAAATAACTAAAAGC
Found at i:12436713 original size:8 final size:9
Alignment explanation
Indices: 12436690--12436764 Score: 64
Period size: 9 Copynumber: 8.1 Consensus size: 9
12436680 CAAAATTATT
12436690 ATTTTATAAA
1 ATTTT-TAAA
12436700 ATTTTTAAA
1 ATTTTTAAA
*
12436709 A-TTTTAAC
1 ATTTTTAAA
* *
12436717 TTTTTTATAT
1 ATTTTTA-AA
12436727 ATTCTTTAGAA
1 ATT-TTTA-AA
12436738 ATTTTTAAA
1 ATTTTTAAA
*
12436747 ATTTTTATA
1 ATTTTTAAA
12436756 A-TTTTAAA
1 ATTTTTAAA
12436764 A
1 A
12436765 AATATATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
8 13 0.24
9 21 0.39
10 12 0.22
11 8 0.15
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (9 bp):
ATTTTTAAA
Found at i:12436804 original size:19 final size:19
Alignment explanation
Indices: 12436769--12436826 Score: 75
Period size: 20 Copynumber: 3.1 Consensus size: 19
12436759 TTAAAAAATA
*
12436769 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
12436787 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
12436806 TGA-AAATTATTTTGAATTTT
1 T-ATAAA-TATTTTGAATTTT
12436826 T
1 T
12436827 TTTTAATTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
18 7 0.19
19 14 0.39
20 15 0.42
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:12436987 original size:23 final size:23
Alignment explanation
Indices: 12436960--12437013 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
12436950 TCAAATTCGA
* *
12436960 AACTTGAATTACTT-ATTTGAGTT
1 AACTTGAATAACTTGATTCGA-TT
*
12436983 GACTTGAATAACTTGATTCGATT
1 AACTTGAATAACTTGATTCGATT
12437006 AACTTGAA
1 AACTTGAA
12437014 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.33, C:0.11, G:0.15, T:0.41
Consensus pattern (23 bp):
AACTTGAATAACTTGATTCGATT
Found at i:12438116 original size:21 final size:21
Alignment explanation
Indices: 12438072--12438133 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
12438062 AATTCAAAAG
12438072 TAAAACATAATATAATATTTATCA
1 TAAAA-ATAA-ATAATA-TTATCA
**
12438096 TAAGGATAAATAATATTATCA
1 TAAAAATAAATAATATTATCA
*
12438117 TAAAAATAAATATTATT
1 TAAAAATAAATAATATT
12438134 TAATTATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
21 20 0.61
22 6 0.18
23 4 0.12
24 3 0.09
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (21 bp):
TAAAAATAAATAATATTATCA
Found at i:12438173 original size:12 final size:12
Alignment explanation
Indices: 12438156--12438181 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
12438146 AATTAAAAAA
12438156 TAAAATTTATTT
1 TAAAATTTATTT
12438168 TAAAATTTATTT
1 TAAAATTTATTT
12438180 TA
1 TA
12438182 TAAAATTACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAAAATTTATTT
Found at i:12440006 original size:31 final size:30
Alignment explanation
Indices: 12439962--12440040 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 30
12439952 AAACAAATTT
**
12439962 AATAAATGCAAAATATATAAAT-TTATTAA
1 AATAAATTAAAAATATATAAATGTTATTAA
*
12439991 ATATTAAATTAAAAATAATATAAATGTTTTTAA
1 A-A-TAAATTAAAAAT-ATATAAATGTTATTAA
*
12440024 AATAATTTAAAAA-ATAT
1 AATAAATTAAAAATATAT
12440041 TATGAACAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
29 5 0.12
30 1 0.02
31 20 0.48
32 9 0.21
33 7 0.17
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (30 bp):
AATAAATTAAAAATATATAAATGTTATTAA
Found at i:12440039 original size:32 final size:32
Alignment explanation
Indices: 12439971--12440036 Score: 84
Period size: 31 Copynumber: 2.1 Consensus size: 32
12439961 TAATAAATGC
12439971 AAAAT-ATATAAATTTATTAAATATTAAATTA
1 AAAATAATATAAATTTATTAAATATTAAATTA
* *
12440002 AAAATAATATAAATGTTTTTAAA-A-TAATTTA
1 AAAATAATATAAAT-TTATTAAATATTAAATTA
12440033 AAAA
1 AAAA
12440037 ATATTATGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 15 0.48
32 9 0.29
33 7 0.23
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (32 bp):
AAAATAATATAAATTTATTAAATATTAAATTA
Found at i:12444033 original size:21 final size:21
Alignment explanation
Indices: 12444007--12444047 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12443997 ACGGGATAGG
12444007 TGATGTGGCTC-GTTAACTAGT
1 TGATGTGGC-CAGTTAACTAGT
12444028 TGATGTGGCCAGTTAACTAG
1 TGATGTGGCCAGTTAACTAG
12444048 CCACGATGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (21 bp):
TGATGTGGCCAGTTAACTAGT
Found at i:12444218 original size:27 final size:27
Alignment explanation
Indices: 12444179--12444232 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
12444169 TTGGATTTCA
12444179 AATTACCAAAATCTAGTTAGGGTTTTG
1 AATTACCAAAATCTAGTTAGGGTTTTG
* * *
12444206 AATTACTAGAATCTAGTTTGGGTTTTG
1 AATTACCAAAATCTAGTTAGGGTTTTG
12444233 GCATGGGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (27 bp):
AATTACCAAAATCTAGTTAGGGTTTTG
Found at i:12444481 original size:3 final size:3
Alignment explanation
Indices: 12444473--12444533 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
12444463 AGTTAACAAT
*
12444473 AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12444521 AAG AAG -AG AAG AA
1 AAG AAG AAG AAG AA
12444534 ATGGAGATGC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12445651 original size:3 final size:3
Alignment explanation
Indices: 12445643--12445669 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
12445633 GATGAATACA
12445643 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
12445670 AGACAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:12446497 original size:18 final size:19
Alignment explanation
Indices: 12446476--12446511 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12446466 TTAAACGAGA
*
12446476 TTAAT-TTTTTATTTAAAT
1 TTAATATTTTTATCTAAAT
12446494 TTAATATTTTTATCTAAA
1 TTAATATTTTTATCTAAA
12446512 CTCTTTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATATTTTTATCTAAAT
Found at i:12451256 original size:21 final size:21
Alignment explanation
Indices: 12451227--12451267 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
12451217 TTGCCAAAGA
* *
12451227 TATGTATTGGATTCAATTGAG
1 TATGAATTGGATTAAATTGAG
*
12451248 TATGAATTGTATTAAATTGA
1 TATGAATTGGATTAAATTGA
12451268 TGTTAAATTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (21 bp):
TATGAATTGGATTAAATTGAG
Found at i:12451759 original size:25 final size:26
Alignment explanation
Indices: 12451728--12451797 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
12451718 CCTGATATAT
12451728 GGCTCTTCGGAGCTTCCCAATTAA-A
1 GGCTCTTCGGAGCTTCCCAATTAATA
* * * * *
12451753 GGTTCTTCATGAGCTTTCCGATTAATT
1 GGCTCTTC-GGAGCTTCCCAATTAATA
*
12451780 GGCTCTCCGGAGCTTCCC
1 GGCTCTTCGGAGCTTCCC
12451798 GATATTGGCT
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
25 7 0.21
26 21 0.62
27 6 0.18
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (26 bp):
GGCTCTTCGGAGCTTCCCAATTAATA
Found at i:12451843 original size:24 final size:24
Alignment explanation
Indices: 12451760--12451881 Score: 68
Period size: 24 Copynumber: 4.9 Consensus size: 24
12451750 AAAGGTTCTT
* *
12451760 CATGAGCTTTCCGATTAATTGGCTCT
1 CATGAGCTTCCCGA-T-ATTGGCTCG
**
12451786 CCGGAGCTTCCCGATATTGGCTCG
1 CATGAGCTTCCCGATATTGGCTCG
* * *
12451810 CTTGAACTTCCTGAT-TATGGCTCG
1 CATGAGCTTCCCGATAT-TGGCTCG
* *
12451834 GATGAGCTTCCC-ATTACATGGCTCG
1 CATGAGCTTCCCGA-TA-TTGGCTCG
* * *
12451859 AAAGAGCTTCCCGTTATATGGCT
1 CATGAGCTTCCCGATAT-TGGCT
12451882 TGAAAGAGCT
Statistics
Matches: 73, Mismatches: 17, Indels: 13
0.71 0.17 0.13
Matches are distributed among these distances:
23 2 0.03
24 35 0.48
25 25 0.34
26 11 0.15
ACGTcount: A:0.19, C:0.26, G:0.23, T:0.32
Consensus pattern (24 bp):
CATGAGCTTCCCGATATTGGCTCG
Found at i:12451898 original size:25 final size:25
Alignment explanation
Indices: 12451826--12451904 Score: 95
Period size: 25 Copynumber: 3.1 Consensus size: 25
12451816 CTTCCTGATT
* * *
12451826 ATGGCTCGGATGAGCTTCCCATTAC
1 ATGGCTCGAAAGAGCTTCCCGTTAC
*
12451851 ATGGCTCGAAAGAGCTTCCCGTTAT
1 ATGGCTCGAAAGAGCTTCCCGTTAC
* *
12451876 ATGGCTTGAAAGAGCTTCTCGTTTAC
1 ATGGCTCGAAAGAGCTTCCCG-TTAC
12451902 ATG
1 ATG
12451905 TTTGCATGAG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 40 0.87
26 6 0.13
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (25 bp):
ATGGCTCGAAAGAGCTTCCCGTTAC
Found at i:12457602 original size:41 final size:41
Alignment explanation
Indices: 12457542--12457660 Score: 211
Period size: 41 Copynumber: 2.9 Consensus size: 41
12457532 TGAGTTTTTG
12457542 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
* * *
12457583 TGGCCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
12457624 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
12457661 AATAATAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.22, C:0.23, G:0.28, T:0.28
Consensus pattern (41 bp):
GGGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTA
Found at i:12458779 original size:7 final size:7
Alignment explanation
Indices: 12458763--12458794 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
12458753 TATTAAATAA
*
12458763 GGTTAAG
1 GGTTAGG
12458770 GGTTAGG
1 GGTTAGG
12458777 GGTTAGG
1 GGTTAGG
12458784 GGTTAGG
1 GGTTAGG
12458791 GGTT
1 GGTT
12458795 TGTGGTTAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.53, T:0.31
Consensus pattern (7 bp):
GGTTAGG
Found at i:12460009 original size:143 final size:142
Alignment explanation
Indices: 12459839--12460197 Score: 553
Period size: 143 Copynumber: 2.5 Consensus size: 142
12459829 GGCGTTTATG
* *
12459839 GCGGTGTTTTTAT-AAAAAACTCCACAAAATAAAATTTACTTTTAAAAAAATAGCGTCATTTTTT
1 GCGGCGTTTTTATAAAAAAACGCCACAAAATAAAATTTACTTTTAAAAAAATAGCG-CATTTTTT
* * *
12459903 TAAATTCCCTCGTTTTATTCCAAATAAAATAATTTTTTGCGGCATTTGTGTA-AAAAACGTCGCA
65 AAAATTCCCTCGTTTTATTCCAAATAAAATAATTTTTTACGGCATTT-TGTACAAAAACGCCGCA
*
12459967 ATAGATAAGCAATA
129 ATAGATAAGAAATA
12459981 GCGGCGTTTTTATAAAAAAACGCCACAAAATAAAATTTACTTTTAAAAAAATAGCGCCATTTTTT
1 GCGGCGTTTTTATAAAAAAACGCCACAAAATAAAATTTACTTTTAAAAAAATAGCG-CATTTTTT
* * * *
12460046 AAAATTCCCTCGTTTTATTCCAAATAGAATAATTTTTTACGGCGTTTTTTACACAAACGCCGCAA
65 AAAATTCCCTCGTTTTATTCCAAATAAAATAATTTTTTACGGCATTTTGTACAAAAACGCCGCAA
12460111 TAGATAAGAAATA
130 TAGATAAGAAATA
* *
12460124 GCGGCGTTTTTATAAAAAAATGCCACAAAATAAAATTTACTTTT-AAAAAATAGTGCAATTTTTT
1 GCGGCGTTTTTATAAAAAAACGCCACAAAATAAAATTTACTTTTAAAAAAATAGCGC-ATTTTTT
12460188 AAAATTCCCT
65 AAAATTCCCT
12460198 ACCCCCTCCC
Statistics
Matches: 201, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
141 1 0.00
142 42 0.21
143 158 0.79
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (142 bp):
GCGGCGTTTTTATAAAAAAACGCCACAAAATAAAATTTACTTTTAAAAAAATAGCGCATTTTTTA
AAATTCCCTCGTTTTATTCCAAATAAAATAATTTTTTACGGCATTTTGTACAAAAACGCCGCAAT
AGATAAGAAATA
Found at i:12460230 original size:21 final size:20
Alignment explanation
Indices: 12460204--12460248 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
12460194 CCCTACCCCC
*
12460204 TCCCCCCGAAATCCCTAACTT
1 TCCCCCCAAAATCCCTAA-TT
*
12460225 TCCCCCTAAAATCCCTAATT
1 TCCCCCCAAAATCCCTAATT
12460245 TCCC
1 TCCC
12460249 ACATCCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.24, C:0.47, G:0.02, T:0.27
Consensus pattern (20 bp):
TCCCCCCAAAATCCCTAATT
Found at i:12462771 original size:17 final size:17
Alignment explanation
Indices: 12462749--12462781 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12462739 AAAATAGAGT
12462749 AACAAAACAGTGCAATA
1 AACAAAACAGTGCAATA
*
12462766 AACAAAATAGTGCAAT
1 AACAAAACAGTGCAAT
12462782 GTTTCTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AACAAAACAGTGCAATA
Found at i:12463484 original size:12 final size:12
Alignment explanation
Indices: 12463466--12463495 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
12463456 ATTCATCAGC
12463466 AATTTGCTTTAA
1 AATTTGCTTTAA
*
12463478 GATTTGCTTTAA
1 AATTTGCTTTAA
12463490 AATTTG
1 AATTTG
12463496 ATCTGTCTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (12 bp):
AATTTGCTTTAA
Found at i:12464281 original size:37 final size:37
Alignment explanation
Indices: 12464240--12464315 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
12464230 AATTCTATTG
12464240 TATTTATATTGCATGGCTGCACCATGTATTTCTTAAC
1 TATTTATATTGCATGGCTGCACCATGTATTTCTTAAC
12464277 TATTTATATTGCATGGCTGCACCATGTATTTCTTAAC
1 TATTTATATTGCATGGCTGCACCATGTATTTCTTAAC
12464314 TA
1 TA
12464316 GTTTGATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.43
Consensus pattern (37 bp):
TATTTATATTGCATGGCTGCACCATGTATTTCTTAAC
Found at i:12464644 original size:5 final size:5
Alignment explanation
Indices: 12464634--12464658 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
12464624 AAATTTAAAA
12464634 AATAT AATAT AATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT
12464659 TTATCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:12464785 original size:43 final size:43
Alignment explanation
Indices: 12464713--12465091 Score: 501
Period size: 43 Copynumber: 8.8 Consensus size: 43
12464703 AGATTATGTT
* *
12464713 TTTAGCGGCGTTTGTGATAAAAAGCGCCGCTAAAGGTTTTGGTC
1 TTTAGCGGCGTTTGTGGT-AAAAGCGCCGCTAAAGGTCTTGGTC
* *
12464757 TTTAGCGGCGTTTGTGGTAAAAGTGCCGCTAAAGGTCTTAGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * **
12464800 TTTAGCGGCGTTTGTGGTATAAGCATCATCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGC-GCCGCTAAAGGTCTTGGTC
* * *
12464844 TTTAGCGGCGTTTTTGGGAAAAGCGCCGCTAAAGGTCTTAGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
12464887 TTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGAC-TGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
* *
12464929 TTTAACAGCGTTTGTGAG-AAAAGCGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTG-GTAAAAGCGCCGCTAAAGGTCTTGGTC
* *
12464972 TTTAGCGGCGTTTGTGGTATAAGCACCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
12465015 TTTAGCGGCGTTTGTGGGAGAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
* * *
12465058 TTTAGCGGCATTTGTGGGAGAAGCGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAG
12465092 TTAGCGACGC
Statistics
Matches: 295, Mismatches: 36, Indels: 9
0.87 0.11 0.03
Matches are distributed among these distances:
42 36 0.12
43 206 0.70
44 53 0.18
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGTAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:12466041 original size:20 final size:20
Alignment explanation
Indices: 12466016--12466054 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
12466006 TACTTTCTTC
12466016 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
12466036 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
12466055 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:12466381 original size:50 final size:51
Alignment explanation
Indices: 12466306--12466498 Score: 183
Period size: 50 Copynumber: 3.7 Consensus size: 51
12466296 TTTCCTGTAC
* * * **
12466306 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAC-CGA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATACTCGA
* ** *
12466356 TGCCTATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCAT-CTCGG
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATACTCGA
* * * * *
12466406 TGCCAACGCTATGTCCCAAACATGGGCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCAT-A-CTC---GA
* *
12466462 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGA
12466499 TCTCATCCCC
Statistics
Matches: 114, Mismatches: 22, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
49 1 0.01
50 79 0.69
53 3 0.03
56 31 0.27
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (51 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATACTCGA
Found at i:12468220 original size:23 final size:23
Alignment explanation
Indices: 12468194--12468237 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12468184 GTAATTATAA
12468194 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* * *
12468217 ATACATTTTTAATTAATATAT
1 ATACATGTGTAATAAATATAT
12468238 ATACATACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:12469568 original size:23 final size:23
Alignment explanation
Indices: 12469541--12469625 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
12469531 TGCTGATTAG
*
12469541 GCACTTTATGTGTCATATATCAA
1 GCACTTTATGTGTCGTATATCAA
* *
12469564 GCACTTTATGTGTCGTATTTCAG
1 GCACTTTATGTGTCGTATATCAA
* **
12469587 GCACCTCGTGTGTCGT-T-TCAA
1 GCACTTTATGTGTCGTATATCAA
12469608 GCAC-TTATGTGTCGTATA
1 GCACTTTATGTGTCGTATA
12469626 CTAATTAGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.18
21 8 0.16
22 1 0.02
23 33 0.65
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (23 bp):
GCACTTTATGTGTCGTATATCAA
Found at i:12470036 original size:25 final size:25
Alignment explanation
Indices: 12470008--12470058 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
12469998 AATGAAATTG
* *
12470008 AGATAGTGAAATATTGCTTACTGAT
1 AGATAATGAAATATTGCCTACTGAT
*
12470033 AGATAATGAAATATTGCCTATTGAT
1 AGATAATGAAATATTGCCTACTGAT
12470058 A
1 A
12470059 TTAATGATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (25 bp):
AGATAATGAAATATTGCCTACTGAT
Found at i:12471296 original size:16 final size:17
Alignment explanation
Indices: 12471267--12471299 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12471257 AGTTACATGT
12471267 CTAAATTGTTAAAAAGGA
1 CTAAATTG-TAAAAAGGA
12471285 CTAAATTG-AAAAAGG
1 CTAAATTGTAAAAAGG
12471300 TGCAAAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.52, C:0.06, G:0.18, T:0.24
Consensus pattern (17 bp):
CTAAATTGTAAAAAGGA
Found at i:12472618 original size:25 final size:25
Alignment explanation
Indices: 12472587--12472665 Score: 88
Period size: 25 Copynumber: 3.1 Consensus size: 25
12472577 CTTCCCGATT
*
12472587 ATGGCTCGGATGAGCTTCCCGTTAC
1 ATGGCTCGAATGAGCTTCCCGTTAC
* *
12472612 ATGGCTC-ACATGAGCTTCCCATTAT
1 ATGGCTCGA-ATGAGCTTCCCGTTAC
* *
12472637 ATGGCTCGAAAGAGCTTCCTGTTTAC
1 ATGGCTCGAATGAGCTTCCCG-TTAC
12472663 ATG
1 ATG
12472666 TTTGCATGAG
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
25 37 0.84
26 7 0.16
ACGTcount: A:0.22, C:0.25, G:0.23, T:0.30
Consensus pattern (25 bp):
ATGGCTCGAATGAGCTTCCCGTTAC
Found at i:12474485 original size:9 final size:9
Alignment explanation
Indices: 12474419--12474598 Score: 58
Period size: 9 Copynumber: 18.3 Consensus size: 9
12474409 AAACTTATTG
12474419 AAATTATAAA
1 AAATTAT-AA
12474429 AAACTTATAA
1 AAA-TTATAA
*
12474439 ATATTAT-A
1 AAATTATAA
12474447 AAA-TATAA
1 AAATTATAA
12474455 TAAATTTATATA
1 -AAA-TTATA-A
12474467 TATAATTTATAA
1 -A-AA-TTATAA
*
12474479 AAATTATTTA
1 AAATTA-TAA
*
12474489 AAATTAAAA
1 AAATTATAA
*
12474498 AAATTGCATTA
1 AAATT--ATAA
* *
12474509 ACATTCTTAA
1 AAATT-ATAA
*
12474519 AAATAATAA
1 AAATTATAA
* *
12474528 AAAATATTA
1 AAATTATAA
12474537 AAATTGATATA
1 AAATT-ATA-A
* *
12474548 AAAATATTA
1 AAATTATAA
*
12474557 AAGTTGATATA
1 AAATT-ATA-A
12474568 AAATTATAA
1 AAATTATAA
* *
12474577 AATTTTAAAA
1 AA-ATTATAA
*
12474587 AAATCATAA
1 AAATTATAA
12474596 AAA
1 AAA
12474599 CTTGAAACTT
Statistics
Matches: 126, Mismatches: 29, Indels: 31
0.68 0.16 0.17
Matches are distributed among these distances:
7 3 0.02
8 4 0.03
9 43 0.34
10 39 0.31
11 25 0.20
12 4 0.03
13 8 0.06
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
AAATTATAA
Found at i:12474577 original size:19 final size:20
Alignment explanation
Indices: 12474527--12474580 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
12474517 AAAAATAATA
12474527 AAAAATATTAAAATTGATAT
1 AAAAATATTAAAATTGATAT
*
12474547 AAAAATATTAAAGTTGATAT
1 AAAAATATTAAAATTGATAT
*
12474567 AAAATTA-TAAAATT
1 AAAAATATTAAAATT
12474581 TTAAAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (20 bp):
AAAAATATTAAAATTGATAT
Found at i:12474789 original size:14 final size:14
Alignment explanation
Indices: 12474770--12474799 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
12474760 ATTCTAACTA
12474770 AGGTTTTTAAAATC
1 AGGTTTTTAAAATC
12474784 AGGTTTTTAAAATC
1 AGGTTTTTAAAATC
12474798 AG
1 AG
12474800 ATTGATGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.40
Consensus pattern (14 bp):
AGGTTTTTAAAATC
Found at i:12474891 original size:16 final size:17
Alignment explanation
Indices: 12474870--12474904 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12474860 TAAATAGAAC
*
12474870 ATTT-AAAATTAAAAAA
1 ATTTAAAAAATAAAAAA
12474886 ATTTAAAAAATAAAAAA
1 ATTTAAAAAATAAAAAA
12474903 AT
1 AT
12474905 GATTGAACCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
ATTTAAAAAATAAAAAA
Found at i:12475040 original size:21 final size:20
Alignment explanation
Indices: 12475016--12475214 Score: 103
Period size: 20 Copynumber: 9.8 Consensus size: 20
12475006 TAGTTCAAGA
*
12475016 TTTATGATTCTTTTTTATAAT
1 TTTAT-ATTATTTTTTATAAT
* * *
12475037 TTTATATTAATTTTAATACT
1 TTTATATTATTTTTTATAAT
*
12475057 TTT-TATAATTTTTTATAAT
1 TTTATATTATTTTTTATAAT
*
12475076 GCTTATGATT-TTTTTTATAGAAT
1 -TTTAT-ATTATTTTTTAT--AAT
12475099 TTTA-A-TATTTTTTATAGAAT
1 TTTATATTATTTTTTAT--AAT
*
12475119 TTTA-AATATGTTTTTAATAA-
1 TTTATATTAT-TTTTT-ATAAT
*
12475139 TTT-TATTGTTTTTTATTAAT
1 TTTATATTATTTTTTA-TAAT
*
12475159 TTGT-TA-TAATTTTTATAAT
1 TT-TATATTATTTTTTATAAT
* * *
12475178 ATTA-ATAATTTTTTATAAG
1 TTTATATTATTTTTTATAAT
*
12475197 TTTATATCAATTTTTTAT
1 TTTATAT-TATTTTTTAT
12475215 TTTTTTAATA
Statistics
Matches: 141, Mismatches: 20, Indels: 34
0.72 0.10 0.17
Matches are distributed among these distances:
18 3 0.02
19 39 0.28
20 52 0.37
21 32 0.23
22 10 0.07
23 5 0.04
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTATATTATTTTTTATAAT
Found at i:12475088 original size:29 final size:29
Alignment explanation
Indices: 12475026--12475089 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
12475016 TTTATGATTC
*
12475026 TTTTTTATAATTTTATATTAATTTTAATA
1 TTTTTTATAATTTTATATTAATCTTAATA
* *
12475055 CTTTTTATAATTTTTTA-TAATGCTT-ATGA
1 TTTTTTATAATTTTATATTAAT-CTTAAT-A
12475084 TTTTTT
1 TTTTTT
12475090 TTATAGAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (29 bp):
TTTTTTATAATTTTATATTAATCTTAATA
Found at i:12475177 original size:19 final size:18
Alignment explanation
Indices: 12475148--12475232 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 18
12475138 ATTTTATTGT
12475148 TTTTTATTAATTTGTTATAA
1 TTTTTA-TAATTT-TTATAA
* *
12475168 TTTTTATAATATTAATAA
1 TTTTTATAATTTTTATAA
*
12475186 TTTTTTATAAGTTTATATCAA
1 -TTTTTATAA-TTTTTAT-AA
*
12475207 TTTTT-T-ATTTTTTTAA
1 TTTTTATAATTTTTATAA
12475223 TATTTTATAA
1 T-TTTTATAA
12475233 AAATATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
16 3 0.06
17 9 0.17
18 7 0.13
19 16 0.31
20 15 0.29
21 2 0.04
ACGTcount: A:0.33, C:0.01, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTTTATAATTTTTATAA
Found at i:12478692 original size:22 final size:22
Alignment explanation
Indices: 12478651--12478692 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12478641 ATTTAATTAT
*
12478651 TTTTCTTTTATGTTCTTTTAAC
1 TTTTCTTTTATGTTCCTTTAAC
* *
12478673 TTTTCTTTTTTTTTCCTTTA
1 TTTTCTTTTATGTTCCTTTA
12478693 TTTTCCTTTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.10, C:0.14, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTTTTATGTTCCTTTAAC
Found at i:12483473 original size:304 final size:303
Alignment explanation
Indices: 12482924--12483524 Score: 945
Period size: 304 Copynumber: 2.0 Consensus size: 303
12482914 TAGTGCCTCT
* * *
12482924 GTTTAGCATTTTGATGCTCTTTAGTGTGATGTAGTTACCCAAGTATCCGAGTTATGTTACTATAG
1 GTTTAGCATTTTGATGCTCTCTAGTGTGATCTAGTTACCCAAGTATCCAAGTTATGTTACTATAG
*
12482989 TTCACTAGGCTATTAAAATTTATGATTGATGTATAAATGATTTGTTAATACATGTGTTTATCCAT
66 TTCACTAGGCTATTAAAATTTATGATTGATATATAAATGATTTGTTAATACATGTGTTTATCCAT
*
12483054 TAAAAGATCTATGCTAGAGAATGATCATACAAGAATGTTTCTTTTTGGTATTGATTCAATGAAAT
131 TAAAAGATCTATGCTAGAGAATGATCATACAAGAATGTCTCTTTTTGGTATTGATTCAATGAAAT
* *
12483119 GTATATATGAATGATTTTAATGAAATTATTGAAGGGCATGAAGTATATGATGAATTATTTTAGTG
196 GTATATATGAACGATTTTAATGAAATTATTGAAGGGCATGAAGTATATGATGAATTATTTCAGTG
*
12483184 CTAATCCAATCTACTTTTTGCAAATGGTTTGTTAGGTTACTATA
261 CTAATCCAAT-TACTTTTTGCAAATGGTTTGTCAGGTTACTATA
**
12483228 GTTTAGCATTTTGATGCTCTCT-GTTGTGATCTAGTTACCTGAGTAAT-CAAGTTATGTTACTAT
1 GTTTAGCATTTTGATGCTCTCTAG-TGTGATCTAGTTACCCAAGT-ATCCAAGTTATGTTACTAT
* * * * *
12483291 AGTTCATTGGGCTATTAAAATTTGTGATTGATATTTAAATTATTTGTTAATACATGTGTTTATCC
64 AGTTCACTAGGCTATTAAAATTTATGATTGATATATAAATGATTTGTTAATACATGTGTTTATCC
* * *
12483356 ATTAAAATATTTATGCTAGAGAATGATCATACAAGAATGTCTCTTTTTGGTATTGATTCGATGAA
129 ATTAAAAGATCTATGCTAGAGAATGATCATACAAGAATGTCTCTTTTTGGTATTGATTCAATGAA
* * *
12483421 ATGTATATATGAACGATTTTGATTAAATTATTGAAGGGCATTAAGTATATGATGAATTATTTCAG
194 ATGTATATATGAACGATTTTAATGAAATTATTGAAGGGCATGAAGTATATGATGAATTATTTCAG
* **
12483486 TGCTAATCGAATTTTTTTTTGCAAATGGTTTGTCAGGTT
259 TGCTAATCCAATTACTTTTTGCAAATGGTTTGTCAGGTT
12483525 TATTTTAATC
Statistics
Matches: 271, Mismatches: 24, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
303 25 0.09
304 244 0.90
305 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (303 bp):
GTTTAGCATTTTGATGCTCTCTAGTGTGATCTAGTTACCCAAGTATCCAAGTTATGTTACTATAG
TTCACTAGGCTATTAAAATTTATGATTGATATATAAATGATTTGTTAATACATGTGTTTATCCAT
TAAAAGATCTATGCTAGAGAATGATCATACAAGAATGTCTCTTTTTGGTATTGATTCAATGAAAT
GTATATATGAACGATTTTAATGAAATTATTGAAGGGCATGAAGTATATGATGAATTATTTCAGTG
CTAATCCAATTACTTTTTGCAAATGGTTTGTCAGGTTACTATA
Found at i:12485654 original size:64 final size:64
Alignment explanation
Indices: 12485553--12485688 Score: 200
Period size: 64 Copynumber: 2.1 Consensus size: 64
12485543 GGCTAAATAG
12485553 AAATAATTAAATTGAATACGATATAACTGAAGATAACTTGATTTGAGTTAAATTTAGATTAATT
1 AAATAATTAAATTGAATACGATATAACTGAAGATAACTTGATTTGAGTTAAATTTAGATTAATT
** * * ** *
12485617 AAATAATTAAATTGAATTTGGTGTAGTTGAAGATAACTTTATTTGAGTTAAATTTAGATTAATT
1 AAATAATTAAATTGAATACGATATAACTGAAGATAACTTGATTTGAGTTAAATTTAGATTAATT
*
12485681 AATTAATT
1 AAATAATT
12485689 GCGAGAGGCT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (64 bp):
AAATAATTAAATTGAATACGATATAACTGAAGATAACTTGATTTGAGTTAAATTTAGATTAATT
Found at i:12495103 original size:18 final size:18
Alignment explanation
Indices: 12495080--12495116 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12495070 AAGGTATAAG
12495080 AAAGGAAATAAAATTTTT
1 AAAGGAAATAAAATTTTT
12495098 AAAGGAAATAAAATTTTT
1 AAAGGAAATAAAATTTTT
12495116 A
1 A
12495117 CTTGTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.32
Consensus pattern (18 bp):
AAAGGAAATAAAATTTTT
Found at i:12505740 original size:17 final size:18
Alignment explanation
Indices: 12505718--12505752 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
12505708 TGCGTAAAGG
12505718 AACAAAT-AAAAAGTAAA
1 AACAAATGAAAAAGTAAA
*
12505735 AACAAATGAAAAATTAAA
1 AACAAATGAAAAAGTAAA
12505753 GCTAAGAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (18 bp):
AACAAATGAAAAAGTAAA
Found at i:12509912 original size:25 final size:25
Alignment explanation
Indices: 12509884--12509981 Score: 106
Period size: 25 Copynumber: 3.9 Consensus size: 25
12509874 GAATCTCTTT
* *
12509884 TGAGCTATATAACGGTAAGCTCATG
1 TGAGCTATATAACGGGAAGCTCATC
* *
12509909 TGAGCCATATAACGGGAAGCTTATC
1 TGAGCTATATAACGGGAAGCTCATC
* * * *
12509934 TAAGTTGTATAACGGGAAGCTTATC
1 TGAGCTATATAACGGGAAGCTCATC
* *
12509959 TGGGCTATATAATGGGAAGCTCA
1 TGAGCTATATAACGGGAAGCTCA
12509982 AATGAGCCAA
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 59 1.00
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.28
Consensus pattern (25 bp):
TGAGCTATATAACGGGAAGCTCATC
Found at i:12510006 original size:24 final size:24
Alignment explanation
Indices: 12509972--12510047 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
12509962 GCTATATAAT
* *
12509972 GGGAAGCTCAAATGAGCCAATATC
1 GGGAAGTTCAAGTGAGCCAATATC
* *
12509996 GGGAAGTTCAAGTGAGTCAATATT
1 GGGAAGTTCAAGTGAGCCAATATC
*
12510020 GGGAAGTTCAAGTAAGCCAATATC
1 GGGAAGTTCAAGTGAGCCAATATC
12510044 GGGA
1 GGGA
12510048 TGTAACACCC
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.36, C:0.14, G:0.29, T:0.21
Consensus pattern (24 bp):
GGGAAGTTCAAGTGAGCCAATATC
Found at i:12512726 original size:25 final size:27
Alignment explanation
Indices: 12512698--12512747 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
12512688 ACCAGTGGTC
12512698 AAATCTCT-C-AATCCATTCAAAATTA
1 AAATCTCTCCTAATCCATTCAAAATTA
* *
12512723 AAATCTGTCCTTATCCATTCAAAAT
1 AAATCTCTCCTAATCCATTCAAAAT
12512748 ACACATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 1 0.05
27 13 0.62
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (27 bp):
AAATCTCTCCTAATCCATTCAAAATTA
Found at i:12518456 original size:14 final size:14
Alignment explanation
Indices: 12518437--12518474 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
12518427 TAGTTGCGGC
12518437 GGCTAGGGTTAGGG
1 GGCTAGGGTTAGGG
12518451 GGCTAGGGTTAGGG
1 GGCTAGGGTTAGGG
12518465 GGCTAGGGTT
1 GGCTAGGGTT
12518475 TTCTTTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.13, C:0.08, G:0.55, T:0.24
Consensus pattern (14 bp):
GGCTAGGGTTAGGG
Found at i:12519006 original size:89 final size:89
Alignment explanation
Indices: 12518893--12519061 Score: 268
Period size: 89 Copynumber: 1.9 Consensus size: 89
12518883 TTGTGGTTTT
* *
12518893 AGTCTGCTCGACTGCAAAGTCAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTTC
1 AGTCTGCTCCACTGCAAACTCAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTTC
*
12518958 AGGGGGATAAGGTTTACTATCCTC
66 AGAGGGATAAGGTTTACTATCCTC
* * *
12518982 AGTCTGCTCCACTGC-AACTCCAGGGAGATAAGACTTGTATCTTCAACTTGCCCTACTGCAACTT
1 AGTCTGCTCCACTGCAAACT-CAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTT
12519046 CAGAGGGATAAGGTTT
65 CAGAGGGATAAGGTTT
12519062 GTTATCTTCG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
88 3 0.04
89 70 0.96
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (89 bp):
AGTCTGCTCCACTGCAAACTCAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTTC
AGAGGGATAAGGTTTACTATCCTC
Found at i:12519056 original size:44 final size:42
Alignment explanation
Indices: 12518903--12519057 Score: 132
Period size: 44 Copynumber: 3.5 Consensus size: 42
12518893 AGTCTGCTCG
** **
12518903 ACTGCAAAGTCAGGGAGATAAGACTTGTATCTTCAACCTACCCC
1 ACTGCAACTTCAGGG-GATAAGACTTGTATCTTCAA-CTTGCCC
** * * *
12518947 ACTGCAACTTCAGGGGGATAAGGTTTACTATCCTC-AGTCTGCTCC
1 ACTGCAACTTCA-GGGGATAAGACTT-GTATCTTCAACT-TGC-CC
*
12518992 ACTGCAACTCCAGGGAGATAAGACTTGTATCTTCAACTTGCCC
1 ACTGCAACTTCAGGG-GATAAGACTTGTATCTTCAACTTGCCC
12519035 TACTGCAACTTCAGAGGGATAAG
1 -ACTGCAACTTCAG-GGGATAAG
12519058 GTTTGTTATC
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
43 3 0.03
44 50 0.57
45 34 0.39
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (42 bp):
ACTGCAACTTCAGGGGATAAGACTTGTATCTTCAACTTGCCC
Found at i:12519080 original size:89 final size:89
Alignment explanation
Indices: 12518913--12519083 Score: 254
Period size: 89 Copynumber: 1.9 Consensus size: 89
12518903 ACTGCAAAGT
*
12518913 CAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTTCAGGGGGATAAGGTTTACTAT
1 CAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTTCAGAGGGATAAGGTTTACTAT
*
12518978 CCTCAGTCTGCTCCACTGCAACTC
66 CCTCAGTCCGCTCCACTGCAACTC
* * * **
12519002 CAGGGAGATAAGACTTGTATCTTCAACTTGCCCTACTGCAACTTCAGAGGGATAAGGTTTGTTAT
1 CAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTTCAGAGGGATAAGGTTTACTAT
*
12519067 CTTC-GATCCGCTCCACT
66 CCTCAG-TCCGCTCCACT
12519084 ACTGATTTAG
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
88 1 0.01
89 72 0.99
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (89 bp):
CAGGGAGATAAGACTTGTATCTTCAACCTACCCCACTGCAACTTCAGAGGGATAAGGTTTACTAT
CCTCAGTCCGCTCCACTGCAACTC
Found at i:12519145 original size:45 final size:45
Alignment explanation
Indices: 12519096--12519832 Score: 956
Period size: 45 Copynumber: 16.4 Consensus size: 45
12519086 TGATTTAGGG
* * * *
12519096 AGACAGGATCTGCAATTTTCGATCTACTTCGCTGCTAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* * * *
12519141 AGACAAGATCTGTTATCTTCGACCTACTTCACTGCCAATCCAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* * * *
12519186 AGACAAGACCTACCATCATCGATCTACTTCGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* *
12519231 AGACAAGATCTACTATCTTC-AGTCTACTTCGCTGCCAATAAAGGA
1 AGACAAGATCTGCTATCTTCGA-TCTACTTCGCTGCCAATACAGGA
* * *
12519276 AGACAAGACCTGCTATCTTC-AGTCTACTTCACTACCAATACAGGA
1 AGACAAGATCTGCTATCTTCGA-TCTACTTCGCTGCCAATACAGGA
*
12519321 AGACAAG-TCCTACTATCTTCGATCTACTTCGCTGCCAATACAGGA
1 AGACAAGAT-CTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* * * *
12519366 AGACAATATCTGTTATCTTCAATCTACTTTGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* *
12519411 AGACAAGATCTGCCATCTTCGATCTACTTCACTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* *
12519456 AGACAAGATCTGCTATCTTC-AGTCTGCTTCGCTGCCAATACAAGA
1 AGACAAGATCTGCTATCTTCGA-TCTACTTCGCTGCCAATACAGGA
* *
12519501 AGACAAGA-CTTGCTATCTTC-AGTCTACTTCGCTGCCAATATAGGT
1 AGACAAGATC-TGCTATCTTCGA-TCTACTTCGCTGCCAATACAGGA
*
12519546 AGACAAGA-CTTGCTATCTTCGATCTACTTCGCTACCAATACAGGA
1 AGACAAGATC-TGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* *
12519591 AGACAAGATCTACTATCTTC-AGTCTACTTTGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGA-TCTACTTCGCTGCCAATACAGGA
*
12519636 AGACAAGA-CTTGCTATCTTC-AGTCTACTTCGCTACCAATACAGGA
1 AGACAAGATC-TGCTATCTTCGA-TCTACTTCGCTGCCAATACAGGA
*
12519681 AGACAAGACCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* *
12519726 AGACACGATCTGCTATCTTCGATCTATTTCGCTGCCAATA-AGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
* * * *
12519770 AGACAAGATCTACCATCTTTGATCTACTTCACTGCCAATACAGGA
1 AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
12519815 AGACAAGATCTGCTATCT
1 AGACAAGATCTGCTATCT
12519833 CATTGATCTG
Statistics
Matches: 610, Mismatches: 69, Indels: 26
0.87 0.10 0.04
Matches are distributed among these distances:
44 43 0.07
45 561 0.92
46 6 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (45 bp):
AGACAAGATCTGCTATCTTCGATCTACTTCGCTGCCAATACAGGA
Found at i:12521085 original size:22 final size:22
Alignment explanation
Indices: 12521059--12521100 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12521049 TTTTTCATTT
12521059 TTCTTTT-TCTTCTTATTCTTGC
1 TTCTTTTATCTTCTT-TTCTTGC
*
12521081 TTCTTTTATTTTCTTTTCTT
1 TTCTTTTATCTTCTTTTCTT
12521101 TTTTGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (22 bp):
TTCTTTTATCTTCTTTTCTTGC
Found at i:12526571 original size:34 final size:35
Alignment explanation
Indices: 12526501--12526571 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
12526491 GCACGCATGC
* *
12526501 ACATGTATATATATAGCAAAATTGGAAATTACAAAT
1 ACATGTATATATATA-CAAAATAGGAAATTAAAAAT
*
12526537 ACATGTATATATATA-TAAATGAGGAAA-TAAAAAT
1 ACATGTATATATATACAAAAT-AGGAAATTAAAAAT
12526571 A
1 A
12526572 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
34 11 0.35
35 5 0.16
36 15 0.48
ACGTcount: A:0.54, C:0.06, G:0.11, T:0.30
Consensus pattern (35 bp):
ACATGTATATATATACAAAATAGGAAATTAAAAAT
Found at i:12527194 original size:350 final size:350
Alignment explanation
Indices: 12526553--12527252 Score: 1382
Period size: 350 Copynumber: 2.0 Consensus size: 350
12526543 ATATATATAT
12526553 AAATGAGGAAATAAAAATAAAAATAAAAATTATTATAATTATAATAGATTTATTTGTAAAATAAC
1 AAATGAGGAAATAAAAATAAAAATAAAAATTATTATAATTATAATAGATTTATTTGTAAAATAAC
12526618 CAAGATAACGAAAAAGGATCGAATTGAAATTTTAAAACAAAATTTGGGGTCAAATCTGAAATAAA
66 CAAGATAACGAAAAAGGATCGAATTGAAATTTTAAAACAAAATTTGGGGTCAAATCTGAAATAAA
*
12526683 TAAAAAAGGGAGGGCCACATTAAACGAGCTGAAAAACTAGAAGGGGCAAAAGGGAAATAATCCCA
131 TAAAAAAGGAAGGGCCACATTAAACGAGCTGAAAAACTAGAAGGGGCAAAAGGGAAATAATCCCA
12526748 TTCTTGCAAAACGCAGAGTTCTAGTAGGGACTAAATTGAAAACACAAAAACAATTCGGGGCAAAA
196 TTCTTGCAAAACGCAGAGTTCTAGTAGGGACTAAATTGAAAACACAAAAACAATTCGGGGCAAAA
12526813 TTAAAATACTAAAAGTACTTGATTGGAAAACATTAAAAAGCGGAAGGGCTAAAAGTGCAATTAGC
261 TTAAAATACTAAAAGTACTTGATTGGAAAACATTAAAAAGCGGAAGGGCTAAAAGTGCAATTAGC
12526878 CCATCCCTTGAAAACACGCGGATCC
326 CCATCCCTTGAAAACACGCGGATCC
12526903 AAATGAGGAAATAAAAATAAAAATAAAAATTATTATAATTATAATAGATTTATTTGTAAAATAAC
1 AAATGAGGAAATAAAAATAAAAATAAAAATTATTATAATTATAATAGATTTATTTGTAAAATAAC
12526968 CAAGATAACGAAAAAGGATCGAATTGAAATTTTAAAACAAAATTTGGGGTCAAATCTGAAATAAA
66 CAAGATAACGAAAAAGGATCGAATTGAAATTTTAAAACAAAATTTGGGGTCAAATCTGAAATAAA
*
12527033 TAAAAAAGGAAGGGCCACATTAAACGCGCTGAAAAACTAGAAGGGGCAAAAGGGAAATAATCCCA
131 TAAAAAAGGAAGGGCCACATTAAACGAGCTGAAAAACTAGAAGGGGCAAAAGGGAAATAATCCCA
12527098 TTCTTGCAAAACGCAGAGTTCTAGTAGGGACTAAATTGAAAACACAAAAACAATTCGGGGCAAAA
196 TTCTTGCAAAACGCAGAGTTCTAGTAGGGACTAAATTGAAAACACAAAAACAATTCGGGGCAAAA
12527163 TTAAAATACTAAAAGTACTTGATTGGAAAACATTAAAAAGCGGAAGGGCTAAAAGTGCAATTAGC
261 TTAAAATACTAAAAGTACTTGATTGGAAAACATTAAAAAGCGGAAGGGCTAAAAGTGCAATTAGC
12527228 CCATCCCTTGAAAACACGCGGATCC
326 CCATCCCTTGAAAACACGCGGATCC
12527253 TCCGAGTCGG
Statistics
Matches: 348, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
350 348 1.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (350 bp):
AAATGAGGAAATAAAAATAAAAATAAAAATTATTATAATTATAATAGATTTATTTGTAAAATAAC
CAAGATAACGAAAAAGGATCGAATTGAAATTTTAAAACAAAATTTGGGGTCAAATCTGAAATAAA
TAAAAAAGGAAGGGCCACATTAAACGAGCTGAAAAACTAGAAGGGGCAAAAGGGAAATAATCCCA
TTCTTGCAAAACGCAGAGTTCTAGTAGGGACTAAATTGAAAACACAAAAACAATTCGGGGCAAAA
TTAAAATACTAAAAGTACTTGATTGGAAAACATTAAAAAGCGGAAGGGCTAAAAGTGCAATTAGC
CCATCCCTTGAAAACACGCGGATCC
Found at i:12537262 original size:80 final size:80
Alignment explanation
Indices: 12537129--12537369 Score: 464
Period size: 80 Copynumber: 3.0 Consensus size: 80
12537119 CAAACTAATG
* *
12537129 ATAAGTGGCATTGTAAGAACGTTTACATTGCGAGAAACAAAACTTACTTCAATAGCTAATCTAAA
1 ATAAGTGGCATTATAAGAATGTTTACATTGCGAGAAACAAAACTTACTTCAATAGCTAATCTAAA
12537194 CGAGTTTAGGGTTTA
66 CGAGTTTAGGGTTTA
12537209 ATAAGTGGCATTATAAGAATGTTTACATTGCGAGAAACAAAACTTACTTCAATAGCTAATCTAAA
1 ATAAGTGGCATTATAAGAATGTTTACATTGCGAGAAACAAAACTTACTTCAATAGCTAATCTAAA
12537274 CGAGTTTAGGGTTTA
66 CGAGTTTAGGGTTTA
12537289 ATAAGTGGCATTATAAGAATGTTTACATTGCGAGAAACAAAACTTACTTCAATAGCTAATCTAAA
1 ATAAGTGGCATTATAAGAATGTTTACATTGCGAGAAACAAAACTTACTTCAATAGCTAATCTAAA
12537354 CGAGTTTAGGGTTTA
66 CGAGTTTAGGGTTTA
12537369 A
1 A
12537370 GGTTTAGGGT
Statistics
Matches: 159, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 159 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (80 bp):
ATAAGTGGCATTATAAGAATGTTTACATTGCGAGAAACAAAACTTACTTCAATAGCTAATCTAAA
CGAGTTTAGGGTTTA
Found at i:12537373 original size:7 final size:7
Alignment explanation
Indices: 12537357--12537387 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
12537347 ATCTAAACGA
12537357 GTTTAGG
1 GTTTAGG
*
12537364 GTTTAAG
1 GTTTAGG
12537371 GTTTAGG
1 GTTTAGG
12537378 GTTTAGG
1 GTTTAGG
12537385 GTT
1 GTT
12537388 AAGAGTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.16, C:0.00, G:0.39, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:12539632 original size:16 final size:17
Alignment explanation
Indices: 12539604--12539635 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
12539594 TAAAATAATT
12539604 TATTTTATGAAATTTAG
1 TATTTTATGAAATTTAG
12539621 TATTTT-TGAAATTTA
1 TATTTTATGAAATTTA
12539636 TACAAAATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (17 bp):
TATTTTATGAAATTTAG
Found at i:12547088 original size:18 final size:20
Alignment explanation
Indices: 12547055--12547094 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
12547045 ATGGAATGAA
12547055 ATATTTAATATAAATAATAT
1 ATATTTAATATAAATAATAT
12547075 ATATTT-ATAT-AATAATAT
1 ATATTTAATATAAATAATAT
12547093 AT
1 AT
12547095 GTAAAAGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATATTTAATATAAATAATAT
Found at i:12548463 original size:19 final size:19
Alignment explanation
Indices: 12548439--12548488 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
12548429 GGAGATGTAA
*
12548439 GGGGGCGTGTGAAGGCGTT
1 GGGGGCGTGTGAAGACGTT
12548458 GGGGGCGTGTGAAGACGTT
1 GGGGGCGTGTGAAGACGTT
* *
12548477 GCGCGCGTGTGA
1 GGGGGCGTGTGA
12548489 GGAGGGGTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.54, T:0.20
Consensus pattern (19 bp):
GGGGGCGTGTGAAGACGTT
Found at i:12549387 original size:88 final size:88
Alignment explanation
Indices: 12549339--12550304 Score: 1344
Period size: 88 Copynumber: 11.0 Consensus size: 88
12549329 AGAATTAGTA
* * * *
12549339 TCTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
*
12549404 AACTGAGGGAGGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
* * * * *
12549427 TCTTCGATCTGTTTCACTGTTGATGCAGGAAGGCAAGATCTACTATCTTCAACTTGCTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
12549492 AACCGAGGGAGGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
* * *
12549515 TCTTCGATCTGCTTCGCCATCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGGTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
* *
12549580 AAGCGAGGGAAGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
*
12549603 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGCCAAGATCTGCTATCTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
12549668 AACCGAGGGAGGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
* * *
12549691 TCTTCGATCTGCTTCGCCGTCGATGCAGGAAGGAAAGATTTGCTATCTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
12549756 AACCGAGGGAGGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
*
12549779 TCTTCGATCTGCTTCACCGTCAATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
* *
12549844 AAACGAAGGAGGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
* * ** *
12549867 CCTTCGATCTGCTTCGCTATCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTACTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
*
12549932 AACCGAAGGAGGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
* * *
12549955 TATTCGATCTGCTTCACCGTCGATGCAAGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
* *
12550020 AAACGAAGGAGGCAAGGCTTGTG
66 AACCGAGGGAGGCAAGGCTTGTG
* ** ** * *
12550043 CCTTCGATCTGCTTTGCTATTGATGCAGGAAGGCAAGATCTACTATCTTCAACCTGCTCCACTAC
1 TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
*
12550108 AACCGAGGGAGACAAGGCTTTGTG
66 AACCGAGGGAGGCAAGGC-TTGTG
* * *
12550132 AT-TTCGATCTGCTTCGCCATCGATGCAGGAAGGCCAGATCTGCTATCTTCAACCTAG-TCCACT
1 -TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCT-GCTCCACT
* * *
12550195 ACAACCTAGGGAGGCAAGGCTGGTA
64 ACAACCGAGGGAGGCAAGGCTTGTG
* * * * * * * ** *
12550220 TCTTCGATCTACTTCGCTGTC-AGTACAGGAAGGCAAGATCTACTATCTTTAACATGCTCTGCTG
1 TCTTCGATCTGCTTCACCGTCGA-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTA
* *
12550284 CAACCCATGGAGGCAAGGCTT
65 CAACCGAGGGAGGCAAGGCTT
12550305 TGTGATTTCA
Statistics
Matches: 785, Mismatches: 87, Indels: 12
0.89 0.10 0.01
Matches are distributed among these distances:
87 3 0.00
88 704 0.90
89 77 0.10
90 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.25
Consensus pattern (88 bp):
TCTTCGATCTGCTTCACCGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTAC
AACCGAGGGAGGCAAGGCTTGTG
Found at i:12550033 original size:44 final size:44
Alignment explanation
Indices: 12549809--12550035 Score: 121
Period size: 44 Copynumber: 5.2 Consensus size: 44
12549799 CAATGCAGGA
*
12549809 AGGCAAGATCTGCTATCTTCAACCTGCTCCACTACAAACGAAGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAACGAAGG
* ** * * * * * *
12549853 AGGCAAG-GCTTG-TGCCTTCGATCTGCT-TCGCTATC-GATGCAGG
1 AGGCAAGATC-TGCTATCTTCAACCTGCTCT-ACTA-CAAACGAAGG
* * *
12549896 AAGGCAAGATCTGCTATCTTCAACCTACTCCACTACAACCGAAGG
1 -AGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAACGAAGG
* * * * * * * *
12549941 AGGCAAG-GCTTG-TGTATTCGATCTGCT-TCACCGT-C-GATGCAAGA
1 AGGCAAGATC-TGCTATCTTCAACCTGCTCT-A-C-TACAAACG-AAGG
12549985 AGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAACGAAGG
1 AGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAACGAAGG
12550029 AGGCAAG
1 AGGCAAG
12550036 GCTTGTGCCT
Statistics
Matches: 124, Mismatches: 41, Indels: 36
0.62 0.20 0.18
Matches are distributed among these distances:
43 34 0.27
44 55 0.44
45 34 0.27
46 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.22, T:0.23
Consensus pattern (44 bp):
AGGCAAGATCTGCTATCTTCAACCTGCTCTACTACAAACGAAGG
Found at i:12551479 original size:7 final size:7
Alignment explanation
Indices: 12551462--12551508 Score: 51
Period size: 7 Copynumber: 6.6 Consensus size: 7
12551452 AGCCTCTCCA
12551462 TTTTCACT
1 TTTTCA-T
12551470 TTTTCATT
1 TTTTCA-T
*
12551478 TTTTCAC
1 TTTTCAT
12551485 TTTTCAT
1 TTTTCAT
*
12551492 TTTT-AA
1 TTTTCAT
12551498 TTTTCAT
1 TTTTCAT
12551505 TTTT
1 TTTT
12551509 TTGACTCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
6 5 0.15
7 15 0.45
8 13 0.39
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (7 bp):
TTTTCAT
Found at i:12551488 original size:15 final size:15
Alignment explanation
Indices: 12551462--12551509 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
12551452 AGCCTCTCCA
12551462 TTTTCACTTTTTCATT
1 TTTTCAC-TTTTCATT
12551478 TTTTCACTTTTCA-T
1 TTTTCACTTTTCATT
*
12551492 TTTT-AATTTTCATT
1 TTTTCACTTTTCATT
12551506 TTTT
1 TTTT
12551510 TGACTCAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 7 0.23
14 10 0.33
15 6 0.20
16 7 0.23
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTTCACTTTTCATT
Found at i:12551501 original size:13 final size:14
Alignment explanation
Indices: 12551470--12551508 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
12551460 CATTTTCACT
*
12551470 TTTTCATTTTTTCAC
1 TTTTCA-TTTTTCAA
12551485 TTTTCATTTTT-AA
1 TTTTCATTTTTCAA
12551498 TTTTCATTTTT
1 TTTTCATTTTT
12551509 TTGACTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 12 0.52
14 5 0.22
15 6 0.26
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCATTTTTCAA
Found at i:12552419 original size:21 final size:20
Alignment explanation
Indices: 12552393--12552446 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
12552383 CTTTTTATCA
*
12552393 TTTTTTATTTGGATGACTTTT
1 TTTTTTATTT-GATCACTTTT
*
12552414 TTTTTTGACTTTGATCATTTTT
1 TTTTTT-A-TTTGATCACTTTT
12552436 TTCTTTTATTT
1 TT-TTTTATTT
12552447 TTTTGCTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 9 0.32
22 12 0.43
23 7 0.25
ACGTcount: A:0.13, C:0.07, G:0.09, T:0.70
Consensus pattern (20 bp):
TTTTTTATTTGATCACTTTT
Found at i:12552457 original size:37 final size:38
Alignment explanation
Indices: 12552416--12552487 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
12552406 TGACTTTTTT
12552416 TTTTGACTTTGATCATT-TTTTTCTTTTATTTTTTTGC
1 TTTTGACTTTGATCATTCTTTTTCTTTTATTTTTTTGC
** *
12552453 TTTTGACTTTGATTTTTCTTTTTCTTTTCTTTTTT
1 TTTTGACTTTGATCATTCTTTTTCTTTTATTTTTT
12552488 GAATCTGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 15 0.48
38 16 0.52
ACGTcount: A:0.08, C:0.11, G:0.07, T:0.74
Consensus pattern (38 bp):
TTTTGACTTTGATCATTCTTTTTCTTTTATTTTTTTGC
Found at i:12552488 original size:37 final size:36
Alignment explanation
Indices: 12552408--12552488 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 36
12552398 TATTTGGATG
12552408 ACTTTTTT-TTTTGACTTTGATCATTTTTTTCTTTT
1 ACTTTTTTGTTTTGACTTTGATCATTTTTTTCTTTT
* **
12552443 ATTTTTTTGCTTTTGACTTTGATTTTTCTTTTTCTTTT
1 ACTTTTTTG-TTTTGACTTTGATCATT-TTTTTCTTTT
12552481 -CTTTTTTG
1 ACTTTTTTG
12552489 AATCTGAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 7 0.18
37 22 0.56
38 10 0.26
ACGTcount: A:0.09, C:0.11, G:0.07, T:0.73
Consensus pattern (36 bp):
ACTTTTTTGTTTTGACTTTGATCATTTTTTTCTTTT
Found at i:12558982 original size:22 final size:22
Alignment explanation
Indices: 12558941--12558984 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
12558931 TAAACTGGAC
*
12558941 ATTTATTTGGTTTATTTTATTT
1 ATTTATTTGGTTTATATTATTT
12558963 ATTTATTTGGGTTT-TATTATTT
1 ATTTATTT-GGTTTATATTATTT
12558985 GGGCTCGGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.18, C:0.00, G:0.11, T:0.70
Consensus pattern (22 bp):
ATTTATTTGGTTTATATTATTT
Found at i:12561790 original size:27 final size:27
Alignment explanation
Indices: 12561722--12562287 Score: 567
Period size: 27 Copynumber: 21.0 Consensus size: 27
12561712 CTGACACCCC
* *
12561722 GAAATACCCCTATAGGATAAAATGAC-
1 GAAATACCCCCATAGGGTAAAATGACT
* * ** *
12561748 AAAATACCTCTTTAGGGTAAACTGACT
1 GAAATACCCCCATAGGGTAAAATGACT
*
12561775 GAAATACCCCCATAGGGTAAAATAACT
1 GAAATACCCCCATAGGGTAAAATGACT
* * * *
12561802 GAAATACCCCTATAGGATAAAATAATT
1 GAAATACCCCCATAGGGTAAAATGACT
* * * *
12561829 AAAATACCCTCGTAGAGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACT
* * *
12561856 GAAGTACCCCCATAGGATAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACT
*
12561883 GAAATACCCTCATAGGGT-AAATGA-T
1 GAAATACCCCCATAGGGTAAAATGACT
*
12561908 CGAAATACCCCCGTAGGGTAAAATGA-T
1 -GAAATACCCCCATAGGGTAAAATGACT
* *
12561935 CGAAATACCCCCATAAGGTAAAATAACT
1 -GAAATACCCCCATAGGGTAAAATGACT
* *
12561963 GAAATACCCCCGTAAGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACT
*
12561990 AAAATACCCCCATAGGGTAAAATGA-T
1 GAAATACCCCCATAGGGTAAAATGACT
*
12562016 CGAAATACCCCTATAGGGTAAAATGA-T
1 -GAAATACCCCCATAGGGTAAAATGACT
* * * *
12562043 CAAAATACCCTCGTAGGGTAAAATGACC
1 -GAAATACCCCCATAGGGTAAAATGACT
** *
12562071 GAAATACCCCTGTAGGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACT
* **
12562098 AAAATACCCTTATAGGGTAAAATGACT
1 GAAATACCCCCATAGGGTAAAATGACT
** *
12562125 GAAATACCCCTGTAGGTTAAAATGAAC-
1 GAAATACCCCCATAGGGTAAAATG-ACT
* *
12562152 AAAATACCCCCATAGGGTAAAATGACC
1 GAAATACCCCCATAGGGTAAAATGACT
* * *
12562179 AAAATACCCTCATAGGGTAGAATGA-T
1 GAAATACCCCCATAGGGTAAAATGACT
*
12562205 CGAAATACCCCCATAGGGTAGAATGA-T
1 -GAAATACCCCCATAGGGTAAAATGACT
*
12562232 CGAAATACCCCCATAGGGTAGAATGA-T
1 -GAAATACCCCCATAGGGTAAAATGACT
12562259 CGAAATACCCCCATAGGGTAAAATGACT
1 -GAAATACCCCCATAGGGTAAAATGACT
12562287 G
1 G
12562288 TTTTACCCCT
Statistics
Matches: 459, Mismatches: 71, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
26 46 0.10
27 409 0.89
28 4 0.01
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (27 bp):
GAAATACCCCCATAGGGTAAAATGACT
Found at i:12562643 original size:28 final size:28
Alignment explanation
Indices: 12562611--12562785 Score: 262
Period size: 28 Copynumber: 6.3 Consensus size: 28
12562601 CACTGTACTG
*
12562611 GTTACTATATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
*
12562639 GTTACTGTATTGGGCTAAGGCACACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
*
12562667 ATTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
*
12562695 ATTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
12562723 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * ** *
12562751 CTTACTATATCAGGCTAAGGCCCACAGT
1 GTTACTGTATTGGGCTAAGGCCCACACT
12562779 G-TACTGT
1 GTTACTGT
12562786 TTCTGAATAG
Statistics
Matches: 135, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
27 5 0.04
28 130 0.96
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:12566053 original size:20 final size:21
Alignment explanation
Indices: 12566028--12566075 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
12566018 TTAGATTAAG
*
12566028 AAATCTTTG-ATAATCTTT-CC
1 AAATCTTTGCA-AATATTTCCC
12566048 AAATCTTTGCAAATATTTCCC
1 AAATCTTTGCAAATATTTCCC
12566069 AAATCTT
1 AAATCTT
12566076 GATTCCAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (21 bp):
AAATCTTTGCAAATATTTCCC
Found at i:12567433 original size:40 final size:40
Alignment explanation
Indices: 12567374--12567493 Score: 141
Period size: 40 Copynumber: 3.0 Consensus size: 40
12567364 AAATATGTTG
12567374 AATTGCACATACGTGCCCCTGTTTGTACTTCAATACCCAA
1 AATTGCACATACGTGCCCCTGTTTGTACTTCAATACCCAA
* * ** **
12567414 AATTGCACATACGTACCCCTGTTTGTACATCGGTACCCTTG
1 AATTGCACATACGTGCCCCTGTTTGTACTTCAATACCC-AA
* * * *
12567455 AATTGCATAGACGTGCCCTTATTTGTACTTCAATACCCA
1 AATTGCACATACGTGCCCCTGTTTGTACTTCAATACCCA
12567494 TGGACATAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
40 34 0.53
41 30 0.47
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (40 bp):
AATTGCACATACGTGCCCCTGTTTGTACTTCAATACCCAA
Found at i:12601569 original size:39 final size:39
Alignment explanation
Indices: 12601453--12601586 Score: 137
Period size: 40 Copynumber: 3.4 Consensus size: 39
12601443 GTTTGGACAA
* * **
12601453 AAAAGGCCACTAAAAATCAAGCATTAGCGGCGCTTTTAAA
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTT-TG
* ** *
12601493 AAAACGACGCTAAAGGTCGAGCATTAGCGGCGCTTTTTGG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTT-G
* *
12601533 AAAACGCCGCTAAAAAT-AAGCATTAGCGGTGTTTTTTG
1 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
12601571 AAAAGCGCCGC-AAAAA
1 AAAA-CGCCGCTAAAAA
12601587 GCCTAAGCCC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 10 0.13
39 23 0.29
40 45 0.58
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTTTG
Done.