Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
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: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 20 of 311
Found at i:5651861 original size:7 final size:7
Alignment explanation
Indices: 5651837--5652016 Score: 78
Period size: 7 Copynumber: 24.7 Consensus size: 7
5651827 ACTAACTAAT
5651837 CTAAACC
1 CTAAACC
*
5651844 TTAAACTC
1 CTAAAC-C
*
5651852 CTAACCC
1 CTAAACC
5651859 CTAAACC
1 CTAAACC
5651866 CTAAACC
1 CTAAACC
5651873 CTAAACC
1 CTAAACC
* *
5651880 ATAAATC
1 CTAAACC
*
5651887 CTAAAAC
1 CTAAACC
*
5651894 ATAAACC
1 CTAAACC
* *
5651901 ATGAACC
1 CTAAACC
*
5651908 ATAAACCC
1 CTAAA-CC
*
5651916 CT-CACC
1 CTAAACC
*
5651922 CTTAACC
1 CTAAACC
*
5651929 CTTAACCC
1 C-TAAACC
5651937 CT-AACAC
1 CTAAAC-C
5651944 CTAAACC
1 CTAAACC
*
5651951 TTAAACC
1 CTAAACC
*
5651958 C-CAACC
1 CTAAACC
5651964 CTTAAATCAC
1 C-TAAA-C-C
5651974 CTTTAAACC
1 C--TAAACC
* *
5651983 ATAATCC
1 CTAAACC
5651990 CTAAACC
1 CTAAACC
*
5651997 CATAATCC
1 C-TAAACC
*
5652005 ATAAACC
1 CTAAACC
*
5652012 TTAAA
1 CTAAA
5652017 ATAGTAACTC
Statistics
Matches: 131, Mismatches: 30, Indels: 24
0.71 0.16 0.13
Matches are distributed among these distances:
6 11 0.08
7 87 0.66
8 23 0.18
9 2 0.02
10 3 0.02
11 5 0.04
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:5651969 original size:21 final size:22
Alignment explanation
Indices: 5651838--5651969 Score: 87
Period size: 21 Copynumber: 6.2 Consensus size: 22
5651828 CTAACTAATC
* *
5651838 TAAACCTTAAACTCCTAACCCC
1 TAAACCTTAAACCCCTAACCCT
* * *
5651860 TAAACCCTAAA-CCCTAAACCA
1 TAAACCTTAAACCCCTAACCCT
* * * *
5651881 TAAATCC-TAAA-ACATAAACCA
1 TAAA-CCTTAAACCCCTAACCCT
* * *
5651902 TGAACCATAAACCCCTCACCCT
1 TAAACCTTAAACCCCTAACCCT
*
5651924 TAACCCTT-AACCCCTAACACC-
1 TAAACCTTAAACCCCTAAC-CCT
5651945 TAAACCTTAAACCCC-AACCCT
1 TAAACCTTAAACCCCTAACCCT
5651966 TAAA
1 TAAA
5651970 TCACCTTTAA
Statistics
Matches: 87, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
20 4 0.05
21 53 0.61
22 30 0.34
ACGTcount: A:0.42, C:0.39, G:0.01, T:0.19
Consensus pattern (22 bp):
TAAACCTTAAACCCCTAACCCT
Found at i:5652365 original size:39 final size:39
Alignment explanation
Indices: 5652322--5652432 Score: 125
Period size: 41 Copynumber: 2.8 Consensus size: 39
5652312 GATCAAGCAT
* *
5652322 TAGCGGCGTTTTTAAAAGGCGCCGCTAAAGGTGTAAT-TA
1 TAGCGGCGTTTTTAAAAAGCGCCGCTAAAGCT-TAATCTA
* * * *
5652361 TAGCGGCGTTTCTTAAAAAAGCGTCGCTAATGCTTGATCTT
1 TAGCGGCGTTT-TT-AAAAAGCGCCGCTAAAGCTTAATCTA
*
5652402 TAGCGGCGTTTTTGAAAAGCGCCGCTAAAGC
1 TAGCGGCGTTTTTAAAAAGCGCCGCTAAAGC
5652433 CACTAAAAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
39 26 0.43
40 7 0.12
41 27 0.45
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (39 bp):
TAGCGGCGTTTTTAAAAAGCGCCGCTAAAGCTTAATCTA
Found at i:5652561 original size:180 final size:180
Alignment explanation
Indices: 5652225--5652619 Score: 546
Period size: 180 Copynumber: 2.2 Consensus size: 180
5652215 CATTTCTTGT
*
5652225 GGCGTTTTTCAAAAAGCGCCGCTAAAGCCACTAAAAGCAGCGTTTTGCAAAATTCTTTTGCGGCG
1 GGCGTTTTT-AAAAAGCGCCGCTAAAGCCACTAAAAGCAGCGTTTTGCAAAATACTTTTGCGGCG
* * * *
5652290 TTTTTTGAAAAACGCCACAAAAGATCAAGCATTAGCGGCGTTTTTAAAAGGCGCCGCTAAAGGTG
65 TTCTTTCAAAAACGCCACAAAAGATCAAGCATTAGCGGCGTTTTTAAAAGGCACCGCTAAAGGTA
* ** *
5652355 TAATTATAGCGGCGTTTCTTAAAAAAGCG-TCGCTAATGCTTGATCTTTAGC
130 TAATTATAGCGGCGTTTCTCAAAAAAGCGCT-GCTAATAATCGATCTTTAGC
*
5652406 GGCGTTTTTGAAAAGCGCCGCTAAAGCCACTAAAAGC-GTCGTTTTGCAAAATACTTTTGCGGCG
1 GGCGTTTTTAAAAAGCGCCGCTAAAGCCACTAAAAGCAG-CGTTTTGCAAAATACTTTTGCGGCG
* * *
5652470 TTCTTTCAAAAATGCCGCTAAAGATCAAGCATTAGCGGCGTTTTCTAAAAGGCACCGCTAAAGGT
65 TTCTTTCAAAAACGCCACAAAAGATCAAGCATTAGCGGCGTTTT-TAAAAGGCACCGCTAAAGGT
* *
5652535 ATACA-TATAGCTGCGTTT-TCAAAAAAGCGCTGCTAATAATCGATCTTTAGT
129 ATA-ATTATAGCGGCGTTTCTCAAAAAAGCGCTGCTAATAATCGATCTTTAGC
** * *
5652586 GGCGTCATTAAAAAGCGCCACTAAATCCACTAAA
1 GGCGTTTTTAAAAAGCGCCGCTAAAGCCACTAAA
5652620 GGCTTGTGGC
Statistics
Matches: 190, Mismatches: 20, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
179 1 0.01
180 145 0.76
181 43 0.23
182 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (180 bp):
GGCGTTTTTAAAAAGCGCCGCTAAAGCCACTAAAAGCAGCGTTTTGCAAAATACTTTTGCGGCGT
TCTTTCAAAAACGCCACAAAAGATCAAGCATTAGCGGCGTTTTTAAAAGGCACCGCTAAAGGTAT
AATTATAGCGGCGTTTCTCAAAAAAGCGCTGCTAATAATCGATCTTTAGC
Found at i:5652738 original size:38 final size:37
Alignment explanation
Indices: 5652671--5652749 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 37
5652661 TAGCAGCGTT
* * *
5652671 TTTTAAAAACGCCGCTAATACTTGATCTTTAGTGGTG
1 TTTTAAAAACGCCACTAATACTTCATCTTTAGTGGCG
*
5652708 TTTTAAAAAGCGCCACTAATGC-TCATTCTTTAGTGGCG
1 TTTTAAAAA-CGCCACTAATACTTCA-TCTTTAGTGGCG
5652746 TTTT
1 TTTT
5652750 TCATTCAAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 11 0.31
38 25 0.69
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (37 bp):
TTTTAAAAACGCCACTAATACTTCATCTTTAGTGGCG
Found at i:5660509 original size:26 final size:26
Alignment explanation
Indices: 5660473--5660524 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5660463 GCAAGAGGAG
* *
5660473 ATGGAATCACTTTACAAAAATAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
5660499 ATGGAATCACTTCACAAAAACAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
5660525 CTGCATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.58, C:0.15, G:0.08, T:0.19
Consensus pattern (26 bp):
ATGGAATCACTTCACAAAAACAAAAA
Found at i:5662399 original size:49 final size:49
Alignment explanation
Indices: 5662294--5662413 Score: 132
Period size: 49 Copynumber: 2.4 Consensus size: 49
5662284 ATCCGGATGA
* * * * * *
5662294 CCCAATAATGATGACTTTTACTGTTTGCATATTCTACCATCCCAAGTGG
1 CCCAACAATGATGGCTTTGAATATTTGCATATTCTACCATCCCAAGCGG
* ***
5662343 CCCAACAATGATGGCTTTGAATATTTGCATATTCTATCATCTTGAGCGG
1 CCCAACAATGATGGCTTTGAATATTTGCATATTCTACCATCCCAAGCGG
* *
5662392 CCTAACAATGATGGTTTTGAAT
1 CCCAACAATGATGGCTTTGAAT
5662414 CATTATTTCG
Statistics
Matches: 59, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 59 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (49 bp):
CCCAACAATGATGGCTTTGAATATTTGCATATTCTACCATCCCAAGCGG
Found at i:5663281 original size:20 final size:20
Alignment explanation
Indices: 5663238--5663277 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5663228 GGTTAACATT
*
5663238 AGTTAATTATTAATTAGTTA
1 AGTTAATTATTAATTAATTA
5663258 AGTTAATTA-TAATTAATTA
1 AGTTAATTATTAATTAATTA
5663277 A
1 A
5663278 AGTTTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AGTTAATTATTAATTAATTA
Found at i:5672313 original size:38 final size:38
Alignment explanation
Indices: 5672262--5672344 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
5672252 AACCCTAATC
* * * *
5672262 CCACCTATTCCACCACCTTTGTTGGTCACTCACATTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACATTGG
*
5672300 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACATTGG
5672338 CCACCTA
1 CCACCTA
5672345 AACCACCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.18, C:0.45, G:0.12, T:0.25
Consensus pattern (38 bp):
CCACCTACTCCACCACCCTTGTTGGCCACCCACATTGG
Found at i:5674886 original size:40 final size:40
Alignment explanation
Indices: 5674824--5675081 Score: 360
Period size: 40 Copynumber: 6.5 Consensus size: 40
5674814 AAGCCAAGTA
* * * *
5674824 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
5674863 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
**
5674903 CCTTCGGGACTTAGCCCGGATATACCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
5674943 CCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
5674983 CCTTCGGGACTTATCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
5675023 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
5675063 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
5675082 TTATCATCCA
Statistics
Matches: 197, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
39 13 0.07
40 184 0.93
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:5685730 original size:68 final size:68
Alignment explanation
Indices: 5685646--5685916 Score: 470
Period size: 68 Copynumber: 4.0 Consensus size: 68
5685636 AAATCAAATA
*
5685646 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGTAGATCTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
5685711 ATC
66 ATC
*
5685714 TCTTTTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
5685779 ATC
66 ATC
* * *
5685782 TCTTCTCCCTGATATGGCGTTGGAGCGGCTAAAAGCCACAACAGATCTCCTTGAAGTTTCAGTGA
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
5685847 ATC
66 ATC
* * *
5685850 TCTTCTCCCTGAAATGGTGTTAGAGCAGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
1 TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
5685915 AT
66 AT
5685917 TAATCGAAGC
Statistics
Matches: 191, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 191 1.00
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.28
Consensus pattern (68 bp):
TCTTCTCCCTGAAATGGCGTTGGAGCGGCTAAAAGCCACAGCAGATCTCCTTGAAGTTTCAGTGG
ATC
Found at i:5686416 original size:38 final size:38
Alignment explanation
Indices: 5686327--5686409 Score: 148
Period size: 38 Copynumber: 2.2 Consensus size: 38
5686317 AACCCTAATC
*
5686327 CCACCTACTCCACCACCCTTGTTGGCCACTCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
*
5686365 CCACCTACTCCACCACTCTTGTTGGCCACCCACCTTGG
1 CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
5686403 CCACCTA
1 CCACCTA
5686410 AACCACCCCA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.17, C:0.48, G:0.12, T:0.23
Consensus pattern (38 bp):
CCACCTACTCCACCACCCTTGTTGGCCACCCACCTTGG
Found at i:5686822 original size:12 final size:13
Alignment explanation
Indices: 5686805--5686854 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
5686795 GAGAGCTTTG
5686805 TTTTATT-TTTTA
1 TTTTATTATTTTA
5686817 TTTTATTATTTT-
1 TTTTATTATTTTA
**
5686829 TACTATTATTTATA
1 TTTTATTATTT-TA
5686843 TTATTATTATTT
1 TT-TTATTATTT
5686855 ATCATGTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 16 0.53
13 5 0.17
14 1 0.03
15 8 0.27
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTTATTATTTTA
Found at i:5686837 original size:15 final size:15
Alignment explanation
Indices: 5686807--5686895 Score: 69
Period size: 15 Copynumber: 5.9 Consensus size: 15
5686797 GAGCTTTGTT
5686807 TTATT-TTT-TATT-
1 TTATTATTTATATTA
* *
5686819 TTATTATTTTTACTA
1 TTATTATTTATATTA
5686834 TTATTTATATTATTATTA
1 TTA-TTAT-TTA-TATTA
* *
5686852 TTTATCATGTATA-TA
1 -TTATTATTTATATTA
5686867 TTATTATTTATATTA
1 TTATTATTTATATTA
5686882 TTATTATATTATAT
1 TTATTAT-TTATAT
5686896 ATGCCCTCTC
Statistics
Matches: 61, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
12 5 0.08
13 3 0.05
14 13 0.21
15 14 0.23
16 12 0.20
17 4 0.07
18 7 0.11
19 3 0.05
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (15 bp):
TTATTATTTATATTA
Found at i:5686838 original size:3 final size:3
Alignment explanation
Indices: 5686814--5686893 Score: 60
Period size: 3 Copynumber: 26.3 Consensus size: 3
5686804 GTTTTATTTT
* * *
5686814 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TTTA TCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA -TTA TTA
5686859 TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
5686894 ATATGCCCTC
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
2 6 0.10
3 46 0.74
4 10 0.16
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:5686840 original size:24 final size:25
Alignment explanation
Indices: 5686808--5686895 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 25
5686798 AGCTTTGTTT
* *
5686808 TATTTTTTATTTTATTATT-TTTAC
1 TATTATTTATATTATTATTATTTAC
5686832 TATTATTTATATTATTATTATTTA-
1 TATTATTTATATTATTATTATTTAC
*
5686856 TCATGTA--TATATTATTATTTATATTAT
1 T-AT-TATTTATATTATTA-TTAT-TTAC
5686883 TATTATATTATAT
1 TATTAT-TTATAT
5686896 ATGCCCTCTC
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
24 28 0.53
25 12 0.23
26 7 0.13
27 1 0.02
28 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (25 bp):
TATTATTTATATTATTATTATTTAC
Found at i:5687206 original size:126 final size:126
Alignment explanation
Indices: 5687094--5687321 Score: 306
Period size: 126 Copynumber: 1.8 Consensus size: 126
5687084 TTATTTTTGC
* *
5687094 TATTACTATTATTATTATATATTA-GTGTATAT-T-TTATGT-ATATATATATTTATATATAGTA
1 TATTACTATTATTATTATATAGTAGGTGTATATCTATTATATAATATATATATTTATATATAGTA
* * *
5687155 TTGTTTTTTA-TTACTTTAAT-TTAATATTTTTATTATATTTGCTTTTTTATTTCTATATT
66 TTATTATTTACTTACTTTAATATTAATATTATTATTATATTTGCTTTTTTATTTCTATATT
* *
5687214 TATTATTATTATTATTATATAGTAGTGTGTATTTCTATTATATACATATATATATTTATATATAG
1 TATTACTATTATTATTATATAGTAG-GTGTATATCTATTATATA-ATATATATATTTATATATAG
* *
5687279 TATTATTATTTACTTTACTTTAATATTATTCTTATTATTATAT
64 TATTATTATTTAC-TTACTTTAATATTAATATTATTATTATAT
5687322 CCAACCCAAT
Statistics
Matches: 90, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
120 22 0.24
122 7 0.08
123 1 0.01
124 5 0.06
126 30 0.33
128 10 0.11
129 15 0.17
ACGTcount: A:0.31, C:0.04, G:0.05, T:0.60
Consensus pattern (126 bp):
TATTACTATTATTATTATATAGTAGGTGTATATCTATTATATAATATATATATTTATATATAGTA
TTATTATTTACTTACTTTAATATTAATATTATTATTATATTTGCTTTTTTATTTCTATATT
Found at i:5689993 original size:20 final size:20
Alignment explanation
Indices: 5689968--5690005 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5689958 CTAGGGATAG
5689968 ATAAGATGCCTTCGACATTA
1 ATAAGATGCCTTCGACATTA
5689988 ATAAGATGCCTTCGACAT
1 ATAAGATGCCTTCGACAT
5690006 CTGCATTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (20 bp):
ATAAGATGCCTTCGACATTA
Found at i:5692319 original size:26 final size:26
Alignment explanation
Indices: 5692283--5692334 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
5692273 GCAAGAGGAG
*
5692283 ATGGAATCACTTTACAAAAACAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
5692309 ATGGAATCACTTCACAAAAACAAAAA
1 ATGGAATCACTTCACAAAAACAAAAA
5692335 CTGTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (26 bp):
ATGGAATCACTTCACAAAAACAAAAA
Found at i:5693631 original size:5 final size:5
Alignment explanation
Indices: 5693621--5693646 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
5693611 TTTTGTGTTC
5693621 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
5693647 ATTTCACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:5694759 original size:20 final size:20
Alignment explanation
Indices: 5694716--5694755 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5694706 GGTTAACATT
*
5694716 AGTTAATTATTAATTAGTTA
1 AGTTAATTATTAATTAATTA
5694736 AGTTAATTA-TAATTAATTA
1 AGTTAATTATTAATTAATTA
5694755 A
1 A
5694756 AGTTTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (20 bp):
AGTTAATTATTAATTAATTA
Found at i:5702724 original size:19 final size:19
Alignment explanation
Indices: 5702678--5702725 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
5702668 GTATATATTT
5702678 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
5702696 TAAATCTTATTT-GGATAGA
1 TAAATTTTATTTAGG-TAGA
5702715 TAAATTTTATT
1 TAAATTTTATT
5702726 CATATTCTAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 6 0.23
19 20 0.77
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:5702787 original size:43 final size:43
Alignment explanation
Indices: 5702739--5702832 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 43
5702729 ATTCTAGAAA
5702739 TATTTT-TATTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
1 TATTTTCT-TTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
* *
5702782 TATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAGGGAAC
1 TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
5702825 TATTTTCT
1 TATTTTCT
5702833 CAATTAGGAT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 47 0.98
44 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (43 bp):
TATTTTCTTTTTATCTTTTAGTAGTTTACTAGAATAAGGGAAC
Found at i:5705377 original size:19 final size:20
Alignment explanation
Indices: 5705353--5705390 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
5705343 GGTACCACCA
5705353 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
5705372 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
5705391 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:5705731 original size:93 final size:93
Alignment explanation
Indices: 5705620--5705790 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
5705610 GCCCCTAAGT
* *
5705620 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
5705685 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
5705713 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
5705778 CGAGTTCGGATGC
66 CGAGTTCGGATGC
5705791 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:5705787 original size:46 final size:46
Alignment explanation
Indices: 5705615--5705787 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
5705605 AACCCGCCCC
* * * * *
5705615 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
5705661 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
5705709 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
5705754 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5705788 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:5710237 original size:19 final size:18
Alignment explanation
Indices: 5710208--5710251 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
5710198 GTATATATTT
*
5710208 TAAATTTATTTAG-GTAGA
1 TAAATTTATTT-GCATAGA
5710226 TAAATCTTATTTGCATAGA
1 TAAAT-TTATTTGCATAGA
5710245 TAAATTT
1 TAAATTT
5710252 TATTCATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (18 bp):
TAAATTTATTTGCATAGA
Found at i:5710317 original size:43 final size:43
Alignment explanation
Indices: 5710264--5710361 Score: 135
Period size: 43 Copynumber: 2.3 Consensus size: 43
5710254 TTCATATTCT
*
5710264 AGAAATATTTT-TATTTTATCTTTTAGTAATTTACTAGAATAAG
1 AGAACTATTTTCT-TTTTATCTTTTAGTAATTTACTAGAATAAG
* * * *
5710307 GGAACTATTTTCTTTTTATGTTTTAGTAGTTTATTAGAATAAG
1 AGAACTATTTTCTTTTTATCTTTTAGTAATTTACTAGAATAAG
5710350 AGAACTATTTTC
1 AGAACTATTTTC
5710362 CCAATTAGGA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
43 47 0.98
44 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (43 bp):
AGAACTATTTTCTTTTTATCTTTTAGTAATTTACTAGAATAAG
Found at i:5718573 original size:29 final size:28
Alignment explanation
Indices: 5718538--5718592 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
5718528 AGTTATACCA
5718538 ATTTGGCTTCGGGCCATGCATATCAGTTG
1 ATTTGGCTTCGGGCCATG-ATATCAGTTG
*
5718567 ATTTGGCTTTGGGCCATGATATCAGT
1 ATTTGGCTTCGGGCCATGATATCAGT
5718593 GCTTCGGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.36
Consensus pattern (28 bp):
ATTTGGCTTCGGGCCATGATATCAGTTG
Found at i:5730389 original size:35 final size:35
Alignment explanation
Indices: 5730343--5730472 Score: 127
Period size: 35 Copynumber: 3.6 Consensus size: 35
5730333 TTTCCTCATT
*
5730343 GAAATACCATACCTACATTTTACAACTCGGTATGG
1 GAAATACCATACCTACATTTTACAACTCAGTATGG
* ** *
5730378 GAAATGCCATACCTACATTTTTTAACTCAGTATGAATTT
1 GAAATACCATACCTACATTTTACAACTCAGTATG----G
*
5730417 GATAATACCATACCTACATTTCACAACTCAGTAT-G
1 GA-AATACCATACCTACATTTTACAACTCAGTATGG
* *
5730452 GATGATAACATACCTACATTT
1 GA-AATACCATACCTACATTT
5730473 CACGCTTTTC
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
35 49 0.63
39 2 0.03
40 27 0.35
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (35 bp):
GAAATACCATACCTACATTTTACAACTCAGTATGG
Found at i:5730465 original size:40 final size:39
Alignment explanation
Indices: 5730344--5730465 Score: 128
Period size: 40 Copynumber: 3.2 Consensus size: 39
5730334 TTCCTCATTG
*
5730344 AAATACCATACCTACATTTTACAACTCGGTATGG--G--
1 AAATACCATACCTACATTTTACAACTCAGTATGGATGAT
* ** *
5730379 AAATGCCATACCTACATTTTTTAACTCAGTATGAATTTGAT
1 AAATACCATACCTACATTTTACAACTCAGTATGGA--TGAT
*
5730420 -AATACCATACCTACATTTCACAACTCAGTATGGATGAT
1 AAATACCATACCTACATTTTACAACTCAGTATGGATGAT
5730458 AACATACC
1 AA-ATACC
5730466 TACATTTCAC
Statistics
Matches: 69, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
35 29 0.42
38 4 0.06
39 2 0.03
40 34 0.49
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (39 bp):
AAATACCATACCTACATTTTACAACTCAGTATGGATGAT
Found at i:5744222 original size:21 final size:22
Alignment explanation
Indices: 5744184--5744231 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
5744174 TAATTTTCAG
* *
5744184 TTTTT-TTTCATGTTCAAGTTT
1 TTTTTATTTCATGTACAAGATT
5744205 TTTTTATTTCAT-TACAAGATT
1 TTTTTATTTCATGTACAAGATT
*
5744226 TCTTTA
1 TTTTTA
5744232 CTCCCCATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.21, C:0.10, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTTATTTCATGTACAAGATT
Found at i:5744844 original size:34 final size:34
Alignment explanation
Indices: 5744800--5744866 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
5744790 GCATGCTTAG
*
5744800 CATGAGGATGATCAAAAAGCACCGAGAAACCTAT
1 CATGAAGATGATCAAAAAGCACCGAGAAACCTAT
* *
5744834 CATGAAGATGATCGAAAAGCGCCGAGAAACCTA
1 CATGAAGATGATCAAAAAGCACCGAGAAACCTA
5744867 CCCTACTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.13
Consensus pattern (34 bp):
CATGAAGATGATCAAAAAGCACCGAGAAACCTAT
Found at i:5747070 original size:19 final size:19
Alignment explanation
Indices: 5747042--5747080 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
5747032 AAAACGAAAG
5747042 AAACGAGAAAA-GGGCCAA
1 AAACGAGAAAATGGGCCAA
5747060 AAACGGAGAAAATGGGCCAA
1 AAAC-GAGAAAATGGGCCAA
5747080 A
1 A
5747081 GTACGAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.21
19 7 0.37
20 8 0.42
ACGTcount: A:0.54, C:0.15, G:0.28, T:0.03
Consensus pattern (19 bp):
AAACGAGAAAATGGGCCAA
Found at i:5753381 original size:17 final size:17
Alignment explanation
Indices: 5753363--5753402 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
5753353 CTGAAATTCT
5753363 TTTCTT-TTCTTTCTTC
1 TTTCTTCTTCTTTCTTC
*
5753379 TTTCTTCTTCTTTATT-
1 TTTCTTCTTCTTTCTTC
5753395 TTTCTTCT
1 TTTCTTCT
5753403 CCTTCGATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.03, C:0.23, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTCTTCTTCTTTCTTC
Found at i:5754083 original size:17 final size:19
Alignment explanation
Indices: 5754056--5754090 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5754046 AGCCAAGTTG
5754056 GGCTGTGTGGGCC-ACACA
1 GGCTGTGTGGGCCTACACA
5754074 GGCT-TGTGGGCCTACAC
1 GGCTGTGTGGGCCTACAC
5754091 TGGCAGGGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.29, G:0.37, T:0.20
Consensus pattern (19 bp):
GGCTGTGTGGGCCTACACA
Found at i:5756127 original size:53 final size:53
Alignment explanation
Indices: 5756047--5756152 Score: 203
Period size: 53 Copynumber: 2.0 Consensus size: 53
5756037 AAAAATCAAA
5756047 TTTGGAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTC
1 TTTGGAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTC
*
5756100 TTTGGAATTGGATCGGGGAAAAGATAAAAGTATTCGACTAATCGACTTGATTC
1 TTTGGAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTC
5756153 ATTGTTTCCA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (53 bp):
TTTGGAATTGGATCGGGGAAAAGATAAAAGTATTCAACTAATCGACTTGATTC
Found at i:5758743 original size:49 final size:48
Alignment explanation
Indices: 5758688--5758804 Score: 135
Period size: 49 Copynumber: 2.4 Consensus size: 48
5758678 TGGATGACCC
* * * *
5758688 AACAATGATGACTTTTACTGTTTGCATATTCTACCATCCCGAGTGGCCT
1 AACAATGATG-CTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
* **
5758737 AACAATGATCGCTTTGAATATTTGCATATTCTATCATCTTGAGCGGCCT
1 AACAATGAT-GCTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
*
5758786 AACAATGATGGTTTTGAAT
1 AACAATGAT-GCTTTGAAT
5758805 TATTATATCG
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 57 0.98
50 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (48 bp):
AACAATGATGCTTTGAATATTTGCATATTCTACCATCCCGAGCGGCCT
Found at i:5761403 original size:41 final size:41
Alignment explanation
Indices: 5761346--5761624 Score: 524
Period size: 41 Copynumber: 6.8 Consensus size: 41
5761336 GAATGTAATA
* *
5761346 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
5761387 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
5761428 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
5761469 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
5761510 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
5761551 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
5761592 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG
1 CAGACTATATGTCTAGCAGGCTTAA-TGCCGGTG
5761625 TACTGAATCA
Statistics
Matches: 235, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
40 3 0.01
41 232 0.99
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (41 bp):
CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:5761649 original size:123 final size:123
Alignment explanation
Indices: 5761346--5761666 Score: 486
Period size: 123 Copynumber: 2.6 Consensus size: 123
5761336 GAATGTAATA
* * * * *
5761346 CAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTATAAGCCTAGCAGGCTTA
5761411 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
66 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
* * *
5761469 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTA
1 CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTATAAGCCTAGCAGGCTTA
5761534 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
66 ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
* *
5761592 CAGACTATATGTCTAGCAGGC-TAAGTGCCGGTG-TAC-TGAATCAGGCTTTAAGCCTAGCAGGC
1 CAGACTATATGTCTAGCAGGCTTAA-TGCCGGTGATACAT--ATCAGACTATAAGCCTAGCAGGC
**
5761654 AAAATGCCGGTGA
63 TTAATGCCGGTGA
5761667 ATCTGTTTAA
Statistics
Matches: 186, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
121 1 0.01
122 6 0.03
123 179 0.96
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (123 bp):
CAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATATCAGACTATAAGCCTAGCAGGCTTA
ATGCCGGTGATACATTTCAGACTATATGTCTAGCAGGCTTAATGCCGGTGATACATTT
Found at i:5767488 original size:18 final size:18
Alignment explanation
Indices: 5767465--5767499 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5767455 TTCATTGCTT
5767465 TTCAAAAGCACTTCTGGC
1 TTCAAAAGCACTTCTGGC
5767483 TTCAAAAGCACTTCTGG
1 TTCAAAAGCACTTCTGG
5767500 AAGAAAAGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.29
Consensus pattern (18 bp):
TTCAAAAGCACTTCTGGC
Found at i:5768066 original size:13 final size:13
Alignment explanation
Indices: 5768050--5768113 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
5768040 TTTAAACCAA
*
5768050 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
*
5768063 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
5768076 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
5768089 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
5768102 ACTTTTCAAAAG
1 ACTTTTCAAAAG
5768114 AAATGAAGAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:5768079 original size:26 final size:26
Alignment explanation
Indices: 5768050--5768113 Score: 101
Period size: 26 Copynumber: 2.5 Consensus size: 26
5768040 TTTAAACCAA
*
5768050 ACTTTTTAAAAGCACTTCTCAAAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
* *
5768076 ACTTTTCCACAGCACTTCTCAAAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
5768102 ACTTTTCAAAAG
1 ACTTTTCAAAAG
5768114 AAATGAAGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.08, T:0.30
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTCTCAAAAGC
Found at i:5768692 original size:21 final size:22
Alignment explanation
Indices: 5768654--5768694 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5768644 CTCAATTAAA
5768654 ATTTATATGAAATCTAATTTAT
1 ATTTATATGAAATCTAATTTAT
* *
5768676 ATTTAT-TTAAATTTAATTT
1 ATTTATATGAAATCTAATTT
5768695 TCTATGTGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTTATATGAAATCTAATTTAT
Found at i:5775479 original size:13 final size:13
Alignment explanation
Indices: 5775461--5775490 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
5775451 AATACTTTCA
*
5775461 AAAAAAATTTAAT
1 AAAAAAATTAAAT
5775474 AAAAAAATTAAAT
1 AAAAAAATTAAAT
5775487 AAAA
1 AAAA
5775491 TATTGTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAATTAAAT
Found at i:5780134 original size:19 final size:20
Alignment explanation
Indices: 5780106--5780155 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
5780096 ATACATAGGT
*
5780106 TTAA-CTTTAATAAAT-TTA
1 TTAATCTTTAATAAATCTAA
*
5780124 TTAATCTTTAATTAATCTAA
1 TTAATCTTTAATAAATCTAA
*
5780144 TCAATCTTTAAT
1 TTAATCTTTAAT
5780156 TCACTTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 4 0.15
19 10 0.37
20 13 0.48
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAATCTTTAATAAATCTAA
Found at i:5780620 original size:65 final size:64
Alignment explanation
Indices: 5780515--5780653 Score: 269
Period size: 65 Copynumber: 2.2 Consensus size: 64
5780505 TTTTGAACAT
5780515 AATTATTCTTGAGACAGAGTTATTCTAAAAAGAGTTGTTTCAAATATTAGTTGCTTTCAACAGG
1 AATTATTCTTGAGACAGAGTTATTCTAAAAAGAGTTGTTTCAAATATTAGTTGCTTTCAACAGG
5780579 ATATTATTCTTGAGACAGAGTTATTCTAAAAAGAGTTGTTTCAAATATTAGTTGCTTTCAACAGG
1 A-ATTATTCTTGAGACAGAGTTATTCTAAAAAGAGTTGTTTCAAATATTAGTTGCTTTCAACAGG
5780644 AATTATTCTT
1 AATTATTCTT
5780654 AAATGACAGT
Statistics
Matches: 74, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
64 10 0.14
65 64 0.86
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.40
Consensus pattern (64 bp):
AATTATTCTTGAGACAGAGTTATTCTAAAAAGAGTTGTTTCAAATATTAGTTGCTTTCAACAGG
Found at i:5782601 original size:43 final size:43
Alignment explanation
Indices: 5782552--5782638 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
5782542 TCATCGACGC
5782552 AAAGATAACTTTAATGTCTTTAATAAATTAGTTCTAGTTACTA
1 AAAGATAACTTTAATGTCTTTAATAAATTAGTTCTAGTTACTA
5782595 AAAGATAACTTTAATGTCTTTAATAAATTAGTTCTAGTTACTA
1 AAAGATAACTTTAATGTCTTTAATAAATTAGTTCTAGTTACTA
5782638 A
1 A
5782639 CTCAAAGTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.41
Consensus pattern (43 bp):
AAAGATAACTTTAATGTCTTTAATAAATTAGTTCTAGTTACTA
Found at i:5783323 original size:22 final size:22
Alignment explanation
Indices: 5783298--5783342 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5783288 ATAATATCTA
*
5783298 TTAATTCATAATTTAA-TTAATT
1 TTAATT-ATAATCTAATTTAATT
*
5783320 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATCTAATTTAATT
5783342 T
1 T
5783343 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTAATTATAATCTAATTTAATT
Found at i:5783328 original size:16 final size:16
Alignment explanation
Indices: 5783309--5783342 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
5783299 TAATTCATAA
5783309 TTTAAT-TAATTTTAAT
1 TTTAATCTAA-TTTAAT
5783325 TTTAATCTAATTTAAT
1 TTTAATCTAATTTAAT
5783341 TT
1 TT
5783343 GGGTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTAATCTAATTTAAT
Found at i:5800606 original size:10 final size:10
Alignment explanation
Indices: 5800593--5800640 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
5800583 TTATTTTCAT
5800593 TTATCTTTAA
1 TTATCTTTAA
* *
5800603 TTATATTAAA
1 TTATCTTTAA
5800613 TTATCTTTAA
1 TTATCTTTAA
* * *
5800623 TTATATGTAT
1 TTATCTTTAA
5800633 TTATCTTT
1 TTATCTTT
5800641 TAGAATTTAA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.60
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:5800636 original size:20 final size:20
Alignment explanation
Indices: 5800591--5800640 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
5800581 ATTTATTTTC
5800591 ATTTATCTTTAATTATATTA
1 ATTTATCTTTAATTATATTA
*
5800611 AATTATCTTTAATTATATGT-
1 ATTTATCTTTAATTATAT-TA
5800631 ATTTATCTTT
1 ATTTATCTTT
5800641 TAGAATTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 26 0.96
21 1 0.04
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTATCTTTAATTATATTA
Found at i:5821917 original size:97 final size:95
Alignment explanation
Indices: 5821797--5821979 Score: 260
Period size: 97 Copynumber: 1.9 Consensus size: 95
5821787 TTTTTAAGAA
* *
5821797 TATGTTGGGCTGAGTAACTGGGGTAAGGTGCTTGGCTGTCATCTCTCCTCGCGTCAAAAAGTTCG
1 TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTATCATCTCT--TCGCGTCAAAAAGTTCG
* *
5821862 ATATGTTCTTAA-AGAAAAATAAAAATTAGGAG
64 ATATATTCCTAAGA-AAAAATAAAAATTAGGAG
** * *
5821894 TATGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTATTATCTCTTCGCGTCAAAAGGTTCGAT
1 TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTATCATCTCTTCGCGTCAAAAAGTTCGAT
5821959 ATATTCCTAAGAAAAAATAAA
66 ATATTCCTAAGAAAAAATAAA
5821980 TAATAATAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
95 35 0.45
96 1 0.01
97 41 0.53
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (95 bp):
TATGTTGGGCTGAGTAACCGGGGTAAGGTGCTTGGCTATCATCTCTTCGCGTCAAAAAGTTCGAT
ATATTCCTAAGAAAAAATAAAAATTAGGAG
Found at i:5822017 original size:14 final size:15
Alignment explanation
Indices: 5821973--5822017 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
5821963 TCCTAAGAAA
5821973 AAAT-AAATAATAAT
1 AAATAAAATAATAAT
*
5821987 -AATTAAATAATAAT
1 AAATAAAATAATAAT
5822001 AAATAAAATAA-AAT
1 AAATAAAATAATAAT
5822015 AAA
1 AAA
5822018 AAGATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 3 0.11
14 16 0.57
15 9 0.32
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATAAAATAATAAT
Found at i:5822026 original size:13 final size:14
Alignment explanation
Indices: 5821973--5822027 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
5821963 TCCTAAGAAA
5821973 AAAT-AAATAATAAT
1 AAATAAAATAA-AAT
*
5821987 -AATTAAATAATAAT
1 AAATAAAATAA-AAT
5822001 AAATAAAATAAAAT
1 AAATAAAATAAAAT
*
5822015 AAA-AAGATAAAAT
1 AAATAAAATAAAAT
5822028 TTAGGGACTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
13 12 0.32
14 16 0.43
15 9 0.24
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (14 bp):
AAATAAAATAAAAT
Found at i:5825194 original size:25 final size:25
Alignment explanation
Indices: 5825111--5825190 Score: 85
Period size: 24 Copynumber: 3.3 Consensus size: 25
5825101 TATATAACGA
5825111 GAAGCTCATAAGAGCCA-TAATCGG
1 GAAGCTCATAAGAGCCATTAATCGG
** * *
5825135 GAAGCTCATGGGAGCCAATAA-CCG
1 GAAGCTCATAAGAGCCATTAATCGG
*
5825159 GTAGCTCCA-AAGAGCCATTAATCGG
1 GAAGCT-CATAAGAGCCATTAATCGG
5825184 GAAGCTC
1 GAAGCTC
5825191 CAAATAGCCA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
24 32 0.73
25 12 0.27
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCATTAATCGG
Found at i:5825207 original size:25 final size:25
Alignment explanation
Indices: 5825108--5825212 Score: 76
Period size: 24 Copynumber: 4.3 Consensus size: 25
5825098 GGCTATATAA
5825108 CGAGAAGCT-CATAAGAGCCA-TAAT
1 CGAGAAGCTCCA-AAGAGCCATTAAT
* ** * *
5825132 CGGGAAGCT-CATGGGAGCCAATAAC
1 CGAGAAGCTCCA-AAGAGCCATTAAT
*
5825157 CG-GTAGCTCCAAAGAGCCATTAAT
1 CGAGAAGCTCCAAAGAGCCATTAAT
* *
5825181 CGGGAAGCTCCAAATAGCCATGT-AT
1 CGAGAAGCTCCAAAGAGCCAT-TAAT
5825206 CGAGAAG
1 CGAGAAG
5825213 TTCAAGCGAG
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
24 33 0.51
25 31 0.48
26 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (25 bp):
CGAGAAGCTCCAAAGAGCCATTAAT
Found at i:5825284 original size:25 final size:27
Alignment explanation
Indices: 5825249--5825299 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
5825239 CTGAGATTCA
*
5825249 TTAATTAGG-AAGCTCACAAAAAGCCT
1 TTAATTAGGAAAACTCACAAAAAGCCT
*
5825275 TTAATT-GGAAAACTCACGAAAAGCC
1 TTAATTAGGAAAACTCACAAAAAGCC
5825300 ATATAACGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.22
Consensus pattern (27 bp):
TTAATTAGGAAAACTCACAAAAAGCCT
Found at i:5834440 original size:57 final size:58
Alignment explanation
Indices: 5834307--5834465 Score: 180
Period size: 59 Copynumber: 2.7 Consensus size: 58
5834297 TTAAATTTAA
* * * *
5834307 AAAAAAACTTAGGTACCGAATTAGGAAAAAAAATGTCAAATTCAAGTACCAAATTGGGAC
1 AAAAAAACTTAGGTACCAAATTA--AGAAAAAATGTCAAGTTCAAGTACCAAATTAGGAC
* * *
5834367 AAAAAAAGTTTAGGTACCAAATTAAGAAAATATGTCAAGTTC-AGATACCGAATTAGG-C
1 AAAAAAA-CTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAAG-TACCAAATTAGGAC
5834425 TAAAAAAA-TTAGGTACCAAATTAAGAAAAAAATGTCAAGTT
1 -AAAAAAACTTAGGTACCAAATTAAG-AAAAAATGTCAAGTT
5834466 TAAATATTAA
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
57 17 0.20
58 17 0.20
59 32 0.37
60 7 0.08
61 14 0.16
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (58 bp):
AAAAAAACTTAGGTACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTAGGAC
Found at i:5835359 original size:26 final size:24
Alignment explanation
Indices: 5835297--5835358 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
5835287 TCACTATTCT
5835297 AAATATTAAAAAATTTATAATTATA
1 AAATA-TAAAAAATTTATAATTATA
* *
5835322 AAATATTAAAAATTTATAAAATTATG
1 AAATATAAAAAATTTAT--AATTATA
5835348 AAAT-TAAAAAA
1 AAATATAAAAAA
5835359 ACTTAACTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 11 0.34
25 11 0.34
26 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATAAAAAATTTATAATTATA
Found at i:5835421 original size:21 final size:22
Alignment explanation
Indices: 5835383--5835441 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
5835373 TTATTAAATT
5835383 AAAT-TAAATTATAAAAACT-ATA
1 AAATATAAA-TAT-AAAACTAATA
5835405 AAATATAAATATAAAACTAATA
1 AAATATAAATATAAAACTAATA
*
5835427 ATATATAAA-ATAAAA
1 AAATATAAATATAAAA
5835442 AAAAGTAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 12 0.35
22 18 0.53
23 4 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATATAAATATAAAACTAATA
Found at i:5836595 original size:56 final size:56
Alignment explanation
Indices: 5836533--5836644 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
5836523 AGTAAATATG
* * *
5836533 TCTGCAACTTGTTTATTGGTTCGTACTTTTTGCAGCTCAATATCTTGAGATAACAC
1 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
5836589 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
1 TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
5836645 ATTTTCTTGA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (56 bp):
TCTGCAACTTGTTCATCGGTTCGTACTTTTTGCAACTCAATATCTTGAGATAACAC
Found at i:5844252 original size:18 final size:20
Alignment explanation
Indices: 5844216--5844258 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
5844206 CAAATAATGT
5844216 AAAAATTATAAGAACATTCA
1 AAAAATTATAAGAACATTCA
*
5844236 AAAAATTTTAA-AA-ATTCA
1 AAAAATTATAAGAACATTCA
5844254 AAAAA
1 AAAAA
5844259 AGTAATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 2 0.09
20 10 0.45
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATTATAAGAACATTCA
Found at i:5849186 original size:19 final size:21
Alignment explanation
Indices: 5849162--5849234 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
5849152 ACTCAAAATA
* *
5849162 ATAATAT-TTTATAAGTA-AT
1 ATAATATATATATAAATATAT
5849181 ATAATAATATATATAAATATAT
1 ATAAT-ATATATATAAATATAT
*
5849203 ATAATATATATATATATATAT
1 ATAATATATATATAAATATAT
5849224 AT-ATATATATA
1 ATAATATATATA
5849235 AAGAAAAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.10
20 11 0.23
21 25 0.52
22 7 0.15
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (21 bp):
ATAATATATATATAAATATAT
Found at i:5849187 original size:22 final size:23
Alignment explanation
Indices: 5849159--5849235 Score: 86
Period size: 22 Copynumber: 3.3 Consensus size: 23
5849149 TTTACTCAAA
* *
5849159 ATAATAATATTTTATAAGTA-AT
1 ATAATAATATTATATAAATATAT
5849181 ATAATAATA-TATATAAATATAT
1 ATAATAATATTATATAAATATAT
*
5849203 ATAATATATATATATATATATATAT
1 ATAATA-ATAT-TATATAAATATAT
5849228 ATATATAA
1 ATA-ATAA
5849236 AGAAAAGAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
21 8 0.17
22 17 0.36
23 3 0.06
25 16 0.34
26 3 0.06
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (23 bp):
ATAATAATATTATATAAATATAT
Found at i:5849192 original size:10 final size:10
Alignment explanation
Indices: 5849159--5849235 Score: 61
Period size: 10 Copynumber: 7.4 Consensus size: 10
5849149 TTTACTCAAA
5849159 ATAATAATAT
1 ATAATAATAT
* *
5849169 TTTATAAGTAAT
1 ATAATAA-T-AT
5849181 ATAATAATAT
1 ATAATAATAT
5849191 AT-ATAA-AT
1 ATAATAATAT
5849199 ATATATAATAT
1 ATA-ATAATAT
5849210 AT-ATATATAT
1 ATAATA-ATAT
5849220 ATATATATATAT
1 ATA-ATA-ATAT
5849232 ATAA
1 ATAA
5849236 AGAAAAGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 15
0.74 0.05 0.20
Matches are distributed among these distances:
8 4 0.07
9 7 0.13
10 19 0.35
11 7 0.13
12 18 0.33
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (10 bp):
ATAATAATAT
Found at i:5849194 original size:2 final size:2
Alignment explanation
Indices: 5849179--5849234 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
5849169 TTTATAAGTA
*
5849179 AT AT A- AT A- AT AT AT AT AA AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5849218 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
5849235 AAGAAAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5855980 original size:14 final size:14
Alignment explanation
Indices: 5855961--5855988 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5855951 AGATATGTTC
5855961 GGTGATGGAAATAA
1 GGTGATGGAAATAA
5855975 GGTGATGGAAATAA
1 GGTGATGGAAATAA
5855989 AAGCTTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.36, T:0.21
Consensus pattern (14 bp):
GGTGATGGAAATAA
Found at i:5856608 original size:30 final size:31
Alignment explanation
Indices: 5856554--5856639 Score: 129
Period size: 30 Copynumber: 2.8 Consensus size: 31
5856544 GAAACATAGG
5856554 AGTGATCAAATTATAAATTTATTAATAATTA
1 AGTGATCAAATTATAAATTTATTAATAATTA
* * *
5856585 AGTGATTAAATTATAAA-TTATTAATTATTG
1 AGTGATCAAATTATAAATTTATTAATAATTA
*
5856615 AGGGATCAAATTATAAATTTATTAA
1 AGTGATCAAATTATAAATTTATTAA
5856640 CCCATCTAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
30 26 0.53
31 23 0.47
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (31 bp):
AGTGATCAAATTATAAATTTATTAATAATTA
Found at i:5861877 original size:56 final size:56
Alignment explanation
Indices: 5861815--5861950 Score: 227
Period size: 56 Copynumber: 2.4 Consensus size: 56
5861805 ACCATGGCAT
5861815 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAATTGGCATCGATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAATTGGCATCGATATGTGATTC
** ** *
5861871 CGATATATGTGTATGAGTAAGACCACGTTTAATACGTTGGCATCTATATGTGATTC
1 CGATATATGTGTGCGAGTAAGACCACGTTTAATAAATTGGCATCGATATGTGATTC
5861927 CGATATATGTGTGCGAGTAAGACC
1 CGATATATGTGTGCGAGTAAGACC
5861951 TTGTCTGGGA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 73 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (56 bp):
CGATATATGTGTGCGAGTAAGACCACGTTTAATAAATTGGCATCGATATGTGATTC
Found at i:5862190 original size:16 final size:16
Alignment explanation
Indices: 5862166--5862196 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5862156 TGGTTATTTA
*
5862166 ATATTTGATGCAAATT
1 ATATATGATGCAAATT
5862182 ATATATGATGCAAAT
1 ATATATGATGCAAAT
5862197 GAAAATATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.39
Consensus pattern (16 bp):
ATATATGATGCAAATT
Found at i:5862206 original size:19 final size:19
Alignment explanation
Indices: 5862182--5862225 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
5862172 GATGCAAATT
5862182 ATATATGATGCAAATG-AAA
1 ATATATG-TGCAAATGAAAA
* *
5862201 ATATATGTGTATATGAAAA
1 ATATATGTGCAAATGAAAA
5862220 ATATAT
1 ATATAT
5862226 TCGGCCAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.50, C:0.02, G:0.14, T:0.34
Consensus pattern (19 bp):
ATATATGTGCAAATGAAAA
Found at i:5865666 original size:11 final size:11
Alignment explanation
Indices: 5865650--5865680 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
5865640 GTAATGTTAA
5865650 AATATATACAT
1 AATATATACAT
5865661 AATATATACAT
1 AATATATACAT
5865672 ATATATATA
1 A-ATATATA
5865681 AAATAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.63
12 7 0.37
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATATACAT
Found at i:5865853 original size:32 final size:34
Alignment explanation
Indices: 5865783--5865854 Score: 80
Period size: 32 Copynumber: 2.2 Consensus size: 34
5865773 TAATAGGTAT
* *
5865783 AATA-ATAAATATAATGATATACGAAAATAATAC
1 AATATATAAATATAATGATATACAAAAATAATAA
*
5865816 TATATATAAA-AT-ATG-TATACAAAGAATAATAA
1 AATATATAAATATAATGATATACAAA-AATAATAA
5865848 AATATAT
1 AATATAT
5865855 GTACTAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
31 7 0.21
32 16 0.48
33 5 0.15
34 5 0.15
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.31
Consensus pattern (34 bp):
AATATATAAATATAATGATATACAAAAATAATAA
Found at i:5866047 original size:22 final size:23
Alignment explanation
Indices: 5865959--5866068 Score: 86
Period size: 22 Copynumber: 4.7 Consensus size: 23
5865949 AGTGTTTAAG
* *
5865959 AATATATACATAAGATGATATGGA
1 AATATATACATAATAT-ATATGAA
* *
5865983 AATATGTACATGGAATAGTATATAAA
1 AATATATACAT--AATA-TATATGAA
5866009 AATATA-AC-TAATA-ATATTGAA
1 AATATATACATAATATATA-TGAA
5866030 AATATATACATAATATATAT-AA
1 AATATATACATAATATATATGAA
*
5866052 AACATATACGAT-ATATA
1 AATATATAC-ATAATATA
5866069 CATATACATT
Statistics
Matches: 71, Mismatches: 7, Indels: 18
0.74 0.07 0.19
Matches are distributed among these distances:
20 3 0.04
21 9 0.13
22 21 0.30
23 8 0.11
24 14 0.20
25 2 0.03
26 13 0.18
27 1 0.01
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (23 bp):
AATATATACATAATATATATGAA
Found at i:5866058 original size:24 final size:23
Alignment explanation
Indices: 5865959--5866059 Score: 82
Period size: 24 Copynumber: 4.3 Consensus size: 23
5865949 AGTGTTTAAG
* **
5865959 AATATATACATAAGATGATATGGA
1 AATATATACATAATAT-ATATAAA
*
5865983 AATATGTACATGGAATAGTATATAAA
1 AATATATACAT--AATA-TATATAAA
*
5866009 AATATA-AC-TAATA-ATATTGAA
1 AATATATACATAATATATA-TAAA
5866030 AATATATACATAATATATATAAA
1 AATATATACATAATATATATAAA
5866053 ACATATA
1 A-ATATA
5866060 CGATATATAC
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
20 3 0.05
21 9 0.15
22 6 0.10
23 9 0.15
24 19 0.31
25 2 0.03
26 13 0.21
27 1 0.02
ACGTcount: A:0.54, C:0.05, G:0.09, T:0.32
Consensus pattern (23 bp):
AATATATACATAATATATATAAA
Found at i:5866143 original size:17 final size:18
Alignment explanation
Indices: 5866110--5866143 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5866100 GGAACTTATT
5866110 AATACGCTACATAGATAC
1 AATACGCTACATAGATAC
*
5866128 AATACG-TACATGGATA
1 AATACGCTACATAGATA
5866144 TAAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.24
Consensus pattern (18 bp):
AATACGCTACATAGATAC
Found at i:5866201 original size:11 final size:11
Alignment explanation
Indices: 5866187--5866252 Score: 57
Period size: 11 Copynumber: 6.1 Consensus size: 11
5866177 TAATATTTGA
5866187 AATATATACAT
1 AATATATACAT
5866198 AATATA-A-A-
1 AATATATACAT
*
5866206 AATATATATAT
1 AATATATACAT
* **
5866217 AATGTAGTTTTAT
1 AATATA--TACAT
5866230 AATATATACAT
1 AATATATACAT
5866241 AATATATACAT
1 AATATATACAT
5866252 A
1 A
5866253 TTAAAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
8 6 0.13
9 2 0.04
10 2 0.04
11 26 0.58
13 9 0.20
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (11 bp):
AATATATACAT
Found at i:5866273 original size:18 final size:20
Alignment explanation
Indices: 5866239--5866277 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
5866229 TAATATATAC
5866239 ATAATATATACATATTAAAA
1 ATAATATATACATATTAAAA
5866259 ATAATA-ATA-ATATTAAAA
1 ATAATATATACATATTAAAA
5866277 A
1 A
5866278 AAACAACTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 3 0.16
20 6 0.32
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATATATACATATTAAAA
Found at i:5868523 original size:75 final size:72
Alignment explanation
Indices: 5868345--5868562 Score: 285
Period size: 75 Copynumber: 3.0 Consensus size: 72
5868335 CTCTTTAAAA
* * * *
5868345 CTCAGCGTGTCTTGAGGCTCAACTCACCTCTTGCAATATGAGTTGA-ATTCTTGAAAAGCAGAAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTG-AAA-CAGAAA
5868409 TTGAAAATAC
64 TT-AAAATAC
* * *
5868419 CTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGATGAACAGAAA
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGA--AACAGAAA
5868484 TTAAAATTAC
64 TTAAAA-TAC
* * *
5868494 CTCAGTGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTCTTTGAAACATAAATT
1 CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACAGAAATT
5868559 AAAA
66 AAAA
5868563 AACAAAAATT
Statistics
Matches: 128, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
73 13 0.10
74 47 0.37
75 66 0.52
76 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (72 bp):
CTCAGCGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAACAGAAATT
AAAATAC
Found at i:5868677 original size:72 final size:72
Alignment explanation
Indices: 5868557--5868715 Score: 205
Period size: 72 Copynumber: 2.2 Consensus size: 72
5868547 GAAACATAAA
* **
5868557 TTAAAAAACAAAAATTGAACATACCTCAGTGTGCCCCGAGGCTCAACTCA-C-CTCAGCAATATG
1 TTAAAAAACAAAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCA-CAATATG
5868620 AGTCGATTT
65 AGTCGA-TT
* * * *
5868629 TTGAAAAACAAATATTGAAAATACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
1 TTAAAAAACAAAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGA
*
5868694 GTTGATT
66 GTCGATT
*
5868701 TTAAAAAACAGAAAT
1 TTAAAAAACAAAAAT
5868716 AAAAATATCA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
72 57 0.77
73 13 0.18
74 4 0.05
ACGTcount: A:0.39, C:0.22, G:0.14, T:0.25
Consensus pattern (72 bp):
TTAAAAAACAAAAATTGAAAATACCTCAGCATGCCCCGAGGCTCAACTCACCTCTCACAATATGA
GTCGATT
Found at i:5868698 original size:159 final size:161
Alignment explanation
Indices: 5868406--5868701 Score: 420
Period size: 159 Copynumber: 1.8 Consensus size: 161
5868396 TGAAAAGCAG
* * *
5868406 AAATTGAAAATACCTCAACGTGCCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGA-TTTTT
** ** * *
5868471 TGATGAACAGAAATTAAAATTACCTCAGTGTGACTTGAGGCTCAACTCACCTCTCGCAATATGAG
65 TGAAAAACAGAAATTAAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAG
5868536 TTGATTTCTTTGAAACATAAATTAAAAAACAA
130 TTGATTTCTTTGAAACATAAATTAAAAAACAA
* **
5868568 AAATTGAACATACCTCAGTGTGCCCCGAGGCTCAACTCACCTC-AGCAATATGAGTCGA-TTTTT
1 AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGATTTTTT
*
5868631 GAAAAACA-AATATTGAAAA-TACCTCAGCATGTCCTGAGGCTCAACTCACCTCTCACAATATGA
66 GAAAAACAGAA-ATT-AAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGA
5868694 GTTGATTT
129 GTTGATTT
5868702 TAAAAAACAG
Statistics
Matches: 119, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
158 2 0.02
159 61 0.51
160 4 0.03
161 13 0.11
162 39 0.33
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.28
Consensus pattern (161 bp):
AAATTGAAAATACCTCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATATGAGTCGATTTTTT
GAAAAACAGAAATTAAAATTACCTCAGCATGACCTGAGGCTCAACTCACCTCTCACAATATGAGT
TGATTTCTTTGAAACATAAATTAAAAAACAA
Found at i:5886593 original size:23 final size:24
Alignment explanation
Indices: 5886566--5886616 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
5886556 TTAATAGGTC
* *
5886566 AAATAAACTATGCTAAT-AATGCT
1 AAATAAACTATACTAATAAATACT
* *
5886589 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
5886613 AAAT
1 AAAT
5886617 TTCTAGAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.53, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:5889548 original size:30 final size:30
Alignment explanation
Indices: 5889514--5889594 Score: 162
Period size: 30 Copynumber: 2.7 Consensus size: 30
5889504 TTTTCGAGCA
5889514 TAGGGGTAAAATGGTCATTTTGTTAAAGTC
1 TAGGGGTAAAATGGTCATTTTGTTAAAGTC
5889544 TAGGGGTAAAATGGTCATTTTGTTAAAGTC
1 TAGGGGTAAAATGGTCATTTTGTTAAAGTC
5889574 TAGGGGTAAAATGGTCATTTT
1 TAGGGGTAAAATGGTCATTTT
5889595 ACCAAAGATG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (30 bp):
TAGGGGTAAAATGGTCATTTTGTTAAAGTC
Found at i:5890090 original size:94 final size:90
Alignment explanation
Indices: 5889929--5890146 Score: 208
Period size: 94 Copynumber: 2.4 Consensus size: 90
5889919 GATTTCTTGT
** * * *
5889929 GTGCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTATAAGTGTCAGTTTAATACCATG
1 GTGCCAGTGTAAGACATGTCT-GGACATGCATCGACCACACGATAAGTGCCAGTGTAAGACCATG
5889994 TCTAGGACATGACATCAGCGT-AGAGATGA
65 TCTAGGACATG-CATCAGC-TAAGAG-T-A
* * * *
5890023 GTGCCAGTGTAAGACGTGTCTGAGACATGCATCGGCCTCGACGATGA-TAGCCAGTGTAAGA-CA
1 GTGCCAGTGTAAGACATGTCTG-GACATGCATCGACCAC-ACGATAAGT-GCCAGTGTAAGACCA
* * *
5890086 TGTCTGGGACTTGCATCAGCTAAGAGTT
63 TGTCTAGGACATGCATCAGCTAAGAGTA
* *
5890114 GTGCTAGTGTAAGACATGTCCGGAACATGCATC
1 GTGCCAGTGTAAGACATGTCTGG-ACATGCATC
5890147 AGCACGTATA
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
90 1 0.01
91 28 0.27
92 2 0.02
93 12 0.12
94 48 0.46
95 13 0.12
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (90 bp):
GTGCCAGTGTAAGACATGTCTGGACATGCATCGACCACACGATAAGTGCCAGTGTAAGACCATGT
CTAGGACATGCATCAGCTAAGAGTA
Found at i:5890224 original size:49 final size:47
Alignment explanation
Indices: 5889931--5890245 Score: 163
Period size: 47 Copynumber: 6.7 Consensus size: 47
5889921 TTTCTTGTGT
* *
5889931 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCACATTAT-AAG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTC--TATGAGGATA
* * * * * *
5889977 GTCAGTTTAATACCATGTCTAGGACATGACATC-AGC-GTA-GA-GATGA
1 GCCAGTGTAAGA-CATGTCTGGGACATG-CATCGACCTCTATGAGGAT-A
* * * * * *
5890023 GTGCCAGTGTAAGACGTGTCTGAGACATGCATCGGCCTCGACGATGATA
1 --GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAGGATA
* * *
5890072 GCCAGTGTAAGACATGTCTGGGACTTGCATC-A--GCTAAGAGTTG-T-
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAG--GATA
* * * * * * *
5890116 GCTAGTGTAAGACATGTCCGGAACATGCATCAGCACGTATAT-ACGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATC-G-ACCTCTATGAGGATA
* *
5890164 GCTAGTATAAGACCATGTCTGGGACATGGCATCGACCTCTATGAGGATA
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACCTCTATGAGGATA
5890213 GCCAGTGTAAGACCATGTCT-GGACATGGCATCG
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
5890246 GCAACTTATC
Statistics
Matches: 203, Mismatches: 42, Indels: 46
0.70 0.14 0.16
Matches are distributed among these distances:
43 1 0.00
44 35 0.17
45 1 0.00
46 15 0.07
47 58 0.29
48 45 0.22
49 40 0.20
50 8 0.04
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.24
Consensus pattern (47 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGACCTCTATGAGGATA
Found at i:5892170 original size:29 final size:28
Alignment explanation
Indices: 5892134--5892214 Score: 80
Period size: 27 Copynumber: 2.9 Consensus size: 28
5892124 CACACCCGGA
5892134 ATAATATAAATCCTCCATAACACACCAGT
1 ATAATAT-AATCCTCCATAACACACCAGT
* *
5892163 ATAATAT-AGCCTCCCA-AACACACTAGT
1 ATAATATAATCCT-CCATAACACACCAGT
*
5892190 A-AAT-TATATCCTCCCTAACACACCA
1 ATAATATA-ATCCTCCATAACACACCA
5892215 ATAAGGCATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
25 1 0.02
26 5 0.12
27 27 0.63
28 3 0.07
29 7 0.16
ACGTcount: A:0.42, C:0.31, G:0.04, T:0.23
Consensus pattern (28 bp):
ATAATATAATCCTCCATAACACACCAGT
Found at i:5892182 original size:27 final size:27
Alignment explanation
Indices: 5892152--5892214 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 27
5892142 AATCCTCCAT
5892152 AACACACCAGTATAA-TATAGCCTCCCA
1 AACACACCAGTA-AATTATAGCCTCCCA
* * *
5892179 AACACACTAGTAAATTATATCCTCCCT
1 AACACACCAGTAAATTATAGCCTCCCA
5892206 AACACACCA
1 AACACACCA
5892215 ATAAGGCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 2 0.06
27 29 0.94
ACGTcount: A:0.41, C:0.33, G:0.05, T:0.21
Consensus pattern (27 bp):
AACACACCAGTAAATTATAGCCTCCCA
Found at i:5892745 original size:17 final size:18
Alignment explanation
Indices: 5892715--5892748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5892705 AATTTTTATT
*
5892715 CAATTTATTCCCTAATTC
1 CAATTTAATCCCTAATTC
5892733 CAATTTAAT-CCTAATT
1 CAATTTAATCCCTAATT
5892749 AACTCTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.44
Consensus pattern (18 bp):
CAATTTAATCCCTAATTC
Found at i:5893184 original size:17 final size:17
Alignment explanation
Indices: 5893162--5893194 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5893152 GTTTTCGTTT
5893162 TGTTC-TCTGTTCTTTTC
1 TGTTCTTCT-TTCTTTTC
5893179 TGTTCTTCTTTCTTTT
1 TGTTCTTCTTTCTTTT
5893195 ATTTTATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (17 bp):
TGTTCTTCTTTCTTTTC
Found at i:5897783 original size:57 final size:57
Alignment explanation
Indices: 5897713--5897825 Score: 208
Period size: 57 Copynumber: 2.0 Consensus size: 57
5897703 AAGGGGATCC
*
5897713 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAATGTCTCAATTATTCT
1 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTCT
*
5897770 ATAGATTGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTC
1 ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTC
5897826 AATCTAGGGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (57 bp):
ATAGATCGAGTTAATGCAACCCTAGGGTGTTAATTAGAGAAAGGTCTCAATTATTCT
Found at i:5899631 original size:13 final size:13
Alignment explanation
Indices: 5899592--5899655 Score: 67
Period size: 13 Copynumber: 4.9 Consensus size: 13
5899582 AGTTCTTCAT
5899592 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
5899605 TGC-TGTGAAAAAG
1 TGCTTTTG-AAAAG
*
5899618 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
5899631 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
*
5899644 TGCTTTGGAAAA
1 TGCTTTTGAAAA
5899656 ATTTAAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
12 3 0.07
13 36 0.86
14 3 0.07
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:5901340 original size:13 final size:13
Alignment explanation
Indices: 5901322--5901350 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5901312 CTCGCCACAC
5901322 CCATGTGCCGCAT
1 CCATGTGCCGCAT
5901335 CCATGTGCCGCAT
1 CCATGTGCCGCAT
5901348 CCA
1 CCA
5901351 ACTCTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.41, G:0.21, T:0.21
Consensus pattern (13 bp):
CCATGTGCCGCAT
Found at i:5909833 original size:18 final size:17
Alignment explanation
Indices: 5909810--5909844 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
5909800 CCCTTCAAGG
5909810 GTTTTGGATTTTCTTTAT
1 GTTTTGGATTTT-TTTAT
*
5909828 GTTTTGTATTTTTTTAT
1 GTTTTGGATTTTTTTAT
5909845 TCTTCTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.11, C:0.03, G:0.14, T:0.71
Consensus pattern (17 bp):
GTTTTGGATTTTTTTAT
Found at i:5913481 original size:162 final size:166
Alignment explanation
Indices: 5913122--5913605 Score: 509
Period size: 162 Copynumber: 2.9 Consensus size: 166
5913112 GTTACACTTG
* * * *
5913122 TATTGCGGTTAATTACCCCTAAAATTAGTTATATGACACATCTTAATCTCCGTAC-ATTACTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
* * * *
5913186 TGGTCATTTCTTTAGCCCACCATGCTTTTTTACACTACACCCTGTACTAGAACCTGACTTACATG
66 TGGTCATTTGTTTAGCCCACCATGCCTTTTTACACGACACCCTGTACTAGAACCAGACTTACATG
* *
5913251 TCAACAATTAGGACTAGTACAGGAATAATGGGCATGTCTT
131 TCAACAATTAGAACTAATACAGG----ATGGGCATGTCTT
** * * * ** * *
5913291 TATTATGGTTGATCACCCCTGAAGTTAGTTGTATGACACATCTCAGTCTTTGTACAACTACTCCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
* * * ** * *
5913356 TGGTCATTTGTTTAGCCCA-CATTCCTTTTTGCGCGACATTCTGTACTGGAATCAGACTTACATG
66 TGGTCATTTGTTTAGCCCACCATGCCTTTTTACACGACACCCTGTACTAGAACCAGACTTACATG
* *
5913420 TCGATAATTAGAAC-AATACA-G-TGGGCATGTCTT
131 TCAACAATTAGAACTAATACAGGATGGGCATGTCTT
* *
5913453 TATTGCAGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTGCTTCA
1 TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
** * * *
5913518 TGGTCATTTGTTTAGCCTGCAATG-CTTTTCTATACGACA-CCTCGTAC-AGAA-CTGAACTTAC
66 TGGTCATTTGTTTAGCCCACCATGCCTTTT-TACACGACACCCT-GTACTAGAACCAG-ACTTAC
* *
5913579 ATGTCGACAATTAGGACTAATACAGGA
128 ATGTCAACAATTAGAACTAATACAGGA
5913606 ATAGTAGGAA
Statistics
Matches: 256, Mismatches: 51, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
161 2 0.01
162 114 0.45
163 18 0.07
164 1 0.00
167 1 0.00
168 5 0.02
169 90 0.35
170 25 0.10
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.34
Consensus pattern (166 bp):
TATTGCGGTTAATTACCCCTGAAGTTAGTTGTATGACACATCTTAGTCTCCGTACAATTACTTCA
TGGTCATTTGTTTAGCCCACCATGCCTTTTTACACGACACCCTGTACTAGAACCAGACTTACATG
TCAACAATTAGAACTAATACAGGATGGGCATGTCTT
Found at i:5917537 original size:75 final size:75
Alignment explanation
Indices: 5917414--5917563 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
5917404 CTCTAAGAAG
**
5917414 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTTTATTGAATGGTTATGGTGGTTCGAGGAGATT
1 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
5917479 ATACTCCTCA
66 ATACTCCTCA
5917489 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
1 CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
5917554 ATACTCCTCA
66 ATACTCCTCA
5917564 TTCCTGCTGT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (75 bp):
CGCTTATTTATAGTCTAAGCTCGACTTACCTTTCCATTGAATGGTTATGGTGGTTCGAGGAGATT
ATACTCCTCA
Found at i:5928052 original size:40 final size:41
Alignment explanation
Indices: 5927992--5928085 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 41
5927982 GGCTATTTGG
*
5927992 AAAAATACATATTGGTTCCACTTGACACAGTGGCGACAGCCA
1 AAAAATATATA-TGGTTCCACTTGACACAGTGGCGACAGCCA
5928034 AAAAATATATAT-GTTCCACTTGACACAGTGGCGACAGCCA
1 AAAAATATATATGGTTCCACTTGACACAGTGGCGACAGCCA
5928074 AAAAATATATAT
1 AAAAATATATAT
5928086 TTTTAAAAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 40 0.78
41 1 0.02
42 10 0.20
ACGTcount: A:0.40, C:0.20, G:0.16, T:0.23
Consensus pattern (41 bp):
AAAAATATATATGGTTCCACTTGACACAGTGGCGACAGCCA
Found at i:5930243 original size:31 final size:31
Alignment explanation
Indices: 5930205--5930322 Score: 209
Period size: 31 Copynumber: 3.8 Consensus size: 31
5930195 ACAAATGACA
5930205 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5930236 AGTGAAAAGTGGTAGCTTCTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5930267 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
5930298 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
5930323 AAGTGACAAG
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 82 1.00
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.26
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:5930496 original size:49 final size:48
Alignment explanation
Indices: 5930395--5930569 Score: 204
Period size: 42 Copynumber: 3.8 Consensus size: 48
5930385 ACTGTATAAT
* * * * *
5930395 ACCATATCTGGGATATGGCATC-AGTGAGATATGTGATT-CGTGTACG
1 ACCATAGCTGGGCTATGGCATCGAATGTGATATGTGATTACGTGTAAG
5930441 ACCATAGCTGGGCTATGGCATCGATATGTGATATGTGATTACGTGTAAG
1 ACCATAGCTGGGCTATGGCATCGA-ATGTGATATGTGATTACGTGTAAG
5930490 ACCATAGCTGGGCTATGGCATCG-A--T-ATA--TGATTACGTGTAAG
1 ACCATAGCTGGGCTATGGCATCGAATGTGATATGTGATTACGTGTAAG
* *
5930532 ACCATAGCTAGGCTATGGCATCAATATGTGAATATGTG
1 ACCATAGCTGGGCTATGGCATCGA-ATGTG-ATATGTG
5930570 TAAAACCATA
Statistics
Matches: 111, Mismatches: 7, Indels: 18
0.82 0.05 0.13
Matches are distributed among these distances:
42 35 0.32
44 4 0.04
45 1 0.01
46 21 0.19
47 2 0.02
48 16 0.14
49 30 0.27
50 2 0.02
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (48 bp):
ACCATAGCTGGGCTATGGCATCGAATGTGATATGTGATTACGTGTAAG
Found at i:5930529 original size:42 final size:42
Alignment explanation
Indices: 5930470--5930597 Score: 175
Period size: 42 Copynumber: 3.0 Consensus size: 42
5930460 ATCGATATGT
5930470 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
* *
5930512 GATATATGATTACGTGTAAGACCATAGCTAGGCTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
* * * * * **
5930554 AATATGTGAATATGTGTAAAACCATAGTTGAACTATGGCATC
1 GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
5930596 GA
1 GA
5930598 GAAAACAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (42 bp):
GATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATC
Found at i:5931621 original size:6 final size:6
Alignment explanation
Indices: 5931610--5931636 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5931600 ACTTAGTAAC
5931610 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
5931637 GAGTAAACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:5932008 original size:20 final size:19
Alignment explanation
Indices: 5931967--5932008 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
5931957 AAAAATTCTG
* *
5931967 AAATTTATATTTTTTTAGA
1 AAATTTATATATTTTTAAA
5931986 AAATTATATATATTTTTAAA
1 AAATT-TATATATTTTTAAA
5932006 AAA
1 AAA
5932009 AATTAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
AAATTTATATATTTTTAAA
Found at i:5932020 original size:21 final size:21
Alignment explanation
Indices: 5931996--5932036 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5931986 AAATTATATA
*
5931996 TATTTTTAAAAAAAATTAAAG
1 TATTTATAAAAAAAATTAAAG
* *
5932017 TATTTATAAAGAAAGTTAAA
1 TATTTATAAAAAAAATTAAA
5932037 AAATTTTAAA
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:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (21 bp):
TATTTATAAAAAAAATTAAAG
Found at i:5933469 original size:18 final size:16
Alignment explanation
Indices: 5933421--5933472 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
5933411 TTATATCCTT
* * *
5933421 TATAAATTTAAAATTC
1 TATAAAATTAAAAATA
*
5933437 TAAAAAATTAAAAATA
1 TATAAAATTAAAAATA
5933453 TATAAAATCTAATAAATA
1 TATAAAAT-TAA-AAATA
5933471 TA
1 TA
5933473 ATATTTGACT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
16 19 0.66
17 3 0.10
18 7 0.24
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TATAAAATTAAAAATA
Found at i:5935533 original size:13 final size:14
Alignment explanation
Indices: 5935506--5935539 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5935496 AACTATCAAA
5935506 GTTTAAAAGCATTT
1 GTTTAAAAGCATTT
5935520 GTTTAAAA-CATTT
1 GTTTAAAAGCATTT
5935533 GCTTTAA
1 G-TTTAA
5935540 CTTTGGGAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (14 bp):
GTTTAAAAGCATTT
Found at i:5937261 original size:39 final size:39
Alignment explanation
Indices: 5937202--5937341 Score: 217
Period size: 39 Copynumber: 3.6 Consensus size: 39
5937192 ATCGTGATCT
** *
5937202 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
5937241 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
5937280 GAAGCCCGGAGGCTAACTGAAGCATATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
* *
5937319 AAAGCCTGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
5937342 TCATTAGAGC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 93 1.00
ACGTcount: A:0.38, C:0.22, G:0.26, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:5940484 original size:12 final size:12
Alignment explanation
Indices: 5940461--5940492 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5940451 GAGTGCATTA
5940461 AAAGTG-TTGAG
1 AAAGTGATTGAG
5940472 AAAGTGATTGAG
1 AAAGTGATTGAG
5940484 AAAGT-ATTG
1 AAAGTGATTG
5940493 TTAACAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (12 bp):
AAAGTGATTGAG
Found at i:5942001 original size:25 final size:25
Alignment explanation
Indices: 5941967--5942016 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
5941957 ATCAGGGACT
5941967 CAATTGAGTGAAATAAAACTCTAAA
1 CAATTGAGTGAAATAAAACTCTAAA
5941992 CAATTGAGTGAAATAAAACTCTAAA
1 CAATTGAGTGAAATAAAACTCTAAA
5942017 AATAGTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (25 bp):
CAATTGAGTGAAATAAAACTCTAAA
Found at i:5944831 original size:30 final size:29
Alignment explanation
Indices: 5944792--5944850 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
5944782 AACACTCTTC
*
5944792 TTCAGCAAATTGATGAACAAAAACTGAAAA
1 TTCAACAAATTGATGAACAAAAACT-AAAA
5944822 TTCAACAAATTGATGAACAAAAACTAAAA
1 TTCAACAAATTGATGAACAAAAACTAAAA
5944851 CTTGTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 4 0.14
30 24 0.86
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.20
Consensus pattern (29 bp):
TTCAACAAATTGATGAACAAAAACTAAAA
Found at i:5948172 original size:24 final size:24
Alignment explanation
Indices: 5948145--5948190 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
5948135 TTATTGTTTC
*
5948145 ATATTTAAAAAAATTTTAAAAATT
1 ATATATAAAAAAATTTTAAAAATT
* * *
5948169 ATATATATATATATTTTAAAAA
1 ATATATAAAAAAATTTTAAAAA
5948191 ATAATAACTC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATAAAAAAATTTTAAAAATT
Found at i:5948682 original size:5 final size:5
Alignment explanation
Indices: 5948672--5948703 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
5948662 AAAATTTGTG
5948672 TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
5948704 TCACAAATTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:5952859 original size:36 final size:36
Alignment explanation
Indices: 5952818--5952921 Score: 181
Period size: 36 Copynumber: 2.8 Consensus size: 36
5952808 AATCTTTAAG
5952818 GATATGCAATCTTAGATATGATACAATCTTAGACAT
1 GATATGCAATCTTAGATATGATACAATCTTAGACAT
*
5952854 GATATGCAATCTTAGATATGATACAATCTTAGATAT
1 GATATGCAATCTTAGATATGATACAATCTTAGACAT
5952890 GATATGCAATCTTAGATATGATATGCAATCTT
1 GATATGCAATCTTAGATATGATA--CAATCTT
5952922 GAAGATATGA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
36 58 0.89
38 7 0.11
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (36 bp):
GATATGCAATCTTAGATATGATACAATCTTAGACAT
Found at i:5952865 original size:19 final size:19
Alignment explanation
Indices: 5952818--5952932 Score: 175
Period size: 19 Copynumber: 6.2 Consensus size: 19
5952808 AATCTTTAAG
5952818 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
5952837 GATA--CAATCTTAGACAT
1 GATATGCAATCTTAGATAT
5952854 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5952873 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5952890 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
5952909 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
5952930 GAT
1 GAT
5952933 CTTGTAATCT
Statistics
Matches: 88, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
17 33 0.38
19 46 0.52
21 9 0.10
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:5952909 original size:14 final size:15
Alignment explanation
Indices: 5952818--5952910 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 15
5952808 AATCTTTAAG
5952818 GATATG-CAATCTTA
1 GATATGACAATCTTA
5952832 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
*
5952849 GACATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
5952868 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
5952885 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
5952904 GATATGA
1 GATATGA
5952911 TATGCAATCT
Statistics
Matches: 70, Mismatches: 2, Indels: 11
0.84 0.02 0.13
Matches are distributed among these distances:
14 6 0.09
17 34 0.49
19 30 0.43
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:5958586 original size:20 final size:22
Alignment explanation
Indices: 5958563--5958611 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
5958553 AACAAAAAAG
5958563 GAAAAAAAT-AAA-AAAAATGA
1 GAAAAAAATAAAATAAAAATGA
5958583 GAAAAAAATAAAAATAAAAATGA
1 GAAAAAAAT-AAAATAAAAATGA
5958606 GAAAAA
1 GAAAAA
5958612 TGAAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.35
22 3 0.12
23 14 0.54
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (22 bp):
GAAAAAAATAAAATAAAAATGA
Found at i:5958590 original size:23 final size:23
Alignment explanation
Indices: 5958564--5958627 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
5958554 ACAAAAAAGG
*
5958564 AAAAA-AATAAAAAAAATGAGAA
1 AAAAATAAAAAAAAAAATGAGAA
*
5958586 AAAAATAAAAATAAAAATGAG--
1 AAAAATAAAAAAAAAAATGAGAA
5958607 AAAAATGAAAAAAGAAAAATG
1 AAAAAT-AAAAAA-AAAAATG
5958628 GAGAGGCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
21 6 0.17
22 10 0.28
23 20 0.56
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (23 bp):
AAAAATAAAAAAAAAAATGAGAA
Found at i:5959657 original size:44 final size:44
Alignment explanation
Indices: 5959458--5959951 Score: 353
Period size: 44 Copynumber: 11.2 Consensus size: 44
5959448 CAAAGAAACA
* * *
5959458 AGATTTGGCATCCCTATGTTTATAGGAAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * **
5959502 AGATCTGACA-CTCCTGTGCTTACAGCGAAGC-TGATCGAAGATTTC
1 AGATTTGGCATC-CCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
* **
5959547 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATTTC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
5959590 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
5959633 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * ** * * **
5959677 AGATCTGACATTCCTGTACTTACAGCGAAGC-AGATCGAAGATTTC
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
*
5959722 AGCA--TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
1 AG-ATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
*
5959765 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * * ** ***
5959809 AGATCTGACATTCCTATGCTTACAACGAAGC-AGATCGAAGATTTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAA-CAAG-TCGAAGATAGC
** * **
5959854 A-ACATGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
* * * * * *
5959897 AGATTTGGCATCCTTGTGCTTACAAGAAACAAATCGAAGACATAGC
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAG--ATAGC
*
5959943 TGATTTGGC
1 AGATTTGGC
5959952 TTTCACGGTT
Statistics
Matches: 350, Mismatches: 80, Indels: 38
0.75 0.17 0.08
Matches are distributed among these distances:
42 2 0.01
43 74 0.21
44 224 0.64
45 35 0.10
46 15 0.04
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAGTCGAAGATAGC
Found at i:5959745 original size:132 final size:132
Alignment explanation
Indices: 5959581--5959936 Score: 604
Period size: 132 Copynumber: 2.7 Consensus size: 132
5959571 GGAACAAGTT
5959581 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
1 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
* *
5959646 CTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTACTTACAGCGAAGCAGA
66 CTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTATACTTACAACGAAGCAGA
5959711 TC
131 TC
5959713 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
1 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
*
5959778 CTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTATGCTTACAACGAAGCAGA
66 CTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTATACTTACAACGAAGCAGA
5959843 TC
131 TC
* * * *
5959845 GAAGATTTTAACATGGCATCCATGTGTTTATAGGGAACAAGTTAAAGATAGCAGATTTGGCATCC
1 GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
* * * * *
5959910 TTGTGCTTACAAGAAACAAATCGAAGA
66 CTGTGTTTATAGGGAACAAATCGAAGA
5959937 CATAGCTGAT
Statistics
Matches: 212, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 212 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (132 bp):
GAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATTTGGCATCC
CTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTATACTTACAACGAAGCAGA
TC
Found at i:5959749 original size:175 final size:175
Alignment explanation
Indices: 5959458--5959826 Score: 605
Period size: 175 Copynumber: 2.1 Consensus size: 175
5959448 CAAAGAAACA
*
5959458 AGATTTGGCATCCCTATGTTTATAGGAAACAAATCGAAGATAGCAGATCTGACACTCCTGTGCTT
1 AGATTTGGCATCCCTATGTTTATAGGAAACAAATCGAAGATAGCAGATCTGACACTCCTGTACTT
* *
5959523 ACAGCGAAGCTGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATT
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
* * *
5959588 TCAGCA-TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGC
131 GCAG-ATTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
* * *
5959633 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTACTT
1 AGATTTGGCATCCCTATGTTTATAGGAAACAAATCGAAGATAGCAGATCTGACACTCCTGTACTT
5959698 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
5959763 GCAGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
131 GCAGA-TTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
* * *
5959809 AGATCTGACATTCCTATG
1 AGATTTGGCATCCCTATG
5959827 CTTACAACGA
Statistics
Matches: 179, Mismatches: 13, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
174 1 0.01
175 127 0.71
176 51 0.28
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (175 bp):
AGATTTGGCATCCCTATGTTTATAGGAAACAAATCGAAGATAGCAGATCTGACACTCCTGTACTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GCAGATTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGC
Found at i:5960250 original size:205 final size:205
Alignment explanation
Indices: 5959898--5960844 Score: 1543
Period size: 206 Copynumber: 4.6 Consensus size: 205
5959888 AAAGATAGCA
* *
5959898 GATTTGGCATCCTTGTGCTTACAAGAAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGTTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGCTT
* *
5959963 ACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTTTGGC
66 ACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
** * *
5960028 GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTTCATATGTTTATACTAAAGCA
131 GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
*
5960093 GATCCAAGGT
196 GATCCAAGAT
*
5960103 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGTTT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGCTT
*
5960168 ACGCTGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
66 ACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
* ** *
5960233 GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATTTGGCCTTCATATGTTTATACTGAAGCA
131 GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
*
5960298 GATCCAAGGT
196 GATCCAAGAT
*
5960308 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACATGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCAC-GGCT
*
5960373 TACGATAAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
65 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
* * *
5960438 GGTCTCCATATTTGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGA
130 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGC
5960503 AGATCCAAGAT
195 AGATCCAAGAT
* *
5960514 GATTTGGCATTCTTGTGCTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACG-GCT
5960579 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
65 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGG
* * * *
5960644 CGTCTCCATATTCGATGGAGGGCAGACACATAGCAGATCTAACCTTCAGATGGTTAGACTGAAGC
130 CGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGC
5960709 AGATCCAAGAT
195 AGATCCAAGAT
* * * * * *
5960720 GGTTTGGTATCCTTGTGCTTACAAGGAGCAAATCGAAGACATAGTTGATTTGGTTTTCGCGTGCT
1 GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACG-GCT
* * *
5960785 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTTAGAAAACAGATCGAAG
65 TACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
5960845 ATAACAGATT
Statistics
Matches: 702, Mismatches: 38, Indels: 3
0.94 0.05 0.00
Matches are distributed among these distances:
205 261 0.37
206 441 0.63
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.29
Consensus pattern (205 bp):
GATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGGCTT
ACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGC
GTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTAACCTTCAGATGTTTATACTGAAGCA
GATCCAAGAT
Done.