Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 56 of 204
Found at i:16441096 original size:24 final size:24
Alignment explanation
Indices: 16441056--16441106 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
16441046 GATTTGATTA
16441056 TTATTATTATATATTTTACTTTA-T
1 TTATTATTATATATTTTA-TTTACT
*
16441080 TTATTATT-TACTTTTTTATTTACT
1 TTATTATTATA-TATTTTATTTACT
16441104 TTA
1 TTA
16441107 CCACTCTTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATTATTATATATTTTATTTACT
Found at i:16443179 original size:14 final size:15
Alignment explanation
Indices: 16443149--16443181 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16443139 CCACTTTTTT
*
16443149 TTTTCTTTTTACTTA
1 TTTTCTTTTTACCTA
16443164 TTTTCTTTTT-CCTA
1 TTTTCTTTTTACCTA
16443178 TTTT
1 TTTT
16443182 TTCCTTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTCTTTTTACCTA
Found at i:16447939 original size:9 final size:9
Alignment explanation
Indices: 16447925--16447958 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
16447915 AGACAGTGGC
16447925 GCAGCAACA
1 GCAGCAACA
16447934 GCAGCAACA
1 GCAGCAACA
*
16447943 GCAGCAGCA
1 GCAGCAACA
*
16447952 GCCGCAA
1 GCAGCAA
16447959 TGGGGGCAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.35, G:0.26, T:0.00
Consensus pattern (9 bp):
GCAGCAACA
Found at i:16452142 original size:40 final size:41
Alignment explanation
Indices: 16452055--16452149 Score: 113
Period size: 40 Copynumber: 2.3 Consensus size: 41
16452045 ATTTTCAATG
* *
16452055 GGCATGCTTAACATGTGAATCAAATTCATAATCAATACAGTC
1 GGCATGCTTAACAGGTGAACCAAATT-ATAATCAATACAGTC
* * *
16452097 GGCATGCTAAACAGGTGAACCGAATT-TAATCAGTACAGT-
1 GGCATGCTTAACAGGTGAACCAAATTATAATCAATACAGTC
16452136 GAGCATGCTTAACA
1 G-GCATGCTTAACA
16452150 TGCAAATCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.02
40 23 0.50
42 22 0.48
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (41 bp):
GGCATGCTTAACAGGTGAACCAAATTATAATCAATACAGTC
Found at i:16454385 original size:22 final size:22
Alignment explanation
Indices: 16454357--16454407 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
16454347 AGAAGAAAGA
*
16454357 TATGTGGCAGTTTATCTACAAT
1 TATGTGGCAGTTTATCGACAAT
* *
16454379 TGTGTGGCCGTTTATCGACAAT
1 TATGTGGCAGTTTATCGACAAT
16454401 TATGTGG
1 TATGTGG
16454408 TGGCTTGTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.25, T:0.39
Consensus pattern (22 bp):
TATGTGGCAGTTTATCGACAAT
Found at i:16463077 original size:40 final size:40
Alignment explanation
Indices: 16462983--16463102 Score: 129
Period size: 40 Copynumber: 3.0 Consensus size: 40
16462973 TCTGGCATGA
* *
16462983 TTCGGGTGGATCAGCTCTTATGAGCTTCTA-TTGGCGTGT
1 TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGGCGTGT
* *
16463022 TTCGAGTGGACCAACTCTTATAAGCTTCTATTTGGCGCAT-T
1 TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGGCG--TGT
* * * *
16463063 TTTG-TTGGATCAACTCTTATGAGCTTCTGTTTGGTGTGT
1 TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGGCGTGT
16463102 T
1 T
16463103 CGGTTTATCT
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
38 1 0.01
39 28 0.42
40 33 0.49
41 4 0.06
42 1 0.01
ACGTcount: A:0.16, C:0.17, G:0.25, T:0.42
Consensus pattern (40 bp):
TTCGAGTGGATCAACTCTTATGAGCTTCTATTTGGCGTGT
Found at i:16463605 original size:15 final size:17
Alignment explanation
Indices: 16463577--16463608 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
16463567 TTCATTATTG
16463577 AAAGGTGATATGATGAA
1 AAAGGTGATATGATGAA
16463594 AAAGG-GAT-TGATGAA
1 AAAGGTGATATGATGAA
16463609 TTGAATGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (17 bp):
AAAGGTGATATGATGAA
Found at i:16471452 original size:37 final size:37
Alignment explanation
Indices: 16471393--16471531 Score: 242
Period size: 37 Copynumber: 3.8 Consensus size: 37
16471383 AGCTCAGACG
* *
16471393 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
16471430 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
16471467 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
16471504 TAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
16471532 TAGAGCTCGG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:16471824 original size:49 final size:47
Alignment explanation
Indices: 16471653--16471918 Score: 379
Period size: 47 Copynumber: 5.6 Consensus size: 47
16471643 TTCGGGACTG
* * * * * * *
16471653 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
* *
16471700 GTCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16471747 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16471794 ATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
* * * *
16471843 ATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGTCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16471892 ATCACATATATACACTTTCACATTCAT
1 ATCACATATATACACTTTCACATTCAT
16471919 TCAAATATAC
Statistics
Matches: 202, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
47 110 0.54
49 92 0.46
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Found at i:16471845 original size:96 final size:94
Alignment explanation
Indices: 16471653--16471918 Score: 397
Period size: 96 Copynumber: 2.8 Consensus size: 94
16471643 TTCGGGACTG
* * * * * *
16471653 ATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATACACTTT
1 ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTT
*
16471718 CACATTCATCACATCGGCTATTAGGCCTT
66 CACATTCATCACATCGGCCATTAGGCCTT
* *
16471747 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACT
1 ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCAC--ATATATACACT
16471812 TTCACATTCATCACATCGGCCATTAGGCCTT
64 TTCACATTCATCACATCGGCCATTAGGCCTT
* *
16471843 ATCACATATATATACACTTTCACATTCATCACATTGGTCATTCGGTCTTATCACATATATACACT
1 ATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACT
16471908 TTCACATTCAT
64 TTCACATTCAT
16471919 TCAAATATAC
Statistics
Matches: 155, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
94 44 0.28
96 68 0.44
98 43 0.28
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (94 bp):
ATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTT
CACATTCATCACATCGGCCATTAGGCCTT
Found at i:16474266 original size:85 final size:84
Alignment explanation
Indices: 16474100--16474277 Score: 338
Period size: 85 Copynumber: 2.1 Consensus size: 84
16474090 TATTTTATTG
*
16474100 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCAACATGTTTATGACATGTTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCAACATGTTTATGACATGTTTTT
16474165 AGCCATAACATCTTGTCCA
66 AGCCATAACATCTTGTCCA
16474184 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTA-CCCAACATGTTTATGACATGTTTT
16474249 TAGCCATAACATCTTGTCCA
65 TAGCCATAACATCTTGTCCA
16474269 CCCATGCTC
1 CCCATGCTC
16474278 ATGGCCGGCC
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
84 39 0.42
85 53 0.58
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.38
Consensus pattern (84 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCAACATGTTTATGACATGTTTTT
AGCCATAACATCTTGTCCA
Found at i:16475968 original size:40 final size:40
Alignment explanation
Indices: 16475938--16476244 Score: 485
Period size: 40 Copynumber: 7.8 Consensus size: 40
16475928 AGCATGATTA
* * *
16475938 CTCTTCGGGACCTAGCCCGGATATAACACCAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
** *
16475978 CTCTTCGGGGTTTAGCACGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
* *
16476018 CTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
16476058 CTCCTCGGGACTTAGCCC-GATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
16476097 CTCCTCGGGACTTAGCCCGGATATAT-ACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
16476136 CTC-CCGGGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
*
16476175 CTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
1 CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
16476215 CTCTTCGGGACTTAGCCCGGATATATCACT
1 CTCTTCGGGACTTAGCCCGGATATATCACT
16476245 CTCAATTCTC
Statistics
Matches: 247, Mismatches: 17, Indels: 6
0.91 0.06 0.02
Matches are distributed among these distances:
38 21 0.09
39 70 0.28
40 156 0.63
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.23
Consensus pattern (40 bp):
CTCTTCGGGACTTAGCCCGGATATATCACTAGCACGAATG
Found at i:16476171 original size:157 final size:160
Alignment explanation
Indices: 16475942--16476244 Score: 486
Period size: 157 Copynumber: 1.9 Consensus size: 160
16475932 TGATTACTCT
* **
16475942 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTTCGGGGTTTAGCACGGATATATCAC
1 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTCCGGGACTTAGCACGGATATATCAC
*
16476007 TAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGACTTA
66 TAGCACGAATGCTCCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGACTTA
16476072 GCCC-GATATATCACTAGCACGAATGCTCC
131 GCCCGGATATATCACTAGCACGAATGCTCC
* * * *
16476101 TCGGGACTTAGCCCGGATAT-ATACTAGCACGAATGCTC-CCGGGACTTAGCCCGGATATATCAC
1 TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTCCGGGACTTAGCACGGATATATCAC
* * *
16476164 TAGCACGAATGCTCCTCGGGACTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGGACTTA
66 TAGCACGAATGCTCCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGACTTA
16476229 GCCCGGATATATCACT
131 GCCCGGATATATCACT
16476245 CTCAATTCTC
Statistics
Matches: 132, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
157 86 0.65
158 27 0.20
159 19 0.14
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (160 bp):
TCGGGACCTAGCCCGGATATAACACCAGCACGAATGCTCTCCGGGACTTAGCACGGATATATCAC
TAGCACGAATGCTCCTCGGAACTTAGCCCGGATACATCACTAGCACGAATGCTCCTCGGGACTTA
GCCCGGATATATCACTAGCACGAATGCTCC
Found at i:16477570 original size:37 final size:37
Alignment explanation
Indices: 16477511--16477649 Score: 242
Period size: 37 Copynumber: 3.8 Consensus size: 37
16477501 AGCTCAGACG
* *
16477511 AAATCTCCACACGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
16477548 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
16477585 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
16477622 TAATCTCCACACGTAGTCATCGGGTCTT
1 AAATCTCCACACGTAGTCATCGGGTCTT
16477650 TAGAGCTCGG
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 99 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:16477918 original size:22 final size:22
Alignment explanation
Indices: 16477890--16477964 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
16477880 TTTCACATTC
16477890 ATCACATCGGCCATTAGGCCTT
1 ATCACATCGGCCATTAGGCCTT
**** *** *
16477912 ATCACATATATACATTTCACATT
1 ATCACAT-CGGCCATTAGGCCTT
16477935 TATCACATCGGCCATTAGGCCTT
1 -ATCACATCGGCCATTAGGCCTT
16477958 ATCACAT
1 ATCACAT
16477965 ATATACACTT
Statistics
Matches: 35, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
22 14 0.40
23 14 0.40
24 7 0.20
ACGTcount: A:0.29, C:0.28, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATCGGCCATTAGGCCTT
Found at i:16478082 original size:49 final size:47
Alignment explanation
Indices: 16477768--16478468 Score: 1089
Period size: 47 Copynumber: 14.6 Consensus size: 47
16477758 CCCTTCGGGA
* * * * * *
16477768 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
16477815 CTTGTCACATATATACAGTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16477862 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
16477909 CTTATCACATATATACA-TTTCACATTTATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16477955 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16478002 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
16478049 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
16478098 CTTATCACATATATACACTTTCACATTCATCATATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
16478145 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
16478194 CTTATCACATATACACACTTTCACATTCATCACATCGACCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
16478241 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16478292 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16478341 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
16478390 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
16478439 CTTATCACATATATACACTTTCACATTCAT
1 CTTATCACATATATACACTTTCACATTCAT
16478469 TCAAATATAC
Statistics
Matches: 613, Mismatches: 32, Indels: 18
0.92 0.05 0.03
Matches are distributed among these distances:
46 45 0.07
47 291 0.47
49 233 0.38
51 44 0.07
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:16478111 original size:96 final size:96
Alignment explanation
Indices: 16477768--16478468 Score: 1114
Period size: 96 Copynumber: 7.3 Consensus size: 96
16477758 CCCTTCGGGA
* * * * * *
16477768 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCTTGTCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
16477831 AGTTTCACATTCATCACATCGGCTATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
16477862 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
16477925 A-TTTCACATTTATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
16477955 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
16478018 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* *
16478049 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
16478114 ACTTTCACATTCATCATATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
* * *
16478145 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATACAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
16478210 ACTTTCACATTCATCACATCGACCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
16478241 CTTATCACATATATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATAT
1 CTTATCAC--ATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATAT
16478306 ATACACTTTCACATTCATCACATCGGCCATTAGGC
62 ATACACTTTCACATTCATCACATCGGCCATTAGGC
16478341 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
* *
16478406 ACACTTTCACATTCATCACATTGGCCATTCGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
16478439 CTTATCAC--ATATATACACTTTCACATTCAT
1 CTTATCACATATATATACACTTTCACATTCAT
16478469 TCAAATATAC
Statistics
Matches: 575, Mismatches: 23, Indels: 16
0.94 0.04 0.03
Matches are distributed among these distances:
93 92 0.16
94 91 0.16
96 206 0.36
98 141 0.25
100 45 0.08
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.34
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:16480788 original size:85 final size:85
Alignment explanation
Indices: 16480659--16480837 Score: 349
Period size: 85 Copynumber: 2.1 Consensus size: 85
16480649 TATTTTATTG
*
16480659 CCCATGCCCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
16480724 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
16480744 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
1 CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
16480809 TAGCCATAACATCTTGTCCA
66 TAGCCATAACATCTTGTCCA
16480829 CCCATGCTC
1 CCCATGCTC
16480838 ATGGCCGGCC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
85 93 1.00
ACGTcount: A:0.26, C:0.28, G:0.08, T:0.37
Consensus pattern (85 bp):
CCCATGCTCTTTATTTTATTAATCCTTACATAATGCACTACCCCAACATGTTTATGACATGTTTT
TAGCCATAACATCTTGTCCA
Found at i:16481418 original size:29 final size:30
Alignment explanation
Indices: 16481299--16482002 Score: 885
Period size: 30 Copynumber: 22.7 Consensus size: 30
16481289 TTGTTAATGG
*
16481299 TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481329 TTAGGGTTTTTAATTAAATTATGTT---G-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481355 TTAGGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481385 TTAGGGTTTTTAATTAAATTAGGTTAAGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481414 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481444 TTAGGATTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
*
16481480 TTAGGGTTTTTAATTAAATTAAGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481509 TTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
* *
16481545 TTAAGGTTTTTAATTAAATTAAGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481575 TTAAGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481605 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
16481641 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481671 TT-GGGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481699 TTAGTGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481728 TTAGGGTTTAGGGTTTTAATTAAATTAGGTTAGGG-
1 TTAGGG--T----TTTTAATTAAATTAGGTTAGGGT
16481763 TTAGGGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481792 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT
1 TTAGGGTTTTTAATT-AA--A--TTA-GGTTAGGGT
16481828 TTAGGGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481857 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481887 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGT
1 TTAGGGTTTTTAATTAAATTAGGTTA--G----GGT
16481923 TTAGGGTTTTTAATTAAATTAGGTTAGGG-
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
*
16481952 TTAGGGTTTTTAATTAAATTAGGTTAGTGT
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGT
16481982 TTAGGGTTTTTAATTAAATTA
1 TTAGGGTTTTTAATTAAATTA
16482003 TAATTTTTAT
Statistics
Matches: 610, Mismatches: 18, Indels: 92
0.85 0.03 0.13
Matches are distributed among these distances:
26 24 0.04
27 1 0.00
28 2 0.00
29 193 0.32
30 195 0.32
31 17 0.03
32 3 0.00
33 7 0.01
34 7 0.01
35 57 0.09
36 104 0.17
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (30 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGT
Found at i:16481500 original size:95 final size:93
Alignment explanation
Indices: 16481299--16482002 Score: 990
Period size: 95 Copynumber: 7.5 Consensus size: 93
16481289 TTGTTAATGG
* *
16481299 TTAGGGTTTTTAATTAAATTAAGTTAGGGTTTAGGGTTTTTAATTAAATTATGTT---GTTA-GG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
*
16481360 ---GTTTTTAATTAAATTAAGTTAGGGT
66 TTTGTTTTTAATTAAATTAGGTTAGGGT
*
16481385 TTAGGGTTTTTAATTAAATTAGGTTAAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGG
* * **
16481449 ATTT-TTAATTAAATTAGGTTAGGGTTAGGGT
65 GTTTGTT--TTTAATTAAATTA-GGTTAGGGT
* *
16481480 TTAGGGTTTTTAATTAAATTAAGTTAGGG-TTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
*
16481544 TTTAAGGTTTTTAATTAAATTAAGTTAGGGT
66 TTT---GTTTTTAATTAAATTAGGTTAGGGT
*
16481575 TTAAGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
16481640 TTTAGGGTTTTTAATTAAATTAGGTTAGGGT
66 TTT---GTTTTTAATTAAATTAGGTTAGGGT
*
16481671 TT-GGGTTTTTAATTAAATTAGGTTAGGG-TTAGTGTTTTTAATTAAATTAGGTTAGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
*
16481734 TTTAGGGTTTTAATTAAATTAGGTTAGGG-
66 TTT--GTTTTTAATTAAATTAGGTTAGGGT
16481763 TTAGGGTTTTTAATTAAATTAGGTTAGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
16481827 TTTAGGGTTTTTAATTAAATTAGGTTAGGG-
66 TTT---GTTTTTAATTAAATTAGGTTAGGGT
*
16481857 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGG
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
16481922 TTTAGGGTTTTTAATTAAATTAGGTTAGGG-
66 TTT---GTTTTTAATTAAATTAGGTTAGGGT
*
16481952 TTAGGGTTTTTAATTAAATTAGGTTAGTGTTTAGGGTTTTTAATTAAATTA
1 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTA
16482003 TAATTTTTAT
Statistics
Matches: 569, Mismatches: 30, Indels: 29
0.91 0.05 0.05
Matches are distributed among these distances:
85 24 0.04
86 27 0.05
88 1 0.00
89 3 0.01
90 1 0.00
92 4 0.01
93 87 0.15
94 108 0.19
95 237 0.42
96 75 0.13
98 2 0.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (93 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGG
TTTGTTTTTAATTAAATTAGGTTAGGGT
Found at i:16481791 original size:23 final size:27
Alignment explanation
Indices: 16481297--16482000 Score: 496
Period size: 29 Copynumber: 22.8 Consensus size: 27
16481287 TTTTGTTAAT
16481297 GGTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAA-T-AGTTAG
16481326 GGTTTAGGGTTTTTAATTAAATTATGTT--
1 GG-TTAGGGTTTTTAATTAAA-TA-GTTAG
16481354 -GTTAGGGTTTTTAATTAAATTAAGTTAG
1 GGTTAGGGTTTTTAATTAAA-T-AGTTAG
*
16481382 GGTTTAGGGTTTTTAATTAAATTAGGTTAA
1 GG-TTAGGGTTTTTAATTAAA-TA-GTTAG
16481412 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAA-TA-GTTAG
*
16481441 GGTTTAGGATTTTTAATTAAATTAGGTTAGGGTTAG
1 GG-TTAGGGTTTTTAATT-AA--A---TA--GTTAG
16481477 GGTTTAGGGTTTTTAATTAAATTAAGTTAG
1 GG-TTAGGGTTTTTAATTAAA-T-AGTTAG
*
16481507 GGTTAGTGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAA-TA-GTTAG
16481536 GGTTAGGGTTTAAGGTTTTTAATTAAATTAAGTTAG
1 GGTTA--G-----GGTTTTTAATTAAA-T-AGTTAG
*
16481572 GGTTTAAGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAA-TA-GTTAG
16481602 GGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GG-TTAGGGTTTTTAATT-AA--A---TA--GTTAG
16481638 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAA-TA-GTTAG
*
16481668 GGTTTGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAA-TA-GTTAG
*
16481697 GGTTAGTGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAA-TA-GTTAG
16481726 GGTTAGGGTTTAGGGTTTTAATTAAATTAGGTTAG
1 GGTTAGGG--T----TTTTAATTAAA-TA-GTTAG
16481761 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAA-TA-GTTAG
16481790 GGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAG
1 GGTTAGGGTTTTTAATT-AA--A---TA--GTTAG
16481825 GGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 GG-TTAGGGTTTTTAATTAAA-TA-GTTAG
16481855 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAA-TA-GTTAG
16481884 GGTTTAGGGTTTTTAATTAAATTAGGTTAGGG
1 GG-TTAGGGTTTTTAATTAAA-TA-GTTA--G
16481916 TTAAGGTTTAGGGTTTTTAATTAAATTAGGTTAG
1 ----GG-TTAGGGTTTTTAATTAAA-TA-GTTAG
16481950 GGTTAGGGTTTTTAATTAAATTAGGTTAG
1 GGTTAGGGTTTTTAATTAAA-TA-GTTAG
*
16481979 TGTTTAGGGTTTTTAATTAAAT
1 -GGTTAGGGTTTTTAATTAAAT
16482001 TATAATTTTT
Statistics
Matches: 608, Mismatches: 13, Indels: 108
0.83 0.02 0.15
Matches are distributed among these distances:
26 23 0.04
27 2 0.00
28 1 0.00
29 217 0.36
30 173 0.28
31 14 0.02
32 3 0.00
33 6 0.01
34 4 0.01
35 48 0.08
36 113 0.19
37 4 0.01
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (27 bp):
GGTTAGGGTTTTTAATTAAATAGTTAG
Found at i:16484238 original size:25 final size:25
Alignment explanation
Indices: 16484188--16484243 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
16484178 CTTTTATAAC
*
16484188 AAATAATAAATTAATAATTATCTAA
1 AAATAATAAATTAATAAATATCTAA
*
16484213 AAATACATAAA-TAA-AAATATCT-T
1 AAATA-ATAAATTAATAAATATCTAA
16484236 AAATAATA
1 AAATAATA
16484244 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 3 0.11
23 5 0.18
24 7 0.25
25 8 0.29
26 5 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (25 bp):
AAATAATAAATTAATAAATATCTAA
Found at i:16484380 original size:20 final size:19
Alignment explanation
Indices: 16484342--16484384 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
16484332 TGAAAATATA
*
16484342 AAAAAAATTAAAATTATTTT
1 AAAAAAATTAAAA-TAATTT
16484362 AAAAAAATATAAAA-AATTT
1 AAAAAAAT-TAAAATAATTT
16484381 AAAA
1 AAAA
16484385 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 8 0.38
20 8 0.38
21 5 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAAAAATTAAAATAATTT
Found at i:16484383 original size:30 final size:31
Alignment explanation
Indices: 16484334--16484399 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 31
16484324 GCCATTGATG
*
16484334 AAAATATAAAAAAAATTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATTTAAAA
*
16484365 AAAATAT-AAAAAATTTAAAATTATTTAAAA
1 AAAATATAAAAAAAATTAAAATTATTTAAAA
16484395 AAAAT
1 AAAAT
16484400 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 26 0.79
31 7 0.21
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAATATAAAAAAAATTAAAATTATTTAAAA
Found at i:16484468 original size:30 final size:30
Alignment explanation
Indices: 16484432--16484491 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
16484422 TTAATATGAA
*
16484432 TTTGAGAGATTTTTGGAAGGAAATTAAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTAAGAG
*
16484462 TTTGAGAGAATTTTGGAAGGAAATTGAGAG
1 TTTGAGAGAATTTTGGAAGGAAATTAAGAG
16484492 GATTTTGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.00, G:0.32, T:0.32
Consensus pattern (30 bp):
TTTGAGAGAATTTTGGAAGGAAATTAAGAG
Found at i:16484491 original size:22 final size:22
Alignment explanation
Indices: 16484463--16484512 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
16484453 AATTAAGAGT
16484463 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
*
16484485 TTGAGAGGATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
16484507 TTGAGA
1 TTGAGA
16484513 TAGGATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.00, G:0.34, T:0.28
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:16489017 original size:2 final size:2
Alignment explanation
Indices: 16489010--16489051 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
16489000 CAAAAGTAAC
16489010 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16489052 GGAGCTAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16489506 original size:20 final size:21
Alignment explanation
Indices: 16489481--16489536 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 21
16489471 TTATCACCTT
16489481 AAAATATTTAAAAATTAC-AA
1 AAAATATTTAAAAATTACAAA
* * *
16489501 AAAATA-TAAAAAAATGCAAA
1 AAAATATTTAAAAATTACAAA
*
16489521 AAAATATTTTAAAATT
1 AAAATATTTAAAAATT
16489537 TTAAAATTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.29
20 14 0.50
21 6 0.21
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATATTTAAAAATTACAAA
Found at i:16489593 original size:59 final size:58
Alignment explanation
Indices: 16489479--16489593 Score: 144
Period size: 59 Copynumber: 2.0 Consensus size: 58
16489469 TATTATCACC
** * *
16489479 TTAAAATATTTAAAAATTACAAAAAATATAAAAAAATGCAAAAAAATATTTTAAAATT
1 TTAAAATATTTAAAAATTACAAAAAATATAAAAAAAAACAAAAAAACATTATAAAATT
*
16489537 TTAAAATTATTT-AAATTTA-AAAAAATATAAAACAAAAAACAAAAAAACATTATAAAA
1 TTAAAA-TATTTAAAAATTACAAAAAATAT-AAA-AAAAAACAAAAAAACATTATAAAA
16489594 ACATTAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
57 9 0.18
58 15 0.31
59 25 0.51
ACGTcount: A:0.66, C:0.04, G:0.01, T:0.29
Consensus pattern (58 bp):
TTAAAATATTTAAAAATTACAAAAAATATAAAAAAAAACAAAAAAACATTATAAAATT
Found at i:16490327 original size:19 final size:20
Alignment explanation
Indices: 16490305--16490349 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
16490295 ACTTTTCCTA
16490305 TTTTTTAATAATTTAAAT-T
1 TTTTTTAATAATTTAAATAT
**
16490324 TTTTTTAATTTTTTAAATAT
1 TTTTTTAATAATTTAAATAT
16490344 TTTTTT
1 TTTTTT
16490350 GTAATTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTTTAATAATTTAAATAT
Found at i:16490406 original size:13 final size:13
Alignment explanation
Indices: 16490388--16490432 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
16490378 AATTTTTAAA
16490388 TAATTTTTGTATT
1 TAATTTTTGTATT
*
16490401 TAATTTTTGTATA
1 TAATTTTTGTATT
16490414 T-ATTTTT-T-TT
1 TAATTTTTGTATT
16490424 ATAATTTTT
1 -TAATTTTT
16490433 AAAGATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 1 0.04
11 2 0.07
12 12 0.43
13 13 0.46
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (13 bp):
TAATTTTTGTATT
Found at i:16490418 original size:12 final size:13
Alignment explanation
Indices: 16490375--16490432 Score: 61
Period size: 12 Copynumber: 4.8 Consensus size: 13
16490365 CTTGTATATT
16490375 TATAA-TTTT-TA
1 TATAATTTTTGTA
*
16490386 AATAATTTTTGTA
1 TATAATTTTTGTA
*
16490399 TTTAATTTTTGTA
1 TATAATTTTTGTA
*
16490412 TAT-ATTTTT-TT
1 TATAATTTTTGTA
16490423 TATAATTTTT
1 TATAATTTTT
16490433 AAAGATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 8 0.21
12 16 0.41
13 15 0.38
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
TATAATTTTTGTA
Found at i:16496195 original size:19 final size:19
Alignment explanation
Indices: 16496173--16496233 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
16496163 ATTAAAGTAG
16496173 GAAAGAAAGAGATATGGGA
1 GAAAGAAAGAGATATGGGA
*
16496192 GAAAGATAGAG--A-GGCGA
1 GAAAGAAAGAGATATGG-GA
* *
16496209 GAGAGAAAGAGATATGAGA
1 GAAAGAAAGAGATATGGGA
16496228 GAAAGA
1 GAAAGA
16496234 TAGAAAGACG
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 2 0.06
17 12 0.36
19 18 0.55
20 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.38, T:0.08
Consensus pattern (19 bp):
GAAAGAAAGAGATATGGGA
Found at i:16496216 original size:36 final size:36
Alignment explanation
Indices: 16496176--16496249 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
16496166 AAAGTAGGAA
* * *
16496176 AGAAAGAGATATGGGAGAAAGATAGAGAGGCGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
16496212 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
1 AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
16496248 AG
1 AG
16496250 GGAAAGGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.38, T:0.08
Consensus pattern (36 bp):
AGAAAGAGATATGAGAGAAAGATAGAAAGACGAGAG
Found at i:16498021 original size:50 final size:50
Alignment explanation
Indices: 16497966--16498159 Score: 178
Period size: 50 Copynumber: 3.9 Consensus size: 50
16497956 CATTGAGGTT
* *
16497966 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA
** * * *
16498016 ATGAGAGATCCCCCGTAAGACCATGTCTGGGAGATGGCATGGGCACCGAT
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA
* * * * **
16498066 ATGAGA-ACTCCCATGTAAAACTATATCTAGGTTATGGCATTGGCA--GTAA
1 ATGAGAGA-TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AA
* * * * * *
16498115 AAGAAACATCCCATGTAAGGCCATGTCTGGGACATGACTTTGGCA
1 ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16498160 TGTTATTATC
Statistics
Matches: 114, Mismatches: 27, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
48 1 0.01
49 34 0.30
50 79 0.69
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAA
Found at i:16502451 original size:10 final size:11
Alignment explanation
Indices: 16502436--16502464 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
16502426 GCAATTTGAT
16502436 AAATAAAAT-A
1 AAATAAAATAA
16502446 AAATAAAATAA
1 AAATAAAATAA
16502457 AAATAAAA
1 AAATAAAA
16502465 GCTATCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.50
11 9 0.50
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:16507422 original size:21 final size:21
Alignment explanation
Indices: 16507376--16507422 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
16507366 AAGTAGTTTT
*
16507376 GAAATGGAAAAGTAATGGATT
1 GAAATGGAAAAGTAATGGATG
16507397 GAAAT-GAAAAGT-ATGGTATG
1 GAAATGGAAAAGTAATGG-ATG
16507417 GTAAAT
1 G-AAAT
16507423 AGTTACATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 4 0.17
20 10 0.43
21 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.28, T:0.26
Consensus pattern (21 bp):
GAAATGGAAAAGTAATGGATG
Found at i:16507671 original size:29 final size:28
Alignment explanation
Indices: 16507597--16507671 Score: 64
Period size: 29 Copynumber: 2.6 Consensus size: 28
16507587 TATAGTTTTT
* *
16507597 AGGTACTATGTACCAGTGTTTCAATTCC
1 AGGTACTATGTACCGGTGTTACAATTCC
* * *
16507625 AGGCACTCTATGT--TGGTGATTACAGTTCC
1 AGGTA--CTATGTACCGGTG-TTACAATTCC
16507654 AGGTACTATGTACCGGTG
1 AGGTACTATGTACCGGTG
16507672 GTGGATACCA
Statistics
Matches: 35, Mismatches: 7, Indels: 9
0.69 0.14 0.18
Matches are distributed among these distances:
27 6 0.17
28 7 0.20
29 16 0.46
30 6 0.17
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (28 bp):
AGGTACTATGTACCGGTGTTACAATTCC
Found at i:16512803 original size:38 final size:38
Alignment explanation
Indices: 16512761--16512834 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
16512751 TTCAGTTCAA
16512761 GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTCGT
1 GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTCGT
*
16512799 GCTAATAAGTTCCTGAATCAAGGTTGTGAAGCTTTC
1 GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTC
16512835 CTAGCCTACG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (38 bp):
GCTAATAAGCTCCTGAATCAAGGTTGTGAAGCTTTCGT
Found at i:16515052 original size:56 final size:50
Alignment explanation
Indices: 16514973--16515162 Score: 188
Period size: 50 Copynumber: 3.7 Consensus size: 50
16514963 GAATGAGATC
*
16514973 CCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGGT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C---GAGA-TATGAGAGGT
* *
16515028 CTCATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAG--ATGAGAGGT
1 C-CATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGAGATATGAGAGGT
** * * **
16515078 CCCCGTAAGACCATGTCTGGGACATGGCATGGGCAC-CGATATGAGAACT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAGATATGAGAGGT
* *
16515127 CCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 -CCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16515163 GTATAGAAAA
Statistics
Matches: 114, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
47 1 0.01
48 1 0.01
49 36 0.32
50 40 0.35
53 3 0.03
55 1 0.01
56 32 0.28
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACGAGATATGAGAGGT
Found at i:16515155 original size:50 final size:50
Alignment explanation
Indices: 16514971--16515211 Score: 220
Period size: 49 Copynumber: 4.7 Consensus size: 50
16514961 GGGAATGAGA
* * **
16514971 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CGA-TATGAGAAC
* * * * **
16515027 TCTCATGTAAGACCATGTCTGGGACATGACGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAAC
* *
16515077 TCCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAAC
* * *
16515126 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--G-TATAGAAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATAT-GAGAAC
* * *
16515174 ATCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16515212 TGTATTATCA
Statistics
Matches: 158, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
47 3 0.02
48 6 0.04
49 74 0.47
50 39 0.25
51 2 0.01
55 1 0.01
56 33 0.21
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGATATGAGAAC
Found at i:16515428 original size:12 final size:12
Alignment explanation
Indices: 16515411--16515449 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
16515401 ATGAGTTATT
16515411 TAAGTAAGCAAG
1 TAAGTAAGCAAG
*
16515423 TAAGTAAACAAG
1 TAAGTAAGCAAG
* *
16515435 TAAGTGAGTAAG
1 TAAGTAAGCAAG
16515447 TAA
1 TAA
16515450 ACAAGCGAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (12 bp):
TAAGTAAGCAAG
Found at i:16515437 original size:20 final size:20
Alignment explanation
Indices: 16515412--16515454 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
16515402 TGAGTTATTT
16515412 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
**
16515432 AAGTAAGTGAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
16515452 AAG
1 AAG
16515455 CGAGTAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.23, T:0.16
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:16521623 original size:50 final size:50
Alignment explanation
Indices: 16521508--16521855 Score: 464
Period size: 50 Copynumber: 6.8 Consensus size: 50
16521498 GATCATAACA
* ** *
16521508 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* ***
16521559 TGTCC-ATGCCATGTCCCAGACATGGTCTTATGGGGGACCTCTCATCTCGG
1 TG-CCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
16521609 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTTATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
16521659 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCACCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
16521709 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGAACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
16521759 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
16521809 TGCCAACGCCATGTCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACG-C----CATGTCCCAGACATGGTCTTACATGGGACCTCT
16521856 TTACCCAAAT
Statistics
Matches: 260, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
49 2 0.01
50 194 0.75
51 31 0.12
52 2 0.01
55 31 0.12
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:16527523 original size:9 final size:9
Alignment explanation
Indices: 16527503--16527542 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
16527493 CATTTTTAAT
16527503 AAATATTAAA
1 AAATA-TAAA
16527513 AAATATAAA
1 AAATATAAA
16527522 AAA-ATAAA
1 AAATATAAA
*
16527530 AAAAATAAA
1 AAATATAAA
16527539 AAAT
1 AAAT
16527543 TATTTTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
8 8 0.29
9 15 0.54
10 5 0.18
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAATATAAA
Found at i:16527531 original size:17 final size:17
Alignment explanation
Indices: 16527509--16527541 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16527499 TAATAAATAT
*
16527509 TAAAAAATATAAAAAAA
1 TAAAAAAAATAAAAAAA
16527526 TAAAAAAAATAAAAAA
1 TAAAAAAAATAAAAAA
16527542 TTATTTTAAA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
TAAAAAAAATAAAAAAA
Found at i:16527552 original size:11 final size:11
Alignment explanation
Indices: 16527538--16527565 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16527528 AAAAAAATAA
16527538 AAAATTATTTT
1 AAAATTATTTT
16527549 AAAATTATTTT
1 AAAATTATTTT
16527560 AAAATT
1 AAAATT
16527566 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:16529050 original size:3 final size:3
Alignment explanation
Indices: 16529042--16529096 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
16529032 TGAAAAAGTA
16529042 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16529090 AAT AAT A
1 AAT AAT A
16529097 GGATTTCATT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:16531809 original size:15 final size:15
Alignment explanation
Indices: 16531789--16531819 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
16531779 AATAAAGAAA
16531789 TCTAGGTGCAAATGT
1 TCTAGGTGCAAATGT
16531804 TCTAGGTGCAAATGT
1 TCTAGGTGCAAATGT
16531819 T
1 T
16531820 ATGAGTACGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (15 bp):
TCTAGGTGCAAATGT
Found at i:16534728 original size:50 final size:49
Alignment explanation
Indices: 16534599--16534783 Score: 189
Period size: 49 Copynumber: 3.8 Consensus size: 49
16534589 TTTTGAGAGG
* **
16534599 TCCCATATAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAC
*
16534648 TCCC-TCGTAAGACCATGTCTGGGACATGGCA-TGTGCACCGATATGAGAAC
1 TCCCAT-GTAAGACCATGTCTGGGACATGGCATTG-GCACCGAGATGAG-AC
* * * * * *
16534698 TCCCATGTAAGACCATATCTGGGATATGGCATTAGCA--GTACAAGAAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAC
* *
16534746 ATCCAATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16534784 TGTTATTATC
Statistics
Matches: 114, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
48 6 0.05
49 76 0.67
50 30 0.26
51 2 0.02
ACGTcount: A:0.29, C:0.23, G:0.26, T:0.23
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAC
Found at i:16540456 original size:26 final size:26
Alignment explanation
Indices: 16540420--16540471 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
16540410 TTGCCAACTG
16540420 AGTTAGAGAAGATTCATAATGTATTC
1 AGTTAGAGAAGATTCATAATGTATTC
16540446 AGTTAGAGAAGATTCATAATGTATTC
1 AGTTAGAGAAGATTCATAATGTATTC
16540472 TATGTGTCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (26 bp):
AGTTAGAGAAGATTCATAATGTATTC
Found at i:16542069 original size:50 final size:50
Alignment explanation
Indices: 16541958--16542204 Score: 223
Period size: 50 Copynumber: 4.8 Consensus size: 50
16541948 ATTTGGGTAA
* *
16541958 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAAGTTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CG-AG--ATG
**
16542014 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGTGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
16542064 AGAGGTCCCCCT-TAAGACCATGTTTGGGACATGGCATGGGCACCGATATG
1 AGAGGT-CCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * *
16542114 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAT-
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-A-GATG
* ** * *
16542163 AAACATCCTATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16542205 TGTTATTATC
Statistics
Matches: 162, Mismatches: 25, Indels: 15
0.80 0.12 0.07
Matches are distributed among these distances:
48 1 0.01
49 40 0.25
50 74 0.46
51 4 0.02
52 2 0.01
53 1 0.01
55 1 0.01
56 39 0.24
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:16548807 original size:13 final size:13
Alignment explanation
Indices: 16548789--16548817 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
16548779 AGACCTCAAG
16548789 ATAATATCCCATA
1 ATAATATCCCATA
16548802 ATAATATCCCATA
1 ATAATATCCCATA
16548815 ATA
1 ATA
16548818 TCCTATTAGG
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:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAATATCCCATA
Found at i:16551954 original size:41 final size:44
Alignment explanation
Indices: 16551872--16551967 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 44
16551862 AATTTTAATT
*
16551872 CAAAAATCTATATTTAAATTAAAATATTAATAAATAAAAATGTTA
1 CAAAAATCTATATTTAAATTAAAATATTAATAAAT-AAAATGTAA
* *
16551917 CAAAAAGTTTATATTTAAATTCAAA-A-T-ATAAAT-AAATGTAA
1 CAAAAA-TCTATATTTAAATTAAAATATTAATAAATAAAATGTAA
16551958 CAAAAATCTA
1 CAAAAATCTA
16551968 ATCTGTGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
40 3 0.07
41 13 0.28
43 6 0.13
44 1 0.02
45 7 0.15
46 16 0.35
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.33
Consensus pattern (44 bp):
CAAAAATCTATATTTAAATTAAAATATTAATAAATAAAATGTAA
Found at i:16560371 original size:7 final size:7
Alignment explanation
Indices: 16560350--16560384 Score: 54
Period size: 7 Copynumber: 5.0 Consensus size: 7
16560340 CATGCAGACC
16560350 ATAAAAA
1 ATAAAAA
16560357 ATATAAAA
1 ATA-AAAA
16560365 ATAAAAA
1 ATAAAAA
16560372 AT-AAAA
1 ATAAAAA
16560378 ATAAAAA
1 ATAAAAA
16560385 TCCAAACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.23
7 13 0.50
8 7 0.27
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:16560375 original size:13 final size:14
Alignment explanation
Indices: 16560353--16560385 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
16560343 GCAGACCATA
16560353 AAAAATATAAAAAT
1 AAAAATATAAAAAT
16560367 AAAAA-ATAAAAAT
1 AAAAATATAAAAAT
16560380 AAAAAT
1 AAAAAT
16560386 CCAAACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (14 bp):
AAAAATATAAAAAT
Found at i:16578204 original size:14 final size:14
Alignment explanation
Indices: 16578172--16578198 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16578162 CAAATTTAAC
16578172 TATACTAAAATGAA
1 TATACTAAAATGAA
16578186 TATACTAAAATGA
1 TATACTAAAATGA
16578199 TCATACAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (14 bp):
TATACTAAAATGAA
Found at i:16578694 original size:24 final size:24
Alignment explanation
Indices: 16578649--16578694 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
16578639 GCTCTTCAGT
* *
16578649 AGCAGTTAGATTGGGCTCCTCGAA
1 AGCAGTTAGAGTGGCCTCCTCGAA
* *
16578673 AGCAGTTTGAGTGGCCTTCTCG
1 AGCAGTTAGAGTGGCCTCCTCG
16578695 GCAGCATAAG
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:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (24 bp):
AGCAGTTAGAGTGGCCTCCTCGAA
Found at i:16584740 original size:27 final size:27
Alignment explanation
Indices: 16584696--16585057 Score: 328
Period size: 27 Copynumber: 13.4 Consensus size: 27
16584686 CTTTCGATTT
16584696 GAAGGGTAAAATGATCGAAATACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* * * *
16584723 GAAAGCTAAAATAATCGAAATACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16584750 TAAGGGTAAAATGATTGAAATACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16584777 AAAGGGTAAAAT-AACGGAAATACCCTC
1 GAAGGGTAAAATGATC-GAAATACCCTC
* * *
16584804 AAAGAGTAAAAT-AACAGAAATACCCTC
1 GAAGGGTAAAATGATC-GAAATACCCTC
* * *
16584831 AAAGGGTAAAATGA-CTAAAATACCCAC
1 GAAGGGTAAAATGATC-GAAATACCCTC
16584858 GAAGGGTAAAATGATCGAAATACCCAT-
1 GAAGGGTAAAATGATCGAAATACCC-TC
*
16584885 GAAGGGTAAAATGA-CGAAAATACCCTT
1 GAAGGGTAAAATGATCG-AAATACCCTC
* * * * *
16584912 GAAGGGTAAAATCACCAAAACACCCCC
1 GAAGGGTAAAATGATCGAAATACCCTC
* *
16584939 GAAGGGTAAAATGATCAAAACACCCTC
1 GAAGGGTAAAATGATCGAAATACCCTC
*
16584966 GAAGGGTAAAATAATCGAAATACCC-C
1 GAAGGGTAAAATGATCGAAATACCCTC
* * * *
16584992 TAAAGGGTAAACTGACCAAAATACCC-C
1 -GAAGGGTAAAATGATCGAAATACCCTC
* *
16585019 GCAGGGTAAAATGA-CTGAAATACCTTC
1 GAAGGGTAAAATGATC-GAAATACCCTC
16585046 -ATAGGGTAAAAT
1 GA-AGGGTAAAAT
16585058 AACCATTATA
Statistics
Matches: 280, Mismatches: 44, Indels: 22
0.81 0.13 0.06
Matches are distributed among these distances:
25 1 0.00
26 23 0.08
27 253 0.90
28 3 0.01
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.17
Consensus pattern (27 bp):
GAAGGGTAAAATGATCGAAATACCCTC
Found at i:16584836 original size:81 final size:79
Alignment explanation
Indices: 16584696--16585060 Score: 380
Period size: 81 Copynumber: 4.5 Consensus size: 79
16584686 CTTTCGATTT
* * *
16584696 GAAGGGTAAAATGATCGAAATACCCTCGAAA-GCTAAAATAATCGAAATACCCCCTAAGGGTAAA
1 GAAGGGTAAAATGATCGAAATACCCTC-AAAGGGTAAAATAA-CGAAATACCCTCAAAGGGTAAA
***
16584760 ATGATTGAAATACCCTC
64 ATGACCAAAATACCC-C
* * *
16584777 AAAGGGTAAAAT-AACGGAAATACCCTCAAAGAGTAAAATAACAGAAATACCCTCAAAGGGTAAA
1 GAAGGGTAAAATGATC-GAAATACCCTCAAAGGGTAAAATAAC-GAAATACCCTCAAAGGGTAAA
*
16584841 ATGACTAAAATACCCAC
64 ATGACCAAAATACCC-C
* * **
16584858 GAAGGGTAAAATGATCGAAATACCCAT-GAAGGGTAAAATGACGAAAATACCCTTGAAGGGTAAA
1 GAAGGGTAAAATGATCGAAATACCC-TCAAAGGGTAAAATAACG-AAATACCCTCAAAGGGTAAA
* *
16584922 ATCACCAAAACACCCCC
64 ATGACCAAAATA-CCCC
* * *
16584939 GAAGGGTAAAATGATCAAAACACCCTCGAAGGGTAAAATAATCGAAATACCC-CTAAAGGGTAAA
1 GAAGGGTAAAATGATCGAAATACCCTCAAAGGGTAAAATAA-CGAAATACCCTC-AAAGGGTAAA
*
16585003 CTGACCAAAATACCCC
64 ATGACCAAAATACCCC
* * *
16585019 GCAGGGTAAAATGA-CTGAAATACCTTCATAGGGTAAAATAAC
1 GAAGGGTAAAATGATC-GAAATACCCTCAAAGGGTAAAATAAC
16585061 CATTATACCC
Statistics
Matches: 240, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
79 2 0.01
80 45 0.19
81 185 0.77
82 8 0.03
ACGTcount: A:0.46, C:0.20, G:0.18, T:0.17
Consensus pattern (79 bp):
GAAGGGTAAAATGATCGAAATACCCTCAAAGGGTAAAATAACGAAATACCCTCAAAGGGTAAAAT
GACCAAAATACCCC
Found at i:16592389 original size:27 final size:27
Alignment explanation
Indices: 16592345--16592790 Score: 395
Period size: 27 Copynumber: 16.5 Consensus size: 27
16592335 TTTTGATTCG
*
16592345 AAGGGTAAAATGATCGAAATATCCTCA
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
16592372 AAGTGTAAAATGACCGAAATACCCCCA
1 AAGGGTAAAATGATCGAAATACCCTCA
*
16592399 AAGGGTAAAATGATCGAAATACCCTCG
1 AAGGGTAAAATGATCGAAATACCCTCA
*
16592426 AAGGGTAAAATAATCGAAATATCCCT-A
1 AAGGGTAAAATGATCGAAATA-CCCTCA
* * *
16592453 AAGGTTAAAATTATCGAAATACCCTTA
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
16592480 AAGGGTAAAAT-AGCTAAAATACCCTCG
1 AAGGGTAAAATGATC-GAAATACCCTCA
*
16592507 AAGGGTAAAATGACCGAAATACCCT-A
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
16592533 GAATGGTAAAATGACCGAAATACCCCCGA
1 -AAGGGTAAAATGATCGAAATACCCTC-A
* * * *
16592562 AA-GGTAAAATGACCGGAATAACCAT-G
1 AAGGGTAAAATGATCGAAAT-ACCCTCA
* * *
16592588 AAGGGTAAAATAATTGAAATACCCTCG
1 AAGGGTAAAATGATCGAAATACCCTCA
*
16592615 AAGGGTAAAATGATCGAAATACTCTCA
1 AAGGGTAAAATGATCGAAATACCCTCA
* * *
16592642 AAGGGTAAAATGATCGAAACACCACCCG
1 AAGGGTAAAATGATCGAAATACC-CTCA
* *
16592670 GAGGGTAAAATGA-CTAATATACCCTCGA
1 AAGGGTAAAATGATCGAA-ATACCCTC-A
* * *
16592698 AA-GGTAAAATGACCAAAATACCAC-CG
1 AAGGGTAAAATGATCGAAATACC-CTCA
* * *
16592724 AAGGGTAAAATGACCAAAATACCCCCA
1 AAGGGTAAAATGATCGAAATACCCTCA
* * * *
16592751 CAGGGTAAAATGATCAAAATACCTTTA
1 AAGGGTAAAATGATCGAAATACCCTCA
*
16592778 TAGGGTAAAATGA
1 AAGGGTAAAATGA
16592791 CCATTATACC
Statistics
Matches: 348, Mismatches: 54, Indels: 34
0.80 0.12 0.08
Matches are distributed among these distances:
26 15 0.04
27 298 0.86
28 34 0.10
29 1 0.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (27 bp):
AAGGGTAAAATGATCGAAATACCCTCA
Found at i:16593154 original size:28 final size:28
Alignment explanation
Indices: 16593113--16593204 Score: 116
Period size: 28 Copynumber: 3.3 Consensus size: 28
16593103 GTTGCATTAT
*
16593113 CACACTGTTACTGTAATAGGCTAAGGCC
1 CACACTGTTTCTGTAATAGGCTAAGGCC
* *
16593141 CACACTGTTTCTGTATTGGGCTAAGGCC
1 CACACTGTTTCTGTAATAGGCTAAGGCC
*
16593169 CACATTGTTAT-TGT-ATCAGGCTAAGGCC
1 CACACTGTT-TCTGTAAT-AGGCTAAGGCC
16593197 CACACTGT
1 CACACTGT
16593205 ACTATTATTG
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.02
28 53 0.96
29 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (28 bp):
CACACTGTTTCTGTAATAGGCTAAGGCC
Found at i:16601520 original size:16 final size:16
Alignment explanation
Indices: 16601499--16601570 Score: 99
Period size: 16 Copynumber: 4.5 Consensus size: 16
16601489 CGTTTGGTTT
16601499 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
* *
16601515 GCTGTAATTGAATAGG
1 GCTGTAATGGAATAGA
* *
16601531 GCTGTAATAGAATAAA
1 GCTGTAATGGAATAGA
16601547 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
*
16601563 ACTGTAAT
1 GCTGTAAT
16601571 AGTATTCTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 48 1.00
ACGTcount: A:0.39, C:0.07, G:0.26, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:16608190 original size:23 final size:20
Alignment explanation
Indices: 16608153--16608193 Score: 55
Period size: 23 Copynumber: 1.9 Consensus size: 20
16608143 TAAAAGAAAT
16608153 AATTATTATTTTTTTAAGTA
1 AATTATTATTTTTTTAAGTA
16608173 AATTGATTAATTTATTTTAAG
1 AATT-ATT-ATTT-TTTTAAG
16608194 AGGGACTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 4 0.22
23 7 0.39
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (20 bp):
AATTATTATTTTTTTAAGTA
Found at i:16610223 original size:17 final size:18
Alignment explanation
Indices: 16610201--16610234 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16610191 TTATTTATAA
16610201 TTTAAA-AAATTAATTAT
1 TTTAAATAAATTAATTAT
*
16610218 TTTAAATAATTTAATTA
1 TTTAAATAAATTAATTA
16610235 AATTAAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTAAATAAATTAATTAT
Found at i:16624245 original size:9 final size:9
Alignment explanation
Indices: 16624231--16624312 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 9
16624221 TTCTAGTTTA
16624231 TTTTATTAT
1 TTTTATTAT
16624240 TTTTATTA-
1 TTTTATTAT
* *
16624248 TTATATTAG
1 TTTTATTAT
16624257 TTTTATTAT
1 TTTTATTAT
**
16624266 TACTATTA-
1 TTTTATTAT
* *
16624274 TTATATTGT
1 TTTTATTAT
16624283 TTTTAGATTAT
1 TTTT--ATTAT
* *
16624294 TTATCTTAT
1 TTTTATTAT
*
16624303 TTTCATTAT
1 TTTTATTAT
16624312 T
1 T
16624313 AGGATTAGTT
Statistics
Matches: 54, Mismatches: 15, Indels: 8
0.70 0.19 0.10
Matches are distributed among these distances:
8 12 0.22
9 35 0.65
11 7 0.13
ACGTcount: A:0.26, C:0.04, G:0.04, T:0.67
Consensus pattern (9 bp):
TTTTATTAT
Found at i:16624248 original size:3 final size:3
Alignment explanation
Indices: 16624228--16624277 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
16624218 TCCTTCTAGT
* *
16624228 TTA TT- TTA TTA TTT TTA TTA TTA -TA TTA GTT- TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
16624271 TTA TTA T
1 TTA TTA T
16624278 ATTGTTTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.15
3 31 0.79
4 2 0.05
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16624254 original size:17 final size:17
Alignment explanation
Indices: 16624228--16624275 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
16624218 TCCTTCTAGT
*
16624228 TTATTTTATTATTTTTA
1 TTATTATATTATTTTTA
*
16624245 TTATTATATTAGTTTTA
1 TTATTATATTATTTTTA
16624262 TTATTACTATTATT
1 TTATTA-TATTATT
16624276 ATATTGTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 21 0.78
18 6 0.22
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (17 bp):
TTATTATATTATTTTTA
Found at i:16624287 original size:26 final size:26
Alignment explanation
Indices: 16624231--16624285 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
16624221 TTCTAGTTTA
**
16624231 TTTTATTATTTTTATTATTATATTAG
1 TTTTATTATTACTATTATTATATTAG
16624257 TTTTATTATTACTATTATTATATT-G
1 TTTTATTATTACTATTATTATATTAG
16624282 TTTT
1 TTTT
16624286 TAGATTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTATTATTACTATTATTATATTAG
Found at i:16624374 original size:27 final size:28
Alignment explanation
Indices: 16624311--16624384 Score: 91
Period size: 27 Copynumber: 2.7 Consensus size: 28
16624301 ATTTTCATTA
* *
16624311 TTAGGATTAGTTTTATTTTTATTATTGC
1 TTAGTATTAGTTTTATTTTTATTACTGC
*
16624339 -TA-TAGTTAGTTCTATTTTTATT-CTGC
1 TTAGTA-TTAGTTTTATTTTTATTACTGC
16624365 TTAGTATTAGTTTTATTTTT
1 TTAGTATTAGTTTTATTTTT
16624385 TGTATTAGGA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.10
27 33 0.85
28 2 0.05
ACGTcount: A:0.20, C:0.05, G:0.12, T:0.62
Consensus pattern (28 bp):
TTAGTATTAGTTTTATTTTTATTACTGC
Found at i:16626033 original size:23 final size:22
Alignment explanation
Indices: 16626007--16626049 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
16625997 TTTTCTAGTT
16626007 TTTTTATCTATTTATCTTATTCA
1 TTTTTATCTATTT-TCTTATTCA
*
16626030 TTTTTGTCTATTTTCTTATT
1 TTTTTATCTATTTTCTTATT
16626050 AGTTTGCTCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTATCTATTTTCTTATTCA
Found at i:16626766 original size:35 final size:35
Alignment explanation
Indices: 16626720--16626789 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
16626710 GTTGTATTAA
16626720 CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
* *
16626755 CCCCTAGTAAACATTGTTGATCCTAACACATTTTT
1 CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
16626790 TTTTCTCTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.30, C:0.27, G:0.07, T:0.36
Consensus pattern (35 bp):
CCCCTAGTAAACATTGCTAATCCTAACACATTTTT
Found at i:16633024 original size:18 final size:18
Alignment explanation
Indices: 16632997--16633082 Score: 75
Period size: 18 Copynumber: 4.6 Consensus size: 18
16632987 CACATTTTTC
16632997 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
* **
16633016 TTCAGTCATATATCCTCAT
1 TTCATTCATAT-TTTTCAT
* **
16633035 TCCAATTCCCATTTTTC-T
1 TTC-ATTCATATTTTTCAT
16633053 TTCATTTCATATTTTTCAT
1 TTCA-TTCATATTTTTCAT
16633072 TTCATTCATAT
1 TTCATTCATAT
16633083 ATCCTTATGC
Statistics
Matches: 51, Mismatches: 12, Indels: 9
0.71 0.17 0.12
Matches are distributed among these distances:
17 1 0.02
18 26 0.51
19 19 0.37
20 5 0.10
ACGTcount: A:0.22, C:0.22, G:0.01, T:0.55
Consensus pattern (18 bp):
TTCATTCATATTTTTCAT
Found at i:16633038 original size:55 final size:56
Alignment explanation
Indices: 16632977--16633106 Score: 192
Period size: 56 Copynumber: 2.3 Consensus size: 56
16632967 CACTAATAGA
16632977 CATTCC-ATGTCACATTTTTC-TTCATTTCATATTTTTCATTTCAGTCATATATCCT
1 CATTCCAAT-TCACATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATCCT
* *
16633032 CATTCCAATTCCCATTTTTCTTTCATTTCATATTTTTCATTTCATTCATATATCCT
1 CATTCCAATTCACATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATCCT
* * *
16633088 TATGCCAATTCTCATTTTT
1 CATTCCAATTCACATTTTT
16633107 ATTTGCCTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
55 16 0.24
56 52 0.76
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (56 bp):
CATTCCAATTCACATTTTTCTTTCATTTCATATTTTTCATTTCAGTCATATATCCT
Found at i:16646224 original size:12 final size:14
Alignment explanation
Indices: 16646207--16646239 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16646197 GATAGGTCAC
16646207 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
16646219 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
16646233 ATGTGTA
1 ATGTGTA
16646240 CTGGATAGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 1 0.05
14 11 0.58
ACGTcount: A:0.24, C:0.09, G:0.27, T:0.39
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:16646234 original size:101 final size:103
Alignment explanation
Indices: 16646119--16646341 Score: 269
Period size: 101 Copynumber: 2.2 Consensus size: 103
16646109 GCATGGACTG
* * *
16646119 TGTGTAGGCCACTATGTGAAAGT-GAAAG-TGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTA
1 TGTGTAGGCTACTATGTGAAACTGGAAAGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTA
* *
16646181 CTACGTATACCAGA-A-TGATAGGTCACATGTGTAGTACTA
64 CCACGTATACCAGATAGTGAT-GATCACATGTGTAGTACTA
* *
16646220 TGTGTAGGCTACTATGTG-TACTGGATAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACC
1 TGTGTAGGCTACTATGTGAAACTGGAAAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACC
* * * *
16646284 ATGTGTATCGGATAGTGATGATCACATGTGTAGTACTA
66 ACGTATACCAGATAGTGATGATCACATGTGTAGTACTA
*
16646322 TGTGCAGGCTACTATGTGAA
1 TGTGTAGGCTACTATGTGAA
16646342 CCGATATCAT
Statistics
Matches: 103, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
100 3 0.03
101 59 0.57
102 37 0.36
103 4 0.04
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (103 bp):
TGTGTAGGCTACTATGTGAAACTGGAAAGCTTCGATCACGTGTGTAGTACTATGTGCAGGCTACC
ACGTATACCAGATAGTGATGATCACATGTGTAGTACTA
Found at i:16646273 original size:51 final size:49
Alignment explanation
Indices: 16646153--16646339 Score: 207
Period size: 51 Copynumber: 3.7 Consensus size: 49
16646143 AAAGTGATGG
* * * ** * *
16646153 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTATACCAGA-ATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATA-G-TTGA
*
16646203 TCACATGTGTAGTACTATGTGTAGGCTACTATGTGTACTGGATAGCTTCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATAG-TT-GA
* *
16646254 TCACGTGTGTAGTACTATGTGCAGGCTACCATGTGTA-TCGGATAGTGATGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACT-GGATAGT--TGA
16646305 TCACATGTGTAGTACTATGTGCAGGCTACTATGTG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGTG
16646340 AACCGATATC
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
50 40 0.34
51 77 0.65
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.32
Consensus pattern (49 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGTGTACTGGATAGTTGA
Found at i:16646289 original size:26 final size:26
Alignment explanation
Indices: 16646259--16646339 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
16646249 TTCGATCACG
16646259 TGTGTAGTACTATGTGCAGGCTACCA
1 TGTGTAGTACTATGTGCAGGCTACCA
* * *
16646285 TGTGTA-T-CGGATAGTG-ATGAT-CACA
1 TGTGTAGTAC-TAT-GTGCAGGCTAC-CA
*
16646310 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACCA
16646336 TGTG
1 TGTG
16646340 AACCGATATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 2 0.05
25 17 0.41
26 20 0.49
27 2 0.05
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACCA
Found at i:16658825 original size:29 final size:29
Alignment explanation
Indices: 16658792--16658850 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
16658782 AATGTTGTCA
16658792 TAAGATCATGATTCATTCCATTTGCATGC
1 TAAGATCATGATTCATTCCATTTGCATGC
16658821 TAAGATCATGATTCATTCCATTTGCATGC
1 TAAGATCATGATTCATTCCATTTGCATGC
16658850 T
1 T
16658851 TACCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.20, G:0.14, T:0.39
Consensus pattern (29 bp):
TAAGATCATGATTCATTCCATTTGCATGC
Found at i:16668608 original size:36 final size:36
Alignment explanation
Indices: 16668556--16668631 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
16668546 ACTAGCTATC
* *
16668556 AAACGGTGTCATTTTGAGAGTTGAGTTCAGAGACCA
1 AAACAGTGTCATTTTGAGAGTTGAGTTCAAAGACCA
* *
16668592 AAACAGTGTCGTTTTGAGAGTTGGGTTCAAAGACCA
1 AAACAGTGTCATTTTGAGAGTTGAGTTCAAAGACCA
16668628 AAAC
1 AAAC
16668632 GGCATCGTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (36 bp):
AAACAGTGTCATTTTGAGAGTTGAGTTCAAAGACCA
Found at i:16668640 original size:36 final size:36
Alignment explanation
Indices: 16668567--16668643 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
16668557 AACGGTGTCA
* **
16668567 TTTTGAGAGTTGAGTTCAGAGACCAAAACAGTGTCG
1 TTTTGAGAGTTGAGTTCAAAGACCAAAACAGCATCG
* *
16668603 TTTTGAGAGTTGGGTTCAAAGACCAAAACGGCATCG
1 TTTTGAGAGTTGAGTTCAAAGACCAAAACAGCATCG
16668639 TTTTG
1 TTTTG
16668644 GCCTCTGACT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (36 bp):
TTTTGAGAGTTGAGTTCAAAGACCAAAACAGCATCG
Found at i:16670555 original size:23 final size:23
Alignment explanation
Indices: 16670525--16670577 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
16670515 ATGTACATCT
16670525 TTATTTTGATCATTTTAGGAAGA
1 TTATTTTGATCATTTTAGGAAGA
16670548 TTATTTTGATCATTTTAGGAAGA
1 TTATTTTGATCATTTTAGGAAGA
16670571 TTATTTT
1 TTATTTT
16670578 AAGAGACGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.28, C:0.04, G:0.15, T:0.53
Consensus pattern (23 bp):
TTATTTTGATCATTTTAGGAAGA
Found at i:16683948 original size:30 final size:30
Alignment explanation
Indices: 16683914--16683971 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16683904 CTGGGCACTT
* *
16683914 CCACACGGGCTGGCCACATGCCCGTGTGAG
1 CCACACGAGCTGGCCACATGCCCATGTGAG
*
16683944 CCACACGAGCTGGGCACATGCCCATGTG
1 CCACACGAGCTGGCCACATGCCCATGTG
16683972 CCAGCCCGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.19, C:0.36, G:0.31, T:0.14
Consensus pattern (30 bp):
CCACACGAGCTGGCCACATGCCCATGTGAG
Found at i:16692272 original size:138 final size:138
Alignment explanation
Indices: 16692024--16692301 Score: 556
Period size: 138 Copynumber: 2.0 Consensus size: 138
16692014 GGTTATAGAG
16692024 CTATTGTCAAAGTTCCAACACGTAAACGTAAAAAGTTAGGTGAAAGAGGAATTGAATGCATACTT
1 CTATTGTCAAAGTTCCAACACGTAAACGTAAAAAGTTAGGTGAAAGAGGAATTGAATGCATACTT
16692089 ATAGGATATGCACATAATAGCAAGGCATATAGGTTCATGGTAATTGAACCAAATGATTCAATTTC
66 ATAGGATATGCACATAATAGCAAGGCATATAGGTTCATGGTAATTGAACCAAATGATTCAATTTC
16692154 AATTAACA
131 AATTAACA
16692162 CTATTGTCAAAGTTCCAACACGTAAACGTAAAAAGTTAGGTGAAAGAGGAATTGAATGCATACTT
1 CTATTGTCAAAGTTCCAACACGTAAACGTAAAAAGTTAGGTGAAAGAGGAATTGAATGCATACTT
16692227 ATAGGATATGCACATAATAGCAAGGCATATAGGTTCATGGTAATTGAACCAAATGATTCAATTTC
66 ATAGGATATGCACATAATAGCAAGGCATATAGGTTCATGGTAATTGAACCAAATGATTCAATTTC
16692292 AATTAACA
131 AATTAACA
16692300 CT
1 CT
16692302 GTTATTGAAT
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 140 1.00
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (138 bp):
CTATTGTCAAAGTTCCAACACGTAAACGTAAAAAGTTAGGTGAAAGAGGAATTGAATGCATACTT
ATAGGATATGCACATAATAGCAAGGCATATAGGTTCATGGTAATTGAACCAAATGATTCAATTTC
AATTAACA
Found at i:16694926 original size:50 final size:50
Alignment explanation
Indices: 16694816--16695013 Score: 184
Period size: 50 Copynumber: 3.9 Consensus size: 50
16694806 ACATTAAGAG
*
16694816 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
*
16694867 GATTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * * * *
16694920 GATGAGAGGTCCCCCGTAAAACCATGTCTGGGACATGGCATGGGTACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * * * * *
16694970 TATGAGAACTCTCATGTAAGACCATATTTAGGATATGGCATTGG
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
16695014 TAGTACAAGA
Statistics
Matches: 121, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
50 74 0.61
51 1 0.01
53 3 0.02
54 6 0.05
55 1 0.01
56 36 0.30
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:16702519 original size:50 final size:50
Alignment explanation
Indices: 16702409--16702608 Score: 188
Period size: 50 Copynumber: 3.9 Consensus size: 50
16702399 ACATTAAGAG
*
16702409 GATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGA
*
16702460 GATTATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * * * *
16702513 GATGAGAGGTCCCCCGTAAAACCATGTCTGGGACATGGCATGGGTACCTA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* ** * * * * *
16702563 TATGAGAACTCTCATGTAAGACCATATTTAGGATATGGCATTGGCA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
16702609 GTACAAGAAA
Statistics
Matches: 122, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
50 75 0.61
51 1 0.01
53 3 0.02
54 6 0.05
55 1 0.01
56 36 0.30
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:16714364 original size:21 final size:20
Alignment explanation
Indices: 16714322--16714360 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16714312 GATATTTATA
16714322 TTATTTTTAATTTAATAAAT
1 TTATTTTTAATTTAATAAAT
*
16714342 TTATTCTTT-ATTTATTAAA
1 TTATT-TTTAATTTAATAAA
16714361 ATTTTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTTTAATTTAATAAAT
Found at i:16715974 original size:38 final size:38
Alignment explanation
Indices: 16715932--16716006 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
16715922 ATTGCATGCC
*
16715932 TACTGTTACTGTTAAACCAAATACATGTTAAACATGTT
1 TACTGTTACTGATAAACCAAATACATGTTAAACATGTT
* * ** *
16715970 TACTGTTATTGATGAACTGAATACATGTTAAGCATGT
1 TACTGTTACTGATAAACCAAATACATGTTAAACATGT
16716007 CTATTGTTTC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (38 bp):
TACTGTTACTGATAAACCAAATACATGTTAAACATGTT
Found at i:16717683 original size:25 final size:24
Alignment explanation
Indices: 16717650--16717704 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
16717640 TCAGTTTATT
*
16717650 TTTAATTATA-TTTAAAATATTTTAA
1 TTTATTTATATTTTAAAA-A-TTTAA
*
16717675 TTTATTTATATTTTCAAAATTTAA
1 TTTATTTATATTTTAAAAATTTAA
16717699 TTTATT
1 TTTATT
16717705 AACATTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 11 0.41
25 10 0.37
26 6 0.22
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
TTTATTTATATTTTAAAAATTTAA
Found at i:16717718 original size:24 final size:24
Alignment explanation
Indices: 16717670--16717725 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
16717660 TTTAAAATAT
* * *
16717670 TTTAATTTATTTATATTTTCAAAA
1 TTTAATTTATTAACATTATCAAAA
*
16717694 TTTAATTTATTAACATTATCTAAA
1 TTTAATTTATTAACATTATCAAAA
*
16717718 TTCAATTT
1 TTTAATTT
16717726 GATGTGGTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (24 bp):
TTTAATTTATTAACATTATCAAAA
Found at i:16718601 original size:21 final size:21
Alignment explanation
Indices: 16718577--16718619 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16718567 ATTGGATAAA
*
16718577 TTTAAAAAATAAATCTAATTT
1 TTTAAAAAATAAATATAATTT
**
16718598 TTTATTAAATAAATATAATTT
1 TTTAAAAAATAAATATAATTT
16718619 T
1 T
16718620 ATATATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTTAAAAAATAAATATAATTT
Found at i:16718647 original size:17 final size:18
Alignment explanation
Indices: 16718606--16718651 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
16718596 TTTTTATTAA
*
16718606 ATAAATATAATTTTATAT
1 ATAAATATGATTTTATAT
16718624 ATAAATATGATTTTAT-T
1 ATAAATATGATTTTATAT
*
16718641 TTAAATATGAT
1 ATAAATATGAT
16718652 AATAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (18 bp):
ATAAATATGATTTTATAT
Found at i:16719030 original size:22 final size:23
Alignment explanation
Indices: 16719005--16719047 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
16718995 AACTTAAAAG
16719005 AAATTAAATATATTTT-ATAATT
1 AAATTAAATATATTTTCATAATT
*
16719027 AAATTAAATATTTTTTCATAA
1 AAATTAAATATATTTTCATAA
16719048 ATATTAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AAATTAAATATATTTTCATAATT
Found at i:16720037 original size:11 final size:11
Alignment explanation
Indices: 16720021--16720058 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16720011 ACTTATTCAA
16720021 TTCTTTTTCTT
1 TTCTTTTTCTT
16720032 TTCTTTTTCTT
1 TTCTTTTTCTT
*
16720043 TT-TGTTTTCCT
1 TTCT-TTTTCTT
16720054 TTCTT
1 TTCTT
16720059 CACTATAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:16720679 original size:62 final size:62
Alignment explanation
Indices: 16720582--16720723 Score: 250
Period size: 62 Copynumber: 2.3 Consensus size: 62
16720572 TCATGTTTCC
*
16720582 AGGCCGTGTAACTCATTGTTTGTGAAATAGGGTCTCACGGCTAG-GAGCACGAGCGTGTGCCT
1 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAGAG-GCACGAGCGTGTGCCT
*
16720644 AGGCCGTGTAACTCACTGTTTGTGAAATAGTGTCTCACGGCTAGAGGCACGAGCGTGTGCCT
1 AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAGAGGCACGAGCGTGTGCCT
16720706 AGGCCGTGTAACTCACTG
1 AGGCCGTGTAACTCACTG
16720724 CTCATGAATT
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
62 76 0.99
63 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (62 bp):
AGGCCGTGTAACTCACTGTTTGTGAAATAGGGTCTCACGGCTAGAGGCACGAGCGTGTGCCT
Found at i:16720745 original size:62 final size:62
Alignment explanation
Indices: 16720582--16720745 Score: 186
Period size: 62 Copynumber: 2.6 Consensus size: 62
16720572 TCATGTTTCC
* * ** ** *
16720582 AGGCCGTGTAACTCATTGTTTGTGAAATAGGGTCTCACGGCTAGGAGCACGAGCGTGTGCCT
1 AGGCCGTGTAACTCACTGCTCATGAAATAAAGTCACACGGCTAGGAGCACGAGCGTGTGCCT
* ** ** *
16720644 AGGCCGTGTAACTCACTGTTTGTGAAATAGTGTCTCACGGCTA-GAGGCACGAGCGTGTGCCT
1 AGGCCGTGTAACTCACTGCTCATGAAATAAAGTCACACGGCTAGGA-GCACGAGCGTGTGCCT
*
16720706 AGGCCGTGTAACTCACTGCTCATGAATTAAAGTCACACGG
1 AGGCCGTGTAACTCACTGCTCATGAAATAAAGTCACACGG
16720746 GCGTGTGTCC
Statistics
Matches: 92, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
61 2 0.02
62 90 0.98
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (62 bp):
AGGCCGTGTAACTCACTGCTCATGAAATAAAGTCACACGGCTAGGAGCACGAGCGTGTGCCT
Found at i:16725597 original size:23 final size:23
Alignment explanation
Indices: 16725564--16725783 Score: 183
Period size: 23 Copynumber: 9.5 Consensus size: 23
16725554 TCATGCTTAA
*
16725564 ATGCTGCCCAATTTGTTGCATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * *
16725587 ATGCTGTCCAATTTTGATGCT-TAA
1 ATGCTGCCCAA-TTTGTTG-TATAT
* *
16725611 ATGCTGTCCAATTTTTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* * *
16725634 ATGCTGCCCAATTTTGGTGTAAAA
1 ATGCTGCCCAA-TTTGTTGTATAT
* * *
16725658 ATGTTGCTCAAATTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* *
16725681 ATGCTGCCCAAATTGTTGAAT-T
1 ATGCTGCCCAATTTGTTGTATAT
* * * *
16725703 ATGCTGTCCAATTTTGGTGTAAAA
1 ATGCTGCCCAA-TTTGTTGTATAT
* *
16725727 ATGCTGCTCAAATTGTTGTATAT
1 ATGCTGCCCAATTTGTTGTATAT
* *
16725750 ATGCTGCCCAAGTTGTTGTATTT
1 ATGCTGCCCAATTTGTTGTATAT
*
16725773 ATGCTGTCCAA
1 ATGCTGCCCAA
16725784 ATTTTGGTGT
Statistics
Matches: 154, Mismatches: 37, Indels: 12
0.76 0.18 0.06
Matches are distributed among these distances:
22 12 0.08
23 97 0.63
24 45 0.29
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (23 bp):
ATGCTGCCCAATTTGTTGTATAT
Found at i:16725610 original size:47 final size:47
Alignment explanation
Indices: 16725556--16725789 Score: 176
Period size: 47 Copynumber: 5.0 Consensus size: 47
16725546 CGGATAGGTC
* *
16725556 ATGCTTAAATGCTGCCCAATTTGTTGCATATATGCTGTCCAATTTTG
1 ATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTTG
* *
16725603 ATGCTTAAATGCTGTCCAATTTTTTGTATATATGCTGCCCAATTTTG
1 ATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTTG
* * * * *
16725650 GTG-TAAAAATGTTGCTCAAATTGTTGTATATATGCTGCCCAAATTGTTG
1 ATGCT-TAAATGCTGCCCAATTTGTTGTATATATGCTGCCC-AATT-TTG
* * * * * * *
16725699 A--ATT--ATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAA-ATTG
1 ATGCTTAAATGCTGCCCAA-TTTGTTGTATATATGCTGCCCAATTTTG
* * * * *
16725742 TTG-TATATATGCTGCCCAAGTTGTTGTATTTATGCTGTCCAAATTTTG
1 ATGCT-TAAATGCTGCCCAATTTGTTGTATATATGCTG-CCCAATTTTG
16725790 GTGTGAGAAT
Statistics
Matches: 143, Mismatches: 32, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
43 3 0.02
44 1 0.01
45 11 0.08
46 30 0.21
47 87 0.61
48 8 0.06
49 3 0.02
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.41
Consensus pattern (47 bp):
ATGCTTAAATGCTGCCCAATTTGTTGTATATATGCTGCCCAATTTTG
Found at i:16725614 original size:24 final size:24
Alignment explanation
Indices: 16725556--16725625 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
16725546 CGGATAGGTC
*
16725556 ATGCTTAAATGCTGCCCAA-TTTG
1 ATGCTTAAATGCTGTCCAATTTTG
* * *
16725579 TTGCATATATGCTGTCCAATTTTG
1 ATGCTTAAATGCTGTCCAATTTTG
16725603 ATGCTTAAATGCTGTCCAATTTT
1 ATGCTTAAATGCTGTCCAATTTT
16725626 TTGTATATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 15 0.38
24 24 0.62
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (24 bp):
ATGCTTAAATGCTGTCCAATTTTG
Found at i:16725819 original size:69 final size:70
Alignment explanation
Indices: 16725611--16725802 Score: 278
Period size: 69 Copynumber: 2.7 Consensus size: 70
16725601 TGATGCTTAA
* * * * * *
16725611 ATGCTGTCCAATTTTTTGTATATATGCTGCCCAATTTTGGTGTAAAAATGTTGCTCAAATTGTTG
1 ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
16725676 TATAT
66 TATAT
*
16725681 ATGCTGCCCAAATTGTTG-AATTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
1 ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
16725745 TATAT
66 TATAT
* * *
16725750 ATGCTGCCCAAGTTGTTGTATTTATGCTGTCCAAATTTTGGTGTGAGAATGCT
1 ATGCTGCCCAAATTGTTGTATTTATGCTGTCC-AATTTTGGTGTAAAAATGCT
16725803 ATCTAATTTG
Statistics
Matches: 109, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
69 64 0.59
70 27 0.25
71 18 0.17
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (70 bp):
ATGCTGCCCAAATTGTTGTATTTATGCTGTCCAATTTTGGTGTAAAAATGCTGCTCAAATTGTTG
TATAT
Found at i:16733414 original size:23 final size:22
Alignment explanation
Indices: 16733348--16733654 Score: 202
Period size: 23 Copynumber: 13.2 Consensus size: 22
16733338 TAAATGCTAC
*
16733348 CCAATTTGTTGCATATATGCTG
1 CCAATTTGTTGTATATATGCTG
* * *
16733370 TCCACTTTTGATTCT-TAAATGCTG
1 -CCA-ATTTG-TTGTATATATGCTG
* *
16733394 TCCCATTTGTTGTATACATGCTG
1 -CCAATTTGTTGTATATATGCTG
*
16733417 CCCAATTTGTTGTATATATGCTA
1 -CCAATTTGTTGTATATATGCTG
* *
16733440 CGCAATTTGTTGCATATATGTTG
1 C-CAATTTGTTGTATATATGCTG
* * *
16733463 TCCAATTTTGATGTTTAAATGCTG
1 -CCAA-TTTGTTGTATATATGCTG
* *
16733487 CCCAATTTGTTGTATATGTCCTG
1 -CCAATTTGTTGTATATATGCTG
* * *
16733510 TCCAATTTTGGTGTAAAAATGCTG
1 -CCAA-TTTGTTGTATATATGCTG
*
16733534 CTCAAATTGTTGTATATATGCTG
1 C-CAATTTGTTGTATATATGCTG
* * *
16733557 CCCAAATTGTTGAATTTATGCTG
1 -CCAATTTGTTGTATATATGCTG
* * *
16733580 TCCAATTTTGATGTAAAAATGCTG
1 -CCAA-TTTGTTGTATATATGCTG
*
16733604 CTCAAATTGTTGTATATATGCTG
1 C-CAATTTGTTGTATATATGCTG
* *
16733627 CCCAAATTGTTGTATTTATGCTG
1 -CCAATTTGTTGTATATATGCTG
16733650 TCCAA
1 -CCAA
16733655 ATTTTGGTGT
Statistics
Matches: 221, Mismatches: 51, Indels: 24
0.75 0.17 0.08
Matches are distributed among these distances:
22 4 0.02
23 149 0.67
24 66 0.30
25 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (22 bp):
CCAATTTGTTGTATATATGCTG
Found at i:16733485 original size:70 final size:70
Alignment explanation
Indices: 16733331--16733658 Score: 206
Period size: 70 Copynumber: 4.7 Consensus size: 70
16733321 ACCGGATAGG
* * * * * *
16733331 TGATGCTTAAATGCTACCCAATTTGTTGCATATATGCTGTCCACTTTTGATTCTTAAATGCTGTC
1 TGATGTTTAAATGCTGCCCAATTTGTTGTATATATGCTGACCACATTTGATTCATAAATGCTGTC
*
16733396 CCATT
66 CAATT
* * * * *
16733401 TGTTGTATACATGCTGCCCAATTTGTTGTATATATGCT-ACGCA-ATTTG-TTGCATATATGTTG
1 TGATGTTTAAATGCTGCCCAATTTGTTGTATATATGCTGAC-CACATTTGATT-CATAAATGCTG
16733463 TCCAATTT
64 TCCAA-TT
* * * * *
16733471 TGATGTTTAAATGCTGCCCAATTTGTTGTATATGTCCTGTCCA-ATTTTGGTGT-AAAAATGCTG
1 TGATGTTTAAATGCTGCCCAATTTGTTGTATATATGCTGACCACA-TTTGAT-TCATAAATGCTG
*
16733534 -CTCAAAT
64 TC-CAATT
* * * * * * * *
16733541 TGTTGTATATATGCTGCCCAAATTGTTGAATTTATGCTGTCCA-ATTTTGATGT-AAAAATGCTG
1 TGATGTTTAAATGCTGCCCAATTTGTTGTATATATGCTGACCACA-TTTGAT-TCATAAATGCTG
*
16733604 -CTCAAAT
64 TC-CAATT
* * * * * * *
16733611 TGTTGTATATATGCTGCCCAAATTGTTGTATTTATGCTGTCCAAATTT
1 TGATGTTTAAATGCTGCCCAATTTGTTGTATATATGCTGACCACATTT
16733659 TGGTGTGAGA
Statistics
Matches: 217, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
68 2 0.01
69 17 0.08
70 180 0.83
71 16 0.07
72 1 0.00
73 1 0.00
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.42
Consensus pattern (70 bp):
TGATGTTTAAATGCTGCCCAATTTGTTGTATATATGCTGACCACATTTGATTCATAAATGCTGTC
CAATT
Found at i:16733530 original size:47 final size:47
Alignment explanation
Indices: 16733338--16733715 Score: 257
Period size: 47 Copynumber: 8.1 Consensus size: 47
16733328 AGGTGATGCT
* * * *
16733338 TAAATGCTACCCAATTTGTTGCATATATGCTGTCCACTTTTGAT-TCT
1 TAAATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGATGT-A
* * *
16733385 TAAATGCTGTCCC-ATTTGTTGTATACATGCTGCCCAA-TTTGTTGTA
1 TAAATGCTG-CCCAATTTGTTGTATATATGCTGTCCAATTTTGATGTA
* * * * * *
16733431 TATATGCTACGCAATTTGTTGCATATATGTTGTCCAATTTTGATGTT
1 TAAATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGATGTA
* * *
16733478 TAAATGCTGCCCAATTTGTTGTATATGTCCTGTCCAATTTTGGTGTA
1 TAAATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGATGTA
* * * * * * *
16733525 AAAATGCTGCTCAAATTGTTGTATATATGCTGCCCAA-ATTGTTGAA
1 TAAATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGATGTA
** * * * * * *
16733571 TTTATGCTGTCCAATTTTGATGTAAAAATGCTG-CTCAA-ATTGTTGTA
1 TAAATGCTGCCCAA-TTTGTTGTATATATGCTGTC-CAATTTTGATGTA
* * * *
16733618 TATATGCTGCCCAAATTGTTGTATTTATGCTGTCCAAATTTTGGTGTGA
1 TAAATGCTGCCCAATTTGTTGTATATATGCTGTCC-AATTTTGATGT-A
* ** * * * * **
16733667 -GAATGCTATCTAATTTGGTATATAAATGCTGTCCAAAATTGATGTA
1 TAAATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGATGTA
16733713 TAA
1 TAA
16733716 GAGCTGTCCA
Statistics
Matches: 253, Mismatches: 67, Indels: 22
0.74 0.20 0.06
Matches are distributed among these distances:
45 2 0.01
46 63 0.25
47 154 0.61
48 33 0.13
49 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.41
Consensus pattern (47 bp):
TAAATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTGATGTA
Found at i:16738311 original size:126 final size:126
Alignment explanation
Indices: 16738086--16738314 Score: 291
Period size: 126 Copynumber: 1.8 Consensus size: 126
16738076 GTGTCAAGCT
* * *
16738086 GTGTGTCCAAGTCATGTAACTCACTATTTATGAATTAAGGTCACACGAGGTAGGGGCATGGACGT
1 GTGTGTCCAAGCCATGTAACTCACTATTTATGAATTAAGGTCACACGAGGTAGGGACATGGACAT
*
16738151 GTGTCTAAGCCATATAAGTCACTATTTGTGAATTAGAGCCACACGGGTTAGGGACATGGGA
66 GTGTCTAAGCCATATAACTCACTATTTGTGAATTAGAGCCACACGGGTTAGGGACATGGGA
* * * * *
16738212 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACATG-GGCTAGGGACACTGG-C
1 GTGTGTCCAAGCCATGTAACTCACTATTTATGAATTAAGGTCACACGAGG-TAGGGACA-TGGAC
* * * * * *
16738275 ATGTGTCTAGGTCGTGTAACTCATTGTTTGTGAATTAGAG
64 ATGTGTCTAAGCCATATAACTCACTATTTGTGAATTAGAG
16738315 TCACGCGGAC
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
125 2 0.02
126 81 0.94
127 3 0.03
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (126 bp):
GTGTGTCCAAGCCATGTAACTCACTATTTATGAATTAAGGTCACACGAGGTAGGGACATGGACAT
GTGTCTAAGCCATATAACTCACTATTTGTGAATTAGAGCCACACGGGTTAGGGACATGGGA
Found at i:16738312 original size:63 final size:63
Alignment explanation
Indices: 16738086--16738318 Score: 231
Period size: 63 Copynumber: 3.7 Consensus size: 63
16738076 GTGTCAAGCT
* * * * *
16738086 GTGTGTCCAAGTCATGTAACTCACTATTTATGAATTA-AGGTCACACGAGG-TAGGGGCATGG-A
1 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGA-GTCACACG-GGCTAGGGACATGGCA
* * * * * * * *
16738148 CGTGTGTCTAAGCCATATAAGTCACTATTTGTGAATTAGAGCCACACGGGTTAGGGACATGGGA
1 -GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGAGTCACACGGGCTAGGGACATGGCA
* *
16738212 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACATGGGCTAGGGACACTGGCA
1 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGAGTCACACGGGCTAGGGACA-TGGCA
* * * *
16738276 -TGTGTCTAGGTCGTGTAACTCATTGTTTGTGAATTAGAGTCAC
1 GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGAGTCAC
16738319 GCGGACGTGT
Statistics
Matches: 144, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
62 2 0.01
63 136 0.94
64 6 0.04
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (63 bp):
GTGTGTCCAAGCCGTGTAACTCACTGTTTGTGAATTAGAGTCACACGGGCTAGGGACATGGCA
Found at i:16739760 original size:37 final size:37
Alignment explanation
Indices: 16739667--16739772 Score: 142
Period size: 37 Copynumber: 2.9 Consensus size: 37
16739657 AAATCTTATT
* *
16739667 ATTATACTGAATGAAGCTCAATCAAGCAAATTATACC
1 ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
* *
16739704 GTTATATTGAATGAAGCTCAATCGAGCAAATCATACC
1 ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
**
16739741 ATTATACTGAATGGCGCTCAA-CTGAGCAAATC
1 ATTATACTGAATGAAGCTCAATC-GAGCAAATC
16739773 TTACTGTTAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
36 1 0.02
37 59 0.98
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (37 bp):
ATTATACTGAATGAAGCTCAATCGAGCAAATCATACC
Found at i:16739783 original size:37 final size:37
Alignment explanation
Indices: 16739656--16739785 Score: 138
Period size: 37 Copynumber: 3.5 Consensus size: 37
16739646 TCTATCAAGC
** *
16739656 CAAATCTTATTATTATACTGAATGAAGCTCAATCAAG
1 CAAATCTTACCATTATACTGAATGAAGCTCAATCGAG
* *
16739693 CAAAT-TATACCGTTATATTGAATGAAGCTCAATCGAG
1 CAAATCT-TACCATTATACTGAATGAAGCTCAATCGAG
* **
16739730 CAAATCATACCATTATACTGAATGGCGCTCAA-CTGAG
1 CAAATCTTACCATTATACTGAATGAAGCTCAATC-GAG
**
16739767 CAAATCTTACTGTTATACT
1 CAAATCTTACCATTATACT
16739786 AACTGATATT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
36 2 0.03
37 75 0.97
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (37 bp):
CAAATCTTACCATTATACTGAATGAAGCTCAATCGAG
Found at i:16741418 original size:25 final size:25
Alignment explanation
Indices: 16741375--16741429 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
16741365 TGAGCATCCT
**
16741375 GATA-TTGGCTCTCTTGAGCTACCC
1 GATAGTTGGCTCTCACGAGCTACCC
*
16741399 GATAGTTGGCTCTCACGAGCTTCCC
1 GATAGTTGGCTCTCACGAGCTACCC
*
16741424 GTTAGT
1 GATAGT
16741430 ACCTCTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.16, C:0.27, G:0.24, T:0.33
Consensus pattern (25 bp):
GATAGTTGGCTCTCACGAGCTACCC
Found at i:16747507 original size:24 final size:24
Alignment explanation
Indices: 16747480--16747531 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
16747470 CAGCTTGAAA
*
16747480 GAGCATCCTGTTATTAGCTCTCAT
1 GAGCATCCTGATATTAGCTCTCAT
* *
16747504 GAGCATCCTGATATTGGCTCTCTT
1 GAGCATCCTGATATTAGCTCTCAT
16747528 GAGC
1 GAGC
16747532 TACCCGGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.35
Consensus pattern (24 bp):
GAGCATCCTGATATTAGCTCTCAT
Found at i:16749510 original size:32 final size:32
Alignment explanation
Indices: 16749469--16749533 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
16749459 ATGTTGTGAC
16749469 ATGTTGTGCACTTGATCAACTTGTGATTTCCT
1 ATGTTGTGCACTTGATCAACTTGTGATTTCCT
*
16749501 ATGTTGTGCACTTTATCAACTTGTGATTTCCT
1 ATGTTGTGCACTTGATCAACTTGTGATTTCCT
16749533 A
1 A
16749534 CTTGTTACCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.20, C:0.18, G:0.17, T:0.45
Consensus pattern (32 bp):
ATGTTGTGCACTTGATCAACTTGTGATTTCCT
Found at i:16749853 original size:43 final size:43
Alignment explanation
Indices: 16749804--16749885 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
16749794 GAGACACTGA
*
16749804 CGTGTGACTCGACCATGCGAGGCACACGGCCTTGCAACACGGC
1 CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACACGGC
* * * *
16749847 CGTGTGACTTGACCGTGTGAGGCACATGGCCTTACAACA
1 CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACA
16749886 TTTCCATGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.22, C:0.30, G:0.29, T:0.18
Consensus pattern (43 bp):
CGTGTGACTCGACCATGCGAGGCACACGGCCTTACAACACGGC
Found at i:16757184 original size:31 final size:31
Alignment explanation
Indices: 16757146--16757208 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
16757136 GTGATAGAAG
*
16757146 GTTTTGAGGTTTCAATTCTTGGGACTGTTAA
1 GTTTTGAGGTTTCAATTCCTGGGACTGTTAA
*
16757177 GTTTTGAGGTTTCGATTCCTGGGACTGTTAA
1 GTTTTGAGGTTTCAATTCCTGGGACTGTTAA
16757208 G
1 G
16757209 GACTGAATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.17, C:0.11, G:0.29, T:0.43
Consensus pattern (31 bp):
GTTTTGAGGTTTCAATTCCTGGGACTGTTAA
Found at i:16758441 original size:58 final size:58
Alignment explanation
Indices: 16758305--16758441 Score: 143
Period size: 58 Copynumber: 2.4 Consensus size: 58
16758295 TCAGCTGGGG
* * * *
16758305 ATGTAAATCCGT-GACCTATTTTGAACTTAGGCATATTTTTTTATATAATCAAATGAGA
1 ATGTAAATCC-TCGAACTGTTTTGAACTTAGGCATATTTTTTGAAATAATCAAATGAGA
** * * * *
16758363 ATGTAAATCCTCGAGTTGTTTTGAACTTAGGCATATTTTTTGAAATACTTAATTGGGA
1 ATGTAAATCCTCGAACTGTTTTGAACTTAGGCATATTTTTTGAAATAATCAAATGAGA
*
16758421 ATGTAAAT-TTACGAACTGTTT
1 ATGTAAATCCT-CGAACTGTTT
16758442 GGAGGTTGCG
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
57 2 0.03
58 63 0.97
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (58 bp):
ATGTAAATCCTCGAACTGTTTTGAACTTAGGCATATTTTTTGAAATAATCAAATGAGA
Found at i:16759134 original size:71 final size:71
Alignment explanation
Indices: 16758488--16759168 Score: 529
Period size: 71 Copynumber: 9.6 Consensus size: 71
16758478 ATAGTTAAGC
* ** * ** * *
16758488 GCTTTTAACTATCGCTAA-T-TGTTTGGAGTTTGC-AGTATTAAACCTGTGAGCCTTAAAATGAT
1 GCTTTTAACTCTCGCTAACTAT-TTTGGAGGCTGCGA-TATTAAACTTGCAAGCCTTAGAATGAC
*
16758550 AGTTGGGA
64 AGCTGGGA
* * * ** *
16758558 GCTTTTAACTCTCGCTAACT-GTTTGGAGGCTGCGGTATTACACTTGTGAGCCTTAGAATGACAA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACTTGCAAGCCTTAGAATGACAG
*
16758622 ATGGGA
66 CTGGGA
* * * * * * * *
16758628 GCTTTTAACCCTCGCAAACTATTTGGGAGGCTAC-AGTTTTAAACCTACAAGCCTTAGAATGATA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGA-TATTAAACTTGCAAGCCTTAGAATGACA
*
16758692 GCTGAGA
65 GCTGGGA
* * * * *
16758699 TCTTTTAACTCTCGCTAACTATTTAGGAGGCTGCGGTTTTAAACCTGCAATG-CTTAGAATGACA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACTTGCAA-GCCTTAGAATGACA
*
16758763 GCTAGGA
65 GCTGGGA
* ** * * ** ** * * *
16758770 GCTTTTTACTCTCTTTAACTGTTTTTGATACTGCGATATTAAACTTGGGAGCCTTACAATGAGAA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACTTGCAAGCCTTAGAATGACAG
16758835 CTGGGA
66 CTGGGA
** * * ** * *
16758841 GCTTTTAGGTCTCGTTAACTATTTTGGAGTCTGC-AGTGCTAAACATGCAAGCCTTAGAATGAAA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGA-TATTAAACTTGCAAGCCTTAGAATGACA
16758905 GCTGGGA
65 GCTGGGA
* * * * * ** *
16758912 GCTTTTAACTCTCACTAGCTATATTAGAGGCTGCGGTATTAAACTTGTGAGCCTTAGAATGACAA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACTTGCAAGCCTTAGAATGACAG
*
16758977 CTGAGA
66 CTGGGA
* * * *
16758983 GCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGC-AGTATTAAATCTATG--AGCCTTGGAATGA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGA-TATTAAA-CT-TGCAAGCCTTAGAATGA
* *
16759045 CAACTAGGA
63 CAGCTGGGA
* * * *
16759054 GCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAAC-TGACAAGCCTTCGAATGATA
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACTTG-CAAGCCTTAGAATGACA
*
16759118 GTTGGGA
65 GCTGGGA
* * * *
16759125 GCTTTTAACTCTTGTTAACTATTTTTGAGGCTGCGGTATTAAAC
1 GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAAC
16759169 CTGTGAGACT
Statistics
Matches: 482, Mismatches: 113, Indels: 31
0.77 0.18 0.05
Matches are distributed among these distances:
68 2 0.00
70 77 0.16
71 397 0.82
72 4 0.01
73 2 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (71 bp):
GCTTTTAACTCTCGCTAACTATTTTGGAGGCTGCGATATTAAACTTGCAAGCCTTAGAATGACAG
CTGGGA
Found at i:16759200 original size:213 final size:209
Alignment explanation
Indices: 16758439--16759242 Score: 691
Period size: 213 Copynumber: 3.8 Consensus size: 209
16758429 TTACGAACTG
* * * * * * ** * *
16758439 TTTGGAGGTTGCGGTGTTAAACCTG-CGAGCCTTAAAATGATAGTTAAGCGCTTTTAACTATCGC
1 TTTGGAGGCTGCAGTATTAAA-CTGACAAGCCTTAGAATGATAGCTGGGAGCTTTTAACTCTCGC
* ** * * *
16758503 TAA-T-TGTTTGGAGTTTGCAGTATTAAACCTGTGAGCCTTAAAATGATAGTTGGGAGCTTTTAA
65 TAACTAT-TTTAGAGGCTGCGGTATTAAACCTGTGAGCCTTAGAATGACAGTT-GGAGCTTTTAA
* * *
16758566 CTCTCGCTAACTG-TTTGGAGGCTGCGGTATTACACTTGTGAGCCTTAGAATGACAAATGGGAGC
128 CTCTCGCTAACTGTTTTGAAGGCTGC-GTATTAAAC-T-TGAGCCTTAGAATGACAACTGGGAGC
* *
16758630 TTTTAACCCTCGCAAACTAT
190 TTTTAACTCTCGCTAACTAT
* * * * *
16758650 TTGGGAGGCTACAGTTTTAAACCT-ACAAGCCTTAGAATGATAGCTGAGATCTTTTAACTCTCGC
1 TTTGGAGGCTGCAGTATTAAA-CTGACAAGCCTTAGAATGATAGCTGGGAGCTTTTAACTCTCGC
* ** * *
16758714 TAACTA-TTTAGGAGGCTGCGGTTTTAAACCTGCAATG-CTTAGAATGACAGCTAGGAGCTTTTT
65 TAACTATTTTA-GAGGCTGCGGTATTAAACCTGTGA-GCCTTAGAATGACAG-TTGGAGCTTTTA
** * *
16758777 ACTCTCTTTAACTGTTTTTGATA--CTGCGATATTAAACTTGGGAGCCTTACAATGAGAACTGGG
127 ACTCTCGCTAACTG-TTTTGA-AGGCTGCG-TATTAAACTT--GAGCCTTAGAATGACAACTGGG
** *
16758840 AGCTTTTAGGTCTCGTTAACTAT
187 AGCTTTTAACTCTCGCTAACTAT
* ** * *
16758863 TTTGGAGTCTGCAGTGCTAAACATG-CAAGCCTTAGAATGAAAGCTGGGAGCTTTTAACTCTCAC
1 TTTGGAGGCTGCAGTATTAAAC-TGACAAGCCTTAGAATGATAGCTGGGAGCTTTTAACTCTCGC
* * * **
16758927 TAGCTATATTAGAGGCTGCGGTATTAAACTTGTGAGCCTTAGAATGACAACTGAGAGCTTTTAAC
65 TAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAGCCTTAGAATGACAGTTG-GAGCTTTTAAC
* * *
16758992 TCTCGTTAACTGTTTTGAAGGCTGCAGTATTAAATCTATGAGCCTTGGAATGACAACTAGGAGCT
129 TCTCGCTAACTGTTTTGAAGGCTGC-GTATTAAA-CT-TGAGCCTTAGAATGACAACTGGGAGCT
* *
16759057 TTTAACTTTTGCTAACTAT
191 TTTAACTCTCGCTAACTAT
* * * *
16759076 TTTGGAGGCTGC-GATATTAAACTGACAAGCCTTCGAATGATAGTTGGGAGCTTTTAACTCTTGT
1 TTTGGAGGCTGCAG-TATTAAACTGACAAGCCTTAGAATGATAGCTGGGAGCTTTTAACTCTCGC
* * * *
16759140 TAACTATTTTTGAGGCTGCGGTATTAAACCTGTGAGACTT-GCAAT-AGTAGTTGTGAGCTTTTC
65 TAACTATTTTAGAGGCTGCGGTATTAAACCTGTGAGCCTTAG-AATGA-CAGTTG-GAGCTTTTA
* * * *
16759203 ATTTTTGCTAACTGTTTTGAAGGTCGTG-ATATTAAACTTG
127 ACTCTCGCTAACTGTTTTGAAGG-C-TGCGTATTAAACTTG
16759243 TATTGGAATT
Statistics
Matches: 477, Mismatches: 88, Indels: 56
0.77 0.14 0.09
Matches are distributed among these distances:
211 61 0.13
212 69 0.14
213 332 0.70
214 11 0.02
215 4 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (209 bp):
TTTGGAGGCTGCAGTATTAAACTGACAAGCCTTAGAATGATAGCTGGGAGCTTTTAACTCTCGCT
AACTATTTTAGAGGCTGCGGTATTAAACCTGTGAGCCTTAGAATGACAGTTGGAGCTTTTAACTC
TCGCTAACTGTTTTGAAGGCTGCGTATTAAACTTGAGCCTTAGAATGACAACTGGGAGCTTTTAA
CTCTCGCTAACTAT
Found at i:16759209 original size:142 final size:142
Alignment explanation
Indices: 16758544--16759240 Score: 342
Period size: 142 Copynumber: 4.9 Consensus size: 142
16758534 TGAGCCTTAA
* * * * * *
16758544 AATGATAGTTGGGAGCTTTTAACTCTCGCTAACTG-TTTGGAGGCTGCGGTATTACACTTGTGAG
1 AATGATAGTTGGGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAGTATTAAACCTATGAG
* * * ** * * * * * *
16758608 CCTTAG-AATGACAAATGGGAGCTTTTAACCCTCGCAAACTATTTGGGAGG-CTAC-AGTTTTAA
66 ACTT-GCAATGACAACTAGGAGCTTTTAACTTTTGCTAACTATTTTGAAGGTC-GCGA-TATTAA
*
16758670 ACCT-ACAAGCCTTAG
128 A-CTGACAAGCCTTCG
* * * * * * * * * ***
16758685 AATGATAGCTGAGATCTTTTAACTCTCGCTAACTATTTAGGAGGCTGCGGTTTTAAACCTGCAAT
1 AATGATAGTTGGGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAGTATTAAACCTATGA-
* * * *
16758750 G-CTTAG-AATGACAGCTAGGAGCTTTTTACTCTCTT--TAACTGTTTTTGATA-CT-GCGATAT
65 GACTT-GCAATGACAACTAGGAGCTTTTAACT-T-TTGCTAACT-ATTTTGA-AGGTCGCGATAT
**
16758809 TAAACTTG-GGAGCCTTAC-
125 TAAAC-TGACAAGCCTT-CG
* ** ** * * * **
16758827 AATGAGAACTGGGAGCTTTTAGGTCTCGTTAACTATTTTGGAGTCTGCAGTGCTAAA-C-ATGCA
1 AATGATAGTTGGGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAGTATTAAACCTATG--
* * * ** * * *
16758890 AGCCTTAG-AATGA-AAGCTGGGAGCTTTTAACTCTCACTAGCTATATT-AGAGG-CTGCGGTAT
64 AGACTT-GCAATGACAA-CTAGGAGCTTTTAACTTTTGCTAACTATTTTGA-AGGTC-GCGATAT
** *
16758951 TAAACTTG-TGAGCCTTAG
125 TAAAC-TGACAAGCCTTCG
* ** * *
16758969 AATGACAACTGAGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAGTATTAAATCTATGAG
1 AATGATAGTTGGGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAGTATTAAACCTATGAG
* * *
16759034 CCTTGGAATGACAACTAGGAGCTTTTAACTTTTGCTAACTATTTTGGAGG-CTGCGATATTAAAC
66 ACTTGCAATGACAACTAGGAGCTTTTAACTTTTGCTAACTATTTTGAAGGTC-GCGATATTAAAC
16759098 TGACAAGCCTTCG
130 TGACAAGCCTTCG
* * * *
16759111 AATGATAGTTGGGAGCTTTTAACTCTTGTTAACTATTTTTG-AGGCTGCGGTATTAAACCTGTGA
1 AATGATAGTTGGGAGCTTTTAACTCTCGTTAACT-GTTTTGAAGGCTGCAGTATTAAACCTATGA
** * * * * * *
16759175 GACTTGCAAT-AGTAGTTGTGAGCTTTTCATTTTTGCTAACTGTTTTGAAGGTCGTGATATTAAA
65 GACTTGCAATGACAACTAG-GAGCTTTTAACTTTTGCTAACTATTTTGAAGGTCGCGATATTAAA
16759239 CT
129 CT
16759241 TGTATTGGAA
Statistics
Matches: 431, Mismatches: 95, Indels: 59
0.74 0.16 0.10
Matches are distributed among these distances:
140 3 0.01
141 45 0.10
142 363 0.84
143 15 0.03
144 5 0.01
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (142 bp):
AATGATAGTTGGGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGCAGTATTAAACCTATGAG
ACTTGCAATGACAACTAGGAGCTTTTAACTTTTGCTAACTATTTTGAAGGTCGCGATATTAAACT
GACAAGCCTTCG
Found at i:16759215 original size:71 final size:71
Alignment explanation
Indices: 16758544--16759240 Score: 226
Period size: 71 Copynumber: 9.8 Consensus size: 71
16758534 TGAGCCTTAA
* * * * * **
16758544 AATGATAGTTGGGAGCTTTTAACTCTCGCTAACT-GTTTGGAGGCTGCGGTATTACACTTG-TGA
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAAC-TGACAA
* *
16758607 GCCTTAG
65 GACTTCG
* ** ** * * * * *
16758614 AATGACAAATGGGAGCTTTTAACCCTCGCAAACTATTTGGGAGGCTAC-AGTTTTAAACCT-ACA
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGA-TATTAAA-CTGACA
* *
16758677 AGCCTTAG
64 AGACTTCG
* * * * * * * *
16758685 AATGATAGCTGAGATCTTTTAACTCTCGCTAACTATTTAGGAGGCTGCGGTTTTAAACCTG-CAA
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAA-CTGACAA
*
16758749 TG-CTTAG
65 -GACTTCG
* * * * * * ** *
16758756 AATGACAGCTAGGAGCTTTTTACTCTCTT--TAACTGTTTTTGATACTGCGATATTAAACTTG-G
1 AATGATAGTTGGGAGCTTTTAACT-T-TTGCTAACTATTTTGGAGGCTGCGATATTAAAC-TGAC
* *
16758818 GAGCCTTAC-
63 AAGACTT-CG
* ** ** * * * * **
16758827 AATGAGAACTGGGAGCTTTTAGGTCTCGTTAACTATTTTGGAGTCTGC-AGTGCTAAACATG-CA
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGA-TATTAAAC-TGACA
* *
16758890 AGCCTTAG
64 AGACTTCG
* * * ** * * * * **
16758898 AATGAAAGCTGGGAGCTTTTAACTCTCACTAGCTATATTAGAGGCTGCGGTATTAAACTTG-TGA
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAAC-TGACAA
* *
16758962 GCCTTAG
65 GACTTCG
* ** * * * * * * **
16758969 AATGACAACTGAGAGCTTTTAACTCTCGTTAACTGTTTTGAAGGCTGC-AGTATTAAATCT-ATG
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGA-TATTAAA-CTGACA
* *
16759032 AGCCTTGG
64 AGACTTCG
* ** *
16759040 AATGACAACTAGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAACTGACAAG
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAACTGACAAG
*
16759105 CCTTCG
66 ACTTCG
* * * * **
16759111 AATGATAGTTGGGAGCTTTTAACTCTTGTTAACTATTTTTGAGGCTGCGGTATTAAACCTG-TGA
1 AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAA-CTGACAA
16759175 GACTT-G
65 GACTTCG
* * * * * *
16759181 CAAT-AGTAGTTGTGAGCTTTTCATTTTTGCTAACTGTTTTGAAGG-TCGTGATATTAAACT
1 -AATGA-TAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCT-GCGATATTAAACT
16759241 TGTATTGGAA
Statistics
Matches: 484, Mismatches: 117, Indels: 52
0.74 0.18 0.08
Matches are distributed among these distances:
69 1 0.00
70 39 0.08
71 436 0.90
72 7 0.01
73 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (71 bp):
AATGATAGTTGGGAGCTTTTAACTTTTGCTAACTATTTTGGAGGCTGCGATATTAAACTGACAAG
ACTTCG
Found at i:16768182 original size:27 final size:29
Alignment explanation
Indices: 16768152--16768205 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
16768142 ATTTTCTTAC
*
16768152 TATT-CAATA-ATTTGATTATAAAAAATG
1 TATTGCAATAGATTAGATTATAAAAAATG
*
16768179 TATTGCATTAGATTAGATTATAAAAAA
1 TATTGCAATAGATTAGATTATAAAAAA
16768206 CTATTTATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 4 0.17
29 15 0.65
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (29 bp):
TATTGCAATAGATTAGATTATAAAAAATG
Found at i:16773137 original size:11 final size:12
Alignment explanation
Indices: 16773111--16773148 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
16773101 CAAAACAGGC
16773111 TTTTAGCGGCGT
1 TTTTAGCGGCGT
*
16773123 TTTTAGTGGCGT
1 TTTTAGCGGCGT
16773135 TTTTAGCGGCGT
1 TTTTAGCGGCGT
16773147 TT
1 TT
16773149 GGACAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.08, C:0.13, G:0.32, T:0.47
Consensus pattern (12 bp):
TTTTAGCGGCGT
Found at i:16773283 original size:40 final size:40
Alignment explanation
Indices: 16773137--16773289 Score: 132
Period size: 40 Copynumber: 3.8 Consensus size: 40
16773127 AGTGGCGTTT
* *
16773137 TTAGCGGCGTTTGGACAAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGTTT-TACAAAAAACGCCGCTAAAAATCGAGCA
* * ** * *
16773178 TTAGTGGCGCTTTACGTAAAACGCTGCTAAAGATCGAGCA
1 TTAGCGGCGTTTTACAAAAAACGCCGCTAAAAATCGAGCA
* ** * *
16773218 TTAGCGGAGTTTCTA-GGAAAGCGCCGCTAAAAAT-TAGCA
1 TTAGCGGCGTTT-TACAAAAAACGCCGCTAAAAATCGAGCA
*
16773257 TTAGCGGCGTTTTTCCAAAAAACGCCGC-AAAAA
1 TTAGCGGCG-TTTTACAAAAAACGCCGCTAAAAA
16773290 GTCTAAGCCC
Statistics
Matches: 88, Mismatches: 21, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
39 18 0.20
40 58 0.66
41 12 0.14
ACGTcount: A:0.35, C:0.21, G:0.23, T:0.22
Consensus pattern (40 bp):
TTAGCGGCGTTTTACAAAAAACGCCGCTAAAAATCGAGCA
Done.