Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 166 of 203
Found at i:52513612 original size:5 final size:5
Alignment explanation
Indices: 52513602--52513628 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
52513592 TTTTTAAAAA
52513602 TATTT TATTT TATTT TATTT TATTT TA
1 TATTT TATTT TATTT TATTT TATTT TA
52513629 ATATTTAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:52514619 original size:11 final size:10
Alignment explanation
Indices: 52514601--52514675 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 10
52514591 AAATTAAAAT
52514601 AAAAATTTTA
1 AAAAATTTTA
52514611 AAAACATTTT-
1 AAAA-ATTTTA
52514621 -AAAA-TTTA
1 AAAAATTTTA
52514629 AAAAA-TTTA
1 AAAAATTTTA
52514638 AAAAGTATTTTTTA
1 AAAA--A--TTTTA
*
52514652 AAAAAATTTA
1 AAAAATTTTA
*
52514662 AAAATTTTTTA
1 AAAA-ATTTTA
52514673 AAA
1 AAA
52514676 TTAAAAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
7 3 0.06
8 1 0.02
9 15 0.28
10 12 0.23
11 13 0.25
12 1 0.02
14 8 0.15
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (10 bp):
AAAAATTTTA
Found at i:52514685 original size:21 final size:21
Alignment explanation
Indices: 52514661--52514705 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
52514651 AAAAAAATTT
*
52514661 AAAAATTTTTTAAAATTAAAA
1 AAAAATATTTTAAAATTAAAA
*
52514682 AAAAGTATTTTAAAATTAAAA
1 AAAAATATTTTAAAATTAAAA
52514703 AAA
1 AAA
52514706 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (21 bp):
AAAAATATTTTAAAATTAAAA
Found at i:52514711 original size:8 final size:9
Alignment explanation
Indices: 52514693--52514717 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52514683 AAAGTATTTT
52514693 AAAATTAAA
1 AAAATTAAA
52514702 AAAATTAAA
1 AAAATTAAA
52514711 AAAATTA
1 AAAATTA
52514718 TTATTATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AAAATTAAA
Found at i:52528138 original size:11 final size:11
Alignment explanation
Indices: 52528118--52528150 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
52528108 ACTTCGCTCG
*
52528118 TAATTATTTTA
1 TAATTATTTTT
52528129 TAA-TATTTTT
1 TAATTATTTTT
52528139 TAATTATTTTT
1 TAATTATTTTT
52528150 T
1 T
52528151 TGAGGGTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TAATTATTTTT
Found at i:52530561 original size:22 final size:23
Alignment explanation
Indices: 52530515--52530561 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
52530505 GGTTATGATA
**
52530515 AAAAATCTTATATTGTAAATCCT
1 AAAAATCTTATATTGTAAAAACT
52530538 AAAAA-CTTATATTGTAAAAACT
1 AAAAATCTTATATTGTAAAAACT
52530560 AA
1 AA
52530562 TTTATCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.51, C:0.11, G:0.04, T:0.34
Consensus pattern (23 bp):
AAAAATCTTATATTGTAAAAACT
Found at i:52530887 original size:14 final size:15
Alignment explanation
Indices: 52530857--52530889 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
52530847 TAAAACTTTT
52530857 TTATAAAGTTATATA
1 TTATAAAGTTATATA
*
52530872 TTATAAA-TTTTATA
1 TTATAAAGTTATATA
52530886 TTAT
1 TTAT
52530890 TTCTTACTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TTATAAAGTTATATA
Found at i:52531509 original size:22 final size:21
Alignment explanation
Indices: 52531463--52531505 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
52531453 TTTTTATCAT
*
52531463 ATTAATAATTTTTTTATAGTA
1 ATTAATAATTTTTTTAAAGTA
52531484 ATTAAT-ATTTTTTTAAATGTA
1 ATTAATAATTTTTTTAAA-GTA
52531505 A
1 A
52531506 ATTATGTAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATTAATAATTTTTTTAAAGTA
Found at i:52535995 original size:236 final size:237
Alignment explanation
Indices: 52535577--52536053 Score: 794
Period size: 236 Copynumber: 2.0 Consensus size: 237
52535567 ATGAGGTAAT
*
52535577 ATAACTCATCAACCCATTAAGAAAAAAATATTTTTTTTAATCACGAGAGACAGGTGACGTAACAG
1 ATAACTCATCAACCCATTAAGAAAAAAATATTTTTTTTAATCACGAGAGACAAGTGACGTAACAG
* * *
52535642 CCCATTTTCAGTGAAATTGGAATATTGGTTTCGAGATCACAAATCTGAGTCATAAAGAAAAATTA
66 CCCATTTTCAGTGAAATTGGAATAGTAGTTTCGAGATCAAAAATCTGAGTCATAAAGAAAAATTA
* * * *
52535707 TTTTAATATTATTTTATTGTCTGCATTATAATAGGAAAGACGTATGAAAATTTTGATAAGAAAAT
131 TTTTAATATTATTTTATGGTATGAATTATAATAGGAAAGACGTATGAAAATTTTGACAAGAAAAT
52535772 TTTACCGATTTCATGTTTAATTGTTAGTAAAGACCAAATTGC
196 TTTACCGATTTCATGTTTAATTGTTAGTAAAGACCAAATTGC
** * *
52535814 ATAA-TCATCAACCCATTAAGAAAAATCTATTTTTTTTAATCACGAGAGACAAGTGATGTAATAG
1 ATAACTCATCAACCCATTAAGAAAAAAATATTTTTTTTAATCACGAGAGACAAGTGACGTAACAG
*
52535878 CCCATTTTCAGTGAAATTGGAATAGTAGTTTCGAGATCAAAAATCTGTGTCATAAAGAAAAATTA
66 CCCATTTTCAGTGAAATTGGAATAGTAGTTTCGAGATCAAAAATCTGAGTCATAAAGAAAAATTA
52535943 TTTTAATATTATTTTATGGTATGAATTATAATAGGAAAGACGTATGAAAATTTTGACAAGAAAAT
131 TTTTAATATTATTTTATGGTATGAATTATAATAGGAAAGACGTATGAAAATTTTGACAAGAAAAT
* * * *
52536008 TTTATCGGTTTCATGTTTAATTGTTAGTAAGGACCAAATTGT
196 TTTACCGATTTCATGTTTAATTGTTAGTAAAGACCAAATTGC
52536050 ATAA
1 ATAA
52536054 AGTGCAAAAG
Statistics
Matches: 223, Mismatches: 17, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
236 219 0.98
237 4 0.02
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (237 bp):
ATAACTCATCAACCCATTAAGAAAAAAATATTTTTTTTAATCACGAGAGACAAGTGACGTAACAG
CCCATTTTCAGTGAAATTGGAATAGTAGTTTCGAGATCAAAAATCTGAGTCATAAAGAAAAATTA
TTTTAATATTATTTTATGGTATGAATTATAATAGGAAAGACGTATGAAAATTTTGACAAGAAAAT
TTTACCGATTTCATGTTTAATTGTTAGTAAAGACCAAATTGC
Found at i:52537376 original size:24 final size:24
Alignment explanation
Indices: 52537343--52537433 Score: 62
Period size: 25 Copynumber: 3.8 Consensus size: 24
52537333 ACCTGTTAAG
*
52537343 CTCACATGAGCTTTCTGTTTCATA
1 CTCATATGAGCTTTCTGTTTCATA
*
52537367 CTCTTATGAG-TTTCCTG-TT-ATA
1 CTCATATGAGCTTT-CTGTTTCATA
* ** * *
52537389 GCCCGGATAAGCTTTCTGTTACATGA
1 -CTCATATGAGCTTTCTGTTTCAT-A
*
52537415 CTCATATGAGCTTCCTGTT
1 CTCATATGAGCTTTCTGTT
52537434 ATATGGCTTG
Statistics
Matches: 49, Mismatches: 12, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
22 3 0.06
23 14 0.29
24 15 0.31
25 16 0.33
26 1 0.02
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (24 bp):
CTCATATGAGCTTTCTGTTTCATA
Found at i:52541348 original size:15 final size:16
Alignment explanation
Indices: 52541328--52541362 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
52541318 TGATCCCCAT
52541328 TTTTCAAAAAATA-AC
1 TTTTCAAAAAATACAC
*
52541343 TTTTCAAAAATTACAC
1 TTTTCAAAAAATACAC
52541359 TTTT
1 TTTT
52541363 ATCCCAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTCAAAAAATACAC
Found at i:52543281 original size:19 final size:19
Alignment explanation
Indices: 52543257--52543294 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
52543247 GGACAATGTG
52543257 ATTGAATATGATTGGTTTT
1 ATTGAATATGATTGGTTTT
52543276 ATTGAATATGATTGGTTTT
1 ATTGAATATGATTGGTTTT
52543295 GGATATGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.21, T:0.53
Consensus pattern (19 bp):
ATTGAATATGATTGGTTTT
Found at i:52550004 original size:21 final size:21
Alignment explanation
Indices: 52549953--52549998 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
52549943 AAGAGTTAGA
* *
52549953 ATTTAGGGTTTAAGGTTTAAG
1 ATTTAGGATTTAAGGTTCAAG
*
52549974 ATTTAGGATTTAAGGTTCATG
1 ATTTAGGATTTAAGGTTCAAG
52549995 ATTT
1 ATTT
52549999 TAGATTCAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.02, G:0.24, T:0.46
Consensus pattern (21 bp):
ATTTAGGATTTAAGGTTCAAG
Found at i:52550011 original size:28 final size:28
Alignment explanation
Indices: 52549980--52550042 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
52549970 TAAGATTTAG
52549980 GATTTAAGGTTCATG-ATTTT-AGATTCAA
1 GATTTAAGGTTCA-GAATTTTGAG-TTCAA
** *
52550008 GATTTGGGGTTCAGAATTTTGAGTTCAG
1 GATTTAAGGTTCAGAATTTTGAGTTCAA
52550036 GATTTAA
1 GATTTAA
52550043 AAAAATAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
27 1 0.04
28 25 0.89
29 2 0.07
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (28 bp):
GATTTAAGGTTCAGAATTTTGAGTTCAA
Found at i:52553614 original size:590 final size:590
Alignment explanation
Indices: 52552496--52553675 Score: 2360
Period size: 590 Copynumber: 2.0 Consensus size: 590
52552486 GGCATTTGTC
52552496 AATTAAGGGAATAAAAAAGCGTCATTGGCTGGTCGGCGGCATTGGCCACTCAGGCGGAGGAGCCG
1 AATTAAGGGAATAAAAAAGCGTCATTGGCTGGTCGGCGGCATTGGCCACTCAGGCGGAGGAGCCG
52552561 AGCTAGAGCTTGCGGCTCCGGAGCCAGATAACAGATCTGCGAGAGCGCTCATGGCTCGAACCTGC
66 AGCTAGAGCTTGCGGCTCCGGAGCCAGATAACAGATCTGCGAGAGCGCTCATGGCTCGAACCTGC
52552626 ATCTCAAGTGCCGCTATGTAATCAGTTGCTTCTTCAAGAATTACCGGTAACGGTTGCTTCCGGCA
131 ATCTCAAGTGCCGCTATGTAATCAGTTGCTTCTTCAAGAATTACCGGTAACGGTTGCTTCCGGCA
52552691 ACCGGGAACCAATCTGCCTAGGACCTTTACTTTTCTTTGAACAGTCGGTACACTTTTTGCTTTCA
196 ACCGGGAACCAATCTGCCTAGGACCTTTACTTTTCTTTGAACAGTCGGTACACTTTTTGCTTTCA
52552756 ATTTCAAAACGCTAACTCTCGGTTTCTTCGACCGGCTAGTCCTTGTTGCGGCAGCAACGGCAGCG
261 ATTTCAAAACGCTAACTCTCGGTTTCTTCGACCGGCTAGTCCTTGTTGCGGCAGCAACGGCAGCG
52552821 GCGGATCCTCTCTGCGATCTCTTCTGCTTTCTAAATTTCAGTTTAAGCCGGCTCGTCAAAATGGC
326 GCGGATCCTCTCTGCGATCTCTTCTGCTTTCTAAATTTCAGTTTAAGCCGGCTCGTCAAAATGGC
52552886 CCGGCTCCACCTGGTTCTCCCTTTAGCAGCAACCGCCAACACTCTATCAGCGGCTTCACGGACAG
391 CCGGCTCCACCTGGTTCTCCCTTTAGCAGCAACCGCCAACACTCTATCAGCGGCTTCACGGACAG
52552951 CTCGACCACCGCGTGGAGCCGAAGGAGAGGGAGTACCGAGACTGACCTGACTCAAAGCTTGAAGA
456 CTCGACCACCGCGTGGAGCCGAAGGAGAGGGAGTACCGAGACTGACCTGACTCAAAGCTTGAAGA
52553016 AGTTTTGAGGAATAGATTTGCTGCTGCGCCTCTGACTTCCATCTGGCATGATCTTCCTTTTGGCT
521 AGTTTTGAGGAATAGATTTGCTGCTGCGCCTCTGACTTCCATCTGGCATGATCTTCCTTTTGGCT
52553081 CCGTT
586 CCGTT
52553086 AATTAAGGGAATAAAAAAGCGTCATTGGCTGGTCGGCGGCATTGGCCACTCAGGCGGAGGAGCCG
1 AATTAAGGGAATAAAAAAGCGTCATTGGCTGGTCGGCGGCATTGGCCACTCAGGCGGAGGAGCCG
52553151 AGCTAGAGCTTGCGGCTCCGGAGCCAGATAACAGATCTGCGAGAGCGCTCATGGCTCGAACCTGC
66 AGCTAGAGCTTGCGGCTCCGGAGCCAGATAACAGATCTGCGAGAGCGCTCATGGCTCGAACCTGC
52553216 ATCTCAAGTGCCGCTATGTAATCAGTTGCTTCTTCAAGAATTACCGGTAACGGTTGCTTCCGGCA
131 ATCTCAAGTGCCGCTATGTAATCAGTTGCTTCTTCAAGAATTACCGGTAACGGTTGCTTCCGGCA
52553281 ACCGGGAACCAATCTGCCTAGGACCTTTACTTTTCTTTGAACAGTCGGTACACTTTTTGCTTTCA
196 ACCGGGAACCAATCTGCCTAGGACCTTTACTTTTCTTTGAACAGTCGGTACACTTTTTGCTTTCA
52553346 ATTTCAAAACGCTAACTCTCGGTTTCTTCGACCGGCTAGTCCTTGTTGCGGCAGCAACGGCAGCG
261 ATTTCAAAACGCTAACTCTCGGTTTCTTCGACCGGCTAGTCCTTGTTGCGGCAGCAACGGCAGCG
52553411 GCGGATCCTCTCTGCGATCTCTTCTGCTTTCTAAATTTCAGTTTAAGCCGGCTCGTCAAAATGGC
326 GCGGATCCTCTCTGCGATCTCTTCTGCTTTCTAAATTTCAGTTTAAGCCGGCTCGTCAAAATGGC
52553476 CCGGCTCCACCTGGTTCTCCCTTTAGCAGCAACCGCCAACACTCTATCAGCGGCTTCACGGACAG
391 CCGGCTCCACCTGGTTCTCCCTTTAGCAGCAACCGCCAACACTCTATCAGCGGCTTCACGGACAG
52553541 CTCGACCACCGCGTGGAGCCGAAGGAGAGGGAGTACCGAGACTGACCTGACTCAAAGCTTGAAGA
456 CTCGACCACCGCGTGGAGCCGAAGGAGAGGGAGTACCGAGACTGACCTGACTCAAAGCTTGAAGA
52553606 AGTTTTGAGGAATAGATTTGCTGCTGCGCCTCTGACTTCCATCTGGCATGATCTTCCTTTTGGCT
521 AGTTTTGAGGAATAGATTTGCTGCTGCGCCTCTGACTTCCATCTGGCATGATCTTCCTTTTGGCT
52553671 CCGTT
586 CCGTT
52553676 GAAGATTCTG
Statistics
Matches: 590, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
590 590 1.00
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (590 bp):
AATTAAGGGAATAAAAAAGCGTCATTGGCTGGTCGGCGGCATTGGCCACTCAGGCGGAGGAGCCG
AGCTAGAGCTTGCGGCTCCGGAGCCAGATAACAGATCTGCGAGAGCGCTCATGGCTCGAACCTGC
ATCTCAAGTGCCGCTATGTAATCAGTTGCTTCTTCAAGAATTACCGGTAACGGTTGCTTCCGGCA
ACCGGGAACCAATCTGCCTAGGACCTTTACTTTTCTTTGAACAGTCGGTACACTTTTTGCTTTCA
ATTTCAAAACGCTAACTCTCGGTTTCTTCGACCGGCTAGTCCTTGTTGCGGCAGCAACGGCAGCG
GCGGATCCTCTCTGCGATCTCTTCTGCTTTCTAAATTTCAGTTTAAGCCGGCTCGTCAAAATGGC
CCGGCTCCACCTGGTTCTCCCTTTAGCAGCAACCGCCAACACTCTATCAGCGGCTTCACGGACAG
CTCGACCACCGCGTGGAGCCGAAGGAGAGGGAGTACCGAGACTGACCTGACTCAAAGCTTGAAGA
AGTTTTGAGGAATAGATTTGCTGCTGCGCCTCTGACTTCCATCTGGCATGATCTTCCTTTTGGCT
CCGTT
Found at i:52556870 original size:6 final size:6
Alignment explanation
Indices: 52556859--52556884 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52556849 AAATAATAAT
52556859 TTTATA TTTATA TTTATA TTTATA TT
1 TTTATA TTTATA TTTATA TTTATA TT
52556885 AAATTACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTATA
Found at i:52556968 original size:7 final size:7
Alignment explanation
Indices: 52556958--52556987 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
52556948 AAAATATAAA
*
52556958 ATTTTAT
1 ATTTAAT
52556965 ATTTAAT
1 ATTTAAT
52556972 ATTTAAT
1 ATTTAAT
52556979 ATTTAAT
1 ATTTAAT
52556986 AT
1 AT
52556988 AATAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:52557027 original size:19 final size:21
Alignment explanation
Indices: 52556981--52557024 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
52556971 TATTTAATAT
*
52556981 TTAATATAATAAAAAATGTTT
1 TTAATATAATAAAAAATGTTA
*
52557002 TTAATATAATAAAACAT-TTA
1 TTAATATAATAAAAAATGTTA
52557022 TTA
1 TTA
52557025 TATTTATGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAATATAATAAAAAATGTTA
Found at i:52562931 original size:11 final size:11
Alignment explanation
Indices: 52562912--52562948 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
52562902 CTAGAAACCC
*
52562912 AAAATTAAAAT
1 AAAAATAAAAT
52562923 AAAAATAAAAT
1 AAAAATAAAAT
52562934 -AAAATAAAAT
1 AAAAATAAAAT
52562944 AAAAA
1 AAAAA
52562949 ACTTAATTAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:52562948 original size:6 final size:5
Alignment explanation
Indices: 52562912--52562947 Score: 54
Period size: 5 Copynumber: 6.8 Consensus size: 5
52562902 CTAGAAACCC
52562912 AAAATT AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAA-T AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
52562948 AACTTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 20 0.69
6 9 0.31
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:52570831 original size:59 final size:59
Alignment explanation
Indices: 52570759--52570872 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 59
52570749 GAGTATGTTG
* *
52570759 AAGCGCGTTACCCTATTATTTATGGGTTGGGTAGGAGTGAGCAAAACTTGATTTGGTTT
1 AAGCGCGTTACCCTATTATTTATGGGTTGGGTAGGAGAGAGCAAAACTCGATTTGGTTT
52570818 AAGCGCGTTACCCTATTATTTATGGGTTGGGTAGGAGAGAGCAAAACTCGATTTG
1 AAGCGCGTTACCCTATTATTTATGGGTTGGGTAGGAGAGAGCAAAACTCGATTTG
52570873 ATTCGAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.25, C:0.13, G:0.29, T:0.32
Consensus pattern (59 bp):
AAGCGCGTTACCCTATTATTTATGGGTTGGGTAGGAGAGAGCAAAACTCGATTTGGTTT
Found at i:52571151 original size:10 final size:9
Alignment explanation
Indices: 52571128--52571161 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
52571118 ATATATTTTT
52571128 TAAAAATTA
1 TAAAAATTA
*
52571137 TAAAAATTC
1 TAAAAATTA
52571146 TAAAAATATA
1 TAAAAAT-TA
52571156 TAAAAA
1 TAAAAA
52571162 AAAGTTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:52572869 original size:26 final size:26
Alignment explanation
Indices: 52572822--52572871 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
52572812 AATAATTAAT
* *
52572822 TTAAATTATATAATTTATTATATTCA
1 TTAAATTATATAATTAAATATATTCA
52572848 TTAAATTAT-TAAGTTAAATATATT
1 TTAAATTATATAA-TTAAATATATT
52572872 TTATTAACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (26 bp):
TTAAATTATATAATTAAATATATTCA
Found at i:52575926 original size:30 final size:30
Alignment explanation
Indices: 52575881--52575939 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
52575871 AATGTAATAC
*
52575881 TATATTTTTATTTGGTATTAATTATATATTT
1 TATATTTTTACTTGGTATTAATTAT-TATTT
52575912 TATA-TTTTACTTGGTATTAATTATTATT
1 TATATTTTTACTTGGTATTAATTATTATT
52575940 GAAAAATCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 19 0.70
31 4 0.15
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.63
Consensus pattern (30 bp):
TATATTTTTACTTGGTATTAATTATTATTT
Found at i:52576605 original size:125 final size:124
Alignment explanation
Indices: 52576371--52576623 Score: 434
Period size: 125 Copynumber: 2.0 Consensus size: 124
52576361 CCATATAAAC
52576371 TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATCCA
1 TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATCCA
52576436 TTACTCAACCACATTAAACACAACATATTAAGCCACACATACATATACATATCAAAATAA
66 TTACTCAACCACATTAAACACAACATATTAAGCCACACA-ACATATACATATCAAAATAA
*
52576496 TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATTTTCATAAATTATCCA
1 TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATCCA
*
52576561 TTACTCAACCACGTTAAACACAACAAACGTATTAAGCCACACATACATATACATATCAAAATA
66 TTACTCAACCACATTAAACACAAC--A--TATTAAGCCACACA-ACATATACATATCAAAATA
52576624 TGTCTAACTC
Statistics
Matches: 122, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
125 87 0.71
127 1 0.01
129 34 0.28
ACGTcount: A:0.43, C:0.22, G:0.02, T:0.33
Consensus pattern (124 bp):
TTATATGCATATTTCTCCAATCATATTATCTCAAATAATACATTATCATATTCATAAATTATCCA
TTACTCAACCACATTAAACACAACATATTAAGCCACACAACATATACATATCAAAATAA
Found at i:52577206 original size:26 final size:25
Alignment explanation
Indices: 52577176--52577237 Score: 81
Period size: 25 Copynumber: 2.4 Consensus size: 25
52577166 ATTCATATTC
52577176 GGGAATGCTCATACAAG-CATATAAAG
1 GGGAA-GCTCATACAAGCCATAT-AAG
* *
52577202 GGGAAGCTCTTTCAAGCCATATAAG
1 GGGAAGCTCATACAAGCCATATAAG
52577227 GGGAAGCTCAT
1 GGGAAGCTCAT
52577238 GTGAGCCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (25 bp):
GGGAAGCTCATACAAGCCATATAAG
Found at i:52577244 original size:25 final size:25
Alignment explanation
Indices: 52577175--52577286 Score: 68
Period size: 25 Copynumber: 4.5 Consensus size: 25
52577165 AATTCATATT
**
52577175 CGGGAATGCTCATACAAG-CATATAAA
1 CGGGAA-GCTCATGTAAGCCATAT-AA
* *
52577201 GGGGAAGCTC-TTTCAAGCCATATAA
1 CGGGAAGCTCATGT-AAGCCATATAA
* * *
52577226 GGGGAAGCTCATGTGAGCCATGTAA
1 CGGGAAGCTCATGTAAGCCATATAA
** ** *
52577251 CGAAAAGCTCATGCCAGCCA-ATAT
1 CGGGAAGCTCATGTAAGCCATATAA
52577275 CGGGAAGCTCAT
1 CGGGAAGCTCAT
52577287 AAAAGAGCCT
Statistics
Matches: 68, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
24 13 0.19
25 43 0.63
26 12 0.18
ACGTcount: A:0.34, C:0.21, G:0.25, T:0.20
Consensus pattern (25 bp):
CGGGAAGCTCATGTAAGCCATATAA
Found at i:52577386 original size:25 final size:25
Alignment explanation
Indices: 52577323--52577387 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
52577313 CGAAAAGCTA
*
52577323 TTAACAGGAAGCTAACAAGAACCAT
1 TTAACAGGAAGCTCACAAGAACCAT
* *
52577348 TTAACGGGAAGCTCACAAGAATCAT
1 TTAACAGGAAGCTCACAAGAACCAT
52577373 TTAACAGGAAGCTCA
1 TTAACAGGAAGCTCA
52577388 TGAGAGCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (25 bp):
TTAACAGGAAGCTCACAAGAACCAT
Found at i:52579153 original size:20 final size:19
Alignment explanation
Indices: 52579102--52579154 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
52579092 CTTGTTTAAA
* *
52579102 AAACAATTTTAACATGATTG
1 AAAC-ATTTTAACTTAATTG
52579122 AAA-ATGTTTAACTTAATTG
1 AAACAT-TTTAACTTAATTG
52579141 AAACCATTTTAACT
1 AAA-CATTTTAACT
52579155 AGATTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 10 0.36
21 2 0.07
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.38
Consensus pattern (19 bp):
AAACATTTTAACTTAATTG
Found at i:52599273 original size:18 final size:19
Alignment explanation
Indices: 52599247--52599286 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
52599237 ATTACTTCTC
*
52599247 AAAAGTATTTTT-AGGCTA
1 AAAAATATTTTTGAGGCTA
52599265 AAAAATATTTTTGAGGCTA
1 AAAAATATTTTTGAGGCTA
52599284 AAA
1 AAA
52599287 TTTTCTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.45, C:0.05, G:0.15, T:0.35
Consensus pattern (19 bp):
AAAAATATTTTTGAGGCTA
Found at i:52621106 original size:3 final size:3
Alignment explanation
Indices: 52621098--52621124 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52621088 TATCAATTGG
52621098 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
52621125 ATGTCTCTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:52630856 original size:20 final size:20
Alignment explanation
Indices: 52630819--52630857 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52630809 GCAGAAATCG
* * *
52630819 AGAGCAAATTAGAGAAAAAT
1 AGAGAAAATAAGAAAAAAAT
52630839 AGAGAAAATAAGAAAAAAA
1 AGAGAAAATAAGAAAAAAA
52630858 GGGGGATTCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.03, G:0.18, T:0.10
Consensus pattern (20 bp):
AGAGAAAATAAGAAAAAAAT
Found at i:52631867 original size:22 final size:21
Alignment explanation
Indices: 52631823--52631909 Score: 86
Period size: 21 Copynumber: 4.0 Consensus size: 21
52631813 ATGAATGTTG
*
52631823 TTTAAATTTATCACATATTAT
1 TTTAAATTTATCATATATTAT
52631844 TTTAAATTTATCATATAATTAT
1 TTTAAATTTATCATAT-ATTAT
* * *
52631866 TTTAAGTTT-TCATGTATCAT
1 TTTAAATTTATCATATATTAT
* *
52631886 TCTTCAAATTTATTATGTATTAT
1 T-TT-AAATTTATCATATATTAT
52631909 T
1 T
52631910 CTATATATTC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 5 0.09
21 22 0.40
22 18 0.33
23 10 0.18
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTAAATTTATCATATATTAT
Found at i:52638542 original size:25 final size:23
Alignment explanation
Indices: 52638481--52638527 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
52638471 AATTCTCAAT
**
52638481 AATAATATTTGGTA-TTTATAAA
1 AATAATATTTATTATTTTATAAA
52638503 AATAATATTTATTATTTTATAAA
1 AATAATATTTATTATTTTATAAA
52638526 AA
1 AA
52638528 ATAGATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
AATAATATTTATTATTTTATAAA
Found at i:52639962 original size:17 final size:17
Alignment explanation
Indices: 52639932--52639973 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
52639922 AAAAATATTA
52639932 TAAAA-ATA-TAAAAAC
1 TAAAATATATTAAAAAC
* *
52639947 TAAATTATATTAAAAAT
1 TAAAATATATTAAAAAC
52639964 TAAAATATAT
1 TAAAATATAT
52639974 AAATTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 4 0.18
16 3 0.14
17 15 0.68
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATATATTAAAAAC
Found at i:52641050 original size:3 final size:3
Alignment explanation
Indices: 52641044--52641082 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
52641034 TTTTTTTTTG
52641044 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
52641083 AAAAATATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:52644957 original size:11 final size:10
Alignment explanation
Indices: 52644936--52645087 Score: 73
Period size: 10 Copynumber: 15.9 Consensus size: 10
52644926 TATTTTTTTA
52644936 ATTTTAAAAT
1 ATTTTAAAAT
52644946 ATTTTAAAAAT
1 ATTTT-AAAAT
*
52644957 AATTTT-TAA-
1 -ATTTTAAAAT
52644966 ATTTTAAAAT
1 ATTTTAAAAT
52644976 ATTTTAAAAAT
1 ATTTT-AAAAT
52644987 ACTTTT----T
1 A-TTTTAAAAT
*
52644994 -TTTT-TAAT
1 ATTTTAAAAT
**
52645002 -TTTTTTAAT
1 ATTTTAAAAT
52645011 --TTTAAAAT
1 ATTTTAAAAT
52645019 ATTTTAAAAAT
1 ATTTT-AAAAT
*
52645030 AATTTT-TAA-
1 -ATTTTAAAAT
52645039 ATTTTAAAAT
1 ATTTTAAAAT
52645049 ATTTTAAAAAT
1 ATTTT-AAAAT
*
52645060 AATTTT-TAA-
1 -ATTTTAAAAT
52645069 ATTTTAAAAT
1 ATTTTAAAAT
52645079 ATTTTAAAA
1 ATTTTAAAA
52645088 ATACTTTTTT
Statistics
Matches: 114, Mismatches: 8, Indels: 40
0.70 0.05 0.25
Matches are distributed among these distances:
5 4 0.04
7 1 0.01
8 26 0.23
9 10 0.09
10 33 0.29
11 21 0.18
12 19 0.17
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:52644969 original size:30 final size:30
Alignment explanation
Indices: 52644929--52644993 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
52644919 ATTTTTTTAT
*
52644929 TTTTTTAATTTTAAAATATTTTAAAAATAA
1 TTTTTAAATTTTAAAATATTTTAAAAATAA
*
52644959 TTTTTAAATTTTAAAATATTTTAAAAATAC
1 TTTTTAAATTTTAAAATATTTTAAAAATAA
52644989 TTTTT
1 TTTTT
52644994 TTTTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTTTAAATTTTAAAATATTTTAAAAATAA
Found at i:52645009 original size:73 final size:72
Alignment explanation
Indices: 52644909--52645066 Score: 280
Period size: 73 Copynumber: 2.2 Consensus size: 72
52644899 CCGATATAAT
52644909 AAATATATTTATTTTTTTATTTTTTTAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAA
1 AAATA-ATTT-TTTTTTTATTTTTTTAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAA
52644974 ATATTTTAA
64 ATATTTTAA
*
52644983 AAATACTTTTTTTTTTAATTTTTTTAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAA
1 AAATAATTTTTTTTTT-ATTTTTTTAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAA
52645048 TATTTTAA
65 TATTTTAA
52645056 AAATAATTTTT
1 AAATAATTTTT
52645067 AAATTTTAAA
Statistics
Matches: 81, Mismatches: 2, Indels: 3
0.94 0.02 0.03
Matches are distributed among these distances:
72 7 0.09
73 69 0.85
74 5 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.58
Consensus pattern (72 bp):
AAATAATTTTTTTTTTATTTTTTTAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAAT
ATTTTAA
Found at i:52645042 original size:30 final size:30
Alignment explanation
Indices: 52645002--52645096 Score: 172
Period size: 30 Copynumber: 3.2 Consensus size: 30
52644992 TTTTTTTAAT
*
52645002 TTTTTTAATTTTAAAATATTTTAAAAATAA
1 TTTTTAAATTTTAAAATATTTTAAAAATAA
52645032 TTTTTAAATTTTAAAATATTTTAAAAATAA
1 TTTTTAAATTTTAAAATATTTTAAAAATAA
*
52645062 TTTTTAAATTTTAAAATATTTTAAAAATAC
1 TTTTTAAATTTTAAAATATTTTAAAAATAA
52645092 TTTTT
1 TTTTT
52645097 TTTAATTTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (30 bp):
TTTTTAAATTTTAAAATATTTTAAAAATAA
Found at i:52645046 original size:103 final size:100
Alignment explanation
Indices: 52644929--52645139 Score: 377
Period size: 103 Copynumber: 2.1 Consensus size: 100
52644919 ATTTTTTTAT
*
52644929 TTTTTTAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAATATTTTAAAAATACTTTTT
1 TTTTTAAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAATATTTTAAAAATAC--TTT
52644994 TTTTTAATTTTTTTAATTTTAAAATATTTTAAAAATAA
64 TTTTTAATTTTTTTAATTTTAAAATATTTTAAAAAT-A
52645032 TTTTTAAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAATATTTTAAAAATACTTTTT
1 TTTTTAAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAATATTTTAAAAATACTTTTT
*
52645097 TTTAATTTTTTTAATTTTAAAATATTTTCAAAATA
66 TTTAATTTTTTTAATTTTAAAATATTTTAAAAATA
52645132 TTTTTAAA
1 TTTTTAAA
52645140 ATACTTTTTT
Statistics
Matches: 106, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
100 9 0.08
101 38 0.36
103 59 0.56
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (100 bp):
TTTTTAAATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAATATTTTAAAAATACTTTTT
TTTAATTTTTTTAATTTTAAAATATTTTAAAAATA
Found at i:52645049 original size:19 final size:18
Alignment explanation
Indices: 52645019--52645083 Score: 61
Period size: 13 Copynumber: 3.8 Consensus size: 18
52645009 ATTTTAAAAT
52645019 ATTTTAAAAATAATTTTTAA
1 ATTTT-AAAAT-ATTTTTAA
52645039 ATTTTAAAATA-TTTTAA
1 ATTTTAAAATATTTTTAA
*
52645056 A----AATA-ATTTTTAA
1 ATTTTAAAATATTTTTAA
52645069 ATTTTAAAATATTTT
1 ATTTTAAAATATTTT
52645084 AAAAATACTT
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
12 1 0.03
13 10 0.27
17 10 0.27
18 6 0.16
19 5 0.14
20 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATTTTAAAATATTTTTAA
Found at i:52645149 original size:41 final size:39
Alignment explanation
Indices: 52645039--52645156 Score: 130
Period size: 41 Copynumber: 2.9 Consensus size: 39
52645029 TAATTTTTAA
* *
52645039 ATTTTAAAATATTTTAAAAATAATTTTTAAATTTTAAAAT
1 ATTTTAAAATATTTTTAAAAT-ATTTTTTAATTTTAAAAT
**
52645079 ATTTTAAAAATACTTTTTTTTAAT-TTTTTTAATTTTAAAAT
1 ATTTT-AAAATA--TTTTTAAAATATTTTTTAATTTTAAAAT
52645120 ATTTTCAAAATATTTTTAAAATACTTTTTTTAATTTT
1 ATTTT-AAAATATTTTTAAAATA--TTTTTTAATTTT
52645157 TTTAATTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
39 8 0.12
40 5 0.08
41 33 0.51
42 12 0.18
43 7 0.11
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (39 bp):
ATTTTAAAATATTTTTAAAATATTTTTTAATTTTAAAAT
Found at i:52645187 original size:31 final size:30
Alignment explanation
Indices: 52645131--52645192 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
52645121 TTTTCAAAAT
* * *
52645131 ATTTTTAAAATACTTTTTTTAATTTTTTTA
1 ATTTTTAAAATAATTTTTGTAATTTTATTA
52645161 ATTTTTAAAATAAATTTTTGGT-ATTTTATTA
1 ATTTTTAAAAT-AATTTTT-GTAATTTTATTA
52645192 A
1 A
52645193 AAAAATGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.41
31 15 0.56
32 1 0.04
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (30 bp):
ATTTTTAAAATAATTTTTGTAATTTTATTA
Found at i:52645187 original size:52 final size:51
Alignment explanation
Indices: 52645069--52645172 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 51
52645059 TAATTTTTAA
52645069 ATTTTAAAATATTTTAAAAATACTTTTTTTTAATTTTTTTAATTTTAAAAT
1 ATTTTAAAATATTTTAAAAATACTTTTTTTTAATTTTTTTAATTTTAAAAT
*
52645120 ATTTTCAAAATATTTTTAAAATAC-TTTTTTTAATTTTTTTAATTTTTAAAAT
1 ATTTT-AAAATATTTTAAAAATACTTTTTTTTAATTTTTTTAA-TTTTAAAAT
52645172 A
1 A
52645173 AATTTTTGGT
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
51 23 0.46
52 27 0.54
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (51 bp):
ATTTTAAAATATTTTAAAAATACTTTTTTTTAATTTTTTTAATTTTAAAAT
Found at i:52646508 original size:3 final size:3
Alignment explanation
Indices: 52646493--52646528 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
52646483 CAAACACAGC
* *
52646493 AGA AGA AGG AGA AGA AGA GGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
52646529 CAAAGGTTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:52647175 original size:17 final size:19
Alignment explanation
Indices: 52647147--52647181 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52647137 ATAATTTTTA
52647147 AAAGTAAAAACC-AAAAAT
1 AAAGTAAAAACCGAAAAAT
52647165 AAAGT-AAAACCGAAAAA
1 AAAGTAAAAACCGAAAAA
52647182 AGTGGGAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.71, C:0.11, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAGTAAAAACCGAAAAAT
Found at i:52647353 original size:30 final size:28
Alignment explanation
Indices: 52647319--52647387 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
52647309 TACCATTAAA
*
52647319 GGCCCATTTTTTTTTAAATTTACCGAAATG
1 GGCCCATTTTTTATT--ATTTACCGAAATG
* * *
52647349 GGCCCGGTATTTTATTATTTACCGGAATG
1 GGCCC-ATTTTTTATTATTTACCGAAATG
52647378 GG-CCATTTTT
1 GGCCCATTTTT
52647388 CCCGAAAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
27 4 0.12
28 2 0.06
29 14 0.44
30 5 0.16
31 7 0.22
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (28 bp):
GGCCCATTTTTTATTATTTACCGAAATG
Found at i:52647925 original size:125 final size:125
Alignment explanation
Indices: 52647685--52647924 Score: 381
Period size: 125 Copynumber: 1.9 Consensus size: 125
52647675 TTTCGGGTTT
*
52647685 AAGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGAGGACGCGCTTTTGCTACAGTTGGT
1 AAGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGAGGACGCGCTTTTACTACAGTTGGT
52647750 CCTGAAAAATAATTTCAAGTTGACGTTTCCGAGAAAATAGTATAAAAAAATGCTTCAAGC
66 CCTGAAAAATAATTTCAAGTTGACGTTTCCGAGAAAATAGTATAAAAAAATGCTTCAAGC
* * * * *
52647810 AAGATGCTTTATTAGAAGAATTTCTAAAATCGTGCCCACGTGGACGTGCTTTTACTATAGTTGGT
1 AAGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGAGGACGCGCTTTTACTACAGTTGGT
* * **
52647875 CCTGAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAAA
66 CCTG-AAAAATAATTTCAAGTTGACGTTTCCGAGAAAATAGTATAAAAAA
52647925 TAATTTGATA
Statistics
Matches: 104, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
125 63 0.61
126 41 0.39
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (125 bp):
AAGATGCTTTATCAGAAGAATTTCTAAAATCGCGCCCACGAGGACGCGCTTTTACTACAGTTGGT
CCTGAAAAATAATTTCAAGTTGACGTTTCCGAGAAAATAGTATAAAAAAATGCTTCAAGC
Found at i:52651261 original size:35 final size:35
Alignment explanation
Indices: 52651222--52651294 Score: 146
Period size: 35 Copynumber: 2.1 Consensus size: 35
52651212 AATACAATTA
52651222 AAATCATTTTGACAAAACATGTAACGTTAGTGGCC
1 AAATCATTTTGACAAAACATGTAACGTTAGTGGCC
52651257 AAATCATTTTGACAAAACATGTAACGTTAGTGGCC
1 AAATCATTTTGACAAAACATGTAACGTTAGTGGCC
52651292 AAA
1 AAA
52651295 AGTTTATAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (35 bp):
AAATCATTTTGACAAAACATGTAACGTTAGTGGCC
Found at i:52652373 original size:105 final size:105
Alignment explanation
Indices: 52652161--52652353 Score: 248
Period size: 105 Copynumber: 1.8 Consensus size: 105
52652151 AGGAGATGCA
* *
52652161 ATTAAATATGGGAATAACTTATATCAGGATAATTCTAAAAAGCATAGTTTTTAGGCACAATTAAA
1 ATTAAATATGAGAATAACTTATATCAGGATAATCCTAAAAAGCATAGTTTTTAGGCACAATTAAA
* * *
52652226 ATATTGTCACATTATCCAATTTTAAAAATAACAAAGTATT
66 ATATTGACACATCATCAAATTTTAAAAATAACAAAGTATT
* * * * *
52652266 ATTATATATGAGAATAATTTATATTAGTATGATCCTAAAAA-CTATAGTTTTTAGGCACCAA-TA
1 ATTAAATATGAGAATAACTTATATCAGGATAATCCTAAAAAGC-ATAGTTTTTAGGCA-CAATTA
52652329 AAAT-TTCGACACATCATCAAATTTT
64 AAATATT-GACACATCATCAAATTTT
52652354 CAAGATATAA
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
104 3 0.04
105 69 0.92
106 3 0.04
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (105 bp):
ATTAAATATGAGAATAACTTATATCAGGATAATCCTAAAAAGCATAGTTTTTAGGCACAATTAAA
ATATTGACACATCATCAAATTTTAAAAATAACAAAGTATT
Found at i:52659651 original size:15 final size:15
Alignment explanation
Indices: 52659633--52659668 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52659623 AGTTTGTGTA
* *
52659633 AAAAAATATATCTAT
1 AAAAAATATATATAG
52659648 AAAAAATATATATAG
1 AAAAAATATATATAG
52659663 AAAAAA
1 AAAAAA
52659669 AAGATTTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
AAAAAATATATATAG
Found at i:52668069 original size:2 final size:2
Alignment explanation
Indices: 52668062--52668099 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
52668052 TAAAGGAGCT
52668062 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
52668100 ATATACCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52669662 original size:10 final size:9
Alignment explanation
Indices: 52669646--52669670 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
52669636 CAGCCAGTTG
52669646 ATTTTTTTT
1 ATTTTTTTT
52669655 ATTTTTTTT
1 ATTTTTTTT
52669664 ATTTTTT
1 ATTTTTT
52669671 AATTAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:52670409 original size:24 final size:24
Alignment explanation
Indices: 52670381--52670434 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
52670371 AAAATTGAAG
*
52670381 CCAAATTGTTATAAACCACTCTCC
1 CCAAATTGTTAAAAACCACTCTCC
* *
52670405 CCAAATTGTTAAAAATCATTCTCC
1 CCAAATTGTTAAAAACCACTCTCC
52670429 CCAAAT
1 CCAAAT
52670435 ACCTCACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.30
Consensus pattern (24 bp):
CCAAATTGTTAAAAACCACTCTCC
Found at i:52670835 original size:14 final size:15
Alignment explanation
Indices: 52670804--52670834 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52670794 GCTAAACATT
52670804 AATTCATAGTAAAAA
1 AATTCATAGTAAAAA
52670819 AATTCATAGTAAAAA
1 AATTCATAGTAAAAA
52670834 A
1 A
52670835 TGCCAACACT
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:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (15 bp):
AATTCATAGTAAAAA
Found at i:52673018 original size:17 final size:17
Alignment explanation
Indices: 52672992--52673024 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52672982 AATAATATTT
*
52672992 ATAAATATATATTTAAA
1 ATAAAAATATATTTAAA
52673009 ATAAAAATATATTTAA
1 ATAAAAATATATTTAA
52673025 TTAATTTATA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAAATATATTTAAA
Found at i:52674083 original size:32 final size:32
Alignment explanation
Indices: 52674047--52674125 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
52674037 ACAACTTTTT
** ** *
52674047 CAGAAAATATTTTCAGGGAATCTGTCAAACAG
1 CAGAAAATATTTTCACAGAATCAATCAAACAC
*
52674079 CAGAAAATATTTTACACAGATTCAATCAAACAC
1 CAGAAAATATTTT-CACAGAATCAATCAAACAC
52674112 CAGAAAATATTTTC
1 CAGAAAATATTTTC
52674126 CAGTAAATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
32 14 0.35
33 26 0.65
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.27
Consensus pattern (32 bp):
CAGAAAATATTTTCACAGAATCAATCAAACAC
Found at i:52674152 original size:20 final size:20
Alignment explanation
Indices: 52674127--52674166 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52674117 AATATTTTCC
*
52674127 AGTAAATCATTTTACAAAAA
1 AGTAAAACATTTTACAAAAA
*
52674147 AGTAAAACATTTTCCAAAAA
1 AGTAAAACATTTTACAAAAA
52674167 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAAAAA
Found at i:52680965 original size:21 final size:21
Alignment explanation
Indices: 52680939--52680979 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
52680929 ATCTGCTCAA
* *
52680939 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
52680960 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
52680980 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:52684592 original size:7 final size:6
Alignment explanation
Indices: 52684572--52684623 Score: 61
Period size: 6 Copynumber: 8.3 Consensus size: 6
52684562 GTATAAAGAG
*
52684572 AAATAA AAATAA AAATAA AAATAA TAAATAA TAAATAA CAAA-AG AAATAA
1 AAATAA AAATAA AAATAA AAATAA -AAATAA -AAATAA -AAATAA AAATAA
52684622 AA
1 AA
52684624 TTATCAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
5 3 0.07
6 22 0.54
7 16 0.39
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:52686993 original size:15 final size:14
Alignment explanation
Indices: 52686972--52687007 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
52686962 ATAATCCTTA
*
52686972 ATAATTATCTTAAT
1 ATAATTATCCTAAT
52686986 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
52687001 ATAATTA
1 ATAATTA
52687008 AAATAGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:52690276 original size:22 final size:21
Alignment explanation
Indices: 52690223--52690276 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
52690213 ATTAACTCAA
*
52690223 TCATATAACATTTCAATTCAT
1 TCATAAAACATTTCAATTCAT
** *
52690244 TCGATTCAACATTTCATTATCAT
1 TC-ATAAAACATTTCAAT-TCAT
52690267 TCATAAAACA
1 TCATAAAACA
52690277 AAGAATCATT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 2 0.08
22 18 0.69
23 6 0.23
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (21 bp):
TCATAAAACATTTCAATTCAT
Found at i:52691313 original size:22 final size:23
Alignment explanation
Indices: 52691260--52691313 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
52691250 TTTTGTACAA
52691260 AATT-ATAAATAATTAAAACTTT
1 AATTAATAAATAATTAAAACTTT
*
52691282 AATTAA-AAATAATTACAA-TTAT
1 AATTAATAAATAATTAAAACTT-T
52691304 AA-TAATAAAT
1 AATTAATAAAT
52691314 GCATAAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 5 0.18
22 22 0.79
23 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (23 bp):
AATTAATAAATAATTAAAACTTT
Found at i:52693863 original size:25 final size:25
Alignment explanation
Indices: 52693829--52693876 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
52693819 ATTTTCCCTA
52693829 TCAGAGGCTACACAAACATATCTTT
1 TCAGAGGCTACACAAACATATCTTT
52693854 TCAGAGGCTACACAAACATATCT
1 TCAGAGGCTACACAAACATATCT
52693877 CCGCATCCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (25 bp):
TCAGAGGCTACACAAACATATCTTT
Found at i:52695092 original size:28 final size:28
Alignment explanation
Indices: 52695060--52695117 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
52695050 CGGATATTCT
52695060 CTTTGGTTGTTAAACTATCAAAAAGAGA
1 CTTTGGTTGTTAAACTATCAAAAAGAGA
52695088 CTTTGGTTGTTAAACTATCAAAAAGAGA
1 CTTTGGTTGTTAAACTATCAAAAAGAGA
52695116 CT
1 CT
52695118 AACTCTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (28 bp):
CTTTGGTTGTTAAACTATCAAAAAGAGA
Found at i:52699329 original size:18 final size:19
Alignment explanation
Indices: 52699295--52699335 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
52699285 ATTTTCAAAA
*
52699295 AAAAATCAAAATAATTTTT
1 AAAAATCAAAATAATTTAT
*
52699314 AAAAATCCAAAT-ATTTAT
1 AAAAATCAAAATAATTTAT
52699332 AAAA
1 AAAA
52699336 TTTTCAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATCAAAATAATTTAT
Found at i:52699582 original size:22 final size:23
Alignment explanation
Indices: 52699557--52699603 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
52699547 GATAACAAAA
*
52699557 TTTTAATTTAA-TGTATATAATT
1 TTTTAATTTAACTGTAAATAATT
*
52699579 TTTTAATTTAACTTTAAATAATT
1 TTTTAATTTAACTGTAAATAATT
52699602 TT
1 TT
52699604 ATTCCATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTAATTTAACTGTAAATAATT
Found at i:52708841 original size:34 final size:35
Alignment explanation
Indices: 52708791--52708864 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 35
52708781 ATTAGGATGA
* * * *
52708791 GGATCAGTTGTTTTTTCACTCGGCCA-GAAAATGT
1 GGATTAGTTGTTTTTTCACTCCGCCATCAAAATGG
* *
52708825 GGATTAGTTTTTTTTTCTCTCCGCCATCAAAATGG
1 GGATTAGTTGTTTTTTCACTCCGCCATCAAAATGG
52708860 GGATT
1 GGATT
52708865 TGTTAATTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
34 22 0.67
35 11 0.33
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.39
Consensus pattern (35 bp):
GGATTAGTTGTTTTTTCACTCCGCCATCAAAATGG
Found at i:52713843 original size:20 final size:21
Alignment explanation
Indices: 52713804--52713872 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 21
52713794 ATTATACCCC
* *
52713804 TATATTGATTTTAAAATAATAT
1 TATATT-ATATTATAATAATAT
52713826 TATATT-TA-TACTAATAATA-
1 TATATTATATTA-TAATAATAT
52713845 TATATTATATTATAATCAATTAT
1 TATATTATATTATAAT-AA-TAT
52713868 TATAT
1 TATAT
52713873 ATGGGTCTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
19 8 0.21
20 14 0.36
21 4 0.10
22 8 0.21
23 5 0.13
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (21 bp):
TATATTATATTATAATAATAT
Found at i:52713947 original size:7 final size:7
Alignment explanation
Indices: 52713935--52713961 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
52713925 ATCTTCTACA
52713935 ATATATC
1 ATATATC
52713942 ATATATC
1 ATATATC
52713949 ATATATC
1 ATATATC
52713956 ATATAT
1 ATATAT
52713962 TTATTTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATATC
Found at i:52714031 original size:16 final size:16
Alignment explanation
Indices: 52714018--52714069 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
52714008 ATTAGAGGCA
52714018 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGTG
*
52714034 TAATGGATTAGAGGTG
1 TAATGGAATAGAGGTG
52714050 TAATGGAATAGAGGTG
1 TAATGGAATAGAGGTG
52714066 TAAT
1 TAAT
52714070 AGCAAATCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.37, C:0.00, G:0.35, T:0.29
Consensus pattern (16 bp):
TAATGGAATAGAGGTG
Found at i:52714054 original size:32 final size:32
Alignment explanation
Indices: 52714007--52714069 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
52713997 CGCTGTATTA
52714007 GATTAGAGGCATAATGGAATAGAGGTGTAATG
1 GATTAGAGGCATAATGGAATAGAGGTGTAATG
**
52714039 GATTAGAGGTGTAATGGAATAGAGGTGTAAT
1 GATTAGAGGCATAATGGAATAGAGGTGTAAT
52714070 AGCAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.02, G:0.35, T:0.27
Consensus pattern (32 bp):
GATTAGAGGCATAATGGAATAGAGGTGTAATG
Found at i:52714153 original size:39 final size:43
Alignment explanation
Indices: 52714048--52714157 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
52714038 GGATTAGAGG
52714048 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
52714093 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
52714133 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
52714158 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:52714320 original size:16 final size:16
Alignment explanation
Indices: 52714283--52714324 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
52714273 TTAATCATAT
*
52714283 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
52714299 TT-AAATATATTATAA
1 TTAAAATATATTATAA
52714314 TTAAAATATAT
1 TTAAAATATAT
52714325 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:52714331 original size:14 final size:15
Alignment explanation
Indices: 52714292--52714333 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52714282 TTTAAACATA
*
52714292 ATTATTATTAAATAT
1 ATTATAATTAAATAT
52714307 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
52714321 A-TATAATTTAATA
1 ATTATAATTAAATA
52714334 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:52714400 original size:33 final size:33
Alignment explanation
Indices: 52714363--52714431 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
52714353 TTCTTATATG
* * *
52714363 AATTTACTCAAATCATAATATATGATACTATAA
1 AATTTACTAAAATCATAATACATAATACTATAA
52714396 AATTTACTAAAATCATAATACATAATACTATAA
1 AATTTACTAAAATCATAATACATAATACTATAA
52714429 AAT
1 AAT
52714432 ATAATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.52, C:0.12, G:0.01, T:0.35
Consensus pattern (33 bp):
AATTTACTAAAATCATAATACATAATACTATAA
Found at i:52716700 original size:16 final size:16
Alignment explanation
Indices: 52716679--52716711 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
52716669 GATACAATAT
*
52716679 AACAAAGGATAAGCAA
1 AACAAAGGATAACCAA
52716695 AACAAAGGATAACCAA
1 AACAAAGGATAACCAA
52716711 A
1 A
52716712 GTAACATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.64, C:0.15, G:0.15, T:0.06
Consensus pattern (16 bp):
AACAAAGGATAACCAA
Found at i:52750881 original size:22 final size:20
Alignment explanation
Indices: 52750851--52750901 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
52750841 TTTGAAAAGA
*
52750851 ATTTTTTTTTCCTATTATTATT
1 ATTTATTTTTCCTATT-TTA-T
*
52750873 ATTTATTTTTTCTATTTTAT
1 ATTTATTTTTCCTATTTTAT
52750893 -TTTATTTTT
1 ATTTATTTTT
52750902 GTAGGAAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 9 0.33
20 1 0.04
21 3 0.11
22 14 0.52
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTATTTTTCCTATTTTAT
Found at i:52750896 original size:19 final size:20
Alignment explanation
Indices: 52750851--52750901 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
52750841 TTTGAAAAGA
52750851 ATTTT-TTTTTCCTATTATT
1 ATTTTATTTTTCCTATTATT
*
52750870 ATTATTTATTTTTTCTATT-TT
1 A-T-TTTATTTTTCCTATTATT
52750891 ATTTTATTTTT
1 ATTTTATTTTT
52750902 GTAGGAAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 6 0.21
22 10 0.36
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (20 bp):
ATTTTATTTTTCCTATTATT
Found at i:52754424 original size:27 final size:28
Alignment explanation
Indices: 52754394--52754446 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
52754384 CAAAATTCAT
*
52754394 ACTTTAATTAT-AAAATAATTAATTTGC
1 ACTTAAATTATGAAAATAATTAATTTGC
* *
52754421 ACTTAAATTATGAACATATTTAATTT
1 ACTTAAATTATGAAAATAATTAATTT
52754447 TAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (28 bp):
ACTTAAATTATGAAAATAATTAATTTGC
Found at i:52761382 original size:19 final size:19
Alignment explanation
Indices: 52761358--52761411 Score: 90
Period size: 19 Copynumber: 2.8 Consensus size: 19
52761348 AATCTTCAAG
52761358 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52761377 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
52761396 GATATGCAATTTTAGA
1 GATATGCAATCTTAGA
52761412 AGATATGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.37, C:0.07, G:0.17, T:0.39
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:52761402 original size:38 final size:40
Alignment explanation
Indices: 52761358--52761434 Score: 104
Period size: 42 Copynumber: 1.9 Consensus size: 40
52761348 AATCTTCAAG
52761358 GATATGCAATCTT-AGATATGA-TATGTAATCTTAGATAT
1 GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
* *
52761396 GATATGCAATTTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT--AAGATATGATTATGTAATCTTAGA
52761435 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 12 0.36
41 8 0.24
42 13 0.39
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (40 bp):
GATATGCAATCTTAAGATATGATTATGTAATCTTAGATAT
Found at i:52767871 original size:44 final size:44
Alignment explanation
Indices: 52767807--52768494 Score: 605
Period size: 44 Copynumber: 15.5 Consensus size: 44
52767797 CAGATCAGTA
* * *
52767807 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCG
1 AAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * *
52767852 AAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * *
52767896 AAGAAAGCAGATCTTGTCTTCATGTATTGG-AGTGAAGTAGATCG
1 AAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * * *
52767940 AAGGTAGTAGATCCTGTCTTCCTATATTGGTAGCAAAGTGGATCG
1 AAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * *
52767985 AAGATGCAGATCTTCTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * * * * *
52768029 AAGAAAGCAGATTTTGTCTTCATGTATTGG-CGTGAAGTAGATCA
1 AAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * *
52768073 AAGATAGCATATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCG
1 AAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * *
52768118 AAGATGCAGATCTTCTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * * * * *
52768162 AAGAAAGCAGATTTTGTCTTCATGTATTGG-CGTGAAGTAGATCA
1 AAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * *
52768206 AAGATAGCATATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCG
1 AAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* **
52768251 AAGATGCAGATCTTGTCTTACC-ATATTGGTGGTTAAGTAGATCG
1 AAGATGCAGATCTTGTCTT-CCTATATTGGTAGCGAAGTAGATCG
* * ** * *
52768295 AAGAAAGCAGATCTTGTCTTCATGCATTGG-CGTGAAGTAGATCG
1 AAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * *
52768339 AAGATGGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCG
1 AAGAT-GCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * *
52768384 AAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATTG
1 AAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* * * * * *
52768428 AAGAAAGCAGATATTGTCTTCATGTATTGG-CGTGAAGTAGATCG
1 AAG-ATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
* *
52768472 AAGATAGCAGACCTTGCCTTCCT
1 AAGAT-GCAGATCTTGTCTTCCT
52768495 GCACCGAAAA
Statistics
Matches: 507, Mismatches: 120, Indels: 33
0.77 0.18 0.05
Matches are distributed among these distances:
43 4 0.01
44 336 0.66
45 167 0.33
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (44 bp):
AAGATGCAGATCTTGTCTTCCTATATTGGTAGCGAAGTAGATCG
Found at i:52768053 original size:133 final size:133
Alignment explanation
Indices: 52767807--52768482 Score: 1145
Period size: 133 Copynumber: 5.1 Consensus size: 133
52767797 CAGATCAGTA
52767807 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
52767872 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGAGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
52767937 TCG
131 TCG
* * * * *
52767940 AAGGTAGTAGATCCTGTCTTCCTATATTGGTAGCAAAGTGGATCGAAGATGCAGATCTTCTCTTC
1 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
52768005 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATTTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
*
52768070 TCA
131 TCG
* *
52768073 AAGATAGCATATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTCTCTTC
1 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
52768138 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATTTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
*
52768203 TCA
131 TCG
* *
52768206 AAGATAGCATATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTA
1 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* ** *
52768271 CCATATTGGTGGTTAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGCATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
52768336 TCG
131 TCG
* * *
52768339 AAGATGGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
52768404 CCATACTGGTGGCGAAGTAGATTGAAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
52768469 TCG
131 TCG
52768472 AAGATAGCAGA
1 AAGATAGCAGA
52768483 CCTTGCCTTC
Statistics
Matches: 510, Mismatches: 33, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 510 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (133 bp):
AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
TCG
Found at i:52768509 original size:89 final size:90
Alignment explanation
Indices: 52767807--52768494 Score: 522
Period size: 89 Copynumber: 7.8 Consensus size: 90
52767797 CAGATCAGTA
* * * * * * * *
52767807 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGACCTTGTCTT
* * *
52767871 CCCATACTGGTGGCGAAGTAGATCG
66 CCTACACTGGTAGCGAAGTAGATCG
* * *
52767896 AAGAAAGCAGATCTTGTCTTCATGTATTGG-AGTGAAGTAGATCGAAGGTAGTAGATCC-TGTCT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGA-CCTTGTCT
* * * *
52767959 TCCTATATTGGTAGCAAAGTGGATCG
65 TCCTACACTGGTAGCGAAGTAGATCG
* * *** * * * * **
52767985 AAG-ATGCAGATCTTCTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATTTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGACCTTGTCTT
* ** * * * *
52768049 CATGTATTGG-CGTGAAGTAGATCA
66 CCTACACTGGTAGCGAAGTAGATCG
* * * * * * * * * *
52768073 AAGATAGCATATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGAT-GCAGATCTTCTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGACCTTGTCTT
* * *
52768137 CCCATACTGGTGGCGAAGTAGATCG
66 CCTACACTGGTAGCGAAGTAGATCG
* * *
52768162 AAGAAAGCAGATTTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAGCATATCC-TGTCT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGA-CCTTGTCT
* * * *
52768225 TCTTATATTGGTAGCGAAGTGGATCG
65 TCCTACACTGGTAGCGAAGTAGATCG
* * * * *
52768251 AAG-ATGCAGATCTTGTCTTACCA--TATTGGTGGTTAAGTAGATCGAAGAAAGCAGATCTTGTC
1 AAGAAAGCAGATCTTGTCTT--CATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGACCTTGTC
* * * * *
52768313 TTCATGCATTGG-CGTGAAGTAGATCG
64 TTCCTACACTGGTAGCGAAGTAGATCG
** * * * * * *
52768339 AAGATGGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGAT-GCAGATCTTGTCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGACCTTGTCTT
* * * *
52768403 CCCATACTGGTGGCGAAGTAGATTG
66 CCTACACTGGTAGCGAAGTAGATCG
* *
52768428 AAGAAAGCAGATATTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGATAGCAGACCTTGCCTT
1 AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGACCTTGTCTT
52768492 CCT
66 CCT
52768495 GCACCGAAAA
Statistics
Matches: 469, Mismatches: 113, Indels: 34
0.76 0.18 0.06
Matches are distributed among these distances:
87 1 0.00
88 152 0.32
89 312 0.67
90 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (90 bp):
AAGAAAGCAGATCTTGTCTTCATGTATTGGTCGTGAAGTAGATCGAAGATAGCAGACCTTGTCTT
CCTACACTGGTAGCGAAGTAGATCG
Found at i:52768605 original size:266 final size:263
Alignment explanation
Indices: 52767807--52768868 Score: 796
Period size: 266 Copynumber: 4.0 Consensus size: 263
52767797 CAGATCAGTA
*
52767807 AAGATAGCAGATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
52767872 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGAGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
* * * * * ** * * ** **
52767937 TCGAAGGTAGTAGATCCTGTCTTCCTATATTGGTAGCAAAGTGGATCGAAGATGCAGATCTT-CT
131 TCAAAGATAGCAGATCCTGCCTTCCTACACCGATAGCGAAGCAGATCGAAGAACCAGATCTTGC-
* * * * * * * ** * *
52768001 CTTCCCATACTGG-TGGCGAAGTAGATCGAAGAAAGCAGATTTTGTCTTCATGTATTGGCGTGAA
195 C-TCCC-T--GGGTTGGCGGAGCAGAGCGAAAAAAGCAGATCTTGTCTTCATGCACCGACGCGAA
* *
52768065 GTAGATCA
256 GCAGATCG
* * *
52768073 AAGATAGCATATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTCTCTTC
1 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
*
52768138 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATTTTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
* * * * ** * ** **
52768203 TCAAAGATAGCATATCCTGTCTTCTTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTC
131 TCAAAGATAGCAGATCCTGCCTTCCTACACCGATAGCGAAGCAGATCGAAGAACCAGATCTTG-C
* * * * * * * ** * *
52768268 TTACCAT--ATTGGTGGTTAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGCATTGGCGTGAA
195 CT-CCCTGGGTTGGCGG---AGCAGAGCGAAAAAAGCAGATCTTGTCTTCATGCACCGACGCGAA
*
52768331 GTAGATCG
256 GCAGATCG
* *
52768339 AAGATGGCAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTC
1 AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
* *
52768404 CCATACTGGTGGCGAAGTAGATTGAAGAAAGCAGATATTGTCTTCATGTATTGGCGTGAAGTAGA
66 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
* * * * * *
52768469 TCGAAGATAGCAGA-CCTTGCCTTCCTGCACCGAAAACGAAGCAAATTGAAGACACCAG-TCTTG
131 TCAAAGATAGCAGATCC-TGCCTTCCTACACCGATAGCGAAGCAGATCGAAGA-ACCAGATCTTG
* *
52768532 CCTCCCTGGGTTGCAGCGGAGCAG-GCTAAAAATAGCAGATCTT-TCTTTCCTGCACCGACAGCG
194 CCTCCCTGGGTTG--GCGGAGCAGAGCGAAAAA-AGCAGATCTTGTC-TTCATGCACCGAC-GCG
52768595 AAGCAGATCG
254 AAGCAGATCG
* * * *** * *
52768605 AAGACACCAG--CCT-TGCCTCACTGGGTT-GTAGCGGAGTAGG--CTAAGAATAGCAGATCTTG
1 AAGATAGCAGATCCTGT-CTTC-CTATATTGGTAGCGAAGT-GGATCGAAG-AT-GCAGATCTTG
* *** * ** * * * * * * * *
52768664 CCTTCCTGCACCGGCAGCGAAGCAGATCCAAGACACCAG-TCTTGCCTCCTTG-GTTGCAGCG-G
61 TCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTG--GCGTG
* * * * * * * *
52768726 -AGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGACATCGAAGCAGATCGAAGACACCAG
124 AAGTAGATCAAAGATAGCAGATCCTGCCTTCCTACACCGATAGCGAAGCAGATCGAAGA-ACCAG
* * ** *
52768790 -CCTTGCTTCCCTGGGTTGCAGCGGAGCAG-GTTAAAAATAGCAGATCTTGTCTTCCTGCACCGA
188 ATCTTGCCTCCCTGGGTTG--GCGGAGCAGAGCGAAAAA-AGCAGATCTTGTCTTCATGCACCGA
52768853 CAGCGAAGCAGATCG
250 C-GCGAAGCAGATCG
52768868 A
1 A
52768869 TGACCCCAGC
Statistics
Matches: 675, Mismatches: 96, Indels: 53
0.82 0.12 0.06
Matches are distributed among these distances:
263 137 0.20
264 39 0.06
265 73 0.11
266 417 0.62
267 5 0.01
268 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (263 bp):
AAGATAGCAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
TCAAAGATAGCAGATCCTGCCTTCCTACACCGATAGCGAAGCAGATCGAAGAACCAGATCTTGCC
TCCCTGGGTTGGCGGAGCAGAGCGAAAAAAGCAGATCTTGTCTTCATGCACCGACGCGAAGCAGA
TCG
Found at i:52768707 original size:44 final size:44
Alignment explanation
Indices: 52768659--52768866 Score: 111
Period size: 43 Copynumber: 4.8 Consensus size: 44
52768649 GAATAGCAGA
*
52768659 TCTTGCCTTCCTGCACCGGCAGCGAAGCAGATCCAAGACACCAG
1 TCTTGCCTTCCTGCACCGGCAGCGAAGCAGATCAAAGACACCAG
*** * * * * * *
52768703 TCTTGCC-TCCTTG--GTTGCAGCGGAGCAGGTTAAAAATAGCAG
1 TCTTGCCTTCC-TGCACCGGCAGCGAAGCAGATCAAAGACACCAG
* * *
52768745 ATCTTGCCTTCCTGCACCGACATCGAAGCAGATCGAAGACACCAG
1 -TCTTGCCTTCCTGCACCGGCAGCGAAGCAGATCAAAGACACCAG
* **** * * * * * *
52768790 CCTTG-CTTCCCTG-GGTTGCAGCGGAGCAGGTTAAAAATAGCAG
1 TCTTGCCTT-CCTGCACCGGCAGCGAAGCAGATCAAAGACACCAG
* *
52768833 ATCTTGTCTTCCTGCACCGACAGCGAAGCAGATC
1 -TCTTGCCTTCCTGCACCGGCAGCGAAGCAGATC
52768867 GATGACCCCA
Statistics
Matches: 110, Mismatches: 45, Indels: 17
0.64 0.26 0.10
Matches are distributed among these distances:
42 19 0.17
43 32 0.29
44 28 0.25
45 31 0.28
ACGTcount: A:0.25, C:0.29, G:0.25, T:0.21
Consensus pattern (44 bp):
TCTTGCCTTCCTGCACCGGCAGCGAAGCAGATCAAAGACACCAG
Found at i:52768774 original size:175 final size:176
Alignment explanation
Indices: 52768475--52768866 Score: 606
Period size: 175 Copynumber: 2.2 Consensus size: 176
52768465 TAGATCGAAG
* * * * **
52768475 ATAGCAGACCTTGCCTTCCTGCACCGAAAACGAAGCAAATTGAAGACACCAGTCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCCAAGACACCAGTCTTGCCTCCCTG
* *
52768540 GGTTGCAGCGGAGCAGGCTAAAAATAGCAGATCTTTCTTTCCTGCACCGACAGCGAAGCAGATCG
66 GGTTGCAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCG
* * *
52768605 AAGACACCAGCCTTGCCTCACTGGGTTGTAGCGGAGTAGGCTAAGA
131 AAGACACCAGCCTTGCCTCACTGGGTTGCAGCGGAGCAGGCTAAAA
* *
52768651 ATAGCAGATCTTGCCTTCCTGCACCGGCAGCGAAGCAGATCCAAGACACCAGTCTTGCCT-CCTT
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCCAAGACACCAGTCTTGCCTCCCTG
* *
52768715 GGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGACATCGAAGCAGATCG
66 GGTTGCAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCG
* * *
52768780 AAGACACCAGCCTTGCTTCCCTGGGTTGCAGCGGAGCAGGTTAAAA
131 AAGACACCAGCCTTGCCTCACTGGGTTGCAGCGGAGCAGGCTAAAA
*
52768826 ATAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATC
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATC
52768867 GATGACCCCA
Statistics
Matches: 196, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
175 143 0.73
176 53 0.27
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (176 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCCAAGACACCAGTCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGCTAAAAATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCG
AAGACACCAGCCTTGCCTCACTGGGTTGCAGCGGAGCAGGCTAAAA
Found at i:52768857 original size:45 final size:44
Alignment explanation
Indices: 52768650--52768863 Score: 123
Period size: 45 Copynumber: 4.9 Consensus size: 44
52768640 GTAGGCTAAG
* * **
52768650 AATAGCAGATCTTGCCTTCCTGCACCGGCAGCGAAGCAGATCCAA
1 AATAGCAGATCTTG-CTTCCTGCACCGACAGCGAAGCAGGTTAAA
* * * * *** *
52768695 GACACCAG-TCTTGCCTCCTTG-GTTG-CAGCGGAGCAGGTTAAA
1 AATAGCAGATCTTGCTTCC-TGCACCGACAGCGAAGCAGGTTAAA
* * **
52768737 AATAGCAGATCTTGCCTTCCTGCACCGACATCGAAGCAGATCGAA
1 AATAGCAGATCTTG-CTTCCTGCACCGACAGCGAAGCAGGTTAAA
* * * * **** *
52768782 GACACCAG-CCTTGCTTCCCTGGGTTG-CAGCGGAGCAGGTTAAA
1 AATAGCAGATCTTGCTT-CCTGCACCGACAGCGAAGCAGGTTAAA
52768825 AATAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAG
1 AATAGCAGATCTTG-CTTCCTGCACCGACAGCGAAGCAG
52768864 ATCGATGACC
Statistics
Matches: 115, Mismatches: 45, Indels: 18
0.65 0.25 0.10
Matches are distributed among these distances:
42 18 0.16
43 32 0.28
44 30 0.26
45 35 0.30
ACGTcount: A:0.26, C:0.29, G:0.25, T:0.21
Consensus pattern (44 bp):
AATAGCAGATCTTGCTTCCTGCACCGACAGCGAAGCAGGTTAAA
Found at i:52768912 original size:88 final size:88
Alignment explanation
Indices: 52768475--52768879 Score: 596
Period size: 88 Copynumber: 4.6 Consensus size: 88
52768465 TAGATCGAAG
* * * * * *
52768475 ATAGCAGACCTTGCCTTCCTGCACCGAAAACGAAGCAAATTGAAGACACCAGTCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
*
52768540 GGTTGCAGCGGAGCAGGCTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * *
52768563 ATAGCAGATCTTTCTTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCACTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
* * * *
52768628 GGTTGTAGCGGAGTAGGCTAAGA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * * *
52768651 ATAGCAGATCTTGCCTTCCTGCACCGGCAGCGAAGCAGATCCAAGACACCAGTCTTGCCT-CCTT
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
52768715 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* *
52768738 ATAGCAGATCTTGCCTTCCTGCACCGACATCGAAGCAGATCGAAGACACCAGCCTTGCTTCCCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
52768803 GGTTGCAGCGGAGCAGGTTAAAA
66 GGTTGCAGCGGAGCAGGTTAAAA
* * *
52768826 ATAGCAGATCTTGTCTTCCTGCACCGACAGCGAAGCAGATCGATGACCCCAGCC
1 ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
52768880 CTATCTCCCT
Statistics
Matches: 283, Mismatches: 33, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
87 76 0.27
88 207 0.73
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.20
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTG
GGTTGCAGCGGAGCAGGTTAAAA
Found at i:52768945 original size:44 final size:44
Alignment explanation
Indices: 52768879--52769044 Score: 226
Period size: 44 Copynumber: 3.8 Consensus size: 44
52768869 TGACCCCAGC
* *
52768879 CCTATCTCCCTGGTTAGCAGTGGAATAGGTTAAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
** *
52768923 CCTATCTCCCTGGTCAATAGTGGAATAGGTTGAAGATTGAGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* * *
52768967 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTGTGAAT
1 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
* *
52769011 CCTATCTCCCTAAG-CAGCAGTGGAGTAGGTTGAA
1 CCTATCTCCCT-GGTCAGCAGTGGAATAGGTTGAA
52769045 AATAGCAGAT
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 105 0.99
45 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (44 bp):
CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTGAAT
Found at i:52770136 original size:22 final size:22
Alignment explanation
Indices: 52770076--52770133 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 22
52770066 AATCTTCAAG
52770076 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
52770095 GATATGCAATTTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
52770117 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
52770134 GATTTAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 12 0.39
22 8 0.26
23 11 0.35
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:52772478 original size:24 final size:24
Alignment explanation
Indices: 52772450--52772501 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
52772440 TTAGTAAGTC
* *
52772450 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACCAATAAATACT
* *
52772474 AAATATATTATACCAATAAATACT
1 AAATAAACTATACCAATAAATACT
52772498 AAAT
1 AAAT
52772502 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.56, C:0.12, G:0.02, T:0.31
Consensus pattern (24 bp):
AAATAAACTATACCAATAAATACT
Found at i:52774683 original size:19 final size:19
Alignment explanation
Indices: 52774659--52774725 Score: 72
Period size: 18 Copynumber: 3.7 Consensus size: 19
52774649 TATAATAAAT
52774659 TATTAATAAAATTTATTTA
1 TATTAATAAAATTTATTTA
*
52774678 TTTTAAT-AAA-TTATTTAA
1 TATTAATAAAATTTATTT-A
52774696 TATT--TAAAATTTATTT-
1 TATTAATAAAATTTATTTA
*
52774712 TAATAATAAAATTT
1 TATTAATAAAATTT
52774726 TAAAATAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
16 4 0.10
17 9 0.22
18 21 0.52
19 6 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTAATAAAATTTATTTA
Found at i:52774725 original size:14 final size:14
Alignment explanation
Indices: 52774708--52774743 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
52774698 TTTAAAATTT
52774708 ATTTTAATAATAA-A
1 ATTTTAA-AATAATA
52774722 ATTTTAAAATAATA
1 ATTTTAAAATAATA
52774736 ATTTTAAA
1 ATTTTAAA
52774744 TGATATTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTTTAAAATAATA
Found at i:52782107 original size:55 final size:55
Alignment explanation
Indices: 52782041--52782153 Score: 199
Period size: 55 Copynumber: 2.1 Consensus size: 55
52782031 TAGGATTTGG
52782041 ATGCTGATAGTTAACTATATTATTTTATATTAAAAAATGTATGATAAATTGAGCT
1 ATGCTGATAGTTAACTATATTATTTTATATTAAAAAATGTATGATAAATTGAGCT
* * *
52782096 ATGCTGATAGTTAACTATATTGTTTTATATTAAAAAATGTATGATGAGTTGAGCT
1 ATGCTGATAGTTAACTATATTATTTTATATTAAAAAATGTATGATAAATTGAGCT
52782151 ATG
1 ATG
52782154 TTGTAGATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (55 bp):
ATGCTGATAGTTAACTATATTATTTTATATTAAAAAATGTATGATAAATTGAGCT
Found at i:52783650 original size:128 final size:128
Alignment explanation
Indices: 52782696--52783631 Score: 1854
Period size: 128 Copynumber: 7.3 Consensus size: 128
52782686 GGTATATCCA
* *
52782696 ATGATGCACTATGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
52782761 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
66 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
52782824 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
52782889 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
66 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
52782952 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
52783017 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
66 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
52783080 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
52783145 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
66 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
52783208 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
52783273 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
66 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
52783336 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
52783401 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
66 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
52783464 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
52783529 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
66 ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
52783592 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTAT
1 ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTAT
52783632 CTGATGATAC
Statistics
Matches: 806, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 806 1.00
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (128 bp):
ATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGTGTGCCAAT
ATATTTCTTCGATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTATTCG
Found at i:52783767 original size:43 final size:43
Alignment explanation
Indices: 52783601--52783863 Score: 207
Period size: 43 Copynumber: 6.1 Consensus size: 43
52783591 GATGATGCAT
* * *
52783601 TGTGTGTGCTAGTATATTTTCTTC-AGTTTATCTGATGATACA--G
1 TGTGTGT-C-AGTATATTTTCTTCGA-TGTATCCGATGATACACTA
* * *
52783644 TGTGTGTACTAGTATGTTTTCTTC-AGTTTATCTGATGATACA-T-
1 TGTGTGT-C-AGTATATTTTCTTCGA-TGTATCCGATGATACACTA
* * *
52783687 TGTGTGTGCTAGTATATTTTCTTCAATTTATCTGATGATACACTA
1 TGTGTGT-C-AGTATATTTTCTTCGATGTATCCGATGATACACTA
* *
52783732 TGTGTGTCAGTATATTTTCTTTGATGTATCCGATGATGCACTA
1 TGTGTGTCAGTATATTTTCTTCGATGTATCCGATGATACACTA
** * * * *
52783775 TGTGTGTCAGTATAGATGCTTCGGTTTATCCGATGA-AGCATTA
1 TGTGTGTCAGTATATTTTCTTCGATGTATCCGATGATA-CACTA
* * * *
52783818 TGTGTGCCAGTATATTTTTTTCGATGTATCCGATGGTGCACTA
1 TGTGTGTCAGTATATTTTCTTCGATGTATCCGATGATACACTA
52783861 TGT
1 TGT
52783864 ACTTGTATAT
Statistics
Matches: 187, Mismatches: 27, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
43 177 0.95
44 3 0.02
45 7 0.04
ACGTcount: A:0.21, C:0.13, G:0.21, T:0.44
Consensus pattern (43 bp):
TGTGTGTCAGTATATTTTCTTCGATGTATCCGATGATACACTA
Found at i:52783767 original size:86 final size:85
Alignment explanation
Indices: 52782822--52783857 Score: 371
Period size: 85 Copynumber: 12.1 Consensus size: 85
52782812 TTTGTTTATT
* * * *
52782822 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTAT-TCAAAGATTCACTATGTGTGCC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCT-GATGATACA-TATGTGTGTC
* * *
52782886 AATATA-TTTCTTCGATTTATC
64 AGTATATTTTCTTTGATGTATC
* * * * ** ** ** *
52782907 TGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTAT-TCGATGATGCAT-TGTGTGTGC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCT-GATGATACATATGTGTGT-C
* * *
52782970 TAGTATATTTTC-TTCAGTTTATT
64 -AGTATATTTTCTTTGA-TGTATC
* * * * * * * * *
52782993 CAAAGATTCACTATGTGTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCAT-TGTGAGTGC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAG-TTTATCTGATGATACATATGT--GTGT
* ** * *
52783055 CAGTGTAGATGAT-TTTG-TTTATT
63 CA--GTATATTTTCTTTGATGTATC
* * * *
52783078 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTAT-TCAAAGATTCACTATGTGTGCC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCT-GATGATACA-TATGTGTGTC
* * *
52783142 AATATA-TTTCTTCGATTTATC
64 AGTATATTTTCTTTGATGTATC
* * * * ** ** ** *
52783163 TGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTAT-TCGATGATGCAT-TGTGTGTGC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCT-GATGATACATATGTGTGT-C
* * *
52783226 TAGTATATTTTC-TTCAGTTTATT
64 -AGTATATTTTCTTTGA-TGTATC
* * * * * * * * *
52783249 CAAAGATTCACTATGTGTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCAT-TGTGAGTGC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAG-TTTATCTGATGATACATATGT--GTGT
* ** * *
52783311 CAGTGTAGATGAT-TTTG-TTTATT
63 CA--GTATATTTTCTTTGATGTATC
* * * *
52783334 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTAT-TCAAAGATTCACTATGTGTGCC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCT-GATGATACA-TATGTGTGTC
* * *
52783398 AATATA-TTTCTTCGATTTATC
64 AGTATATTTTCTTTGATGTATC
* * * * ** ** ** *
52783419 TGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTGTTTAT-TCGATGATGCAT-TGTGTGTGC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCT-GATGATACATATGTGTGT-C
* * *
52783482 TAGTATATTTTC-TTCAGTTTATT
64 -AGTATATTTTCTTTGA-TGTATC
* * * * * * * * *
52783505 CAAAGATTCACTATGTGTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCAT-TGTGAGTGC
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAG-TTTATCTGATGATACATATGT--GTGT
* ** * *
52783567 CAGTGTAGATGAT-TTTG-TTTATT
63 CA--GTATATTTTCTTTGATGTATC
*
52783590 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCTGATGATACA-GTGTGTGTACT
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCTGATGATACATATGTGTGT-C-
* * *
52783654 AGTATGTTTTC-TTCAGTTTATC
64 AGTATATTTTCTTTGA-TGTATC
* * *
52783676 TGATGATACATTGTGTGTGCTAGTATATTTTCTTCAATTTATCTGATGATACACTATGTGTGTCA
1 CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCTGATGATACA-TATGTGTGTCA
52783741 GTATATTTTCTTTGATGTATC
65 GTATATTTTCTTTGATGTATC
** * * *
52783762 CGATGATGCACTATGTGTGT-C-AGTATAGATGCTTCGGTTTATCCGATGA-AGCATTATGTGTG
1 CGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATCTGATGATA-CA-TATGTGTG
*
52783824 CCAGTATATTTT-TTTCGATGTATC
62 TCAGTATATTTTCTTT-GATGTATC
*
52783848 CGATGGTGCA
1 CGATGATGCA
52783858 CTATGTACTT
Statistics
Matches: 716, Mismatches: 173, Indels: 123
0.71 0.17 0.12
Matches are distributed among these distances:
83 20 0.03
84 31 0.04
85 302 0.42
86 299 0.42
87 44 0.06
88 20 0.03
ACGTcount: A:0.22, C:0.13, G:0.21, T:0.44
Consensus pattern (85 bp):
CGATGATGCATTGTGTGTGCTAGTATATTTTCTTCAGTTTATCTGATGATACATATGTGTGTCAG
TATATTTTCTTTGATGTATC
Found at i:52783767 original size:129 final size:130
Alignment explanation
Indices: 52782690--52783863 Score: 298
Period size: 128 Copynumber: 9.2 Consensus size: 130
52782680 TCCTTTGGTA
* * * * * *
52782690 TATCCAATGATGCACTA--TGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGA-TCACTATGT
* * * * * * * * * ** ** ***
52782753 GTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTG
65 GTGTCAGTATAGATGCTTCAG-TTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
*
52782816 TT
129 TG
* * * * * *
52782818 TATTCGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGA-TCACTATGT
* * * * * * * * * ** ** ***
52782881 GTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTG
65 GTGTCAGTATAGATGCTTCAG-TTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
*
52782944 TT
129 TG
* * * * * *
52782946 TATTCGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGA-TCACTATGT
* * * * * * * * * ** ** ***
52783009 GTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTG
65 GTGTCAGTATAGATGCTTCAG-TTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
*
52783072 TT
129 TG
* * * * * *
52783074 TATTCGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGA-TCACTATGT
* * * * * * * * * ** ** ***
52783137 GTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTG
65 GTGTCAGTATAGATGCTTCAG-TTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
*
52783200 TT
129 TG
* * * * * *
52783202 TATTCGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGA-TCACTATGT
* * * * * * * * * ** ** ***
52783265 GTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTG
65 GTGTCAGTATAGATGCTTCAG-TTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
*
52783328 TT
129 TG
* * * * * *
52783330 TATTCGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGA-TCACTATGT
* * * * * * * * * ** ** ***
52783393 GTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTG
65 GTGTCAGTATAGATGCTTCAG-TTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
*
52783456 TT
129 TG
* * * * * *
52783458 TATTCGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATTCAAAGATTCACTATGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGA-TCACTATGT
* * * * * * * * * ** ** ***
52783521 GTGCCAATATA-TTTCTTC-GATTTATCTGATGATGCATTGTGAGTGCCAGTGTAGATGATTTTG
65 GTGTCAGTATAGATGCTTCAG-TTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
*
52783584 TT
129 TG
* * * *
52783586 TATTCGATGATGCA-T-TGTGTGTGCTAGTATATTTTCTTCAGTTTATCTGATGAT-AC-AGTGT
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGATCACTA-TGT
* * * * *
52783647 GTGTACTAGTAT-GTTTTCTTCAGTTTATCTGATGATA-CATTGTGTGTGCTAGTATATTTTCTT
65 GTGT-C-AGTATAG-ATGCTTCAGTTTATCCGATGA-AGCATTATGTGTGCCAGTATATTTTCTT
*
52783710 CAATT
126 CAATG
* *
52783715 TATCTGATGATACACTATGTGTGT-C-AGTATATTTTCTT-TGATGTATCCGATGATGCACTATG
1 TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAG-TGTATCCGATGAT-CACTATG
* * *
52783777 TGTGTCAGTATAGATGCTTCGGTTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTTTTCGA
64 TGTGTCAGTATAGATGCTTCAGTTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAA
52783842 TG
129 TG
* *
52783844 TATCCGATGGTGCACTATGT
1 TATCCGATGATACACTATGT
52783864 ACTTGTATAT
Statistics
Matches: 992, Mismatches: 37, Indels: 33
0.93 0.03 0.03
Matches are distributed among these distances:
125 1 0.00
126 8 0.01
127 3 0.00
128 818 0.82
129 140 0.14
130 5 0.01
131 16 0.02
132 1 0.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (130 bp):
TATCCGATGATACACTATGTGTGTGCTAGTATATTTTCTTCAGTGTATCCGATGATCACTATGTG
TGTCAGTATAGATGCTTCAGTTTATCCGATGAAGCATTATGTGTGCCAGTATATTTTCTTCAATG
Found at i:52786510 original size:11 final size:11
Alignment explanation
Indices: 52786494--52786518 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52786484 AAATTCTGTG
52786494 TTTTCTTTTTT
1 TTTTCTTTTTT
52786505 TTTTCTTTTTT
1 TTTTCTTTTTT
52786516 TTT
1 TTT
52786519 CTGCGATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:52791361 original size:7 final size:7
Alignment explanation
Indices: 52791349--52791386 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
52791339 CAAATTTCTG
52791349 AAAAAGA
1 AAAAAGA
52791356 AAAAAGA
1 AAAAAGA
52791363 AAAAAGA
1 AAAAAGA
*
52791370 AAAAATA
1 AAAAAGA
52791377 AAAAAGA
1 AAAAAGA
52791384 AAA
1 AAA
52791387 GACAAAGTCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.87, C:0.00, G:0.11, T:0.03
Consensus pattern (7 bp):
AAAAAGA
Found at i:52797278 original size:42 final size:43
Alignment explanation
Indices: 52797162--52797295 Score: 139
Period size: 42 Copynumber: 3.1 Consensus size: 43
52797152 ATAGGATTCT
* * **
52797162 GATATGTGATTTCGTGTAA-AACCTCGTCTGGGATGTTGGCATC
1 GATATGAGATTTCGTGTAAGACCCT-GTCTGGGACATTGGCATC
* * *
52797205 GATTTGAGATTTATGTGTAAGACCATGTCTGGGACATTGGCATC
1 GATATGAGATTT-CGTGTAAGACCCTGTCTGGGACATTGGCATC
* *
52797249 GTATAT-A-ATTTCGTGTAAGACCCTGTCTGGGACAGTGTCATC
1 G-ATATGAGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATC
52797291 GATAT
1 GATAT
52797296 TTGATAACAT
Statistics
Matches: 76, Mismatches: 12, Indels: 8
0.79 0.12 0.08
Matches are distributed among these distances:
41 4 0.05
42 28 0.37
43 14 0.18
44 24 0.32
45 6 0.08
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (43 bp):
GATATGAGATTTCGTGTAAGACCCTGTCTGGGACATTGGCATC
Found at i:52800503 original size:134 final size:133
Alignment explanation
Indices: 52800035--52800507 Score: 409
Period size: 134 Copynumber: 3.5 Consensus size: 133
52800025 AGTTTGCTGG
* * *
52800035 TTTACAATCACACCTTAAGTTCATTAATTTACGATCATGAAGAATTCAATTAGCGTTATT-CAAT
1 TTTACAATCACAGCTTAAGTTCATTAATTTACGATCATGAACAATTCAATTAGAGTT-TTCCAAT
* * ** *
52800099 TTATGAATGCA-AA-TCTATTCAAACAATTTTTTGATTTACGATCACAATCGATATTATTAAAGT
65 TTATG-AT-CACAACTCCATTCAAACAGTTTGATGATTTACGATCACAATC-ATATTATTAAAGA
52800162 TCACTT-A
127 TCA-TTGA
* * * * * * * *
52800169 TTTACGATCACAGCTTAAGTTCATTTATTTATGATCATGAACGATTCACTTCGAG-TTCCCTGAT
1 TTTACAATCACAGCTTAAGTTCATTAATTTACGATCATGAACAATTCAATTAGAGTTTTCC-AAT
* * * ** * * **
52800233 TTACGACCGCAACTCCATTCAAACAGTTTGATGATTTAAAATGAAAATTGGTATTATTAAAGAT-
65 TTATGATCACAACTCCATTCAAACAGTTTGATGATTTACGATCACAA-TCATATTATTAAAGATC
* *
52800297 TTCTAA
129 AT-TGA
* * * * * * ** *
52800303 TTTACAATCAAAACTTAAGTTCATTGATTTATGATAATGAACGATTCAATTAGAGTTCACCGATT
1 TTTACAATCACAGCTTAAGTTCATTAATTTACGATCATGAACAATTCAATTAGAGTTTTCCAATT
* *
52800368 TATGATCACAACTCCATTCAAACAGTTTGGTGATTTACGATCACAACTCATATTATTAAAGCTCA
66 TATGATCACAACTCCATTCAAACAGTTTGATGATTTACGATCACAA-TCATATTATTAAAGATCA
*
52800433 TTGG
130 TTGA
* * * * * * *
52800437 TTTACGATCATAGCTTAAGTTTATTCATTTACGATCATGCACAATGCAATTAGAGTTTTTCAATT
1 TTTACAATCACAGCTTAAGTTCATTAATTTACGATCATGAACAATTCAATTAGAGTTTTCCAATT
52800502 TATGAT
66 TATGAT
52800508 TGAGCTATCG
Statistics
Matches: 266, Mismatches: 64, Indels: 18
0.76 0.18 0.05
Matches are distributed among these distances:
132 3 0.01
133 6 0.02
134 252 0.95
135 5 0.02
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (133 bp):
TTTACAATCACAGCTTAAGTTCATTAATTTACGATCATGAACAATTCAATTAGAGTTTTCCAATT
TATGATCACAACTCCATTCAAACAGTTTGATGATTTACGATCACAATCATATTATTAAAGATCAT
TGA
Found at i:52812562 original size:15 final size:15
Alignment explanation
Indices: 52812529--52812566 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
52812519 ATGATAGTTT
52812529 TAATATATATGTATTA
1 TAATA-ATATGTATTA
52812545 TAATAATAT-TATTAA
1 TAATAATATGTATT-A
52812560 TAATAAT
1 TAATAAT
52812567 TAAAATGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 12 0.57
16 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TAATAATATGTATTA
Found at i:52826764 original size:42 final size:43
Alignment explanation
Indices: 52826699--52826846 Score: 178
Period size: 43 Copynumber: 3.5 Consensus size: 43
52826689 CAACGTTAAC
* * *
52826699 GTCCTAGACGTGATTTTACATGTAATCACAAATCGATGCCACT
1 GTCCCAGACGTGGTCTTACATGTAATCACAAATCGATGCCACT
*
52826742 GTCCCAGACGTGGT-TTACATGTAATCACAAATCGATGTCACT
1 GTCCCAGACGTGGTCTTACATGTAATCACAAATCGATGCCACT
* * *
52826784 GTCCCAGACAG-GGTCTTACACGAAAAT-ACAAGTCGATGCCAAC-
1 GTCCCAGAC-GTGGTCTTACATG-TAATCACAAATCGATGCC-ACT
52826827 GTCCCAGACGTGGTCTTACA
1 GTCCCAGACGTGGTCTTACA
52826847 CAAAAAAACA
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
42 40 0.43
43 48 0.52
44 5 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (43 bp):
GTCCCAGACGTGGTCTTACATGTAATCACAAATCGATGCCACT
Found at i:52826821 original size:43 final size:43
Alignment explanation
Indices: 52826726--52826895 Score: 181
Period size: 43 Copynumber: 4.0 Consensus size: 43
52826716 ACATGTAATC
* *
52826726 ACAAATCGATGCC-ACTGTCCCAGACGTGGT-TTACATG-TAAT
1 ACAAATCGATGCCAAC-GTCCCAGACGTGGTCTTACACGAAAAT
*
52826767 CACAAATCGATGTC-ACTGTCCCAGACAG-GGTCTTACACGAAAAT
1 -ACAAATCGATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAAT
* * *
52826811 ACAAGTCGATGCCAACGTCCCAGACGTGGTCTTACACAAAAAA
1 ACAAATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAAT
* *
52826854 ACAAGTTGAAT-CCAACGTCCCAGACGTGGTCTTACACGAAAA
1 ACAAATCG-ATGCCAACGTCCCAGACGTGGTCTTACACGAAAA
52826896 CACTTACCAG
Statistics
Matches: 113, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
42 28 0.25
43 78 0.69
44 7 0.06
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (43 bp):
ACAAATCGATGCCAACGTCCCAGACGTGGTCTTACACGAAAAT
Found at i:52832772 original size:41 final size:41
Alignment explanation
Indices: 52832684--52832795 Score: 118
Period size: 41 Copynumber: 2.7 Consensus size: 41
52832674 AGCCAATTTA
* *
52832684 AAAAAAACGCTTCCAATTGAAAGCGTTTTCAGATGAAATTC
1 AAAAAAACGCTTCCAAGTAAAAGCGTTTTCAGATGAAATTC
* * * *
52832725 AGAAAAACGCTTCCAAGTAAAAGTGTTTTCAGGTG-ATTTGC
1 AAAAAAACGCTTCCAAGTAAAAGCGTTTTCAGATGAAATT-C
* * * *
52832766 AAAAAAACGCTTTCAACTAGAAGCGCTTTC
1 AAAAAAACGCTTCCAAGTAAAAGCGTTTTC
52832796 TACCACATCA
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
40 3 0.05
41 55 0.95
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (41 bp):
AAAAAAACGCTTCCAAGTAAAAGCGTTTTCAGATGAAATTC
Found at i:52837926 original size:21 final size:22
Alignment explanation
Indices: 52837900--52837945 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
52837890 AACTACTACT
* *
52837900 AATAATTATTAAATTAAAT-AA
1 AATAATAATAAAATTAAATGAA
52837921 AATAATAATAAAATTAAATGAA
1 AATAATAATAAAATTAAATGAA
52837943 AAT
1 AAT
52837946 GTGAATAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
AATAATAATAAAATTAAATGAA
Found at i:52846881 original size:7 final size:7
Alignment explanation
Indices: 52846871--52846896 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
52846861 TGAAAATTAG
52846871 GATTTGA
1 GATTTGA
52846878 GATTTGA
1 GATTTGA
52846885 GATTTGA
1 GATTTGA
52846892 GATTT
1 GATTT
52846897 TTGAAAGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (7 bp):
GATTTGA
Found at i:52850644 original size:45 final size:43
Alignment explanation
Indices: 52850556--52850661 Score: 108
Period size: 45 Copynumber: 2.4 Consensus size: 43
52850546 GGAATGTATA
* *
52850556 GAAATAGAGAAATGGAAAACATTTAGAAATGATTATGGTTTTCTTC
1 GAAAT-GAGAAATGG-AAACATTTAGAAATGAATATGGGTTTC-TC
* *
52850602 GAAATGGAGAAATGGAATCATTT-GAAAATGAATGTGGGTTTCTC
1 GAAAT-GAGAAATGGAAACATTTAG-AAATGAATATGGGTTTCTC
*
52850646 AAAATG-GAAATGGAAA
1 GAAATGAGAAATGGAAA
52850662 TGAAAAATGA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 9 0.17
43 1 0.02
44 7 0.13
45 21 0.40
46 14 0.27
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.28
Consensus pattern (43 bp):
GAAATGAGAAATGGAAACATTTAGAAATGAATATGGGTTTCTC
Found at i:52854923 original size:67 final size:67
Alignment explanation
Indices: 52854780--52855095 Score: 316
Period size: 67 Copynumber: 4.7 Consensus size: 67
52854770 GATTGTTTCG
* * * * **
52854780 CTCTCTATGTTGTCATA-CTGGAGCTATGGTCTTACACATTATACCCCATGCTTAATATCTTGGT
1 CTCTCTATGTTGCCATAGCT-GAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCCTGAC
**
52854844 GGA
65 AAA
* * * * * * *
52854847 CTATTTATGTTTCCATAGCTGAGCTATGATCTTACATATTATACCTCATGTTTAATGTCCCGACA
1 CTCTCTATGTTGCCATAGCTGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCCTGACA
*
52854912 GA
66 AA
* *** *
52854914 CTCTCTATGTTGCCATAGCCGAGC-ACAATCTTACACATTATACCCCATGTTTAATG-CCTTAGC
1 CTCTCTATGTTGCCATAGCTGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCCTGA-C
52854977 AAA
65 AAA
* * * * *
52854980 CTCTCTATGTTGCCATAGTTGAGATGTGGTCTTACACATTAAACCCCATGTTTAATGTTCTAGA-
1 CTCTCTATGTTGCCATAGCTGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCCT-GAC
52855044 AAA
65 AAA
* **
52855047 CTCTCTATGTTGCCATAACCAAGCTATGGTCTTACACATTATACCCCAT
1 CTCTCTATGTTGCCATAGCTGAGCTATGGTCTTACACATTATACCCCAT
52855096 TATAACCCAT
Statistics
Matches: 202, Mismatches: 42, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
65 3 0.01
66 52 0.26
67 142 0.70
68 4 0.02
69 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (67 bp):
CTCTCTATGTTGCCATAGCTGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCCTGACA
AA
Found at i:52855050 original size:133 final size:134
Alignment explanation
Indices: 52854809--52855095 Score: 326
Period size: 133 Copynumber: 2.1 Consensus size: 134
52854799 GGAGCTATGG
* * *** * * *
52854809 TCTTACACATTATACCCCATGCTTAATATCTTGGTGGACTATTTATGTTTCCATAGCTGAGCTAT
1 TCTTACACATTATACCCCATGCTTAATACCTTAGCAAACTATCTATGTTGCCATAGCTGAGATAT
* * * * * * *
52854874 GATCTTACATATTATACCTCATGTTTAATGTCCCGACAGACTCTCTATGTTGCCATAGCCGAGC-
66 GATCTTACACATTAAACCCCATGTTTAATGTCCAGACAAACTCTCTATGTTGCCATAACCAAGCT
52854938 ACAA
131 ACAA
* * * * *
52854942 TCTTACACATTATACCCCATGTTTAATGCCTTAGCAAACTCTCTATGTTGCCATAGTTGAGATGT
1 TCTTACACATTATACCCCATGCTTAATACCTTAGCAAACTATCTATGTTGCCATAGCTGAGATAT
* *
52855007 GGTCTTACACATTAAACCCCATGTTTAATGTTCTAGA-AAACTCTCTATGTTGCCATAACCAAGC
66 GATCTTACACATTAAACCCCATGTTTAATG-TCCAGACAAACTCTCTATGTTGCCATAACCAAGC
***
52855071 TATGG
130 TACAA
52855076 TCTTACACATTATACCCCAT
1 TCTTACACATTATACCCCAT
52855096 TATAACCCAT
Statistics
Matches: 127, Mismatches: 25, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
133 102 0.80
134 25 0.20
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (134 bp):
TCTTACACATTATACCCCATGCTTAATACCTTAGCAAACTATCTATGTTGCCATAGCTGAGATAT
GATCTTACACATTAAACCCCATGTTTAATGTCCAGACAAACTCTCTATGTTGCCATAACCAAGCT
ACAA
Found at i:52868586 original size:67 final size:67
Alignment explanation
Indices: 52868477--52869115 Score: 678
Period size: 67 Copynumber: 9.6 Consensus size: 67
52868467 CTGTATGCTG
* * * * * * * *
52868477 CCATAGCCGAGCTTTAGTCTTACACGTCATACCCCATGTTTAATGTCTTGACAGACCCTTTATGT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
52868542 TT
66 TT
* * * * *
52868544 CCATAG-CTAAGCTATGGTCTTACGCATTATATCTCATGTTTAATGTCTTGGC-GAACTCTTTAT
1 CCATAGTC-GAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAG-ACTCTCTAT
52868607 -TTT
64 GTTT
** ** * *
52868610 CCATAGTCGAGCTATGACCTTACACATTATACCTTATGTTTAATGTCCTGACAGACTCTCTATGT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
*
52868675 TA
66 TT
* * * *
52868677 CCATAGTCGAGATATGGTTTTACACATTATACCCTATGTTTAATGTCTTGG-AGAACTTTCTATG
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAG-ACTCTCTATG
52868741 TTGT
65 TT-T
* * * * * * * * * *
52868745 -CATAGTCAAGCTATGGTGTCACAGATTATACCCCATATTTAATATCCTGGAAAACTCTCTATAT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
*
52868809 TG
66 TT
* * * * * * * *
52868811 CAATTGTTGAGCTATGGTTTTACACATTATATCCCATGTTTAATTTTTTGGCAAACTCTCTATGT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
*
52868876 TG
66 TT
* * * *
52868878 CCATAGTCAAGCTATGGTCTTACACATTATGCCCCATGTTTAATGTCTTGGTAGACTCTTTATGT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
52868943 TT
66 TT
* * *
52868945 CCATAGTTGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCCTGGCGGACTCTCTATGT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
52869010 TGT
66 T-T
* * *
52869013 -CATAGTCGAGCTATGGTCTTACACATTATAACCCATGTTTAATGTCTTGGCGGAGTCTCTATGT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
*
52869077 TG
66 TT
**
52869079 CCATAGTCGAGCTATAATCTTACACATTATACCCCAT
1 CCATAGTCGAGCTATGGTCTTACACATTATACCCCAT
52869116 TATAGCCCAT
Statistics
Matches: 477, Mismatches: 84, Indels: 22
0.82 0.14 0.04
Matches are distributed among these distances:
66 57 0.12
67 418 0.88
68 2 0.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (67 bp):
CCATAGTCGAGCTATGGTCTTACACATTATACCCCATGTTTAATGTCTTGGCAGACTCTCTATGT
TT
Found at i:52880485 original size:13 final size:13
Alignment explanation
Indices: 52880467--52880496 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
52880457 AGCCCAAACT
52880467 CAATTACCCAACC
1 CAATTACCCAACC
52880480 CAATTACCCAACC
1 CAATTACCCAACC
52880493 CAAT
1 CAAT
52880497 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:52880651 original size:9 final size:9
Alignment explanation
Indices: 52880639--52880713 Score: 80
Period size: 9 Copynumber: 8.2 Consensus size: 9
52880629 ATAAAAAAAT
52880639 TTCGGGTAA
1 TTCGGGTAA
*
52880648 TTCGGGTATTT
1 TTCGGGTA--A
52880659 TTC-GGTAA
1 TTCGGGTAA
**
52880667 TTCGATTAA
1 TTCGGGTAA
*
52880676 TTCGGTTAA
1 TTCGGGTAA
*
52880685 TTCGGTTAA
1 TTCGGGTAA
52880694 TTCGGGTAA
1 TTCGGGTAA
52880703 TTCGGGTAA
1 TTCGGGTAA
52880712 TT
1 TT
52880714 TTAACCAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
8 3 0.05
9 47 0.82
10 4 0.07
11 3 0.05
ACGTcount: A:0.21, C:0.11, G:0.25, T:0.43
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:52880889 original size:12 final size:12
Alignment explanation
Indices: 52880872--52880896 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52880862 AGTAATTTCG
52880872 GGTCGGTTAACC
1 GGTCGGTTAACC
52880884 GGTCGGTTAACC
1 GGTCGGTTAACC
52880896 G
1 G
52880897 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:52882124 original size:28 final size:26
Alignment explanation
Indices: 52882080--52882131 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
52882070 ATATTATTAA
52882080 TATAATATATAAATGTTATAATAAGG
1 TATAATATATAAATGTTATAATAAGG
*
52882106 TATAATATATTATTATGTTATAATAA
1 TATAATATA-TA-AATGTTATAATAA
52882132 ACATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 9 0.39
27 2 0.09
28 12 0.52
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (26 bp):
TATAATATATAAATGTTATAATAAGG
Found at i:52882606 original size:41 final size:41
Alignment explanation
Indices: 52882551--52882753 Score: 217
Period size: 41 Copynumber: 4.9 Consensus size: 41
52882541 ACTTTATATT
*
52882551 AATAATATTCAGGCTTTATGCCTAGCAGGCTTTATGTCGGTG
1 AATAATA-TCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
* * * *
52882593 AATTATAACAGGCTTTATGTCTAGCAGGCTTTATGCCGGTT
1 AATAATATCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
* *
52882634 AATAATATCAGGCTTTATGCCTAGCACGCTTCATGCCGGTG
1 AATAATATCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
* ** * *
52882675 TACCATATCAGGCTTTATGCCTAGCAGGCTTTGTGCCGATG
1 AATAATATCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
* * ** * * * *
52882716 TATCATATTTGGATTTGTGTCTAGTAGGCTTTATGCCG
1 AATAATATCAGGCTTTATGCCTAGCAGGCTTTATGCCG
52882754 ATATGGTATC
Statistics
Matches: 135, Mismatches: 26, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
41 129 0.96
42 6 0.04
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
AATAATATCAGGCTTTATGCCTAGCAGGCTTTATGCCGGTG
Done.