Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 130 of 433
Found at i:40023453 original size:62 final size:62
Alignment explanation
Indices: 40023382--40023507 Score: 252
Period size: 62 Copynumber: 2.0 Consensus size: 62
40023372 GGATATGAAA
40023382 ACCCTGAACCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAGCCAAGTGTTGAACTTGAATTT
1 ACCCTGAACCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAGCCAAGTGTTGAACTTGAATTT
40023444 ACCCTGAACCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAGCCAAGTGTTGAACTTGAATTT
1 ACCCTGAACCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAGCCAAGTGTTGAACTTGAATTT
40023506 AC
1 AC
40023508 AACTCCCATG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 64 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (62 bp):
ACCCTGAACCAAGGGTTGAGCCAGAAGAAGAACCAGTCAAGCCAAGTGTTGAACTTGAATTT
Found at i:40025549 original size:94 final size:94
Alignment explanation
Indices: 40025402--40025621 Score: 282
Period size: 94 Copynumber: 2.3 Consensus size: 94
40025392 TATGTGTGCT
*
40025402 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGCATGAGAGCCAGTGTAAGACATGTCTAGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGCACGAGAGCCAGTGTAAGACATGTCTAGG
** **
40025467 ACATGCATCGGCCTCGTGATATTTAAGCC
66 ACATGCATCGGCCTCGCAATATACAAGCC
* * * * *
40025496 AGTGGAAGACATGTCTGGGACATGCATC-GGCATTGAG-ACGAGAGCTAGTGTAAGACATGTCTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCA--CAGCACGAGAGCCAGTGTAAGACATGTCTA
* *
40025559 GGACATGGATCGGCCTCGCAATATACAAGCT
64 GGACATGCATCGGCCTCGCAATATACAAGCC
*
40025590 AGTGTAAGACCTGTCTGGGACATGGCATCAGC
1 AGTGTAAGACATGTCTGGGACAT-GCATCAGC
40025622 TTGTTGTGTG
Statistics
Matches: 107, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
93 3 0.03
94 96 0.90
95 7 0.07
96 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAGCACGAGAGCCAGTGTAAGACATGTCTAGG
ACATGCATCGGCCTCGCAATATACAAGCC
Found at i:40025571 original size:46 final size:46
Alignment explanation
Indices: 40025402--40025756 Score: 204
Period size: 46 Copynumber: 7.5 Consensus size: 46
40025392 TATGTGTGCT
* *
40025402 AGTGTAAGACATGTCTGGGACATGCATCAGCCA--CAGCATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GGCATTGAG-ATGAGAGCC
* * * *
40025448 AGTGTAAGACATGTCTAGGACATGCATCGGCCTCGTGATATTTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCAT--TGAGA-TGAGAGCC
* * *
40025496 AGTGGAAGACATGTCTGGGACATGCATCGGCATTGAGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAGAGCC
* * * * * * *
40025542 AGTGTAAGACATGTCTCGGACATGGATCGGCCTCGCA-ATATACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATTG-AGAT-GA-GAGCC
* * * * * *
40025590 AGTGTAAGACCTGTCTGGGACATGGCATCAGC-TT--GTTGTGTGTC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCATTGAGATGAGAGCC
* * * * *
40025634 AGTGTAAGAC-CGATCTGGGACATGGCATTGACATCGATAGATGAGAGCT
1 AGTGTAAGACATG-TCTGGGACAT-GCATCGGCATTG--AGATGAGAGCC
* * * * * *
40025683 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGCTATATGAAAACC
1 AGTGTAAGACATGTCTGGGACAT-GCATCGGCATTG--AGATGAGAGCC
40025732 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
40025757 GAGTCGGTAT
Statistics
Matches: 237, Mismatches: 53, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
43 1 0.00
44 27 0.11
45 4 0.02
46 66 0.28
47 2 0.01
48 61 0.26
49 62 0.26
50 14 0.06
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGATGAGAGCC
Found at i:40025700 original size:49 final size:49
Alignment explanation
Indices: 40025439--40025757 Score: 218
Period size: 48 Copynumber: 6.7 Consensus size: 49
40025429 CAGCCACAGC
* * * *
40025439 ATGAGAGCCAGTGTAAGACATGTCTAGGACAT-GCATCGGCCTCGTGATA-
1 ATGAGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATC--GATAG
* * * * * *
40025488 TTTA-AGCCAGTGGAAGACATGTCTGGGACAT-GCATCGGCATTG--AG
1 ATGAGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAG
* * * * *
40025533 ACGAGAGCTAGTGTAAGACATGTCTCGGACATGG-ATCGGCCTCGCA-AT
1 ATGAGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCG-ATAG
* * * *
40025581 AT-ACAAGCTAGTGTAAGACCTGTCTGGGACATGGCATCAGC-TTG-TTG
1 ATGA-GAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAG
* * * *
40025628 -TGTG-TC-AGTGTAAGACC-GATCTGGGACATGGCATTGACATCGATAG
1 ATGAGAGCTAGTGTAAGACCTG-TCTGGGACATGGCATCGGCATCGATAG
* * *
40025674 ATGAGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGCTAT
1 ATGAGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAG
* * *
40025723 ATGAAAACCAGTGTAAGACCATGTCTGGGACATGG
1 ATGAGAGCTAGTGTAAGACC-TGTCTGGGACATGG
40025758 AGTCGGTATC
Statistics
Matches: 212, Mismatches: 41, Indels: 33
0.74 0.14 0.12
Matches are distributed among these distances:
43 1 0.00
44 28 0.13
45 4 0.02
46 36 0.17
47 5 0.02
48 66 0.31
49 57 0.27
50 15 0.07
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (49 bp):
ATGAGAGCTAGTGTAAGACCTGTCTGGGACATGGCATCGGCATCGATAG
Found at i:40030596 original size:36 final size:36
Alignment explanation
Indices: 40030556--40030627 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
40030546 TGCCAAACCT
40030556 GTAGGGTATACTGACTTATGACACACAGCCAAGTCA
1 GTAGGGTATACTGACTTATGACACACAGCCAAGTCA
**
40030592 GTAGGGTATACTGACTTATGACACATGGCCAAGTCA
1 GTAGGGTATACTGACTTATGACACACAGCCAAGTCA
40030628 CACACCCGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (36 bp):
GTAGGGTATACTGACTTATGACACACAGCCAAGTCA
Found at i:40031643 original size:41 final size:41
Alignment explanation
Indices: 40031536--40031647 Score: 111
Period size: 41 Copynumber: 2.7 Consensus size: 41
40031526 TCGGTACACT
*
40031536 ACTAAGTGCCAATACATAGCCGAAGCTATTATAATTTTGCAC
1 ACTAAGTGCC-ATACATAGCCGAAGCTATTATAATCTTGCAC
** ** **
40031578 ACTAACCGCC-TCACATAGTGGAAGCTATCT-TGGTCTTGCAC
1 ACTAAGTGCCAT-ACATAGCCGAAGCTAT-TATAATCTTGCAC
*
40031619 ACTAAGTGCCATATATAGCCGAAGCTATT
1 ACTAAGTGCCATACATAGCCGAAGCTATT
40031648 CCGAATCGTA
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
40 2 0.04
41 43 0.78
42 10 0.18
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (41 bp):
ACTAAGTGCCATACATAGCCGAAGCTATTATAATCTTGCAC
Found at i:40035640 original size:42 final size:43
Alignment explanation
Indices: 40035474--40035645 Score: 136
Period size: 43 Copynumber: 4.1 Consensus size: 43
40035464 ACATATCGTA
* * * * *
40035474 CAATGCTAATGTCCCAGACGTTGTCTTACATGTAATCATATCT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT
* * * * * * * * *
40035517 CGATGCCACTGTCCCAAATAGGGTCTTACACG-AAACAAAAAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT
* * * *
40035559 -GATGTCAAAGTCCTAGACATGGTCTTACATGTAATCACATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT
*
40035601 CAATGCCAATGTCCCAGA-GTGGTCTTACATG-AATACACATAT
1 CAATGCCAATGTCCCAGACATGGTCTTACATGTAAT-CACATAT
40035643 CAA
1 CAA
40035646 AAATCCTATG
Statistics
Matches: 97, Mismatches: 29, Indels: 7
0.73 0.22 0.05
Matches are distributed among these distances:
41 26 0.27
42 35 0.36
43 36 0.37
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (43 bp):
CAATGCCAATGTCCCAGACATGGTCTTACATGTAATCACATAT
Found at i:40039611 original size:28 final size:28
Alignment explanation
Indices: 40039579--40039643 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
40039569 ATTTACTAGA
*
40039579 ATACCCCTATGTATGCAAAATTACCATT
1 ATACCCCTATGTATGCAAAATGACCATT
* * *
40039607 ATACCTCTATGTATGCTAAATGACCTTT
1 ATACCCCTATGTATGCAAAATGACCATT
40039635 ATACCCCTA
1 ATACCCCTA
40039644 GGGTTAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (28 bp):
ATACCCCTATGTATGCAAAATGACCATT
Found at i:40039850 original size:29 final size:28
Alignment explanation
Indices: 40039749--40039839 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
40039739 AGGAAGCGTC
40039749 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAATTATCTGTT
*
40039777 CTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCACTGCCACAAATTATCTGTT
*
40039805 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAATTATCTGT-T
40039834 CTGGTG
1 CTGGTG
40039840 ACTCTGTCAC
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.32
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAATTATCTGTT
Found at i:40039864 original size:56 final size:55
Alignment explanation
Indices: 40039749--40039864 Score: 137
Period size: 56 Copynumber: 2.1 Consensus size: 55
40039739 AGGAAGCGTC
* *
40039749 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACAAATTATCTGTT
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCAC-AATTATCTGTT
* * *
40039805 CTGGTGGC-ACTGCCACAAAATATCTGTATCTGGTGACTCTGTCAC-ATTTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACAATTATCTGT-T
40039861 CTGG
1 CTGG
40039865 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
55 9 0.17
56 29 0.56
57 14 0.27
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (55 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACAATTATCTGTT
Found at i:40040332 original size:18 final size:18
Alignment explanation
Indices: 40040293--40040333 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
40040283 TAATAAGGCC
* *
40040293 TTTTAATTATTTTTATGG
1 TTTTAATTACTTTTATGA
*
40040311 TTTTAATTACTTTTATTA
1 TTTTAATTACTTTTATGA
40040329 TTTTA
1 TTTTA
40040334 TTTTACTATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTAATTACTTTTATGA
Found at i:40041838 original size:93 final size:93
Alignment explanation
Indices: 40041726--40041897 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40041716 GCCCATAAGT
* *
40041726 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40041791 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40041819 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40041884 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
40041898 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40041893 original size:46 final size:46
Alignment explanation
Indices: 40041718--40041893 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40041708 TGTAACCCGC
* * *
40041718 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
40041764 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
40041814 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
40041857 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40041894 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:40044322 original size:30 final size:30
Alignment explanation
Indices: 40044278--40044366 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
40044268 CAAAGATAAC
40044278 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
40044307 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
40044337 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
40044367 CGATACTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:40044326 original size:15 final size:15
Alignment explanation
Indices: 40044278--40044357 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
40044268 CAAAGATAAC
*
40044278 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
40044292 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
40044307 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
40044322 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
40044337 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
40044352 AAGAAA
1 AAGAAA
40044358 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:40044366 original size:15 final size:15
Alignment explanation
Indices: 40044289--40044366 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
40044279 AGAAAACCGA
40044289 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
40044304 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
40044318 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
40044333 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
40044349 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
40044364 ATA
1 ATA
40044367 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:40047428 original size:93 final size:93
Alignment explanation
Indices: 40047316--40047487 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40047306 GCCCATAAGT
* *
40047316 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40047381 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40047409 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40047474 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
40047488 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40047483 original size:46 final size:46
Alignment explanation
Indices: 40047308--40047483 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
40047298 TGTAACCCGC
* * *
40047308 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
40047354 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
40047404 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
40047447 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40047484 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:40056413 original size:40 final size:40
Alignment explanation
Indices: 40056351--40056648 Score: 449
Period size: 40 Copynumber: 7.5 Consensus size: 40
40056341 AAGCCAAGTA
* * ***
40056351 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTTGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
40056390 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40056430 CCTTCGGGACTTAGCCCGGATATAGTAACTCGGACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40056470 CCTTCGGGACTTAGCCCGGATATAGTAACTCGGACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40056510 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40056550 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
40056590 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40056630 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
40056649 TTATCATCCA
Statistics
Matches: 243, Mismatches: 13, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
39 13 0.05
40 230 0.95
ACGTcount: A:0.26, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40057931 original size:21 final size:20
Alignment explanation
Indices: 40057905--40057946 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
40057895 ACATGAGAGC
*
40057905 CTTTCTCTTTTTTTTCTTTTT
1 CTTTCTCTTTCTTTT-TTTTT
40057926 CTTTCTCTTTCTTTTTTTTT
1 CTTTCTCTTTCTTTTTTTTT
40057946 C
1 C
40057947 ATCATCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (20 bp):
CTTTCTCTTTCTTTTTTTTT
Found at i:40068817 original size:28 final size:28
Alignment explanation
Indices: 40068752--40068852 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
40068742 ATAGTGAATC
*
40068752 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
40068781 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40068809 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
40068839 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40068853 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40076772 original size:28 final size:28
Alignment explanation
Indices: 40076707--40076807 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
40076697 ATAGTGAATC
*
40076707 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
40076736 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
40076764 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
40076794 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40076808 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:40101630 original size:32 final size:33
Alignment explanation
Indices: 40101588--40101680 Score: 100
Period size: 32 Copynumber: 2.8 Consensus size: 33
40101578 CAAGCCCATC
*
40101588 GGGCCTAAGCCC-ATTCAGATAACAGTGATACT
1 GGGCCTAAGCCCTATTCAGATAACAGTGAAACT
* * * *
40101620 GGGCCAAAGCCCTTTTCAGATTACA-TTAAACT
1 GGGCCTAAGCCCTATTCAGATAACAGTGAAACT
*
40101652 GGGCCTTAGCCCCTTATTCAGATAACAGT
1 GGGCCTAAG-CCC-TATTCAGATAACAGT
40101681 ATGGCCCAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
32 23 0.48
33 13 0.27
34 11 0.23
35 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (33 bp):
GGGCCTAAGCCCTATTCAGATAACAGTGAAACT
Found at i:40102020 original size:26 final size:26
Alignment explanation
Indices: 40101991--40102043 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
40101981 TCCAACATGC
*
40101991 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGAT-AATTTATCTCCTAGGGGT
* *
40102017 ATTTCGATACTTTATCTCCTAGGGGT
1 ATTTAGATAATTTATCTCCTAGGGGT
40102043 A
1 A
40102044 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGATAATTTATCTCCTAGGGGT
Found at i:40103335 original size:24 final size:25
Alignment explanation
Indices: 40103290--40103349 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
40103280 TTGGCCGGCC
40103290 AACTCCTACT-CCTTGATCAGCTCCT
1 AACTCCT-CTCCCTTGATCAGCTCCT
*
40103315 AACTCCTCTCCCTT-ATTAGCTCCT
1 AACTCCTCTCCCTTGATCAGCTCCT
* *
40103339 AAATCTTCTCC
1 AACTCCTCTCC
40103350 TGACCGCCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 20 0.65
25 11 0.35
ACGTcount: A:0.20, C:0.40, G:0.05, T:0.35
Consensus pattern (25 bp):
AACTCCTCTCCCTTGATCAGCTCCT
Found at i:40109918 original size:26 final size:26
Alignment explanation
Indices: 40109889--40109941 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
40109879 TCCAACATGC
40109889 ATTTAGGTCAATTTA-CTCCTAGGGGT
1 ATTTAGGT-AATTTATCTCCTAGGGGT
* *
40109915 ATTTCGGTACTTTATCTCCTAGGGGT
1 ATTTAGGTAATTTATCTCCTAGGGGT
40109941 A
1 A
40109942 AAACTATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (26 bp):
ATTTAGGTAATTTATCTCCTAGGGGT
Found at i:40120231 original size:26 final size:26
Alignment explanation
Indices: 40120202--40120254 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
40120192 AATAACATCA
40120202 AGATGTTCTTCATTGTAATCATCCAG
1 AGATGTTCTTCATTGTAATCATCCAG
40120228 AGATGTTCTTCATTGTAATCATCCAG
1 AGATGTTCTTCATTGTAATCATCCAG
40120254 A
1 A
40120255 CCTTCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (26 bp):
AGATGTTCTTCATTGTAATCATCCAG
Found at i:40131029 original size:15 final size:15
Alignment explanation
Indices: 40131008--40131045 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
40130998 GTAAATTCTA
40131008 TTTTATTTTTTTA-T
1 TTTTATTTTTTTACT
*
40131022 TATTTATTATTTTACT
1 T-TTTATTTTTTTACT
40131038 TTTTATTT
1 TTTTATTT
40131046 ATCTTGGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 17 0.85
16 2 0.10
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTTTTACT
Found at i:40134049 original size:22 final size:21
Alignment explanation
Indices: 40134021--40134072 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
40134011 AACAGAAAAT
40134021 ACCATAACAAAAATGAACTCAA
1 ACCATAACAAAAAT-AACTCAA
* *
40134043 ACCATAAGCAAACATAACTGAA
1 ACCATAA-CAAAAATAACTCAA
40134065 ACCA-AACA
1 ACCATAACA
40134073 TGGAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 2 0.07
21 2 0.07
22 17 0.63
23 6 0.22
ACGTcount: A:0.58, C:0.25, G:0.06, T:0.12
Consensus pattern (21 bp):
ACCATAACAAAAATAACTCAA
Found at i:40136428 original size:29 final size:27
Alignment explanation
Indices: 40136337--40136448 Score: 82
Period size: 29 Copynumber: 4.0 Consensus size: 27
40136327 TACATACATG
* *
40136337 CATATAGCCCACTAGGCCCAATCTTATT
1 CATATGGCCCACTAGGCCCAAT-TCATT
* * *
40136365 CAAATGGCCTATCT-GGCCCAGTTCATATT
1 CATATGGCCCA-CTAGGCCCAATTC--ATT
* *
40136394 CTTATGGCCTACTAGGCCCAATTCACCTT
1 CATATGGCCCACTAGGCCCAATTCA--TT
* *
40136423 CATATGGCCCATTAGGCCCAAATCAT
1 CATATGGCCCACTAGGCCCAATTCAT
40136449 ATTATACTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
27 3 0.05
28 17 0.26
29 46 0.70
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (27 bp):
CATATGGCCCACTAGGCCCAATTCATT
Found at i:40137964 original size:16 final size:16
Alignment explanation
Indices: 40137943--40137974 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
40137933 AAGTTCGAGA
40137943 TTTCGAGAATTTTAGG
1 TTTCGAGAATTTTAGG
*
40137959 TTTCGAGATTTTTAGG
1 TTTCGAGAATTTTAGG
40137975 GCATTACAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.22, C:0.06, G:0.25, T:0.47
Consensus pattern (16 bp):
TTTCGAGAATTTTAGG
Found at i:40143061 original size:18 final size:18
Alignment explanation
Indices: 40143021--40143063 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40143011 ATGTTTTAGA
*
40143021 GAAAACTGTGTTTTCATC
1 GAAAACCGTGTTTTCATC
* *
40143039 AAAAACCGTGTTTTCATT
1 GAAAACCGTGTTTTCATC
40143057 GAAAACC
1 GAAAACC
40143064 TTTCTTAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (18 bp):
GAAAACCGTGTTTTCATC
Found at i:40144180 original size:29 final size:29
Alignment explanation
Indices: 40144099--40144213 Score: 90
Period size: 29 Copynumber: 4.0 Consensus size: 29
40144089 TACATACATG
* * *
40144099 CATATAGCCCACTAGGCCCAA-TCTTATT
1 CATATGGCCCACTAGACCCAATTCATATT
* * *
40144127 CAAATGGCCCATCT-GGCCCAGTTCATATT
1 CATATGGCCCA-CTAGACCCAATTCATATT
* * **
40144156 CTTATGGCCCACTAGACCTAATTCACCTT
1 CATATGGCCCACTAGACCCAATTCATATT
* * *
40144185 CATATGGCCCATTAGGCCCAAATCATATT
1 CATATGGCCCACTAGACCCAATTCATATT
40144214 ATACTCATGC
Statistics
Matches: 66, Mismatches: 18, Indels: 5
0.74 0.20 0.06
Matches are distributed among these distances:
28 17 0.26
29 49 0.74
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (29 bp):
CATATGGCCCACTAGACCCAATTCATATT
Found at i:40144322 original size:19 final size:19
Alignment explanation
Indices: 40144295--40144332 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40144285 TAGCCTATTA
40144295 GGCCAATTTAGCCC-ATTCT
1 GGCCAATTT-GCCCAATTCT
*
40144314 GGCCCATTTGCCCAATTCT
1 GGCCAATTTGCCCAATTCT
40144333 CAACCTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.18, C:0.34, G:0.16, T:0.32
Consensus pattern (19 bp):
GGCCAATTTGCCCAATTCT
Found at i:40146637 original size:14 final size:15
Alignment explanation
Indices: 40146620--40146648 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
40146610 GCACAAAAAT
40146620 TTCACACAT-ACAAA
1 TTCACACATAACAAA
40146634 TTCACACATAACAAA
1 TTCACACATAACAAA
40146649 CACAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
TTCACACATAACAAA
Found at i:40154529 original size:24 final size:24
Alignment explanation
Indices: 40154497--40154547 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
40154487 AGAAATTACA
40154497 TTAGTTTGTTTAAAAACCTAGAAG
1 TTAGTTTGTTTAAAAACCTAGAAG
40154521 TTAGTTTGTTTAAAAACCTAGAAG
1 TTAGTTTGTTTAAAAACCTAGAAG
40154545 TTA
1 TTA
40154548 AATCCTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (24 bp):
TTAGTTTGTTTAAAAACCTAGAAG
Found at i:40158199 original size:13 final size:15
Alignment explanation
Indices: 40158171--40158203 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
40158161 TTTATCCAAT
40158171 TTTTATGTGATTAAA
1 TTTTATGTGATTAAA
40158186 TTTTAT-TG-TTAAA
1 TTTTATGTGATTAAA
40158199 TTTTA
1 TTTTA
40158204 AATTTGATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (15 bp):
TTTTATGTGATTAAA
Found at i:40161312 original size:6 final size:7
Alignment explanation
Indices: 40161295--40161319 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40161285 TAAAATCTAA
40161295 AAAAAAT
1 AAAAAAT
40161302 AAAAAAT
1 AAAAAAT
40161309 AAAAAAT
1 AAAAAAT
40161316 AAAA
1 AAAA
40161320 TAATTTGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:40164153 original size:21 final size:22
Alignment explanation
Indices: 40164123--40164166 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40164113 AAAAATTCAA
*
40164123 TAAATAAAAATTAT-TAAATAT
1 TAAATAAAAATAATATAAATAT
*
40164144 TAAATTAAAATAATATAAATAT
1 TAAATAAAAATAATATAAATAT
40164166 T
1 T
40164167 TTTAAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATAAAAATAATATAAATAT
Found at i:40164172 original size:32 final size:33
Alignment explanation
Indices: 40164121--40164190 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 33
40164111 ATAAAAATTC
*
40164121 AATAAATAAAAATTATTAAATA-TT-AAATTAA
1 AATAAATAAAAATTATTAAAAATTTAAAATTAA
* *
40164152 AATAATATAAATATTTTTAAAAATTTAAAATTAA
1 AATAA-ATAAAAATTATTAAAAATTTAAAATTAA
*
40164186 TATAA
1 AATAA
40164191 GCGGGCTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 5 0.16
32 14 0.44
33 2 0.06
34 11 0.34
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (33 bp):
AATAAATAAAAATTATTAAAAATTTAAAATTAA
Found at i:40169396 original size:24 final size:24
Alignment explanation
Indices: 40169369--40169414 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40169359 TCAATGAATG
*
40169369 GATTATGGAGAAAATCAAGGAGAA
1 GATTAGGGAGAAAATCAAGGAGAA
* *
40169393 GATTGGGGAGAAAATCATGGAG
1 GATTAGGGAGAAAATCAAGGAG
40169415 GAATTTTAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.04, G:0.35, T:0.17
Consensus pattern (24 bp):
GATTAGGGAGAAAATCAAGGAGAA
Found at i:40170991 original size:27 final size:27
Alignment explanation
Indices: 40170961--40171027 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
40170951 GACCTCAGTT
**
40170961 TGTAAAATTACTAAAATACCGTTGTAG
1 TGTAAAATTACTAAAATACCCCTGTAG
*
40170988 TGTAAAATTACCAAAATACCCCTGTAG
1 TGTAAAATTACTAAAATACCCCTGTAG
* *
40171015 GGTAAAATGACTA
1 TGTAAAATTACTA
40171028 TTTTGCCATT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (27 bp):
TGTAAAATTACTAAAATACCCCTGTAG
Found at i:40171463 original size:27 final size:26
Alignment explanation
Indices: 40171385--40171463 Score: 68
Period size: 27 Copynumber: 2.9 Consensus size: 26
40171375 GCTTTGTGAA
*
40171385 GATCATATTTACCAGTGGTTATGTGTC
1 GATCATATTTACCA-TGGCTATGTGTC
* ** * *
40171412 TATCATATTTATTGATGACTCTGTGTC
1 GATCATATTTA-CCATGGCTATGTGTC
*
40171439 GATCATATTTACCCATGGCTGTGTG
1 GATCATATTTA-CCATGGCTATGTG
40171464 CCAATTATAT
Statistics
Matches: 39, Mismatches: 12, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
27 38 0.97
28 1 0.03
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (26 bp):
GATCATATTTACCATGGCTATGTGTC
Found at i:40172878 original size:38 final size:36
Alignment explanation
Indices: 40172803--40172879 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 36
40172793 TTTCAAAAAT
*
40172803 AATATTATTTTAATAAATTTTAAATTAGATTAAATTA
1 AATATTATCTTAATAAATTTT-AATTAGATTAAATTA
40172840 AATACTTATCTTAATAATATTTT-ATTA-ATTTAATATTA
1 AATA-TTATCTTAATAA-ATTTTAATTAGA-TTAA-ATTA
40172878 AA
1 AA
40172880 GTGATTAAGT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
36 1 0.03
37 12 0.34
38 17 0.49
39 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (36 bp):
AATATTATCTTAATAAATTTTAATTAGATTAAATTA
Found at i:40177685 original size:23 final size:23
Alignment explanation
Indices: 40177655--40177700 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
40177645 AGAAGTTAAC
40177655 CAAGTGGATTTAACAACTACTGT
1 CAAGTGGATTTAACAACTACTGT
40177678 CAAGTGGATTTAACAACTACTGT
1 CAAGTGGATTTAACAACTACTGT
40177701 AATGATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (23 bp):
CAAGTGGATTTAACAACTACTGT
Found at i:40178282 original size:10 final size:10
Alignment explanation
Indices: 40178267--40178324 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
40178257 TAAAAAATTA
40178267 TATTTTTTAT
1 TATTTTTTAT
40178277 TATTTTTTAT
1 TATTTTTTAT
* *
40178287 TATATTGTTAC
1 TAT-TTTTTAT
*
40178298 TATTTCATTAT
1 TATTT-TTTAT
* *
40178309 TATTTATTAC
1 TATTTTTTAT
40178319 TATTTT
1 TATTTT
40178325 GTTGTTACTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
10 24 0.60
11 16 0.40
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (10 bp):
TATTTTTTAT
Found at i:40178310 original size:32 final size:34
Alignment explanation
Indices: 40178273--40178337 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
40178263 ATTATATTTT
40178273 TTATTATTT-TT-TATTATATTGTTACTATTTCA
1 TTATTATTTATTATATTATATTGTTACTATTTCA
* *
40178305 TTATTATTTATTACTATTTTGTTGTTACTATTT
1 TTATTATTTATTA-TATTATATTGTTACTATTT
40178338 GGATATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 9 0.32
33 2 0.07
35 17 0.61
ACGTcount: A:0.23, C:0.06, G:0.05, T:0.66
Consensus pattern (34 bp):
TTATTATTTATTATATTATATTGTTACTATTTCA
Found at i:40178318 original size:21 final size:22
Alignment explanation
Indices: 40178283--40178323 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
40178273 TTATTATTTT
*
40178283 TTATTATATTGTTACTATTTCA
1 TTATTATATTATTACTATTTCA
40178305 TTATTAT-TTATTACTATTT
1 TTATTATATTATTACTATTT
40178324 TGTTGTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTATATTATTACTATTTCA
Found at i:40179327 original size:29 final size:29
Alignment explanation
Indices: 40179271--40179327 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
40179261 ATTTGAACCA
*
40179271 TAAATAAAATTTCATGTATATAATTATAT
1 TAAATAAAATTTCATGTATATAAGTATAT
40179300 TAAATTAAAATTT-ATGTATCA-AAGTATA
1 TAAA-TAAAATTTCATGTAT-ATAAGTATA
40179328 CACTTGATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.49, C:0.04, G:0.05, T:0.42
Consensus pattern (29 bp):
TAAATAAAATTTCATGTATATAAGTATAT
Found at i:40182338 original size:25 final size:25
Alignment explanation
Indices: 40182304--40182352 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
40182294 CTATAGAAGT
40182304 ATGCTTCTTGCCTTTTCCTTTTGAG
1 ATGCTTCTTGCCTTTTCCTTTTGAG
40182329 ATGCTTCTTGCCTTTTCCTTTTGA
1 ATGCTTCTTGCCTTTTCCTTTTGA
40182353 TGGAGCTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.53
Consensus pattern (25 bp):
ATGCTTCTTGCCTTTTCCTTTTGAG
Found at i:40185405 original size:21 final size:20
Alignment explanation
Indices: 40185379--40185418 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
40185369 TTATTTTTAT
40185379 TTATATATAAGAAACATAAAA
1 TTATAT-TAAGAAACATAAAA
* *
40185400 TTATATTTAGAAATATAAA
1 TTATATTAAGAAACATAAA
40185419 CAACTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.35
Consensus pattern (20 bp):
TTATATTAAGAAACATAAAA
Found at i:40187095 original size:17 final size:16
Alignment explanation
Indices: 40187073--40187104 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
40187063 ATCCTCTCAA
40187073 TCTCAAAACTCATATCC
1 TCTCAAAACTC-TATCC
40187090 TCTCAAAACTCTATC
1 TCTCAAAACTCTATC
40187105 AAATTCTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (16 bp):
TCTCAAAACTCTATCC
Found at i:40189513 original size:42 final size:42
Alignment explanation
Indices: 40189464--40189623 Score: 167
Period size: 42 Copynumber: 3.6 Consensus size: 42
40189454 TTCATTTTCT
** * *
40189464 CGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 CGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
* * *
40189506 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
* *
40189548 CGATGCTATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATAT
1 CGATGCCATAGCCCAGCTATGGTCTTACAC---AT---AT-TCACATAA
*
40189597 CGATCCCATAGCCCAGCTATGGTCTTA
1 CGATGCCATAGCCCAGCTATGGTCTTA
40189624 GACGAATCAC
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 63 0.64
45 2 0.02
48 2 0.02
49 31 0.32
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (42 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAA
Found at i:40189700 original size:47 final size:46
Alignment explanation
Indices: 40189546--40189789 Score: 191
Period size: 47 Copynumber: 5.0 Consensus size: 46
40189536 ATATTCATAT
* * *
40189546 ACCGATGCTATAGCCCAGCTATGGTCTTACACGTAATCACATATCAC
1 ACCGATGCCATAGCCCAGATATGGTCTTATACGT-ATCACATATCAC
* * * * * *
40189593 ATATCGATCCCATAGCCCAGCTATGGTCTTAGACGAATCACATATCTC
1 --ACCGATGCCATAGCCCAGATATGGTCTTATACGTATCACATATCAC
* * * *
40189641 ACTGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCAC
1 ACCGATGCCATAGCCCAGATATGGTCTTATAC-GTATCACATATCAC
* * * *
40189688 ACCGATGCCATATCCCAGATATGGTTTTATACGAAAGCACATGATCAC
1 ACCGATGCCATAGCCCAGATATGGTCTTATACG-TATCACAT-ATCAC
* * *
40189736 ATCTCTCCGATGCCATAGCCCAGCTATGGTATTATACGGAAATCACATATCAC
1 A-----CCGATGCCATAGCCCAGATATGGTCTTATAC-G-TATCACATATCAC
40189789 A
1 A
40189790 TGTTGCCATG
Statistics
Matches: 162, Mismatches: 24, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
46 27 0.17
47 46 0.28
48 17 0.10
49 29 0.18
53 34 0.21
54 9 0.06
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (46 bp):
ACCGATGCCATAGCCCAGATATGGTCTTATACGTATCACATATCAC
Found at i:40189758 original size:53 final size:53
Alignment explanation
Indices: 40189629--40189790 Score: 158
Period size: 53 Copynumber: 3.1 Consensus size: 53
40189619 TCTTAGACGA
* * * * * *
40189629 ATCACATATCTCACTGATGCCATATCCCAGATATGGTCTTATACAG-TAGCATAT
1 ATCACATCTCTC-C-GATGCCATAGCCCAGATATGGTATTATACGGAAAGCACAT
* *
40189683 ATCACA-----CCGATGCCATATCCCAGATATGGTTTTATAC-GAAAGCACAT
1 ATCACATCTCTCCGATGCCATAGCCCAGATATGGTATTATACGGAAAGCACAT
* *
40189730 GATCACATCTCTCCGATGCCATAGCCCAGCTATGGTATTATACGGAAATCACAT
1 -ATCACATCTCTCCGATGCCATAGCCCAGATATGGTATTATACGGAAAGCACAT
40189784 ATCACAT
1 ATCACAT
40189791 GTTGCCATGG
Statistics
Matches: 93, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
46 1 0.01
47 34 0.37
48 7 0.08
49 1 0.01
53 35 0.38
54 15 0.16
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (53 bp):
ATCACATCTCTCCGATGCCATAGCCCAGATATGGTATTATACGGAAAGCACAT
Found at i:40195558 original size:46 final size:45
Alignment explanation
Indices: 40195456--40195671 Score: 188
Period size: 46 Copynumber: 4.7 Consensus size: 45
40195446 CATATCTGTA
* *
40195456 CCGATGCCATGTCCCAGACATGGTCTTACACTGAC-ACATCTCGTA-G
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTCATCTCG-AGG
* * *
40195502 CTGATGCATGTCCCAAACATGTCTTACACTGGCTTACGTCTCGAGG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGCTT-CATCTCGAGG
* * * *
40195548 CCGATGCATGTCCCAGACATGTCTTACACTGGCACTCGTCTCAATG
1 CCGATGCATGTCCCAGACATGTCTTACACTGGC-TTCATCTCGAGG
** * *
40195594 CC-ATTGCCATGTCTTAGACATGGTCTTACACTGGCTCTCATAAT-GTGG
1 CCGA-TG-CATGTCCCAGACAT-GTCTTACACTGGCT-TCAT-CTCGAGG
*
40195642 CCGATGCATGTCCTAGACATGTCTTACACT
1 CCGATGCATGTCCCAGACATGTCTTACACT
40195672 AGCTCACACA
Statistics
Matches: 141, Mismatches: 19, Indels: 20
0.78 0.11 0.11
Matches are distributed among these distances:
44 12 0.09
45 15 0.11
46 65 0.46
47 26 0.18
48 21 0.15
49 2 0.01
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.28
Consensus pattern (45 bp):
CCGATGCATGTCCCAGACATGTCTTACACTGGCTTCATCTCGAGG
Found at i:40202035 original size:29 final size:28
Alignment explanation
Indices: 40202001--40202103 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
40201991 TACTCAATCA
*
40202001 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
40202030 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
40202059 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
40202088 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
40202104 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:40206360 original size:29 final size:28
Alignment explanation
Indices: 40206323--40206442 Score: 134
Period size: 29 Copynumber: 4.2 Consensus size: 28
40206313 CATGATTGTG
40206323 AATGTGATTTGGGCCTCATGGGCCATATA
1 AATGTGATTTGGGCCT-ATGGGCCATATA
*
40206352 AATATGATTTGGGCCTGATGGGCCATATA
1 AATGTGATTTGGGCCT-ATGGGCCATATA
* ** **
40206381 CATGTGAAGTGGGCCTAATGAACCATATA
1 AATGTGATTTGGGCCT-ATGGGCCATATA
40206410 AATGTGA-TTGGGCCTAGTGGGCCATATA
1 AATGTGATTTGGGCCTA-TGGGCCATATA
*
40206438 CATGT
1 AATGT
40206443 ATGTGAGTTT
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
27 1 0.01
28 20 0.26
29 55 0.72
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (28 bp):
AATGTGATTTGGGCCTATGGGCCATATA
Found at i:40207901 original size:46 final size:46
Alignment explanation
Indices: 40207851--40208026 Score: 209
Period size: 46 Copynumber: 3.8 Consensus size: 46
40207841 TGGTTGAGCA
40207851 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40207897 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40207942 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
40207990 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40208027 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 61 0.55
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40208007 original size:93 final size:93
Alignment explanation
Indices: 40207848--40208019 Score: 310
Period size: 93 Copynumber: 1.8 Consensus size: 93
40207838 GGATGGTTGA
*
40207848 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
40207913 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40207941 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
40208005 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
40208020 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
92 2 0.03
93 74 0.97
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40214721 original size:69 final size:70
Alignment explanation
Indices: 40214590--40214721 Score: 221
Period size: 69 Copynumber: 1.9 Consensus size: 70
40214580 AGTTTATTAC
* * * *
40214590 TAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTAC
1 TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTAC
40214655 TTAGT
66 TTAGT
40214660 TAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
1 TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGT
40214722 GTTATGTGCT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
69 36 0.62
70 22 0.38
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (70 bp):
TAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTGTCCAAATTAGGACAAAATCATGGTAC
TTAGT
Found at i:40215596 original size:39 final size:39
Alignment explanation
Indices: 40215478--40215610 Score: 185
Period size: 39 Copynumber: 3.4 Consensus size: 39
40215468 ATATTTGATG
* *
40215478 TATATCCTGACTTAAGATCCGCAGGCTTCGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAAT
* * * *
40215517 TATATCCGGGCTTAAAGACTCGCAGGCTTCGTGCTAGAAT
1 TATATCCGGACTTAAGGTC-CGCAGGCTTCGTGCTGGAAT
*
40215557 TGTATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAAT
1 TATATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAAT
*
40215596 TATATCCGGGCTTAA
1 TATATCCGGACTTAA
40215611 ATGTAACACC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 46 0.57
40 34 0.43
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAAGGTCCGCAGGCTTCGTGCTGGAAT
Found at i:40216268 original size:18 final size:18
Alignment explanation
Indices: 40216235--40216286 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
40216225 GGCTTTAACC
40216235 CATTA-CAGAATAAGAAA
1 CATTATCAGAATAAGAAA
*
40216252 CATTATCAGAACT-AGAAT
1 CATTATCAGAA-TAAGAAA
* *
40216270 CATAATCAGAATCAGAA
1 CATTATCAGAATAAGAA
40216287 TTAGGTGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.20
18 23 0.77
19 1 0.03
ACGTcount: A:0.52, C:0.15, G:0.12, T:0.21
Consensus pattern (18 bp):
CATTATCAGAATAAGAAA
Found at i:40216304 original size:25 final size:25
Alignment explanation
Indices: 40216273--40216327 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
40216263 CTAGAATCAT
* *
40216273 AATCAGAATCAGAATTAGGTGACAG
1 AATCAGAATCAGAATCAGGTAACAG
*
40216298 AATCAGAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
40216323 AATCA
1 AATCA
40216328 AAAATCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.20
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTAACAG
Found at i:40216517 original size:27 final size:26
Alignment explanation
Indices: 40216475--40216576 Score: 105
Period size: 27 Copynumber: 3.8 Consensus size: 26
40216465 GCTCAGTTAT
* *
40216475 CAGATATTGTGATAGAGTCACCAGATA
1 CAGATATTGTGGTAGAGCCACCAGA-A
*
40216502 CAGATATTGTGGTAGAGCCACTAGAA
1 CAGATATTGTGGTAGAGCCACCAGAA
* *
40216528 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGTAGAGCCACCAG-AA
* * *
40216556 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGTAGAGCCAC
40216577 TTAACAGAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
26 7 0.11
27 50 0.77
28 8 0.12
ACGTcount: A:0.36, C:0.19, G:0.24, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGGTAGAGCCACCAGAA
Found at i:40216602 original size:54 final size:54
Alignment explanation
Indices: 40216493--40216596 Score: 131
Period size: 54 Copynumber: 2.0 Consensus size: 54
40216483 GTGATAGAGT
* * * * **
40216493 CACCAGATACAGATATTGTGGTAGAGCCACTAGAACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATAATGTGGCAAAGCCACTAGAACAGATATACGTGGCATAGC
*
40216547 CACCAGAAACAGATAATGTGGCAAAGCCACT-TAACAGA-ATACGTGGCATA
1 CACCAGAAACAGATAATGTGGCAAAGCCACTAGAACAGATATACGTGGCATA
40216597 AAGCCATGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
52 10 0.23
53 6 0.14
54 27 0.63
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (54 bp):
CACCAGAAACAGATAATGTGGCAAAGCCACTAGAACAGATATACGTGGCATAGC
Found at i:40216763 original size:22 final size:22
Alignment explanation
Indices: 40216735--40216799 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
40216725 GCAAATACGT
*
40216735 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
40216757 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
* *
40216779 TTGACACAAATCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
40216800 AAGGCTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:40217076 original size:16 final size:16
Alignment explanation
Indices: 40217055--40217085 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40217045 ATCCCAACCC
*
40217055 ATGCAACATGTCATGT
1 ATGCAAAATGTCATGT
40217071 ATGCAAAATGTCATG
1 ATGCAAAATGTCATG
40217086 CCTATATTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.29
Consensus pattern (16 bp):
ATGCAAAATGTCATGT
Found at i:40217283 original size:27 final size:27
Alignment explanation
Indices: 40217226--40217497 Score: 334
Period size: 27 Copynumber: 10.1 Consensus size: 27
40217216 GGGGCAAAAT
* * * *
40217226 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
40217252 GGTAATTCCACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40217279 AGTAATTCTACCATACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
40217306 AGTAATTCTACCCTACATGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40217333 GATAATTCTACCCTACAAGGGT-TTT-
1 GGTAATTCTACCCTACAGGGGTATTTC
40217358 GTGATAATTCTACCCTACAGGGGTATTTC
1 G-G-TAATTCTACCCTACAGGGGTATTTC
*
40217387 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40217414 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
40217441 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
40217468 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
40217495 GGT
1 GGT
40217498 CATTTTGTAA
Statistics
Matches: 216, Mismatches: 25, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
25 1 0.00
26 15 0.07
27 195 0.90
28 4 0.02
29 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.33
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:40217569 original size:27 final size:26
Alignment explanation
Indices: 40217539--40217879 Score: 342
Period size: 27 Copynumber: 12.7 Consensus size: 26
40217529 CTGTAAATCA
* * *
40217539 AGGGTACTTTGGTAATTTTACAAGTCG
1 AGGGTATTTTGGTAATTTTACAA-ACC
*** ** *
40217566 AGGGTATTTCAATAATTTTACAGGTCG
1 AGGGTATTTTGGTAATTTTACA-AACC
** * **
40217593 AGGGTATTTCAGTAATTTCACAAATT
1 AGGGTATTTTGGTAATTTTACAAACC
*
40217619 AGGGATATTTTGGTAATTTT-CAAACT
1 AGGG-TATTTTGGTAATTTTACAAACC
*
40217645 AGGGGTATTTTGATAATTTTACAAACC
1 A-GGGTATTTTGGTAATTTTACAAACC
40217672 AGGGGTATTTTGGTAATTTTACAAACC
1 A-GGGTATTTTGGTAATTTTACAAACC
* *
40217699 AGGGGTATTTTGGTAATTTTATAAACAA
1 A-GGGTATTTTGGTAATTTTACAAAC-C
*
40217727 AGGGTATTTTAGTAATTTTACAAACC
1 AGGGTATTTTGGTAATTTTACAAACC
* **
40217753 AGGGGTATTTTTGTAATTTTGTAAACC
1 A-GGGTATTTTGGTAATTTTACAAACC
40217780 AAGGGTATTTTGGTAATTTTACAAACC
1 -AGGGTATTTTGGTAATTTTACAAACC
* *
40217807 AGGAGTATTTTGGTGATTTTATAAACC
1 AGG-GTATTTTGGTAATTTTACAAACC
*
40217834 AAGGGTATTTTCGTAATTTTACAAACC
1 -AGGGTATTTTGGTAATTTTACAAACC
40217861 AGAGGTATTTTGGTAATTT
1 AG-GGTATTTTGGTAATTT
40217880 GGTAAACTAA
Statistics
Matches: 269, Mismatches: 35, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
26 30 0.11
27 234 0.87
28 5 0.02
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (26 bp):
AGGGTATTTTGGTAATTTTACAAACC
Found at i:40217886 original size:54 final size:54
Alignment explanation
Indices: 40217619--40217879 Score: 398
Period size: 54 Copynumber: 4.8 Consensus size: 54
40217609 TTCACAAATT
* * *
40217619 AGGGATATTTTGGTAATTTT-CAAACTAGGGGTATTTTGATAATTTTACAAACCA
1 AGGG-TATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
* *
40217673 GGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACAA
1 AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
* * *
40217727 AGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTTGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
* *
40217781 AGGGTATTTTGGTAATTTTACAAACCAGGAGTATTTTGGTGATTTTATAAACCA
1 AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
* *
40217835 AGGGTATTTTCGTAATTTTACAAACCAGAGGTATTTTGGTAATTT
1 AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTT
40217880 GGTAAACTAA
Statistics
Matches: 187, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
53 15 0.08
54 172 0.92
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (54 bp):
AGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCA
Found at i:40218784 original size:39 final size:39
Alignment explanation
Indices: 40218725--40218856 Score: 158
Period size: 39 Copynumber: 3.4 Consensus size: 39
40218715 TGTTACATTA
* * *
40218725 AAGACCCGCAGGCTTCGTGCTGGAATTGTATCCGGACTT
1 AAGATCCGCAGGCTTCGTGCTGGAACTATATCCGGACTT
*
40218764 AAGATCCGCAGGCTTCGTGCTGGTACTATATCCGGACTT
1 AAGATCCGCAGGCTTCGTGCTGGAACTATATCCGGACTT
* * * * *
40218803 AAGGTCCGCAGGCTTTGTACTGGTACTATATCCGGGCTT
1 AAGATCCGCAGGCTTCGTGCTGGAACTATATCCGGACTT
*
40218842 AA-AGTCCGTAGGCTT
1 AAGA-TCCGCAGGCTT
40218857 TGTGTTGGTG
Statistics
Matches: 82, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
39 82 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.28
Consensus pattern (39 bp):
AAGATCCGCAGGCTTCGTGCTGGAACTATATCCGGACTT
Found at i:40220510 original size:16 final size:16
Alignment explanation
Indices: 40220489--40220531 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
40220479 GTAGATCAGC
40220489 AAAAGCTGAAATACCG
1 AAAAGCTGAAATACCG
* *
40220505 AAAAGCCGAAATGCCG
1 AAAAGCTGAAATACCG
*
40220521 AAAAGTTGAAA
1 AAAAGCTGAAA
40220532 GTTTGGCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.21, T:0.12
Consensus pattern (16 bp):
AAAAGCTGAAATACCG
Found at i:40220796 original size:29 final size:29
Alignment explanation
Indices: 40220747--40220858 Score: 127
Period size: 29 Copynumber: 3.9 Consensus size: 29
40220737 CATGACTGTG
*
40220747 AATGTGATTTGGTCCTAATGGGCCATATA
1 AATGTGATTTGGGCCTAATGGGCCATATA
*
40220776 AATGTGATTTGGGCCTGATGGGCCATATA
1 AATGTGATTTGGGCCTAATGGGCCATATA
* * * * * *
40220805 CATGTAAATTGGGCTTAATGAGTCATATA
1 AATGTGATTTGGGCCTAATGGGCCATATA
* *
40220834 AATGTGA-TTCGGCCTAGTGGGCCAT
1 AATGTGATTTGGGCCTAATGGGCCAT
40220859 GTACAGGTAT
Statistics
Matches: 67, Mismatches: 16, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
28 13 0.19
29 54 0.81
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (29 bp):
AATGTGATTTGGGCCTAATGGGCCATATA
Found at i:40227609 original size:93 final size:93
Alignment explanation
Indices: 40227450--40227620 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
40227440 GGATGGTTGA
* *
40227450 GCATCCGAACTCGTTGAGTTGAGTCCTGAGTTCACTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCTGAGTTCACTATGGATGCGAACGCCCGAACTCGTTGAGT
40227515 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40227543 GCATCCGAACTCGTTGAGTTGAGTCC-GAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCTGAGTTCAC-TATGGATGCGAACGCCCGAACTCGTTGAG
40227607 TTGAGTCCGAGTTC
65 TTGAGTCCGAGTTC
40227621 ACTTAGGGGC
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 8 0.11
93 66 0.89
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCTGAGTTCACTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40227624 original size:46 final size:46
Alignment explanation
Indices: 40227454--40227625 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
40227444 GGTTGAGCAT
* *
40227454 CCGAACTCGTTGAGTTGAGTCCTGAGTTCAC-TATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCC-GAGTTCACTTATGGATGCGAACGC
* * *
40227500 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---GC
40227545 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
40227593 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40227626 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 9, Indels: 20
0.79 0.07 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 8 0.07
46 54 0.50
47 28 0.26
48 4 0.04
50 4 0.04
51 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:40235073 original size:46 final size:46
Alignment explanation
Indices: 40235023--40235195 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
40235013 TGGTTGAGCA
40235023 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40235069 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
40235114 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
40235162 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
40235196 GGGGCGGGTT
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 61 0.56
47 29 0.27
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40235179 original size:93 final size:93
Alignment explanation
Indices: 40235020--40235190 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40235010 GGATGGTTGA
* *
40235020 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40235085 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
40235113 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40235178 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
40235191 ACTTAGGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40255197 original size:40 final size:40
Alignment explanation
Indices: 40255123--40255344 Score: 358
Period size: 40 Copynumber: 5.6 Consensus size: 40
40255113 AACCCAAGTA
* * *
40255123 CCTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATA
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
40255162 CCTTCGGGTCTTAGCCCGGAAATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
* *
40255202 CCTTCGAGATTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40255242 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40255282 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40255322 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
40255345 CATTCGAATA
Statistics
Matches: 170, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
39 12 0.07
40 157 0.92
41 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:40257495 original size:23 final size:25
Alignment explanation
Indices: 40257469--40257515 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
40257459 TATCATTCAT
*
40257469 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
40257492 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
40257516 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:40257836 original size:46 final size:46
Alignment explanation
Indices: 40257776--40258036 Score: 306
Period size: 46 Copynumber: 5.9 Consensus size: 46
40257766 TTTGACGTGA
* * * * ** ** *
40257776 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATACCAGGT
** * *
40257822 TGCCATGGTATCTTTCAACCATGGTCTTATTC-TTTCATGCCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATACCAGGT
* *
40257867 TGCCATGGTATCTTTCAACTATGGTCTTACACATCTCATACCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATACCAGGT
*
40257913 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATACCAGGT
*
40257959 TGCCATGGTATCTTTCAACCATAGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATACCAGGT
40257997 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATA
40258037 TCAGAGAGCA
Statistics
Matches: 188, Mismatches: 19, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
38 32 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 39 0.21
46 108 0.57
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATACCAGGT
Found at i:40257885 original size:91 final size:87
Alignment explanation
Indices: 40257776--40258036 Score: 305
Period size: 91 Copynumber: 2.9 Consensus size: 87
40257766 TTTGACGTGA
* * * *
40257776 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTTTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACTATGGTCTTACACA----TT-TCAGGTTGCCATGGTATCTTTCAAC
** *
40257841 CATGGTCTTATTC-TTTCATGCCACGT
61 CATGGTCTTACACATTTCATACCACGT
40257867 TGCCATGGTATCTTTCAACTATGGTCTTACACATCTCATACCAGGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACTATGGTCTTACACAT-T--T--CAGGTTGCCATGGTATCTTTCAAC
* *
40257932 CATGGTCTTACACATTTCATATCAGGT
61 CATGGTCTTACACATTTCATACCACGT
* *
40257959 TGCCATGGTATCTTTCAACCATAGTCTTACACA---CAGGTTGCCATGGTATCTTTCAACCATGG
1 TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCAGGTTGCCATGGTATCTTTCAACCATGG
40258021 TCTTACACATTTCATA
66 TCTTACACATTTCATA
40258037 TCAGAGAGCA
Statistics
Matches: 153, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
84 45 0.29
87 1 0.01
88 1 0.01
89 1 0.01
91 64 0.42
92 41 0.27
ACGTcount: A:0.22, C:0.25, G:0.15, T:0.38
Consensus pattern (87 bp):
TGCCATGGTATCTTTCAACTATGGTCTTACACATTTCAGGTTGCCATGGTATCTTTCAACCATGG
TCTTACACATTTCATACCACGT
Found at i:40258005 original size:38 final size:38
Alignment explanation
Indices: 40257954--40258029 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
40257944 CATTTCATAT
40257954 CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
*
40257992 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
40258030 TTTCATATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATAGTCTTACACA
Found at i:40260176 original size:11 final size:11
Alignment explanation
Indices: 40260160--40260207 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
40260150 CTTTATATAC
40260160 TAATAAAATAA
1 TAATAAAATAA
40260171 TAATAAAATATA
1 TAATAAAATA-A
* * *
40260183 TTATTAAAGTAT
1 -TAATAAAATAA
40260195 TAATAAAATAA
1 TAATAAAATAA
40260206 TA
1 TA
40260208 TTTATCTAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
11 20 0.69
12 1 0.03
13 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:40260190 original size:24 final size:24
Alignment explanation
Indices: 40260154--40260209 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
40260144 TTCTTTCTTT
*
40260154 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* * *
40260178 ATATATTATTAAAGTATTAATAAA
1 ATATATTAATAAAATAATAATAAA
40260202 ATAATATT
1 AT-ATATT
40260210 TATCTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:40270389 original size:30 final size:30
Alignment explanation
Indices: 40270355--40270415 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40270345 TCCTTAACTC
40270355 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
40270385 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
40270415 A
1 A
40270416 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:40274151 original size:13 final size:13
Alignment explanation
Indices: 40274133--40274170 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
40274123 CTATGTCCCT
40274133 CACACGGTCGAGA
1 CACACGGTCGAGA
*
40274146 CACACGGCCGAGA
1 CACACGGTCGAGA
40274159 CACACGGTCGAG
1 CACACGGTCGAG
40274171 TCTTTGCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.29, C:0.34, G:0.32, T:0.05
Consensus pattern (13 bp):
CACACGGTCGAGA
Found at i:40275324 original size:42 final size:42
Alignment explanation
Indices: 40275274--40275380 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
40275264 ACATCGATGT
* * * **
40275274 CATATCCCATATATGGTCTTATACAAATTCTCATT-TTGACGC
1 CATATCCCAGATATGGTCTTACACAAAATC-CATTATCAACGC
* ** *
40275316 CATGTCCCAGACGTGGTCTTACACAAAATCCCTTATCAACGC
1 CATATCCCAGATATGGTCTTACACAAAATCCATTATCAACGC
40275358 CATATCCCAGATATGGTCTTACA
1 CATATCCCAGATATGGTCTTACA
40275381 TGATAACTCA
Statistics
Matches: 52, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 3 0.06
42 49 0.94
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.31
Consensus pattern (42 bp):
CATATCCCAGATATGGTCTTACACAAAATCCATTATCAACGC
Found at i:40278030 original size:41 final size:41
Alignment explanation
Indices: 40277973--40278055 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
40277963 TGGTAAAAGA
40277973 ATGATATATTTTAGGATATCAAATTTCCAAGAAAGAGTTGG
1 ATGATATATTTTAGGATATCAAATTTCCAAGAAAGAGTTGG
40278014 ATGATATATTTTAGGATATCAAATTTCCAAGAAAGAGTTGG
1 ATGATATATTTTAGGATATCAAATTTCCAAGAAAGAGTTGG
40278055 A
1 A
40278056 AATGGATAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (41 bp):
ATGATATATTTTAGGATATCAAATTTCCAAGAAAGAGTTGG
Found at i:40281081 original size:34 final size:34
Alignment explanation
Indices: 40281035--40281099 Score: 121
Period size: 34 Copynumber: 1.9 Consensus size: 34
40281025 TCAGAAGGGG
40281035 CTAATCTCCCAGTGACATTTAATCAAGCATTGCA
1 CTAATCTCCCAGTGACATTTAATCAAGCATTGCA
*
40281069 CTAATCTTCCAGTGACATTTAATCAAGCATT
1 CTAATCTCCCAGTGACATTTAATCAAGCATT
40281100 AATGGCCCAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (34 bp):
CTAATCTCCCAGTGACATTTAATCAAGCATTGCA
Found at i:40285657 original size:24 final size:24
Alignment explanation
Indices: 40285625--40285699 Score: 132
Period size: 24 Copynumber: 3.1 Consensus size: 24
40285615 TTTGATTCAA
*
40285625 TTCCAGAACTAAACATTAATTTAG
1 TTCCCGAACTAAACATTAATTTAG
40285649 TTCCCGAACTAAACATTAATTTAG
1 TTCCCGAACTAAACATTAATTTAG
*
40285673 TTCCCGAACTAAACATTAATTCAG
1 TTCCCGAACTAAACATTAATTTAG
40285697 TTC
1 TTC
40285700 AATTTATCAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.33
Consensus pattern (24 bp):
TTCCCGAACTAAACATTAATTTAG
Found at i:40286291 original size:19 final size:20
Alignment explanation
Indices: 40286245--40286297 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
40286235 TTTGTCTTTA
40286245 TATAATTAATATTTAATTAACC
1 TATAATT-A-ATTTAATTAACC
*
40286267 TA-AATTAATTTAATTAA-T
1 TATAATTAATTTAATTAACC
40286285 TATAATT-ATTTAA
1 TATAATTAATTTAA
40286298 CCTTAAGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
18 8 0.28
19 14 0.48
20 1 0.03
21 4 0.14
22 2 0.07
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (20 bp):
TATAATTAATTTAATTAACC
Found at i:40291833 original size:39 final size:39
Alignment explanation
Indices: 40291779--40292050 Score: 445
Period size: 39 Copynumber: 7.0 Consensus size: 39
40291769 AAGACACTGA
*
40291779 AAATGTATCTGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
40291818 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
40291857 AAATATATCCGGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
*
40291896 AAATGTATCCGGACTAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* * *
40291935 AAATGTATCCGAGCCAAAGTCCCGCAGGCTTCGTGCTGA
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
40291974 AAATGTATCCAGGCCAAAGTCCCGCAGGCTTCGTGCTGG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
* *
40292013 AAATGTATCCGGGTTAAAGTCCCGCAGGCTTTGTGCTG
1 AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTG
40292051 ATAATATAAT
Statistics
Matches: 216, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 216 1.00
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.23
Consensus pattern (39 bp):
AAATGTATCCGGGCTAAAGTCCCGCAGGCTTCGTGCTGG
Found at i:40293630 original size:29 final size:29
Alignment explanation
Indices: 40293569--40293667 Score: 168
Period size: 28 Copynumber: 3.5 Consensus size: 29
40293559 ACAGTAAGTC
40293569 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATTCAAACT
40293597 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
40293626 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
40293654 CGCACACTTAGTGC
1 CGCACACTTAGTGC
40293668 CAATCTCATT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 34 0.49
29 34 0.49
30 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTATACAATTCAAACT
Found at i:40300459 original size:19 final size:19
Alignment explanation
Indices: 40300437--40300475 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
40300427 TGTGACAATT
40300437 ACATAATAATCCAAGAAAC
1 ACATAATAATCCAAGAAAC
40300456 ACATAATAATCCAAGAAAC
1 ACATAATAATCCAAGAAAC
40300475 A
1 A
40300476 TACTCATAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (19 bp):
ACATAATAATCCAAGAAAC
Found at i:40322074 original size:2 final size:2
Alignment explanation
Indices: 40322067--40322130 Score: 94
Period size: 2 Copynumber: 32.5 Consensus size: 2
40322057 TATGTTTAGA
*
40322067 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG TG AG A-
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
40322108 AG AG AG AG AG AG AA AG AG TG AG A
1 AG AG AG AG AG AG AG AG AG AG AG A
40322131 ACAGCCAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
AG
Found at i:40322759 original size:22 final size:23
Alignment explanation
Indices: 40322732--40322774 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
40322722 AAAAAATTAT
40322732 AAAATTATTATTT-AATTATTCA
1 AAAATTATTATTTAAATTATTCA
*
40322754 AAAATTCTTATTTAAATTATT
1 AAAATTATTATTTAAATTATT
40322775 AAATTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (23 bp):
AAAATTATTATTTAAATTATTCA
Found at i:40335882 original size:40 final size:40
Alignment explanation
Indices: 40335755--40335884 Score: 154
Period size: 40 Copynumber: 3.2 Consensus size: 40
40335745 ATGCTGGAAA
* * *
40335755 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* * * **
40335795 CTACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCA
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
* *
40335835 TTCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACATGG
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGA-GTGG
40335875 TTATATCCGG
1 TTATATCCGG
40335885 TTATATTCCG
Statistics
Matches: 73, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 72 0.99
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (40 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTGG
Found at i:40335883 original size:80 final size:80
Alignment explanation
Indices: 40335717--40335884 Score: 196
Period size: 80 Copynumber: 2.1 Consensus size: 80
40335707 AAATTGAATG
* *
40335717 ATATCCGGGCTAAGCCCCGAAGACAATCATGCTGGAAATTATATCCGGGTTAAGACCCGAAGGCA
1 ATATCCGGGCTAAGACCCGAAGACAATCATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
*
40335782 ATTGTGCTAGTGGCT
66 ATTGTGCTAATGGCT
* * * * ** *
40335797 ACATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTCATTCTATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGACAATCATGCTG-GAAATTATATCCGGGCTAAGACCCGAAGGC
* *
40335861 ATTTGTGC-ACATGGTT
65 AATTGTGCTA-ATGGCT
40335877 ATATCCGG
1 ATATCCGG
40335885 TTATATTCCG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
79 2 0.03
80 71 0.97
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (80 bp):
ATATCCGGGCTAAGACCCGAAGACAATCATGCTGGAAATTATATCCGGGCTAAGACCCGAAGGCA
ATTGTGCTAATGGCT
Found at i:40338840 original size:11 final size:10
Alignment explanation
Indices: 40338824--40338858 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
40338814 ATGATGACAA
40338824 AAAGAAAAGAG
1 AAAGAAAA-AG
40338835 AAAGAAAAAG
1 AAAGAAAAAG
*
40338845 AAAAAAAAAG
1 AAAGAAAAAG
40338855 AAAG
1 AAAG
40338859 GCTCTCATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 14 0.64
11 8 0.36
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:40340175 original size:40 final size:40
Alignment explanation
Indices: 40340118--40340437 Score: 500
Period size: 40 Copynumber: 8.0 Consensus size: 40
40340108 GATGATAACT
* * **
40340118 GGGCTAAGTCCCGAAGGCATTTGCGCTAGTGGCTAGT-TCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TATCC
*
40340158 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40340198 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
40340238 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40340278 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40340318 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
40340358 GGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* * *
40340398 GGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
40340438 AGTTAAATCC
Statistics
Matches: 264, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
39 3 0.01
40 261 0.99
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:40341875 original size:46 final size:46
Alignment explanation
Indices: 40341808--40341899 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
40341798 TGTTACAGAA
*
40341808 AATCCCGGTTGAATAAAAAGGGATGTCAGATGGATAAATCATTGTT
1 AATCCCAGTTGAATAAAAAGGGATGTCAGATGGATAAATCATTGTT
* *
40341854 AATCCCAGTTGAATAAAAAGGGATGTCCGATGGATAAATTATTGTT
1 AATCCCAGTTGAATAAAAAGGGATGTCAGATGGATAAATCATTGTT
40341900 TATATAACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.37, C:0.11, G:0.23, T:0.29
Consensus pattern (46 bp):
AATCCCAGTTGAATAAAAAGGGATGTCAGATGGATAAATCATTGTT
Found at i:40368349 original size:116 final size:116
Alignment explanation
Indices: 40368145--40368365 Score: 352
Period size: 116 Copynumber: 1.9 Consensus size: 116
40368135 AAATTGAATG
*
40368145 AAATAATTGTATAGACCGAAAATTGGATCAAACCAGAGATAATCAGGGAAAAGCAAAAATTTTAA
1 AAATAATTGTATAGACCGAAAATTGGATCAAACCAGAGATAATCAGGGAAAACCAAAAATTTTAA
40368210 ATTAGTCCTTAAAGTTTAAACTTGTTTGCTATTTTTCCCATATAGGTTCAT
66 ATTAGTCCTTAAAGTTTAAACTTGTTTGCTATTTTTCCCATATAGGTTCAT
* ** * * *
40368261 AAATAATTGTATAGACTGGTAATTGGATCAAATCAGAGATAATCGGGGAAAACCAAAAATTTTAG
1 AAATAATTGTATAGACCGAAAATTGGATCAAACCAGAGATAATCAGGGAAAACCAAAAATTTTAA
* * *
40368326 ATTAGTCTTTAAAGTTTCAACTTGTTTGCTGTTTTTCCCA
66 ATTAGTCCTTAAAGTTTAAACTTGTTTGCTATTTTTCCCA
40368366 GGTATGTTCA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
116 95 1.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.34
Consensus pattern (116 bp):
AAATAATTGTATAGACCGAAAATTGGATCAAACCAGAGATAATCAGGGAAAACCAAAAATTTTAA
ATTAGTCCTTAAAGTTTAAACTTGTTTGCTATTTTTCCCATATAGGTTCAT
Found at i:40371937 original size:25 final size:25
Alignment explanation
Indices: 40371890--40371938 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
40371880 AAACTAAAAA
*
40371890 TACTGTAGATAGTATATTCTGAAAC
1 TACTGTAGATAGTATACTCTGAAAC
* *
40371915 TACTGTAGGTAGTATACTGTGAAA
1 TACTGTAGATAGTATACTCTGAAA
40371939 ACACTCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (25 bp):
TACTGTAGATAGTATACTCTGAAAC
Found at i:40379246 original size:17 final size:17
Alignment explanation
Indices: 40379224--40379264 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
40379214 TGAATTCTAG
40379224 TAGCTATAACAATCAAA
1 TAGCTATAACAATCAAA
**
40379241 TAGCTATAATGATCAAA
1 TAGCTATAACAATCAAA
40379258 TAGCTAT
1 TAGCTAT
40379265 GGAATTCAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (17 bp):
TAGCTATAACAATCAAA
Found at i:40384468 original size:39 final size:39
Alignment explanation
Indices: 40384359--40384518 Score: 178
Period size: 39 Copynumber: 4.1 Consensus size: 39
40384349 TATTACAGAT
* * * * *
40384359 TATAATGAGATTTAGCATTTGTTGCAGATCCTCGAGTAA
1 TATAATGAGATCTAGCCTTTGTTGCAGATTCTTGGGTAA
**
40384398 TATAACAAGATCTAGCCTTTGTTGCAGATTCTTGGGTAA
1 TATAATGAGATCTAGCCTTTGTTGCAGATTCTTGGGTAA
* * *
40384437 TATAATGAGATCTAGCCTTTATTGCAAATTCTTAGGTAA
1 TATAATGAGATCTAGCCTTTGTTGCAGATTCTTGGGTAA
* ** *
40384476 TATAATGAGATCTAACCCTTT-TTGTGGATTCTCGGGTAA
1 TATAATGAGATCT-AGCCTTTGTTGCAGATTCTTGGGTAA
40384515 TATA
1 TATA
40384519 TGACATAGGT
Statistics
Matches: 102, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
39 96 0.94
40 6 0.06
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (39 bp):
TATAATGAGATCTAGCCTTTGTTGCAGATTCTTGGGTAA
Found at i:40389206 original size:46 final size:46
Alignment explanation
Indices: 40389098--40389463 Score: 176
Period size: 46 Copynumber: 7.7 Consensus size: 46
40389088 ATATTATGAG
** *
40389098 AGCCAGTGTAAGACCATGTTTGGGACATGTCATCAGTATTGAGATG-A
1 AGCCAGTGTAAGACCATGTTTGGGACATG-CATC-GGCTCGAGATGTA
*
40389145 GAGCTAGTGTAAGA-CATGTTTGGGACATGCATCGGCCTCGAGATGTA
1 -AGCCAGTGTAAGACCATGTTTGGGACATGCATCGG-CTCGAGATGTA
* ** * *
40389192 AGCCAGTTTAAGA-CATGCCTGGGACATGCATTGGCTACAAGATGT-
1 AGCCAGTGTAAGACCATGTTTGGGACATGCATCGGCT-CGAGATGTA
* * * * *
40389237 -GTCAGTGTAAGACCATGTTTGGGATATGGCATCGACACGTGTAGAGGT-
1 AGCCAGTGTAAGACCATGTTTGGGACAT-GCATCGGCTC--G-AGATGTA
* * * * *
40389285 -GTCAGCGTAAGACCATGTCTGGGACATGGCATCGGCACGGATATGTGA
1 AGCCAGTGTAAGACCATGTTTGGGACAT-GCATCGGCTC-GAGATGT-A
* * * * ** *
40389333 GAGCTAGTGTAAGACTATGTCTGGGACATGACGTCGGC-CTTGATTTCAA
1 -AGCCAGTGTAAGACCATGTTTGGGACATG-CATCGGCTCGAGATGT--A
* * * *
40389382 TAGTCAGTGTAAGACCATGTTTGGGATATGACATCGACTTGATGGATG--
1 -AGCCAGTGTAAGACCATGTTTGGGACATG-CATCGGCTCGA--GATGTA
* * *
40389430 AGCTAGTGTAAGACCATGTCTGGTACATGGCATC
1 AGCCAGTGTAAGACCATGTTTGGGACAT-GCATC
40389464 AACATCATAC
Statistics
Matches: 246, Mismatches: 54, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
44 10 0.04
45 15 0.06
46 57 0.23
47 44 0.18
48 55 0.22
49 33 0.13
50 29 0.12
52 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.30, T:0.27
Consensus pattern (46 bp):
AGCCAGTGTAAGACCATGTTTGGGACATGCATCGGCTCGAGATGTA
Found at i:40391003 original size:35 final size:35
Alignment explanation
Indices: 40390962--40391028 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
40390952 ACATACATAG
*
40390962 ATTCACAATATAACATTTATAATTATTTAAACTAA
1 ATTCACAATATAACATTTATAATGATTTAAACTAA
40390997 ATTCACAATATAACATTTATAATGATTTAAAC
1 ATTCACAATATAACATTTATAATGATTTAAAC
40391029 ATAATTACCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (35 bp):
ATTCACAATATAACATTTATAATGATTTAAACTAA
Found at i:40397316 original size:40 final size:40
Alignment explanation
Indices: 40397243--40397322 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
40397233 ACACACTATG
* * *
40397243 TGGGGATAAAATCGACCCACCCATCCCTGCACACCGTAAA
1 TGGGGATAAAATCGACCCACCCAACCCTACACACCATAAA
* **
40397283 TGGGGATATAATCGACCCATTCAACCCTACACACCATAAA
1 TGGGGATAAAATCGACCCACCCAACCCTACACACCATAAA
40397323 ATACCGCATC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.35, C:0.33, G:0.15, T:0.17
Consensus pattern (40 bp):
TGGGGATAAAATCGACCCACCCAACCCTACACACCATAAA
Found at i:40404562 original size:8 final size:8
Alignment explanation
Indices: 40404551--40404591 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
40404541 TGGTTAAGAT
40404551 GTGTGTTG
1 GTGTGTTG
40404559 GTGTGTTG
1 GTGTGTTG
40404567 GTGTGTTG
1 GTGTGTTG
40404575 GTGTGTTG
1 GTGTGTTG
40404583 GTGTGTTG
1 GTGTGTTG
40404591 G
1 G
40404592 AGGTCTAGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (8 bp):
GTGTGTTG
Found at i:40405398 original size:17 final size:19
Alignment explanation
Indices: 40405370--40405405 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
40405360 TCAGGCAAAT
40405370 GGGCTGTGTGGG-CCACAC
1 GGGCTGTGTGGGCCCACAC
40405388 GGGCT-TGTGGGCCCACAC
1 GGGCTGTGTGGGCCCACAC
40405406 AGTGAACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.11, C:0.31, G:0.42, T:0.17
Consensus pattern (19 bp):
GGGCTGTGTGGGCCCACAC
Found at i:40408757 original size:22 final size:22
Alignment explanation
Indices: 40408732--40408776 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
40408722 GAATCTTCTA
40408732 AAGCTCCAAACAACTTCGAATC
1 AAGCTCCAAACAACTTCGAATC
40408754 AAGCTCCAAACAACTTCGAATC
1 AAGCTCCAAACAACTTCGAATC
40408776 A
1 A
40408777 TCTTAGGACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.31, G:0.09, T:0.18
Consensus pattern (22 bp):
AAGCTCCAAACAACTTCGAATC
Found at i:40409146 original size:16 final size:16
Alignment explanation
Indices: 40409125--40409162 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40409115 ATTTTTCTCA
*
40409125 TAAAAATAT-TAATATT
1 TAAAAATATAAAATA-T
40409141 TAAAAATATAAAATAT
1 TAAAAATATAAAATAT
40409157 TAAAAA
1 TAAAAA
40409163 CTTTTATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAAATATAAAATAT
Found at i:40409199 original size:23 final size:23
Alignment explanation
Indices: 40409157--40409203 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
40409147 TATAAAATAT
40409157 TAAAAACTTTTATAAAATTATAAA
1 TAAAAAC-TTTATAAAATTATAAA
40409181 TAAAAAC-TTATAAATATTATAAA
1 TAAAAACTTTATAAA-ATTATAAA
40409204 AACTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 7 0.32
23 8 0.36
24 7 0.32
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
TAAAAACTTTATAAAATTATAAA
Found at i:40409204 original size:19 final size:19
Alignment explanation
Indices: 40409180--40409233 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
40409170 AAAATTATAA
*
40409180 ATAAAAACTTATAAATATT
1 ATAAAAACTTATAAAAATT
40409199 ATAAAAAC-TATAAAAATT
1 ATAAAAACTTATAAAAATT
*
40409217 CTAATAAA-TTATAAAAA
1 ATAA-AAACTTATAAAAA
40409234 AAAAACCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAAAAACTTATAAAAATT
Found at i:40409215 original size:20 final size:19
Alignment explanation
Indices: 40409135--40409233 Score: 55
Period size: 19 Copynumber: 5.1 Consensus size: 19
40409125 TAAAAATATT
40409135 AATATTTAAAAA-TAT-AA
1 AATATTTAAAAACTATAAA
40409152 AATA-TTAAAAACTTTTATAAA
1 AATATTTAAAAAC---TATAAA
** *
40409173 ATTATAAATAAAAACT-TATA
1 A--ATATTTAAAAACTATAAA
40409193 AATATTATAAAAACTATAAA
1 AATATT-TAAAAACTATAAA
* *
40409213 AAT-TCTAATAAATTATAAA
1 AATATTTAA-AAACTATAAA
40409232 AA
1 AA
40409234 AAAAACCATA
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
16 7 0.11
17 4 0.06
18 6 0.09
19 20 0.31
20 13 0.20
21 4 0.06
23 3 0.05
24 7 0.11
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (19 bp):
AATATTTAAAAACTATAAA
Found at i:40409856 original size:10 final size:9
Alignment explanation
Indices: 40409837--40409979 Score: 54
Period size: 9 Copynumber: 14.8 Consensus size: 9
40409827 TATAAAGTTA
40409837 AAAAATTAT
1 AAAAATTAT
40409846 AAAAATATAT
1 AAAAAT-TAT
**
40409856 ATTAATTATT
1 AAAAATTA-T
**
40409866 AGTAATTAT
1 AAAAATTAT
*
40409875 AAAACTTAT
1 AAAAATTAT
*
40409884 AAAAACTCATT
1 AAAAA-TTA-T
* * *
40409895 ATAAGTTCT
1 AAAAATTAT
40409904 AATAAATTAT
1 AA-AAATTAT
*
40409914 AAAAAATTGT
1 -AAAAATTAT
*
40409924 AAAATTTAT
1 AAAAATTAT
40409933 AATAAAATTAT
1 -A-AAAATTAT
40409944 AAAATATTA-
1 AAAA-ATTAT
*
40409953 AAACTAAATAT
1 AAA--AATTAT
* *
40409964 AGAATTTAT
1 AAAAATTAT
40409973 AAAAATT
1 AAAAATT
40409980 CATATACTGG
Statistics
Matches: 97, Mismatches: 25, Indels: 24
0.66 0.17 0.16
Matches are distributed among these distances:
9 43 0.44
10 38 0.39
11 16 0.16
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (9 bp):
AAAAATTAT
Found at i:40409941 original size:20 final size:19
Alignment explanation
Indices: 40409910--40409977 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 19
40409900 TTCTAATAAA
*
40409910 TTATAAAAAATTGTAAAAT
1 TTATAAAAAATTATAAAAT
40409929 TTATAATAAAATTATAAAAT
1 TTATAA-AAAATTATAAAAT
*
40409949 ATTA-AAACTAAA-TATAGAAT
1 -TTATAAA--AAATTATAAAAT
40409969 TTATAAAAA
1 TTATAAAAA
40409978 TTCATATACT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
18 2 0.05
19 10 0.24
20 24 0.57
21 6 0.14
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.35
Consensus pattern (19 bp):
TTATAAAAAATTATAAAAT
Found at i:40410693 original size:9 final size:9
Alignment explanation
Indices: 40410679--40410910 Score: 69
Period size: 9 Copynumber: 25.7 Consensus size: 9
40410669 AACGAATTTT
40410679 TTTTTATAA
1 TTTTTATAA
*
40410688 TTTTTATAC
1 TTTTTATAA
*
40410697 TTTTTGT--
1 TTTTTATAA
*
40410704 TTTTTATGA
1 TTTTTATAA
*
40410713 TTTATTAGAA
1 TTT-TTATAA
* **
40410723 TTTATATGT
1 TTTTTATAA
*
40410732 TTTTTATGA
1 TTTTTATAA
40410741 TTTTT-TATA
1 TTTTTATA-A
40410750 TTTTT-TAA
1 TTTTTATAA
40410758 GTTTTTATAAA
1 -TTTTTAT-AA
* *
40410769 ATTTTAAATA
1 TTTTTATA-A
40410779 TGTTTTATAAA
1 T-TTTTAT-AA
*
40410790 TTGTATCATAA
1 TT-T-TTATAA
*
40410801 TTTAT-TAA
1 TTTTTATAA
40410809 TTTTTATAA
1 TTTTTATAA
*
40410818 TTTTTTGTAA
1 -TTTTTATAA
* *
40410828 TATTTACAA
1 TTTTTATAA
**
40410837 TTTTT-TTC
1 TTTTTATAA
40410845 TTTTTATAA
1 TTTTTATAA
*
40410854 CTTTATATCAA
1 -TTTTTAT-AA
40410865 -TTTTAT--
1 TTTTTATAA
40410871 TTTTTAT--
1 TTTTTATAA
40410878 TTTTT-T-A
1 TTTTTATAA
40410885 TTTTTA-ACA
1 TTTTTATA-A
40410894 TTTTTATGATA
1 TTTTTAT-A-A
40410905 TTTTTA
1 TTTTTA
40410911 ATGATTTCTA
Statistics
Matches: 166, Mismatches: 33, Indels: 46
0.68 0.13 0.19
Matches are distributed among these distances:
6 1 0.01
7 22 0.13
8 14 0.08
9 71 0.43
10 30 0.18
11 24 0.14
12 4 0.02
ACGTcount: A:0.28, C:0.03, G:0.04, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:40410761 original size:28 final size:27
Alignment explanation
Indices: 40410678--40410763 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 27
40410668 AAACGAATTT
* *
40410678 TTTTTTAT-AATTTTTATACTTTTT-G
1 TTTTTTATGATTTTTTATAATTTTTAG
* * *
40410703 TTTTTTATGATTTATTAGAATTTATATG
1 TTTTTTATGATTTTTTATAATTTTTA-G
*
40410731 TTTTTTATGATTTTTTATATTTTTTAAG
1 TTTTTTATGATTTTTTATAATTTTT-AG
40410759 TTTTT
1 TTTTT
40410764 ATAAAATTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
25 8 0.17
26 11 0.23
28 28 0.58
29 1 0.02
ACGTcount: A:0.22, C:0.01, G:0.07, T:0.70
Consensus pattern (27 bp):
TTTTTTATGATTTTTTATAATTTTTAG
Done.