Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009639.1 Hibiscus syriacus cultivar Beakdansim tig00117048_pilon, whole genome shotgun sequence
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: 15077257
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 62
Found at i:5678206 original size:51 final size:51
Alignment explanation
Indices: 5678130--5678233 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
5678120 ACCGATCTGA
5678130 TGGGCAACCTCTGTTTCTGAAGGTTTCCCTATCTTTAAAAGGTGAAAACTT
1 TGGGCAACCTCTGTTTCTGAAGGTTTCCCTATCTTTAAAAGGTGAAAACTT
5678181 TGGGCAACCTCTGTTTCTGAAGGTTTCCCTATCTTTAAAAGGTGAAAACTT
1 TGGGCAACCTCTGTTTCTGAAGGTTTCCCTATCTTTAAAAGGTGAAAACTT
5678232 TG
1 TG
5678234 AACACGACCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.25, C:0.19, G:0.20, T:0.36
Consensus pattern (51 bp):
TGGGCAACCTCTGTTTCTGAAGGTTTCCCTATCTTTAAAAGGTGAAAACTT
Found at i:5680573 original size:36 final size:35
Alignment explanation
Indices: 5680527--5680952 Score: 419
Period size: 36 Copynumber: 11.5 Consensus size: 35
5680517 AAAAATATTT
* *
5680527 ATATATTATATAGTCTTTAAAACATTTTGAAAACTA
1 ATATAATATATAGTTTTTAAAACATTTTGAAAA-TA
5680563 ATATAATATATAGTTTTTAAAACATTTTTTGAAAA-A
1 ATATAATATATAGTTTTTAAAACA--TTTTGAAAATA
*
5680599 TATATATTATATAGTTTTTAAAACATTTTGAAAAATA
1 -ATATAATATATAGTTTTTAAAACATTTTG-AAAATA
5680636 ATATAATATATA-TTTTTAAAACATTTTTTGAAAATA
1 ATATAATATATAGTTTTTAAAACA--TTTTGAAAATA
* * **
5680672 TATATATTATATAGATTTTAAAACACCTTGAAAACTA
1 -ATATAATATATAGTTTTTAAAACATTTTGAAAA-TA
5680709 ATATAATATATAGTTTTTAAAACATTTTTTGAAAATA
1 ATATAATATATAGTTTTTAAAACA--TTTTGAAAATA
* * *
5680746 TATATATTATATAATTTTTGAAACATTTTGAAAATAA
1 -ATATAATATATAGTTTTTAAAACATTTTGAAAAT-A
*
5680783 ATATTATATATAGTTTTTAAAACATTTTTGAAAAT-
1 ATATAATATATAGTTTTTAAAACA-TTTTGAAAATA
*
5680818 ATATATTATATAGTTTTTAAAACATTTTGGAAATATA
1 ATATAATATATAGTTTTTAAAACATTTT-GAAA-ATA
* * *
5680855 TATAATATTATATAGTTTTTTGAAAAATCTTTTTGGAAAATGC
1 -AT-ATAATATATAG-TTTTT--AAAA-CATTTT-GAAAAT-A
*
5680898 ATATAATATATAGTTTTTAAAATAACATTTTAGAAATTA
1 ATATAATATATAGTTTTT--AA-AACATTTT-GAAAATA
*
5680937 ATATATTATATA-TTTT
1 ATATAATATATAGTTTT
5680953 CGAAATTGTT
Statistics
Matches: 334, Mismatches: 30, Indels: 50
0.81 0.07 0.12
Matches are distributed among these distances:
34 4 0.01
35 42 0.13
36 105 0.31
37 55 0.16
38 53 0.16
39 22 0.07
40 23 0.07
41 12 0.04
42 8 0.02
43 10 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.46
Consensus pattern (35 bp):
ATATAATATATAGTTTTTAAAACATTTTGAAAATA
Found at i:5680613 original size:73 final size:72
Alignment explanation
Indices: 5680526--5680952 Score: 540
Period size: 73 Copynumber: 5.7 Consensus size: 72
5680516 TAAAAATATT
*
5680526 TATATATTATATAGTCTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAACATTTT
1 TATATATTATATAGTTTTTAAAACATTTTGAAAA-TAATATAATATATAGTTTTTAAAACATTTT
5680591 TTGAAAAA
65 TTGAAAAA
5680599 TATATATTATATAGTTTTTAAAACATTTTGAAAAATAATATAATATATA-TTTTTAAAACATTTT
1 TATATATTATATAGTTTTTAAAACATTTTG-AAAATAATATAATATATAGTTTTTAAAACATTTT
5680663 TTGAAAATA
65 TTGAAAA-A
* **
5680672 TATATATTATATAGATTTTAAAACACCTTGAAAACTAATATAATATATAGTTTTTAAAACATTTT
1 TATATATTATATAGTTTTTAAAACATTTTGAAAA-TAATATAATATATAGTTTTTAAAACATTTT
5680737 TTGAAAATA
65 TTGAAAA-A
* * *
5680746 TATATATTATATAATTTTTGAAACATTTTGAAAATAAATATTATATATAGTTTTTAAAACA-TTT
1 TATATATTATATAGTTTTTAAAACATTTTGAAAAT-AATATAATATATAGTTTTTAAAACATTTT
5680810 TTG-AAAA
65 TTGAAAAA
*
5680817 TATATATTATATAGTTTTTAAAACATTTTGGAAATATATATAATATTATATAGTTTTTTGAAAA-
1 TATATATTATATAGTTTTTAAAACATTTT-GAAA-ATA-AT-ATAATATATAG-TTTTT-AAAAC
*
5680881 ATCTTTTTGGAAAA
60 AT-TTTTTGAAAAA
* * *
5680895 TGCATATAATATATAGTTTTTAAAATAACATTTTAGAAATTAATATATTATATA-TTTT
1 T--ATATATTATATAGTTTTT--AA-AACATTTT-GAAAATAATATAATATATAGTTTT
5680953 CGAAATTGTT
Statistics
Matches: 318, Mismatches: 17, Indels: 33
0.86 0.05 0.09
Matches are distributed among these distances:
71 28 0.09
72 34 0.11
73 96 0.30
74 90 0.28
75 6 0.02
76 4 0.01
77 6 0.02
78 9 0.03
80 27 0.08
81 2 0.01
82 4 0.01
83 12 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (72 bp):
TATATATTATATAGTTTTTAAAACATTTTGAAAATAATATAATATATAGTTTTTAAAACATTTTT
TGAAAAA
Found at i:5680904 original size:44 final size:39
Alignment explanation
Indices: 5680438--5680952 Score: 360
Period size: 36 Copynumber: 13.6 Consensus size: 39
5680428 TATTATATAT
* * **
5680438 ATATATATACACATTATATAG-TTTGAAAACATTTTTAAA
1 ATATATATA-ATATTATATAGTTTTTAAAACATTTTGGAA
* * **
5680477 ATATATATATATATATAATATAGTTTTGACAAGCATGTTTAAAA
1 ATATATATA-ATAT-T-ATATAGTTTTTA-AAACAT-TTTGGAA
* *
5680521 ATATTTAT-ATATTATATAGTCTTTAAAACATTTT-GAA
1 ATATATATAATATTATATAGTTTTTAAAACATTTTGGAA
* *
5680558 A-ACTA-AT-ATAATATATAGTTTTTAAAACATTTTTTGAA
1 ATA-TATATAATATTATATAGTTTTTAAAACA-TTTTGGAA
5680596 A-A-ATAT-ATATTATATAGTTTTTAAAACATTTT-GAA
1 ATATATATAATATTATATAGTTTTTAAAACATTTTGGAA
* * *
5680631 AAATA-AT-ATAATATATA-TTTTTAAAACATTTTTTGAA
1 ATATATATAATATTATATAGTTTTTAAAACA-TTTTGGAA
* **
5680668 A-ATATAT-ATATTATATAGATTTTAAAACACCTT-GAA
1 ATATATATAATATTATATAGTTTTTAAAACATTTTGGAA
* *
5680704 A-ACTA-AT-ATAATATATAGTTTTTAAAACATTTTTTGAA
1 ATA-TATATAATATTATATAGTTTTTAAAACA-TTTTGGAA
* *
5680742 A-ATATAT-ATATTATATAATTTTTGAAACATTTT-GAA
1 ATATATATAATATTATATAGTTTTTAAAACATTTTGGAA
* * *
5680778 A-ATAAATATTA-TATATAGTTTTTAAAACATTTTTG-A
1 ATATATATAATATTATATAGTTTTTAAAACATTTTGGAA
5680814 A-A-ATAT-ATATTATATAGTTTTTAAAACATTTTGGAA
1 ATATATATAATATTATATAGTTTTTAAAACATTTTGGAA
*
5680850 ATATATATAATATTATATAGTTTTTTGAAAAATCTTTTTGGAA
1 ATATATATAATATTATATAG-TTTTT--AAAA-CATTTTGGAA
** * *
5680893 A-ATGCAT-ATAATATATAGTTTTTAAAATAACATTTTAGAA
1 ATATATATAATATTATATAGTTTTT--AA-AACATTTTGGAA
5680933 AT-TA-AT-ATATTATATA-TTTT
1 ATATATATAATATTATATAGTTTT
5680953 CGAAATTGTT
Statistics
Matches: 403, Mismatches: 41, Indels: 65
0.79 0.08 0.13
Matches are distributed among these distances:
34 2 0.00
35 41 0.10
36 108 0.27
37 63 0.16
38 52 0.13
39 39 0.10
40 34 0.08
41 19 0.05
42 17 0.04
43 15 0.04
44 13 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (39 bp):
ATATATATAATATTATATAGTTTTTAAAACATTTTGGAA
Found at i:5680982 original size:18 final size:20
Alignment explanation
Indices: 5680961--5681027 Score: 84
Period size: 22 Copynumber: 3.2 Consensus size: 20
5680951 TTCGAAATTG
5680961 TTTTTATTTTTA-TT-TTTA
1 TTTTTATTTTTATTTATTTA
5680979 TTTTTATTATTTTATTTATTTA
1 TTTTTA-T-TTTTATTTATTTA
5681001 TTTATTATTTCTTATTTATTTA
1 TTT-TTATTT-TTATTTATTTA
5681023 TTTTT
1 TTTTT
5681028 TCTGTTTAGG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.14
19 1 0.02
20 5 0.12
21 6 0.14
22 22 0.51
23 3 0.07
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (20 bp):
TTTTTATTTTTATTTATTTA
Found at i:5680993 original size:8 final size:9
Alignment explanation
Indices: 5680962--5681026 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 9
5680952 TCGAAATTGT
5680962 TTTTATTT-
1 TTTTATTTA
5680970 TTATT-TTTA
1 TT-TTATTTA
5680979 TTTT-TATTA
1 TTTTAT-TTA
5680988 TTTTATTTA
1 TTTTATTTA
5680997 -TTTATTTA
1 TTTTATTTA
5681005 TTATT-TCTTA
1 TT-TTAT-TTA
5681015 -TTTATTTA
1 TTTTATTTA
5681023 TTTT
1 TTTT
5681027 TTCTGTTTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 17
0.74 0.00 0.26
Matches are distributed among these distances:
8 21 0.44
9 21 0.44
10 6 0.12
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTATTTA
Found at i:5680993 original size:20 final size:20
Alignment explanation
Indices: 5680968--5681025 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 20
5680958 TTGTTTTTAT
*
5680968 TTTTATTT-TTATTTTTATTA
1 TTTTATTTATT-TATTTATTA
5680988 TTTTATTTATTTATTTATTA
1 TTTTATTTATTTATTTATTA
5681008 TTTCTTATTTATTTATTT
1 -TT-TTATTTATTTATTT
5681026 TTTCTGTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 16 0.47
21 4 0.12
22 14 0.41
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTATTTATTTATTTATTA
Found at i:5680993 original size:26 final size:27
Alignment explanation
Indices: 5680961--5681027 Score: 84
Period size: 28 Copynumber: 2.4 Consensus size: 27
5680951 TTCGAAATTG
5680961 TTTTTATTTTTATTT-TTATTT-TTAT
1 TTTTTATTTTTATTTATTATTTCTTAT
5680986 TATTTTATTTATTTATTTATTATTTCTTAT
1 T-TTTTA-TT-TTTATTTATTATTTCTTAT
5681016 TTATTTATTTTT
1 TT-TTTATTTTT
5681028 TCTGTTTAGG
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
25 1 0.03
26 5 0.14
27 2 0.06
28 10 0.28
29 9 0.25
30 9 0.25
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (27 bp):
TTTTTATTTTTATTTATTATTTCTTAT
Found at i:5680998 original size:4 final size:4
Alignment explanation
Indices: 5680975--5681025 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
5680965 TATTTTTATT
* *
5680975 TTTA TTTT TATTA TTTTA TTTA TTTA TTTA -TTA TTT- CTTA TTTA TTTA
1 TTTA TTTA T-TTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5681023 TTT
1 TTT
5681026 TTTCTGTTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 5 0.13
4 28 0.72
5 5 0.13
6 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5681030 original size:18 final size:17
Alignment explanation
Indices: 5680963--5681028 Score: 75
Period size: 18 Copynumber: 3.9 Consensus size: 17
5680953 CGAAATTGTT
5680963 TTTATTT-TTATTTTTA
1 TTTATTTATTATTTTTA
*
5680979 TTTTTATTATT-TTATTTA
1 TTTAT-TTATTATT-TTTA
5680997 TTTATTTATTATTTCTTA
1 TTTATTTATTATTT-TTA
5681015 TTTATTTATT-TTTT
1 TTTATTTATTATTTT
5681029 CTGTTTAGGG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
16 5 0.12
17 13 0.30
18 25 0.58
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTATTTATTATTTTTA
Found at i:5682385 original size:23 final size:23
Alignment explanation
Indices: 5682359--5682421 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
5682349 TTTATTATTC
5682359 TTTTTTTATTTATTATTTTATCA
1 TTTTTTTATTTATTATTTTATCA
** ** *
5682382 TTTTTTTAAGTATTGGTTTATTA
1 TTTTTTTATTTATTATTTTATCA
5682405 TTTTTATT-TTTATTATT
1 TTTTT-TTATTTATTATT
5682422 ATTTTTGCCT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
23 28 0.93
24 2 0.07
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTTTTTATTTATTATTTTATCA
Found at i:5683535 original size:17 final size:18
Alignment explanation
Indices: 5683503--5683536 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5683493 CTCACTAACC
*
5683503 CTTTTATTTTTTTGTTCT
1 CTTTTATTTTTGTGTTCT
5683521 CTTTTA-TTTTGTGTTC
1 CTTTTATTTTTGTGTTC
5683537 ATCGTTTGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.06, C:0.12, G:0.09, T:0.74
Consensus pattern (18 bp):
CTTTTATTTTTGTGTTCT
Found at i:5687963 original size:84 final size:82
Alignment explanation
Indices: 5687625--5688397 Score: 637
Period size: 84 Copynumber: 9.3 Consensus size: 82
5687615 AGGCTATATG
* * * * * * * *
5687625 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
5687690 CTAGAAGGGTTATCTGTCA
65 CTAGAAGGGTTATCTG-CA
* * * * * *
5687709 CCAAAGCCCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACGTCATTTGAAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
5687774 AAGAAGGGCTATCTG--
66 TAGAAGGGTTATCTGCA
** * * * * * * * *
5687789 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
5687854 CTAGAAGGGTTATCTGTCA
65 CTAGAAGGGTTATCTG-CA
* * * *
5687873 CCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAATTTGCAGCACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* *
5687938 TAAAAGGGTTGTCTGCCAA
66 TAGAAGGGTTATCTG-C-A
* * * * *
5687957 CAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGGCACATCATCTGCAGCATAGCTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGCAGCATAACTTAAGT
* *
5688021 CGAGAAGGGCTATCTG--
65 CTAGAAGGGTTATCTGCA
** * * * *
5688037 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGT
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
5688102 -TGAGAAGGGTTATTTTCCAA
65 CT-AGAAGGGTTA-TCTGC-A
* * * *
5688122 CCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCATCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * * *
5688187 GATAAGGGCTATATG--
66 TAGAAGGGTTATCTGCA
* * * * * * * * *
5688202 CCAAAGATCC-CCGAGTTCAATTACACTCAGCATCGACGGCACATCATTTACAGTATAACTCAAG
1 CCAAAGA-CCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGCAGCATAACTTAAG
* * *
5688266 GCTAGAAAGATTATCTGTCA
64 TCTAGAAGGGTTATCTG-CA
* * * * *
5688286 CTAAATACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
* * *
5688351 GAGAAGGGCTATTTGCCAA
66 TAGAAGGGTTATCTG-C-A
* * *
5688370 CCGAAGACCTTCGAGTTTGATTACGCTC
1 CCAAAGACCTTCGAGTTCGACTACGCTC
5688398 TCAGAGGAAA
Statistics
Matches: 529, Mismatches: 139, Indels: 42
0.75 0.20 0.06
Matches are distributed among these distances:
80 71 0.13
81 110 0.21
82 3 0.01
83 124 0.23
84 195 0.37
85 26 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (82 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTC
TAGAAGGGTTATCTGCA
Found at i:5688043 original size:164 final size:163
Alignment explanation
Indices: 5687626--5688369 Score: 642
Period size: 164 Copynumber: 4.5 Consensus size: 163
5687616 GGCTATATGC
* * * * * * * * * *
5687626 CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
* * * * * * *
5687691 TAGAAGGGTTATCTGTCACCAAAG-CCCTTCAAGTTTGACTACGCTCAGC-TCCAAGGCACGTCA
65 GAGAAGGGCTATCTG---CCAAAGACCC-CCGAGTTCGACTACACTCAGCATCCAAGGCACATCA
* * *
5687754 TTTGAAGCATAGCTTAAGTC-AAGAAGGGCTATCTG-C-
126 TTTGCAGCATAACTTAAGTCTAA-AAGGGTTATCTGCCA
** * * * * * * * *
5687790 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGGC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
* * *** * * *
5687855 TAGAAGGGTTATCTGTCACCAAAGACATTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATAAT
65 GAGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGACTACACTCAGCATCCAAGGCACATCAT
* *
5687919 TTGCAGCACAACTTAAGTCTAAAAGGGTTGTCTGCCAA
127 TTGCAGCATAACTTAAGTCTAAAAGGGTTATCTGCC-A
* * * *
5687957 CAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGGCACATCATCTGCAGCATAGCTTAAGT
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCATATCATTTGCAGCATAGCTTAAGT
* * * *
5688021 CGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTT
64 CGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCATCCAAGGCACATCATTT
* * *
5688086 GCAGCATAACTTAAGT-TGAGAAGGGTTATTTTCCAA
129 GCAGCATAACTTAAGTCT-AAAAGGGTTATCTGCC-A
* *
5688122 CCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCATCATAGCTTAAGTC
1 -CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
* * * * * * * *
5688187 GATAAGGGCTATATGCCAAAGATCCCCGAGTTCAATTACACTCAGCATCGACGGCACATCATTTA
65 GAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCATCCAAGGCACATCATTTG
* * * * *
5688252 CAGTATAACTCAAGGCTAGAAA-GATTATCTGTCA
130 CAGCATAACTTAAGTCTA-AAAGGGTTATCTGCCA
* *
5688286 CTAAATACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTC
*
5688351 GAGAAGGGCTATTTGCCAA
65 GAGAAGGGCTATCTGCCAA
5688370 CCGAAGACCT
Statistics
Matches: 495, Mismatches: 71, Indels: 28
0.83 0.12 0.05
Matches are distributed among these distances:
163 1 0.00
164 248 0.50
165 177 0.36
166 8 0.02
167 38 0.08
168 23 0.05
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (163 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAGCTTAAGTCG
AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGACTACACTCAGCATCCAAGGCACATCATTTGC
AGCATAACTTAAGTCTAAAAGGGTTATCTGCCA
Found at i:5688063 original size:248 final size:248
Alignment explanation
Indices: 5687625--5688204 Score: 772
Period size: 248 Copynumber: 2.3 Consensus size: 248
5687615 AGGCTATATG
* * * * * * * * *
5687625 CCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGG
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGCAGCATAACTTAAGT
* * * * *
5687690 CTAGAAGGGTTATCTGTCACCAAAGCCCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACGTCAT
65 CTAAAAGGGTTATCTGCCACAAAAGACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCAT
*
5687755 TTGAAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGC
130 CTGAAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGC
*
5687820 TTCGAGGGCATATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGT-C-A
195 TTCGAGGGCACATCATTTACAGCATAACTCAA-GCTGAGAAGGGTTAT-TGTCCAA
* * *
5687873 CCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAATTTGCAGCACAACTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTC
* **
5687938 TAAAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGGCACATCA
66 TAAAAGGGTTATCTGCC-ACAAAAGACCTTCAAGTTTGACTACGCTCAGCTCCAA-GGCACATCA
* *
5688002 TCTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAG
129 TCTGAAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAG
* * * *
5688067 CTTCGAGGGCACATCATTTGCAGCATAACTTAAGTTGAGAAGGGTTATTTTCCAA
194 CTTCGAGGGCACATCATTTACAGCATAACTCAAGCTGAGAAGGGTTATTGTCCAA
* * *
5688122 CCAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCATCATAGCTTAAGTC
1 CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTC
* * * *
5688187 GATAAGGGCTATATGCCA
66 TAAAAGGGTTATCTGCCA
5688205 AAGATCCCCG
Statistics
Matches: 288, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
247 47 0.16
248 169 0.59
249 72 0.25
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (248 bp):
CCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTC
TAAAAGGGTTATCTGCCACAAAAGACCTTCAAGTTTGACTACGCTCAGCTCCAAGGCACATCATC
TGAAGCATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTACAGCATAACTCAAGCTGAGAAGGGTTATTGTCCAA
Found at i:5688370 original size:413 final size:412
Alignment explanation
Indices: 5687594--5688397 Score: 1180
Period size: 413 Copynumber: 1.9 Consensus size: 412
5687584 AAACTATTTT
*
5687594 CAGCATAGCATAAGTCGAGAAAGGCTATATGCCAAAGACCCTCGAGTTCGATTACACTCAGCTTC
1 CAGCATAGCATAAGTCGAGAAAGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
*
5687659 GAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGCCCTTCAAG
66 GAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCAAG
* * *
5687724 TTTGACTACGCTCAGCTCCAAGGCACGTCATTTGAAGCATAGCTTAAGTCAAGAAGGGCTATCTG
131 TTCGACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAGCTTAAGTCAAGAAGGGCTATATG
* * * *
5687789 CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCATATCATTTACAGCATAACTCAAGG
196 CCAAAGACCCCCGAGTTCAATTACACTCAGCATCGACGGCACATCATTTACAGCATAACTCAAGG
* *
5687854 CTAGAAGGGTTATCTGTCACCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAAT
261 CTAGAAAGATTATCTGTCACCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAAT
* * * *
5687919 TTGCAGCACAACTTAAGTCTAAAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTTGACTACGCT
326 TTGCAGCACAACTTAAGTCGAAAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCT
5687984 CAGCTCAACGGCACATCATCTG
391 CAGCTCAACGGCACATCATCTG
* * *
5688006 CAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
1 CAGCATAGCATAAGTCGAGAAAGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
* * * *
5688071 GAGGGCACATCATTTGCAGCATAACTTAA-GTTGAGAAGGGTTAT-TTTCCAACCAAAGACCTTC
66 GAGGGCACATCATTTACAGCATAACTCAAGGCT-AGAAGGGTTATCTGT-C-ACCAAAGACCTTC
* * * * * * *
5688134 GAGTTCGACTATGCTCAGCTCCAAGGCATATCATTTGCATCATAGCTTAAGTCGATAAGGGCTAT
128 AAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAGCTTAAGTCAAGAAGGGCTAT
* *
5688199 ATGCCAAAGATCCCCGAGTTCAATTACACTCAGCATCGACGGCACATCATTTACAGTATAACTCA
193 ATGCCAAAGACCCCCGAGTTCAATTACACTCAGCATCGACGGCACATCATTTACAGCATAACTCA
* * * *
5688264 AGGCTAGAAAGATTATCTGTCACTAAATACCTTCGAGTTCGACTACGCTTAGCTCCAAGGCATAT
258 AGGCTAGAAAGATTATCTGTCACCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATAT
* * * * * ** *
5688329 CATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATTTGCCAACCGAAGACCTTCGAGTTTGATTAC
323 AATTTGCAGCACAACTTAAGTCGAAAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGACTAC
5688394 GCTC
388 GCTC
5688398 TCAGAGGAAA
Statistics
Matches: 346, Mismatches: 43, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
411 4 0.01
412 100 0.29
413 242 0.70
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (412 bp):
CAGCATAGCATAAGTCGAGAAAGGCTATATGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTC
GAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCAAG
TTCGACTACGCTCAGCTCCAAGGCACATCATTTGAAGCATAGCTTAAGTCAAGAAGGGCTATATG
CCAAAGACCCCCGAGTTCAATTACACTCAGCATCGACGGCACATCATTTACAGCATAACTCAAGG
CTAGAAAGATTATCTGTCACCAAAGACATTCGAGTTCGACTACGCTCAGCTCCAAGGCATATAAT
TTGCAGCACAACTTAAGTCGAAAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTTGACTACGCT
CAGCTCAACGGCACATCATCTG
Found at i:5689117 original size:36 final size:35
Alignment explanation
Indices: 5689003--5689429 Score: 385
Period size: 36 Copynumber: 11.4 Consensus size: 35
5688993 ATATATACAC
* *
5689003 ATTATATAG-TTTGAAAACATTTTTAAAATATATAT
1 ATTATATAGTTTTTAAAACATTTTGAAAATA-ATAT
* * *
5689038 ATAATATATAGTTTTGACAAGCATGTTTAAAAAATATTTATAT
1 AT--TATATAGTTTTTA-AAACAT-TTT-GAAAATA---ATAT
5689081 ATTATATAGTTTTTAAAACATTTTGAAAACTAATAT
1 ATTATATAGTTTTTAAAACATTTTGAAAA-TAATAT
* *
5689117 AATATATAGTTTTTAAAACATTTTTTGAATATATATAT
1 ATTATATAGTTTTTAAAACA--TTTTGAAAATA-ATAT
*
5689155 ATTATATAGTTTTTAAAACATCTTGAAAACTAATAT
1 ATTATATAGTTTTTAAAACATTTTGAAAA-TAATAT
*
5689191 AATT-TATAGTTTTTAAAACATTTTTTTAAAATATATAT
1 -ATTATATAGTTTTTAAAACA--TTTTGAAAATA-ATAT
* *
5689229 ATTATATAATTTTTGAAACATTTTGAAAATAAATAT
1 ATTATATAGTTTTTAAAACATTTTGAAAAT-AATAT
*
5689265 AATATATAGTTTTTAAAACATTTTTGAAAAT-ATAT
1 ATTATATAGTTTTTAAAACA-TTTTGAAAATAATAT
5689300 ATTATATAGTTTTTAAAACATTTTGAAAATATATATAAT
1 ATTATATAGTTTTTAAAACATTTTG-AAA-ATA-AT-AT
* *
5689339 ATTATATAGTTTTTGAAAAATCTTTTTGGAAAATGCATAT
1 ATTATATAGTTTTT--AAAA-CATTTT-GAAAAT-AATAT
* *
5689379 AATATATAGTTTTTAAAATAACATTTTAGAAATTAATAT
1 ATTATATAGTTTTT--AA-AACATTTT-GAAAATAATAT
5689418 ATTATATA-TTTT
1 ATTATATAGTTTT
5689430 CGAAATTGTT
Statistics
Matches: 333, Mismatches: 28, Indels: 59
0.79 0.07 0.14
Matches are distributed among these distances:
34 5 0.02
35 28 0.08
36 82 0.25
37 30 0.09
38 71 0.21
39 37 0.11
40 36 0.11
41 28 0.08
42 8 0.02
43 8 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (35 bp):
ATTATATAGTTTTTAAAACATTTTGAAAATAATAT
Found at i:5689169 original size:74 final size:73
Alignment explanation
Indices: 5688993--5689429 Score: 454
Period size: 74 Copynumber: 5.8 Consensus size: 73
5688983 TTATATATAT
* * * * *
5688993 ATATATACACATTATATAG-TTTGAAAACATTTTTAAAATATATATATAATATATAGTTTTGACA
1 ATATATATATATTATATAGTTTTTAAAACA-TTTTGAAA-ATA-ATATAATATATAGTTTTTA-A
* ***
5689057 AGCATGTTTAAAAA
62 AACAT-TTT-TTGA
*
5689071 ATATTTATATATTATATAGTTTTTAAAACATTTTGAAAACTAATATAATATATAGTTTTTAAAAC
1 ATATATATATATTATATAGTTTTTAAAACATTTTGAAAA-TAATATAATATATAGTTTTTAAAAC
5689136 ATTTTTTGA
65 ATTTTTTGA
* *
5689145 ATATATATATATTATATAGTTTTTAAAACATCTTGAAAACTAATATAATTTATAGTTTTTAAAAC
1 ATATATATATATTATATAGTTTTTAAAACATTTTGAAAA-TAATATAATATATAGTTTTTAAAAC
*
5689210 ATTTTTTTA
65 ATTTTTTGA
* * *
5689219 AAATATATATATTATATAATTTTTGAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAAC
1 ATATATATATATTATATAGTTTTTAAAACATTTTGAAAAT-AATATAATATATAGTTTTTAAAAC
5689284 A-TTTTTGA
65 ATTTTTTGA
5689292 A-A-ATATATATTATATAGTTTTTAAAACATTTTGAAAATATATATAATATTATATAGTTTTTGA
1 ATATATATATATTATATAGTTTTTAAAACATTTTGAAAATA-ATAT-A-A-TATATAGTTTTT-A
5689355 AAA-ATCTTTTTGGA
61 AAACAT-TTTTT-GA
* ** * * *
5689369 AAATGCATATAATATATAGTTTTTAAAATAACATTTTAGAAATTAATATATTATATA-TTTT
1 ATATATATATATTATATAGTTTTT--AA-AACATTTT-GAAAATAATATAATATATAGTTTT
5689430 CGAAATTGTT
Statistics
Matches: 315, Mismatches: 27, Indels: 34
0.84 0.07 0.09
Matches are distributed among these distances:
70 1 0.00
71 38 0.12
72 2 0.01
73 9 0.03
74 143 0.45
75 7 0.02
76 10 0.03
77 22 0.07
78 30 0.10
79 32 0.10
81 3 0.01
82 12 0.04
83 6 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (73 bp):
ATATATATATATTATATAGTTTTTAAAACATTTTGAAAATAATATAATATATAGTTTTTAAAACA
TTTTTTGA
Found at i:5689461 original size:18 final size:20
Alignment explanation
Indices: 5689440--5689486 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
5689430 CGAAATTGTT
5689440 TTTATTTTTATTA-TT-TTA
1 TTTATTTTTATTATTTCTTA
5689458 TTTATTTATTTATTATTTCTTA
1 TTTA-TT-TTTATTATTTCTTA
5689480 TTTATTT
1 TTTATTT
5689487 ATTTTTTCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 4 0.16
19 2 0.08
20 8 0.32
21 4 0.16
22 7 0.28
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTATTTTTATTATTTCTTA
Found at i:5689463 original size:4 final size:4
Alignment explanation
Indices: 5689440--5689490 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
5689430 CGAAATTGTT
* *
5689440 TTTA TTTT TATTA TTTTA TTTA TTTA TTTA -TTA TTT- CTTA TTTA TTTA
1 TTTA TTTA T-TTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5689488 TTT
1 TTT
5689491 TTTCTGTTCA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
3 5 0.13
4 28 0.72
5 5 0.13
6 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:5689465 original size:22 final size:21
Alignment explanation
Indices: 5689440--5689492 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
5689430 CGAAATTGTT
*
5689440 TTTATTTTTATTATTTTATTTA
1 TTTATTTTTATT-TCTTATTTA
5689462 TTTATTTATTATTTCTTATTTA
1 TTTATTT-TTATTTCTTATTTA
5689484 TTTATTTTT
1 TTTATTTTT
5689493 TCTGTTCAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 2 0.07
22 22 0.76
23 5 0.17
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTATTTTTATTTCTTATTTA
Found at i:5689487 original size:18 final size:18
Alignment explanation
Indices: 5689459--5689495 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
5689449 ATTATTTTAT
5689459 TTATTTATTTATTATTTC
1 TTATTTATTTATTATTTC
*
5689477 TTATTTATTTATTTTTTC
1 TTATTTATTTATTATTTC
5689495 T
1 T
5689496 GTTCAGGGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTATTTATTATTTC
Found at i:5690337 original size:39 final size:37
Alignment explanation
Indices: 5690202--5690415 Score: 206
Period size: 36 Copynumber: 5.7 Consensus size: 37
5690192 ATACCGCATC
* *
5690202 GAAAATATATATATTATATAATTTTTGAAACATTTT-
1 GAAAATATATATATTATATAGTTTTTAAAACATTTTG
* *
5690238 GAAAATAAATAT-TATATATAGTTTTTAAAACATTTTT
1 GAAAATATATATAT-TATATAGTTTTTAAAACATTTTG
5690275 G-AAA-ATATATATTATATAGTTTTTAAAACATTTTG
1 GAAAATATATATATTATATAGTTTTTAAAACATTTTG
*
5690310 GAAATATATATAATATTATATAGTTTTTTGAAAAATCTTTTTG
1 GAAA-ATATAT-ATATTATATAG-TTTTT--AAAA-CATTTTG
** * *
5690353 GAAAATGCATATAATATATAGTTTTTAAAATAACATTTTA
1 GAAAATATATATATTATATAGTTTTT--AA-AACATTTTG
*
5690393 GAAATTA-ATATATTATATA-TTTT
1 GAAAATATATATATTATATAGTTTT
5690416 CGAAATTGTT
Statistics
Matches: 151, Mismatches: 15, Indels: 22
0.80 0.08 0.12
Matches are distributed among these distances:
35 29 0.19
36 37 0.25
37 2 0.01
38 8 0.05
39 22 0.15
40 23 0.15
41 12 0.08
42 8 0.05
43 10 0.07
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
GAAAATATATATATTATATAGTTTTTAAAACATTTTG
Found at i:5690371 original size:80 final size:73
Alignment explanation
Indices: 5690208--5690415 Score: 214
Period size: 71 Copynumber: 2.8 Consensus size: 73
5690198 CATCGAAAAT
* * *
5690208 ATATATATTATATAATTTTTGAAACATTTTGAAA-ATAAATATTA-TATATAG-TTTTTAAAACA
1 ATATATATTATATAGTTTTTAAAACATTTTGAAATAT-AATAATATTATATAGTTTTTTAAAACA
5690270 TTTTTGAAA
65 TTTTTGAAA
5690279 ATATATATTATATAGTTTTTAAAACATTTTGGAAATATATATAATATTATATAGTTTTTTGAAAA
1 ATATATATTATATAGTTTTTAAAACATTTT-GAAATATA-ATAATATTATATAGTTTTTT-AAAA
5690344 -ATCTTTTTGGAAA
63 CA--TTTTT-GAAA
*
5690357 ATGCATATAATATATAGTTTTTAAAATAACATTTTAGAAAT-TAAT-ATATTATATA-TTTT
1 AT--ATATATTATATAGTTTTT--AA-AACATTTT-GAAATATAATAATATTATATAGTTTT
5690416 CGAAATTGTT
Statistics
Matches: 118, Mismatches: 5, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
71 28 0.24
72 5 0.04
73 7 0.06
74 7 0.06
75 6 0.05
76 4 0.03
77 5 0.04
78 6 0.05
79 4 0.03
80 27 0.23
81 2 0.02
82 4 0.03
83 13 0.11
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (73 bp):
ATATATATTATATAGTTTTTAAAACATTTTGAAATATAATAATATTATATAGTTTTTTAAAACAT
TTTTGAAA
Found at i:5690455 original size:4 final size:4
Alignment explanation
Indices: 5690432--5690482 Score: 52
Period size: 4 Copynumber: 12.8 Consensus size: 4
5690422 TGTTTTTATT
* *
5690432 TTTA TTTT TATTA TTTTA TTTA TTTA TTTA TTT- TTT- CTTA TTTA TTTA
1 TTTA TTTA T-TTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
5690480 TTT
1 TTT
5690483 TTTCTGTTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 5 0.12
4 29 0.73
5 5 0.12
6 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:5690460 original size:22 final size:22
Alignment explanation
Indices: 5690426--5690485 Score: 50
Period size: 24 Copynumber: 2.6 Consensus size: 22
5690416 CGAAATTGTT
* *
5690426 TTTATTTTTATTTTTATTATTTTA
1 TTTATTTAT-TTTTTATTA-TTAA
* *
5690450 TTTATTTATTTATTTTTTCTT-A
1 TTTATTTATTT-TTTATTATTAA
5690472 TTTATTTATTTTTT
1 TTTATTTATTTTTT
5690486 CTGTTTAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 3 0.09
22 12 0.38
23 4 0.12
24 13 0.41
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (22 bp):
TTTATTTATTTTTTATTATTAA
Found at i:5690484 original size:18 final size:18
Alignment explanation
Indices: 5690426--5690487 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 18
5690416 CGAAATTGTT
*
5690426 TTTA-TTTTTATT-TTTA
1 TTTATTTTTTCTTATTTA
*
5690442 -TTATTTTAT-TTATTTA
1 TTTATTTTTTCTTATTTA
5690458 TTTATTTTTTCTTATTTA
1 TTTATTTTTTCTTATTTA
5690476 TTTATTTTTTCT
1 TTTATTTTTTCT
5690488 GTTTAGGGTC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
15 5 0.12
16 8 0.20
17 8 0.20
18 19 0.47
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTATTTTTTCTTATTTA
Found at i:5691409 original size:992 final size:988
Alignment explanation
Indices: 5689242--5691206 Score: 2769
Period size: 992 Copynumber: 2.0 Consensus size: 988
5689232 ATATAATTTT
** * * **** *
5689242 TGAAACATTTTGAAAATAAATATAATATATAGTTTTTAAAACATTTTTGAAAATATATATTATAT
1 TGAAACATGATGAAAATAAAAATGATATATAGGGCGTAAAACATTCTTGAAAATATATATTATAT
** * * * * * * * * ** *
5689307 AGTTTTTAAAACATTTTGAAAATATATATAATATTATATAGT-TTTTGAAAAATCTTTTTGGAAA
66 AGTTTGGAAAACATCTGGGAAAGAGATATAAGATGACATAGTGGGTGGAAAAATCTTTTTGGAAA
* * * * ** * * * * * * *
5689371 ATGCATATAATATATAGTTTTTAAAATAACATTTTAGAAATTAATATATTATATATTTTCGAAAT
131 ACGCATAGAATAGAGAGAATTT-AAAGAACATTCTACAAATTAAGAGA-TAAAGATTTTCGAAAT
5689436 TG------TTTTTATTTTTATTATTTTATTTATTTATTTATTATTTCTTATTTATTTATTTTTTC
194 TGTTTTTATTTTTATTTTTATTATTTTATTTATTTATTTATTATTTCTTATTTATTTATTTTTTC
5689495 TGTTCAGGGTCCAAAATGAGGTTCGAATAGTCCAAGAGTTGGGCCTGAACCAGCCCAGCAGCGTC
259 TGTTCAGGGTCCAAAATGAGGTTCGAATAGTCCAAGAGTTGGGCCTGAACCAGCCCAGCAGCGTC
* *
5689560 TAGGGTTTCTCAACTTAGTCCCAACGCCGCACAACTTACGACCGTTAGATCAAGGAGTGATCAAC
324 TAGGGTTTCTCAACTTAGACCCAACGCCGCACAACTTACGACCGTTAGATCAAGCAGTGATCAAC
5689625 GGCTCAATTCGCGTGATAACTAGGGTTCTGAAGCCCCAAATATCTCATCAAATGCGCAGCCAGAT
389 GGCTCAATTCGCGTGATAACTAGGGTTCTGAAGCCCCAAATATCTCATCAAATGCGCAGCCAGAT
* * * *
5689690 CCAGATCGTTGGATCTGATCCAATCCAACGGTCATAAATGTCCCAGAACGTTCTGGAATGCAAGA
454 CCAGACCGTTGGATCTGACCCAATCCAACAGTCAGAAATGTCCCAGAACGTTCTGGAATGCAAGA
*
5689755 CGAGATTGCAAATCGTCCATCGACCGAGATCCCCGGTACCCGAAGCTGGAATCCTCACAACAACA
519 CGAGATTGCAAATCGTCCACCGACCGAGATCCCCGGTACCCGAAGCTGGAATCCTCACAACAACA
* * * * *
5689820 TCCCAGAAAATGGGTATCCTACATACCGAGAATCGCGCCACGAACACCAAACGGGATTGACCCAT
584 GCCCAGAAAATGGGTATCATACATACCGAGAATCGCGCCACGAACACCAAACAGGACTAACCCAT
* * *
5689885 CTCGTGATGTTCAGCAACGTTCACCGGCCGAGAGGGTATAAATACCCCCAGACAGAACGAAACCA
649 CCCGTGATGTTCAGCAACATTCACCAGCCGAGAGGGTATAAATACCCCCAGACAGAACGAAACCA
5689950 AGGGGGAATCATCAAAGTGCACAAAGCACCACCAGAGAACAGCATCCACAAAACACAGTAAACCA
714 AGGGGGAATCATCAAAGTGCACAAAGCACCACCAGAGAACAGCATCCACAAAACACAGTAAACCA
5690015 AGATATCAACAGTACACAACCAGATCGAAAAACCAAACGCACAAGAGAGAACCAACAACAGAACC
779 AGATATCAACAGTACACAACCAGATCGAAAAACCAAACGCACAAGAGAGAACCAACAACAGAACC
* *
5690080 CACGAGTAAACCAAAAACCAAAGGCAACATCACAAAACTGAAACCATAGAAAATACCAAAGGCCG
844 CACGAGTAAACCAAAAACCAAAGGCAACATCACAAAACCGAAACCACAGAAAATACCAAAGGCCG
* * * * * * *
5690145 AAGCACCGCAAAAATCCAAGCAAAATATAAAACAAAGCAAAGTCAAGATACCGCATCGAAAATAT
909 AAGCACCCCAAAAATCCAAGCAAAATATAAAAAAAAGCAAAGTCAAAAGACCCCATCGAAAACAG
* * * * *
5690210 ATATATTATATAATTTT
974 AGATATCAGAGAA--TG
** * * **** *
5690227 TGAAACATTTTGAAAATAAATATTATATATAGTTTTTAAAACATTTTTGAAAATATATATTATAT
1 TGAAACATGATGAAAATAAAAATGATATATAGGGCGTAAAACATTCTTGAAAATATATATTATAT
** * * * * * * * *** *
5690292 AGTTTTTAAAACATTTTGGAAATATATATAATATTATATAGTTTTTTGAAAAATCTTTTTGGAAA
66 AGTTTGGAAAACATCTGGGAAAGAGATATAAGATGACATAGTGGGTGGAAAAATCTTTTTGGAAA
* * * * ** * * * * * * *
5690357 ATGCATATAATATATAGTTTTTAAAATAACATTTTAGAAATTAATATATTATATATTTTCGAAAT
131 ACGCATAGAATAGAGAGAATTT-AAAGAACATTCTACAAATTAAGAGA-TAAAGATTTTCGAAAT
*
5690422 TGTTTTTATTTTTATTTTTATTATTTTATTTATTTATTTATTTTTTCTTATTTATTTATTTTTTC
194 TGTTTTTATTTTTATTTTTATTATTTTATTTATTTATTTATTATTTCTTATTTATTTATTTTTTC
*
5690487 TGTTTAGGGTCCAAAATGAGGTTCGAATAGTCCAAGAGTTGGGCCTGAACCAGCCCAGCAGCGTC
259 TGTTCAGGGTCCAAAATGAGGTTCGAATAGTCCAAGAGTTGGGCCTGAACCAGCCCAGCAGCGTC
*
5690552 TAGGGTTTCTCAACTTAGACCCAACGCCGCACAACTTACGGCCGTTAGATCAAGCAGTGATCAAC
324 TAGGGTTTCTCAACTTAGACCCAACGCCGCACAACTTACGACCGTTAGATCAAGCAGTGATCAAC
*
5690617 GGCTCAATTCGCGTGATAACTAGGGTTCTGAAGCCCCAAATATCTCATCAAATGTGCAGCCAGAT
389 GGCTCAATTCGCGTGATAACTAGGGTTCTGAAGCCCCAAATATCTCATCAAATGCGCAGCCAGAT
5690682 CCAGACCGTTGGATCTGACCCAATCCAACAGTCAGAAATGTCCCAGAACGTTCTGGAATGCAAGA
454 CCAGACCGTTGGATCTGACCCAATCCAACAGTCAGAAATGTCCCAGAACGTTCTGGAATGCAAGA
5690747 CGAGATTGCAAATCGTCCACCGACCGAGATCCCCGGTACCCGAAGCTGGAATCCTCACAACAACA
519 CGAGATTGCAAATCGTCCACCGACCGAGATCCCCGGTACCCGAAGCTGGAATCCTCACAACAACA
5690812 GCCC-GAAAAATGGGTATCATACATACCGAGAATCGCGCCACGAACACCAAACAGGACTAACCCA
584 GCCCAG-AAAATGGGTATCATACATACCGAGAATCGCGCCACGAACACCAAACAGGACTAACCCA
* * *
5690876 TCCCGTGATGTTC-GACAACATTCACCAGCCGATAGGGTATAAATACCCCCAGATAGAATGAAAC
648 TCCCGTGATGTTCAG-CAACATTCACCAGCCGAGAGGGTATAAATACCCCCAGACAGAACGAAAC
*
5690940 CAAGGGGGAATCATCAACAGTGCACAAAGCACCACCAGAGAACAGCATCCACAAAACATAGTAAA
712 CAAGGGGGAATCATCAA-AGTGCACAAAGCACCACCAGAGAACAGCATCCACAAAACACAGTAAA
*
5691005 CCAAGATATCAACAGTACACAACCAGATCGAAAAACCAAACGCACAAGAGAGAACCCACAACAGA
776 CCAAGATATCAACAGTACACAACCAGATCGAAAAACCAAACGCACAAGAGAGAACCAACAACAGA
* *
5691070 ACCCATGAGTAAACCAAGAACCAAAGGCAACATCACAAAACCGAAACCACAGAAAATACCAAAGG
841 ACCCACGAGTAAACCAAAAACCAAAGGCAACATCACAAAACCGAAACCACAGAAAATACCAAAGG
* *
5691135 CCGAAGCCCCCCAAAAATCCAAGCAAAATATAAAAAAAAGCAAAGTCAAAAGACCCCGTCGAAAA
906 CCGAAGCACCCCAAAAATCCAAGCAAAATATAAAAAAAAGCAAAGTCAAAAGACCCCATCGAAAA
5691200 CCAGAGA
971 -CAGAGA
5691207 ACCGAGGAGT
Statistics
Matches: 929, Mismatches: 40, Indels: 13
0.95 0.04 0.01
Matches are distributed among these distances:
985 105 0.11
986 89 0.10
991 2 0.00
992 501 0.54
993 229 0.25
994 3 0.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (988 bp):
TGAAACATGATGAAAATAAAAATGATATATAGGGCGTAAAACATTCTTGAAAATATATATTATAT
AGTTTGGAAAACATCTGGGAAAGAGATATAAGATGACATAGTGGGTGGAAAAATCTTTTTGGAAA
ACGCATAGAATAGAGAGAATTTAAAGAACATTCTACAAATTAAGAGATAAAGATTTTCGAAATTG
TTTTTATTTTTATTTTTATTATTTTATTTATTTATTTATTATTTCTTATTTATTTATTTTTTCTG
TTCAGGGTCCAAAATGAGGTTCGAATAGTCCAAGAGTTGGGCCTGAACCAGCCCAGCAGCGTCTA
GGGTTTCTCAACTTAGACCCAACGCCGCACAACTTACGACCGTTAGATCAAGCAGTGATCAACGG
CTCAATTCGCGTGATAACTAGGGTTCTGAAGCCCCAAATATCTCATCAAATGCGCAGCCAGATCC
AGACCGTTGGATCTGACCCAATCCAACAGTCAGAAATGTCCCAGAACGTTCTGGAATGCAAGACG
AGATTGCAAATCGTCCACCGACCGAGATCCCCGGTACCCGAAGCTGGAATCCTCACAACAACAGC
CCAGAAAATGGGTATCATACATACCGAGAATCGCGCCACGAACACCAAACAGGACTAACCCATCC
CGTGATGTTCAGCAACATTCACCAGCCGAGAGGGTATAAATACCCCCAGACAGAACGAAACCAAG
GGGGAATCATCAAAGTGCACAAAGCACCACCAGAGAACAGCATCCACAAAACACAGTAAACCAAG
ATATCAACAGTACACAACCAGATCGAAAAACCAAACGCACAAGAGAGAACCAACAACAGAACCCA
CGAGTAAACCAAAAACCAAAGGCAACATCACAAAACCGAAACCACAGAAAATACCAAAGGCCGAA
GCACCCCAAAAATCCAAGCAAAATATAAAAAAAAGCAAAGTCAAAAGACCCCATCGAAAACAGAG
ATATCAGAGAATG
Found at i:5691854 original size:23 final size:23
Alignment explanation
Indices: 5691819--5691868 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
5691809 TTTATTATTC
** *
5691819 TTTTTTATTTATTATTTTATCAT
1 TTTTTTAAGTATTAGTTTATCAT
* *
5691842 TTTTTTAAGTATTGGTTTATTAT
1 TTTTTTAAGTATTAGTTTATCAT
5691865 TTTT
1 TTTT
5691869 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.02, G:0.06, T:0.72
Consensus pattern (23 bp):
TTTTTTAAGTATTAGTTTATCAT
Found at i:5691876 original size:12 final size:12
Alignment explanation
Indices: 5691807--5691886 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
5691797 TTTCTTTACC
*
5691807 TTTTTATTATTCT
1 TTTTTATTATT-A
5691820 TTTTTATTTATTA
1 TTTTTA-TTATTA
*
5691833 -TTTTATCATT-
1 TTTTTATTATTA
* *
5691843 TTTTTAAGTATTGG
1 TTTTT-ATTATT-A
*
5691857 TTTATTATTTTTA
1 TTT-TTATTATTA
5691870 TTTTTATTATTA
1 TTTTTATTATTA
5691882 TTTTT
1 TTTTT
5691887 GCCTAACATC
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
11 8 0.15
12 22 0.42
13 9 0.17
14 12 0.23
15 2 0.04
ACGTcount: A:0.20, C:0.03, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:5702086 original size:20 final size:20
Alignment explanation
Indices: 5702029--5702086 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
5702019 TTCTTTGTTG
5702029 CCTTTTCTTGAAAATCATTT
1 CCTTTTCTTGAAAATCATTT
** ** *
5702049 TTTTTTCTT---CTTCTTTT
1 CCTTTTCTTGAAAATCATTT
5702066 CCTTTTCTTGAAAATCATTT
1 CCTTTTCTTGAAAATCATTT
5702086 C
1 C
5702087 ACAGCACTAT
Statistics
Matches: 25, Mismatches: 10, Indels: 6
0.61 0.24 0.15
Matches are distributed among these distances:
17 12 0.48
20 13 0.52
ACGTcount: A:0.17, C:0.21, G:0.03, T:0.59
Consensus pattern (20 bp):
CCTTTTCTTGAAAATCATTT
Found at i:5702505 original size:18 final size:19
Alignment explanation
Indices: 5702479--5702520 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5702469 GTGTTATGCC
*
5702479 AGTAAAAATTAAAA-AAAA
1 AGTAAAAATCAAAATAAAA
*
5702497 AGTAGAAATCAAAATAAAA
1 AGTAAAAATCAAAATAAAA
5702516 A-TAAA
1 AGTAAA
5702521 TTAAAAGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (19 bp):
AGTAAAAATCAAAATAAAA
Found at i:5702966 original size:28 final size:28
Alignment explanation
Indices: 5702889--5702983 Score: 102
Period size: 28 Copynumber: 3.3 Consensus size: 28
5702879 ATTTAACTAC
* *
5702889 TTAAAGTAATTTTTAGTCGAAATAAGTAT
1 TTAAAGT-ATTTTTAATCAAAATAAGTAT
* * *
5702918 CTAAACTTATTTTTTTATCAAAATAAGTAT
1 TTAAA-GTA-TTTTTAATCAAAATAAGTAT
5702948 TTAAAGTATTTTTAATCAAAAT-AGATAT
1 TTAAAGTATTTTTAATCAAAATAAG-TAT
5702976 TTAAAGTA
1 TTAAAGTA
5702984 ATCAATTTGT
Statistics
Matches: 55, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
27 2 0.04
28 24 0.44
29 7 0.13
30 22 0.40
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.43
Consensus pattern (28 bp):
TTAAAGTATTTTTAATCAAAATAAGTAT
Found at i:5705670 original size:81 final size:81
Alignment explanation
Indices: 5705570--5706210 Score: 922
Period size: 81 Copynumber: 7.9 Consensus size: 81
5705560 TTCCTCTAAT
* * * * * * *
5705570 GGCATTTAACCCTTCATCTAACTTGCATTATTGGCACCTTTTTGTCAAATGCAAAGTTAGGCATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
*
5705635 TAATCTTTTACCCAAA
66 TAATCTTTTACTCAAA
* * * * *
5705651 AGCGTTTAACCTTTCATCTAACTAGCATGATTGGCACCTTTCTTCCAAATGCACAATTAGGCATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
* * *
5705716 TAACCTTTCACTAAAA
66 TAATCTTTTACTCAAA
* * * *
5705732 GGCATTTAACCTTTCATCTAACTAGCATAATTGGCACCTTTCTGCCAAATGCACATTTAGACATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
5705797 TAATCTTTTACTCAAA
66 TAATCTTTTACTCAAA
** * * * **
5705813 GGTTTTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGCCTAACACACAGTTAGGCATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
5705878 TAATCTTTTACTCAAA
66 TAATCTTTTACTCAAA
* * *
5705894 GGCATTTAACCATTCATCTAACTAGCATAATTGACACATTTCTGCCAAATGCACAGTTAGGCATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
5705959 TAATCTTTTACTCAAA
66 TAATCTTTTACTCAAA
* * * *
5705975 GGCATTTAACATTTCATCTAACTAGCATGATTGACACATTTCTACCAAATGCACAATTAGGCATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
5706040 TAATCTTTTACTCAAA
66 TAATCTTTTACTCAAA
* *
5706056 GGCATTTGACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGACATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
5706121 TAATCTTTTACTCAAA
66 TAATCTTTTACTCAAA
* * *
5706137 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCATATTTCTTCCAAATGCACAGTTAGACATT
1 GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
*
5706202 TAATTTTTT
66 TAATCTTTT
5706211 TTACTCATAA
Statistics
Matches: 505, Mismatches: 55, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 505 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (81 bp):
GGCATTTAACCTTTCATCTAACTAGCATGATTGGCACATTTCTGCCAAATGCACAGTTAGGCATT
TAATCTTTTACTCAAA
Found at i:5705737 original size:22 final size:23
Alignment explanation
Indices: 5705709--5705752 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
5705699 ATGCACAATT
5705709 AGGCATTTAACCTTTCA-CTAAA
1 AGGCATTTAACCTTTCATCTAAA
5705731 AGGCATTTAACCTTTCATCTAA
1 AGGCATTTAACCTTTCATCTAA
5705753 CTAGCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (23 bp):
AGGCATTTAACCTTTCATCTAAA
Found at i:5706646 original size:19 final size:19
Alignment explanation
Indices: 5706622--5706671 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
5706612 TCTATATTAT
5706622 AGTATCGATACTCCCTTTC
1 AGTATCGATACTCCCTTTC
*** *
5706641 AGTATCGATACTTTTTTTT
1 AGTATCGATACTCCCTTTC
5706660 AGTATCGATACT
1 AGTATCGATACT
5706672 AATGGAATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.12, T:0.44
Consensus pattern (19 bp):
AGTATCGATACTCCCTTTC
Found at i:5712845 original size:81 final size:81
Alignment explanation
Indices: 5712739--5713152 Score: 535
Period size: 81 Copynumber: 5.1 Consensus size: 81
5712729 TCTTTCCTTT
* * ** * * * **
5712739 AAAGGCATTTAACCTTTCGTATAACTTTCATTATTGGCACCTTTTTGTTAAATGCACAATTAGGC
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTAGCACCTTTCTGCCAAATGCACAATTAGGC
* *
5712804 ATTTATTCTTTTACCC
66 ATTTAATCTTTTACTC
* * * *
5712820 AAAGTCATTTAACCTTTCATCTAACTAGCATGATTAACACCTTTCTGCCGAATGCATAATTAGGC
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTAGCACCTTTCTGCCAAATGCACAATTAGGC
5712885 ATTTAATCTTTTACTC
66 ATTTAATCTTTTACTC
* * * * *
5712901 AAAGGCATTTAACCTTTCATCTAACTAGCATAATTAGCACATTTCTGCCAAATGAACAGTTAGAC
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTAGCACCTTTCTGCCAAATGCACAATTAGGC
5712966 ATTTAATCTTTTACTC
66 ATTTAATCTTTTACTC
* ** *
5712982 AAAGGCATTTAACCTTTCATCTAACTAGCATGATT-GAAATTTTTCTGCCAAATGCACAGTTAGG
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTAG-CACCTTTCTGCCAAATGCACAATTAGG
*
5713046 CATTTAATATTTTACTC
65 CATTTAATCTTTTACTC
* * *
5713063 AAAGACATTTAACCTTTCATCTAACTAGCGTGATT-GACACCTTTCTGCCAAATACACAATTAGG
1 AAAGGCATTTAACCTTTCATCTAACTAGCATGATTAG-CACCTTTCTGCCAAATGCACAATTAGG
5713127 CATTTAATCTTTTACTC
65 CATTTAATCTTTTACTC
*
5713144 AAAGACATT
1 AAAGGCATT
5713153 GTCGTAACCG
Statistics
Matches: 293, Mismatches: 39, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
80 1 0.00
81 292 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (81 bp):
AAAGGCATTTAACCTTTCATCTAACTAGCATGATTAGCACCTTTCTGCCAAATGCACAATTAGGC
ATTTAATCTTTTACTC
Found at i:5715220 original size:15 final size:15
Alignment explanation
Indices: 5715200--5715231 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5715190 TTTGGGCCTG
5715200 TAATAATAATAATAT
1 TAATAATAATAATAT
5715215 TAATAATAATAATAT
1 TAATAATAATAATAT
5715230 TA
1 TA
5715232 TAAAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAATAATAATAATAT
Found at i:5715597 original size:133 final size:138
Alignment explanation
Indices: 5715431--5715758 Score: 398
Period size: 133 Copynumber: 2.4 Consensus size: 138
5715421 AATCTAGCAA
5715431 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
5715496 AAACTCTATCTGGAAA-CT-GACCCTCAA-AAGG-AGTT-GTTGATTCAACTTCATATG-TGATG
66 AAACTCTATCTGAAAATATAGACCCTCAAGAAGGTAGTTCGTTCATTCAACTCCATA-GATGATG
*
5715555 AATTAAGGC
130 AATCAAGGC
*
5715564 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * * * * ** *
5715629 GAACTTTCTTTGAAAATATAGATCCTCAAGTGAGGTTTTTCTTTCATTCAACTCCATAGATGATG
66 AAACTCTATCTGAAAATATAGACCCTCAAG-AAGGTAGTTCGTTCATTCAACTCCATAGATGATG
**
5715694 AATCAAGTT
130 AATCAAGGC
* ** * *
5715703 AAGATCAAACAAGTTGTTCTCATTATGAACGTCTTCTTCCTCTTCAGATGAGTTCT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCT
5715759 CATTATAAAC
Statistics
Matches: 165, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
133 75 0.45
134 1 0.01
135 8 0.05
137 3 0.02
138 3 0.02
139 75 0.45
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (138 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
AAACTCTATCTGAAAATATAGACCCTCAAGAAGGTAGTTCGTTCATTCAACTCCATAGATGATGA
ATCAAGGC
Found at i:5715930 original size:122 final size:121
Alignment explanation
Indices: 5715710--5716290 Score: 747
Period size: 122 Copynumber: 4.7 Consensus size: 121
5715700 GTTAAGATCA
* * * *
5715710 AACAAGTTGTTCTCATTATGAACGTCTTCTTCCTCTTCAGATGAG---TTCTCATTATAAACCCT
1 AACAAGTTCTTCTCATTATGAAC-TTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * *
5715772 TCTAGAAATGTTGATGCTGATCTATCTCGTTCTGTGATAGAGTCGAGCAAAAGGTTG
65 TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTG
*
5715829 AACAAGCTCTTCTCATTATGAACTTTGTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTTT-TCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * * *
5715894 TTTGGAAATGTTGATGCTGATCTATCTCCTTTTGTGATAAAGTCATGCAAAAGGTTG
65 TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTG
* *
5715951 AACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCCTCAGATGAATTCTTCTCATTATGAACTCT
1 AACAAGTTCTTCTCATTATGAACTT-TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCT
* * *
5716016 TCTAGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAGAGTCAAGCAAAAGGTTG
65 TCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTG
* *
5716073 AACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAAATGAGTTCTTCTCATTATGAATTCT
1 AACAAGTTCTTCTCATTATGAACTT-TTCTTCCTCTTC-----AG-----------ATGAGTTCT
*
5716138 TCTCATTATGAACTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCAAGCA
49 TCTCATTATGAACTCTTCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCA
*
5716203 AAATGTTG
114 AAAGGTTG
5716211 AACAAGTTCTTCTCATTATGAACTTCCTT-TTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
1 AACAAGTTCTTCTCATTATGAACTT--TTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTC
5716275 TTCTGGAAATGTTGAT
64 TTCTGGAAATGTTGAT
5716291 CCATCAAGTG
Statistics
Matches: 411, Mismatches: 29, Indels: 41
0.85 0.06 0.09
Matches are distributed among these distances:
118 2 0.00
119 39 0.09
122 250 0.61
123 1 0.00
127 2 0.00
133 2 0.00
138 113 0.27
139 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (121 bp):
AACAAGTTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTT
CTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCAAGCAAAAGGTTG
Found at i:5716140 original size:19 final size:16
Alignment explanation
Indices: 5716113--5716156 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
5716103 TCCTCTTCAA
*
5716113 ATGAGTTCTTCTCATT
1 ATGAATTCTTCTCATT
5716129 ATGAATTCTTCTCATT
1 ATGAATTCTTCTCATT
*
5716145 ATGAACTCTTCT
1 ATGAATTCTTCT
5716157 GGAAATGTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (16 bp):
ATGAATTCTTCTCATT
Found at i:5716244 original size:138 final size:138
Alignment explanation
Indices: 5715991--5716278 Score: 522
Period size: 138 Copynumber: 2.1 Consensus size: 138
5715981 TCCTCCTCAG
*
5715991 ATGAATTCTTCTCATTATGAACTCTTCTAGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAG
1 ATGAATTCTTCTCATTATGAACTCTTCTAGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAG
5716056 AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAAATGAGTTC
66 AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAAATGAGTTC
5716121 TTCTCATT
131 TTCTCATT
*
5716129 ATGAATTCTTCTCATTATGAACTCTTCTGGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAG
1 ATGAATTCTTCTCATTATGAACTCTTCTAGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAG
* * *
5716194 AGTCAAGCAAAATGTTGAACAAGTTCTTCTCATTATGAACTTCCTTTTCCTCTTCAGATGAGTTC
66 AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAAATGAGTTC
5716259 TTCTCATT
131 TTCTCATT
*
5716267 ATGAACTCTTCT
1 ATGAATTCTTCT
5716279 GGAAATGTTG
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
138 144 1.00
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (138 bp):
ATGAATTCTTCTCATTATGAACTCTTCTAGAAATGTTGATGTTGATCTATCTCCTTCTGTGATAG
AGTCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCCTCTTCCTCTTCAAATGAGTTC
TTCTCATT
Found at i:5716703 original size:22 final size:22
Alignment explanation
Indices: 5716678--5716756 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
5716668 AATAAAGCTT
* * *
5716678 TCATATTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGTGAATCTA
5716700 TCATCTTTGAAGAGTGAATCTA
1 TCATCTTTGAAGAGTGAATCTA
5716722 TCATCTTTGAAGAGTGAATCTA
1 TCATCTTTGAAGAGTGAATCTA
5716744 TCATCTTTGAAGA
1 TCATCTTTGAAGA
5716757 ATGTAGATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGTGAATCTA
Found at i:5717226 original size:54 final size:54
Alignment explanation
Indices: 5717119--5717230 Score: 179
Period size: 54 Copynumber: 2.1 Consensus size: 54
5717109 ATAATAACTA
* * **
5717119 GTTCGTAAAACATTTGACAACATATTCATCCTTTCCTGTGGCTTCTGTACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTACACAGAT
*
5717173 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTACCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTACACAGAT
5717227 GTTC
1 GTTC
5717231 ATCAGTGAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCATGTGGCTTCTACACAGAT
Found at i:5722004 original size:15 final size:15
Alignment explanation
Indices: 5721984--5722015 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5721974 TGCAATTAAT
5721984 AATGAATGTATGCAA
1 AATGAATGTATGCAA
5721999 AATGAATGTATGCAA
1 AATGAATGTATGCAA
5722014 AA
1 AA
5722016 GGTATTGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:5725946 original size:22 final size:23
Alignment explanation
Indices: 5725903--5725954 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
5725893 ATTTCAAGAA
*
5725903 AATATAT-TAATTTTTATATTTT
1 AATATATATAATTTTTAGATTTT
*
5725925 AATATATAT-ATTTTTAGGTTTT
1 AATATATATAATTTTTAGATTTT
*
5725947 TATATATA
1 AATATATA
5725955 AGATGTTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 25 0.96
23 1 0.04
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
AATATATATAATTTTTAGATTTT
Found at i:5726092 original size:14 final size:14
Alignment explanation
Indices: 5726060--5726097 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
5726050 ACATTTCCCT
5726060 AAAAA-TAATAAAA
1 AAAAATTAATAAAA
5726073 AAAAATTAATAAAA
1 AAAAATTAATAAAA
**
5726087 TTAAATTAATA
1 AAAAATTAATA
5726098 TACATAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.23
14 17 0.77
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAAATTAATAAAA
Found at i:5727456 original size:3 final size:3
Alignment explanation
Indices: 5727448--5727538 Score: 107
Period size: 3 Copynumber: 31.0 Consensus size: 3
5727438 TTTGGGCCTG
* * *
5727448 TAA TAA TAA TAA TAA TAT TGA TAA TAA TAA TAA TAA TAA TAA T-A TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5727495 TTA TAA TTAA -AA TAA TAA TTA TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5727539 ATAAAATGGA
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
2 6 0.08
3 65 0.88
4 3 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:5739183 original size:66 final size:66
Alignment explanation
Indices: 5739077--5739206 Score: 181
Period size: 66 Copynumber: 2.0 Consensus size: 66
5739067 GGTATAAAGA
* * * *
5739077 CTCTGGAAGGTTCAGTCGCTGTTGGTAATTCCTTGTATAGGTTCATCATCGACT-AGTAATTCCT
1 CTCTGGAAGGTTCAGTCGATGCTGGTAATTCCTTGTATAGGTTCAACACCGACTGA-TAATTCCT
5739141 AT
65 AT
* * *
5739143 CTCTGGCAGGTTCAGTCGATGCTGGTATTTCCTTTTATAGGTTCAACACCGACTGATAATTCCT
1 CTCTGGAAGGTTCAGTCGATGCTGGTAATTCCTTGTATAGGTTCAACACCGACTGATAATTCCT
5739207 TATAGACCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
66 55 0.98
67 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (66 bp):
CTCTGGAAGGTTCAGTCGATGCTGGTAATTCCTTGTATAGGTTCAACACCGACTGATAATTCCTA
T
Found at i:5743360 original size:31 final size:31
Alignment explanation
Indices: 5743336--5743442 Score: 110
Period size: 31 Copynumber: 3.3 Consensus size: 31
5743326 TCAGTCACTG
5743336 CTGGTAATTCCTTGTATAGGTTCAGCACCGA
1 CTGGTAATTCCTTGTATAGGTTCAGCACCGA
* *
5743367 CTGGTAATTCTTATCTCTG-GTAGGTTCAGTCACTG-
1 CTGGTAATTC----CT-TGTATAGGTTCAG-CACCGA
* *
5743402 CTGATAATTCCTTTTATAGGTTCAGCACCGA
1 CTGGTAATTCCTTGTATAGGTTCAGCACCGA
5743433 CTGGTAATTC
1 CTGGTAATTC
5743443 TTTATGGACC
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
30 5 0.08
31 30 0.49
35 20 0.33
36 6 0.10
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (31 bp):
CTGGTAATTCCTTGTATAGGTTCAGCACCGA
Found at i:5743421 original size:66 final size:66
Alignment explanation
Indices: 5743315--5743444 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
5743305 GGTATGAAGA
* *
5743315 CTCTGGAATGTTCAGTCACTGCTGGTAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCTTA
1 CTCTGGAAGGTTCAGTCACTGCTGATAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCTTA
5743380 T
66 T
* *
5743381 CTCTGGTAGGTTCAGTCACTGCTGATAATTCCTTTTATAGGTTCAGCACCGACTGGTAATTCTT
1 CTCTGGAAGGTTCAGTCACTGCTGATAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCTT
5743445 TATGGACCTA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (66 bp):
CTCTGGAAGGTTCAGTCACTGCTGATAATTCCTTGTATAGGTTCAGCACCGACTGGTAATTCTTA
T
Found at i:5743501 original size:31 final size:31
Alignment explanation
Indices: 5743463--5743546 Score: 100
Period size: 31 Copynumber: 2.7 Consensus size: 31
5743453 TAAGGTGACC
**
5743463 CTTGGGTAGGCTCTGCGGCCCCGAGATTTTT
1 CTTGGGTAGGCTCTGCGGCCCCGAGAACTTT
* *
5743494 CTTGGGTAGGC-CTCGTGGCCCTGAGAACTTT
1 CTTGGGTAGGCTCT-GCGGCCCCGAGAACTTT
5743525 CTTGGGTAGGCTCT-CAGGCCCC
1 CTTGGGTAGGCTCTGC-GGCCCC
5743547 AAGGTGCTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
30 2 0.05
31 40 0.91
32 2 0.05
ACGTcount: A:0.11, C:0.29, G:0.32, T:0.29
Consensus pattern (31 bp):
CTTGGGTAGGCTCTGCGGCCCCGAGAACTTT
Found at i:5745257 original size:138 final size:138
Alignment explanation
Indices: 5745037--5745442 Score: 447
Period size: 138 Copynumber: 2.9 Consensus size: 138
5745027 ATTCGCATTA
* * * * * * * *
5745037 AGGAAGTCTGATTGTCTGAAGATGACACTGCTCCTTCGGGTTGAGGAGATCTGGTCGGTGGACGA
1 AGGAAGTATGGTTATCTGAAGATGACGCTACTTCTACGCGTTGAGGAGATCTGGTCGGTGGACGA
* *
5745102 AATTTTTCCTATGTGATGAGGACGTCTACCTATATTTAGGGATAATTTGGAGACAACACGGTTCC
66 CA-TTATCCTATGTGATGAGGACGTCTACCTATATTTAGGGATAATTTGGAGACAACACGGTTCC
5745167 TACATGATG
130 TACATGATG
* * * * * *
5745176 AGGAAGTCTGGTTATCTGAGGATGACGTTGCTT-TACGTGTTGAGAAGATCTGGTCGGTGGACGA
1 AGGAAGTATGGTTATCTGAAGATGACGCTACTTCTACGCGTTGAGGAGATCTGGTCGGTGGACGA
** * * * *
5745240 CATTGATCCTACATGATGAGGACATCTAGCC-ATCTTTAGGGATAATTTGGAGACAATAAGGTTC
66 CATT-ATCCTATGTGATGAGGACGTCTA-CCTATATTTAGGGATAATTTGGAGACAACACGGTTC
**
5745304 CTATGTGATG
129 CTACATGATG
** *
5745314 AGGAAGTATGGTTATCTGAAGATGACGCTACTTCTACGCGTTGAGGAGATCTGGTCAATGGATGA
1 AGGAAGTATGGTTATCTGAAGATGACGCTACTTCTACGCGTTGAGGAGATCTGGTCGGTGGACGA
* * * * * * *
5745379 CATTATTCCTATGTGATAAGTACGTCTAGCTATTTTTTAGGGATAATTTAGAAATAACACGGTT
66 CATTA-TCCTATGTGATGAGGACGTCTACCTA-TATTTAGGGATAATTTGGAGACAACACGGTT
5745443 GAAATGACCA
Statistics
Matches: 221, Mismatches: 40, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
137 2 0.01
138 117 0.53
139 77 0.35
140 25 0.11
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (138 bp):
AGGAAGTATGGTTATCTGAAGATGACGCTACTTCTACGCGTTGAGGAGATCTGGTCGGTGGACGA
CATTATCCTATGTGATGAGGACGTCTACCTATATTTAGGGATAATTTGGAGACAACACGGTTCCT
ACATGATG
Found at i:5746088 original size:66 final size:68
Alignment explanation
Indices: 5746008--5746241 Score: 264
Period size: 66 Copynumber: 3.5 Consensus size: 68
5745998 TGTCTCGGGT
* * * * * * *
5746008 GAGATAAAATTTTGTTTTGAGTGAAA-TATTTCAAAAATTT-TGCTTCAAGGGAAAATTGTCTCA
1 GAGACAAAACTTTGTTTTGAGAGAAACAATTTCAAAAGTTTATGTTTCAAGGGAAAACTGTCTCA
5746071 AGC
66 AGC
** * ** *
5746074 GAGATGAAACTTTGTTTCGAGAGAAACAATTTCAATGGTTTATGTTTC-AGGAAAAACTGTCTCA
1 GAGACAAAACTTTGTTTTGAGAGAAACAATTTCAAAAGTTTATGTTTCAAGGGAAAACTGTCTCA
5746138 AGC
66 AGC
* *
5746141 GAGACAAAACTTTGTTTTGAGAGAAACAATCTC-AAAGTTTATGTTTCAAGAG-AAACTGTCTCA
1 GAGACAAAACTTTGTTTTGAGAGAAACAATTTCAAAAGTTTATGTTTCAAGGGAAAACTGTCTCA
5746204 AGC
66 AGC
* *
5746207 GAGACAAAACTTTGTTTTTAG-GAAAACAATCTCAA
1 GAGACAAAACTTTGTTTTGAGAG-AAACAATTTCAA
5746242 GAGAGATCAA
Statistics
Matches: 143, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
65 1 0.01
66 78 0.55
67 59 0.41
68 5 0.03
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (68 bp):
GAGACAAAACTTTGTTTTGAGAGAAACAATTTCAAAAGTTTATGTTTCAAGGGAAAACTGTCTCA
AGC
Found at i:5747534 original size:45 final size:45
Alignment explanation
Indices: 5747483--5747599 Score: 209
Period size: 45 Copynumber: 2.6 Consensus size: 45
5747473 AATTTTGTAT
5747483 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
5747528 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
1 CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
* *
5747573 CAATATACTTGCCA-TTATTTCATAAGC
1 CAATATACTTACCATTTATTCCATAAGC
5747600 ATGCTTACCA
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
44 12 0.17
45 58 0.83
ACGTcount: A:0.32, C:0.22, G:0.07, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTAC
Found at i:5747716 original size:40 final size:40
Alignment explanation
Indices: 5747672--5747752 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
5747662 ATATGAGTCA
* * *
5747672 AATGTTGCA-TCAAAGTGTTGAGGTCGAGCTTTGCTCACCT
1 AATGTTGCACT-AAAGTGCTGAGGTCGAGCTTTACCCACCT
**
5747712 AATGTTGCACTGTAGTGCTGAGGTCGAGCTTTACCCACCT
1 AATGTTGCACTAAAGTGCTGAGGTCGAGCTTTACCCACCT
5747752 A
1 A
5747753 GTACACTGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (40 bp):
AATGTTGCACTAAAGTGCTGAGGTCGAGCTTTACCCACCT
Found at i:5750663 original size:2 final size:2
Alignment explanation
Indices: 5750656--5750684 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5750646 AGCTTTATTG
5750656 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5750685 ATTGCCTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5753773 original size:81 final size:81
Alignment explanation
Indices: 5753674--5754071 Score: 532
Period size: 81 Copynumber: 4.9 Consensus size: 81
5753664 CTATTCCAAA
* * *
5753674 AGTAAAAGATTAATGGCCTAGCTATGCATTTGGCAGAAATGTGTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
5753739 AGGTTAAATACCGTTG
66 AGGTTAAATACCGTTG
* * *
5753755 AGTAAAAGATTAATGGCCTAGCTATACATTTGGCAGAAAGGTGTCAATTATGCCAGTTAAATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
* * * *
5753820 CGATTAAATATCATTG
66 AGGTTAAATACCGTTG
* * *
5753836 AGTAAAAGATTAATGTCCTAGTTGTACATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
**
5753901 CA-GTTAAATATAGTTG
66 -AGGTTAAATACCGTTG
* * * *
5753917 AGTAAAAGATTAATGGCCTAGCTGTGCATCTGGTAGAAAGATGTCAATTATGCCAATTAGAT-AA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
5753981 ACGGTTAAATACCGTTG
66 A-GGTTAAATACCGTTG
** * *
5753998 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGATAGAAAAGAT-TCAATTATGCAAGTTAGATGA
1 AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAG-AAAGGTGTCAATTATGCCAGTTAGATGA
*
5754062 AAGGCTAAAT
65 AAGGTTAAAT
5754072 GCATTTGGGT
Statistics
Matches: 282, Mismatches: 30, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
79 1 0.00
80 2 0.01
81 270 0.96
82 9 0.03
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (81 bp):
AGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCGTTG
Found at i:5759523 original size:16 final size:16
Alignment explanation
Indices: 5759493--5759525 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5759483 ATTATTGATG
5759493 AATTTGTAAGTAAATA
1 AATTTGTAAGTAAATA
5759509 AATTT-TAAGTCAAATA
1 AATTTGTAAGT-AAATA
5759525 A
1 A
5759526 TAAATAACTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.36
Consensus pattern (16 bp):
AATTTGTAAGTAAATA
Found at i:5760941 original size:61 final size:61
Alignment explanation
Indices: 5760846--5760971 Score: 180
Period size: 61 Copynumber: 2.1 Consensus size: 61
5760836 TATGAACCTA
** *
5760846 AGTGCCAATACACATAAGGTCGGGCCCACCATATGCACTAAATGTTGTTTATATACACTAT
1 AGTGCCAATACACATAAGGTCGGGCCCACCATATGCACTAAATGTCCTTTATATACAATAT
* * * * *
5760907 AGTGCTAATACACATAAGGTTGTGCCCACCATATGCACTAAGTGTCCTTTATATATAATAT
1 AGTGCCAATACACATAAGGTCGGGCCCACCATATGCACTAAATGTCCTTTATATACAATAT
5760968 AGTG
1 AGTG
5760972 GTAAACTGAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 57 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.30
Consensus pattern (61 bp):
AGTGCCAATACACATAAGGTCGGGCCCACCATATGCACTAAATGTCCTTTATATACAATAT
Found at i:5761788 original size:32 final size:32
Alignment explanation
Indices: 5761711--5761796 Score: 111
Period size: 32 Copynumber: 2.7 Consensus size: 32
5761701 AGTATAGTTT
* *
5761711 GCATATTAAATAATAGTCTGCATGTGATAGTT
1 GCATATTAAATAATAGTTTGCATGTGATAGTA
* *
5761743 GCTTGTTAAATAATAGTTTGCATGTGATAGTA
1 GCATATTAAATAATAGTTTGCATGTGATAGTA
* *
5761775 GCATATTATATAAT-GGTTGCAT
1 GCATATTAAATAATAGTTTGCAT
5761797 TGCATATGGT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
31 7 0.15
32 39 0.85
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.40
Consensus pattern (32 bp):
GCATATTAAATAATAGTTTGCATGTGATAGTA
Found at i:5762282 original size:42 final size:42
Alignment explanation
Indices: 5762218--5762336 Score: 177
Period size: 42 Copynumber: 2.8 Consensus size: 42
5762208 TTCCCCGAAA
5762218 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATATTT
1 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATATTT
* * * *
5762260 TCTTC-TGTTTGTTTCATGTAATTCATTTTCCGAAAAATGTTT
1 TC-CCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATATTT
*
5762302 TCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAA
5762337 TGTAATTCAT
Statistics
Matches: 67, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
41 1 0.01
42 65 0.97
43 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (42 bp):
TCCCGTGTTTGTTTCATGTAATTCGTTTTCCGGAAAATATTT
Found at i:5762417 original size:14 final size:14
Alignment explanation
Indices: 5762398--5762435 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
5762388 ACTTACGGAT
5762398 TCATTTTCCGTAAG
1 TCATTTTCCGTAAG
5762412 TCATTTTCCGTAAG
1 TCATTTTCCGTAAG
5762426 TCATTTTCCG
1 TCATTTTCCG
5762436 AACTTTTCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.13, T:0.45
Consensus pattern (14 bp):
TCATTTTCCGTAAG
Found at i:5762565 original size:29 final size:33
Alignment explanation
Indices: 5762528--5762592 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 33
5762518 CATCAAAATA
*
5762528 TTAATTA-TTAAAAT-ATTTAA-AATATATTTT
1 TTAATTATTTAAAATAATATAATAATATATTTT
*
5762558 TTAA-TATTTAAAATAATATAATATTATATTTT
1 TTAATTATTTAAAATAATATAATAATATATTTT
5762590 TTA
1 TTA
5762593 GTTTAATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 2 0.07
30 11 0.37
31 5 0.17
32 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTAATTATTTAAAATAATATAATAATATATTTT
Found at i:5762586 original size:22 final size:21
Alignment explanation
Indices: 5762539--5762588 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5762529 TAATTATTAA
* *
5762539 AATATTTAAAATATATTTTTT
1 AATATTTAAAATATATATATT
5762560 AATATTTAAAATAATATAATATT
1 AATATTTAAAAT-ATAT-ATATT
5762583 -ATATTT
1 AATATTT
5762589 TTTAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.48
22 10 0.40
23 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATATTTAAAATATATATATT
Found at i:5762598 original size:30 final size:31
Alignment explanation
Indices: 5762550--5762617 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 31
5762540 ATATTTAAAA
5762550 TATATTTTTTAATATTTAAAATAATATAAT-AT
1 TATATTTTTTAATATTT--AATAATATAATAAT
*
5762582 TATATTTTTT-A-GTTTAATAATATAATCAAT
1 TATATTTTTTAATATTTAATAATATAAT-AAT
5762612 TATATT
1 TATATT
5762618 ATAATAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
28 11 0.33
30 11 0.33
31 1 0.03
32 10 0.30
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (31 bp):
TATATTTTTTAATATTTAATAATATAATAAT
Found at i:5762622 original size:23 final size:23
Alignment explanation
Indices: 5762596--5762663 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
5762586 TTTTTTAGTT
5762596 TAATAATATAATCA-ATTATATTA
1 TAATAATATAA-CATATTATATTA
*
5762619 TAATAATATAAGATATTATATTA
1 TAATAATATAACATATTATATTA
*
5762642 TAATAATATAAGATATTATATT
1 TAATAATATAACATATTATATT
5762664 TTTTTTATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
22 1 0.02
23 42 0.98
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (23 bp):
TAATAATATAACATATTATATTA
Found at i:5762682 original size:32 final size:30
Alignment explanation
Indices: 5762634--5762742 Score: 100
Period size: 32 Copynumber: 3.6 Consensus size: 30
5762624 ATATAAGATA
*
5762634 TTATATTATAATAATATA-AGATATTATATTTTT
1 TTATATTTTAATAATATATA-ATA--AT-TTTTT
5762667 TT-TATTTTAATAATATATAATAATTTTTT
1 TTATATTTTAATAATATATAATAATTTTTT
*
5762696 TTATATATTTAATAATGA-ATAAT-ATTATTT
1 TTATAT-TTTAATAAT-ATATAATAATTTTTT
* *
5762726 ATATATTTAAATAATAT
1 TTATATTTTAATAATAT
5762743 TTTAGTAAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
28 1 0.01
29 15 0.22
30 16 0.24
31 14 0.21
32 18 0.27
33 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TTATATTTTAATAATATATAATAATTTTTT
Found at i:5762708 original size:28 final size:28
Alignment explanation
Indices: 5762661--5762740 Score: 85
Period size: 28 Copynumber: 2.8 Consensus size: 28
5762651 AAGATATTAT
5762661 ATTTTTTTTAT-T-TTAATAATATAT-AATA
1 ATTTTTTTTATATATT--TAATA-ATGAATA
5762689 ATTTTTTTTATATATTTAATAATGAATA
1 ATTTTTTTTATATATTTAATAATGAATA
* *
5762717 ATATTATTTATATATTTAAATAAT
1 ATTTTTTTTATATATTT-AATAAT
5762741 ATTTTAGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
27 2 0.04
28 35 0.76
29 7 0.15
30 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (28 bp):
ATTTTTTTTATATATTTAATAATGAATA
Found at i:5762912 original size:18 final size:20
Alignment explanation
Indices: 5762885--5762922 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
5762875 TAATAAAATT
5762885 ATAAAAAAA-TA-TTTAATA
1 ATAAAAAAATTATTTTAATA
*
5762903 ATAAATAAATTATTTTAATA
1 ATAAAAAAATTATTTTAATA
5762923 TTTTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 2 0.12
20 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATAAAAAAATTATTTTAATA
Found at i:5763131 original size:20 final size:20
Alignment explanation
Indices: 5763072--5763121 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
5763062 TTTCCAGATG
5763072 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
5763092 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
5763112 TTTTCCAGAA
1 TTTTCCAGAA
5763122 TTCAAATTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:5763150 original size:15 final size:15
Alignment explanation
Indices: 5763104--5763154 Score: 70
Period size: 14 Copynumber: 3.5 Consensus size: 15
5763094 TTCCAGAAAT
**
5763104 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
5763119 G-AATTCAAATT-CA
1 GTAATTCAAATTCCA
5763132 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
5763147 GTAATTCA
1 GTAATTCA
5763155 TTTTCTGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 3 0.09
14 18 0.56
15 11 0.34
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:5765564 original size:35 final size:36
Alignment explanation
Indices: 5765505--5765604 Score: 114
Period size: 35 Copynumber: 2.8 Consensus size: 36
5765495 TTTCGTCCTA
*
5765505 CTAT-GATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTATGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
5765542 CTA-GGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTATGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
5765577 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTATGGATTCAACTCCTAAA-ATAGGAT
5765605 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
35 22 0.40
36 18 0.33
37 15 0.27
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (36 bp):
CTATGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:5766040 original size:11 final size:11
Alignment explanation
Indices: 5766020--5766103 Score: 53
Period size: 11 Copynumber: 7.3 Consensus size: 11
5766010 TTAATTATTT
*
5766020 TTATTCTAATA
1 TTATTTTAATA
*
5766031 TTATTTTAATG
1 TTATTTTAATA
* *
5766042 TTTTTTTAAAA
1 TTATTTTAATA
*
5766053 GTTATTATATATA
1 -TTATTTTA-ATA
5766066 TATATTTATAACTA
1 T-TATTT-TAA-TA
*
5766080 TTA-TTTATTA
1 TTATTTTAATA
*
5766090 TTATTTTACTA
1 TTATTTTAATA
5766101 TTA
1 TTA
5766104 ACGTATATAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
10 5 0.09
11 28 0.50
12 9 0.16
13 9 0.16
14 5 0.09
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.60
Consensus pattern (11 bp):
TTATTTTAATA
Found at i:5766293 original size:16 final size:16
Alignment explanation
Indices: 5766272--5766305 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5766262 CATGTATTTA
5766272 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
5766288 TATTATTTTACTTTAT
1 TATTATATTACATTAT
5766304 TA
1 TA
5766306 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:5766310 original size:21 final size:22
Alignment explanation
Indices: 5766286--5766335 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
5766276 ATATTACATT
*
5766286 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
*
5766307 ATTATT-TTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
5766328 TTTATTAT
1 ATTATTAT
5766336 ATATATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 11 0.46
21 12 0.50
22 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:5771026 original size:8 final size:8
Alignment explanation
Indices: 5771015--5771084 Score: 52
Period size: 8 Copynumber: 8.5 Consensus size: 8
5771005 CAAAAAGGGC
5771015 AAAAAGAA
1 AAAAAGAA
5771023 AAAAAGAA
1 AAAAAGAA
* *
5771031 AAGAAGCA
1 AAAAAGAA
*
5771039 AAAAAGGA
1 AAAAAGAA
*
5771047 AAAAACAA
1 AAAAAGAA
5771055 GAACAAA-AA
1 -AA-AAAGAA
*
5771064 AGAAAGAA
1 AAAAAGAA
*
5771072 CAAAAATAA
1 -AAAAAGAA
5771081 AAAA
1 AAAA
5771085 GGGGACAAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
7 3 0.06
8 33 0.67
9 10 0.20
10 3 0.06
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5771049 original size:22 final size:21
Alignment explanation
Indices: 5771031--5771086 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
5771021 AAAAAAAGAA
5771031 AAGAAGCAAAAAAGGAAAAAAC
1 AAGAA-CAAAAAAGGAAAAAAC
*
5771053 AAGAACAAAAAA-GAAAGAAC
1 AAGAACAAAAAAGGAAAAAAC
* *
5771073 AAAAATAAAAAAGG
1 AAGAACAAAAAAGG
5771087 GGACAAAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.57
21 8 0.27
22 5 0.17
ACGTcount: A:0.75, C:0.07, G:0.16, T:0.02
Consensus pattern (21 bp):
AAGAACAAAAAAGGAAAAAAC
Found at i:5771719 original size:22 final size:22
Alignment explanation
Indices: 5771691--5771741 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
5771681 CCCCATCAAT
5771691 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
5771713 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
5771735 CCTTTGA
1 CCTTTGA
5771742 CCAAACACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:5772637 original size:36 final size:36
Alignment explanation
Indices: 5772590--5772694 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
5772580 GTGCTCACCA
5772590 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
* * *
5772626 TTGTCTCTCTTGAGACAGTTCCCCTTTAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * * *
5772663 TTTTCTCCCCTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
5772695 TAAACATTGA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
36 30 0.51
37 29 0.49
ACGTcount: A:0.25, C:0.26, G:0.12, T:0.37
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:5772694 original size:37 final size:37
Alignment explanation
Indices: 5772590--5772699 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
5772580 GTGCTCACCA
* *
5772590 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCCCCTGAGACAGTTTCCCTTGAAACAAAACT
* * * * *
5772626 TTGTCTCTCTTGAGACAGTTCCCCTTTAAACAAAATT
1 TTGTCTCCCCTGAGACAGTTTCCCTTGAAACAAAACT
* *
5772663 TTTTCTCCCCTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCCCCTGAGACAGTTTCCCTTGAAACA-AAAC
5772700 ATTGAAAACA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
36 29 0.47
37 30 0.48
38 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.12, T:0.36
Consensus pattern (37 bp):
TTGTCTCCCCTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:5772784 original size:102 final size:102
Alignment explanation
Indices: 5772608--5773065 Score: 736
Period size: 102 Copynumber: 4.5 Consensus size: 102
5772598 CTTGAGACAG
** * * * * * *
5772608 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTCCCCTTTAAACAAAATTTTTTCTCCCC
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
5772673 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* ** *
5772710 TTTCCCTTGAAATGAGTTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTCCGTCTCCAT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
5772775 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
5772812 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCTT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
5772877 TGAGACAGTTTCTTTTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
5772914 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* *
5772979 TGAGACAGTTTCTCTTTAAACATAAACATTGAAAGCA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
5773016 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACA
1 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACA
5773066 TAAACATTGA
Statistics
Matches: 329, Mismatches: 27, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 329 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:5772880 original size:37 final size:36
Alignment explanation
Indices: 5772812--5773000 Score: 121
Period size: 37 Copynumber: 5.4 Consensus size: 36
5772802 ATTGGAAACA
** *
5772812 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCT-TTGAGACAG
5772848 TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCT-CTTTGAGACAG
** * *
5772885 TTTCTTTTGAAACATAAA--------CATTGAAAACA-
1 TTTCCCTTGAAACA-AAATTTTGTCTCTTTG-AGACAG
** *
5772914 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCT-TTGAGACAG
* *
5772950 TTTCCCTCGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCT-CTTTGAGACAG
* *
5772987 TTTCTCTTTAAACA
1 TTTCCCTTGAAACA
5773001 TAAACATTGA
Statistics
Matches: 115, Mismatches: 22, Indels: 31
0.68 0.13 0.18
Matches are distributed among these distances:
27 2 0.02
29 14 0.12
30 4 0.03
35 4 0.03
36 26 0.23
37 59 0.51
38 6 0.05
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAAATTTTGTCTCTTTGAGACAG
Found at i:5773055 original size:65 final size:65
Alignment explanation
Indices: 5772965--5773128 Score: 283
Period size: 65 Copynumber: 2.5 Consensus size: 65
5772955 CTCGAAACAA
* * * *
5772965 AATTTTGTCTCCCTTGAGACAGTTTCTCTTTAAACATAAACATTGAAAGCATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
*
5773030 AATTTCGTCTCTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
5773095 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAA
1 AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAA
5773129 TAAAATTTTG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 93 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (65 bp):
AATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATG
Found at i:5773074 original size:167 final size:169
Alignment explanation
Indices: 5772848--5773162 Score: 510
Period size: 167 Copynumber: 1.9 Consensus size: 169
5772838 CTTGAGATAG
* *
5772848 TTTCCCTTGAAACAAAATTTTGTCTCCTTTGAGACAGTTTCTTTTGAAACATAAACATTGAAAAC
1 TTTCCCTTGAAACAAAATTTCGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
* *
5772913 ATTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTCGAAACAAAATTTTGTCTCCC
66 ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
5772978 TTGAGACAG-TTTCTCTTTAAACATAAACATTGAAAGCA
131 TTGAGACAGTTTTCTCTTTAAACATAAACATTGAAAGCA
** *
5773016 TTTCCCTTGAAA-TGAATTTCGTCT-CTCTTGAGATAGTTTCTCTTGAAACATAAACATTGAAAA
1 TTTCCCTTGAAACAAAATTTCGTCTCCT-TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAA
* * *
5773079 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAATAAAATTTTGTCTCC
65 CATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCC
5773144 CTTGAGACAGTTTTCTCTT
130 CTTGAGACAGTTTTCTCTT
5773163 GAAGTATCAT
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
166 2 0.01
167 113 0.84
168 20 0.15
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (169 bp):
TTTCCCTTGAAACAAAATTTCGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAAC
ATTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAGTTTCCCTCGAAACAAAATTTTGTCTCCC
TTGAGACAGTTTTCTCTTTAAACATAAACATTGAAAGCA
Found at i:5773142 original size:37 final size:37
Alignment explanation
Indices: 5773081--5773165 Score: 118
Period size: 37 Copynumber: 2.3 Consensus size: 37
5773071 ATTGAAAACA
* * *
5773081 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGACAG-
1 TTTCTCTTGAAATAAATTTCGTCTCCCTTGAGACAGT
*
5773117 TTTCTCTTGAAATAAAATTTTGTCTCCCTTGAGACAGT
1 TTTCTCTTGAAAT-AAATTTCGTCTCCCTTGAGACAGT
5773155 TTTCTCTTGAA
1 TTTCTCTTGAA
5773166 GTATCATCTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 12 0.28
37 20 0.47
38 11 0.26
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (37 bp):
TTTCTCTTGAAATAAATTTCGTCTCCCTTGAGACAGT
Found at i:5773308 original size:37 final size:37
Alignment explanation
Indices: 5773238--5773309 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
5773228 TGGAACTAAG
* * **
5773238 TTTTGTCTCTCTTGAGACAGTTTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
* *
5773275 TTTTGTCTCCCTTAAGACTGTTTCCCTTGAAACAA
1 TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAA
5773310 CAAATATCTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 29 1.00
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.42
Consensus pattern (37 bp):
TTTTGTCTCCCTTAAGACAGTTTCCCTTAAAACAAAA
Found at i:5774007 original size:105 final size:102
Alignment explanation
Indices: 5773655--5774303 Score: 667
Period size: 98 Copynumber: 6.4 Consensus size: 102
5773645 GGTTTTAGCT
* * * * *
5773655 AGAGTCAATTTCGACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAA
**
5773720 CGAAGGGACGGCTGGTTGTCAACAATAATTTCCCAGTTTC
66 CGAAGGGACGGCTGACTGTCAACAA-AATTT--CAGTTTC
* *
5773760 AGGGCCAATTTCAACTTCAC-GACGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACA
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACA
* * ** *
5773824 GCGAAGGGGCGGCTGACTGTTGAC-AAA---CAATTTC
65 ACGAAGGGACGGCTGACTGTCAACAAAATTTCAGTTTC
* * * * *
5773858 GGAGCCAATCTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAA
*
5773923 CGAAGGGACGGCTGGCTGTCAACAATAATTTCCCAGTTTC
66 CGAAGGGACGGCTGACTGTCAACAA-AATTT--CAGTTTC
* * * * *
5773963 AGGGCCAATTTCAACTTCACAGTGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAG
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAA
* * * *
5774028 CGAAGGGGCGGCTGACTGTCGAC--AA--GCAATTTC
66 CGAAGGGACGGCTGACTGTCAACAAAATTTCAGTTTC
* * * * * *
5774061 GGAGCCAATCTCAACTTCACAGCGAAGGATATTGTACTCGAGATAACACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAA
* * *
5774126 CGAAGGGATGGCTGATTGTCAACAAGATTTC-G-TTC
66 CGAAGGGACGGCTGACTGTCAACAAAATTTCAGTTTC
* *
5774161 AGAGTCAATTTCAACTTCACAGCGAAGGATATT--ACGCTCGAGACAGCACAAGCTCAACTTCAC
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC-C-CGAGACAACACAAGCTCAACTTCAC
* * * *
5774224 AGCGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCGGTTCC
64 AACGAAGGGACGGCTGACTGTCAAC-AA-AATTT--CAGTTTC
* * *
5774267 AGAACCAATTTCAAATTCACAGCGGAGGATATTGGAC
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGAC
5774304 TCGGAACAAT
Statistics
Matches: 444, Mismatches: 77, Indels: 43
0.79 0.14 0.08
Matches are distributed among these distances:
98 161 0.36
99 2 0.00
100 79 0.18
101 2 0.00
102 7 0.02
103 2 0.00
104 3 0.01
105 155 0.35
106 31 0.07
108 2 0.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.21
Consensus pattern (102 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCGAGACAACACAAGCTCAACTTCACAA
CGAAGGGACGGCTGACTGTCAACAAAATTTCAGTTTC
Found at i:5774017 original size:203 final size:203
Alignment explanation
Indices: 5773668--5774258 Score: 955
Period size: 203 Copynumber: 2.9 Consensus size: 203
5773658 GTCAATTTCG
* *
5773668 ACTTCACAGTGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
5773733 GGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCAC-GACGAAGGATATTGGAC
66 GGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAG-CGAAGGATATTGGAC
* *
5773797 CCAAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTTGACAAACAATTTCGGAG
130 CCAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAACAATTTCGGAG
5773862 CCAATCTCA
195 CCAATCTCA
5773871 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* *
5773936 GGCTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAGTGAAGGATATTGGACC
66 GGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
*
5774001 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAGCAATTTCGGAGC
131 CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAACAATTTCGGAGC
5774066 CAATCTCA
196 CAATCTCA
* * *
5774074 ACTTCACAGCGAAGGATATTGTACTCGAGATAACACAAGTTCAACTTCACAACGAAGGGATGGCT
1 ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
* * * *
5774139 GATTGTCAACAA-GATTT--C-G-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATT--ACG
66 GGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGAC-
* *
5774197 CTCGAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCAACAAACAATTTC
130 C-CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAACAATTTC
5774259 CCGGTTCCAG
Statistics
Matches: 366, Mismatches: 19, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
196 2 0.01
197 1 0.00
198 90 0.25
199 1 0.00
200 1 0.00
202 4 0.01
203 266 0.73
204 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.21
Consensus pattern (203 bp):
ACTTCACAGCGAAGGATATTGAACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCT
GGTTGTCAACAATAATTTCCCAGTTTCAGGGCCAATTTCAACTTCACAGCGAAGGATATTGGACC
CAAGACAGCACAAGCTCAACTTCACAGCGAAGGGGCGGCTGACTGTCGACAAACAATTTCGGAGC
CAATCTCA
Found at i:5774830 original size:35 final size:37
Alignment explanation
Indices: 5774767--5774835 Score: 115
Period size: 35 Copynumber: 1.9 Consensus size: 37
5774757 TTTCGTCCTA
5774767 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
*
5774804 CTAGGATTC-AACTC-CTAAAATAGGATAGAATT
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATT
5774836 TTTCTATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 17 0.55
36 5 0.16
37 9 0.29
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTATG
Found at i:5775559 original size:16 final size:16
Alignment explanation
Indices: 5775538--5775571 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5775528 CATGTATTTA
5775538 TATTATATTACATTAT
1 TATTATATTACATTAT
* *
5775554 TATTATTTTACTTTAT
1 TATTATATTACATTAT
5775570 TA
1 TA
5775572 AATTATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATATTACATTAT
Found at i:5775576 original size:21 final size:22
Alignment explanation
Indices: 5775552--5775602 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
5775542 ATATTACATT
*
5775552 ATTATTATTTTACTTTATTA-A
1 ATTATTATTTTACGTTATTATA
*
5775573 ATTATT-TTTTTCGTTATTATA
1 ATTATTATTTTACGTTATTATA
*
5775594 TTTATTATT
1 ATTATTATT
5775603 ATATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.44
21 12 0.48
22 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (22 bp):
ATTATTATTTTACGTTATTATA
Found at i:5776622 original size:16 final size:16
Alignment explanation
Indices: 5776601--5776648 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
5776591 ATTCTCTTAA
5776601 CTTCCTTGTAATTTTC
1 CTTCCTTGTAATTTTC
5776617 CTTCCTTGTAATTTTC
1 CTTCCTTGTAATTTTC
*
5776633 CTTCCTTTTAATTTTC
1 CTTCCTTGTAATTTTC
5776649 TTCTTACTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.12, C:0.25, G:0.04, T:0.58
Consensus pattern (16 bp):
CTTCCTTGTAATTTTC
Found at i:5783572 original size:10 final size:10
Alignment explanation
Indices: 5783560--5783608 Score: 57
Period size: 10 Copynumber: 4.9 Consensus size: 10
5783550 AAAGACCGCA
5783560 AAAGAAAGAA-
1 AAAGAAA-AAG
5783570 AAAGAAAAAG
1 AAAGAAAAAG
5783580 AAAGAAAAAG
1 AAAGAAAAAG
*
5783590 AAAAGAGAAAG
1 -AAAGAAAAAG
5783601 AAA-AAAAA
1 AAAGAAAAA
5783609 CCAAAGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 6 0.17
10 20 0.57
11 9 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:5783575 original size:6 final size:6
Alignment explanation
Indices: 5783564--5783605 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
5783554 ACCGCAAAAG
*
5783564 AAAGAA AAAGAA AAAG-- AAAGAA AAAG-A AAAGAG AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
5783606 AAACCAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 4 0.13
5 5 0.16
6 22 0.71
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:5783578 original size:16 final size:16
Alignment explanation
Indices: 5783559--5783605 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
5783549 GAAAGACCGC
5783559 AAAAGAAAGAAAAAGA
1 AAAAGAAAGAAAAAGA
5783575 AAAAGAAAGAAAAAGA
1 AAAAGAAAGAAAAAGA
5783591 AAAGAGAAAGAAAAA
1 AAA-AGAAAGAAAAA
5783606 AAACCAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 19 0.63
17 11 0.37
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAGAAAAAGA
Found at i:5783874 original size:16 final size:16
Alignment explanation
Indices: 5783862--5783895 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
5783852 TTATATAGTT
5783862 ATTA-TATACTATATA
1 ATTAGTATACTATATA
5783877 ATTAGTATACTATATA
1 ATTAGTATACTATATA
5783893 ATT
1 ATT
5783896 GCATGTTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTAGTATACTATATA
Found at i:5783874 original size:18 final size:17
Alignment explanation
Indices: 5783826--5783892 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
5783816 GTGCATATTA
* *
5783826 TATTATATATTAAATAG
1 TATTATATACTATATAG
** *
5783843 TATTGCATATTATATAG
1 TATTATATACTATATAG
5783860 TTATTATATACTATATA-
1 -TATTATATACTATATAG
5783877 -ATTAGTATACTATATA
1 TATTA-TATACTATATA
5783893 ATTGCATGTT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
15 4 0.10
16 11 0.26
17 14 0.33
18 13 0.31
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (17 bp):
TATTATATACTATATAG
Found at i:5790672 original size:12 final size:12
Alignment explanation
Indices: 5790606--5790674 Score: 57
Period size: 12 Copynumber: 5.3 Consensus size: 12
5790596 ATTATTTATT
* *
5790606 TATTACTATTAC
1 TATTATTATTAG
5790618 TATTATTATTAG
1 TATTATTATTAG
* *
5790630 TATTATTTGTTGG
1 TATTA-TTATTAG
5790643 TATTATTAATTATAAG
1 TATTATT-A-T-T-AG
5790659 TATTATTATTAG
1 TATTATTATTAG
5790671 TATT
1 TATT
5790675 TTTTATATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
12 23 0.50
13 11 0.24
14 2 0.04
15 2 0.04
16 8 0.17
ACGTcount: A:0.32, C:0.03, G:0.09, T:0.57
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:5797655 original size:19 final size:20
Alignment explanation
Indices: 5797612--5797659 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
5797602 ATACCAACAA
*
5797612 TATCGATACTTACCCTTGGG
1 TATCGATACTTACCCTTGAG
5797632 TATCGATACTCT-CCC-TGAG
1 TATCGATACT-TACCCTTGAG
5797651 TATCGATAC
1 TATCGATAC
5797660 CAAAAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 12 0.46
20 13 0.50
21 1 0.04
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (20 bp):
TATCGATACTTACCCTTGAG
Found at i:5819084 original size:52 final size:52
Alignment explanation
Indices: 5819006--5819128 Score: 219
Period size: 52 Copynumber: 2.4 Consensus size: 52
5818996 ACCTTGACAT
* *
5819006 TGTAAGAGCATCGAGAGATTGCCTGGGGTTTTGGTAAAACATGTCTTGGCAA
1 TGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGAAAAACATGTCTTGGCAA
*
5819058 TGTAAGAGCATCGGGAGATCGCCTGGGGTTTTGGAAAAACATGTCTTGGCAA
1 TGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGAAAAACATGTCTTGGCAA
5819110 TGTAAGAGCATCGAGAGAT
1 TGTAAGAGCATCGAGAGAT
5819129 AACATTTTGT
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.26
Consensus pattern (52 bp):
TGTAAGAGCATCGAGAGATCGCCTGGGGTTTTGGAAAAACATGTCTTGGCAA
Found at i:5824141 original size:8 final size:8
Alignment explanation
Indices: 5824128--5824157 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
5824118 TAGTTTCAAA
5824128 AAAAAAAC
1 AAAAAAAC
5824136 AAAAAAAC
1 AAAAAAAC
5824144 AAAAAAAC
1 AAAAAAAC
5824152 AAAAAA
1 AAAAAA
5824158 CTGTGAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:5832593 original size:90 final size:88
Alignment explanation
Indices: 5832436--5832609 Score: 294
Period size: 89 Copynumber: 2.0 Consensus size: 88
5832426 CCTAACTCAC
*
5832436 CCTTTTATAGCCAAGTTACCCTAATCATATTAGAGTTTTATTATTTCAAATTAATTTAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGAGTTTTATTATTTCAAATTAATTAAATCTATA
*
5832501 TTTAATTAATTAGAATTTAATAAT
66 TTTAATTAATT-GAAATTAATAAT
* *
5832525 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGAG-TTTTATTATTTCAAATTAATTAAATCTAT
5832590 ATTTAATTAATTGAAATTAA
65 ATTTAATTAATTGAAATTAA
5832610 ATATTTGGGA
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 40 0.50
90 40 0.50
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGAGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAATAAT
Found at i:5834279 original size:64 final size:64
Alignment explanation
Indices: 5834166--5834289 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
5834156 GTGCACCAAG
* * *** *
5834166 TGTGCATCAATGTATAAAATGCATTCGATGTTTGAAAATAGCTTGAGTGCATCGGTGCATTTCT
1 TGTGCATCAATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTTCT
* * *
5834230 TGTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-AACCCAAGTGCATCGATGCAT
1 TGTGCATCAATGCATAAAATGCATTCGATGTTTGAA-AATAACCCAAGTGCATCGATGCAT
5834290 AGAGAGTGCA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 48 0.96
65 2 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (64 bp):
TGTGCATCAATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTTCT
Found at i:5834573 original size:19 final size:20
Alignment explanation
Indices: 5834535--5834574 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
5834525 TTTGAAATTA
*
5834535 CTCCCCCTTACTATAACATTT
1 CTCCCCCTTA-TAAAACATTT
5834556 CTCCCCCTT-TAAAACATTT
1 CTCCCCCTTATAAAACATTT
5834575 TACACTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.25, C:0.38, G:0.00, T:0.38
Consensus pattern (20 bp):
CTCCCCCTTATAAAACATTT
Found at i:5841824 original size:7 final size:7
Alignment explanation
Indices: 5841812--5841838 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5841802 ATGGAATTAT
5841812 ATTTGGA
1 ATTTGGA
5841819 ATTTGGA
1 ATTTGGA
5841826 ATTTGGA
1 ATTTGGA
5841833 ATTTGG
1 ATTTGG
5841839 TAGAAAAATT
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:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (7 bp):
ATTTGGA
Found at i:5843489 original size:59 final size:59
Alignment explanation
Indices: 5843390--5843526 Score: 195
Period size: 59 Copynumber: 2.3 Consensus size: 59
5843380 CAGCAGGCTG
** * *
5843390 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCATGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
* * *
5843449 CATATTCGGGACTATACTTAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
5843508 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
5843527 CGGTGCTAAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
58 2 0.03
59 65 0.97
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACGACCTTATGTGT
Found at i:5843768 original size:60 final size:60
Alignment explanation
Indices: 5843698--5843817 Score: 240
Period size: 60 Copynumber: 2.0 Consensus size: 60
5843688 TTCAGTTATG
5843698 ATATTTTGATCATGGTAAAATTTATTACATTATTTATTATTTTAATTACCTCACTAAGTA
1 ATATTTTGATCATGGTAAAATTTATTACATTATTTATTATTTTAATTACCTCACTAAGTA
5843758 ATATTTTGATCATGGTAAAATTTATTACATTATTTATTATTTTAATTACCTCACTAAGTA
1 ATATTTTGATCATGGTAAAATTTATTACATTATTTATTATTTTAATTACCTCACTAAGTA
5843818 TATACTTAGC
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.48
Consensus pattern (60 bp):
ATATTTTGATCATGGTAAAATTTATTACATTATTTATTATTTTAATTACCTCACTAAGTA
Found at i:5850688 original size:59 final size:59
Alignment explanation
Indices: 5850589--5850725 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 59
5850579 CAGCAGGCTG
** * *
5850589 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACAACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACAACCTTATATGT
* ** * *
5850648 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGGCACGACCTTATATGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACAACCTTATATGT
5850707 CATATTCGGG-ATAGCACTA
1 CATATTCGGGAATA-CACTA
5850726 CGGTGCTTAT
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 1 0.02
59 63 0.98
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGGCACAACCTTATATGT
Found at i:5851346 original size:22 final size:22
Alignment explanation
Indices: 5851315--5851356 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5851305 ATTACAAAAG
*
5851315 GGGAACCGATTCCCCTACTACA
1 GGGAACCGATTCCCCCACTACA
*
5851337 GGGAATCGATTCCCCCACTA
1 GGGAACCGATTCCCCCACTA
5851357 TTCACTGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.19
Consensus pattern (22 bp):
GGGAACCGATTCCCCCACTACA
Found at i:5852734 original size:64 final size:64
Alignment explanation
Indices: 5852602--5852780 Score: 200
Period size: 64 Copynumber: 2.8 Consensus size: 64
5852592 TGGAACACTT
* * * * **
5852602 AGTGCATCGGTGCACCA-AGTGTGCATCGATGCATACAATGCATTCGATGTTTGAAAATAGCCTG
1 AGTGCATCGATGCA-TAGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCC
* ** *
5852666 AGTGCATCGATGCATTGCTTGTGCATCGATGCATAAAATGCATTCGATGTTTTAATAA-AACCCC
1 AGTGCATCGATGCATAGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCC
* * * *
5852730 AGTGCATCGATGCATAGAGAGTACATTGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGATGCATAGAGTGTGCATCGATGCATAAAATGCATTCGATGTT
5852781 CAATTTATTC
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
64 94 0.98
65 2 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (64 bp):
AGTGCATCGATGCATAGAGTGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCC
Found at i:5854801 original size:61 final size:61
Alignment explanation
Indices: 5854698--5854821 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 61
5854688 CCTAAGTGAC
* *
5854698 AATACACATAAGTTCGTGCCCACCATATGCACTTAGTTTCCTTTATACACACTACAATGCT
1 AATACACATAAGTTCGTGCCCACCATATGCACTAAGTGTCCTTTATACACACTACAATGCT
* *
5854759 AATACACATAAGATT-GTGTCCC-CCATATGCACTAAGTGTCCTTTATATACACTATAATGCT
1 AATACACATAAG-TTCGTG-CCCACCATATGCACTAAGTGTCCTTTATACACACTACAATGCT
5854820 AA
1 AA
5854822 ACCGAATGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 52 0.91
62 5 0.09
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.31
Consensus pattern (61 bp):
AATACACATAAGTTCGTGCCCACCATATGCACTAAGTGTCCTTTATACACACTACAATGCT
Found at i:5855283 original size:2 final size:2
Alignment explanation
Indices: 5855278--5855311 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5855268 ATAAAAAATC
5855278 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5855312 ACAAATATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5870310 original size:44 final size:45
Alignment explanation
Indices: 5870261--5870352 Score: 150
Period size: 45 Copynumber: 2.1 Consensus size: 45
5870251 TTAGTTAATG
* *
5870261 TGAATGTAATG-AAATAATAATAATGAGAAATATGCAAGAATGCA
1 TGAATGTAATGAAAAGAAAAATAATGAGAAATATGCAAGAATGCA
*
5870305 TGAATGTAATGAAAAGAAAAATAATGAGAAATATGCAATAATGCA
1 TGAATGTAATGAAAAGAAAAATAATGAGAAATATGCAAGAATGCA
5870350 TGA
1 TGA
5870353 TGCGTGAAGT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 11 0.25
45 33 0.75
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.24
Consensus pattern (45 bp):
TGAATGTAATGAAAAGAAAAATAATGAGAAATATGCAAGAATGCA
Found at i:5872297 original size:16 final size:15
Alignment explanation
Indices: 5872271--5872301 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5872261 AAGAAATATC
5872271 AAATAAAAATTAAAT
1 AAATAAAAATTAAAT
5872286 AAATAAATAATTAAAT
1 AAATAAA-AATTAAAT
5872302 CAAAGAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAATAAAAATTAAAT
Found at i:5884063 original size:29 final size:28
Alignment explanation
Indices: 5884026--5884093 Score: 77
Period size: 29 Copynumber: 2.4 Consensus size: 28
5884016 TCAAAAAAAG
5884026 AAAAAATATTAATAAAATA-ATAAATAAA
1 AAAAAATATTAATAAAATATAT-AATAAA
* *
5884054 AAAATAATATTAGTATAATATATAATAAA
1 AAAA-AATATTAATAAAATATATAATAAA
5884083 AATAAAA-ATTA
1 AA-AAAATATTA
5884094 TTTTTAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 8 0.23
29 23 0.66
30 4 0.11
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (28 bp):
AAAAAATATTAATAAAATATATAATAAA
Found at i:5884209 original size:13 final size:14
Alignment explanation
Indices: 5884185--5884313 Score: 68
Period size: 13 Copynumber: 10.1 Consensus size: 14
5884175 AAAACTCTAT
5884185 AATATATTTTCAAA
1 AATATATTTTCAAA
5884199 AATAT-TTTTCAAA
1 AATATATTTTCAAA
* *
5884212 ACTATATATT---A
1 AATATATTTTCAAA
* *
5884223 TATACATTTTC-AA
1 AATATATTTTCAAA
5884236 AA-ATATTTTCAAA
1 AATATATTTTCAAA
* *
5884249 ACTATATATT---A
1 AATATATTTTCAAA
*
5884260 TATATATTTTC-AA
1 AATATATTTTCAAA
5884273 AATAT-TTTT-AAA
1 AATATATTTTCAAA
* *
5884285 AACTATATATT-ATA
1 AA-TATATTTTCAAA
*
5884299 TATATATTTTCAAA
1 AATATATTTTCAAA
5884313 A
1 A
5884314 TGTTTTCCAA
Statistics
Matches: 84, Mismatches: 20, Indels: 22
0.67 0.16 0.17
Matches are distributed among these distances:
11 15 0.18
12 15 0.18
13 32 0.38
14 22 0.26
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATATTTTCAAA
Found at i:5884254 original size:37 final size:37
Alignment explanation
Indices: 5884086--5884427 Score: 356
Period size: 38 Copynumber: 9.1 Consensus size: 37
5884076 TAATAAAAAT
* * * *
5884086 AAAAATTATTTTTAAAAATATGTATTATATATGCTTTT-
1 AAAAA-TATTTTCAAAACTATATATTATATAT-ATTTTC
* ** * *
5884124 AAAAATTGTTTTTGAAACCATATAATATATATATTTTC
1 AAAAA-TATTTTCAAAACTATATATTATATATATTTTC
* *
5884162 AAAAATTATTTTTAAAAC--TCTA-TA-ATATATTTTC
1 AAAAA-TATTTTCAAAACTATATATTATATATATTTTC
*
5884196 AAAAATATTTTTCAAAACTATATATTATATACATTTTC
1 AAAAATA-TTTTCAAAACTATATATTATATATATTTTC
5884234 AAAAATATTTTCAAAACTATATATTATATATATTTTC
1 AAAAATATTTTCAAAACTATATATTATATATATTTTC
*
5884271 -AAAATATTTTTAAAAACTATATATTATATATATATTTTC
1 AAAAATA-TTTTCAAAACTATATA-T-TATATATATTTTC
* *
5884310 -AAAATGTTTTCCAAAACTATATATTATATATATGTTC
1 AAAAATATTTT-CAAAACTATATATTATATATATTTTC
* *
5884347 AAAAATGTTTTCAAAAACTATATATTATATATATATATTA
1 AAAAATATTTTC-AAAACTATATATTATATATAT-T-TTC
*
5884387 AAAAATGTTTTCAAAAACTATATATTATATATATTTTC
1 AAAAATATTTTC-AAAACTATATATTATATATATTTTC
5884425 AAA
1 AAA
5884428 TATTATACTA
Statistics
Matches: 269, Mismatches: 21, Indels: 28
0.85 0.07 0.09
Matches are distributed among these distances:
33 2 0.01
34 24 0.09
35 2 0.01
36 12 0.04
37 63 0.23
38 100 0.37
39 30 0.11
40 36 0.13
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (37 bp):
AAAAATATTTTCAAAACTATATATTATATATATTTTC
Found at i:5888366 original size:10 final size:10
Alignment explanation
Indices: 5888352--5888483 Score: 99
Period size: 10 Copynumber: 12.5 Consensus size: 10
5888342 AAAAAGACAT
5888352 AAAAAAGATAG
1 AAAAAA-ATAG
5888363 AAAAAAGAGATAG
1 -AAAAA-A-ATAG
*
5888376 -AAAAGATAG
1 AAAAAAATAG
5888385 AGAGAAAAATAG
1 A-A-AAAAATAG
*
5888397 AAAGGAAAA-AA
1 AAA--AAAATAG
5888408 AAGAAAAATAG
1 AA-AAAAATAG
*
5888419 AGAAAAATAG
1 AAAAAAATAG
5888429 AAAAAAAATAG
1 -AAAAAAATAG
5888440 AAAAAAATAG
1 AAAAAAATAG
*
5888450 -AAAAAAGAG
1 AAAAAAATAG
*
5888459 AAAAAAAGAG
1 AAAAAAATAG
*
5888469 AAAAAAAGAG
1 AAAAAAATAG
5888479 AAAAA
1 AAAAA
5888484 GGAAAAGAAA
Statistics
Matches: 103, Mismatches: 7, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
9 12 0.12
10 47 0.46
11 20 0.19
12 18 0.17
13 6 0.06
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (10 bp):
AAAAAAATAG
Found at i:5888435 original size:11 final size:11
Alignment explanation
Indices: 5888327--5888475 Score: 82
Period size: 11 Copynumber: 13.8 Consensus size: 11
5888317 CGACACAGAG
*
5888327 AGAAAAAATAT
1 AGAAAAAAAAT
* *
5888338 ATAAAAAAAGAC
1 AGAAAAAAA-AT
* *
5888350 ATAAAAAAGAT
1 AGAAAAAAAAT
5888361 AGAAAAAAGAGAT
1 AGAAAAAA-A-AT
*
5888374 AG--AAAAGAT
1 AGAAAAAAAAT
*
5888383 AGAGAGAAAAAT
1 AGA-AAAAAAAT
5888395 AGAAAGGAAAAA-
1 AGAAA--AAAAAT
*
5888407 A-AAGAAAAAT
1 AGAAAAAAAAT
*
5888417 AG-AGAAAAAT
1 AGAAAAAAAAT
5888427 AGAAAAAAAAT
1 AGAAAAAAAAT
5888438 AG-AAAAAAAT
1 AGAAAAAAAAT
*
5888448 AG--AAAAAAG
1 AGAAAAAAAAT
*
5888457 AG-AAAAAAAG
1 AGAAAAAAAAT
5888467 AGAAAAAAA
1 AGAAAAAAA
5888476 GAGAAAAAGG
Statistics
Matches: 111, Mismatches: 14, Indels: 26
0.74 0.09 0.17
Matches are distributed among these distances:
9 17 0.15
10 30 0.27
11 37 0.33
12 18 0.16
13 9 0.08
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (11 bp):
AGAAAAAAAAT
Done.