Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 43 of 150
Found at i:12082965 original size:15 final size:14
Alignment explanation
Indices: 12082945--12082993 Score: 64
Period size: 15 Copynumber: 3.4 Consensus size: 14
12082935 CTATGCTTTA
12082945 AGGGTTAGGGGATTT
1 AGGGTTAGGGG-TTT
12082960 AGGGTTAGGGG-TT
1 AGGGTTAGGGGTTT
*
12082973 AGGGATTTGGGGTTT
1 AGGG-TTAGGGGTTT
12082988 AGGGTT
1 AGGGTT
12082994 TCAACAGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
13 6 0.19
14 8 0.26
15 17 0.55
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.35
Consensus pattern (14 bp):
AGGGTTAGGGGTTT
Found at i:12082972 original size:22 final size:22
Alignment explanation
Indices: 12082941--12082991 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
12082931 AGTGCTATGC
*
12082941 TTTAAGGGTTAGGGGATTTAGGG
1 TTTAGGGGTTA-GGGATTTAGGG
*
12082964 -TTAGGGGTTAGGGATTTGGGG
1 TTTAGGGGTTAGGGATTTAGGG
12082985 TTTAGGG
1 TTTAGGG
12082992 TTTCAACAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.35
Consensus pattern (22 bp):
TTTAGGGGTTAGGGATTTAGGG
Found at i:12082992 original size:21 final size:21
Alignment explanation
Indices: 12082945--12082993 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
12082935 CTATGCTTTA
12082945 AGGGTTAGGGGATTTAGGGTT
1 AGGGTTAGGGGATTTAGGGTT
*
12082966 AGGGGTTA-GGGATTTGGGGTTT
1 A-GGGTTAGGGGATTTAGGG-TT
12082988 AGGGTT
1 AGGGTT
12082994 TCAACAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.16, C:0.00, G:0.49, T:0.35
Consensus pattern (21 bp):
AGGGTTAGGGGATTTAGGGTT
Found at i:12083394 original size:15 final size:17
Alignment explanation
Indices: 12083366--12083400 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
12083356 GGATAGGACC
12083366 AAAATATAAGAAAATAT
1 AAAATATAAGAAAATAT
12083383 AAAATA-AA-AAAATAT
1 AAAATATAAGAAAATAT
12083398 AAA
1 AAA
12083401 TGAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 2 0.11
17 6 0.33
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (17 bp):
AAAATATAAGAAAATAT
Found at i:12084029 original size:2 final size:2
Alignment explanation
Indices: 12084024--12084056 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12084014 TTTGTACTTG
*
12084024 TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12084057 GTTATATGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:12084467 original size:194 final size:194
Alignment explanation
Indices: 12084157--12084553 Score: 494
Period size: 194 Copynumber: 2.0 Consensus size: 194
12084147 GTCTTTGAAA
* * * *
12084157 AATGGGAATACGGGTTTTGTTTAACTGTCTCAATTGCTTCTCGACAAAACCCAGTTTACAACATT
1 AATGGGAATACAGGTGTTGTTTAACTGTCTCAATTGCTTCTCAACAAAACCCAGTTTACAACATA
* * * *
12084222 TCTGACGTTATAAAATCTTGATTCCTTACTGATTCTGCTGAATTTGTGTTTATGGTTGTCGATAT
66 TCCGAAGCTATAAAATCTTGATTCCTTACTGATTCTGCTGAATTTGTGTTTATGATTGTCGATAT
* * * * *
12084287 ATGATGTTTGTTGTTGTATATTGCTTTTGAGTTTTACAAAAGTCGAAGAGAAA-CATTTTTAAG
131 ATGATATTTGTTGCTATATATTGCTTTTGAGTTTTACAAAAGTCGAAGAAAAATCACTTTTAAG
* * * * **
12084350 AATGGGAATTCAGGTGTTGTTTAACTGTC-CGAATTTCTTCTTAACAAAACCCCATTTTATGACA
1 AATGGGAATACAGGTGTTGTTTAACTGTCTC-AATTGCTTCTCAACAAAA-CCCAGTTTACAACA
* * * *
12084414 TATCCGAAGCTATGAAATCTTGATTCCTTGA-TGTTTCTGCTGGATTTGTGTTTATGATTGTTGA
64 TATCCGAAGCTATAAAATCTTGATTCCTT-ACTGATTCTGCTGAATTTGTGTTTATGATTGTCGA
* * * *
12084478 TATATGCTATTTGTTGCTATATATTGCTTTTGAGTTTTTCAAGAGTCGAAGAAAAATGACTTTTA
128 TATATGATATTTGTTGCTATATATTGCTTTTGAGTTTTACAAAAGTCGAAGAAAAATCACTTTTA
12084543 AG
193 AG
*
12084545 AACGGGAAT
1 AATGGGAAT
12084554 CTGTTTGTCG
Statistics
Matches: 172, Mismatches: 28, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
192 1 0.01
193 41 0.24
194 113 0.66
195 17 0.10
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.41
Consensus pattern (194 bp):
AATGGGAATACAGGTGTTGTTTAACTGTCTCAATTGCTTCTCAACAAAACCCAGTTTACAACATA
TCCGAAGCTATAAAATCTTGATTCCTTACTGATTCTGCTGAATTTGTGTTTATGATTGTCGATAT
ATGATATTTGTTGCTATATATTGCTTTTGAGTTTTACAAAAGTCGAAGAAAAATCACTTTTAAG
Found at i:12086161 original size:43 final size:43
Alignment explanation
Indices: 12086052--12086324 Score: 354
Period size: 43 Copynumber: 6.4 Consensus size: 43
12086042 TAAAAAGTCA
** * * * *
12086052 TGTT-TTTAGCGGCGTTTGT-CAAAAAGAGCCACTAAAAGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
* * * * *
12086093 TCTT-TATAGTGGCGTTTGTTGTAGAAGCGCCGCTAAAGGTCA
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
* * * *
12086135 TGATCTTTAGCGGCATTTGTGTTAGAAGCGCCGTTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
* *
12086178 TGTTCTTTAGCGACGTTTGTGTTAGAAGCGCCGCTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
*
12086221 TGTTCTTTAGCGGCGTTTGTGGTAGAAGAGCCGCTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
*
12086264 TGTTCTTTAGCGGTGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
1 TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
12086307 TGTTCTTTAGCGGCGTTT
1 TGTTCTTTAGCGGCGTTT
12086325 ATTTTTAAAA
Statistics
Matches: 201, Mismatches: 29, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
41 16 0.08
42 17 0.08
43 168 0.84
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.35
Consensus pattern (43 bp):
TGTTCTTTAGCGGCGTTTGTGGTAGAAGCGCCGCTAAAGGTCT
Found at i:12086406 original size:25 final size:25
Alignment explanation
Indices: 12086372--12086432 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
12086362 ACAGTGGCAT
*
12086372 TTTTTGCGGCGCTTGCCGCAAATAC
1 TTTTAGCGGCGCTTGCCGCAAATAC
12086397 TTTTAGCGGCGCTTGCCGCAAATAC
1 TTTTAGCGGCGCTTGCCGCAAATAC
12086422 TTTTAGCGGCG
1 TTTTAGCGGCG
12086433 TTAAAAGCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (25 bp):
TTTTAGCGGCGCTTGCCGCAAATAC
Found at i:12086465 original size:22 final size:22
Alignment explanation
Indices: 12086435--12086477 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
12086425 TAGCGGCGTT
* *
12086435 AAAAGCGCCACTAAAGGCCTAA
1 AAAAACGCCACTAAAAGCCTAA
12086457 AAAAACGCCACTAAAAGCCTA
1 AAAAACGCCACTAAAAGCCTA
12086478 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.28, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAACGCCACTAAAAGCCTAA
Found at i:12087872 original size:18 final size:21
Alignment explanation
Indices: 12087832--12087877 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
12087822 AATTATAAAT
12087832 TTTTTTATATATTCTTTAGAA
1 TTTTTTATATATTCTTTAGAA
*
12087853 TTTTTTAT-T-TT-TTTATAA
1 TTTTTTATATATTCTTTAGAA
12087871 TTTTTTA
1 TTTTTTA
12087878 AAATATAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 13 0.54
19 2 0.08
20 1 0.04
21 8 0.33
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (21 bp):
TTTTTTATATATTCTTTAGAA
Found at i:12087877 original size:10 final size:10
Alignment explanation
Indices: 12087832--12087877 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
12087822 AATTATAAAT
12087832 TTTTTTATATA
1 TTTTTTATA-A
* *
12087843 TTCTTTAGAA
1 TTTTTTATAA
12087853 TTTTTTAT--
1 TTTTTTATAA
12087861 TTTTTTATAA
1 TTTTTTATAA
12087871 TTTTTTA
1 TTTTTTA
12087878 AAATATAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
8 8 0.28
10 14 0.48
11 7 0.24
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:12087917 original size:19 final size:20
Alignment explanation
Indices: 12087893--12087937 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
12087883 TAAAGTTTAA
12087893 AATTTTTAAAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
12087912 AA-TTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
12087931 AATTTTT
1 AATTTTT
12087938 TAAATTTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.38
19 11 0.46
20 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:12087942 original size:19 final size:19
Alignment explanation
Indices: 12087893--12087943 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 19
12087883 TAAAGTTTAA
*
12087893 AATTTTTAAAAATATTTTG
1 AATTTTTAAAATTATTTTG
*
12087912 AATTTTAAAAATTATTTTG
1 AATTTTTAAAATTATTTTG
*
12087931 AATTTTTTAAATT
1 AATTTTTAAAATT
12087944 TTTGTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (19 bp):
AATTTTTAAAATTATTTTG
Found at i:12088717 original size:13 final size:13
Alignment explanation
Indices: 12088696--12088732 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
12088686 TTAGAATGAA
12088696 GGAGAACACAAGT
1 GGAGAACACAAGT
*
12088709 GGTGAACACAA--
1 GGAGAACACAAGT
12088720 GGAGAACACAAGT
1 GGAGAACACAAGT
12088733 CGCAACCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.50
13 10 0.50
ACGTcount: A:0.46, C:0.16, G:0.30, T:0.08
Consensus pattern (13 bp):
GGAGAACACAAGT
Found at i:12090426 original size:15 final size:15
Alignment explanation
Indices: 12090406--12090436 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12090396 CAACTCTAAG
12090406 TATCAAAACACCAAT
1 TATCAAAACACCAAT
*
12090421 TATCAAAACCCCAAT
1 TATCAAAACACCAAT
12090436 T
1 T
12090437 GACATACTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (15 bp):
TATCAAAACACCAAT
Found at i:12104293 original size:20 final size:20
Alignment explanation
Indices: 12104270--12104318 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12104260 AAGGCACTAG
12104270 AGTGCAAACAGAGACACCAA
1 AGTGCAAACAGAGACACCAA
* *
12104290 AGTGTGAAA-AGAGGCACCAA
1 AGTG-CAAACAGAGACACCAA
12104310 AGTGCAAAC
1 AGTGCAAAC
12104319 CCATACAAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.12
20 18 0.75
21 3 0.12
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (20 bp):
AGTGCAAACAGAGACACCAA
Found at i:12128801 original size:20 final size:20
Alignment explanation
Indices: 12128778--12128826 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12128768 CAATGTTTAT
*
12128778 ACAGAGTCACCGAA-GTGCAA
1 ACAGAGGCA-CGAATGTGCAA
12128798 ACAGAGGCACGAATGTGCAA
1 ACAGAGGCACGAATGTGCAA
*
12128818 TCAGAGGCA
1 ACAGAGGCA
12128827 TTAAAGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.39, C:0.22, G:0.29, T:0.10
Consensus pattern (20 bp):
ACAGAGGCACGAATGTGCAA
Found at i:12128835 original size:20 final size:20
Alignment explanation
Indices: 12128790--12128839 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
12128780 AGAGTCACCG
*
12128790 AAGTGCAAACAGAGGCACGA
1 AAGTGCAATCAGAGGCACGA
* **
12128810 ATGTGCAATCAGAGGCATTA
1 AAGTGCAATCAGAGGCACGA
12128830 AAGTGCAATC
1 AAGTGCAATC
12128840 CCGTACAAGC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.18, G:0.26, T:0.16
Consensus pattern (20 bp):
AAGTGCAATCAGAGGCACGA
Found at i:12148295 original size:55 final size:55
Alignment explanation
Indices: 12148211--12148320 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
12148201 CCACTATTCA
12148211 AGTGGTTGTTTTAATTTTTTAAGAAAATAATTTTGATGGCCTAGAAAAATAGCAG
1 AGTGGTTGTTTTAATTTTTTAAGAAAATAATTTTGATGGCCTAGAAAAATAGCAG
12148266 AGTGGTTGTTTTAATTTTTTAAGAAAATAATTTTGATGGCCTAGAAAAATAGCAG
1 AGTGGTTGTTTTAATTTTTTAAGAAAATAATTTTGATGGCCTAGAAAAATAGCAG
12148321 CAATTTGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.36, C:0.05, G:0.20, T:0.38
Consensus pattern (55 bp):
AGTGGTTGTTTTAATTTTTTAAGAAAATAATTTTGATGGCCTAGAAAAATAGCAG
Found at i:12150598 original size:50 final size:50
Alignment explanation
Indices: 12150357--12150598 Score: 256
Period size: 50 Copynumber: 4.9 Consensus size: 50
12150347 GATAATAACA
* * * *
12150357 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGTTTTCT-GTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCG--G
* * * * ** * * *
12150406 TACCAATGCCATATCCCAAATATGGTCTTACATGGGAGTTCTCATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
* ** *
12150456 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
** * *
12150506 TGCCAACACAATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
12150556 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTT
12150599 TACCCAAATG
Statistics
Matches: 158, Mismatches: 32, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
49 32 0.20
50 121 0.77
51 4 0.03
52 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:12160768 original size:43 final size:43
Alignment explanation
Indices: 12160632--12160788 Score: 133
Period size: 43 Copynumber: 3.7 Consensus size: 43
12160622 TGTTATCTCG
* * * *
12160632 TGTAAGACCACGTCTGGGGC-GTTGGCATCGAT-TTGAGATTTACA
1 TGTAAGACCATGTCTAGGACAG-TGGCATCGATATT-TGA-TTACA
* * * * *
12160676 TGTAAGACCATGTCTGGGACATTGGCATC-ATATATGATTTCG
1 TGTAAGACCATGTCTAGGACAGTGGCATCGATATTTGATTACA
* *
12160718 TGTAAGACCCTGTCTAGGACCGTGGCATCGATATTTGATTACA
1 TGTAAGACCATGTCTAGGACAGTGGCATCGATATTTGATTACA
* *
12160761 TGTAAGACCACGTCTGGGAC-GTTGGCAT
1 TGTAAGACCATGTCTAGGACAG-TGGCAT
12160789 TGTACAAGCT
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 29 0.32
43 37 0.40
44 26 0.28
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (43 bp):
TGTAAGACCATGTCTAGGACAGTGGCATCGATATTTGATTACA
Found at i:12160778 original size:85 final size:86
Alignment explanation
Indices: 12160629--12160788 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 86
12160619 ATATGTTATC
** *
12160629 TCGTGTAAGACCACGTCTGGGGCGTTGGCATCGATTTGAGATTTACATGTAAGACCATGTCTGGG
1 TCGTGTAAGACCACGTCTGGACCGTTGGCATCGATTTGAGATTTACATGTAAGACCACGTCTGGG
12160694 ACATTGGCATCATATATGATT
66 ACATTGGCATCATATATGATT
*
12160715 TCGTGTAAGACC-CTGTCTAGGACCG-TGGCATCGATATT-TGA-TTACATGTAAGACCACGTCT
1 TCGTGTAAGACCAC-GTCT-GGACCGTTGGCATCGAT-TTGAGATTTACATGTAAGACCACGTCT
*
12160776 GGGACGTTGGCAT
63 GGGACATTGGCAT
12160789 TGTACAAGCT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
85 32 0.48
86 28 0.42
87 6 0.09
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (86 bp):
TCGTGTAAGACCACGTCTGGACCGTTGGCATCGATTTGAGATTTACATGTAAGACCACGTCTGGG
ACATTGGCATCATATATGATT
Found at i:12165907 original size:13 final size:13
Alignment explanation
Indices: 12165889--12165913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12165879 TTTACTGGAA
12165889 TCTTATTTCTTTC
1 TCTTATTTCTTTC
12165902 TCTTATTTCTTT
1 TCTTATTTCTTT
12165914 TTCATTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.72
Consensus pattern (13 bp):
TCTTATTTCTTTC
Found at i:12168962 original size:26 final size:26
Alignment explanation
Indices: 12168931--12168984 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
12168921 GAAGTTAGGA
12168931 TTGGTTTAGTATTTCAGTTCATTGGC
1 TTGGTTTAGTATTTCAGTTCATTGGC
*
12168957 TTGGTTTAGTGTTTCAGTTCATTGGC
1 TTGGTTTAGTATTTCAGTTCATTGGC
12168983 TT
1 TT
12168985 TCTTAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.13, C:0.11, G:0.24, T:0.52
Consensus pattern (26 bp):
TTGGTTTAGTATTTCAGTTCATTGGC
Found at i:12169898 original size:23 final size:22
Alignment explanation
Indices: 12169872--12169914 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
12169862 ATCACTATTA
12169872 TTAAATATATTTATTAATTTAGT
1 TTAAATATATTTATT-ATTTAGT
*
12169895 TTAAATATATTTCTTATTTA
1 TTAAATATATTTATTATTTA
12169915 TCATGACCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (22 bp):
TTAAATATATTTATTATTTAGT
Found at i:12171133 original size:16 final size:16
Alignment explanation
Indices: 12171112--12171180 Score: 102
Period size: 16 Copynumber: 4.3 Consensus size: 16
12171102 TTTGGTTCGC
* *
12171112 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
* *
12171128 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
12171144 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
12171160 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
12171176 TGTAA
1 TGTAA
12171181 AAGCAAATCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 51 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:12171252 original size:44 final size:45
Alignment explanation
Indices: 12171160--12171254 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 45
12171150 GGAATAGAGG
*
12171160 TGTAATGGAATAGAGGTGTAAAAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAAAAGCAAATCAACTGTTTGGTTGAA
* * ***
12171205 TGTAATGGAATAGAGGCGTAATAG-TAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAAAAGCAAATCAACTGTTTGGTTGAA
12171249 TGTAAT
1 TGTAAT
12171255 AGAGGTGTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 22 0.50
45 22 0.50
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.33
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAAAAGCAAATCAACTGTTTGGTTGAA
Found at i:12171432 original size:16 final size:16
Alignment explanation
Indices: 12171395--12171436 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12171385 TTAATCATAT
*
12171395 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
12171411 TT-AAATATATTATAA
1 TTAAAATATATTATAA
12171426 TTAAAATATAT
1 TTAAAATATAT
12171437 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:12171443 original size:14 final size:15
Alignment explanation
Indices: 12171404--12171445 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
12171394 TTTAAACATA
*
12171404 ATTATTATTAAATAT
1 ATTATAATTAAATAT
12171419 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
12171433 A-TATAATTTAATA
1 ATTATAATTAAATA
12171446 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:12173321 original size:11 final size:11
Alignment explanation
Indices: 12173307--12173333 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12173297 AAAAATTAAT
12173307 ACAAAAGTTTC
1 ACAAAAGTTTC
12173318 ACAAAAGTTTC
1 ACAAAAGTTTC
12173329 ACAAA
1 ACAAA
12173334 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:12176752 original size:18 final size:18
Alignment explanation
Indices: 12176738--12176775 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12176728 ACCCTTCTTC
12176738 TCCCTTTTCCCCTTCCCCT
1 TCCC-TTTCCCCTTCCCCT
12176757 TCCCTTTCCCCTTCCCCT
1 TCCCTTTCCCCTTCCCCT
12176775 T
1 T
12176776 GGGTTGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCCTTTCCCCTTCCCCT
Found at i:12176755 original size:6 final size:6
Alignment explanation
Indices: 12176744--12176775 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12176734 CTTCTCCCTT
*
12176744 TTCCCC TTCCCC TTCCCT TTCCCC TTCCCC TT
1 TTCCCC TTCCCC TTCCCC TTCCCC TTCCCC TT
12176776 GGGTTGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (6 bp):
TTCCCC
Found at i:12179931 original size:26 final size:25
Alignment explanation
Indices: 12179902--12180068 Score: 88
Period size: 26 Copynumber: 6.8 Consensus size: 25
12179892 ATTTTTGTTG
12179902 AATTATATTTAATAATAATTATTTTA
1 AATTATATTT-ATAATAATTATTTTA
*
12179928 AATTATATTT-T-ATAA-TATTATA
1 AATTATATTTATAATAATTATTTTA
* * *
12179950 TATTATGATTT-TAGTAAATTCA-TATA
1 AATTAT-ATTTATAAT-AATT-ATTTTA
* * **
12179976 AA-AATATTTAATACTAAGAATTTT-
1 AATTATATTT-ATAATAATTATTTTA
* *
12180000 -ATTA-AATTAT-AT-ATTTTTGTTA
1 AATTATATTTATAATAATTATT-TTA
12180022 AATTATATTTAATAATAATTATTTTA
1 AATTATATTT-ATAATAATTATTTTA
12180048 AATTATATTTTATAAT-ATTAT
1 AATTATA-TTTATAATAATTAT
12180069 ATATTATAAT
Statistics
Matches: 107, Mismatches: 17, Indels: 35
0.67 0.11 0.22
Matches are distributed among these distances:
20 3 0.03
21 3 0.03
22 13 0.12
23 17 0.16
24 11 0.10
25 15 0.14
26 36 0.34
27 9 0.08
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (25 bp):
AATTATATTTATAATAATTATTTTA
Found at i:12179949 original size:59 final size:59
Alignment explanation
Indices: 12179875--12180073 Score: 210
Period size: 59 Copynumber: 3.3 Consensus size: 59
12179865 ATTACTAAGA
*
12179875 ATTTTATTAAATTATATATTTTTGTTGAATTATATTTAATAATAATTATTTTAAATTAT
1 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTAT
* ** * * * * * *
12179934 ATTTTA-TAATATTATATA-TTATGATTTTAGTAAATTCATATAA-AAATA-TTTAATACTAAGA
1 ATTTTATTAA-ATTATATATTTTTG-TTAAATTATATTTA-ATAATAATTATTTTAA-A-TTA-T
12179995 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTAT
1 ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTAT
12180054 ATTTTA-TAATATTATATATT
1 ATTTTATTAA-ATTATATATT
12180074 ATAATTTTAG
Statistics
Matches: 111, Mismatches: 18, Indels: 22
0.74 0.12 0.15
Matches are distributed among these distances:
58 15 0.14
59 44 0.40
60 12 0.11
61 28 0.25
62 12 0.11
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (59 bp):
ATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTATTTTAAATTAT
Found at i:12180002 original size:120 final size:120
Alignment explanation
Indices: 12179858--12180095 Score: 449
Period size: 120 Copynumber: 2.0 Consensus size: 120
12179848 CAATCATTAG
* *
12179858 AATATTTATTACTAAGAATTTTATTAAATTATATATTTTTGTTGAATTATATTTAATAATAATTA
1 AATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTA
*
12179923 TTTTAAATTATATTTTATAATATTATATATTATGATTTTAGTAAATTCATATAAA
66 TTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATATAAA
12179978 AATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTA
1 AATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTA
12180043 TTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATATA
66 TTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATATA
12180096 TTCTATTAAA
Statistics
Matches: 115, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 115 1.00
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (120 bp):
AATATTTAATACTAAGAATTTTATTAAATTATATATTTTTGTTAAATTATATTTAATAATAATTA
TTTTAAATTATATTTTATAATATTATATATTATAATTTTAGTAAATTCATATAAA
Found at i:12180067 original size:15 final size:15
Alignment explanation
Indices: 12180023--12180078 Score: 57
Period size: 15 Copynumber: 4.0 Consensus size: 15
12180013 TTTTTGTTAA
*
12180023 ATTATATTTAATAAT
1 ATTATATTTTATAAT
*
12180038 AAT-TA-TTT-TAA-
1 ATTATATTTTATAAT
12180049 ATTATATTTTATAAT
1 ATTATATTTTATAAT
*
12180064 ATTATATATTATAAT
1 ATTATATTTTATAAT
12180079 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.06
12 5 0.15
13 5 0.15
14 5 0.15
15 16 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTATATTTTATAAT
Found at i:12180096 original size:24 final size:22
Alignment explanation
Indices: 12180049--12180102 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
12180039 ATTATTTTAA
12180049 ATTATATTTTATAATATTATAT
1 ATTATATTTTATAATATTATAT
12180071 ATTATAATTTTAGTAA-ATTCATAT
1 ATTAT-ATTTTA-TAATATT-ATAT
*
12180095 ATTCTATT
1 ATTATATT
12180103 AAATTACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.18
23 12 0.43
24 11 0.39
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.56
Consensus pattern (22 bp):
ATTATATTTTATAATATTATAT
Found at i:12180321 original size:21 final size:21
Alignment explanation
Indices: 12180295--12180347 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
12180285 CGCTGTTTCT
*
12180295 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
12180316 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
*
12180337 AATCACACCGC
1 AATCTCACCGC
12180348 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.32, C:0.38, G:0.09, T:0.21
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:12183133 original size:84 final size:84
Alignment explanation
Indices: 12182992--12183159 Score: 318
Period size: 84 Copynumber: 2.0 Consensus size: 84
12182982 TAAGCATAAG
12182992 TTAGTTCAGTTTTCCTTTATTTCCCATGACACTAGTCTACAGAATGAGAACTTACTGTAGTTGCT
1 TTAGTTCAGTTTTCCTTTATTTCCCATGACACTAGTCTACAGAATGAGAACTTACTGTAGTTGCT
12183057 ACATAAAATAAAGGGGGAA
66 ACATAAAATAAAGGGGGAA
* *
12183076 TTAGTTCAGTTTTCCTTTATTTCCCATGACACTAGTTTACAGGATGAGAACTTACTGTAGTTGCT
1 TTAGTTCAGTTTTCCTTTATTTCCCATGACACTAGTCTACAGAATGAGAACTTACTGTAGTTGCT
12183141 ACATAAAATAAAGGGGGAA
66 ACATAAAATAAAGGGGGAA
12183160 AGGAGAAAGA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (84 bp):
TTAGTTCAGTTTTCCTTTATTTCCCATGACACTAGTCTACAGAATGAGAACTTACTGTAGTTGCT
ACATAAAATAAAGGGGGAA
Found at i:12185512 original size:15 final size:17
Alignment explanation
Indices: 12185476--12185512 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
12185466 TCCCCTCCCC
12185476 TTAAAAAGATCTACCTA
1 TTAAAAAGATCTACCTA
*
12185493 TTAAAAA-ATTTACC-A
1 TTAAAAAGATCTACCTA
12185508 TTAAA
1 TTAAA
12185513 CGATGACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 6 0.32
16 6 0.32
17 7 0.37
ACGTcount: A:0.51, C:0.14, G:0.03, T:0.32
Consensus pattern (17 bp):
TTAAAAAGATCTACCTA
Found at i:12186027 original size:17 final size:18
Alignment explanation
Indices: 12186005--12186038 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
12185995 CTAGTTGTTG
12186005 TTTTAA-TAATTTTTATT
1 TTTTAATTAATTTTTATT
12186022 TTTTAATTAATTTTTAT
1 TTTTAATTAATTTTTAT
12186039 AACTTCTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTAATTAATTTTTATT
Found at i:12186067 original size:10 final size:10
Alignment explanation
Indices: 12186005--12186078 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
12185995 CTAGTTGTTG
12186005 TTTTAATAAT
1 TTTTAATAAT
12186015 TTTT-AT--T
1 TTTTAATAAT
12186022 TTTTAATTAAT
1 TTTTAA-TAAT
12186033 TTTT-ATAACT
1 TTTTAATAA-T
*
12186043 TCTT-ATAAT
1 TTTTAATAAT
*
12186052 TCTTAATAAT
1 TTTTAATAAT
*
12186062 TTTTAAATAAA
1 TTTT-AATAAT
12186073 TTTTAA
1 TTTTAA
12186079 ATTTTATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 14
0.76 0.04 0.20
Matches are distributed among these distances:
7 5 0.09
8 1 0.02
9 11 0.20
10 23 0.43
11 14 0.26
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:12186099 original size:18 final size:18
Alignment explanation
Indices: 12186012--12186099 Score: 58
Period size: 18 Copynumber: 4.7 Consensus size: 18
12186002 TTGTTTTAAT
* *
12186012 AATTTTTAT-TTTTTAATT
1 AATTTTTATAATTTT-ATA
12186030 AATTTTTATAACTTCTTAT-
1 AATTTTTATAA-TT-TTATA
*
12186049 AATTCTTAATAATTTT-TA
1 AATT-TTTATAATTTTATA
12186067 AATAAATTTTA-AATTTTATA
1 AAT---TTTTATAATTTTATA
12186087 AATTTTTATAATT
1 AATTTTTATAATT
12186100 ATTTGAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 20
0.71 0.04 0.25
Matches are distributed among these distances:
17 6 0.11
18 18 0.32
19 12 0.21
20 18 0.32
21 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTTATAATTTTATA
Found at i:12188862 original size:16 final size:16
Alignment explanation
Indices: 12188841--12188876 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
12188831 TTTGGTTCAC
12188841 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12188857 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12188873 TGTA
1 TGTA
12188877 ATAGCTAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12188941 original size:44 final size:45
Alignment explanation
Indices: 12188857--12188947 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
12188847 GGATTAGAGG
* * *
12188857 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
12188902 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
12188946 TG
1 TG
12188948 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:12189133 original size:18 final size:17
Alignment explanation
Indices: 12189112--12189146 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12189102 TTATTATTAA
*
12189112 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12189130 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12189147 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12189283 original size:156 final size:156
Alignment explanation
Indices: 12188999--12189469 Score: 798
Period size: 156 Copynumber: 3.0 Consensus size: 156
12188989 TAGAATACCC
* *
12188999 TTAGCATAAAATTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
12189064 TTATCAGTAATAAATATTTTAATCATGTTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATGTTTAAACATAATTATTATTAAATATATTTTAATTAAAA
12189129 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
12189155 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTAATGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
12189220 TTATCAGTAATAAATATTTTAATCATGTTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 TTATCAGTAATAAATATTTTAATCATGTTTAAACATAATTATTATTAAATATATTTTAATTAAAA
12189285 TATATAATTTAATAAAATTCTTATAA
131 TATATAATTTAATAAAATTCTTATAA
*
12189311 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * * * * ****
12189376 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATACATTATAATTTTGG
66 TTATCAGTAATAAATATTTTAATCATGTTTAAACATAATTATTATTAAATATATTTTAATTAAAA
*
12189441 TATATAATTTAGTAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTT-ATAA
12189468 TT
1 TT
12189470 CATATTCTTA
Statistics
Matches: 298, Mismatches: 16, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
156 292 0.98
157 6 0.02
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.48
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
TTATCAGTAATAAATATTTTAATCATGTTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTTAATAAAATTCTTATAA
Found at i:12189289 original size:18 final size:17
Alignment explanation
Indices: 12189268--12189302 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12189258 TTATTATTAA
*
12189268 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12189286 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12189303 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:12198102 original size:26 final size:25
Alignment explanation
Indices: 12198033--12198127 Score: 129
Period size: 25 Copynumber: 3.8 Consensus size: 25
12198023 CACCCTAATA
12198033 TTACCC-AGTAAAATTTTGACGATT
1 TTACCCTAGTAAAATTTTGACGATT
* * *
12198057 TTACCCCAATAAAATTTTGACAATT
1 TTACCCTAGTAAAATTTTGACGATT
*
12198082 TTACCCTTTGTAAAATTTTGACGATT
1 TTACCC-TAGTAAAATTTTGACGATT
*
12198108 TTACCCTGGTAAAATTTTGA
1 TTACCCTAGTAAAATTTTGA
12198128 GAAAATTTGT
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
24 6 0.10
25 35 0.56
26 21 0.34
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.40
Consensus pattern (25 bp):
TTACCCTAGTAAAATTTTGACGATT
Found at i:12200363 original size:43 final size:43
Alignment explanation
Indices: 12200295--12200422 Score: 168
Period size: 43 Copynumber: 3.0 Consensus size: 43
12200285 TTATCTTAGA
*
12200295 AAAAAAGGAATTT-AAAAAGTGGAGAAGATAATCTTGGGTTGTTG
1 AAAAAA-GAATTTAAAAAAAT-GAGAAGATAATCTTGGGTTGTTG
*
12200339 AAAAAATAATTTAAAAAAATGAGAAGATAATCTTGGGTTGTTG
1 AAAAAAGAATTTAAAAAAATGAGAAGATAATCTTGGGTTGTTG
* * * * *
12200382 AAAAAAGAACTTAAAAAGAGGAGAAGATAAACATGGGTTGT
1 AAAAAAGAATTTAAAAAAATGAGAAGATAATCTTGGGTTGT
12200423 CGGATTTACC
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
43 63 0.84
44 12 0.16
ACGTcount: A:0.48, C:0.03, G:0.23, T:0.25
Consensus pattern (43 bp):
AAAAAAGAATTTAAAAAAATGAGAAGATAATCTTGGGTTGTTG
Found at i:12209404 original size:16 final size:15
Alignment explanation
Indices: 12209371--12209412 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
12209361 AGATGATAAT
12209371 TATTAATATATAATTA
1 TATTAAT-TATAATTA
*
12209387 TATTCATTATAATATA
1 TATTAATTATAAT-TA
12209403 TATTAATTAT
1 TATTAATTAT
12209413 TATCAGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 6 0.26
16 17 0.74
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTAATTATAATTA
Found at i:12209997 original size:20 final size:21
Alignment explanation
Indices: 12209950--12209999 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
12209940 GGTGGTAAGA
*
12209950 TCAATTT-TTCTCTTAAATTT
1 TCAATTTATTATCTTAAATTT
12209970 T-AATTTTATTATC-TAAATTT
1 TCAA-TTTATTATCTTAAATTT
12209990 TCAATTTATT
1 TCAATTTATT
12210000 GAATTATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.08
20 18 0.69
21 6 0.23
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (21 bp):
TCAATTTATTATCTTAAATTT
Found at i:12213681 original size:21 final size:21
Alignment explanation
Indices: 12213657--12213701 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
12213647 TTTTAATGCT
*
12213657 TGATTTATATA-GGTTTGGTCA
1 TGATATATATATGGTTTGG-CA
*
12213678 TGATATATATATGTTTTGGCA
1 TGATATATATATGGTTTGGCA
12213699 TGA
1 TGA
12213702 AGTAATTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.27, C:0.04, G:0.22, T:0.47
Consensus pattern (21 bp):
TGATATATATATGGTTTGGCA
Found at i:12221949 original size:21 final size:21
Alignment explanation
Indices: 12221925--12221964 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
12221915 ATGCTTGAGT
12221925 TATATA-GTTTTGGTCATGATA
1 TATATATGTTTTGG-CATGATA
12221946 TATATATGTTTTGGCATGA
1 TATATATGTTTTGGCATGA
12221965 AGTAATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (21 bp):
TATATATGTTTTGGCATGATA
Found at i:12223905 original size:48 final size:49
Alignment explanation
Indices: 12223819--12224025 Score: 233
Period size: 48 Copynumber: 4.3 Consensus size: 49
12223809 TCGGAATAAA
* * * * * *
12223819 AACAGATTTCTCGGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAAT
1 AACAGAGTTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAC
* * * * * **
12223868 AACAGA-TTCTCGGTGGCCTGTACATAGTCTGTGCCACCCTTGTATCTT
1 AACAGAGTTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAC
*
12223916 AACA-AGTTATTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAC
1 AACAGAGTTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAC
* *
12223964 AACAGA-ATATCGGTGGCCTGCACACAGTCCGTGTCACCCTTGTGTCAC
1 AACAGAGTTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAC
*
12224012 AACAGA-ATATCGGT
1 AACAGAGTTATCGGT
12224026 ACGCATAGTA
Statistics
Matches: 137, Mismatches: 19, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
47 1 0.01
48 129 0.94
49 7 0.05
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (49 bp):
AACAGAGTTATCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCAC
Found at i:12224002 original size:96 final size:96
Alignment explanation
Indices: 12223831--12224006 Score: 262
Period size: 96 Copynumber: 1.8 Consensus size: 96
12223821 CAGATTTCTC
* * * * * *
12223831 GGTGGCCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTCTCGGTGGCCTGTACATAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTGTAACAACAGAATATCGGTGGCCTGCACACAGT
*
12223896 CTGTGCCACCCTTGTATCTTAACAAGTTATT
66 CCGTGCCACCCTTGTATCTTAACAAGTTATT
* *
12223927 GGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCACAACAGAATATCGGTGGCCTGCACACAGT
1 GGTGGCCTGCACACAGTCCGTACCACCCTTGTGTAACAACAGAATATCGGTGGCCTGCACACAGT
*
12223992 CCGTGTCACCCTTGT
66 CCGTGCCACCCTTGT
12224007 GTCACAACAG
Statistics
Matches: 70, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 70 1.00
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.27
Consensus pattern (96 bp):
GGTGGCCTGCACACAGTCCGTACCACCCTTGTGTAACAACAGAATATCGGTGGCCTGCACACAGT
CCGTGCCACCCTTGTATCTTAACAAGTTATT
Found at i:12236547 original size:30 final size:30
Alignment explanation
Indices: 12236465--12236550 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 30
12236455 TTTGAGGGAT
12236465 TTAATGAGAATTTTCAAAAAA-TTTGGTAGGC
1 TTAATGAGAA-TTT-AAAAAATTTTGGTAGGC
* * *
12236496 CTAATTAGAACTTTAACAAATTTTGG-AGGC
1 TTAATGAGAA-TTTAAAAAATTTTGGTAGGC
*
12236526 TTAATGAGAGTTCTAAAAAATTTTG
1 TTAATGAGAATT-TAAAAAATTTTG
12236551 AAATGCTTCA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
29 2 0.04
30 27 0.60
31 16 0.36
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.36
Consensus pattern (30 bp):
TTAATGAGAATTTAAAAAATTTTGGTAGGC
Found at i:12236953 original size:22 final size:21
Alignment explanation
Indices: 12236923--12236977 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
12236913 AAAGGTAATT
* *
12236923 TTATCATTTTAATAGATTATAA
1 TTATAATTTTAAAAGATTA-AA
12236945 TTATAATTTTTAAAAGATTAAA
1 TTATAA-TTTTAAAAGATTAAA
*
12236967 TTAAAATTTTA
1 TTATAATTTTA
12236978 TATAAAAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.17
22 12 0.41
23 12 0.41
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (21 bp):
TTATAATTTTAAAAGATTAAA
Found at i:12236962 original size:23 final size:22
Alignment explanation
Indices: 12236929--12236976 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 22
12236919 AATTTTATCA
* *
12236929 TTTTAATAGATTATAATTATAAT
1 TTTTAAAAGATTA-AATTAAAAT
12236952 TTTTAAAAGATTAAATTAAAAT
1 TTTTAAAAGATTAAATTAAAAT
12236974 TTT
1 TTT
12236977 ATATAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTTAAAAGATTAAATTAAAAT
Found at i:12237011 original size:11 final size:11
Alignment explanation
Indices: 12236995--12237019 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12236985 GATCTAAATG
12236995 TAAAGTATGCA
1 TAAAGTATGCA
12237006 TAAAGTATGCA
1 TAAAGTATGCA
12237017 TAA
1 TAA
12237020 GAATATTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (11 bp):
TAAAGTATGCA
Found at i:12237490 original size:45 final size:44
Alignment explanation
Indices: 12237401--12237493 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
12237391 ATTACAACAT
*
12237401 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
*
12237445 CATTCCATTCAACCAAACA-ATTGAATTACTATTAC-GCCTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAG-CTCTATTC
12237490 CATT
1 CATT
12237494 ACACCTCTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 23 0.52
45 20 0.45
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.32
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGCTCTATTC
Found at i:12237500 original size:16 final size:16
Alignment explanation
Indices: 12237475--12237512 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
12237465 TTGAATTACT
*
12237475 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
12237491 ATTACACCTCTATTCT
1 ATTACACCTCTATTCC
12237507 ATTACA
1 ATTACA
12237513 GTAAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:12243645 original size:12 final size:13
Alignment explanation
Indices: 12243621--12243649 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12243611 GGACTATAAC
12243621 TATTGCATTTATT
1 TATTGCATTTATT
12243634 TATTGC-TTTATT
1 TATTGCATTTATT
12243646 TATT
1 TATT
12243650 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:12256226 original size:15 final size:15
Alignment explanation
Indices: 12256206--12256234 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12256196 TTCATTCACA
12256206 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
12256221 CACCGTGTTATCAA
1 CACCGTGTTATCAA
12256235 GCAACAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:12257350 original size:14 final size:14
Alignment explanation
Indices: 12257328--12257367 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
12257318 CATTCATCCA
*
12257328 TAATTAATTAATTT
1 TAATCAATTAATTT
*
12257342 TAATCAATTGATTT
1 TAATCAATTAATTT
12257356 TAATC-ATTAATT
1 TAATCAATTAATT
12257368 AAGGTACTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (14 bp):
TAATCAATTAATTT
Found at i:12271115 original size:306 final size:306
Alignment explanation
Indices: 12270550--12271163 Score: 1129
Period size: 306 Copynumber: 2.0 Consensus size: 306
12270540 TGTTTAGGGC
* *
12270550 CTCATGTGACTCGACTTGCATGCCACTTCGATCTCCTTGACACACCGAAGCAGTCCTCCTCGCTT
1 CTCATATGACTCGACTTGCATGCCACTTCGATCTCCTCGACACACCGAAGCAGTCCTCCTCGCTT
*
12270615 ACACTAGTCGGCCAGATGTCCCCGCAAGGATTATTGAGCATCACCCATATGAGGATGATTGAGTG
66 ACACTAGTCGGCCAGATGTCCCCGCAAGGATTATTGAGCATCACCCATATGAGGATGATTGAGCG
* *
12270680 ACTTTATGGAGTGGATCCACCTCAGTACCAATTATCTCATTTTGGTCCTCAGGATGAACCCGAGG
131 ACTTTATAGAGTGGATCCACCTCAGTACCAATTATCTCATTTTGATCCTCAGGATGAACCCGAGG
*
12270745 ACTTCACTGACGATGTCCCCTTCTATCACAAGGATCCACCTCATCATCCACCTTCAAGTCACCGT
196 ACTTCACTAACGATGTCCCCTTCTATCACAAGGATCCACCTCATCATCCACCTTCAAGTCACCGT
*
12270810 CCTGCTTCTTCTGCTGCTACCTTAGTGAACCTCTCCGAGTGGTTCA
261 CCTGCTTCTTCTGCTGCTACCTTAGCGAACCTCTCCGAGTGGTTCA
*
12270856 CTCATATGACTTGACTTGCATGCCACTTCGATCTCCTCGACACACCGAAGCAGTCCTCCTCGCTT
1 CTCATATGACTCGACTTGCATGCCACTTCGATCTCCTCGACACACCGAAGCAGTCCTCCTCGCTT
* *
12270921 ACACTAGTCGGCCAGATGTCCCCGCAAGGATTATTGAGCATGAGCCATATGAGGATGATTGAGCG
66 ACACTAGTCGGCCAGATGTCCCCGCAAGGATTATTGAGCATCACCCATATGAGGATGATTGAGCG
12270986 ACTTTATAGAGTGGATCCACCTCAGTACCAATTATCTCATTTTGATCCTCAGGATGAACCCGAGG
131 ACTTTATAGAGTGGATCCACCTCAGTACCAATTATCTCATTTTGATCCTCAGGATGAACCCGAGG
*
12271051 ACTTCACTAACGATGTCCCCTTCTATCACACGGATCCACCTCATCATCCACCTTCAAGTCACCGT
196 ACTTCACTAACGATGTCCCCTTCTATCACAAGGATCCACCTCATCATCCACCTTCAAGTCACCGT
12271116 CCTGCTTCTTCTGCTGCTACCTTAGCGAACCTCTCCGAGTGGTTCA
261 CCTGCTTCTTCTGCTGCTACCTTAGCGAACCTCTCCGAGTGGTTCA
12271162 CT
1 CT
12271164 TGTTTCGAGT
Statistics
Matches: 297, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
306 297 1.00
ACGTcount: A:0.23, C:0.31, G:0.19, T:0.28
Consensus pattern (306 bp):
CTCATATGACTCGACTTGCATGCCACTTCGATCTCCTCGACACACCGAAGCAGTCCTCCTCGCTT
ACACTAGTCGGCCAGATGTCCCCGCAAGGATTATTGAGCATCACCCATATGAGGATGATTGAGCG
ACTTTATAGAGTGGATCCACCTCAGTACCAATTATCTCATTTTGATCCTCAGGATGAACCCGAGG
ACTTCACTAACGATGTCCCCTTCTATCACAAGGATCCACCTCATCATCCACCTTCAAGTCACCGT
CCTGCTTCTTCTGCTGCTACCTTAGCGAACCTCTCCGAGTGGTTCA
Found at i:12271404 original size:26 final size:26
Alignment explanation
Indices: 12271341--12271404 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 26
12271331 TTTTTAGTTG
* * *
12271341 TTTTATTTTTATGTTCTTAGACTTAT
1 TTTTATTTTTATATTCTTAAACTAAT
*
12271367 TTTGT-TTCTTATATT-TTAAACTAAAT
1 TTT-TATTTTTATATTCTTAAACT-AAT
12271393 TTTTATTTTTAT
1 TTTTATTTTTAT
12271405 GGTTGTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
25 7 0.23
26 22 0.73
27 1 0.03
ACGTcount: A:0.23, C:0.06, G:0.05, T:0.66
Consensus pattern (26 bp):
TTTTATTTTTATATTCTTAAACTAAT
Found at i:12274770 original size:28 final size:27
Alignment explanation
Indices: 12274722--12274775 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
12274712 TACATACATA
12274722 TGTATAATAAAAATAATTTAATATAGGT
1 TGTATAATAAAAATAATTTAA-ATAGGT
12274750 TGTATAA-ATAAAA-AATATTAAATAGG
1 TGTATAATA-AAAATAAT-TTAAATAGG
12274776 GATATTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (27 bp):
TGTATAATAAAAATAATTTAAATAGGT
Found at i:12281502 original size:24 final size:23
Alignment explanation
Indices: 12281464--12281689 Score: 166
Period size: 24 Copynumber: 9.6 Consensus size: 23
12281454 TTCACATCAT
* *
12281464 AATTTGGACAGCATAAATACAAC
1 AATTTGGGCAGCATATATACAAC
*
12281487 AATTTTGGGCAACATATATACAAC
1 AA-TTTGGGCAGCATATATACAAC
* * * *
12281511 AATTTGAGCAGCATTTTTACACC
1 AATTTGGGCAGCATATATACAAC
* * * *
12281534 AAAATTGGACAGCATAAATTCAAC
1 -AATTTGGGCAGCATATATACAAC
12281558 AATTTGGGCAGCATATATACAAC
1 AATTTGGGCAGCATATATACAAC
* * * *
12281581 AATTTGAGCAGCATTTTTACACC
1 AATTTGGGCAGCATATATACAAC
* *
12281604 AAAATTGGACAGCATATATACAAC
1 -AATTTGGGCAGCATATATACAAC
* * *
12281628 AATTTTGGACAGCATTTA-AGCATC
1 AA-TTTGGGCAGCATATATA-CAAC
* ** *
12281652 AAAATTGGATAGCATATATGCAAC
1 -AATTTGGGCAGCATATATACAAC
*
12281676 AAATTGGGCAGCAT
1 AATTTGGGCAGCAT
12281690 TTAAGCATCA
Statistics
Matches: 156, Mismatches: 40, Indels: 14
0.74 0.19 0.07
Matches are distributed among these distances:
23 71 0.46
24 83 0.53
25 2 0.01
ACGTcount: A:0.41, C:0.17, G:0.15, T:0.27
Consensus pattern (23 bp):
AATTTGGGCAGCATATATACAAC
Found at i:12281584 original size:70 final size:71
Alignment explanation
Indices: 12281431--12281642 Score: 313
Period size: 70 Copynumber: 3.0 Consensus size: 71
12281421 GGACAACATT
* * * * *
12281431 TATATACCA-AATTAGA-CAGCATTTTCACATCATAATTTGGACAGCATAAATACAACAATTTTG
1 TATATACAACAATTTGAGCAGCATTTTTACACCA-AAATTGGACAGCATAAATACAACAATTTTG
*
12281494 GGCAACA
65 GGCAGCA
*
12281501 TATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAGCATAAATTCAACAA-TTTGG
1 TATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAGCATAAATACAACAATTTTGG
12281565 GCAGCA
66 GCAGCA
*
12281571 TATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAGCATATATACAACAATTTTGG
1 TATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAGCATAAATACAACAATTTTGG
*
12281636 ACAGCA
66 GCAGCA
12281642 T
1 T
12281643 TTAAGCATCA
Statistics
Matches: 129, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
70 75 0.58
71 40 0.31
72 14 0.11
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (71 bp):
TATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGACAGCATAAATACAACAATTTTGG
GCAGCA
Found at i:12281660 original size:48 final size:47
Alignment explanation
Indices: 12281561--12281699 Score: 174
Period size: 47 Copynumber: 2.9 Consensus size: 47
12281551 ATTCAACAAT
* * *
12281561 TTGGGCAGCATATATACAACAATTT-GAGCAGCATTTTTA-CACCAAAA
1 TTGGACAGCATATATACAACAATTTGGA-CAGCA-TTTAAGCATCAAAA
12281608 TTGGACAGCATATATACAACAATTTTGGACAGCATTTAAGCATCAAAA
1 TTGGACAGCATATATACAACAA-TTTGGACAGCATTTAAGCATCAAAA
* * * *
12281656 TTGGATAGCATATATGCAACAAATTGGGCAGCATTTAAGCATCA
1 TTGGACAGCATATATACAACAATTTGGACAGCATTTAAGCATCA
12281700 CCTATTCGGT
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
47 45 0.55
48 35 0.43
49 2 0.02
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (47 bp):
TTGGACAGCATATATACAACAATTTGGACAGCATTTAAGCATCAAAA
Found at i:12283731 original size:31 final size:31
Alignment explanation
Indices: 12283696--12283757 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
12283686 TGTTTCGTTT
12283696 TTTTTATTATAATAA-CTTTATAA-TATATATA
1 TTTTT-TTATAATAACCTTTATAACTA-ATATA
*
12283727 TTTTTTTATTATAACCTTTATAACTAATATA
1 TTTTTTTATAATAACCTTTATAACTAATATA
12283758 AAAACTATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 8 0.29
31 18 0.64
32 2 0.07
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (31 bp):
TTTTTTTATAATAACCTTTATAACTAATATA
Found at i:12289265 original size:71 final size:70
Alignment explanation
Indices: 12289181--12289331 Score: 171
Period size: 71 Copynumber: 2.1 Consensus size: 70
12289171 GATAGCTCTT
* * * * *
12289181 ATACATCAATTTGGACATCATTTATATACCA-AATTAGA-TAGTATTTTCACACCAAAATTTGGA
1 ATACAACAATTTGGACAGCA--TATATACAACAATTAGAGCAGCATTTTCACACCAAAA-TTGGA
12289244 CAGCATAA
63 CAGCATAA
* * * *
12289252 ATACAACAATTTGGGCAGCATATATACAACAATTTGAGCAGCATTTTTACACCAAAATTGGATAG
1 ATACAACAATTTGGACAGCATATATACAACAATTAGAGCAGCATTTTCACACCAAAATTGGACAG
*
12289317 CATAT
66 CATAA
12289322 ATACAACAAT
1 ATACAACAAT
12289332 ATATATATTT
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
69 8 0.12
70 27 0.40
71 33 0.49
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.30
Consensus pattern (70 bp):
ATACAACAATTTGGACAGCATATATACAACAATTAGAGCAGCATTTTCACACCAAAATTGGACAG
CATAA
Found at i:12289270 original size:23 final size:23
Alignment explanation
Indices: 12289236--12289295 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
12289226 TTCACACCAA
*
12289236 AATTTGGACAGCATAAATACAAC
1 AATTTGGGCAGCATAAATACAAC
*
12289259 AATTTGGGCAGCATATATACAAC
1 AATTTGGGCAGCATAAATACAAC
*
12289282 AATTTGAGCAGCAT
1 AATTTGGGCAGCAT
12289296 TTTTACACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (23 bp):
AATTTGGGCAGCATAAATACAAC
Found at i:12289302 original size:23 final size:23
Alignment explanation
Indices: 12289236--12289331 Score: 88
Period size: 23 Copynumber: 4.1 Consensus size: 23
12289226 TTCACACCAA
*
12289236 AATTTG-GACAGCATAAATACAAC
1 AATTTGAG-CAGCATATATACAAC
*
12289259 AATTTGGGCAGCATATATACAAC
1 AATTTGAGCAGCATATATACAAC
* * *
12289282 AATTTGAGCAGCATTTTTACACC
1 AATTTGAGCAGCATATATACAAC
* *
12289305 AAAATTG-GATAGCATATATACAAC
1 -AATTTGAG-CAGCATATATACAAC
12289329 AAT
1 AAT
12289332 ATATATATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
23 42 0.71
24 17 0.29
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.27
Consensus pattern (23 bp):
AATTTGAGCAGCATATATACAAC
Found at i:12289998 original size:37 final size:37
Alignment explanation
Indices: 12289922--12290143 Score: 173
Period size: 37 Copynumber: 6.0 Consensus size: 37
12289912 ATTCTAAATG
* * * *
12289922 GCTCAAACGAGTAATGTCTACT-ATTATACTGAATA-T
1 GCTCAAAAGAGCAATATCTACTGATAATACTGAA-AGT
* *
12289958 GCTCAAATGAGCAATATCTACTGA-AACTACTGAACGT
1 GCTCAAAAGAGCAATATCTACTGATAA-TACTGAAAGT
* *
12289995 GCTCAAAAGAGCAATATCTACTGATTATATTGAAAGTT
1 GCTCAAAAGAGCAATATCTACTGATAATACTGAAAG-T
* * * * * *
12290033 GCTCAAATGAGCGATATCCACTGATTATACTGAATGG
1 GCTCAAAAGAGCAATATCTACTGATAATACTGAAAGT
* * * * *
12290070 GCTCAAACGACCAATATTTACT-AAATATATTGAAAGT
1 GCTCAAAAGAGCAATATCTACTGATA-ATACTGAAAGT
* * * *
12290107 GCTCAAAAGGGCAATGTCTACTAATTATACTGAAAGT
1 GCTCAAAAGAGCAATATCTACTGATAATACTGAAAGT
12290144 TGCTTAGACA
Statistics
Matches: 146, Mismatches: 33, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
36 21 0.14
37 91 0.62
38 34 0.23
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (37 bp):
GCTCAAAAGAGCAATATCTACTGATAATACTGAAAGT
Found at i:12290044 original size:75 final size:74
Alignment explanation
Indices: 12289921--12290140 Score: 223
Period size: 75 Copynumber: 3.0 Consensus size: 74
12289911 AATTCTAAAT
* * *
12289921 GGCTCAAACGAGTAATGTCTACTATTATACTG-AA-TATGCTCAAATGAGCAATATCTACTGA-A
1 GGCTCAAACGAGCAATATCTACTATTATATTGAAAGT-TGCTCAAATGAGCAATATCTACTGATA
12289983 ACTACTGAACG
65 A-TACTGAACG
* * * * *
12289994 TGCTCAAAAGAGCAATATCTACTGATTATATTGAAAGTTGCTCAAATGAGCGATATCCACTGATT
1 GGCTCAAACGAGCAATATCTACT-ATTATATTGAAAGTTGCTCAAATGAGCAATATCTACTGATA
*
12290059 ATACTGAATG
65 ATACTGAACG
* * * * * * * *
12290069 GGCTCAAACGACCAATATTTACTAAATATATTGAAAG-TGCTCAAAAGGGCAATGTCTACTAATT
1 GGCTCAAACGAGCAATATCTACT-ATTATATTGAAAGTTGCTCAAATGAGCAATATCTACTGATA
12290133 ATACTGAA
65 ATACTGAA
12290141 AGTTGCTTAG
Statistics
Matches: 122, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
73 19 0.16
74 37 0.30
75 64 0.52
76 2 0.02
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (74 bp):
GGCTCAAACGAGCAATATCTACTATTATATTGAAAGTTGCTCAAATGAGCAATATCTACTGATAA
TACTGAACG
Found at i:12290141 original size:112 final size:112
Alignment explanation
Indices: 12289944--12290203 Score: 315
Period size: 112 Copynumber: 2.3 Consensus size: 112
12289934 AATGTCTACT
** * * * *
12289944 ATTATACTGAATATGCTCAAATGAGCAATATCTACTGAAACTACTGAACGTGCTCAAAAGAGCAA
1 ATTATACTGAATGGGCTCAAACGACCAATATCTACTGAAAATACTGAAAGTGCTCAAAAGAGCAA
* * **
12290009 TATCTACTGATTATATTGAAAGTTGCTCAAATGAGCGATATCCACTG
66 TATCTACTAATTATACTGAAAGTTGCTCAAACAAGCGATATCCACTG
* * *
12290056 ATTATACTGAATGGGCTCAAACGACCAATATTTACT-AAATATATTGAAAGTGCTCAAAAGGGCA
1 ATTATACTGAATGGGCTCAAACGACCAATATCTACTGAAA-ATACTGAAAGTGCTCAAAAGAGCA
* * * *
12290120 ATGTCTACTAATTATACTGAAAGTTGCTTAGACAAGCGATATCCATTG
65 ATATCTACTAATTATACTGAAAGTTGCTCAAACAAGCGATATCCACTG
* * * *
12290168 ATTACACTGAATGGGCTCAAACAAGCGATATCTACT
1 ATTATACTGAATGGGCTCAAACGACCAATATCTACT
12290204 TGTTATATAG
Statistics
Matches: 125, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
111 3 0.02
112 122 0.98
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (112 bp):
ATTATACTGAATGGGCTCAAACGACCAATATCTACTGAAAATACTGAAAGTGCTCAAAAGAGCAA
TATCTACTAATTATACTGAAAGTTGCTCAAACAAGCGATATCCACTG
Found at i:12292868 original size:17 final size:18
Alignment explanation
Indices: 12292846--12292886 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
12292836 CAATTTTCCT
12292846 TTCACAT-TC-AATATTAA
1 TTCACATATCAAATA-TAA
12292863 TTCACATATCAAATATAA
1 TTCACATATCAAATATAA
12292881 TTCACA
1 TTCACA
12292887 ATTTATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 11 0.50
19 4 0.18
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.37
Consensus pattern (18 bp):
TTCACATATCAAATATAA
Found at i:12299990 original size:23 final size:23
Alignment explanation
Indices: 12299964--12300016 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
12299954 ATAAGTGCCA
*
12299964 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
12299987 CACTGGA-ATGTAACCGAAGCTAC
1 CACT-GATATGTAACCGAAGCTAC
12300010 CACTGAT
1 CACTGAT
12300017 CAATAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 2 0.07
23 23 0.85
24 2 0.07
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAACCGAAGCTAC
Found at i:12307699 original size:3 final size:3
Alignment explanation
Indices: 12307691--12307733 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
12307681 GGAAATCTAG
12307691 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12307734 GGCCAAAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12308469 original size:10 final size:10
Alignment explanation
Indices: 12308456--12308505 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
12308446 AAGTAATAAT
12308456 ATTATTAAAA
1 ATTATTAAAA
12308466 ATTA-TAAAA
1 ATTATTAAAA
*
12308475 AAT-TTAAAA
1 ATTATTAAAA
*
12308484 ATTATAAAAA
1 ATTATTAAAA
*
12308494 ATTATTTAAA
1 ATTATTAAAA
12308504 AT
1 AT
12308506 ATTTTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
9 14 0.42
10 19 0.58
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
ATTATTAAAA
Found at i:12308481 original size:18 final size:18
Alignment explanation
Indices: 12308460--12308496 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
12308450 AATAATATTA
12308460 TTAAAAATTATAAAAAAT
1 TTAAAAATTATAAAAAAT
12308478 TTAAAAATTATAAAAAAT
1 TTAAAAATTATAAAAAAT
12308496 T
1 T
12308497 ATTTAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAAAATTATAAAAAAT
Found at i:12309757 original size:9 final size:9
Alignment explanation
Indices: 12309743--12309791 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
12309733 TTTGGTTAAA
12309743 AATTAACCG
1 AATTAACCG
12309752 AATTAACCG
1 AATTAACCG
*
12309761 AATTACCCG
1 AATTAACCG
12309770 AATTAACCG
1 AATTAACCG
*
12309779 AATTAACCA
1 AATTAACCG
12309788 AATT
1 AATT
12309792 GAATCACTAC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.45, C:0.22, G:0.08, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:12322329 original size:37 final size:38
Alignment explanation
Indices: 12322283--12322376 Score: 111
Period size: 37 Copynumber: 2.5 Consensus size: 38
12322273 ATCTTACTGC
* *
12322283 TATATTGAATGAAGCTCAATC-AAGCAAATCATACCGT
1 TATACTGAATGAAGCTCAATCTAAGCAAATCATACCAT
* * * *
12322320 TGTACTGAATGAAGCACAA-CTGAGCAATTCATACCAT
1 TATACTGAATGAAGCTCAATCTAAGCAAATCATACCAT
*
12322357 TATACTGAATGATGCTCAAT
1 TATACTGAATGAAGCTCAAT
12322377 TTAGTAAATC
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
36 1 0.02
37 45 0.98
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (38 bp):
TATACTGAATGAAGCTCAATCTAAGCAAATCATACCAT
Found at i:12326885 original size:48 final size:48
Alignment explanation
Indices: 12326814--12327048 Score: 425
Period size: 48 Copynumber: 4.9 Consensus size: 48
12326804 TTACCGAATT
12326814 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATC
1 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATC
*
12326862 GATTTGAGATCCCGTATAAGACCATATATGGGATATGGCATCGGCATC
1 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATC
** *
12326910 GATTTGAGATCTTGTATAAGACCATATCTGGGATATGGCATCGACATC
1 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATC
*
12326958 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGTATC
1 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATC
12327006 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCG
1 GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCG
12327049 ATATGAGACT
Statistics
Matches: 178, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 178 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (48 bp):
GATTTGAGATCCCGTATAAGACCATATCTGGGATATGGCATCGGCATC
Found at i:12329858 original size:16 final size:18
Alignment explanation
Indices: 12329831--12329863 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12329821 TAGAATTGGG
12329831 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
12329848 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
12329864 GTTAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:12334158 original size:25 final size:23
Alignment explanation
Indices: 12334113--12334166 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 23
12334103 AGGCACCTGC
*
12334113 AACAAACAAACTCAAGAGAAACAAA
1 AACAAACAAACCCAAGAG-AA-AAA
*
12334138 AACAAACAATACCCATG-GAAAAA
1 AACAAACAA-ACCCAAGAGAAAAA
12334161 AACAAA
1 AACAAA
12334167 AACGGATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
23 9 0.35
24 2 0.08
25 10 0.38
26 5 0.19
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.06
Consensus pattern (23 bp):
AACAAACAAACCCAAGAGAAAAA
Found at i:12335210 original size:3 final size:3
Alignment explanation
Indices: 12335202--12335229 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12335192 CGAGTATATG
12335202 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
12335230 TATGTTTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:12335326 original size:11 final size:11
Alignment explanation
Indices: 12335312--12335364 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
12335302 ATTCAATGGT
12335312 TATTTTAATTC
1 TATTTTAATTC
* *
12335323 TATTTTGAGTC
1 TATTTTAATTC
12335334 TATTTTGAATTC
1 TATTTT-AATTC
12335346 ATATATTTAATT-
1 -TAT-TTTAATTC
12335358 TATTTTA
1 TATTTTA
12335365 GAAATTTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.60
Consensus pattern (11 bp):
TATTTTAATTC
Found at i:12340019 original size:15 final size:15
Alignment explanation
Indices: 12339999--12340033 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
12339989 AGATTCTTTC
12339999 AAAAAAAATCAAAAT
1 AAAAAAAATCAAAAT
12340014 AAAAAAAATCAAAAT
1 AAAAAAAATCAAAAT
12340029 AAAAA
1 AAAAA
12340034 TGAGAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.83, C:0.06, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAAATCAAAAT
Found at i:12342407 original size:44 final size:44
Alignment explanation
Indices: 12342359--12342743 Score: 158
Period size: 44 Copynumber: 8.3 Consensus size: 44
12342349 ATGTTAAAGT
12342359 GGAGCAGATTAAAGCCAGAAATCTCATCTCCCTGAGATTACAGC
1 GGAGCAGATTAAAGCCAGAAATCTCATCTCCCTGAGATTACAGC
* * * *
12342403 GGAGCAGATTGAAGCTC-GTAA-CCCTATCTCCCTGAGATTACAGT
1 GGAGCAGATTAAAGC-CAGAAATCTC-ATCTCCCTGAGATTACAGC
* ** * * *
12342447 GGAGCGGATTAAA-ATA-AAGGATCTTATCTCTCTGA-AGTTACAGTAGA
1 GGAGCAGATTAAAGCCAGAA--ATCTCATCTCCCTGAGA-TTAC---AGC
* * *
12342494 GTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGC
1 G--GA--G---CAGATTAAAGCCAGAAATCTCATCTCCCTGAGATTACAGC
* * *
12342545 GGAGCAGATTAAAGCTAGTAATC-CTATCTCCCTGAGATTACAGT
1 GGAGCAGATTAAAGCCAGAAATCTC-ATCTCCCTGAGATTACAGC
* ** * * *
12342589 GGAGCGGATTAAA-ATA-AAGGATCTTATCTCTCTGAAGTTATAGTAGAGTACATC
1 GGAGCAGATTAAAGCCAGAA--ATCTCATCTCCCTG-AG----A-T----TACAGC
* * * * *
12342643 GCATCAAATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGC
1 GGAGCAGATTAAAGCCAGAAATCTCATCTCCCTGAGATTACAGC
* * * *
12342687 GGAGCAGATTGAAGCTAGTAATC-CTATCTCCCTGAGATTACAGT
1 GGAGCAGATTAAAGCCAGAAATCTC-ATCTCCCTGAGATTACAGC
*
12342731 GGAGCGGATTAAA
1 GGAGCAGATTAAA
12342744 ATAAAGGATC
Statistics
Matches: 253, Mismatches: 51, Indels: 74
0.67 0.13 0.20
Matches are distributed among these distances:
42 2 0.01
43 5 0.02
44 168 0.66
45 4 0.02
47 4 0.02
48 1 0.00
49 6 0.02
50 1 0.00
51 4 0.02
53 2 0.01
54 49 0.19
55 3 0.01
56 4 0.02
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (44 bp):
GGAGCAGATTAAAGCCAGAAATCTCATCTCCCTGAGATTACAGC
Found at i:12342537 original size:142 final size:142
Alignment explanation
Indices: 12342363--12342791 Score: 777
Period size: 142 Copynumber: 3.0 Consensus size: 142
12342353 TAAAGTGGAG
* * * *
12342363 CAGATTAAAGCCAGAAATCTCATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTCGTAACCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
*
12342428 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAG
*
12342493 AGTAGATCGCAT
131 AGTACATCGCAT
* *
12342505 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTATAGCGGAGCAGATTAAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
12342570 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAG
12342635 AGTACATCGCAT
131 AGTACATCGCAT
*
12342647 CAAATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
12342712 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAG
12342777 AGTACATCGCAT
131 AGTACATCGCAT
12342789 CAG
1 CAG
12342792 GTCTTATCTC
Statistics
Matches: 275, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
142 275 1.00
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTATAGTAG
AGTACATCGCAT
Found at i:12342910 original size:50 final size:50
Alignment explanation
Indices: 12342886--12343078 Score: 170
Period size: 50 Copynumber: 3.9 Consensus size: 50
12342876 CCACATCGGT
* *
12342886 GAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCTACAACAAC
1 GAATCTTGCTTCCCCGACATTGCAGTGCAAAAGATTAAAGCCACAACAAC
* * * *** * * * * * * * * *
12342936 GTATCTTACCTCTTAGGCAATCCAGCGGAACAGATTAAAGCCACATCGAT
1 GAATCTTGCTTCCCCGACATTGCAGTGCAAAAGATTAAAGCCACAACAAC
* *
12342986 GAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCCACAACAGC
1 GAATCTTGCTTCCCCGACATTGCAGTGCAAAAGATTAAAGCCACAACAAC
* * * **
12343036 GAATCATGCTTCCCCGACACTACAGTTAAAAAGATTAAAGCCA
1 GAATCTTGCTTCCCCGACATTGCAGTGCAAAAGATTAAAGCCA
12343079 TAATGGCAAA
Statistics
Matches: 105, Mismatches: 38, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 105 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (50 bp):
GAATCTTGCTTCCCCGACATTGCAGTGCAAAAGATTAAAGCCACAACAAC
Found at i:12343071 original size:100 final size:100
Alignment explanation
Indices: 12342869--12343078 Score: 267
Period size: 100 Copynumber: 2.1 Consensus size: 100
12342859 AGTGGAACAA
* *
12342869 ATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCTACAACA
1 ATTAAAGCCACATCGATGAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCCACAACA
* * ** * * * *
12342934 ACGTATCTTACCTCTTAGGCAATCCAGCGGAACAG
66 ACGAATCATACCTCCCAGACAATACAGCGAAAAAG
12342969 ATTAAAGCCACATCGATGAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCCACAACA
1 ATTAAAGCCACATCGATGAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCCACAACA
* * * * * **
12343034 GCGAATCATGCTTCCCCGACACTACAGTTAAAAAG
66 ACGAATCATACCTCCCAGACAATACAGCGAAAAAG
12343069 ATTAAAGCCA
1 ATTAAAGCCA
12343079 TAATGGCAAA
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
100 93 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (100 bp):
ATTAAAGCCACATCGATGAATCTTGCTTCCCCGACATTGCAGTTCAAAAGATTAAAGCCACAACA
ACGAATCATACCTCCCAGACAATACAGCGAAAAAG
Found at i:12349547 original size:44 final size:44
Alignment explanation
Indices: 12349434--12349547 Score: 104
Period size: 44 Copynumber: 2.6 Consensus size: 44
12349424 TGTCGGCTTT
* * * * * *
12349434 AATCTGTTCCATTACAACTTCAGGGAGATAAGATTTGCCATCTTC
1 AATCTGCTCCACTACTAC-TCAGGGAGATAAGATCTACAATCTTC
* * *
12349479 GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC
1 AATCTGCTCCACTACTACTCAGGGAGATAAGATCTACAATCTTC
* *
12349523 AA-CTTTCTCCACTGCTACTCAGGGA
1 AATC-TGCTCCACTACTACTCAGGGA
12349548 AACAAGGCTT
Statistics
Matches: 54, Mismatches: 14, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.74
45 13 0.24
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTACTACTCAGGGAGATAAGATCTACAATCTTC
Found at i:12349595 original size:132 final size:132
Alignment explanation
Indices: 12349459--12350082 Score: 888
Period size: 132 Copynumber: 4.8 Consensus size: 132
12349449 AACTTCAGGG
** * *
12349459 AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
* * * * * *
12349524 ACTTTCTCCACTGCTACTCAGGGAAACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
66 ACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
12349589 AA
131 AA
** *
12349591 AGATAAGATTTTCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTATAAT-TTCC
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTT-C
** ** * * * * *
12349655 AATTTTCTCCGTTGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATTTGTTTCCCATTATCTTG
65 AACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTG
12349720 GAA
130 GAA
* *
12349723 AGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGTGAGATAAG-------ATCTTCA
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
12349781 ACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
66 ACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
12349846 AA
131 AA
* * *
12349848 AGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCCATAATCTTCA
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
*
12349913 ACCTTCTCCTCTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
66 ACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
12349978 AA
131 AA
*
12349980 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGAT-TCATAATCTTC
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ATAATCTTC
* *
12350044 AACCTTCTCCGCTATTGCTTAGGGAGACAAGGCTTGGTG
65 AACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTG
12350083 TTTCACCAAT
Statistics
Matches: 447, Mismatches: 35, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
125 111 0.25
126 2 0.00
131 2 0.00
132 332 0.74
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (132 bp):
AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCA
ACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG
AA
Found at i:12349857 original size:257 final size:258
Alignment explanation
Indices: 12349459--12350082 Score: 867
Period size: 257 Copynumber: 2.4 Consensus size: 258
12349449 AACTTCAGGG
** *
12349459 AGATAAGATTTGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCA
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG------AATCTTCA
* * * * *
12349524 ACTTTCTCCACTGCTACTCAGGGAAACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
60 ACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGG
** * *
12349589 AAAGATAAGATTTTCCGTCTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTATAAT-TT
125 AAAGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCCATAATCTT
** * * * *
12349653 CCAATTTTCTCCGT-TGCTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATTTGTTTCCCATTATC
190 -CAACCTTCTCC-TCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATC
12349717 TTGGAA
253 TTGGAA
* *
12349723 AGATAAGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGTGAGATAAG-ATCTTCAACCTTC
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAATCTTCAACCTTC
*
12349787 TCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGAT
66 TCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGGAAAGAT
*
12349852 AAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGGGAGATAAGATCCATAATCTTCAACCT
131 AAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCCATAATCTTCAACCT
*
12349917 TCTCCTCTACTGCTTAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
196 TCTCCTCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
*
12349980 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTACTTAGGGAGATAAGATTCATAATCTTCA
1 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG------AATCTTCA
* *
12350045 ACCTTCTCCGCTATTGCTTAGGGAGACAAGGCTTGGTG
60 ACCTTCTCCACTACTGCTTAGGGAGACAAGGCTTGGTG
12350083 TTTCACCAAT
Statistics
Matches: 323, Mismatches: 28, Indels: 18
0.88 0.08 0.05
Matches are distributed among these distances:
256 1 0.00
257 231 0.72
258 2 0.01
264 89 0.28
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (258 bp):
AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAATCTTCAACCTTC
TCCACTACTGCTTAGGGAGACAAGGCTTGGTGGCTCAAATCTGCTTCCCACTATCTTGGAAAGAT
AAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGAGAGATAAGATCCATAATCTTCAACCT
TCTCCTCTACTGCTCAGGGAGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
Found at i:12349897 original size:44 final size:44
Alignment explanation
Indices: 12349848--12350070 Score: 139
Period size: 44 Copynumber: 5.1 Consensus size: 44
12349838 TATCTTGGAA
* * *
12349848 AGATAAGATTCGCCGTCTTCGATCTACTCCACTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* *** * * *
12349892 AGATAAGATCCATAATCTTCAACCTTCTCCTCTACTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * *** * * *
12349936 AGACAAGGCTT-GGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTCACCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
12349980 AGATAAGATTCACCGTCTTCGATCTGCTCCACTACTACTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
*** * * * *
12350024 AGATAAGATTCATAATCTTCAACCTTCTCCGCTATTGCTTAGGG
1 AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
12350068 AGA
1 AGA
12350071 CAAGGCTTGG
Statistics
Matches: 131, Mismatches: 40, Indels: 16
0.70 0.21 0.09
Matches are distributed among these distances:
42 6 0.05
43 7 0.05
44 107 0.82
45 6 0.05
46 5 0.04
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.30
Consensus pattern (44 bp):
AGATAAGATTCACCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:12363209 original size:14 final size:14
Alignment explanation
Indices: 12363190--12363222 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
12363180 GCCATGTTTG
12363190 TTTGGGCCACTAAA
1 TTTGGGCCACTAAA
*
12363204 TTTGGGCCACTGAA
1 TTTGGGCCACTAAA
12363218 TTTGG
1 TTTGG
12363223 TTTTGGGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.33
Consensus pattern (14 bp):
TTTGGGCCACTAAA
Found at i:12364916 original size:14 final size:14
Alignment explanation
Indices: 12364897--12364927 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12364887 AAGTGAGAAA
*
12364897 TGAGAGAAGAGTTG
1 TGAGAGAAGAGATG
12364911 TGAGAGAAGAGATG
1 TGAGAGAAGAGATG
12364925 TGA
1 TGA
12364928 ATGAGGGATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.42, T:0.19
Consensus pattern (14 bp):
TGAGAGAAGAGATG
Found at i:12365718 original size:31 final size:32
Alignment explanation
Indices: 12365680--12365750 Score: 92
Period size: 31 Copynumber: 2.2 Consensus size: 32
12365670 GCTCTATGGG
*
12365680 GCGACACCGCGAT-GACAGTAAGGT-CTTTGAA
1 GCGACACCGCGATAG-CAGTAAGGTCCTTCGAA
*
12365711 GCGACACCGCGATAGCGGTAAGGTCCTTCGAA
1 GCGACACCGCGATAGCAGTAAGGTCCTTCGAA
*
12365743 GTGACACC
1 GCGACACC
12365751 TCCAAGAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.27, C:0.27, G:0.30, T:0.17
Consensus pattern (32 bp):
GCGACACCGCGATAGCAGTAAGGTCCTTCGAA
Found at i:12365914 original size:27 final size:28
Alignment explanation
Indices: 12365810--12365912 Score: 122
Period size: 27 Copynumber: 3.8 Consensus size: 28
12365800 AGTCCGACGA
*
12365810 GACATTAAACATAGGGTAG-TCTGCCGT
1 GACATTAAACATAGGGTAGTTCTGCCGG
** *
12365837 GACATTAAACACGGGGTA-TTCTGCCAG
1 GACATTAAACATAGGGTAGTTCTGCCGG
* *
12365864 GACATTAAACATAGAGTAGTTC-GTCGG
1 GACATTAAACATAGGGTAGTTCTGCCGG
*
12365891 GACATCAAACATAGGGTAGTTC
1 GACATTAAACATAGGGTAGTTC
12365913 GTTAGGACGT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
27 60 0.95
28 3 0.05
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (28 bp):
GACATTAAACATAGGGTAGTTCTGCCGG
Found at i:12365920 original size:27 final size:27
Alignment explanation
Indices: 12365810--12365929 Score: 93
Period size: 27 Copynumber: 4.4 Consensus size: 27
12365800 AGTCCGACGA
* *
12365810 GACATTAAACATAGGGTAG-TC-TGCCG
1 GACATTAAACATAGAGTAGTTCGT-CAG
** * *
12365836 TGACATTAAACACGGGGTA-TTCTGCCAG
1 -GACATTAAACATAGAGTAGTTC-GTCAG
*
12365864 GACATTAAACATAGAGTAGTTCGTCGG
1 GACATTAAACATAGAGTAGTTCGTCAG
* * *
12365891 GACATCAAACATAGGGTAGTTCGTTAG
1 GACATTAAACATAGAGTAGTTCGTCAG
*
12365918 GACGTTAAACAT
1 GACATTAAACAT
12365930 GAGATAAAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 8
0.76 0.15 0.08
Matches are distributed among these distances:
27 69 0.93
28 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (27 bp):
GACATTAAACATAGAGTAGTTCGTCAG
Found at i:12369343 original size:21 final size:21
Alignment explanation
Indices: 12369297--12369343 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
12369287 AGGACATGGT
* *
12369297 TGTGTGGCTACTTCACACGCC
1 TGTGTGACTACTTCACACACC
* *
12369318 CGTGTGACTACTTCACACATC
1 TGTGTGACTACTTCACACACC
12369339 TGTGT
1 TGTGT
12369344 ACACTAATCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.30, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTGTGACTACTTCACACACC
Found at i:12382608 original size:14 final size:16
Alignment explanation
Indices: 12382579--12382611 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
12382569 GTGCAGGATG
12382579 AAGGAGAGAAGAGAGA
1 AAGGAGAGAAGAGAGA
12382595 AAGGAGA-AAG-GAGA
1 AAGGAGAGAAGAGAGA
12382609 AAG
1 AAG
12382612 AAAATGAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
15 3 0.18
16 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (16 bp):
AAGGAGAGAAGAGAGA
Found at i:12384234 original size:12 final size:12
Alignment explanation
Indices: 12384217--12384243 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12384207 CACCGCACCA
12384217 GCCCCAGCCCCC
1 GCCCCAGCCCCC
12384229 GCCCCAGCCCCC
1 GCCCCAGCCCCC
12384241 GCC
1 GCC
12384244 TGATTGGCGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.07, C:0.74, G:0.19, T:0.00
Consensus pattern (12 bp):
GCCCCAGCCCCC
Found at i:12384720 original size:13 final size:13
Alignment explanation
Indices: 12384702--12384728 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12384692 ATACCGACTC
12384702 ATATAAACATATA
1 ATATAAACATATA
12384715 ATATAAACATATA
1 ATATAAACATATA
12384728 A
1 A
12384729 ACACAAAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
ATATAAACATATA
Found at i:12385822 original size:98 final size:98
Alignment explanation
Indices: 12385650--12385844 Score: 354
Period size: 98 Copynumber: 2.0 Consensus size: 98
12385640 ACAATAGAAT
*
12385650 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
*
12385715 TCTAGAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
12385748 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
12385813 TTTAAAATCCCAAATTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
12385845 TTATTTTTAA
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:12386540 original size:24 final size:25
Alignment explanation
Indices: 12386511--12386558 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12386501 ATATAAATAT
12386511 GAAAATATTC-ATTAAAAAATATAG
1 GAAAATATTCGATTAAAAAATATAG
* *
12386535 GAAAATATTCGTTTAAAATATATA
1 GAAAATATTCGATTAAAAAATATA
12386559 TATGTGTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.54, C:0.04, G:0.08, T:0.33
Consensus pattern (25 bp):
GAAAATATTCGATTAAAAAATATAG
Found at i:12387209 original size:19 final size:19
Alignment explanation
Indices: 12387185--12387313 Score: 213
Period size: 19 Copynumber: 6.8 Consensus size: 19
12387175 AATCATATAT
12387185 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
**
12387204 TCTAAGATTATATATCATA
1 TCTAAGATTGCATATCATA
12387223 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12387242 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
12387261 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
12387280 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
12387299 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
12387314 TCTCAAAAAT
Statistics
Matches: 102, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 102 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:12387232 original size:38 final size:38
Alignment explanation
Indices: 12387162--12387313 Score: 223
Period size: 38 Copynumber: 3.9 Consensus size: 38
12387152 AAATTAAATC
*
12387162 TCTAAGATTACAAAATCATATATTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATC--ATA-TCTAAGATTGCATATCATA
*
12387204 TCTAAGATTATATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
*
12387242 TCTAAGATTACATATCATATCTAGGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
12387280 TCTAGGATTGCATATCATATCTAAGATTGCATAT
1 TCTAAGATTACATATCATATCTAAGATTGCATAT
12387314 TCTCAAAAAT
Statistics
Matches: 103, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
38 86 0.83
39 3 0.03
41 4 0.04
42 10 0.10
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:12387785 original size:132 final size:132
Alignment explanation
Indices: 12387543--12388191 Score: 903
Period size: 132 Copynumber: 4.9 Consensus size: 132
12387533 TTGCAACTGC
* * * * *
12387543 AGGGAGATAAGA-CTTACAATCTTCAACCTATTCCACTGCTGACCAGGG-AGATAGGATTACTGA
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGG
* * * *
12387606 CTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCCACCATCTTCGATTTACTCCACTACT
64 CTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACT
12387671 GCTT
129 GCTT
* ** * *
12387675 AGGGAGATAAGATCTGAAATCTTCAAACTATTCCACTATTGCCTAGGGAAGTAGAATTACTAGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * * *
12387740 TCAATGTACTGCACTGTAACCACAGGGAGGTAAAATCCGCTATCTTCAATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
12387805 TT
131 TT
* * *
12387807 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAGTTATTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* *
12387872 TCAATGTACTCCATTATAACCACAGGGAGGTAAAATCCACCATCTTCGATCTGCTCCACTACTGC
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
12387937 TT
131 TT
12387939 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
1 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
* * *
12388004 TTAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTTCACTGTCAA
66 TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCAC--T-AC
12388069 TGC--
128 TGCTT
* ** * * **
12388072 AGGAAGGCAAGATCT-ACTATCTTTAATCTATTCCACTGCTGCGTAGGGAAGTAGAATTACTGGC
1 AGGGAGATAAGATCTGA-AATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGC
*
12388136 TTCAATGTACTCCACAATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
65 TTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCT
12388192 TCGTTGTCAA
Statistics
Matches: 467, Mismatches: 44, Indels: 11
0.89 0.08 0.02
Matches are distributed among these distances:
132 348 0.75
133 114 0.24
134 1 0.00
135 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (132 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCT
TCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGC
TT
Found at i:12387842 original size:44 final size:44
Alignment explanation
Indices: 12387649--12387980 Score: 123
Period size: 44 Copynumber: 7.5 Consensus size: 44
12387639 AAAATCCACC
* *
12387649 ATCTTCGATTTACTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAA
* * * * *
12387693 ATCTTCAAACTATTCCACTATTGCCTAGGGA-AGT-AGAAT-T-ACT
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGA-TAAG-ATCTGA-A
* * * ** * * * **
12387736 AGCTTCAATGTACTGCACTGTAAC--CACAGGGAGGTAAAATCCGCT
1 ATCTTCAATCTACTCCAC--T-ACTGCTTAGGGAGATAAGATCTGAA
*
12387781 ATCTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAA
* ** **
12387825 ATCTTCAATCTATTCCACTGTTGCCCAGGGA-AGTAGAGTTAT-TG--
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGA-TA-AG--ATCTGAA
* * * * ** * * * *
12387869 -GCTTCAATGTACTCCATTA-TAACCACAGGGAGGTAAAATC-CACC
1 ATCTTCAATCTACTCCACTACT--GCTTAGGGAGATAAGATCTGA-A
* *
12387913 ATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAA
1 ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAA
* *
12387957 ATCTTCAATCTATTCCACTGCTGC
1 ATCTTCAATCTACTCCACTACTGC
12387981 CCAGGGAAGT
Statistics
Matches: 200, Mismatches: 62, Indels: 52
0.64 0.20 0.17
Matches are distributed among these distances:
41 2 0.01
42 4 0.02
43 34 0.17
44 120 0.60
45 34 0.17
46 4 0.02
47 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (44 bp):
ATCTTCAATCTACTCCACTACTGCTTAGGGAGATAAGATCTGAA
Found at i:12389540 original size:1 final size:1
Alignment explanation
Indices: 12389536--12389602 Score: 71
Period size: 1 Copynumber: 67.0 Consensus size: 1
12389526 CCATTTTTCC
* * * * * * *
12389536 TTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTGTTTTTTGTTTTTTTTGTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12389601 TT
1 TT
12389603 AAATCTGAAC
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:12389549 original size:7 final size:7
Alignment explanation
Indices: 12389539--12389600 Score: 83
Period size: 7 Copynumber: 8.9 Consensus size: 7
12389529 TTTTTCCTTT
12389539 TTTTTTG
1 TTTTTTG
12389546 TTTTTTTG
1 -TTTTTTG
12389554 TTTTTTTG
1 -TTTTTTG
12389562 TTTTTTG
1 TTTTTTG
12389569 TTTTTTG
1 TTTTTTG
12389576 TTTTTT-
1 TTTTTTG
*
12389582 TTGTTTG
1 TTTTTTG
12389589 TTTTTT-
1 TTTTTTG
12389595 TTTTTT
1 TTTTTT
12389601 TTAAATCTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
6 11 0.22
7 25 0.49
8 15 0.29
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (7 bp):
TTTTTTG
Found at i:12389549 original size:8 final size:8
Alignment explanation
Indices: 12389538--12389599 Score: 85
Period size: 8 Copynumber: 7.9 Consensus size: 8
12389528 ATTTTTCCTT
12389538 TTTTTTTG
1 TTTTTTTG
12389546 TTTTTTTG
1 TTTTTTTG
12389554 TTTTTTTG
1 TTTTTTTG
12389562 -TTTTTTG
1 TTTTTTTG
12389569 -TTTTTTG
1 TTTTTTTG
12389576 TTTTTTTTG
1 -TTTTTTTG
12389585 TTTGTTTT-
1 TTT-TTTTG
12389593 TTTTTTT
1 TTTTTTT
12389600 TTTAAATCTG
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
7 18 0.35
8 22 0.43
9 11 0.22
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (8 bp):
TTTTTTTG
Found at i:12389569 original size:23 final size:22
Alignment explanation
Indices: 12389536--12389602 Score: 95
Period size: 21 Copynumber: 3.1 Consensus size: 22
12389526 CCATTTTTCC
12389536 TTTTTTTTTGTTTTTTTGTTTT
1 TTTTTTTTTGTTTTTTTGTTTT
12389558 TTTGTTTTTTG-TTTTTTG-TTT
1 TTT-TTTTTTGTTTTTTTGTTTT
*
12389579 TTTTTGTTTGTTTTTTT-TTTT
1 TTTTTTTTTGTTTTTTTGTTTT
12389600 TTT
1 TTT
12389603 AAATCTGAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
20 6 0.15
21 18 0.44
22 10 0.24
23 7 0.17
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (22 bp):
TTTTTTTTTGTTTTTTTGTTTT
Found at i:12393852 original size:98 final size:98
Alignment explanation
Indices: 12393670--12393864 Score: 345
Period size: 98 Copynumber: 2.0 Consensus size: 98
12393660 ACAATAAAAT
*
12393670 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
12393735 TCTAGAATCTCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
12393768 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
* *
12393833 TTTAAAATCCCAAATTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
12393865 TTATTTTTAA
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
TTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:12394547 original size:22 final size:23
Alignment explanation
Indices: 12394522--12394574 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
12394512 ATATACATAT
12394522 AAATAT-GAAAATATTCATTAAA
1 AAATATAGAAAATATTCATTAAA
* *
12394544 AAATATAGGAAAATATTCGTTTAA
1 AAATATA-GAAAATATTCATTAAA
12394568 AAATATA
1 AAATATA
12394575 TATATGTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 6 0.22
24 21 0.78
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (23 bp):
AAATATAGAAAATATTCATTAAA
Done.