Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 129 of 214
Found at i:39187334 original size:18 final size:17
Alignment explanation
Indices: 39187308--39187343 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
39187298 TTTGGTTATA
39187308 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
39187326 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
39187343 T
1 T
39187344 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:39188265 original size:2 final size:2
Alignment explanation
Indices: 39188258--39188282 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39188248 TTTGTTCTTT
39188258 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39188283 GGGGCACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39190207 original size:43 final size:43
Alignment explanation
Indices: 39190120--39190282 Score: 217
Period size: 43 Copynumber: 3.8 Consensus size: 43
39190110 AGCTCGTACA
* *
39190120 ATGCCAACGTCCCAGACGTGGTCTTACATG-TAATCACAAA-TCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAAT-A-AAAGTCG
* *
39190163 ATGTC-ACTGTCCCAGACAG-GGTCTTACACGAAAATAGAAGTCG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACACGAAAATAAAAGTCG
39190206 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAATAAAAGTCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAATAAAAGTCG
*
39190249 ATGCCAACGTCTCAGACGTGGTCTTACACGAAAA
1 ATGCCAACGTCCCAGACGTGGTCTTACACGAAAA
39190283 AAATTATCAG
Statistics
Matches: 107, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
42 5 0.05
43 96 0.90
44 6 0.06
ACGTcount: A:0.33, C:0.26, G:0.21, T:0.21
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGAAAATAAAAGTCG
Found at i:39192509 original size:7 final size:7
Alignment explanation
Indices: 39192497--39192524 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
39192487 TCACGAACAT
39192497 AAAAATA
1 AAAAATA
39192504 AAAAATA
1 AAAAATA
39192511 AAAAATA
1 AAAAATA
39192518 AAAAATA
1 AAAAATA
39192525 CAGAGATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:39193334 original size:8 final size:8
Alignment explanation
Indices: 39193321--39193346 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
39193311 TATTTCTCAC
39193321 TATTATAT
1 TATTATAT
39193329 TATTATAT
1 TATTATAT
39193337 TATTATAT
1 TATTATAT
39193345 TA
1 TA
39193347 AAAATGGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATAT
Found at i:39195987 original size:58 final size:57
Alignment explanation
Indices: 39195953--39196096 Score: 168
Period size: 58 Copynumber: 2.5 Consensus size: 57
39195943 TTAGTTCATA
39195953 TAATAATAATTATATTAAGAATTTTATAAAATTATATATTATTTTATTAAATTATATT
1 TAATAATAATTATATTAAGAATTTTATAAAATTATATATTATTTTATTAAATTATA-T
* ** * * *
39196011 TAATAATAATTATATTAA-AATATGGTTAAATTATTTATTATTTTTATTAAATTATTTT
1 TAATAATAATTATATTAAGAATTTTATAAAATTATATATTA-TTTTATTAAATTA-TAT
*
39196069 TAATAATAATCT-TATTAA-AATTTAATAA
1 TAATAATAAT-TATATTAAGAATTTTATAA
39196097 CAATAACAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 17 0.23
58 54 0.74
59 2 0.03
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (57 bp):
TAATAATAATTATATTAAGAATTTTATAAAATTATATATTATTTTATTAAATTATAT
Found at i:39196283 original size:16 final size:16
Alignment explanation
Indices: 39196264--39196302 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
39196254 CTAATTACAA
39196264 CTCTATTCAATTGCAG
1 CTCTATTCAATTGCAG
39196280 CTCTATTCAATTGCAG
1 CTCTATTCAATTGCAG
39196296 CTCTATT
1 CTCTATT
39196303 TCATTACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.41
Consensus pattern (16 bp):
CTCTATTCAATTGCAG
Found at i:39207986 original size:50 final size:50
Alignment explanation
Indices: 39207871--39208113 Score: 405
Period size: 50 Copynumber: 4.8 Consensus size: 50
39207861 GATAATAACA
* ** *
39207871 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
39207922 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
39207972 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
39208022 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
39208072 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
39208114 TTACCCAAAT
Statistics
Matches: 180, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
50 147 0.82
51 33 0.18
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:39208229 original size:13 final size:13
Alignment explanation
Indices: 39208208--39208238 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39208198 GCTTAGATCA
*
39208208 TCATCAAATAAAT
1 TCATAAAATAAAT
39208221 TCATAAAATAAAT
1 TCATAAAATAAAT
39208234 TCATA
1 TCATA
39208239 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:39208486 original size:30 final size:30
Alignment explanation
Indices: 39208451--39208508 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
39208441 CCTCGACTCT
*
39208451 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
39208481 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
39208509 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:39211384 original size:18 final size:18
Alignment explanation
Indices: 39211331--39211384 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
39211321 AAATAGTGTC
* *
39211331 ATTCATTTCCAAAACATT
1 ATTCATTTACAAAACGTT
*
39211349 ATTCATTTACAAATCGTT
1 ATTCATTTACAAAACGTT
39211367 ATTCAATTT-CAAAACGTT
1 ATTC-ATTTACAAAACGTT
39211385 TTCTTATTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
18 27 0.87
19 4 0.13
ACGTcount: A:0.37, C:0.19, G:0.04, T:0.41
Consensus pattern (18 bp):
ATTCATTTACAAAACGTT
Found at i:39215088 original size:70 final size:70
Alignment explanation
Indices: 39215005--39215148 Score: 270
Period size: 70 Copynumber: 2.1 Consensus size: 70
39214995 ATATTAAATC
*
39215005 ACAATTTCATACAATTTCTTCTTGTAAATTAAACGATGTTAAATATATAATTAGGGTTTGACTGA
1 ACAATTTCATACAATTTCTTCTCGTAAATTAAACGATGTTAAATATATAATTAGGGTTTGACTGA
39215070 TAAAA
66 TAAAA
*
39215075 ACAATTTCATACAATTTCTTCTCGTAAATTAAACGATGTTAAATATATAATTAGGGTTTGGCTGA
1 ACAATTTCATACAATTTCTTCTCGTAAATTAAACGATGTTAAATATATAATTAGGGTTTGACTGA
39215140 TAAAA
66 TAAAA
39215145 ACAA
1 ACAA
39215149 CCGTACCGTA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (70 bp):
ACAATTTCATACAATTTCTTCTCGTAAATTAAACGATGTTAAATATATAATTAGGGTTTGACTGA
TAAAA
Found at i:39226831 original size:249 final size:248
Alignment explanation
Indices: 39226393--39226886 Score: 841
Period size: 249 Copynumber: 2.0 Consensus size: 248
39226383 TCTTCTCATG
39226393 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCACTCGTAGT
1 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCACTCGTAGT
* *
39226458 ATGCGATATCATTTTCCTAATTTTAAACCTGTCTTTAGTAGATGTTTTTGCCTACTTGATTCATA
66 ATGCGATATCATTTTCCTAATTCTAAACCTGTCTTTAGTAGATGTTTCTGCCTACTTGATTCATA
39226523 AATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATAGC
131 AATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATAGC
*
39226588 CGATTGAAG-TTTTCTGGGAAATAAGGTGTGAGACAAAAAAAGTATCATGGAGGT
196 CGATGGAAGTTTTTC-GGGAAATAAGGTGTGAGAC-AAAAAAGTATCATGGAGGT
*
39226642 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCAAC-CGTGG
1 GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTC-ACTCGTAG
39226706 TATGCGATATCATTTTCCTAATTCTAAACC-GCTCTTTAGTAGATGTTTCTGCCTACTTGATTCA
65 TATGCGATATCATTTTCCTAATTCTAAACCTG-TCTTTAGTAGATGTTTCTGCCTACTTGATTCA
* * * *
39226770 TAAATACATAAAATCTTGTTTTTGGTTCTTCATTGTGTATTTTGTCCCGGTAAGAATTTTAGATA
129 TAAATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATA
* *
39226835 GCTGATGGAAGTTTTTCGGGAAATAAGGTGTGAGACGAAAAAGTATCATGGA
194 GCCGATGGAAGTTTTTCGGGAAATAAGGTGTGAGACAAAAAAGTATCATGGA
39226887 AGCCCTAGGA
Statistics
Matches: 232, Mismatches: 10, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
248 16 0.07
249 209 0.90
250 7 0.03
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (248 bp):
GTAAGCATTTCATTGACATGGATTGCAGCATATGAACTTTGTTTGATTCGGTATTCACTCGTAGT
ATGCGATATCATTTTCCTAATTCTAAACCTGTCTTTAGTAGATGTTTCTGCCTACTTGATTCATA
AATACATAAAATCTTGTTCTTGGTTCTTCATTGAGTATTTTGTCCCAGAAAGAATTTTAGATAGC
CGATGGAAGTTTTTCGGGAAATAAGGTGTGAGACAAAAAAGTATCATGGAGGT
Found at i:39238726 original size:40 final size:40
Alignment explanation
Indices: 39238668--39238874 Score: 279
Period size: 40 Copynumber: 5.2 Consensus size: 40
39238658 AAATGCTTTT
* * *
39238668 TGAATGCACAAACGTGCCCCTGTTTGTACTTTGGTACCCT
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCC
* ** *
39238708 TAAATGCACATACATGCCCCTGTTTGTACTTTTTTATCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCC
* * *
39238748 TGAATGCACATACGTGCCCCTGTTTGTACTTCGATACCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCC
*
39238788 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTGCCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCC
** *
39238828 TGAATGCACATACATGCCATTGTTTGTACTTTGGCACCCCC
1 TGAATGCACATACATGCCCCTGTTTGTACTTTGGTA-CCCC
39238869 TGAATG
1 TGAATG
39238875 TTTATAATGT
Statistics
Matches: 145, Mismatches: 21, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
40 135 0.93
41 10 0.07
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (40 bp):
TGAATGCACATACATGCCCCTGTTTGTACTTTGGTACCCC
Found at i:39238768 original size:20 final size:20
Alignment explanation
Indices: 39238745--39238845 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
39238735 ACTTTTTTAT
39238745 CCCTGAATGCACATACGTGC
1 CCCTGAATGCACATACGTGC
** * * *
39238765 CCCTGTTTGTAC-TTCGATAC
1 CCCTGAATGCACATACG-TGC
*
39238785 CCCTGAATGCACATACATGC
1 CCCTGAATGCACATACGTGC
** * * **
39238805 CCCTGTTTGTACTTTGGTGC
1 CCCTGAATGCACATACGTGC
*
39238825 CCCTGAATGCACATACATGC
1 CCCTGAATGCACATACGTGC
39238845 C
1 C
39238846 ATTGTTTGTA
Statistics
Matches: 54, Mismatches: 25, Indels: 4
0.65 0.30 0.05
Matches are distributed among these distances:
19 3 0.06
20 49 0.91
21 2 0.04
ACGTcount: A:0.21, C:0.33, G:0.18, T:0.29
Consensus pattern (20 bp):
CCCTGAATGCACATACGTGC
Found at i:39241627 original size:24 final size:24
Alignment explanation
Indices: 39241585--39241637 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
39241575 GCTAGGATAA
* *
39241585 TTAAAATATTATCTGTTAACATAT
1 TTAAAATATTATCTATTAACACAT
*
39241609 TTAAAATATTAT-TAATTAATACAT
1 TTAAAATATTATCT-ATTAACACAT
39241633 TTAAA
1 TTAAA
39241638 TGTTACGGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.45
Consensus pattern (24 bp):
TTAAAATATTATCTATTAACACAT
Found at i:39242738 original size:69 final size:69
Alignment explanation
Indices: 39242658--39242798 Score: 255
Period size: 69 Copynumber: 2.0 Consensus size: 69
39242648 CAGTATCATA
39242658 TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
1 TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
39242723 CATC
66 CATC
* * *
39242727 TTAACATCATACTTCAAGCAAAAGATCTTTCTCAGGTCAACTTAATTTGTTTGAGCATATATATA
1 TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
39242792 CATC
66 CATC
39242796 TTA
1 TTA
39242799 TAGGAAACAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (69 bp):
TTAACATCATACTTCAAGCAAAAGAACTTTCTCAGGTCAAATTAATGTGTTTGAGCATATATATA
CATC
Found at i:39252898 original size:3 final size:3
Alignment explanation
Indices: 39252890--39252916 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
39252880 TGAAGTTGAT
39252890 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
39252917 AATGGCCGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:39253455 original size:21 final size:21
Alignment explanation
Indices: 39253409--39253455 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
39253399 AGGGTCAGTT
*
39253409 CTTCATTGCTTAAAAAAAGTA
1 CTTCTTTGCTTAAAAAAAGTA
39253430 CTTCTTTGCTTAAAAAAAGTA
1 CTTCTTTGCTTAAAAAAAGTA
39253451 CTTCT
1 CTTCT
39253456 GACTCCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (21 bp):
CTTCTTTGCTTAAAAAAAGTA
Found at i:39254038 original size:13 final size:13
Alignment explanation
Indices: 39254022--39254074 Score: 72
Period size: 13 Copynumber: 4.1 Consensus size: 13
39254012 TTTAAACTAA
39254022 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
39254035 ACTTTTTC-ATAGC
1 AC-TTTTCAAAAGC
*
39254048 ACTTTTCAAAATC
1 ACTTTTCAAAAGC
39254061 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
39254074 A
1 A
39254075 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
12 5 0.15
13 24 0.71
14 5 0.15
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.36
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:39258486 original size:25 final size:25
Alignment explanation
Indices: 39258449--39258526 Score: 104
Period size: 25 Copynumber: 3.2 Consensus size: 25
39258439 ACACCCAGCC
*
39258449 GTGTCCCA-GCCCGTGTGCCAGGCT
1 GTGTCACACGCCCGTGTGCCAGGCT
39258473 GTGTCACACGCCCGTGTGCCAGGCT
1 GTGTCACACGCCCGTGTGCCAGGCT
* * * *
39258498 ATGTCACACGCCCATGTGTCAGGCC
1 GTGTCACACGCCCGTGTGCCAGGCT
39258523 GTGT
1 GTGT
39258527 AACTCTCGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 7 0.15
25 40 0.85
ACGTcount: A:0.13, C:0.35, G:0.31, T:0.22
Consensus pattern (25 bp):
GTGTCACACGCCCGTGTGCCAGGCT
Found at i:39261684 original size:99 final size:98
Alignment explanation
Indices: 39261505--39261683 Score: 272
Period size: 99 Copynumber: 1.8 Consensus size: 98
39261495 TCTTAAAACC
* *
39261505 GAATGTATATTCACTATAAACATGAATAGTTGAATGCATATATACATATATGCTTAATAAATATT
1 GAATGTATATTCACTATAAACATGAATAGTCGAATGCATATATACA-ATATGCTTAACAAATATT
*
39261570 AGCTCCAAATGTATATACACTTTGAACATGAACT
65 AGCACCAAATGTATATACACTTTGAACATGAACT
* *
39261604 GAATGTATATTTACTATAAACGTGAATAGTCGAATGCATATATAC-ATATGCTTAACAAATATTA
1 GAATGTATATTCACTATAAACATGAATAGTCGAATGCATATATACAATATGCTTAACAAATATTA
*
39261668 -CAACCAATTGTATATA
66 GC-ACCAAATGTATATA
39261684 TGTATTTATC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
96 1 0.01
97 30 0.41
99 42 0.58
ACGTcount: A:0.42, C:0.13, G:0.11, T:0.34
Consensus pattern (98 bp):
GAATGTATATTCACTATAAACATGAATAGTCGAATGCATATATACAATATGCTTAACAAATATTA
GCACCAAATGTATATACACTTTGAACATGAACT
Found at i:39261738 original size:35 final size:35
Alignment explanation
Indices: 39261671--39261739 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 35
39261661 AATATTACAA
* * * *
39261671 CCAATTGTATATATGTATTTATCACCTGCATATAT
1 CCAATTGCATATATGTACTTAACACCTACATATAT
**
39261706 CCAATTGCATATATGTACTTAACATGTACATATA
1 CCAATTGCATATATGTACTTAACACCTACATATA
39261740 ACTAAACCTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (35 bp):
CCAATTGCATATATGTACTTAACACCTACATATAT
Found at i:39262155 original size:41 final size:41
Alignment explanation
Indices: 39262110--39262264 Score: 240
Period size: 41 Copynumber: 3.8 Consensus size: 41
39262100 TGATTCAGTA
* *
39262110 CACCGGCAATT-AGCCTACTAGACGTAAAGTCTGAAATATTT
1 CACCGGC-ATTAAGCCTGCTAGACGTAAAGTCTGAAACATTT
39262151 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTT
* * *
39262192 CACCAGCATTAAGCTTGCTAGACGTAAAGTCTAAAACATTT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTT
*
39262233 CACCGGCATCAAGCCTGCTAGACGTAAAGTCT
1 CACCGGCATTAAGCCTGCTAGACGTAAAGTCT
39262265 ATAAAATCCA
Statistics
Matches: 105, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 3 0.03
41 102 0.97
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACGTAAAGTCTGAAACATTT
Found at i:39268140 original size:37 final size:37
Alignment explanation
Indices: 39268090--39268168 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
39268080 TTATTACGAA
* * *
39268090 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
39268127 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
39268164 GTCTT
1 GTCTT
39268169 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:39268446 original size:47 final size:47
Alignment explanation
Indices: 39268286--39268604 Score: 548
Period size: 47 Copynumber: 6.7 Consensus size: 47
39268276 GCCCTTCGGG
*
39268286 ACTTATCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTT-TCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
*
39268336 ACTTTCACATTCATCACATCGGCCATTAGGCCCTATCACATATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATAC
39268385 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
*
39268432 ACTTTCACATTCATCACATCGGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
* *
39268479 ACTTTCACATTCATCACATCCGCCATTAGGCATTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
39268526 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
39268573 ACTTTCACATTCATCACATCGGCCATTAGGCC
1 ACTTTCACATTCATCACATCGGCCATTAGGCC
39268605 ATACTATCAT
Statistics
Matches: 264, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
47 177 0.67
49 83 0.31
50 4 0.02
ACGTcount: A:0.30, C:0.30, G:0.08, T:0.31
Consensus pattern (47 bp):
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
Found at i:39273837 original size:46 final size:45
Alignment explanation
Indices: 39273764--39273893 Score: 197
Period size: 46 Copynumber: 2.8 Consensus size: 45
39273754 ACAATGCTAT
*
39273764 AACTCAGTATGGTTTTCTTCACCGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTT-ACTGAAATACCATACCTACTTTTCAC
39273810 AACTCAGTATGGTTTTCGTTACTGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTACTTTTCAC
* * *
39273856 AACTCAGCATGGTTTTCTTTACTAAAATATCATACCTA
1 AACTCAGTATGGTTTTC-TTACTGAAATACCATACCTA
39273894 TGTTCCACAC
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 76 0.97
47 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (45 bp):
AACTCAGTATGGTTTTCTTACTGAAATACCATACCTACTTTTCAC
Found at i:39275006 original size:10 final size:10
Alignment explanation
Indices: 39274993--39275029 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
39274983 ATGACACTCC
39274993 ATAAATATTT
1 ATAAATATTT
39275003 ATAAAAATATTT
1 AT--AAATATTT
39275015 ATAAATATTT
1 ATAAATATTT
39275025 ATAAA
1 ATAAA
39275030 AATATTTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 15 0.60
12 10 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAAATATTT
Found at i:39275012 original size:12 final size:12
Alignment explanation
Indices: 39274995--39275038 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
39274985 GACACTCCAT
39274995 AAATATTTATAA
1 AAATATTTATAA
39275007 AAATATTTAT--
1 AAATATTTATAA
39275017 AAATATTTATAA
1 AAATATTTATAA
39275029 AAATATTTAT
1 AAATATTTAT
39275039 GGCTCAGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.33
12 20 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
AAATATTTATAA
Found at i:39275021 original size:22 final size:22
Alignment explanation
Indices: 39274993--39275038 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
39274983 ATGACACTCC
39274993 ATAAATATTTATAAAAATATTT
1 ATAAATATTTATAAAAATATTT
39275015 ATAAATATTTATAAAAATATTT
1 ATAAATATTTATAAAAATATTT
39275037 AT
1 AT
39275039 GGCTCAGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAATATTTATAAAAATATTT
Found at i:39276438 original size:40 final size:41
Alignment explanation
Indices: 39276394--39276539 Score: 177
Period size: 41 Copynumber: 3.6 Consensus size: 41
39276384 AGGGGCACCA
* * *
39276394 AAGTACAAAAAGGGGCATGTATGTGCAATTTAGAAGTA-CG
1 AAGTACAAACAGGGGCATGTATGTGCAATTCAGAGGTACCG
* * **
39276434 AAGTACAAACAGGGGCATGTCTGTGCAATTCAGGGGTATTG
1 AAGTACAAACAGGGGCATGTATGTGCAATTCAGAGGTACCG
* * *
39276475 AAGTACAAACAGGGGCATTTACGTACAATTCAGAGGTACCG
1 AAGTACAAACAGGGGCATGTATGTGCAATTCAGAGGTACCG
* *
39276516 AAGTACAAACAGAGGCACGTATGT
1 AAGTACAAACAGGGGCATGTATGT
39276540 AAAACTCATA
Statistics
Matches: 88, Mismatches: 17, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 33 0.38
41 55 0.62
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.21
Consensus pattern (41 bp):
AAGTACAAACAGGGGCATGTATGTGCAATTCAGAGGTACCG
Found at i:39276489 original size:20 final size:20
Alignment explanation
Indices: 39276464--39276527 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
39276454 CTGTGCAATT
39276464 CAGGGGTATTGAAGTACAAA
1 CAGGGGTATTGAAGTACAAA
* * * *
39276484 CAGGGGCATTTACGTACAATT
1 CAGGGGTATTGAAGTACAA-A
* **
39276505 CAGAGGTACCGAAGTACAAA
1 CAGGGGTATTGAAGTACAAA
39276525 CAG
1 CAG
39276528 AGGCACGTAT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.19
Consensus pattern (20 bp):
CAGGGGTATTGAAGTACAAA
Found at i:39281201 original size:3 final size:3
Alignment explanation
Indices: 39281193--39281237 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
39281183 ATATTTTAGC
39281193 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
39281238 TCCTACTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:39281608 original size:29 final size:29
Alignment explanation
Indices: 39281539--39281613 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
39281529 TTGGTGTTAA
39281539 TTTATTTATTTATTTACATGCTCGTTATTAT
1 TTTATTT-TTTATTTACATGCTC-TTATTAT
39281570 TTT-TTTTTTATTTA-AGTGCT-TTAATT-T
1 TTTATTTTTTATTTACA-TGCTCTT-ATTAT
39281597 TTTATTTGTTTATTTAC
1 TTTATTT-TTTATTTAC
39281614 TTTTATTTGT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
27 6 0.15
28 7 0.18
29 20 0.51
30 3 0.08
31 3 0.08
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (29 bp):
TTTATTTTTTATTTACATGCTCTTATTAT
Found at i:39281619 original size:18 final size:17
Alignment explanation
Indices: 39281596--39281634 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
39281586 TGCTTTAATT
*
39281596 TTTTATTTGTTTATTTAC
1 TTTTATTTGTTGATTT-C
39281614 TTTTATTTGTTGATTTC
1 TTTTATTTGTTGATTTC
39281631 TTTT
1 TTTT
39281635 CATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTGATTTC
Found at i:39281963 original size:109 final size:109
Alignment explanation
Indices: 39281749--39282062 Score: 449
Period size: 110 Copynumber: 2.9 Consensus size: 109
39281739 AACGAAAATT
*
39281749 TTTTCAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* * *
39281814 CGATTTCTCTCGTTCAACCAAATGACTTAATATCCTTTTC-AAAA
66 CGATTTTTCTCGTTCAACCAAATG-CTAAATAGCCTTTTCAAAAA
39281858 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
39281923 CGATTTTTTCTCGTTCAACCAAATAGCTAAATAGCC-TTTCAAAAA
66 CGA-TTTTTCTCGTTCAACCAAAT-GCTAAATAGCCTTTTCAAAAA
* * * * * *
39281968 TTTCAAAATAAGGCAATATTTTGCATTTGGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTT
1 TTTTAAAATAAGGCAATGTTTTGCGTTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
*
39282032 TCGA--TTTCTCGTTTAACCAAATTGCTAAATA
65 TCGATTTTTCTCGTTCAACCAAA-TGCTAAATA
39282063 TCCTCTTGAA
Statistics
Matches: 189, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
107 24 0.13
108 1 0.01
109 71 0.38
110 81 0.43
111 12 0.06
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (109 bp):
TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATGCTAAATAGCCTTTTCAAAAA
Found at i:39285470 original size:8 final size:8
Alignment explanation
Indices: 39285453--39285492 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
39285443 GACTCGAAAG
39285453 AAAAAT-A
1 AAAAATCA
39285460 AAAAATCAA
1 AAAAATC-A
39285469 AAAAATCA
1 AAAAATCA
*
39285477 AAAAATAA
1 AAAAATCA
39285485 AAAAATCA
1 AAAAATCA
39285493 TAAGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
7 6 0.21
8 15 0.52
9 8 0.28
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAATCA
Found at i:39285474 original size:16 final size:16
Alignment explanation
Indices: 39285453--39285492 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
39285443 GACTCGAAAG
39285453 AAAAAT-AAAAAATCAA
1 AAAAATCAAAAAAT-AA
39285469 AAAAATCAAAAAATAA
1 AAAAATCAAAAAATAA
39285485 AAAAATCA
1 AAAAATCA
39285493 TAAGAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.80, C:0.07, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAATCAAAAAATAA
Found at i:39285502 original size:16 final size:16
Alignment explanation
Indices: 39285453--39285503 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
39285443 GACTCGAAAG
*
39285453 AAAAAT-AAAAAATCAA
1 AAAAATCAAAAAA-GAA
*
39285469 AAAAATCAAAAAATAA
1 AAAAATCAAAAAAGAA
* *
39285485 AAAAATCATAAGAGAA
1 AAAAATCAAAAAAGAA
39285501 AAA
1 AAA
39285504 GAAAGAAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 24 0.80
17 6 0.20
ACGTcount: A:0.78, C:0.06, G:0.04, T:0.12
Consensus pattern (16 bp):
AAAAATCAAAAAAGAA
Found at i:39285506 original size:6 final size:6
Alignment explanation
Indices: 39285497--39285535 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
39285487 AAATCATAAG
39285497 AGAAAA AGAAAGA AGGAAAA AG-AAA AGAAAA AGAAAA AG
1 AGAAAA AGAAA-A A-GAAAA AGAAAA AGAAAA AGAAAA AG
39285536 GAGAAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.17
6 17 0.57
7 4 0.13
8 4 0.13
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (6 bp):
AGAAAA
Found at i:39285523 original size:15 final size:14
Alignment explanation
Indices: 39285498--39285537 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 14
39285488 AATCATAAGA
39285498 GAAAAAGAAAGAAG
1 GAAAAAGAAAGAAG
39285512 GAAAAAG-AA-AA-
1 GAAAAAGAAAGAAG
39285523 GAAAAAGAAA-AAG
1 GAAAAAGAAAGAAG
39285536 GA
1 GA
39285538 GAAGTCAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.29
12 6 0.25
13 4 0.17
14 7 0.29
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
GAAAAAGAAAGAAG
Found at i:39286719 original size:43 final size:44
Alignment explanation
Indices: 39286649--39286764 Score: 128
Period size: 43 Copynumber: 2.7 Consensus size: 44
39286639 CCCAAAAAGG
* * * *
39286649 GCGGCTCAAATTTTGAAACAAAATGGGGCACGG-AGTGATTAGA
1 GCGGCTCAAATTTTGGATCAAATTGGGGCACGGTAGTGATCAGA
* * *
39286692 GCGGCTTAAATTTTGGATCAAATTGGGGCATGGTGGTGATCAGA
1 GCGGCTCAAATTTTGGATCAAATTGGGGCACGGTAGTGATCAGA
* * *
39286736 GCAGCTCAAATTTT-GATCAGATCGGGGCA
1 GCGGCTCAAATTTTGGATCAAATTGGGGCA
39286765 TATGATGATC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 41 0.67
44 20 0.33
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (44 bp):
GCGGCTCAAATTTTGGATCAAATTGGGGCACGGTAGTGATCAGA
Found at i:39287980 original size:50 final size:50
Alignment explanation
Indices: 39287898--39289501 Score: 835
Period size: 50 Copynumber: 32.1 Consensus size: 50
39287888 TTTGCAATTC
* * * * *
39287898 AAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGA-TGCAGTGGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGAC-ATTGCAGTTGA
** * * *
39287948 GCAGATTGAAGCTACAACGGCGAATCTCACTTCCCTGACATTGCAATT-C
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * * **
39287997 AAATATTGAAGCCACAACGGTGAATCTTAC-TCCCAGGCGA-TGCAGCAGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGAC-ATTGCAGTTGA
* * * * *
39288046 ACAGATTGAAGCTACGACGGCGAATCTCACTTCCCCGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * ** **
39288096 AAAGATTGAAGCTACAACAGCGAATCTAACCTCCCTGGTGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCC-AGACATTGCAGTTGA
* * * * * * *
39288146 ACAGATCGAAGCTACGACGGTGAATCTCACTTCCCCGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * ** * * * **
39288196 AAATATTGAAGCCACAATGGTAAATCTTACTTCCTAGGCGA-TGCAGGGGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGAC-ATTGCAGTTGA
** * * * * *
39288246 GCAGATTGAAGCTACAACAGCAAATCTCACTTCCCCGACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * * * * *
39288296 AAAGATCGAAGCCACAACGGTGAATCTTATTTCCTAGGCAGTGCAGTTGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * ** * * *
39288346 ACAGATTGAAGCTACAACAGTGGATCTTGCTTCCTC-GACATTGTAATTTA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCC-CAGACATTGCAGTTGA
* * * * * * * **
39288396 AAAGATCGAAGCCACAACAGTGAATCTTATTTCCCAGGCGA-TGCAGCAGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGAC-ATTGCAGTTGA
* * *
39288446 ATAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGTAGTTTA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * * **
39288496 AAAGATCGAAGCCACAACGGTGAATCGT-ATTTCCCAGGCGA-TGCAGCGGA
1 AAAGATTGAAGCTACAACGGCGAATC-TCACTTCCCAGAC-ATTGCAGTTGA
* * * *
39288546 ATAGATTGAAGCTACGACGGCGAATCTCACTTCCTC-GACATTGCAATTTA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCC-CAGACATTGCAGTTGA
* * * * * ** **
39288596 AAAGATTGAAGCCACAATGGCGAATCTTATTTCCCAGGCGCTGCAGCGGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * * * *
39288646 ACAGATTGAAGCTACGACGGTGAATCTCACTTTCTC-GACATTGTAATTCA
1 AAAGATTGAAGCTACAACGGCGAATCTCAC-TTCCCAGACATTGCAGTTGA
* * **
39288696 AAAGATTGAAG-TCACAACGGCAAATCTCATTTCCCTAG-CGA-TGCAGCGGA
1 AAAGATTGAAGCT-ACAACGGCGAATCTCACTTCCC-AGAC-ATTGCAGTTGA
* * * * *
39288746 ACAGATTGAAGCTACAATGGCGAATCTCACTTCCCCA-ACATTACAATTCA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTT-CCCAGACATTGCAGTTGA
* * ** * *
39288796 AAAGATTGAAGCCACCAA-GGCGAATCTTACCTT-CCAGACGGTACAGTGGA
1 AAAGATTGAAGCTA-CAACGGCGAATCTCA-CTTCCCAGACATTGCAGTTGA
* * * ** * *
39288846 ACAGATTGAAGCTACAACGGCAAATTTTGCTTCCCCGACATTGC-GATTAA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAG-TTGA
* * * * * ** **
39288896 AAAGATTGAA-CCACAACGGCGAATCTTACTCCCCCGGCGGTGCAGCAGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * ** * * ** *
39288945 ACAGATTGAAGCTACTACAACGAATTTTACTTCCTTGACATTGCAATT-A
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * *
39288994 AACAAATTGAAGCTACGACGGCGAATCTCACTTCCCTGACATTGCAATTTA
1 AA-AGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* * * * * * **
39289045 AAAGATCGAAGCCACAACGGCGAATCTTATTTCCCAGGCGA-TGTAGCGGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGAC-ATTGCAGTTGA
* * * *
39289095 ACAGATTGAAGCTACGACGGCGAATCTCACTTTCCC-GACATTGCAATTCA
1 AAAGATTGAAGCTACAACGGCGAATCTCAC-TTCCCAGACATTGCAGTTGA
* * * *
39289145 AAAGATTGAAG-TCACAACGGCAAATCTCATTTCCCTAG-CAATGCAGTGGA
1 AAAGATTGAAGCT-ACAACGGCGAATCTCACTTCCC-AGACATTGCAGTTGA
* * * *
39289195 ACAAG-TTGAAGCTACGATGGCGAATCTCACTTCCCCAG-CATTGCAATTCA
1 A-AAGATTGAAGCTACAACGGCGAATCTCACTT-CCCAGACATTGCAGTTGA
* * * * * *** * *
39289245 AAAGATTAAAGCCACCAA-GGCAAATCTTACTTTCCAGATGGTACAGTGGA
1 AAAGATTGAAGCTA-CAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* ** * *
39289295 ATAGATTGAAGCTACAACGGCGAATCTTGCTTCCCTGACATTGC-GATTAA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAG-TTGA
* * * * * **
39289345 AAAGATTGAAGCCACAACGGCGAATCTTACTCCCCCAG-TAGTGCAGCGGA
1 AAAGATTGAAGCTACAACGGCGAATCTCACT-TCCCAGACATTGCAGTTGA
* * * ** ** * *
39289395 ACAGATTGAAGCTACAACAGCGAATTTTGCTTCCTTGACATTGCA-ATCA
1 AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
* *
39289444 AATAGATTGAAGCTACAACGGCGAATCTTACTTCCTC-GACATTGTAGTT-A
1 AA-AGATTGAAGCTACAACGGCGAATCTCACTTCC-CAGACATTGCAGTTGA
39289494 AACAGATT
1 AA-AGATT
39289502 AGAGATGACA
Statistics
Matches: 1132, Mismatches: 364, Indels: 116
0.70 0.23 0.07
Matches are distributed among these distances:
48 10 0.01
49 135 0.12
50 939 0.83
51 48 0.04
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
AAAGATTGAAGCTACAACGGCGAATCTCACTTCCCAGACATTGCAGTTGA
Found at i:39288171 original size:100 final size:99
Alignment explanation
Indices: 39287889--39289021 Score: 1238
Period size: 100 Copynumber: 11.4 Consensus size: 99
39287879 AAACCATAGT
* * *
39287889 TTGCAATTC-AAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGTGGAGCAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGATGCAGCGGAACAGA
*
39287953 TTGAAGCTACAACGGCGAATCTCACTTCCCTGACA
65 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * *
39287988 TTGCAATTC-AAATATTGAAGCCACAACGGTGAATCTTACTCCCAGGCGATGCAGCAGAACAGAT
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTATTCCCAGGCGATGCAGCGGAACAGAT
*
39288052 TGAAGCTACGACGGCGAATCTCACTTCCCCGACA
66 TGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * * * *
39288086 TTGCAATTCAAAAGATTGAAGCTACAACAGCGAATCTAACCTCCCTGGTGATGCAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGATGCAGCGGAACAGA
* * *
39288151 TCGAAGCTACGACGGTGAATCTCACTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * ** * * *
39288186 TTGCAATTCAAAATATTGAAGCCACAATGGTAAATCTTACTTCCTAGGCGATGCAGGGGAGCAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGATGCAGCGGAACAGA
* *
39288251 TTGAAGCTACAACAGCAAATCTCACTTCCCCGACA
65 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * **
39288286 TTGCAATTCAAAAGATCGAAGCCACAACGGTGAATCTTATTTCCTAGGC-AGTGCAGTTGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGA-TGCAGCGGAACAG
* * * ** *
39288350 ATTGAAGCTACAACAGTGGATCTTGCTTCCTCGACA
64 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * * * * *
39288386 TTGTAATTTAAAAGATCGAAGCCACAACAGTGAATCTTATTTCCCAGGCGATGCAGCAGAATAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGATGCAGCGGAACAGA
*
39288451 TTGAAGCTACAACGGCGAATCTCACTTCCCAGACA
65 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * * * * *
39288486 TTGTAGTTTAAAAGATCGAAGCCACAACGGTGAATCGTATTTCCCAGGCGATGCAGCGGAATAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGATGCAGCGGAACAGA
* *
39288551 TTGAAGCTACGACGGCGAATCTCACTTCCTCGACA
65 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * *
39288586 TTGCAATTTAAAAGATTGAAGCCACAATGGCGAATCTTATTTCCCAGGCGCTGCAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGATGCAGCGGAACAGA
* * * *
39288651 TTGAAGCTACGACGGTGAATCTCACTTTCTCGACA
65 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * *
39288686 TTGTAATTCAAAAGATTGAAGTCACAACGGCAAATCTCATTTCCCTA-GCGATGCAGCGGAACAG
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCC-AGGCGATGCAGCGGAACAG
* *
39288750 ATTGAAGCTACAATGGCGAATCTCACTTCCCCAACA
64 ATTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * * *
39288786 TTACAATTCAAAAGATTGAAGCCACCAA-GGCGAATCTTACCTT-CCAGACGGTACAGTGGAACA
1 TTGCAATTCAAAAGATTGAAGCCA-CAACGGCGAATCTTA--TTCCCAGGCGATGCAGCGGAACA
* * **
39288849 GATTGAAGCTACAACGGCAAATTTTGCTTCCCCGACA
63 GATTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * * * * *
39288886 TTGCGATTAAAAAGATTGAA-CCACAACGGCGAATCTTACTCCCCCGGCGGTGCAGCAGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTA-TTCCCAGGCGATGCAGCGGAACAGA
* ** * * **
39288950 TTGAAGCTACTACAACGAATTTTACTTCCTTGACA
65 TTGAAGCTACAACGGCGAATCTCACTTCCCCGACA
* * *
39288985 TTGCAATT-AAACAAATTGAAGCTACGACGGCGAATCT
1 TTGCAATTCAAA-AGATTGAAGCCACAACGGCGAATCT
39289022 CACTTCCCTG
Statistics
Matches: 893, Mismatches: 129, Indels: 23
0.85 0.12 0.02
Matches are distributed among these distances:
98 71 0.08
99 136 0.15
100 679 0.76
101 7 0.01
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.23
Consensus pattern (99 bp):
TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTATTCCCAGGCGATGCAGCGGAACAGAT
TGAAGCTACAACGGCGAATCTCACTTCCCCGACA
Found at i:39291280 original size:12 final size:10
Alignment explanation
Indices: 39291253--39291283 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39291243 TTTTTTAAAC
39291253 TTATATATTT
1 TTATATATTT
39291263 TTATATATTT
1 TTATATATTT
*
39291273 TTACATATTT
1 TTATATATTT
39291283 T
1 T
39291284 ACCACTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:39291544 original size:18 final size:17
Alignment explanation
Indices: 39291521--39291559 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
39291511 TGCTTTAATT
*
39291521 TTTTATTTGTTTATTTAC
1 TTTTATTTGTTGATTT-C
39291539 TTTTATTTGTTGATTTC
1 TTTTATTTGTTGATTTC
39291556 TTTT
1 TTTT
39291560 CATTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
TTTTATTTGTTGATTTC
Found at i:39291915 original size:110 final size:108
Alignment explanation
Indices: 39291675--39291987 Score: 445
Period size: 110 Copynumber: 2.9 Consensus size: 108
39291665 ACGAAAATTT
* *
39291675 TTTC-AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAATATGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* * * *
39291739 CGATTTCTCTCGTTCAACCAAATGACTTAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATG-CTAAATAGCCTTTCAAAAA
*
39291783 TTTTAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
39291848 CGATTTTTTCTCGTTCAACCAAATAGCTAAATAGCCTTTCAAAAA
66 CGA-TTTTTCTCGTTCAACCAAAT-GCTAAATAGCCTTTCAAAAA
* * *
39291893 TTTCAAAATAAGGCAATGTTTTGCATTTGGGAAATTCGAG-GAACGTGCCCTAAGGTGCTGGGTT
1 TTTCAAAATAAGGCAATGTTTTGCATTT-GGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* *
39291957 TCGA--TTTCTCGTTTAACCAAATTGCCAAATA
65 TCGATTTTTCTCGTTCAACCAAA-TGCTAAATA
39291988 TCCTCTTAAA
Statistics
Matches: 187, Mismatches: 13, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
107 23 0.12
108 4 0.02
109 61 0.33
110 87 0.47
111 12 0.06
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (108 bp):
TTTCAAAATAAGGCAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATGCTAAATAGCCTTTCAAAAA
Found at i:39292393 original size:35 final size:35
Alignment explanation
Indices: 39292347--39292498 Score: 180
Period size: 35 Copynumber: 4.3 Consensus size: 35
39292337 CACTCTCTGT
39292347 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
**
39292382 TTGGTGTGTTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
* * **
39292417 TTGCTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
* * * * *
39292452 TTGCTGTGTTTTGGAGGGAATGGCT-TGTGTGAGCA
1 TTGGTGTGTTTCGGAGGGACTAGCTCT-TATGAGCA
39292487 TCTGGTGTGTTT
1 T-TGGTGTGTTT
39292499 TGGTTGGACT
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
34 1 0.01
35 93 0.90
36 9 0.09
ACGTcount: A:0.14, C:0.13, G:0.33, T:0.39
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGACTAGCTCTTATGAGCA
Found at i:39297101 original size:32 final size:32
Alignment explanation
Indices: 39297027--39297135 Score: 114
Period size: 32 Copynumber: 3.4 Consensus size: 32
39297017 TGGTTCTATG
* * *
39297027 AAATGATAACAAATATCAGCTTTTCATTTTGTG
1 AAATGATAACAAATATCAAC-TTTAATTTTGTA
* *
39297060 AATTTATAACAAATTAT-AACTTTAATTTTGTA
1 AAATGATAACAAA-TATCAACTTTAATTTTGTA
* *
39297092 AAATGATAACAAATATCAA-TTAACATTTTGTT
1 AAATGATAACAAATATCAACTTTA-ATTTTGTA
39297124 AAATGATAACAA
1 AAATGATAACAA
39297136 TATTCCTCTA
Statistics
Matches: 64, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
31 6 0.09
32 42 0.66
33 13 0.20
34 3 0.05
ACGTcount: A:0.45, C:0.09, G:0.07, T:0.39
Consensus pattern (32 bp):
AAATGATAACAAATATCAACTTTAATTTTGTA
Found at i:39299472 original size:18 final size:17
Alignment explanation
Indices: 39299430--39299470 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
39299420 GAAAATATTA
39299430 ATAAAAATAGAATTTAG
1 ATAAAAATAGAATTTAG
*
39299447 ATAGAAATAGAATTTTAG
1 ATAAAAATAGAA-TTTAG
39299465 -TAAAAA
1 ATAAAAA
39299471 ATTTTAAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
ATAAAAATAGAATTTAG
Found at i:39299499 original size:11 final size:11
Alignment explanation
Indices: 39299477--39299530 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
39299467 AAAAATTTTA
39299477 AGAGAGAATTTG
1 AGAGA-AATTTG
39299489 AGAGAAATTTG
1 AGAGAAATTTG
* *
39299500 AAAGAATTTTG
1 AGAGAAATTTG
39299511 AGAG-AATGTTG
1 AGAGAAAT-TTG
*
39299522 TGAGAAATT
1 AGAGAAATT
39299531 AGTAGGGGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
10 2 0.06
11 25 0.71
12 8 0.23
ACGTcount: A:0.43, C:0.00, G:0.28, T:0.30
Consensus pattern (11 bp):
AGAGAAATTTG
Found at i:39300808 original size:35 final size:35
Alignment explanation
Indices: 39300762--39300828 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
39300752 TCTTTGTGTG
* *
39300762 AATGGTGGAAAAGAAGTTACAGATATAGGTATGTC
1 AATGGTAGAAAAGAAGTTACAAATATAGGTATGTC
39300797 AATGGTAGAAAAGAAGTTACAAATATAGGTAT
1 AATGGTAGAAAAGAAGTTACAAATATAGGTAT
39300829 TTTCTGAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.04, G:0.25, T:0.25
Consensus pattern (35 bp):
AATGGTAGAAAAGAAGTTACAAATATAGGTATGTC
Found at i:39302438 original size:5 final size:5
Alignment explanation
Indices: 39302397--39302435 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
39302387 CAAGAACCCA
*
39302397 AGGCT AGGCT AGGCT AGGCT AGGCT AGGCT AGGCC AGGC
1 AGGCT AGGCT AGGCT AGGCT AGGCT AGGCT AGGCT AGGC
39302436 CAGACATGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.21, C:0.23, G:0.41, T:0.15
Consensus pattern (5 bp):
AGGCT
Found at i:39312583 original size:12 final size:12
Alignment explanation
Indices: 39312566--39312603 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
39312556 TGCGAAGCCA
39312566 CACATGAGATCG
1 CACATGAGATCG
39312578 CACATGAGATCG
1 CACATGAGATCG
* *
39312590 CATATGAGACCG
1 CACATGAGATCG
39312602 CA
1 CA
39312604 TAAACACGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.24, T:0.16
Consensus pattern (12 bp):
CACATGAGATCG
Found at i:39316858 original size:21 final size:21
Alignment explanation
Indices: 39316832--39316872 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39316822 ATCTGCTCAA
* *
39316832 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
39316853 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
39316873 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:39335744 original size:46 final size:46
Alignment explanation
Indices: 39335671--39335855 Score: 271
Period size: 46 Copynumber: 4.0 Consensus size: 46
39335661 ACAAGGCTAT
* *
39335671 AACTCAGTATGGTTTTCTTCACGGAAATACCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * * *
39335717 AACTCAGCATGGTTTTCTTTACCGAAATACCATACCTACTTTTTAC
1 AACTCAGTATGATTTTCTTCACCGAAATACCATACCTACTTTTCAC
* *
39335763 AACTCAGTATGATTTTCTTTACCGAAATATCATACCTACTTTTCAC
1 AACTCAGTATGATTTTCTTCACCGAAATACCATACCTACTTTTCAC
* * *
39335809 AACTCAGTATGATTTTCTTCACTGGAATACCATACCTACGTTTCAC
1 AACTCAGTATGATTTTCTTCACCGAAATACCATACCTACTTTTCAC
39335855 A
1 A
39335856 CTTTTCCGTG
Statistics
Matches: 126, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.29, C:0.25, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGATTTTCTTCACCGAAATACCATACCTACTTTTCAC
Found at i:39337130 original size:16 final size:17
Alignment explanation
Indices: 39337084--39337131 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
39337074 AAATTCTTTT
39337084 TAAATCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
39337101 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
39337118 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
39337132 TTCTAAATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:39348795 original size:6 final size:6
Alignment explanation
Indices: 39348784--39348822 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
39348774 AGTAGATGAT
39348784 GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCT
1 GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCTGAG GCT
39348823 AATTTTAATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.15, C:0.18, G:0.49, T:0.18
Consensus pattern (6 bp):
GCTGAG
Found at i:39362573 original size:62 final size:62
Alignment explanation
Indices: 39362476--39362599 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
39362466 TGTAATCCTA
*
39362476 GAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAGATCG
1 GAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAAATCG
39362538 GAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAAATCG
1 GAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAAATCG
39362600 AGTTAATGAG
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.43, C:0.16, G:0.19, T:0.23
Consensus pattern (62 bp):
GAAATAGGACGACATAAATCTACCAGATTAGAGTCAAATCTAATAGTGGAATCCATAAATCG
Found at i:39373117 original size:36 final size:36
Alignment explanation
Indices: 39373070--39373150 Score: 126
Period size: 36 Copynumber: 2.2 Consensus size: 36
39373060 GGCCCAAGTT
*
39373070 ACGCCCAAAAGGAGGCCTAAATCAGCGCTCCATATC
1 ACGCCCAAAAGGAGGCCCAAATCAGCGCTCCATATC
* * *
39373106 ACGCCCAAAAGGAGGCCCAAATCTGTGCTCTATATC
1 ACGCCCAAAAGGAGGCCCAAATCAGCGCTCCATATC
39373142 ACGCCCAAA
1 ACGCCCAAA
39373151 TACACGACCC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.33, C:0.33, G:0.19, T:0.15
Consensus pattern (36 bp):
ACGCCCAAAAGGAGGCCCAAATCAGCGCTCCATATC
Found at i:39375169 original size:68 final size:69
Alignment explanation
Indices: 39375040--39375174 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 69
39375030 TGATTAAACT
* * *
39375040 TAATCACTTTAATATTAAATTAGCATAATAGTTATCAAGATAAATATTAAATTAAAATTAATATT
1 TAATCACTTTAATATTAAATTAACAAAATAGCTATCAAGATAAATATTAAATTAAAATTAATATT
39375105 AAGA
66 AAGA
* * * * * *
39375109 TAATCAGTTTAATATTAAATTAATAAAATA-CTATTAAGATAAGTATTAAATTTAATTTAATATT
1 TAATCACTTTAATATTAAATTAACAAAATAGCTATCAAGATAAATATTAAATTAAAATTAATATT
39375173 AA
66 AA
39375175 ACTATTAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
68 31 0.54
69 26 0.46
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.40
Consensus pattern (69 bp):
TAATCACTTTAATATTAAATTAACAAAATAGCTATCAAGATAAATATTAAATTAAAATTAATATT
AAGA
Found at i:39379824 original size:21 final size:21
Alignment explanation
Indices: 39379800--39379883 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
39379790 GTGTTTTATT
*
39379800 TTCTGTTCAACTCTTATGAGT
1 TTCTGTTCAACTCTTATGAGC
*
39379821 TTCTGTTCAACTCTTACGAGC
1 TTCTGTTCAACTCTTATGAGC
*
39379842 TTCTGTTCAGCTCTT-TCGAGC
1 TTCTGTTCAACTCTTAT-GAGC
*
39379863 TTCTGTTCAGCT-TT-TGAGC
1 TTCTGTTCAACTCTTATGAGC
39379882 TT
1 TT
39379884 TTGATTGGAG
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
19 6 0.10
20 3 0.05
21 49 0.84
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTGTTCAACTCTTATGAGC
Found at i:39381801 original size:21 final size:21
Alignment explanation
Indices: 39381777--39381816 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39381767 AAACTGCCTG
*
39381777 CTATGTCGCGACACGCCCCTA
1 CTATGTCGCAACACGCCCCTA
*
39381798 CTATGTCGCAACAGGCCCC
1 CTATGTCGCAACACGCCCC
39381817 CTTATGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.42, G:0.20, T:0.17
Consensus pattern (21 bp):
CTATGTCGCAACACGCCCCTA
Found at i:39382056 original size:17 final size:19
Alignment explanation
Indices: 39382024--39382058 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
39382014 GAGACAAATT
39382024 ATTCTTAGGTTTTTATTTC
1 ATTCTTAGGTTTTTATTTC
39382043 ATTCTTA-G-TTTTATTT
1 ATTCTTAGGTTTTTATTT
39382059 TGTTTACATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 1 0.06
19 7 0.44
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.66
Consensus pattern (19 bp):
ATTCTTAGGTTTTTATTTC
Found at i:39383566 original size:28 final size:30
Alignment explanation
Indices: 39383534--39383660 Score: 158
Period size: 30 Copynumber: 4.4 Consensus size: 30
39383524 TTTTATTTAT
39383534 TTAGGGTTTAAG-GTTTTAGAA-AAA-TAAA
1 TTAGGGTTTAAGTGTTTTA-AATAAATTAAA
39383562 TTAGGGTTTAGAG-GTTTTAAA-AAA-TAAA
1 TTAGGGTTTA-AGTGTTTTAAATAAATTAAA
* *
39383590 TTAGGGTTTATGTTTTTTAAATAAATTAAA
1 TTAGGGTTTAAGTGTTTTAAATAAATTAAA
* *
39383620 TTAGGGTTTATGTTTTTTAAATAAATTAAA
1 TTAGGGTTTAAGTGTTTTAAATAAATTAAA
39383650 TTAGGGTTTAA
1 TTAGGGTTTAA
39383661 AGATTTTTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
27 1 0.01
28 36 0.39
29 11 0.12
30 44 0.48
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (30 bp):
TTAGGGTTTAAGTGTTTTAAATAAATTAAA
Found at i:39383955 original size:125 final size:126
Alignment explanation
Indices: 39383775--39384447 Score: 937
Period size: 125 Copynumber: 5.4 Consensus size: 126
39383765 TTTTTCAGTG
* *
39383775 AGCAAAAGTACT-AAAAAGAGCTCCCAGCTGGACGCTATTTTTCTACAGTAGTTTCTGAAAAAAT
1 AGCAAAAGTACTGAAAAA-AGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAAT
* * * ** * *
39383839 AATTTTGAGAAGATGATTCTAAAAAAATAAGGTAAAAAACATTTCAAGAAAGATGCACTGTC
65 AATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * * *
39383901 AGCAAAAGTACTGAAAAAAGCTCTCACTTGGATGCTC-TTTTCTATAGTAGTTTCTGAAAAAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
* * * *
39383965 ATTTTGGGAAGATAGTTTTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTTTC
66 ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * *
39384026 AGCAAAAGTA-TCGAAAAAAGCTCCCACCTGGACACTCTTTTTCTACAATAATTTCTGAAAAAAT
1 AGCAAAAGTACT-GAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAAT
* *
39384090 AA--TTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAATGCTTCAAGCAGGATGCACTGTT
65 AATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
39384150 AGCAAAAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTG-AAAAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
* * *
39384214 ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAAAGCTTCAAGCAGGATGCACTTTT
66 ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * * * *
39384275 AGCAAAAGTACTAAAAAAAGCTCCCACCTAGATGCTCTTTTTCTATAGTAGTTTTTGAAAAAATA
1 AGCAAAAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
* *
39384340 ATTTTGAGAAGATGGTTCT-AAATAAATAGGGTCAAAAACGCTTCAAGCAGGATGCATTGTC
66 ATTTTGAGAAGATGGTTCTGAAA-AAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
* * * * *
39384401 AGCAAAAGTACTAAAAAAATCTCCCACCTAGAAGCTTTTTTTCTACA
1 AGCAAAAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACA
39384448 ATACATCCTA
Statistics
Matches: 490, Mismatches: 49, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
123 8 0.02
124 105 0.21
125 219 0.45
126 153 0.31
127 5 0.01
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (126 bp):
AGCAAAAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
ATTTTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTC
Found at i:39384215 original size:249 final size:249
Alignment explanation
Indices: 39383775--39384447 Score: 938
Period size: 249 Copynumber: 2.7 Consensus size: 249
39383765 TTTTTCAGTG
* * *
39383775 AGCAAAAGTACTAAAAAGAGCTCCCAGCTGGACGCTATTTTTCTACAGTAGTTTCTGAAAAAATA
1 AGCAAAAGTAC-AAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
* * ** * *
39383840 ATTTTGAGAAGATGATTCTAAAAAAATAAGGTAAAAAACATTTCAAGAAAGATGCACTGTCAGCA
65 A-TTTGAGAAGATGGTTCT-AAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTCAGCA
* * * *
39383905 AAAGTACTGAAAAAAGCTCTCACTTGGATGCTC-TTTTCTATAGTAGTTTCTGAAAAAATAATTT
128 AAAGTACTGAAAAAAGCTCCCACCTGGAAGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTT
* * *
39383969 TGGGAAGATAGTTTTGAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTTTC
193 TGAGAAGATAGTTCTGAAAAAATAGGGTAAAAAAAGCTTCAAGCAGGATGCACTTTC
* * * *
39384026 AGCAAAAGTATCGAAAAAAGCTCCCACCTGGACACTCTTTTTCTACAATAATTTCTGAAAAAATA
1 AGCAAAAGTA-CAAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
* *
39384091 A-TTGAGAAGATGGTTCTGAAAAAATAGGGTAAAAAATGCTTCAAGCAGGATGCACTGTTAGCAA
65 ATTTGAGAAGATGGTTCT-AAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTCAGCAA
*
39384155 AAGTACTGAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTG-AAAAATAATTTT
129 AAGTACTGAAAAAAGCTCCCACCTGGAAGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTTT
* *
39384219 GAGAAGATGGTTCTGAAAAAATAGGGTAAAAAAAGCTTCAAGCAGGATGCACTTTT
194 GAGAAGATAGTTCTGAAAAAATAGGGTAAAAAAAGCTTCAAGCAGGATGCACTTTC
* * * *
39384275 AGCAAAAGTACTAAAAAAAGCTCCCACCTAGATGCTCTTTTTCTATAGTAGTTTTTGAAAAAATA
1 AGCAAAAGTAC-AAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATA
* *
39384340 ATTTTGAGAAGATGGTTCTAAATAAATAGGGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCA
65 A-TTTGAGAAGATGGTTCTAAA-AAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTCAGCA
* * * *
39384405 AAAGTACTAAAAAAATCTCCCACCTAGAAGCTTTTTTTCTACA
128 AAAGTACTGAAAAAAGCTCCCACCTGGAAGCTCTTTTTCTACA
39384448 ATACATCCTA
Statistics
Matches: 374, Mismatches: 42, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
248 1 0.00
249 202 0.54
250 21 0.06
251 149 0.40
252 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (249 bp):
AGCAAAAGTACAAAAAAAGCTCCCACCTGGACGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAA
TTTGAGAAGATGGTTCTAAAAAATAGGGTAAAAAACGCTTCAAGCAGGATGCACTGTCAGCAAAA
GTACTGAAAAAAGCTCCCACCTGGAAGCTCTTTTTCTACAGTAGTTTCTGAAAAAATAATTTTGA
GAAGATAGTTCTGAAAAAATAGGGTAAAAAAAGCTTCAAGCAGGATGCACTTTC
Found at i:39384547 original size:25 final size:25
Alignment explanation
Indices: 39384518--39384588 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
39384508 TTACAGCAAG
*
39384518 AGAAATT-AGAGAAGTTTAGAAGAAT
1 AGAAATTGA-AGAAGTTCAGAAGAAT
* *
39384543 AGAAATTGAAAAAGTTCAGAAGAGT
1 AGAAATTGAAGAAGTTCAGAAGAAT
* *
39384568 ATAAATTGAAGAAGTTGAGAA
1 AGAAATTGAAGAAGTTCAGAA
39384589 TGTATAAGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 38 0.97
26 1 0.03
ACGTcount: A:0.52, C:0.01, G:0.24, T:0.23
Consensus pattern (25 bp):
AGAAATTGAAGAAGTTCAGAAGAAT
Found at i:39385910 original size:15 final size:16
Alignment explanation
Indices: 39385884--39385915 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
39385874 TTTTGAATAT
39385884 TATTGTTATTATTTAA
1 TATTGTTATTATTTAA
39385900 TATTG-TATTATTTAA
1 TATTGTTATTATTTAA
39385915 T
1 T
39385916 GTACTCATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
TATTGTTATTATTTAA
Found at i:39386609 original size:17 final size:18
Alignment explanation
Indices: 39386589--39386622 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
39386579 TAATCACCAC
*
39386589 TAATATT-ATTTTGTTTG
1 TAATATTCAATTTGTTTG
39386606 TAATATTCAATTTGTTT
1 TAATATTCAATTTGTTT
39386623 TTGAATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.62
Consensus pattern (18 bp):
TAATATTCAATTTGTTTG
Found at i:39388652 original size:27 final size:27
Alignment explanation
Indices: 39388622--39388766 Score: 157
Period size: 27 Copynumber: 5.4 Consensus size: 27
39388612 GGGTATAATA
* * *
39388622 GTCATTTTACCCCATGAGAGTTTTTCG
1 GTCATTTTACCCAATGAGGGTATTTCG
* *
39388649 GTCATTTTACCCAATGGGGGTATTTCA
1 GTCATTTTACCCAATGAGGGTATTTCG
* * *
39388676 GTTATTCTACCCAATGGGGGTATTTCG
1 GTCATTTTACCCAATGAGGGTATTTCG
* *
39388703 GTTATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCAATGAGGGTATTTCG
* * *
39388730 GTCATTTTACTCTATGA-GGTATTTTG
1 GTCATTTTACCCAATGAGGGTATTTCG
*
39388756 GTTATTTTACC
1 GTCATTTTACC
39388767 TATTTTGAGG
Statistics
Matches: 102, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
26 17 0.17
27 85 0.83
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCAATGAGGGTATTTCG
Found at i:39402587 original size:17 final size:17
Alignment explanation
Indices: 39402565--39402598 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
39402555 TAATCCCAAA
*
39402565 CAAAATCAATAAAAACT
1 CAAAATCAAAAAAAACT
*
39402582 CAAAATTAAAAAAAACT
1 CAAAATCAAAAAAAACT
39402599 GCAATGTTAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAAATCAAAAAAAACT
Found at i:39402982 original size:12 final size:12
Alignment explanation
Indices: 39402965--39403000 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
39402955 AATAAGTCTG
39402965 AAAAATAAAATA
1 AAAAATAAAATA
39402977 AAAAATAACAAT-
1 AAAAATAA-AATA
39402989 AAAAATAAAATA
1 AAAAATAAAATA
39403001 TAGTTCGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 3 0.14
12 16 0.73
13 3 0.14
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:39414380 original size:42 final size:43
Alignment explanation
Indices: 39414278--39414387 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 43
39414268 CAATGCTAAC
* * *
39414278 GTCCCAGACATGGTCTTACATGAAATTGAATATTGATGTCACT
1 GTCCCAGACATGGTCTTACATGAAATTCAATATCGATGTCAAT
* * *
39414321 ATCCCAGATAGGGTCTTACATGAAA-TC-ATATACGATGTCAAT
1 GTCCCAGACATGGTCTTACATGAAATTCAATAT-CGATGTCAAT
* *
39414363 GTCCCAGACATGATCTTACACGAAA
1 GTCCCAGACATGGTCTTACATGAAA
39414388 ATCTCAAATC
Statistics
Matches: 55, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 4 0.07
42 29 0.53
43 22 0.40
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (43 bp):
GTCCCAGACATGGTCTTACATGAAATTCAATATCGATGTCAAT
Found at i:39421764 original size:23 final size:23
Alignment explanation
Indices: 39421732--39421850 Score: 157
Period size: 23 Copynumber: 5.2 Consensus size: 23
39421722 AGTGCCACAT
* *
39421732 TGATATGTAGCCGAAGCTACCCC
1 TGATATGTAGTCGAAGCTACCAC
* *
39421755 TGATACGTAGTCGTAGCTACCAC
1 TGATATGTAGTCGAAGCTACCAC
*
39421778 TGAAATGTAGTCGAAGCTACCAC
1 TGATATGTAGTCGAAGCTACCAC
* * *
39421801 TGATAGGTAGCCGTAGCTACCAC
1 TGATATGTAGTCGAAGCTACCAC
*
39421824 TGAAATGTAGTCGAAGCTACCAC
1 TGATATGTAGTCGAAGCTACCAC
39421847 TGAT
1 TGAT
39421851 CAATAACACT
Statistics
Matches: 80, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 80 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (23 bp):
TGATATGTAGTCGAAGCTACCAC
Found at i:39421804 original size:46 final size:46
Alignment explanation
Indices: 39421736--39421850 Score: 194
Period size: 46 Copynumber: 2.5 Consensus size: 46
39421726 CCACATTGAT
* * *
39421736 ATGTAGCCGAAGCTACCCCTGATACGTAGTCGTAGCTACCACTGAA
1 ATGTAGTCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
*
39421782 ATGTAGTCGAAGCTACCACTGATAGGTAGCCGTAGCTACCACTGAA
1 ATGTAGTCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
39421828 ATGTAGTCGAAGCTACCACTGAT
1 ATGTAGTCGAAGCTACCACTGAT
39421851 CAATAACACT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (46 bp):
ATGTAGTCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
Found at i:39424991 original size:18 final size:19
Alignment explanation
Indices: 39424950--39424993 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
39424940 TTCCCTTAAA
*
39424950 AGGAATTGGTAGGGTTAGC
1 AGGAGTTGGTAGGGTTAGC
39424969 A-GAGTTGGTAGGGTTAG-
1 AGGAGTTGGTAGGGTTAGC
39424986 AGGAGTTG
1 AGGAGTTG
39424994 AGAGTAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.25, C:0.02, G:0.45, T:0.27
Consensus pattern (19 bp):
AGGAGTTGGTAGGGTTAGC
Found at i:39435208 original size:3 final size:3
Alignment explanation
Indices: 39435200--39435234 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
39435190 TAAAAAGAGG
39435200 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
39435235 CCTTAAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:39445344 original size:16 final size:16
Alignment explanation
Indices: 39445323--39445355 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
39445313 TTCGCTGTAT
39445323 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
39445339 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
39445355 T
1 T
39445356 AGCAAATCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.21
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:39445609 original size:18 final size:17
Alignment explanation
Indices: 39445588--39445622 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39445578 TTATTATTAA
*
39445588 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39445606 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39445623 TCTTAATAAT
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:39450464 original size:21 final size:21
Alignment explanation
Indices: 39450440--39450479 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39450430 AAATATAATC
39450440 ATTAA-ATATTTGTAATTATAT
1 ATTAACATATTTGT-ATTATAT
39450461 ATTAACATATTTGTATTAT
1 ATTAACATATTTGTATTAT
39450480 TTTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
ATTAACATATTTGTATTATAT
Found at i:39455281 original size:28 final size:27
Alignment explanation
Indices: 39455250--39455307 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
39455240 ATTCGCTACG
*
39455250 AAGGCTGTTCTTTTCAAGATTCACCACA
1 AAGG-TGTTCATTTCAAGATTCACCACA
* * *
39455278 AAGGTTTTCATTTCATGATTTACCACA
1 AAGGTGTTCATTTCAAGATTCACCACA
39455305 AAG
1 AAG
39455308 AATTTTCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (27 bp):
AAGGTGTTCATTTCAAGATTCACCACA
Found at i:39455297 original size:27 final size:27
Alignment explanation
Indices: 39455216--39455307 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 27
39455206 TCATAATCCG
* * *
39455216 CCACAAAAGGTATTTCCTTTCATAATTCG
1 CCAC-AAAGGT-TTTCATTTCATGATTCA
* * * * *
39455245 CTACGAAGGCTGTTCTTTTCAAGATTCA
1 CCACAAAGG-TTTTCATTTCATGATTCA
*
39455273 CCACAAAGGTTTTCATTTCATGATTTA
1 CCACAAAGGTTTTCATTTCATGATTCA
39455300 CCACAAAG
1 CCACAAAG
39455308 AATTTTCTTT
Statistics
Matches: 49, Mismatches: 13, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
27 22 0.45
28 23 0.47
29 4 0.08
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (27 bp):
CCACAAAGGTTTTCATTTCATGATTCA
Found at i:39455318 original size:27 final size:27
Alignment explanation
Indices: 39455261--39455318 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
39455251 AGGCTGTTCT
*
39455261 TTTCAAGATTCACCACAAAGGTTTTCA
1 TTTCAAGATTCACCACAAAGATTTTCA
* *
39455288 TTTCATGATTTACCACAAAGAATTTTC-
1 TTTCAAGATTCACCACAAAG-ATTTTCA
39455315 TTTC
1 TTTC
39455319 TTGACATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (27 bp):
TTTCAAGATTCACCACAAAGATTTTCA
Found at i:39458185 original size:36 final size:36
Alignment explanation
Indices: 39458138--39458210 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
39458128 ATTCGAACCC
39458138 ATGCTTTTACTTACATCAAAGTGTATGATCACACAT
1 ATGCTTTTACTTACATCAAAGTGTATGATCACACAT
39458174 ATGCTTTTACTTACATCAAAGTGTATGATCACACAT
1 ATGCTTTTACTTACATCAAAGTGTATGATCACACAT
39458210 A
1 A
39458211 CATAGTCTGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (36 bp):
ATGCTTTTACTTACATCAAAGTGTATGATCACACAT
Found at i:39459629 original size:21 final size:21
Alignment explanation
Indices: 39459601--39459681 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 21
39459591 GACATGGTCG
39459601 TGTGGTTACTCCACACGCCCA
1 TGTGGTTACTCCACACGCCCA
* * *
39459622 TATGGTTACTCCACACTCTCA
1 TGTGGTTACTCCACACGCCCA
**
39459643 TGTGGTTACTCCACACGCCTG
1 TGTGGTTACTCCACACGCCCA
*
39459664 TGTGGTTACTCCATACGC
1 TGTGGTTACTCCACACGC
39459682 TCGTATGCAC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.30
Consensus pattern (21 bp):
TGTGGTTACTCCACACGCCCA
Found at i:39462550 original size:42 final size:43
Alignment explanation
Indices: 39462470--39462550 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
39462460 AAATATAATC
*
39462470 ATAAAATTAAATATAAAATATTTAAAAAATAATATTAAAAGAA
1 ATAAAATGAAATATAAAATATTTAAAAAATAATATTAAAAGAA
*
39462513 ATAAAATGAAATATAAAGA-A-TTAAAAAATTATATTAAA
1 ATAAAATGAAATATAAA-ATATTTAAAAAATAATATTAAA
39462551 TAATAAGTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
42 17 0.49
43 17 0.49
44 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (43 bp):
ATAAAATGAAATATAAAATATTTAAAAAATAATATTAAAAGAA
Found at i:39469091 original size:3 final size:3
Alignment explanation
Indices: 39469083--39469108 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
39469073 GCTTTAGTTT
39469083 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
39469109 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:39472230 original size:41 final size:41
Alignment explanation
Indices: 39472168--39472370 Score: 226
Period size: 41 Copynumber: 4.6 Consensus size: 41
39472158 GACTATACGT
39472168 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
39472209 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
39472250 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCC-G-G---TG----A---TCTGAATCAGGTTATAAAC
* * * *
39472303 CTAGTAGGCTAAGTGCCGGTGATCTGAATTAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* *
39472344 CTTGCAGGCTAAGCGCCGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
39472371 TTAAATTAAG
Statistics
Matches: 140, Mismatches: 9, Indels: 25
0.80 0.05 0.14
Matches are distributed among these distances:
41 90 0.64
42 6 0.04
43 1 0.01
44 1 0.01
46 2 0.01
48 2 0.01
50 1 0.01
51 1 0.01
52 1 0.01
53 35 0.25
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:39472289 original size:12 final size:12
Alignment explanation
Indices: 39472272--39472296 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39472262 GTGCCGGTGA
39472272 TCTGAATCAGGT
1 TCTGAATCAGGT
39472284 TCTGAATCAGGT
1 TCTGAATCAGGT
39472296 T
1 T
39472297 ATAAACCTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (12 bp):
TCTGAATCAGGT
Found at i:39472312 original size:53 final size:53
Alignment explanation
Indices: 39472231--39472331 Score: 193
Period size: 53 Copynumber: 1.9 Consensus size: 53
39472221 GTGCTGGTGA
39472231 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
1 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
*
39472284 TCTGAATCAGGTTATAAACCTAGTAGGCTAAGTGCCGGTGATCTGAAT
1 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAAT
39472332 TAGGCTATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (53 bp):
TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGT
Found at i:39472351 original size:94 final size:95
Alignment explanation
Indices: 39472190--39472370 Score: 292
Period size: 94 Copynumber: 1.9 Consensus size: 95
39472180 GTGCCGGTGA
* *
39472190 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAACCTAGC
1 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCTAGC
*
39472255 AGGCTAAGTGCCGGTG-ATCTGAATCAGGT
66 AGGCTAAGCGCCGGTGAATCTGAATCAGGT
* * * *
39472284 TCTGAATCAGGTTATAAACCTAGTAGGCTAAGTGCCGGTGATCTGAATTAGGCTATAAGCCTTGC
1 TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCTAGC
39472349 AGGCTAAGCGCCGGTGAATCTG
66 AGGCTAAGCGCCGGTGAATCTG
39472371 TTAAATTAAG
Statistics
Matches: 79, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
94 74 0.94
95 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.27, T:0.27
Consensus pattern (95 bp):
TCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAACCTAGC
AGGCTAAGCGCCGGTGAATCTGAATCAGGT
Found at i:39473149 original size:40 final size:39
Alignment explanation
Indices: 39473084--39473210 Score: 193
Period size: 39 Copynumber: 3.3 Consensus size: 39
39473074 AATAAATATA
* *
39473084 TTTATTTTTTAAATTTTTAAA-ATTTTTAAAATACTTTT
1 TTTATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
39473122 TTTATTATTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTTATT-TTTTTAATTTTAAAATATTTTTAAAATACTTTT
**
39473162 TAAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTTATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
*
39473201 TTTAATTTTT
1 TTTATTTTTT
39473211 AAAATAAATA
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.08
39 53 0.66
40 21 0.26
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTATTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
Found at i:39473150 original size:11 final size:11
Alignment explanation
Indices: 39473136--39473201 Score: 63
Period size: 11 Copynumber: 6.4 Consensus size: 11
39473126 TTATTTTTAA
39473136 TTTTAAAATAT
1 TTTTAAAATAT
39473147 TTTTAAAATACT
1 TTTTAAAATA-T
39473159 TTTT-AAAT-T
1 TTTTAAAATAT
*
39473168 TTTT----TAA
1 TTTTAAAATAT
39473175 TTTTAAAATAT
1 TTTTAAAATAT
39473186 TTTTAAAATACT
1 TTTTAAAATA-T
39473198 TTTT
1 TTTT
39473202 TTAATTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
9 5 0.11
11 26 0.57
12 10 0.22
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:39473161 original size:29 final size:30
Alignment explanation
Indices: 39473088--39473169 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 30
39473078 AATATATTTA
* *
39473088 TTTTTTAAAT-TTTTAAAATTTTTAAAATAC
1 TTTTTAAAATATTTTTAAA-TTTTAAAATAC
** *
39473118 TTTTTTTATTATTTTT-AATTTTAAAATA-
1 TTTTTAAAATATTTTTAAATTTTAAAATAC
39473146 TTTTTAAAATACTTTTTAAATTTT
1 TTTTTAAAATA-TTTTTAAATTTT
39473170 TTTAATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
28 8 0.19
29 15 0.35
30 16 0.37
31 4 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTAAAATATTTTTAAATTTTAAAATAC
Found at i:39475878 original size:27 final size:27
Alignment explanation
Indices: 39475848--39475905 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
39475838 ATATTTATAT
39475848 ATAT-AAATAATAATAATTTTAAAAAAA
1 ATATCAAA-AATAATAATTTTAAAAAAA
* * * *
39475875 ATATCAGAAATACTGATTTTAAGAAAA
1 ATATCAAAAATAATAATTTTAAAAAAA
39475902 ATAT
1 ATAT
39475906 GGAAAAAAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (27 bp):
ATATCAAAAATAATAATTTTAAAAAAA
Found at i:39477487 original size:132 final size:132
Alignment explanation
Indices: 39477280--39477707 Score: 626
Period size: 132 Copynumber: 3.2 Consensus size: 132
39477270 TAGTGTTTTA
* * * * * *
39477280 ATCTACTCCTCTGCAACTTTAGGGAGATAAGA-CT-TGTAGCTTCAACCTTCTCCACTGCTGCTT
1 ATCTGCTCCACTGCAAC-TTAGGGAGATAAGATCTAT-AATCTTCAACCTTCTCCGCTGCTGCTC
* * *
39477343 AGGGAGACAAGGCTTGGTGGCTTTAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTC
64 AGGGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTC
39477408 TTCG
129 TTCG
* * *
39477412 ATCTGCTCCACTGCAACTTAGGAAGATAAGATCTATAATCTTCATCCTTCTCTGCTGCTGCTCAG
1 ATCTGCTCCACTGCAACTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAG
* *
39477477 GAAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTT
66 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
39477542 CG
131 CG
* ** *
39477544 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTACTGCTCAG
1 ATCTGCTCCACTGCAACTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAG
*
39477609 GGAGATAAGGCTTGGTGTCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
66 GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
39477674 CG
131 CG
* *
39477676 ATCTGCTCTACTGTAACTTCAGGGAGATAAGA
1 ATCTGCTCCACTGCAACTT-AGGGAGATAAGA
39477708 CTACTGGTTA
Statistics
Matches: 264, Mismatches: 29, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
131 13 0.05
132 238 0.90
133 13 0.05
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (132 bp):
ATCTGCTCCACTGCAACTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTGCTGCTCAG
GGAGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTT
CG
Found at i:39492732 original size:13 final size:13
Alignment explanation
Indices: 39492714--39492739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39492704 ATATTATAAA
39492714 ACATTTAAAATAT
1 ACATTTAAAATAT
39492727 ACATTTAAAATAT
1 ACATTTAAAATAT
39492740 TATAAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
ACATTTAAAATAT
Found at i:39495892 original size:20 final size:20
Alignment explanation
Indices: 39495867--39495907 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
39495857 TCCAATATTG
39495867 ACACGGCAATACTCGTGAAT
1 ACACGGCAATACTCGTGAAT
39495887 ACACGGCAATACTCGTGAAT
1 ACACGGCAATACTCGTGAAT
39495907 A
1 A
39495908 ACTCACAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ACACGGCAATACTCGTGAAT
Found at i:39496772 original size:25 final size:25
Alignment explanation
Indices: 39496743--39496802 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
39496733 GAAACTCTTT
39496743 AGAGCCATATAACGAGAAGCTC-ATG
1 AGAGCCATATAACGAGAAGCTCTA-G
* * * *
39496768 TGAGCTAAATAACGGGAAGCTCTAG
1 AGAGCCATATAACGAGAAGCTCTAG
39496793 AGAGCCATAT
1 AGAGCCATAT
39496803 TTTAGGAAGC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 26 0.96
26 1 0.04
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.18
Consensus pattern (25 bp):
AGAGCCATATAACGAGAAGCTCTAG
Found at i:39498415 original size:20 final size:20
Alignment explanation
Indices: 39498381--39498422 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
39498371 AACTATTTAA
** *
39498381 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
39498401 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
39498421 AT
1 AT
39498423 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:39505281 original size:23 final size:22
Alignment explanation
Indices: 39505229--39505281 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
39505219 TCCACGTCTT
*
39505229 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
39505251 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
39505274 TTTCTTTT
1 TTTCTTTT
39505282 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:39512140 original size:32 final size:32
Alignment explanation
Indices: 39512099--39512165 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
39512089 GGGAGAATGT
39512099 CACGGGCCAAAGTGCAAAGCCCGTGACCATGC
1 CACGGGCCAAAGTGCAAAGCCCGTGACCATGC
39512131 CACGGGCCAAAGTGCAAAGCCCGTGACCATGC
1 CACGGGCCAAAGTGCAAAGCCCGTGACCATGC
39512163 CAC
1 CAC
39512166 AAGAAGCGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.36, G:0.27, T:0.09
Consensus pattern (32 bp):
CACGGGCCAAAGTGCAAAGCCCGTGACCATGC
Found at i:39514395 original size:50 final size:50
Alignment explanation
Indices: 39514253--39514494 Score: 218
Period size: 50 Copynumber: 4.7 Consensus size: 50
39514243 GATAATAACA
* ** * *
39514253 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATATTTCTTATAC--
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* ** *
39514302 TGCCAATGTCATATCCCAGACATGGTCTTACATGGGAGTTCTCATATTGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * * ** *
39514352 TGCCCATGTCATGTCCCAGATATGGTTTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
39514402 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
39514458 TGCCAATGCCATGTTCCAAACATGGTCTTACATGGGA
1 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGA
39514495 TCTCATCACC
Statistics
Matches: 156, Mismatches: 29, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
49 41 0.26
50 78 0.50
53 2 0.01
56 35 0.22
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:39529007 original size:22 final size:23
Alignment explanation
Indices: 39528982--39529038 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
39528972 TGCACTAATG
39528982 AACAGAGAGCACTA-AAGTGCTA
1 AACAGAGAGCACTATAAGTGCTA
*
39529004 AACAGAGAGCAC-ATATGTGCTA
1 AACAGAGAGCACTATAAGTGCTA
* *
39529026 AACGGAGAACACT
1 AACAGAGAGCACT
39529039 TCCTGCTAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.97
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.14
Consensus pattern (23 bp):
AACAGAGAGCACTATAAGTGCTA
Found at i:39530085 original size:24 final size:24
Alignment explanation
Indices: 39530058--39530104 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
39530048 ATAAGTAAAT
39530058 TATACATATTATTACAAATGTATG
1 TATACATATTATTACAAATGTATG
* * *
39530082 TATATATTTTATTACACATGTAT
1 TATACATATTATTACAAATGTAT
39530105 TTTATTATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (24 bp):
TATACATATTATTACAAATGTATG
Found at i:39530664 original size:16 final size:16
Alignment explanation
Indices: 39530643--39530674 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
39530633 TTTGTTGAGT
39530643 ATGACTCATATTTCAG
1 ATGACTCATATTTCAG
39530659 ATGACTCATATTTCAG
1 ATGACTCATATTTCAG
39530675 TTAAATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
ATGACTCATATTTCAG
Found at i:39533088 original size:2 final size:2
Alignment explanation
Indices: 39533081--39533145 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
39533071 TCCGTCATCC
39533081 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
39533123 CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT C
39533146 GACTTCCTTT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:39535462 original size:27 final size:27
Alignment explanation
Indices: 39535432--39535519 Score: 140
Period size: 27 Copynumber: 3.3 Consensus size: 27
39535422 CCTAAACCCC
* *
39535432 AATGTAAAAACTTTATGATTTCATTAA
1 AATGTAAAAACCTTATGGTTTCATTAA
*
39535459 AATGTAAAAACCCTATGGTTTCATTAA
1 AATGTAAAAACCTTATGGTTTCATTAA
*
39535486 AATGTAAAAACCTTATGGTTTTATTAA
1 AATGTAAAAACCTTATGGTTTCATTAA
39535513 AATGTAA
1 AATGTAA
39535520 CACCTACTTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.43, C:0.09, G:0.10, T:0.38
Consensus pattern (27 bp):
AATGTAAAAACCTTATGGTTTCATTAA
Found at i:39536880 original size:19 final size:19
Alignment explanation
Indices: 39536855--39536895 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
39536845 TCTATGGCAT
* *
39536855 AAAAAAAGAGATAGAAATAG
1 AAAAAAA-AGAAAAAAATAG
39536875 AAAAAAAAGAAAAAAATAG
1 AAAAAAAAGAAAAAAATAG
39536894 AA
1 AA
39536896 TGATTGTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAATAG
Found at i:39547508 original size:16 final size:16
Alignment explanation
Indices: 39547486--39547553 Score: 109
Period size: 16 Copynumber: 4.2 Consensus size: 16
39547476 TTTGGTTCGC
*
39547486 TGTATTGGATTAGACG
1 TGTATTGGATTAGAGG
* *
39547502 CGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
39547518 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39547534 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
39547550 TGTA
1 TGTA
39547554 ATAGCAAATC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.26, C:0.03, G:0.34, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:39547810 original size:18 final size:17
Alignment explanation
Indices: 39547789--39547823 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39547779 TTATTATTAA
*
39547789 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
39547807 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
39547824 TCTTAATAAT
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:39547877 original size:157 final size:156
Alignment explanation
Indices: 39547683--39547991 Score: 573
Period size: 157 Copynumber: 2.0 Consensus size: 156
39547673 CCCTTAACAT
*
39547683 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTATTATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
* *
39547748 TAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
39547813 TTTAATAAAATTCTTAATAATTAGCAG
131 -TTAATAAAATTCTTAATAATTAGCAG
*
39547840 AAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
1 AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
39547905 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
66 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
39547970 TTAATAAAATTCTTAATAATTA
131 TTAATAAAATTCTTAATAATTA
39547992 ATATTCTTAT
Statistics
Matches: 148, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
156 22 0.15
157 126 0.85
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (156 bp):
AAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAATATCAA
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
TTAATAAAATTCTTAATAATTAGCAG
Found at i:39547963 original size:16 final size:16
Alignment explanation
Indices: 39547926--39547967 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39547916 TTAATCATAT
*
39547926 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
39547942 TT-AAATATATTATAA
1 TTAAAATATATTATAA
39547957 TTAAAATATAT
1 TTAAAATATAT
39547968 AATTAATAAA
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:39547970 original size:13 final size:15
Alignment explanation
Indices: 39547935--39547973 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
39547925 TTTAAACATA
*
39547935 ATTATTATTAAATAT
1 ATTATAATTAAATAT
39547950 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
39547964 A-TATAATTAA
1 ATTATAATTAA
39547974 TAAAATTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.39
14 3 0.13
15 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:39548093 original size:14 final size:15
Alignment explanation
Indices: 39548044--39548095 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
39548034 ATAAAATATA
39548044 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
39548059 TATTAAATATATTAT
1 AATTAAATATATTAT
39548074 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
39548087 AATTTAATA
1 AATTAAATA
39548096 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:39548141 original size:120 final size:120
Alignment explanation
Indices: 39547929--39548442 Score: 928
Period size: 120 Copynumber: 4.3 Consensus size: 120
39547919 ATCATATTTA
39547929 AACATAATTATTATTAAATATATTATAATTAAAATATATAA-TTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
39547993 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
39548048 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
39548113 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
39548168 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
39548233 TATTCTTATATGAATTTACTCTAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
39548288 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
39548353 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAT-ATAAA-TT
* *
39548408 GAA-ATAATTAATATTAAATATATTTTAATTAAAAT
1 -AACATAATTATTATTAAATATATTATAATTAAAAT
39548443 TTATTGTTTA
Statistics
Matches: 385, Mismatches: 6, Indels: 7
0.97 0.02 0.02
Matches are distributed among these distances:
119 48 0.12
120 335 0.87
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:39548213 original size:14 final size:15
Alignment explanation
Indices: 39548164--39548335 Score: 60
Period size: 15 Copynumber: 11.6 Consensus size: 15
39548154 GTAAAATATA
39548164 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
39548179 TATTAAATATATTAT
1 AATTAAATATATTAT
*
39548194 AATTAAAATATATAATTT
1 AATT-AAATATAT--TAT
* *
39548212 AATAAAAT-TCTTAAT
1 AATTAAATATATT-AT
*
39548227 AATT-AATATTCTTAT
1 AATTAAATA-TATTAT
* * * *
39548242 -A-TGAATTTACTCT
1 AATTAAATATATTAT
* *
39548255 AATCATAATATATGAT
1 AATTA-AATATATTAT
*
39548271 ACTGTAAA-ATA-TA-
1 AAT-TAAATATATTAT
39548284 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
39548299 TATTAAATATATTAT
1 AATTAAATATATTAT
39548314 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
39548327 AATTTAATA
1 AATTAAATA
39548336 AAATTCTTAA
Statistics
Matches: 115, Mismatches: 24, Indels: 37
0.65 0.14 0.21
Matches are distributed among these distances:
12 3 0.03
13 17 0.15
14 23 0.20
15 38 0.33
16 24 0.21
17 5 0.04
18 5 0.04
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:39554321 original size:17 final size:18
Alignment explanation
Indices: 39554289--39554323 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
39554279 TTACCCTTGC
*
39554289 TACAAATATTAATTTATT
1 TACAAATATGAATTTATT
39554307 TACAAAT-TGAATTTATT
1 TACAAATATGAATTTATT
39554324 GTTTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (18 bp):
TACAAATATGAATTTATT
Found at i:39554362 original size:17 final size:15
Alignment explanation
Indices: 39554332--39554368 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
39554322 TTGTTTTAAT
39554332 TTATTAAATAAAATA
1 TTATTAAATAAAATA
39554347 TTATTAGAATTAAAATA
1 TTATTA-AA-TAAAATA
39554364 TTATT
1 TTATT
39554369 TTAAGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.30
16 2 0.10
17 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (15 bp):
TTATTAAATAAAATA
Done.