Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 8 of 279
Found at i:2365086 original size:19 final size:17
Alignment explanation
Indices: 2365062--2365108 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
2365052 AATTAAAGTA
*
2365062 ATAAAAAATAATACTATAT
1 ATAAAAAAT-ATA-TATAC
*
2365081 ATAAAATATATATATAC
1 ATAAAAAATATATATAC
2365098 AT-AAAAATATA
1 ATAAAAAATATA
2365109 CACTAATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
16 8 0.32
17 6 0.24
18 3 0.12
19 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATATATATAC
Found at i:2365104 original size:18 final size:19
Alignment explanation
Indices: 2365065--2365113 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
2365055 TAAAGTAATA
*
2365065 AAAAATA-ATACTATATAT
1 AAAAATATATACTATACAT
2365083 -AAAATATATA-TATACAT
1 AAAAATATATACTATACAT
*
2365100 AAAAATATACACTA
1 AAAAATATATACTA
2365114 ATATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 12 0.46
18 12 0.46
19 2 0.08
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATACTATACAT
Found at i:2365340 original size:3 final size:3
Alignment explanation
Indices: 2365327--2365410 Score: 63
Period size: 3 Copynumber: 28.3 Consensus size: 3
2365317 GAGGGCATAT
2365327 ATA AT- ATA ATA ATA AT- ATA A-A A-A ATA ATA TATA CATGA GA-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA -AT-A -ATA ATA
* *
2365371 ATA ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA ATA ATA A
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
2365411 ATAAAACAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
2 11 0.16
3 47 0.70
4 7 0.10
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2365379 original size:27 final size:26
Alignment explanation
Indices: 2365327--2365414 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 26
2365317 GAGGGCATAT
*
2365327 ATAATATAATAATAATATAAAA-AATA
1 ATAATATAATAATAGTA-AAAATAATA
*
2365353 AT-ATATACAT--GAG-AAATAATAATA
1 ATAATATA-ATAATAGTAAA-AATAATA
2365377 ATAATATAAATAATAGTAAAAATAATA
1 ATAATAT-AATAATAGTAAAAATAATA
2365404 ATAATA-AATAA
1 ATAATATAATAA
2365415 AACAAAGCTC
Statistics
Matches: 51, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
22 2 0.04
23 3 0.06
24 7 0.14
25 16 0.31
26 5 0.10
27 15 0.29
28 3 0.06
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
ATAATATAATAATAGTAAAAATAATA
Found at i:2371438 original size:28 final size:28
Alignment explanation
Indices: 2371398--2371455 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
2371388 GTTCCGATAT
2371398 CATGGAGATGTTATTGATGCATTCATTC
1 CATGGAGATGTTATTGATGCATTCATTC
2371426 CATGGAGATGTTATTGATGCATTCATTC
1 CATGGAGATGTTATTGATGCATTCATTC
2371454 CA
1 CA
2371456 GCAAACAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.38
Consensus pattern (28 bp):
CATGGAGATGTTATTGATGCATTCATTC
Found at i:2375553 original size:3 final size:3
Alignment explanation
Indices: 2375536--2375580 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
2375526 AAAGTAGAAT
* *
2375536 AGA AGA AAA ATA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2375581 GGGAGGGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (3 bp):
AGA
Found at i:2379652 original size:22 final size:21
Alignment explanation
Indices: 2379624--2379675 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
2379614 AATAGAAACG
2379624 AATAGAATTCTAGTTCTCAAAA
1 AATAGAATTCTA-TTCTCAAAA
* *
2379646 AATAGAACT-TATTCTTAAAA
1 AATAGAATTCTATTCTCAAAA
2379666 AATA-AATTCT
1 AATAGAATTCT
2379676 CACTACTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 13 0.50
21 2 0.08
22 8 0.31
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.35
Consensus pattern (21 bp):
AATAGAATTCTATTCTCAAAA
Found at i:2382579 original size:25 final size:25
Alignment explanation
Indices: 2382522--2382581 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
2382512 GAGCTGTAAA
*
2382522 CGGTAAGCTCATATAAGCTGAATAT
1 CGGTAAGCTCATACAAGCTGAATAT
** * *
2382547 CGACAAGCTCATACGAGTTGAATAT
1 CGGTAAGCTCATACAAGCTGAATAT
2382572 CGGTAAGCTC
1 CGGTAAGCTC
2382582 TCTTGAATTA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (25 bp):
CGGTAAGCTCATACAAGCTGAATAT
Found at i:2388794 original size:21 final size:20
Alignment explanation
Indices: 2388754--2388796 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2388744 CCCCTACAGC
*
2388754 TTTGAAAATTTGCAATGTTT
1 TTTGAAAATTTACAATGTTT
2388774 TTTGAAAAATTCTACAA-GTTT
1 TTTG-AAAATT-TACAATGTTT
2388795 TT
1 TT
2388797 GATTTAGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.49
Consensus pattern (20 bp):
TTTGAAAATTTACAATGTTT
Found at i:2392604 original size:17 final size:17
Alignment explanation
Indices: 2392584--2392622 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
2392574 AGTCTTAAAG
2392584 GATTTACAATCTTAGAA
1 GATTTACAATCTTAGAA
**
2392601 GATTTTTAATCTTAGAA
1 GATTTACAATCTTAGAA
2392618 GATTT
1 GATTT
2392623 GATTTCGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.44
Consensus pattern (17 bp):
GATTTACAATCTTAGAA
Found at i:2398182 original size:49 final size:49
Alignment explanation
Indices: 2398003--2398182 Score: 177
Period size: 49 Copynumber: 3.7 Consensus size: 49
2397993 TGGGATAAGA
* * **
2398003 TGTCGATGCCATGTCCCAAACATGGTCTTACACTGGCTAGCA-C-ATCAA
1 TGTCGATGCCATGTCCCAGACA-GGTCTTACACTGGCTATCATCTATCGG
* * ** * *
2398051 AGTCGATGCCATGTTCCAGACAGGTCTTACACTAACTTTCATATATCGAG
1 TGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCG-G
* * * * * *
2398101 -GCCGATGTCGTGTCCCAGACAGGTCTTGCACTGGCTCTCATCTATTGG
1 TGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGG
2398149 TGTCGATGCCATGTCCCAGACAGGTCTTACACTG
1 TGTCGATGCCATGTCCCAGACAGGTCTTACACTG
2398183 ACACACAACA
Statistics
Matches: 104, Mismatches: 24, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
47 15 0.14
48 20 0.19
49 69 0.66
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (49 bp):
TGTCGATGCCATGTCCCAGACAGGTCTTACACTGGCTATCATCTATCGG
Found at i:2398349 original size:46 final size:44
Alignment explanation
Indices: 2398246--2398367 Score: 142
Period size: 46 Copynumber: 2.7 Consensus size: 44
2398236 TCTCGAGGCT
*
2398246 GATGCATGTCCCAAACATGTT-TTACACTAGCTTCGTCTCAATGTC
1 GATGCATGTCCCAGACAT-TTCTTACACTAGCTTC-TCTCAATGTC
*
2398291 TATGCATGTCCCAGACATTTCTTACACTAGCTT-TCAT-AATGTAGCC
1 GATGCATGTCCCAGACATTTCTTACACTAGCTTCTC-TCAATGT---C
*
2398337 GATGCATGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATTTCTTACACTAGC
2398368 ACATATATCA
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
43 7 0.10
44 3 0.04
45 28 0.41
46 30 0.44
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (44 bp):
GATGCATGTCCCAGACATTTCTTACACTAGCTTCTCTCAATGTC
Found at i:2404377 original size:24 final size:23
Alignment explanation
Indices: 2404328--2404377 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
2404318 GAGTTACCTG
**
2404328 TTAAACTTAATGAGCTTCCTGTT
1 TTAAACTTAATGAGCTTCCTAAT
* *
2404351 TTAAACTCTTATGAGTTTCCTAAT
1 TTAAACT-TAATGAGCTTCCTAAT
2404375 TTA
1 TTA
2404378 GCCTAGATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (23 bp):
TTAAACTTAATGAGCTTCCTAAT
Found at i:2410592 original size:19 final size:18
Alignment explanation
Indices: 2410544--2410597 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
2410534 TATAATATCG
*
2410544 AAAATCAATGATAAAA-TT
1 AAAATCAAT-TTAAAATTT
2410562 AAAAT-AATTTTAAAATTT
1 AAAATCAA-TTTAAAATTT
2410580 AAAAATCAATTTAAAATT
1 -AAAATCAATTTAAAATT
2410598 AAGATAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 7 0.23
18 8 0.26
19 14 0.45
20 2 0.06
ACGTcount: A:0.59, C:0.04, G:0.02, T:0.35
Consensus pattern (18 bp):
AAAATCAATTTAAAATTT
Found at i:2410599 original size:18 final size:18
Alignment explanation
Indices: 2410544--2410599 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
2410534 TATAATATCG
*
2410544 AAAATCAATGATAAAATT-
1 AAAATCAAT-TTAAAATTA
2410562 AAAAT-AATTTTAAAATTTA
1 AAAATCAA-TTTAAAA-TTA
2410581 AAAATCAATTTAAAATTA
1 AAAATCAATTTAAAATTA
2410599 A
1 A
2410600 GATAATAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
17 7 0.21
18 12 0.36
19 12 0.36
20 2 0.06
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.34
Consensus pattern (18 bp):
AAAATCAATTTAAAATTA
Found at i:2414490 original size:28 final size:28
Alignment explanation
Indices: 2414459--2414551 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 28
2414449 ATTATTTAAA
2414459 ATTTCATTTTTCGATAAAAATACATAAG
1 ATTTCATTTTTCGATAAAAATACATAAG
* **** * * *
2414487 ATTTTATAAAACTAATAAAAAAAATTACTTAAT
1 ATTTCATTTTTC-GAT---AAAAA-TACATAAG
2414520 ATTTCATTTTTCGATAAAAATACATAAG
1 ATTTCATTTTTCGATAAAAATACATAAG
2414548 ATTT
1 ATTT
2414552 TATAAAACTA
Statistics
Matches: 44, Mismatches: 16, Indels: 10
0.63 0.23 0.14
Matches are distributed among these distances:
28 17 0.39
29 7 0.16
32 7 0.16
33 13 0.30
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (28 bp):
ATTTCATTTTTCGATAAAAATACATAAG
Found at i:2414504 original size:29 final size:29
Alignment explanation
Indices: 2414472--2414568 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
2414462 TCATTTTTCG
2414472 ATAAAAATACATAAGATTTTATAAAACTA
1 ATAAAAATACATAAGATTTTATAAAACTA
* * * **** *
2414501 ATAAAAAAAATTACTTAATATTTCATTTTTC-G
1 AT---AAAAA-TACATAAGATTTTATAAAACTA
2414533 ATAAAAATACATAAGATTTTATAAAACTA
1 ATAAAAATACATAAGATTTTATAAAACTA
2414562 ATAAAAA
1 ATAAAAA
2414569 CATTTATAGA
Statistics
Matches: 47, Mismatches: 16, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
28 13 0.28
29 14 0.30
32 7 0.15
33 13 0.28
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.34
Consensus pattern (29 bp):
ATAAAAATACATAAGATTTTATAAAACTA
Found at i:2414511 original size:61 final size:61
Alignment explanation
Indices: 2414444--2414568 Score: 232
Period size: 61 Copynumber: 2.0 Consensus size: 61
2414434 ATTTAAAAAT
*
2414444 AAAAAATTATTTAAAATTTCATTTTTCGATAAAAATACATAAGATTTTATAAAACTAATAA
1 AAAAAATTACTTAAAATTTCATTTTTCGATAAAAATACATAAGATTTTATAAAACTAATAA
*
2414505 AAAAAATTACTTAATATTTCATTTTTCGATAAAAATACATAAGATTTTATAAAACTAATAA
1 AAAAAATTACTTAAAATTTCATTTTTCGATAAAAATACATAAGATTTTATAAAACTAATAA
2414566 AAA
1 AAA
2414569 CATTTATAGA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.53, C:0.07, G:0.03, T:0.37
Consensus pattern (61 bp):
AAAAAATTACTTAAAATTTCATTTTTCGATAAAAATACATAAGATTTTATAAAACTAATAA
Found at i:2418656 original size:16 final size:17
Alignment explanation
Indices: 2418635--2418672 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2418625 TTCTATATTG
*
2418635 ATTTTACT-TTTATTTT
1 ATTTTACTATGTATTTT
2418651 ATTTTACTACTGTATTTT
1 ATTTTACTA-TGTATTTT
2418669 ATTT
1 ATTT
2418673 AAATAAGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
18 11 0.58
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.68
Consensus pattern (17 bp):
ATTTTACTATGTATTTT
Found at i:2418761 original size:29 final size:29
Alignment explanation
Indices: 2418728--2418799 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
2418718 ACAAATTCTT
2418728 AATGAACAAGTTCTTCATCGCGAACTCTC
1 AATGAACAAGTTCTTCATCGCGAACTCTC
*
2418757 AATGAACAAGTTCTTTATCGCGAACTCTC
1 AATGAACAAGTTCTTCATCGCGAACTCTC
2418786 AATGAACAAGTTCT
1 AATGAACAAGTTCT
2418800 CCATTTCTTC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (29 bp):
AATGAACAAGTTCTTCATCGCGAACTCTC
Found at i:2428661 original size:46 final size:46
Alignment explanation
Indices: 2428596--2428775 Score: 227
Period size: 46 Copynumber: 3.9 Consensus size: 46
2428586 TTATCTTTGA
* * * ** *
2428596 CATGATGCCATAGTGTCTTTCAATTATGGTCTTACTCATTTTCTGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTGT
** * *
2428642 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTGT
*
2428688 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTC-TGT
* *
2428734 CATGTTGTCATGATATCTTTCAACCATGGTCTTACACATTTT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTT
2428776 ATTTCAGAAA
Statistics
Matches: 117, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
45 3 0.03
46 111 0.95
47 3 0.03
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTTCTGT
Found at i:2428729 original size:21 final size:21
Alignment explanation
Indices: 2428705--2428774 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 21
2428695 CCATGGTATC
2428705 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTACACA
* * *
2428726 TTTCATATCATGTTGTCATGATATC-
1 TTTCA-ACCATG--GTC-TTACA-CA
2428751 TTTCAACCATGGTCTTACACA
1 TTTCAACCATGGTCTTACACA
2428772 TTT
1 TTT
2428775 TATTTCAGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 1 0.03
21 11 0.30
22 8 0.22
24 8 0.22
25 8 0.22
26 1 0.03
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (21 bp):
TTTCAACCATGGTCTTACACA
Found at i:2432554 original size:19 final size:19
Alignment explanation
Indices: 2432530--2432570 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
2432520 TGAGTGGACG
2432530 ATAGTGGACCTTGAATTTC
1 ATAGTGGACCTTGAATTTC
2432549 ATAGTGGACCTTGAATTTC
1 ATAGTGGACCTTGAATTTC
2432568 ATA
1 ATA
2432571 ATTTATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (19 bp):
ATAGTGGACCTTGAATTTC
Found at i:2440663 original size:20 final size:19
Alignment explanation
Indices: 2440638--2440681 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2440628 TGGAAAATAA
*
2440638 TTTCTAAAAAATGATTTACT
1 TTTCT-AAAAATAATTTACT
*
2440658 TTTCTAGAAATAATTTACT
1 TTTCTAAAAATAATTTACT
2440677 TTTCT
1 TTTCT
2440682 GGTGTTTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (19 bp):
TTTCTAAAAATAATTTACT
Found at i:2442077 original size:32 final size:32
Alignment explanation
Indices: 2442031--2442091 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
2442021 TGTCAATCAT
*
2442031 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCCAACAAGCATAAAACATAATAAA
*
2442063 TTCAATATCTAACAAGCATAAAACATAAT
1 TTCAATATCCAACAAGCATAAAACATAAT
2442092 CAATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (32 bp):
TTCAATATCCAACAAGCATAAAACATAATAAA
Found at i:2442095 original size:27 final size:30
Alignment explanation
Indices: 2442031--2442104 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
2442021 TGTCAATCAT
* *
2442031 TTCAATATCCAACAAGCTTAAAACATAATAAA
1 TTCAATATCTAACAAGCATAAAAC--AATAAA
2442063 TTCAATATCTAACAAGCATAAAAC-AT-AA
1 TTCAATATCTAACAAGCATAAAACAATAAA
2442091 -TCAATATCTAACAA
1 TTCAATATCTAACAA
2442105 ATTCAAGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.35
28 2 0.05
29 2 0.05
32 22 0.55
ACGTcount: A:0.53, C:0.19, G:0.03, T:0.26
Consensus pattern (30 bp):
TTCAATATCTAACAAGCATAAAACAATAAA
Found at i:2444366 original size:22 final size:22
Alignment explanation
Indices: 2444313--2444366 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
2444303 GGGAAAAATT
*
2444313 TTGGCTTTTATTGAAATAAAAC
1 TTGGCTTTTGTTGAAATAAAAC
2444335 TTGGCTTTTGTTGAAATAAAAC
1 TTGGCTTTTGTTGAAATAAAAC
2444357 TTGGCTTTTG
1 TTGGCTTTTG
2444367 ATCAATGGGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.44
Consensus pattern (22 bp):
TTGGCTTTTGTTGAAATAAAAC
Found at i:2453645 original size:178 final size:177
Alignment explanation
Indices: 2453415--2453807 Score: 547
Period size: 178 Copynumber: 2.2 Consensus size: 177
2453405 TACTTCAAGG
* * * * * *
2453415 AGATAAGATTCACTGTTTTTGATCTGCCCCACTGCTATCTCGAGGAGACAAAATCTACAATCTTC
1 AGATAAGATTCACCG-TATTGATTTGCTCCACTGCTAGCTCGAAGAGACAAAATCTACAATCTTC
*
2453480 AGT-TTGCTCCCTTGCTACCTCAGGAAGATAATACTACAATCTTCAACCTACTCCCTTGCTACCT
65 AGTCTT-CTCCCTTGCTACCTCAGGAAGATAAGACTACAATCTTCAACCTACTCCCTTGCTACCT
* * * *
2453544 TAGGAAGATAAGGCTGGTGACTAAAATCTGCT-TCTCTGCTACCTCGGGA
129 CAAGAAGATAAAGCTGGTGACTAAAATCTGCTCCCT-TGCTACCTCGGGA
* *
2453593 AGATAAGATTCGCCGTATTCGATTTGCTCCACTGCTAGCTCGAAGAGACAAAATCTGCAATCTTC
1 AGATAAGATTCACCGTATT-GATTTGCTCCACTGCTAGCTCGAAGAGACAAAATCTACAATCTTC
*
2453658 AGTCTTCTCCCTTGCTACCTTAGGAAGATAAGACTACAATCTTCAACCTACTCCCTTGCTACCTC
65 AGTCTTCTCCCTTGCTACCTCAGGAAGATAAGACTACAATCTTCAACCTACTCCCTTGCTACCTC
* * *
2453723 AAGAAGATAAAGCTGGTGGCTAAAATCTGCTCCCTTGTTACCTTGGGA
130 AAGAAGATAAAGCTGGTGACTAAAATCTGCTCCCTTGCTACCTCGGGA
* * *
2453771 AGATAAGATTCACCATCTGTGATTTGCTCCATTGCTA
1 AGATAAGATTCACCGTAT-TGATTTGCTCCACTGCTA
2453808 TTTCAGGGAA
Statistics
Matches: 190, Mismatches: 21, Indels: 8
0.87 0.10 0.04
Matches are distributed among these distances:
177 3 0.02
178 182 0.96
179 5 0.03
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (177 bp):
AGATAAGATTCACCGTATTGATTTGCTCCACTGCTAGCTCGAAGAGACAAAATCTACAATCTTCA
GTCTTCTCCCTTGCTACCTCAGGAAGATAAGACTACAATCTTCAACCTACTCCCTTGCTACCTCA
AGAAGATAAAGCTGGTGACTAAAATCTGCTCCCTTGCTACCTCGGGA
Found at i:2455133 original size:55 final size:55
Alignment explanation
Indices: 2455062--2455221 Score: 175
Period size: 55 Copynumber: 2.9 Consensus size: 55
2455052 TTTTTCATTG
**
2455062 GGTCTCAAAGTACCCTTTGCGGGTTTTCACCTTGGCC-C-C-CT-TTTTTTTTAAA
1 GGTCTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGCCTCTCTCTCTTTTTTTT-AA
* * * *
2455114 GAATGTCTCAAAGCGCCCTTTGCGGGTTCTCACTTTAGCCTCTTCTCTCTTTTTTTTTA
1 G---GTCTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGCCTC-TCTCTCTTTTTTTTAA
*
2455173 GGTCTCAAAGCGCCCTTTTGCGGGTTTTCACCTTGGCCTCTCCCTCTTT
1 GGTCTCAAAGCGCCC-TTTGCGGGTTTTCACCTTGGCCTCTCTCTCTTT
2455222 AGGTGAAATA
Statistics
Matches: 89, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
52 1 0.01
55 31 0.35
56 23 0.26
57 21 0.24
58 1 0.01
59 4 0.04
60 8 0.09
ACGTcount: A:0.12, C:0.29, G:0.17, T:0.41
Consensus pattern (55 bp):
GGTCTCAAAGCGCCCTTTGCGGGTTTTCACCTTGGCCTCTCTCTCTTTTTTTTAA
Found at i:2466199 original size:11 final size:11
Alignment explanation
Indices: 2466159--2466191 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
2466149 ATGTAAATTA
*
2466159 AAACACACAA-
1 AAACAAACAAT
2466169 AAACAAACAAT
1 AAACAAACAAT
2466180 AAACAAACAAT
1 AAACAAACAAT
2466191 A
1 A
2466192 CATAAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.73, C:0.21, G:0.00, T:0.06
Consensus pattern (11 bp):
AAACAAACAAT
Found at i:2477869 original size:43 final size:44
Alignment explanation
Indices: 2477821--2477909 Score: 119
Period size: 43 Copynumber: 2.0 Consensus size: 44
2477811 GAAGTGTAGT
*
2477821 TGTTATAGAA-AAGGTTGACTGTATA-CTTGAATTATCTAATGGC
1 TGTTATA-AAGAAGGTTGACTATATAGCTTGAATTATCTAATGGC
* *
2477864 TGTTATAAAGAAGGTTGATTATATATGCTTGAATTTTCTAATGGC
1 TGTTATAAAGAAGGTTGACTATATA-GCTTGAATTATCTAATGGC
2477909 T
1 T
2477910 ACATTTTTCT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
42 2 0.05
43 20 0.50
45 18 0.45
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (44 bp):
TGTTATAAAGAAGGTTGACTATATAGCTTGAATTATCTAATGGC
Found at i:2478445 original size:21 final size:23
Alignment explanation
Indices: 2478405--2478446 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
2478395 TCATTCATGT
2478405 TAAACATTTAAAACAAATAAATC
1 TAAACATTTAAAACAAATAAATC
*
2478428 TAAAC-TTT-AAACACATAAA
1 TAAACATTTAAAACAAATAAA
2478447 AGTGTTTCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 3 0.17
23 5 0.28
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAACATTTAAAACAAATAAATC
Found at i:2483211 original size:26 final size:26
Alignment explanation
Indices: 2483182--2483289 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2483172 TGGTACAAAT
2483182 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
2483208 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2483234 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2483260 TGATAATGAGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2483286 TGAT
1 TGAT
2483290 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2488100 original size:45 final size:45
Alignment explanation
Indices: 2488049--2488138 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
2488039 ATAGGTTTGA
2488049 TATTTTGATTATATATATGTTGATATTTAAGATTCATGTTAATAT
1 TATTTTGATTATATATATGTTGATATTTAAGATTCATGTTAATAT
*
2488094 TATTTTGATTATATATATGTTGATATTTGAGATTCATGTTAATAT
1 TATTTTGATTATATATATGTTGATATTTAAGATTCATGTTAATAT
2488139 GTTTGAGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.02, G:0.12, T:0.53
Consensus pattern (45 bp):
TATTTTGATTATATATATGTTGATATTTAAGATTCATGTTAATAT
Found at i:2492117 original size:20 final size:20
Alignment explanation
Indices: 2492078--2492131 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
2492068 TTTTCTACTA
*
2492078 AAAC-TTATCATTTGATAACC
1 AAACATTATCATAT-ATAACC
2492098 ATAACA-TATCATATATAACC
1 A-AACATTATCATATATAACC
*
2492118 AACCATTATCATAT
1 AAACATTATCATAT
2492132 TACAACATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 3 0.10
20 16 0.55
21 10 0.34
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.33
Consensus pattern (20 bp):
AAACATTATCATATATAACC
Found at i:2493746 original size:5 final size:5
Alignment explanation
Indices: 2493728--2493800 Score: 137
Period size: 5 Copynumber: 14.4 Consensus size: 5
2493718 TTTACTTAAT
2493728 TATAA TAGTAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TA-TAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
2493779 TATAA TATAA TATAA TATAA TA
1 TATAA TATAA TATAA TATAA TA
2493801 ATATTTTCTT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
5 62 0.93
6 5 0.07
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:2494005 original size:20 final size:20
Alignment explanation
Indices: 2493978--2494029 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
2493968 TAATCCTTAT
**
2493978 ACCTAATTAACCTTAATTTAA
1 ACCTAATTAACC-TAATCAAA
*
2493999 A-CTAATTCACCTAATCAAA
1 ACCTAATTAACCTAATCAAA
2494018 ACCTAATTAACC
1 ACCTAATTAACC
2494030 ACACAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.27
20 18 0.69
21 1 0.04
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (20 bp):
ACCTAATTAACCTAATCAAA
Found at i:2499207 original size:29 final size:29
Alignment explanation
Indices: 2499174--2499612 Score: 461
Period size: 29 Copynumber: 15.1 Consensus size: 29
2499164 ATCGATTAAA
* ** * *
2499174 GAAAAGGGATAGTTTCGACTATCGACTAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
2499203 GAAAAGGGGTGGTGACGACCATC-AATTAT
1 GAAAAGGGATGGTGACGACCATCGAA-TAT
* ** *
2499232 GAAAAGGGATCGTGACCTCCATCAAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
2499261 GAAAAGGGATGGTGACGACCTTCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* *
2499290 CAAAAGGGATGGTGACAACCATCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* * *
2499319 AAAAAGAGATGGTGACGACTATCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
2499348 GAAAAGGGATGGTGACAACCATCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
2499377 GAAAAGGGATGGTGACGACCATCGACTAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* ** *
2499406 GAAAAGGGATAGTTTCGACTATC-AACTAT
1 GAAAAGGGATGGTGACGACCATCGAA-TAT
* ** * *
2499435 GAAAAGGGATAGTTTCGACTATCGACTAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
* ** * * * *
2499464 GAAAAGGGATAGTTTCAACTATTGACTAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
2499493 GAAAAGGGATGGTGACGACCATCGATTAAT
1 GAAAAGGGATGGTGACGACCATCGAAT-AT
*
2499523 GAAAAGGGATGGT-TCTGACCATCGAATAT
1 GAAAAGGGATGGTGAC-GACCATCGAATAT
* **
2499552 GAAAATGGATGGTTTCGACCATCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
*
2499581 GAAAAGGGATGGTGACGACTATCGAATAT
1 GAAAAGGGATGGTGACGACCATCGAATAT
2499610 GAA
1 GAA
2499613 CCATCGAATA
Statistics
Matches: 353, Mismatches: 50, Indels: 14
0.85 0.12 0.03
Matches are distributed among these distances:
28 2 0.01
29 321 0.91
30 30 0.08
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (29 bp):
GAAAAGGGATGGTGACGACCATCGAATAT
Found at i:2502556 original size:44 final size:44
Alignment explanation
Indices: 2502435--2503068 Score: 335
Period size: 44 Copynumber: 14.0 Consensus size: 44
2502425 GATCTGTGAC
* *
2502435 TTATAGCTTTAATCTGAC-CCACTGCAACTTCAAGGAGATGAGAT
1 TTATAGCTTTAATCTG-CTCCACTGCAACTTCAGGGAGATAAGAT
* * * * * *
2502479 TCACTATCTTCAATCTACTCCACTGCTACTTCAGGGAGATAAGGT
1 TTA-TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
2502524 TTATAGCTTTAATTTGCTCTACTGCAACTTCAGAGAGAGAAGATT
1 TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T
* ** * * * * *
2502569 TTCTTTCTTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGAC
1 TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * * *
2502613 TTGTTGCTTTAATCTGTTCCACTGTAACTTCAAGGAGATAAGAT
1 TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
** * * * *
2502657 TCGTGGCTTTAATCTTCTCCACTGTAACTTCAGGGAGACAAGAT
1 TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
** * * *
2502701 TCGT-GACTTTAATCTGCTCCACTGTAACTTTAGAGAGATAAGAT
1 TTATAG-CTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*** * * * *
2502745 TCGCCA-TTTTCAATCTACTCCACTGCAACTTCAGGGAGTTGAGAT
1 T-TATAGCTTT-AATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
** * * * * * *
2502790 TCGTAACTTCAACCTGTTCCACTGCAACTTCAAGGAGATAAGGT
1 TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
2502834 TTATGGCTTTAATCTACTCCACTGAAACTTCAAGGAGATAAGAT
1 TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* *
2502878 TCGCCATGATAACTTCAAT-TCGC-CCTACTGCAACTTCAGGG-GTATAAGATT
1 T-----T-ATAGCTTTAATCT-GCTCC-ACTGCAACTTCAGGGAG-ATAAGA-T
* * * * * *
2502929 TGTAACTTGTAGCTTAAATCAGTTCCACTACAACTTTAGGGAAATAAGAT
1 T-T-A----TAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
*** * * * * * * *
2502979 CCGCTATCTTCAACCTGCTCCACTACAACTTCAGGAATATAAGGT
1 -TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * *
2503024 TAATGGCTTTAATCTGCTCCACTGCAACTTCGGGGAGATAAGAT
1 TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
2503068 T
1 T
2503069 GGCTGTGGTT
Statistics
Matches: 443, Mismatches: 121, Indels: 52
0.72 0.20 0.08
Matches are distributed among these distances:
43 1 0.00
44 244 0.55
45 130 0.29
47 2 0.00
49 5 0.01
50 29 0.07
51 30 0.07
52 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
TTATAGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
Found at i:2502711 original size:88 final size:88
Alignment explanation
Indices: 2502441--2502880 Score: 379
Period size: 89 Copynumber: 5.0 Consensus size: 88
2502431 TGACTTATAG
** * * * ** * *
2502441 CTTTAATCTGACCCACTGCAACTTCAAGGAGATGAGATTCACTATCTTCAATCTACTCCACTGCT
1 CTTTAATCTGTTCCACTGTAACTTCAAGGAGATAAGATTC-GTGGCTTTAATCTACTCCACTGCA
* **
2502506 ACTTCAGGGAGATAAGGTTTAT-A
65 ACTTCAGGGAGATAAGATTCGTGA
* * * * * ** * *
2502529 GCTTTAATTTGCTCTACTGCAACTTC-AGAGAGAGAAGATTTTC-TTTCTTCAGTCTACTCCACT
1 -CTTTAATCTGTTCCACTGTAACTTCAAG-GAGATAAGA--TTCGTGGCTTTAATCTACTCCACT
*
2502592 GCAACTTTAGGGAGATAAGACTT-GTTG-
62 GCAACTTCAGGGAGATAAGA-TTCG-TGA
* *
2502619 CTTTAATCTGTTCCACTGTAACTTCAAGGAGATAAGATTCGTGGCTTTAATCTTCTCCACTGTAA
1 CTTTAATCTGTTCCACTGTAACTTCAAGGAGATAAGATTCGTGGCTTTAATCTACTCCACTGCAA
*
2502684 CTTCAGGGAGACAAGATTCGTGA
66 CTTCAGGGAGATAAGATTCGTGA
* * ****
2502707 CTTTAATCTGCTCCACTGTAACTT-TAGAGAGATAAGATTCGCCATTTTCAATCTACTCCACTGC
1 CTTTAATCTGTTCCACTGTAACTTCAAG-GAGATAAGATTCGTGGCTTT-AATCTACTCCACTGC
* * *
2502771 AACTTCAGGGAGTTGAGATTCGTAA
64 AACTTCAGGGAGATAAGATTCGTGA
* * * * ** *
2502796 CTTCAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTTATGGCTTTAATCTACTCCACTGAAA
1 CTTTAATCTGTTCCACTGTAACTTCAAGGAGATAAGATTCGTGGCTTTAATCTACTCCACTGCAA
*
2502861 CTTCAAGGAGATAAGATTCG
66 CTTCAGGGAGATAAGATTCG
2502881 CCATGATAAC
Statistics
Matches: 285, Mismatches: 53, Indels: 27
0.78 0.15 0.07
Matches are distributed among these distances:
87 9 0.03
88 107 0.38
89 159 0.56
90 7 0.02
91 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (88 bp):
CTTTAATCTGTTCCACTGTAACTTCAAGGAGATAAGATTCGTGGCTTTAATCTACTCCACTGCAA
CTTCAGGGAGATAAGATTCGTGA
Found at i:2502738 original size:177 final size:177
Alignment explanation
Indices: 2502438--2502880 Score: 516
Period size: 177 Copynumber: 2.5 Consensus size: 177
2502428 CTGTGACTTA
** * ** *
2502438 TAGCTTTAATCTGACCCACTGCAACTTCAAGGAGATGAGATTCACTATCTTCAATCTACTCCACT
1 TAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGATTCA-TGGCTTTAATCTACTCCACT
* ** * *
2502503 GCT-ACTTCAGGGAGATAAGGTTTATAGCTTTAATTTGCTCTACTGCAACTTCAGAGAGAGAAGA
65 G-TAACTTCAGGGAGATAAGATTCGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGAGAAGA
** * * *
2502567 TT-TTCTTTCTTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTT-G
129 TTCGCCATT-TTCAATCTACTCCACTGCAACTTCAGGGAGATAAGA-TTCG
* * * *
2502616 TTGCTTTAATCTGTTCCACTGTAACTTCAAGGAGATAAGATTCGTGGCTTTAATCTTCTCCACTG
1 TAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGATTCATGGCTTTAATCTACTCCACTG
* * * *
2502681 TAACTTCAGGGAGACAAGATTCGT-GACTTTAATCTGCTCCACTGTAACTTTAGAGAGATAAGAT
66 TAACTTCAGGGAGATAAGATTCGTAG-CTTTAATCTGCTCCACTGCAACTTCAGAGAGAGAAGAT
* *
2502745 TCGCCATTTTCAATCTACTCCACTGCAACTTCAGGGAGTTGAGATTCG
130 TCGCCATTTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCG
* * * * *
2502793 TAACTTCAACCTGTTCCACTGCAACTTCAAGGAGATAAGGTTTATGGCTTTAATCTACTCCACTG
1 TAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGATTCATGGCTTTAATCTACTCCACTG
* *
2502858 AAACTTCAAGGAGATAAGATTCG
66 TAACTTCAGGGAGATAAGATTCG
2502881 CCATGATAAC
Statistics
Matches: 223, Mismatches: 38, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
176 4 0.02
177 178 0.80
178 41 0.18
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (177 bp):
TAGCTTTAATCTGTTCCACTGCAACTTCAAGGAGATAAGATTCATGGCTTTAATCTACTCCACTG
TAACTTCAGGGAGATAAGATTCGTAGCTTTAATCTGCTCCACTGCAACTTCAGAGAGAGAAGATT
CGCCATTTTCAATCTACTCCACTGCAACTTCAGGGAGATAAGATTCG
Found at i:2502760 original size:133 final size:132
Alignment explanation
Indices: 2502441--2502884 Score: 389
Period size: 133 Copynumber: 3.3 Consensus size: 132
2502431 TGACTTATAG
* * * *
2502441 CTTTAATCTGAC-CCACTGCAACTTCAAGGAGATGAGATTCACTATCTTCAATCTACTCCACTGC
1 CTTTAATCT-ACTCCACTGCAACTTCAAGGAGATAAGATTCGCCATTTTCAATCTACTCCACTG-
* ** * * *
2502505 T-ACTTCAGGGAGATAAGGTTTATAGCTTTAAT-TTGCTCTACTGCAACTTCAGAGAGAGAAGAT
64 TAACTTCAGGGAGATAAGATTCGTAGCTTTAATCTT-CTCCACTGCAACTTCAGGGAGACAAGA-
**
2502568 TTTCTTT
127 -TTCTGA
* * * * **** **
2502575 CTTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTT-GTTGCTTT-AATCTGTTCCACTGT
1 CTTTAATCTACTCCACTGCAACTTCAAGGAGATAAGA-TTCGCCATTTTCAATCTACTCCACTGT
* * *
2502638 AACTTCAAGGAGATAAGATTCGTGGCTTTAATCTTCTCCACTGTAACTTCAGGGAGACAAGATTC
65 AACTTCAGGGAGATAAGATTCGTAGCTTTAATCTTCTCCACTGCAACTTCAGGGAGACAAGATTC
2502703 GTGA
130 -TGA
* * * *
2502707 CTTTAATCTGCTCCACTGTAACTT-TAGAGAGATAAGATTCGCCATTTTCAATCTACTCCACTGC
1 CTTTAATCTACTCCACTGCAACTTCAAG-GAGATAAGATTCGCCATTTTCAATCTACTCCACTGT
* * * * * * * *
2502771 AACTTCAGGGAGTTGAGATTCGTAACTTCAACCTGT-TCCACTGCAACTTCAAGGAGATAAGGTT
65 AACTTCAGGGAGATAAGATTCGTAGCTTTAATCT-TCTCCACTGCAACTTCAGGGAGACAA-GAT
* *
2502835 TATGG
128 TCTGA
*
2502840 CTTTAATCTACTCCACTGAAACTTCAAGGAGATAAGATTCGCCAT
1 CTTTAATCTACTCCACTGCAACTTCAAGGAGATAAGATTCGCCAT
2502885 GATAACTTCA
Statistics
Matches: 247, Mismatches: 52, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
131 6 0.02
132 35 0.14
133 164 0.66
134 40 0.16
135 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (132 bp):
CTTTAATCTACTCCACTGCAACTTCAAGGAGATAAGATTCGCCATTTTCAATCTACTCCACTGTA
ACTTCAGGGAGATAAGATTCGTAGCTTTAATCTTCTCCACTGCAACTTCAGGGAGACAAGATTCT
GA
Found at i:2508577 original size:25 final size:25
Alignment explanation
Indices: 2508528--2508599 Score: 62
Period size: 24 Copynumber: 2.9 Consensus size: 25
2508518 TATGCATAAC
*
2508528 AACATATAAGAATATGATAAT-AAA
1 AACATATATGAATATGATAATAAAA
*
2508552 AACATATATGCATAATGAT-ATGAAAA
1 AACATATATGAAT-ATGATAAT-AAAA
2508578 ATACATATAT-ATATAT-ATAATA
1 A-ACATATATGA-ATATGATAATA
2508600 TACTATTAGA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
24 13 0.33
25 8 0.21
26 8 0.21
27 10 0.26
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.31
Consensus pattern (25 bp):
AACATATATGAATATGATAATAAAA
Found at i:2524276 original size:22 final size:20
Alignment explanation
Indices: 2524241--2524281 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2524231 TCTATATGAA
*
2524241 AACATTAAAAATATGTACAT
1 AACATTAAAAATATATACAT
2524261 AACATATATAAAATATATACA
1 AACAT-TA-AAAATATATACA
2524282 ATATATACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
AACATTAAAAATATATACAT
Found at i:2524477 original size:24 final size:24
Alignment explanation
Indices: 2524429--2524481 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2524419 ATAGCTGACA
*
2524429 ATATTAAAATATATACATAACAAC
1 ATATAAAAATATATACATAACAAC
2524453 ATATAAAAATATAATAACA-AA-AAC
1 ATATAAAAATAT-AT-ACATAACAAC
2524477 ATATA
1 ATATA
2524482 TGCATAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 19 0.73
25 4 0.15
26 3 0.12
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (24 bp):
ATATAAAAATATATACATAACAAC
Found at i:2525386 original size:26 final size:27
Alignment explanation
Indices: 2525344--2525397 Score: 101
Period size: 26 Copynumber: 2.0 Consensus size: 27
2525334 ATCGCAAAGG
2525344 TAAGATTTTTTTTCGTGTTTTTAAATA
1 TAAGATTTTTTTTCGTGTTTTTAAATA
2525371 TAAGA-TTTTTTTCGTGTTTTTAAATA
1 TAAGATTTTTTTTCGTGTTTTTAAATA
2525397 T
1 T
2525398 TCTTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.26, C:0.04, G:0.11, T:0.59
Consensus pattern (27 bp):
TAAGATTTTTTTTCGTGTTTTTAAATA
Found at i:2526738 original size:14 final size:14
Alignment explanation
Indices: 2526719--2526746 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2526709 GATTTTCACG
2526719 AACAGAAATTGAAA
1 AACAGAAATTGAAA
2526733 AACAGAAATTGAAA
1 AACAGAAATTGAAA
2526747 TTACCTCAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.07, G:0.14, T:0.14
Consensus pattern (14 bp):
AACAGAAATTGAAA
Found at i:2526894 original size:89 final size:87
Alignment explanation
Indices: 2526503--2526890 Score: 480
Period size: 89 Copynumber: 4.4 Consensus size: 87
2526493 CATTTCTTAA
* * * * **
2526503 AGGCTCAACTCACTTCTTGCAATATGAGTTGATTTTTGAA-AGCAGAATTTGCAAAACAGATTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAGAGCAGAAATTGAAAAACAGAAATT
*
2526567 GAAAATACCTCGGCATGTGACCC-G
66 GAAAATACCTCAGC--GTG-CCCTG
* * * * **
2526591 AGGCTCAACTCACCTCTCGTAATATGAGTTGATTCTTGAAAAGCATAAATTGAAAAAACATTAAT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAGAGCAGAAATTG-AAAAACAGAAAT
2526656 TGAAAATACCTCAGCGTG-CCTCG
65 TGAAAATACCTCAGCGTGCCCT-G
* * *
2526679 AGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTCACGAACAGAAATTGAAAAACAGAAATT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAGAGCAGAAATTGAAAAACAGAAATT
* *
2526743 GAAATTACCTCAGCGTGTCCTG
66 GAAAATACCTCAGCGTGCCCTG
*
2526765 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTCG-AAAGCAGAA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAAGAGCAGAAATT-GAAAAACAGAA
*
2526829 ATCGAAAATACCTCAGCGTGCCCTG
63 ATTGAAAATACCTCAGCGTGCCCTG
*
2526854 AGGCTCAACTCACCTCTCGCAATAGGAGTTGATTTTT
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
2526891 TTGACAAACA
Statistics
Matches: 261, Mismatches: 30, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
86 62 0.24
87 21 0.08
88 71 0.27
89 85 0.33
90 22 0.08
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (87 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAGAGCAGAAATTGAAAAACAGAAATT
GAAAATACCTCAGCGTGCCCTG
Found at i:2526964 original size:75 final size:75
Alignment explanation
Indices: 2526827--2526969 Score: 241
Period size: 75 Copynumber: 1.9 Consensus size: 75
2526817 TCGAAAGCAG
*
2526827 AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTGATTTTTT
1 AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTAATTTTTT
2526892 TGACAAACAT
66 TGACAAACAT
* * * *
2526902 AAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTT
1 AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTAATTTTTT
2526967 TGA
66 TGA
2526970 GAAGAAGAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (75 bp):
AAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTAATTTTTT
TGACAAACAT
Found at i:2526981 original size:75 final size:75
Alignment explanation
Indices: 2526824--2526986 Score: 238
Period size: 75 Copynumber: 2.2 Consensus size: 75
2526814 AATTCGAAAG
* *
2526824 CAGAAATCGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTGATTT
1 CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTAATTT
2526889 TTTTGACAAA
66 TTTTGACAAA
* * * *
2526899 CATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTT
1 CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTAATTT
*
2526964 TTTTGAGAAGA
66 TTTTGACAA-A
*
2526975 -AGAAATTTAAAA
1 CAGAAATTGAAAA
2526987 AACATCTATT
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
75 76 0.99
76 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.28
Consensus pattern (75 bp):
CAGAAATTGAAAATACCTCAGCGTGCCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTAATTT
TTTTGACAAA
Found at i:2527144 original size:250 final size:243
Alignment explanation
Indices: 2526646--2527438 Score: 839
Period size: 250 Copynumber: 3.3 Consensus size: 243
2526636 TAAATTGAAA
*
2526646 AAACATTAATTGAAAATACCTCAGCGTG-CCTCGAGGCTCAACTCACCTCTCGCAATATGAGTTG
1 AAACATAAATTGAAAATACCTCAGCGTGTCCT-GAGGCTCAACTCACCTCTCGCAATATGAGTTG
* * * *
2526710 A--TTTTCACGAA-CAGAAATTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCA
65 ATTTTTTTA-GAAGAAGAAATT-AAAAA-A-CAATTGAAAATACCTCAGCGTGTCCTGAGGCTCA
* *
2526772 ACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAGAGCAGAAATTCG-AAAGCAGAAATCGAAA
126 ACTCACCTCTCGCAATATGAGTTGA--TTTTTGAA-A-CATAAATT-GAAAAACAGAAATCGAAA
* *
2526836 ATACCTCAGCGTG-CCCTGAGGCTCAACTCACCTCTCGCAATAGGAGTTGATTTTTTTGAC
186 ATACCTCAGCATGTCCC-GAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGAC
* *
2526896 AAACATAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAA
1 AAACATAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
* *
2526961 TTTTTTTGAGAAGAAGAAATTTAAAAAACATCTATTGAAAATACCTCGGCGTATGACCTGAGGCT
66 TTTTTTT-AGAAGAAGAAA-TTAAAAAACA---ATTGAAAATACCTCAGCG--TGTCCTGAGGCT
* * *
2527026 TAACTCACCTCTCACAATATGAGTTGATTTTTGAAACATAAATTGAAAAACAGAAATCAAAAATA
124 CAACTCACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAAAACAGAAATCGAAAATA
* *
2527091 CCTCAGCATGTCCCGAGGCTCAACTCACTTCCCGCAATATGAGTTGATTTTTGAC
189 CCTCAGCATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
* * * * * * *
2527146 AAATAGT-AATTGAAAATACCGCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATAGGAGTTG
1 AAACA-TAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTG
** * *
2527210 --TTTTTT----GAA-AAA-TCCAAAA-AATTGACAATACCTCAGCGTGTCCCGAGGCTCAACTC
65 ATTTTTTTAGAAGAAGAAATTAAAAAACAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTC
* * * * *
2527266 ATCTCTTGCAATATGAGTTGA-TTTT------T---TT-AAAAAAAGAATTTGAAAATACCTCAG
130 ACCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAAAACAGAAATCGAAAATACCTCAG
** * *
2527320 CATGTCTTGAGGCTCAACTCACCTCTCACAATATGAGTTGATTTTTGAA
195 CATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
* * *
2527369 AAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGAGTTGA
1 AAACATAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
2527434 TTTTT
66 TTTTT
2527439 GAAAAAAGCA
Statistics
Matches: 469, Mismatches: 57, Indels: 59
0.80 0.10 0.10
Matches are distributed among these distances:
223 118 0.25
224 2 0.00
225 4 0.01
227 1 0.00
233 4 0.01
234 33 0.07
236 16 0.03
239 1 0.00
240 5 0.01
242 3 0.01
243 3 0.01
248 6 0.01
250 119 0.25
251 6 0.01
252 71 0.15
253 15 0.03
254 26 0.06
256 36 0.08
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (243 bp):
AAACATAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
TTTTTTTAGAAGAAGAAATTAAAAAACAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCA
CCTCTCGCAATATGAGTTGATTTTTGAAACATAAATTGAAAAACAGAAATCGAAAATACCTCAGC
ATGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAC
Found at i:2527208 original size:73 final size:73
Alignment explanation
Indices: 2527068--2527591 Score: 534
Period size: 73 Copynumber: 7.0 Consensus size: 73
2527058 GAAACATAAA
** * * *
2527068 TTGAAAAACAGAAATCAAAAATACCTCAGCATGTCCCGAGGCTCAACTCACTTCCCGCAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2527133 GTTGATTT
66 GTTGATTT
* * * * * * * *
2527141 TTGACAAATAGTAATTGAAAATACCGCAACGTGCCCCGAGGCTCAACTCACCTCTAGCAATAGGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
*
2527206 GTTGTTTT
66 GTTGATTT
* * * *
2527214 TTGAAAAATCCAAAAAATTGACAATACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTTGCAATA
1 TTGAAAAA--C-AGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATA
2527279 TGAGTTGATTTT
63 TGAGTTGA-TTT
* * * * ** *
2527291 TTTAAAAAAAGAATTTGAAAATACCTCAGCATGTCTTGAGGCTCAACTCACCTCTCACAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2527356 GTTGATTT
66 GTTGATTT
* * *
2527364 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
2527429 GTTGATTT
66 GTTGATTT
** * *
2527437 TTGAAAAAAGCAGAAATT-AAAAGTACCTCAATGTG-CCTTGAGGCTCGACTCACCTCTCGCAAT
1 TTG-AAAAA-CAGAAATTGAAAA-TACCTCAGCGTGTCC-CGAGGCTCAACTCACCTCTCGCAAT
*
2527500 ATGAGTTG-GTT
62 ATGAGTTGATTT
** *
2527511 TTGACAAACAGAAACAGAAATTGAAAATACCTCAGCACGTGAGCCGAGGGTCAACTCACCT-TCC
1 TTG----A-A-AAACAGAAATTGAAAATACCTCAG--CGTGTCCCGAGGCTCAACTCACCTCT-C
*
2527575 GCACTATGAGTTGATTT
57 GCAATATGAGTTGATTT
2527592 AAAAAATAGA
Statistics
Matches: 373, Mismatches: 59, Indels: 30
0.81 0.13 0.06
Matches are distributed among these distances:
73 137 0.37
74 67 0.18
75 49 0.13
76 51 0.14
77 12 0.03
78 16 0.04
79 8 0.02
80 30 0.08
81 3 0.01
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (73 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTT
Found at i:2527531 original size:147 final size:146
Alignment explanation
Indices: 2527068--2527532 Score: 530
Period size: 147 Copynumber: 3.2 Consensus size: 146
2527058 GAAACATAAA
* * * *
2527068 TTGAAAAACAGAAATCA-AAAATACCTCAGCATGTCCCGAGGCTCAACTCACTTCCCGCAATATG
1 TTGAAAAACAGAAA-CAGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATG
* * * * * ** *
2527132 AGTTGATTTTTGACAAATAGTAATTGAAAATACCGCAACGTGCCCCGAGGCTCAACTCACCTCTA
65 AGTTGATTTTTGAAAAAAAGAAATTGAAAATACCTCAATGTGCCTTGAGGCTCAACTCACCTCTC
* *
2527197 GCAATAGGAGTTGTTTT
130 GCAATATGAGTTGATTT
* * *
2527214 TTGAAAAATCCA-AAAAATTGACAA-TACCTCAGCGTGTCCCGAGGCTCAACTCATCTCTTGCAA
1 TTGAAAAA--CAGAAACA--GA-AATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAA
* *
2527277 TATGAGTTGATTTTTTTAAAAAAAGAATTTGAAAATACCTCAGCATGT--CTTGAGGCTCAACTC
61 TATGAGTTGA-TTTTTGAAAAAAAGAAATTGAAAATACCTCA--ATGTGCCTTGAGGCTCAACTC
*
2527340 ACCTCTCACAATATGAGTTGATTT
123 ACCTCTCGCAATATGAGTTGATTT
** * *
2527364 TTGAAAAACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGTAATATGA
1 TTGAAAAACAGAAACAGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
*
2527429 GTTGATTTTTGAAAAAAGCAGAAATT-AAAAGTACCTCAATGTGCCTTGAGGCTCGACTCACCTC
66 GTTGATTTTTGAAAAAA--AGAAATTGAAAA-TACCTCAATGTGCCTTGAGGCTCAACTCACCTC
*
2527493 TCGCAATATGAGTTG-GTT
128 TCGCAATATGAGTTGATTT
*
2527511 TTGACAAACAGAAACAGAAATT
1 TTGAAAAACAGAAACAGAAATT
2527533 GAAAATACCT
Statistics
Matches: 270, Mismatches: 33, Indels: 31
0.81 0.10 0.09
Matches are distributed among these distances:
146 26 0.10
147 75 0.28
148 50 0.19
149 48 0.18
150 68 0.25
152 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (146 bp):
TTGAAAAACAGAAACAGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGA
GTTGATTTTTGAAAAAAAGAAATTGAAAATACCTCAATGTGCCTTGAGGCTCAACTCACCTCTCG
CAATATGAGTTGATTT
Found at i:2553026 original size:22 final size:20
Alignment explanation
Indices: 2552991--2553031 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
2552981 TCTATATGAA
*
2552991 AACATTAAAAATATGTACAT
1 AACATTAAAAATATATACAT
2553011 AACATATATAAAATATATACA
1 AACAT-TA-AAAATATATACA
2553032 ATATATACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (20 bp):
AACATTAAAAATATATACAT
Found at i:2553206 original size:24 final size:24
Alignment explanation
Indices: 2553179--2553231 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2553169 ATAGCTGACA
*
2553179 ATATTAAAATAT-AT-ACATAACAAC
1 ATATAAAAATATGATAACA-AA-AAC
2553203 ATATAAAAATATGATAACAAAAAC
1 ATATAAAAATATGATAACAAAAAC
2553227 ATATA
1 ATATA
2553232 TGCATAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 19 0.73
25 4 0.15
26 3 0.12
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATAAAAATATGATAACAAAAAC
Found at i:2559263 original size:3 final size:3
Alignment explanation
Indices: 2559255--2559308 Score: 65
Period size: 3 Copynumber: 18.0 Consensus size: 3
2559245 AATATGCAGG
* * *
2559255 AAT AAT AAT AAC AAT AAT GAA- AAT GAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT
2559300 AAT AAT AAT
1 AAT AAT AAT
2559309 GAATGAATGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.05
3 39 0.91
4 2 0.05
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2559315 original size:4 final size:4
Alignment explanation
Indices: 2559306--2559338 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
2559296 TAATAATAAT
2559306 AATG AATG AATG AATG AATG AATG AATG AATG A
1 AATG AATG AATG AATG AATG AATG AATG AATG A
2559339 TTTAAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (4 bp):
AATG
Found at i:2571351 original size:8 final size:10
Alignment explanation
Indices: 2571327--2571359 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
2571317 CATTAAGAAC
2571327 ATATTTTATT
1 ATATTTTATT
2571337 ATATTTTATT
1 ATATTTTATT
2571347 AT-TTTTA-T
1 ATATTTTATT
2571355 ATATT
1 ATATT
2571360 ATTTAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 3 0.14
9 7 0.32
10 12 0.55
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
ATATTTTATT
Found at i:2573124 original size:11 final size:11
Alignment explanation
Indices: 2573108--2573137 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2573098 TTATAGGCAT
2573108 AAGAAGTACAA
1 AAGAAGTACAA
*
2573119 AAGAAGTATAA
1 AAGAAGTACAA
2573130 AAGAAGTA
1 AAGAAGTA
2573138 GAGATCTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.13
Consensus pattern (11 bp):
AAGAAGTACAA
Found at i:2578910 original size:14 final size:13
Alignment explanation
Indices: 2578869--2578922 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
2578859 CCCAATTTCC
2578869 AATTTTATATTTTT
1 AATTTTA-ATTTTT
*
2578883 AATCTTTAAATTTT
1 AAT-TTTAATTTTT
2578897 AATTTTAGATTTTT
1 AATTTTA-ATTTTT
*
2578911 AAGTTTCAATTT
1 AA-TTTTAATTT
2578923 CAAATTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.12
14 22 0.65
15 8 0.24
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (13 bp):
AATTTTAATTTTT
Found at i:2578911 original size:21 final size:20
Alignment explanation
Indices: 2578869--2578922 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
2578859 CCCAATTTCC
2578869 AATTTTATATTTTTAATCTTTA
1 AATTTTA-A-TTTTAATCTTTA
*
2578891 AATTTTAATTTTAGATTTTTA
1 AATTTTAATTTTA-ATCTTTA
* *
2578912 AGTTTCAATTT
1 AATTTTAATTT
2578923 CAAATTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 16 0.57
22 7 0.25
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (20 bp):
AATTTTAATTTTAATCTTTA
Found at i:2578928 original size:28 final size:29
Alignment explanation
Indices: 2578861--2578930 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
2578851 CTTTAATCCC
* *
2578861 CAATTTCCAATTTTATATTTTTAATCTTT
1 CAATTTCAAATTTTAGATTTTTAATCTTT
* * *
2578890 AAATTT-TAATTTTAGATTTTTAA-GTTT
1 CAATTTCAAATTTTAGATTTTTAATCTTT
2578917 CAATTTCAAATTTT
1 CAATTTCAAATTTT
2578931 CAACCCTCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 8 0.24
28 21 0.62
29 5 0.15
ACGTcount: A:0.31, C:0.09, G:0.03, T:0.57
Consensus pattern (29 bp):
CAATTTCAAATTTTAGATTTTTAATCTTT
Found at i:2578929 original size:21 final size:21
Alignment explanation
Indices: 2578887--2578930 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
2578877 ATTTTTAATC
* * *
2578887 TTTAAATTTTAATTTTAGATT
1 TTTAAATTTCAATTTCAAATT
*
2578908 TTTAAGTTTCAATTTCAAATT
1 TTTAAATTTCAATTTCAAATT
2578929 TT
1 TT
2578931 CAACCCTCAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
TTTAAATTTCAATTTCAAATT
Found at i:2579505 original size:28 final size:28
Alignment explanation
Indices: 2579465--2579523 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
2579455 AAGTTTAGAG
2579465 GTTGTAGCACCCCAAACCCGGCCCAGAA
1 GTTGTAGCACCCCAAACCCGGCCCAGAA
2579493 GTTGTAGCACCCCAAACCCGGCCCAGAA
1 GTTGTAGCACCCCAAACCCGGCCCAGAA
2579521 GTT
1 GTT
2579524 ATGGCCGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.37, G:0.22, T:0.14
Consensus pattern (28 bp):
GTTGTAGCACCCCAAACCCGGCCCAGAA
Found at i:2588773 original size:26 final size:26
Alignment explanation
Indices: 2588742--2588849 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2588732 TGAAATGCCC
*
2588742 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
2588768 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
2588794 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
2588820 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
2588846 ATCA
1 ATCA
2588850 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:2595731 original size:26 final size:26
Alignment explanation
Indices: 2595695--2595804 Score: 202
Period size: 26 Copynumber: 4.2 Consensus size: 26
2595685 CATGAAATTC
2595695 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
2595721 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
2595747 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
2595773 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
2595799 TTATCA
1 TTATCA
2595805 ATTTGTATCA
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.37, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:2597595 original size:55 final size:55
Alignment explanation
Indices: 2597511--2597614 Score: 199
Period size: 55 Copynumber: 1.9 Consensus size: 55
2597501 AATCCGAGGT
2597511 TGAAAATTTATTTTAATATTATTTTTTGTGTTTACAGCATGGTATGTGATATGTG
1 TGAAAATTTATTTTAATATTATTTTTTGTGTTTACAGCATGGTATGTGATATGTG
*
2597566 TGAAAGTTTATTTTAATATTATTTTTTGTGTTTACAGCATGGTATGTGA
1 TGAAAATTTATTTTAATATTATTTTTTGTGTTTACAGCATGGTATGTGA
2597615 CATGATAAAG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 48 1.00
ACGTcount: A:0.27, C:0.04, G:0.18, T:0.51
Consensus pattern (55 bp):
TGAAAATTTATTTTAATATTATTTTTTGTGTTTACAGCATGGTATGTGATATGTG
Found at i:2597645 original size:55 final size:55
Alignment explanation
Indices: 2597511--2597645 Score: 157
Period size: 55 Copynumber: 2.5 Consensus size: 55
2597501 AATCCGAGGT
* * * * *
2597511 TGAAAATTTATTTTAATATTATTTTTTGTGTTTACAGCATGGTATGTGATATGTG
1 TGAAAGTTTATGTTAATATGATTTTTTGTGTTTACAGCATGGTATGTGACATGTA
* *
2597566 TGAAAGTTTATTTTAATATTATTTTTTGTGTTTACAGCATGGTATGTGACATG-A
1 TGAAAGTTTATGTTAATATGATTTTTTGTGTTTACAGCATGGTATGTGACATGTA
* *
2597620 T-AAAGGTTTGTGGTTAATGTGATTTT
1 TGAAA-GTTTAT-GTTAATATGATTTT
2597646 GATTTGGTAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
53 3 0.04
54 6 0.08
55 62 0.87
ACGTcount: A:0.27, C:0.04, G:0.20, T:0.50
Consensus pattern (55 bp):
TGAAAGTTTATGTTAATATGATTTTTTGTGTTTACAGCATGGTATGTGACATGTA
Found at i:2598418 original size:12 final size:12
Alignment explanation
Indices: 2598397--2598429 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
2598387 TAGACACATG
2598397 GGCC-TGTGGTC
1 GGCCGTGTGGTC
2598408 GGCCGTGTGGTC
1 GGCCGTGTGGTC
2598420 GGCCGTGTGG
1 GGCCGTGTGG
2598430 CCTAGTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.00, C:0.24, G:0.52, T:0.24
Consensus pattern (12 bp):
GGCCGTGTGGTC
Found at i:2601030 original size:26 final size:26
Alignment explanation
Indices: 2600999--2601051 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
2600989 TGTGAAAAAG
*
2600999 AAAGATGGCACGATGTGAATGTGTAT
1 AAAGATGGCACGATGAGAATGTGTAT
2601025 AAAGATGGCACGATGAGAATGTGTAT
1 AAAGATGGCACGATGAGAATGTGTAT
2601051 A
1 A
2601052 GATTACAGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.30, T:0.25
Consensus pattern (26 bp):
AAAGATGGCACGATGAGAATGTGTAT
Found at i:2603526 original size:429 final size:429
Alignment explanation
Indices: 2602727--2605299 Score: 5029
Period size: 429 Copynumber: 6.0 Consensus size: 429
2602717 AACTTGCTGA
*
2602727 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTAACTATTTCTATTGTTTGAGATAGAGATC
1 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
* *
2602792 CAAGGTTTACATCGCAGTTTTAGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTTAGT
66 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
2602857 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
131 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
2602922 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
196 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
2602987 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
261 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
2603052 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
326 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
2603117 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
391 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
2603156 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
1 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
2603221 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
66 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
2603286 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
131 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
2603351 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
196 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
2603416 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
261 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
2603481 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
326 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
2603546 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
391 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
2603585 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
1 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
2603650 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
66 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
2603715 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
131 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
* *
2603780 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTGCCATTGATTGAATTCACAT
196 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
*
2603845 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAATATTTATGTGGTCGAAAATGT
261 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
*
2603910 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAAGGTTGATATGATTAGAGA
326 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
*
2603975 GACTGAAGAAAAAGTGAAAATGATTCGTGATAGTTTGAG
391 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
2604014 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
1 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
2604079 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
66 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
2604144 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
131 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
2604209 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
196 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
2604274 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
261 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
* *
2604339 AGAACACTGTTGTACTAGATTGAGCTTAGCAAGAGTAAGATCCACAGGGTTGATATGATTAGAGA
326 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
2604404 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
391 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
2604443 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
1 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
2604508 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
66 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
*
2604573 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTTAGATACTTGAGGATATGTT
131 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
2604638 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
196 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
*
2604703 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTTGAAAATGT
261 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
*
2604768 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGTGA
326 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
2604833 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
391 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
2604872 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
1 GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
2604937 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
66 CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
2605002 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
131 ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
2605067 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
196 GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
2605132 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
261 ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
2605197 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
326 AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
2605262 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGA
391 GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGA
2605300 AACCAGTGTC
Statistics
Matches: 2121, Mismatches: 23, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
429 2121 1.00
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.31
Consensus pattern (429 bp):
GTTGTATATTTCTCAGATTATGAGGTTGCACGGTGTACCTATTTCTATTGTTTGAGATAGAGATC
CAAGGTTTACATCGCAGTTTTGGAAGAAACTACAAGATGCATTAGGTACAAAGCTACACTTCAGT
ACTGCATTTCATTCACAAATAGATGGTCAATCCGAGCGAGTTATTCAGATACTTGAGGATATGTT
GAGATGTTGCATACTTGAGTTCGTAAGTACGTGGGAAAAGTATTTCCCATTGATTGAATTCACGT
ATAATAACAGTTTTCAATCGAGCATTAAAATGGCACCGTATGAAGATTTATGTGGTCGAAAATGT
AGAACACTGTTGTACTAGACTGAGCTTAGCAAGAATAAGATCCACAGGGTTGATATGATTAGAGA
GACTGAAGAAAAAGTGAAAGTGATTCGTGATAGTTTGAG
Found at i:2606551 original size:30 final size:30
Alignment explanation
Indices: 2606507--2606569 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
2606497 ATGTCAATTA
*
2606507 GGGGTTAATTTGTG-A-AAATGTGAAAATAT
1 GGGGTTAATATGTGAATAAAT-TGAAAATAT
*
2606536 GGGGTTTAATATGTGAATAAATTTAAAATAT
1 GGGG-TTAATATGTGAATAAATTGAAAATAT
2606567 GGG
1 GGG
2606570 CTACTAGGGG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 9 0.31
31 12 0.41
32 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.27, T:0.35
Consensus pattern (30 bp):
GGGGTTAATATGTGAATAAATTGAAAATAT
Found at i:2607186 original size:47 final size:47
Alignment explanation
Indices: 2607127--2607257 Score: 174
Period size: 47 Copynumber: 2.8 Consensus size: 47
2607117 GTGCAAATGA
*
2607127 TACCTTGATTTGGCTATAGGCCATGGTATAGGTA-TTCAAAGAGGAGT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTTC-AAGAGAAGT
* ** *
2607174 TACCTTGATTTGGCTACAGGCCATGGTATAGGTACTTCGTGATAAGT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTTCAAGAGAAGT
* * *
2607221 TACCTTGATTTGGCTATTGGTCATGGTATATGTACTT
1 TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTT
2607258 ATCGATAGAG
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
47 71 0.96
48 3 0.04
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.37
Consensus pattern (47 bp):
TACCTTGATTTGGCTATAGGCCATGGTATAGGTACTTCAAGAGAAGT
Found at i:2608664 original size:48 final size:48
Alignment explanation
Indices: 2608588--2608871 Score: 309
Period size: 48 Copynumber: 5.9 Consensus size: 48
2608578 AAAGGGTAAG
* * * * * *
2608588 ATGCCGATGCTATGTCCCAGACATGGTCTTACACTAGCTCCCGTAACA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAATA
* * * * *
2608636 ATGCCAATGCCATGTTCCAAACATGGTCTTACATTGGCTCACATATTG
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAATA
* * * * *
2608684 AGGCTGATGCCATG-TCCTAGACATAGTCTTACACTAGCTCTCATAATA
1 ATGCCGATGCCATGTTCC-AAACATGGTCTTACACTAGCTCACATAATA
* * * * *
2608732 ATGCTGATGCCATGTTCCAAACATGGTCTTTCACTGGCTCACATATTG
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAATA
* * * *
2608780 AGGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAACA
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAATA
* *
2608828 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACAT
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACAT
2608872 GTACCCTAAC
Statistics
Matches: 191, Mismatches: 43, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
47 3 0.02
48 185 0.97
49 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (48 bp):
ATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCTCACATAATA
Found at i:2608757 original size:96 final size:96
Alignment explanation
Indices: 2608590--2608871 Score: 440
Period size: 96 Copynumber: 2.9 Consensus size: 96
2608580 AGGGTAAGAT
* * * **
2608590 GCCGATGCTATGTCCCAGACATGGTCTTACACTAGCTCCCGTAACAATGCCAATGCCATGTTCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCTGATGCCATGTTCCA
*
2608655 AACATGGTCTTACATTGGCTCACATATTGAG
66 AACATGGTCTTACACTGGCTCACATATTGAG
* * * *
2608686 GCTGATGCCATGTCCTAGACATAGTCTTACACTAGCTCTCATAATAATGCTGATGCCATGTTCCA
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCTGATGCCATGTTCCA
*
2608751 AACATGGTCTTTCACTGGCTCACATATTGAG
66 AACATGGTCTTACACTGGCTCACATATTGAG
*
2608782 GCCGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTCATAACAATG-TCGATGCCATGTTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCT-GATGCCATGTTCC
2608846 AAACATGGTCTTACACTGGCTCACAT
65 AAACATGGTCTTACACTGGCTCACAT
2608872 GTACCCTAAC
Statistics
Matches: 168, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
95 1 0.01
96 167 0.99
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (96 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACAATGCTGATGCCATGTTCCA
AACATGGTCTTACACTGGCTCACATATTGAG
Found at i:2611509 original size:26 final size:26
Alignment explanation
Indices: 2611480--2611530 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
2611470 ATTGTTATAT
2611480 GGCTCTTCGTGAGCTTCCCGATTAAA
1 GGCTCTTCGTGAGCTTCCCGATTAAA
* *
2611506 GGCTCTTTGTGAGCTTCCTGATTAA
1 GGCTCTTCGTGAGCTTCCCGATTAA
2611531 TGGATATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (26 bp):
GGCTCTTCGTGAGCTTCCCGATTAAA
Found at i:2615351 original size:16 final size:17
Alignment explanation
Indices: 2615330--2615362 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2615320 TATTTTAAAC
*
2615330 TTTGTTT-TTGGTTTTT
1 TTTGTTTGTCGGTTTTT
2615346 TTTGTTTGTCGGTTTTT
1 TTTGTTTGTCGGTTTTT
2615363 GGTATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.03, G:0.21, T:0.76
Consensus pattern (17 bp):
TTTGTTTGTCGGTTTTT
Found at i:2631239 original size:40 final size:40
Alignment explanation
Indices: 2631141--2631483 Score: 424
Period size: 40 Copynumber: 8.6 Consensus size: 40
2631131 TCCTCGTTCA
* * * * *
2631141 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
2631180 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2631220 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2631260 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
2631300 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
2631340 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * *
2631380 AAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAATAACTCGCACG
** * * * *
2631420 AATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
2631460 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
2631484 CAGCATTCAA
Statistics
Matches: 275, Mismatches: 23, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
39 39 0.14
40 224 0.81
41 12 0.04
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:2631492 original size:41 final size:41
Alignment explanation
Indices: 2631415--2631492 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
2631405 TTTGTATCTC
* * *
2631415 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
2631456 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
2631493 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:2642936 original size:23 final size:23
Alignment explanation
Indices: 2642910--2642981 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 23
2642900 TGTGATGCAA
2642910 ATATCTATGTTTGTTTAGCCATT
1 ATATCTATGTTTGTTTAGCCATT
* * **
2642933 ATAT-GATGTCATGAGTATG--ATT
1 ATATCTATGT-TTGTTTA-GCCATT
*
2642955 ATATCTATGTTTGTTTAGCCCTT
1 ATATCTATGTTTGTTTAGCCATT
2642978 ATAT
1 ATAT
2642982 GATGTCATGA
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
21 1 0.03
22 15 0.43
23 18 0.51
24 1 0.03
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (23 bp):
ATATCTATGTTTGTTTAGCCATT
Found at i:2642941 original size:22 final size:22
Alignment explanation
Indices: 2642916--2642986 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
2642906 GCAAATATCT
2642916 ATGTTTGTTTAGCCATTATATG
1 ATGTTTGTTTAGCCATTATATG
* ** *
2642938 ATGTCATGAGTATG--ATTATATCT
1 ATGT-TTGTTTA-GCCATTATAT-G
*
2642961 ATGTTTGTTTAGCCCTTATATG
1 ATGTTTGTTTAGCCATTATATG
2642983 ATGT
1 ATGT
2642987 CATGAGTATG
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
21 1 0.03
22 19 0.54
23 14 0.40
24 1 0.03
ACGTcount: A:0.24, C:0.10, G:0.18, T:0.48
Consensus pattern (22 bp):
ATGTTTGTTTAGCCATTATATG
Found at i:2642974 original size:45 final size:45
Alignment explanation
Indices: 2642910--2642999 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
2642900 TGTGATGCAA
2642910 ATATCTATGTTTGTTTAGCCATTATATGATGTCATGAGTATGATT
1 ATATCTATGTTTGTTTAGCCATTATATGATGTCATGAGTATGATT
*
2642955 ATATCTATGTTTGTTTAGCCCTTATATGATGTCATGAGTATGATT
1 ATATCTATGTTTGTTTAGCCATTATATGATGTCATGAGTATGATT
2643000 TGTTTGAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.47
Consensus pattern (45 bp):
ATATCTATGTTTGTTTAGCCATTATATGATGTCATGAGTATGATT
Found at i:2647657 original size:15 final size:15
Alignment explanation
Indices: 2647637--2647692 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
2647627 GTGTCTTGGG
2647637 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
2647652 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
* *
2647667 TTTC-TCAATCTTGGA
1 TTTCTTTATTC-TGGA
2647682 TTTCTTTATTC
1 TTTCTTTATTC
2647693 AGTTTTCTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 4 0.12
15 25 0.76
16 4 0.12
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:2650041 original size:47 final size:47
Alignment explanation
Indices: 2649972--2650134 Score: 201
Period size: 47 Copynumber: 3.5 Consensus size: 47
2649962 NNNNNNNNNN
*
2649972 AACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAGGCATCCG
* * *
2650019 AACTCGTTGAGTTGAGTCCGAGTTCACT--TATG-GA-T-GCGAATGTCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCA-TGAAATGTAACTAG-GCA--TCCG
*
2650065 AACTCGTTGAGTTGAGTCCTAGTTCATGAAATGTAACTAGGCATCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAGGCATCCG
*
2650112 AACTCGTTGAGTTGAGTCTGAGT
1 AACTCGTTGAGTTGAGTCCGAGT
2650135 ACACTTATGG
Statistics
Matches: 97, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 2 0.02
46 32 0.33
47 53 0.55
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (47 bp):
AACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAGGCATCCG
Found at i:2650082 original size:46 final size:46
Alignment explanation
Indices: 2650015--2650190 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
2650005 TAACTAGGCA
2650015 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
2650061 TCCGAACTCGTTGAGTTGAGTCCTAGTTCA-TGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
2650106 CATCCGAACTCGTTGAGTTGAGTCTGAGTACACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
2650154 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2650191 GCAGGTTACA
Statistics
Matches: 106, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 62 0.58
47 27 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2650140 original size:93 final size:93
Alignment explanation
Indices: 2649972--2650183 Score: 361
Period size: 93 Copynumber: 2.3 Consensus size: 93
2649962 NNNNNNNNNN
*
2649972 AACTCGTTGAGTTGAGTCCGAGTTCGTGAAATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTC
1 AACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTC
* * *
2650037 CGAGTTCACTTATGGATGCGAATGTCCG
66 CGAGTACACTTATGGATGCGAACGCCCG
*
2650065 AACTCGTTGAGTTGAGTCCTAGTTCATGAAATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTC
1 AACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTC
*
2650130 TGAGTACACTTATGGATGCGAACGCCCG
66 CGAGTACACTTATGGATGCGAACGCCCG
*
2650158 AGCTCGTTGAGTTGAGTCCGAGTTCA
1 AACTCGTTGAGTTGAGTCCGAGTTCA
2650184 CTTATGGGCA
Statistics
Matches: 111, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 111 1.00
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (93 bp):
AACTCGTTGAGTTGAGTCCGAGTTCATGAAATGTAACTAGGCATCCGAACTCGTTGAGTTGAGTC
CGAGTACACTTATGGATGCGAACGCCCG
Found at i:2654381 original size:43 final size:41
Alignment explanation
Indices: 2654285--2654394 Score: 109
Period size: 42 Copynumber: 2.6 Consensus size: 41
2654275 GACTTATGAT
2654285 TTACATGTAAGACCATGTCTAGGACATCGGCATCATATTTG
1 TTACATGTAAGACCATGTCTAGGACATCGGCATCATATTTG
* *
2654326 --ACATCGCATAAGACCTTGTCTGGGACAGT-GGCATCAATATTTGG
1 TTACAT-G--TAAGACCATGTCTAGGACA-TCGGCATC-ATATTT-G
* *
2654370 TTACATGTAAGACCACGTCGAGGAC
1 TTACATGTAAGACCATGTCTAGGAC
2654395 GTTAATATTG
Statistics
Matches: 55, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
39 4 0.07
40 1 0.02
42 23 0.42
43 21 0.38
44 1 0.02
45 1 0.02
46 4 0.07
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (41 bp):
TTACATGTAAGACCATGTCTAGGACATCGGCATCATATTTG
Found at i:2654968 original size:23 final size:22
Alignment explanation
Indices: 2654927--2654971 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
2654917 TATTTAGCCA
*
2654927 TGTGATATGGCTTGGTTTTGGT
1 TGTGATATGGCTTGATTTTGGT
*
2654949 TGTGATTATGGTTTGATTTTGGT
1 TGTGA-TATGGCTTGATTTTGGT
2654972 ATATGAAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.11, C:0.02, G:0.33, T:0.53
Consensus pattern (22 bp):
TGTGATATGGCTTGATTTTGGT
Found at i:2657838 original size:144 final size:143
Alignment explanation
Indices: 2657573--2657851 Score: 522
Period size: 144 Copynumber: 1.9 Consensus size: 143
2657563 TGATTTCATC
2657573 TCCACTTTCTGAGTCTTCACAGCTAACCCCCTCAGAATAATTAGATGGCTCTTGGTTCGCATCTA
1 TCCACTTTCTGAGTCTTCACAGCTAACCCCCTCAGAATAATTAGATGGCTCTTGGTTCGCATCTA
* *
2657638 TATCTTTACCCCACATTTAAAGCATAAGCAACTTGATTAACCTAGGCATACTTCTTAGGAGGTTT
66 TATCTTCACCCCACATTTAAAGCATAAGCAACTTGATCAACCTAGGCATACTTCTTAGGAGGTTT
2657703 AATTTAGCAAACA
131 AATTTAGCAAACA
*
2657716 TCCACTTTTCTGAGTCTTCACAGCTAACCGCCTCAGAATAATTAGATGGCTCTTGGTTCGCATCT
1 TCCAC-TTTCTGAGTCTTCACAGCTAACCCCCTCAGAATAATTAGATGGCTCTTGGTTCGCATCT
2657781 ATATCTTCACCCCACATTTAAAGCATAAGCAACTTGATCAACCTAGGCATACTTCTTAGGAGGTT
65 ATATCTTCACCCCACATTTAAAGCATAAGCAACTTGATCAACCTAGGCATACTTCTTAGGAGGTT
2657846 TAATTT
130 TAATTT
2657852 CTCTTCTAGT
Statistics
Matches: 132, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
143 5 0.04
144 127 0.96
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (143 bp):
TCCACTTTCTGAGTCTTCACAGCTAACCCCCTCAGAATAATTAGATGGCTCTTGGTTCGCATCTA
TATCTTCACCCCACATTTAAAGCATAAGCAACTTGATCAACCTAGGCATACTTCTTAGGAGGTTT
AATTTAGCAAACA
Found at i:2659256 original size:3 final size:3
Alignment explanation
Indices: 2659248--2659305 Score: 57
Period size: 3 Copynumber: 19.3 Consensus size: 3
2659238 AAATAGATAT
* * *
2659248 TTA TTA TTA TAA TTA TTAA TTA TTA TTG TT- TATA TTA TTA TTT TTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA TTA
2659294 TTA TTA -TA TTA T
1 TTA TTA TTA TTA T
2659306 GGAATAAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
2 3 0.07
3 39 0.85
4 4 0.09
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2659286 original size:15 final size:15
Alignment explanation
Indices: 2659248--2659300 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
2659238 AAATAGATAT
**
2659248 TTATTATTATAATTA
1 TTATTATTATTTTTA
2659263 TTAATTATTATTGTTTA
1 TT-ATTATTATT-TTTA
2659280 -TATTATTATTTTTA
1 TTATTATTATTTTTA
2659294 TTATTAT
1 TTATTAT
2659301 ATTATGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
15 17 0.52
16 9 0.27
17 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTATTATTATTTTTA
Found at i:2659619 original size:16 final size:17
Alignment explanation
Indices: 2659592--2659632 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
2659582 TATATAGTAA
*
2659592 AGAAATAAAAAGAAAAG
1 AGAAAGAAAAAGAAAAG
*
2659609 A-AAAGAAAAAGAAAGG
1 AGAAAGAAAAAGAAAAG
2659625 AGAAAGAA
1 AGAAAGAA
2659633 GCAGACAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (17 bp):
AGAAAGAAAAAGAAAAG
Found at i:2660081 original size:17 final size:18
Alignment explanation
Indices: 2660059--2660094 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2660049 TAAATGAGTT
2660059 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
2660076 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
2660094 A
1 A
2660095 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:2660307 original size:20 final size:20
Alignment explanation
Indices: 2660279--2660345 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
2660269 ATGTTACATT
*
2660279 TAAATTTATATGTATGGTAG
1 TAAAATTATATGTATGGTAG
*
2660299 TAAAATTATA---A-GGTATT
1 TAAAATTATATGTATGGTA-G
*
2660316 TAAATTTATATGTATGGTAG
1 TAAAATTATATGTATGGTAG
*
2660336 TAAAACTATA
1 TAAAATTATA
2660346 AGGTAAGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 10
0.69 0.12 0.19
Matches are distributed among these distances:
16 4 0.11
17 10 0.28
20 18 0.50
21 4 0.11
ACGTcount: A:0.42, C:0.01, G:0.15, T:0.42
Consensus pattern (20 bp):
TAAAATTATATGTATGGTAG
Found at i:2660314 original size:21 final size:21
Alignment explanation
Indices: 2660290--2660350 Score: 60
Period size: 17 Copynumber: 3.1 Consensus size: 21
2660280 AAATTTATAT
2660290 GTATGGTAGTAAAATTATAAG
1 GTATGGTAGTAAAATTATAAG
* *
2660311 GTAT--T--TAAATTTAT-AT
1 GTATGGTAGTAAAATTATAAG
*
2660327 GTATGGTAGTAAAACTATAAG
1 GTATGGTAGTAAAATTATAAG
2660348 GTA
1 GTA
2660351 AGTATCAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 10
0.67 0.11 0.22
Matches are distributed among these distances:
16 5 0.17
17 8 0.27
18 1 0.03
19 1 0.03
20 7 0.23
21 8 0.27
ACGTcount: A:0.41, C:0.02, G:0.20, T:0.38
Consensus pattern (21 bp):
GTATGGTAGTAAAATTATAAG
Found at i:2660317 original size:37 final size:37
Alignment explanation
Indices: 2660276--2660350 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2660266 TAAATGTTAC
*
2660276 ATTTAAATTTATATGTATGGTAGTAAAATTATAAGGT
1 ATTTAAATTTATATGTATGGTAGTAAAACTATAAGGT
2660313 ATTTAAATTTATATGTATGGTAGTAAAACTATAAGGT
1 ATTTAAATTTATATGTATGGTAGTAAAACTATAAGGT
2660350 A
1 A
2660351 AGTATCAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.01, G:0.16, T:0.41
Consensus pattern (37 bp):
ATTTAAATTTATATGTATGGTAGTAAAACTATAAGGT
Found at i:2660652 original size:21 final size:22
Alignment explanation
Indices: 2660619--2660668 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
2660609 AGGCACTTTA
* *
2660619 TGTGTCGTATATCAGGTACCTCG
1 TGTGTCG-ATATCAAGCACCTCG
*
2660642 TGTGTCG-TATCAAGCACCTTG
1 TGTGTCGATATCAAGCACCTCG
2660663 TGTGTC
1 TGTGTC
2660669 ATTTTAGGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 17 0.71
23 7 0.29
ACGTcount: A:0.16, C:0.22, G:0.26, T:0.36
Consensus pattern (22 bp):
TGTGTCGATATCAAGCACCTCG
Found at i:2667978 original size:26 final size:26
Alignment explanation
Indices: 2667949--2668056 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
2667939 TGGTACAAAT
2667949 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
2667975 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2668001 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
2668027 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
2668053 TGAT
1 TGAT
2668057 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:2677989 original size:43 final size:43
Alignment explanation
Indices: 2677925--2678008 Score: 141
Period size: 43 Copynumber: 2.0 Consensus size: 43
2677915 AACATGTAAC
* *
2677925 ACATCCCTAATGAACTCGGACCTCTCAACGAGCTCGGATGCTT
1 ACATCCATAATGAACTCGGACCTCTCAACGAGCTCAGATGCTT
*
2677968 ACATCCATAATGAACTTGGACCTCTCAACGAGCTCAGATGC
1 ACATCCATAATGAACTCGGACCTCTCAACGAGCTCAGATGC
2678009 CACATATCTC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.23
Consensus pattern (43 bp):
ACATCCATAATGAACTCGGACCTCTCAACGAGCTCAGATGCTT
Found at i:2684331 original size:131 final size:132
Alignment explanation
Indices: 2683867--2684521 Score: 474
Period size: 132 Copynumber: 4.9 Consensus size: 132
2683857 AGAAAATACA
* * * * ** *
2683867 AGTGAAATTTCGAAGAGACATTCGATTATTTTGAACAAACGGGGGATTGCAACCCAGCACGA-TA
1 AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACAC-ATTA
* *** * * *
2683931 GGGCACTATTCCCCGAATTGCCAAACATCGAACATTT--CTTCAGTTTTCAAGAGTTTTTAGAAA
65 GGGCACGATTCCGAAAATTGCCAAACATCAAAC-TTTGCCTTCA-TTTTAAAGAATTTTTA-AAA
*
2683994 -ACATG
127 GACACG
* ** * * ** *
2683999 AGTGAAA-TTCTAAAGGGATCTTCGATCGTTTTGAACAAATGAAAAAGCGCAACCCAGCACGA-T
1 AGTGAAATTTC-AAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACAC-ATT
* * * * ** **
2684062 AGGGCACGATTCTCG--AATTGCCAAACATCGAACATCGCATTTGTTTTAAAGGGTTTTCTTAAA
64 AGGGCACGATTC-CGAAAATTGCCAAACATCAAACTTTGCCTTCATTTTAAA-GAATTT-TT--A
* *
2684125 AAAAACATG
124 AAAGACACG
* * * ** ** *
2684134 AATGAAAACTT-AAAGGAACGTTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGA-T
1 AGTG-AAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACAC-ATT
* * ** * * *
2684197 AGGGCATGATTCC-AAAATTGTCAAACA-CCGAGTATTGCCTTCATTTTAAAGGATTTTTAGAAG
64 AGGGCACGATTCCGAAAATTGCCAAACATCAAACT-TTGCCTTCATTTTAAAGAATTTTTAAAAG
2684260 AC-CTG
128 ACAC-G
* *
2684265 AGTGAAATTTCAAAGGGATATTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACACATTAG
1 AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACATTAG
* ** * *
2684330 GGCGCGATTCCGCGAATTGCCAAATATCAAACTTTGCCTTCATTTTAAAGAATTTTTAAAAGGCA
66 GGCACGATTCCGAAAATTGCCAAACATCAAACTTTGCCTTCATTTTAAAGAATTTTTAAAAGACA
2684395 CG
131 CG
** * *
2684397 AGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGCGAAATTGCAACCCAACACGTTAG
1 AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACATTAG
* * * * * * *
2684462 GGCACTATTCCGGAAATTGCCAAATATCGAA-TCTCGTCTTCGTTTTAAAGAATTTTTAAA
66 GGCACGATTCCGAAAATTGCCAAACATCAAACT-TTGCCTTCATTTTAAAGAATTTTTAAA
2684522 TGAATACTTA
Statistics
Matches: 419, Mismatches: 83, Indels: 42
0.77 0.15 0.08
Matches are distributed among these distances:
130 7 0.02
131 90 0.21
132 211 0.50
133 9 0.02
134 11 0.03
135 86 0.21
136 3 0.01
137 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (132 bp):
AGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACGAGAAATTGCAACCCAACACATTAG
GGCACGATTCCGAAAATTGCCAAACATCAAACTTTGCCTTCATTTTAAAGAATTTTTAAAAGACA
CG
Found at i:2684378 original size:267 final size:267
Alignment explanation
Indices: 2683887--2684485 Score: 597
Period size: 266 Copynumber: 2.3 Consensus size: 267
2683877 CGAAGAGACA
* ** ** **
2683887 TTCGATTATTTTGAACAAACGGGGGATTGCAACCCAGCACGATAGGGCACTATTCCCCGAATTGC
1 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCAAAATTGC
* * *
2683952 CAAACATCGAACATTTCTTCAGTTTTCAAGAGTTTTTAGAAAACATGAGTGAAATTCTAAAGGGA
66 CAAACACCGAACATTCCTTCAGTTTTAAAGAGTTTTTAGAAAACATGAGTGAAATTCTAAAGGGA
* * * * *
2684017 TCTTCGATCGTTTTGAACAAATGAAAAAGCGCAACCCAGCACGATAGGGCACGATTCTCGAATTG
131 TATTCGATCATTTTGAACAAACGAAAAAGCGCAACCCAACACGATAGGGCACGATTCGCGAATTG
* **
2684082 CCAAACATCGAACATCGCATTTGTTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAAAACTTAA
196 CCAAACATCAAACATCGCATTCATTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAAAACTTAA
2684147 AGGAACG
261 AGGAACG
2684154 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCA-TGATT-CCAAAATTG
1 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACT-ATTCCCAAAATTG
* ** * *
2684217 TCAAACACCGAGTATTGCCTTCA-TTTTAAAG-GATTTTTAGAAGACCTGAGTGAAATT-TCAAA
65 CCAAACACCGAACATT-CCTTCAGTTTTAAAGAG-TTTTTAGAAAACATGAGTGAAATTCT-AAA
* * * * ** *
2684279 GGGATATTTGATTATTTTGAGCAAACGAGAAATTGCAACCCAACAC-ATTAGGGCGCGATTCCGC
127 GGGATATTCGATCATTTTGAACAAACGAAAAAGCGCAACCCAACACGA-TAGGGCACGATT-CGC
* * * * ** ** * *
2684343 GAATTGCCAAATATCAAACTTTGCCTTCATTTTAAA-GAATTT-TT--AAAAGGCACGAGTGAAA
190 GAATTGCCAAACATCAAACATCGCATTCATTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAAA
** * * **
2684404 TTTTGAAGGGATA
255 ACTTAAAGGAACG
* ** * * **
2684417 TTCGATTATTTTGAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACTATTCCGGAAATTGC
1 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCAAAATTGC
2684482 CAAA
66 CAAA
2684486 TATCGAATCT
Statistics
Matches: 270, Mismatches: 54, Indels: 19
0.79 0.16 0.06
Matches are distributed among these distances:
263 67 0.25
264 12 0.04
265 5 0.02
266 103 0.38
267 83 0.31
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.27
Consensus pattern (267 bp):
TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCAAAATTGC
CAAACACCGAACATTCCTTCAGTTTTAAAGAGTTTTTAGAAAACATGAGTGAAATTCTAAAGGGA
TATTCGATCATTTTGAACAAACGAAAAAGCGCAACCCAACACGATAGGGCACGATTCGCGAATTG
CCAAACATCAAACATCGCATTCATTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAAAACTTAA
AGGAACG
Found at i:2687780 original size:221 final size:221
Alignment explanation
Indices: 2687471--2688459 Score: 1466
Period size: 221 Copynumber: 4.5 Consensus size: 221
2687461 CCCCTGCCAA
* * * * * *
2687471 TACAGAGACGCCAAATCTGCTATCTTCAATCTGCTCTCCGCC-GCTACAGAGACGACAAATCTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCTGC
* * *
2687535 TATCTTCGATCTACTCTTCGCCGCTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGT
66 TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGC
* *
2687600 CACTACAAAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCT
131 CGCTACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCT
*
2687665 GCTATCTTCGATATGCTCTCCGCCGC
196 GCTATCTTCGATCTGCTCTCCGCCGC
* *
2687691 TACAGAGATC-CCAAATCTGTTATCTTCGATTTGCTCCCCACCTGATACAGAGATGCCAAATCTG
1 TACAGAGA-CGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCTG
* *
2687755 CTATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAAGCTGCTATCTTCGATCTGCTCTCCG
65 CTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCG
* * *
2687820 CCGCTACAGAGACGA-CAAATCTGTTATCTTCGATCTGCTCTCTGCCGCTACAGAGATGCCAAAT
130 CCGCTACAGAGAC-ACCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAAT
* * *
2687884 CTGCTATCTTTGATCTACTCTCCGCCGT
194 CTGCTATCTTCGATCTGCTCTCCGCCGC
2687912 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCTGC
* * * * **
2687977 TATATTCGATCTGCTCTTCGCCGCTACAAAGACGCCAAATCTGCTATCTTCAATCTGCTCTTTGC
66 TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGC
* ** * * * *
2688042 TGCTACAGAGATGCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGCTTCAGAGATGCCAAATCT
131 CGCTACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCT
2688107 GCTATCTTCGATCTGCTCTCCGCCGC
196 GCTATCTTCGATCTGCTCTCCGCCGC
* * * *
2688133 TACGGGGACGCCAAATCTGTTAACTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCTGC
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCTGC
* *
2688198 TATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGC
66 TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGC
* * *
2688263 CGCTACAGAGACACCAAATCTGCTATATTCGATCTGCTCTCTGCCACTACAGAGACGCCAAATCT
131 CGCTACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCT
* *
2688328 GCTATCTTTGATCTGCTCTCCTCCGC
196 GCTATCTTCGATCTGCTCTCCGCCGC
* ** *
2688354 TACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTTCGCC--ACTACAGAGACGCCAAATCTG
1 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGA-TACAGAGATGCCAAATCTG
2688417 CTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCT
65 CTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCT
2688460 ATTATCTGCT
Statistics
Matches: 689, Mismatches: 74, Indels: 12
0.89 0.10 0.02
Matches are distributed among these distances:
219 1 0.00
220 96 0.14
221 591 0.86
222 1 0.00
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.28
Consensus pattern (221 bp):
TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGATACAGAGATGCCAAATCTGC
TATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGC
CGCTACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGACGCCAAATCT
GCTATCTTCGATCTGCTCTCCGCCGC
Found at i:2688466 original size:44 final size:44
Alignment explanation
Indices: 2687471--2688459 Score: 1377
Period size: 44 Copynumber: 22.4 Consensus size: 44
2687461 CCCCTGCCAA
*
2687471 TACAGAGACGCCAAATCTGCTATCTTCAATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * *
2687515 TACAGAGACGACAAATCTGCTATCTTCGATCTACTCTTCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* *
2687559 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGTCAC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * * *
2687603 TACAAAGACACCAAATCTGTTATCTTCGATCTGCTCTCCGCCAC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
*
2687647 TACAGAGACGCCAAATCTGCTATCTTCGATATGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * * * *
2687691 TACAGAGATC-CCAAATCTGTTATCTTCGATTTGCTCCCCACCTGA
1 TACAGAGA-CGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC-GC
*
2687736 TACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* *
2687780 TACAGAGATGCCAAAGCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * *
2687824 TACAGAGACGACAAATCTGTTATCTTCGATCTGCTCTCTGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * * *
2687868 TACAGAGATGCCAAATCTGCTATCTTTGATCTACTCTCCGCCGT
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * *
2687912 TACAGAGACGCCAAATCTGTTATCTTCGATCTGCTCCCCGCCTGA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC-GC
* * *
2687957 TACAGAGATGCCAAATCTGCTATATTCGATCTGCTCTTCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * ** *
2688001 TACAAAGACGCCAAATCTGCTATCTTCAATCTGCTCTTTGCTGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * *
2688045 TACAGAGATGCCAAATCTGTTATCTTTGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* *
2688089 TTCAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * * * * * *
2688133 TACGGGGACGCCAAATCTGTTAACTTCGATCTACTCCCCGCCTGA
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCC-GC
*
2688178 TACAGAGATGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* *
2688222 TACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * * *
2688266 TACAGAGACACCAAATCTGCTATATTCGATCTGCTCTCTGCCAC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* *
2688310 TACAGAGACGCCAAATCTGCTATCTTTGATCTGCTCTCCTCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
* * * *
2688354 TACAGAGACACCAAATCTGTTATCTTCGATCTGCTCTTCGCCAC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
2688398 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
1 TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
2688442 TACAGAGACGCCAAATCT
1 TACAGAGACGCCAAATCT
2688460 ATTATCTGCT
Statistics
Matches: 829, Mismatches: 111, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
44 717 0.86
45 112 0.14
ACGTcount: A:0.23, C:0.33, G:0.17, T:0.28
Consensus pattern (44 bp):
TACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCGC
Found at i:2689690 original size:5 final size:5
Alignment explanation
Indices: 2689680--2689756 Score: 72
Period size: 5 Copynumber: 15.4 Consensus size: 5
2689670 TGGCCTATCA
*
2689680 TTTTC TTTTC TTTTC TTCT- TTTTC TTTTTC TTCTT- TATTTC -TTTC
1 TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TT-TTC T-TTTC TTTTC
*
2689725 TTTTC TTTTC TTTTC TTCT- TTTTC TTCTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT-TTC TT
2689757 CTTTTTTTTT
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
4 10 0.17
5 37 0.62
6 13 0.22
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:2689704 original size:9 final size:8
Alignment explanation
Indices: 2689680--2689764 Score: 71
Period size: 9 Copynumber: 9.5 Consensus size: 8
2689670 TGGCCTATCA
2689680 TTTTCTTTT
1 TTTTC-TTT
2689689 CTTTTCTTCT
1 -TTTTCTT-T
2689699 TTTTCTTT
1 TTTTCTTT
2689707 TTCTTCTTT
1 TT-TTCTTT
*
2689716 ATTTCTTT
1 TTTTCTTT
2689724 CTTTTCTTTT
1 -TTTTC-TTT
2689734 CTTTTCTTCT
1 -TTTTCTT-T
2689744 TTTTCTTCT
1 TTTTCTT-T
*
2689753 TCTTCTTT
1 TTTTCTTT
2689761 TTTT
1 TTTT
2689765 TTTGAAGATC
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
8 13 0.20
9 37 0.56
10 16 0.24
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTTT
Found at i:2689710 original size:15 final size:15
Alignment explanation
Indices: 2689685--2689767 Score: 95
Period size: 15 Copynumber: 5.7 Consensus size: 15
2689675 TATCATTTTC
2689685 TTTTC-TTTTCTTCT
1 TTTTCTTTTTCTTCT
2689699 TTTTCTTTTTCTTCTT
1 TTTTCTTTTTCTTC-T
2689715 TATTTCTTTCTT-TTC-
1 T-TTTCTTT-TTCTTCT
2689730 TTTTC-TTTTCTTCT
1 TTTTCTTTTTCTTCT
*
2689744 TTTTCTTCTTCTTCT
1 TTTTCTTTTTCTTCT
2689759 TTTT-TTTTT
1 TTTTCTTTTT
2689768 GAAGATCTCA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
12 2 0.03
13 5 0.08
14 18 0.30
15 21 0.35
16 2 0.03
17 10 0.17
18 2 0.03
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTCTTTTTCTTCT
Found at i:2692338 original size:19 final size:19
Alignment explanation
Indices: 2692314--2692355 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2692304 TGGGAAATTT
2692314 AATGCAAATG-ATGCGATG
1 AATGCAAATGCATGCGATG
*
2692332 CAATGCAAATGCATGTGATG
1 -AATGCAAATGCATGCGATG
2692352 AATG
1 AATG
2692356 GAAAGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.24
Consensus pattern (19 bp):
AATGCAAATGCATGCGATG
Found at i:2694404 original size:267 final size:267
Alignment explanation
Indices: 2693913--2694511 Score: 590
Period size: 266 Copynumber: 2.3 Consensus size: 267
2693903 CGAAGAGACA
* ** ** *
2693913 TTCGATTATTTTGAACAAACGGGGGATTGCAACCCAGCACGATAGGGCACTATTCCCCGAATTGC
1 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCCAAATTGC
* * * *
2693978 CAAACATCGAACATTTCTTCCGTTTTCAAGAGTTTTTAGAAAACGTGAGTGAAATTCTAAAGGGA
66 CAAACACCGAACATTCCTTCCGTTTTAAAGAGTTTTTAGAAAACCTGAGTGAAATTCTAAAGGGA
* * * * *
2694043 TCTTCGATCGTTTTGAACAAATGAAAAAGCGCAACCCAGCACGATAGGGCACGATTCTCGAATTG
131 TATTCGATCATTTTGAACAAATCAAAAAGCGCAACCCAACACGATAGGGCACGATTCGCGAATTG
* **
2694108 CCAAACATCGAACATCGCATTTGTTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAAAACTTAA
196 CCAAACATCAAACATCGCATTCATTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAAAACTTAA
2694173 AGGAACG
261 AGGAACG
2694180 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCA-TGA-TCCCCAAATTG
1 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACT-ATTCCCCAAATTG
* **
2694243 TCAAACACCGAGTATTGCCTT-CGTTTTAAAG-GATTTTTA-AAAGACCTGAGTGAAATT-TCAA
65 CCAAACACCGAACATT-CCTTCCGTTTTAAAGAG-TTTTTAGAAA-ACCTGAGTGAAATTCT-AA
* * * ** * *
2694304 AGGGATATTTGATTATTTTGAGCAAA-CAAGAAATTGCAACCCAACACGTTAGGGCGCGATTCCG
126 AGGGATATTCGATCATTTTGAACAAATCAA-AAAGCGCAACCCAACACGATAGGGCACGATT-CG
* * ** * ** ** * *
2694368 CGAATTGCCAAATATCAAACTTTTCCTTCATTTTAAA-GAATTT-TT--AAAAGGCACGAGTGAA
189 CGAATTGCCAAACATCAAACATCGCATTCATTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAA
** * * **
2694429 ATTTTGAAGGGATA
254 AACTTAAAGGAACG
* ** * * **
2694443 TTCGATTATTTTGAACAAACGCGAAATTGCAACCCAACACGTTAGGGCACTATTCCGGAAATTGC
1 TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCCAAATTGC
2694508 CAAA
66 CAAA
2694512 TATCGAATCT
Statistics
Matches: 270, Mismatches: 53, Indels: 21
0.78 0.15 0.06
Matches are distributed among these distances:
263 65 0.24
264 14 0.05
265 9 0.03
266 104 0.39
267 78 0.29
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (267 bp):
TTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCACTATTCCCCAAATTGC
CAAACACCGAACATTCCTTCCGTTTTAAAGAGTTTTTAGAAAACCTGAGTGAAATTCTAAAGGGA
TATTCGATCATTTTGAACAAATCAAAAAGCGCAACCCAACACGATAGGGCACGATTCGCGAATTG
CCAAACATCAAACATCGCATTCATTTTAAAGGGTTTTCTTAAAAAAAACATGAATGAAAACTTAA
AGGAACG
Found at i:2694432 original size:132 final size:133
Alignment explanation
Indices: 2693892--2694547 Score: 468
Period size: 132 Copynumber: 5.0 Consensus size: 133
2693882 TAGAAAATAC
* * * ** ** * *
2693892 GAGTGAAATTTCGAAGAGACATTCGATTATTTTGAACAAACGGGGGATTGCAACCCAGCACGATA
1 GAGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACAAGAAATTGCAACCCAACACGTTA
* * * * * *
2693957 GGGCACTATTCCCCG-AATTGCCAAACATCG-AACAT--TTCTTCCGTTTTCAAGAGTTTTTAGA
66 GGGCACGATT-CCGGAAATTGCCAAATATCGAAAC-TCGTCCTT-CGTTTTAAAGAATTTTTA-A
*
2694018 AA-ACGT
127 AAGACCT
* ** * ** * *
2694024 GAGTGAAA-TTCTAAAGGGATCTTCGATCGTTTTGAACAAATGAA-AAAGCGCAACCCAGCACGA
1 GAGTGAAATTTC-AAAGGGATATTCGATTATTTTGAACAAA-CAAGAAATTGCAACCCAACACGT
* * * **
2694087 TAGGGCACGATTCTC-G-AATTGCCAAACATCG-AACATCG-CATTTGTTTTAAAGGGTTTTCTT
64 TAGGGCACGATTC-CGGAAATTGCCAAATATCGAAAC-TCGTCCTTCGTTTTAAA-GAATTT-TT
* *
2694148 AAAAAAAACAT
125 --AAAAGACCT
* * * ** * ** * *
2694159 GAATGAAAACTT-AAAGGAACGTTCGATTATTTTGAACAAACGAGAAATCACAACCCAGCACGAT
1 GAGTG-AAATTTCAAAGGGATATTCGATTATTTTGAACAAACAAGAAATTGCAACCCAACACGTT
* ** * * * * * *
2694223 AGGGCATGA-TCCCCAAATTGTCAAACACCGAGTA-TTG-CCTTCGTTTTAAAGGATTTTTAAAA
65 AGGGCACGATTCCGGAAATTGCCAAATATCGA-AACTCGTCCTTCGTTTTAAAGAATTTTTAAAA
2694285 GACCT
129 GACCT
* *
2694290 GAGTGAAATTTCAAAGGGATATTTGATTATTTTGAGCAAACAAGAAATTGCAACCCAACACGTTA
1 GAGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACAAGAAATTGCAACCCAACACGTTA
* ** *
2694355 GGGCGCGATTCCGCG-AATTGCCAAATATC-AAACTTTTCCTTCATTTTAAAGAATTTTTAAAAG
66 GGGCACGATTCCG-GAAATTGCCAAATATCGAAACTCGTCCTTCGTTTTAAAGAATTTTTAAAAG
*
2694418 GCAC-
130 AC-CT
** **
2694422 GAGTGAAATTTTGAAGGGATATTCGATTATTTTGAACAAACGCGAAATTGCAACCCAACACGTTA
1 GAGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACAAGAAATTGCAACCCAACACGTTA
* *
2694487 GGGCACTATTCCGGAAATTGCCAAATATCGAATCTCGT-CTTCGTTTTAAAGAATTTTTAAA
66 GGGCACGATTCCGGAAATTGCCAAATATCGAAACTCGTCCTTCGTTTTAAAGAATTTTTAAA
2694548 TGAATACTTA
Statistics
Matches: 421, Mismatches: 78, Indels: 50
0.77 0.14 0.09
Matches are distributed among these distances:
130 6 0.01
131 96 0.23
132 208 0.49
133 11 0.03
134 11 0.03
135 83 0.20
136 3 0.01
137 3 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (133 bp):
GAGTGAAATTTCAAAGGGATATTCGATTATTTTGAACAAACAAGAAATTGCAACCCAACACGTTA
GGGCACGATTCCGGAAATTGCCAAATATCGAAACTCGTCCTTCGTTTTAAAGAATTTTTAAAAGA
CCT
Found at i:2697565 original size:5 final size:5
Alignment explanation
Indices: 2697555--2697582 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
2697545 CTGTGTGATC
2697555 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
2697583 CACAGTCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:2698995 original size:18 final size:17
Alignment explanation
Indices: 2698974--2699025 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 17
2698964 ACTTTGGGTT
2698974 TTTTATAAATATTTTGAA
1 TTTTA-AAATATTTTGAA
2698992 TTTTAAAA-A--TT--A
1 TTTTAAAATATTTTGAA
2699004 TTTTAAAAATATTTTGAA
1 TTTT-AAAATATTTTGAA
2699022 TTTT
1 TTTT
2699026 TTTTGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
12 5 0.18
13 4 0.14
14 3 0.11
16 3 0.11
17 3 0.11
18 10 0.36
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (17 bp):
TTTTAAAATATTTTGAA
Found at i:2709436 original size:21 final size:21
Alignment explanation
Indices: 2709410--2709542 Score: 124
Period size: 21 Copynumber: 6.3 Consensus size: 21
2709400 TGAATATGCC
* * *
2709410 AACAGAAGCTAACAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * *
2709431 AACAGAAACTCATAAGTGTTA
1 AACAGAAGCTCATAAGAGCTA
2709452 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
2709473 AACAAAAACTCGTAAGAGATG
1 AACAGAAGCTCATAAGAGCTA
* * *
2709494 AACAGAAGCTCGTAAGAGATG
1 AACAGAAGCTCATAAGAGCTA
2709515 AACAGAAGCTCGA-AAGAGCTA
1 AACAGAAGCTC-ATAAGAGCTA
2709536 AACAGAA
1 AACAGAA
2709543 AGTAAAACAT
Statistics
Matches: 92, Mismatches: 19, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
21 92 1.00
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.14
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:2709458 original size:42 final size:42
Alignment explanation
Indices: 2709410--2709542 Score: 142
Period size: 42 Copynumber: 3.2 Consensus size: 42
2709400 TGAATATGCC
* * * *
2709410 AACAGAAGCTAACAAGAGCTGAACAGAAACTCATAAGTGTTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGATA
* * * *
2709452 AACAGAAGCTCATAAGAGCTAAACAAAAACTCGTAAGAGATG
1 AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGATA
* * * *
2709494 AACAGAAGCTCGTAAGAGATGAACAGAAGCTCGA-AAGAGCTA
1 AACAGAAGCTCATAAGAGCTGAACAGAAACTC-ATAAGAGATA
2709536 AACAGAA
1 AACAGAA
2709543 AGTAAAACAT
Statistics
Matches: 74, Mismatches: 16, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.14
Consensus pattern (42 bp):
AACAGAAGCTCATAAGAGCTGAACAGAAACTCATAAGAGATA
Found at i:2730460 original size:17 final size:17
Alignment explanation
Indices: 2730438--2730474 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2730428 ATGTCTAATA
* *
2730438 TTATCTAGAGTTGTCGT
1 TTATCTAGAGGTGTCAT
2730455 TTATCTAGAGGTGTCAT
1 TTATCTAGAGGTGTCAT
2730472 TTA
1 TTA
2730475 CACTGACCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.22, C:0.11, G:0.22, T:0.46
Consensus pattern (17 bp):
TTATCTAGAGGTGTCAT
Found at i:2733229 original size:16 final size:16
Alignment explanation
Indices: 2733196--2733225 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2733186 TTATTAATAT
2733196 TTTTATTTATTTCTTA
1 TTTTATTTATTTCTTA
2733212 TTTTA-TTATTTCTT
1 TTTTATTTATTTCTT
2733226 TATTACTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTATTTCTTA
Found at i:2735524 original size:30 final size:30
Alignment explanation
Indices: 2735490--2735550 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2735480 TCCTTAACTC
*
2735490 AAACTTTGGCAAAATTACAATTTTTCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
2735520 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
2735550 A
1 A
2735551 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:2735835 original size:30 final size:30
Alignment explanation
Indices: 2735801--2735861 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
2735791 TCCTTAACTC
*
2735801 AAACTTTGGCAAAATTACAATTTTTCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
* * * *
2735831 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
2735861 A
1 A
2735862 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.39
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:2735949 original size:311 final size:311
Alignment explanation
Indices: 2735386--2736006 Score: 1242
Period size: 311 Copynumber: 2.0 Consensus size: 311
2735376 CTTTCCCGAT
2735386 TTTCAATTTTTCTCCCATTCTAGATTCAAATCTCATTTTCCGGGATCTAAAACATCATATTTTAC
1 TTTCAATTTTTCTCCCATTCTAGATTCAAATCTCATTTTCCGGGATCTAAAACATCATATTTTAC
2735451 TTATTTAATTAATGTAATATTCAAAACAGTCCTTAACTCAAACTTTGGCAAAATTACAATTTTTC
66 TTATTTAATTAATGTAATATTCAAAACAGTCCTTAACTCAAACTTTGGCAAAATTACAATTTTTC
2735516 CCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAATTCATCCCTTATTC
131 CCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAATTCATCCCTTATTC
2735581 TTATGTTTTATGGAATGTTGATCAGTTTTCCCTTCTATGGCAACATCAAATTCTCACTCTAACAC
196 TTATGTTTTATGGAATGTTGATCAGTTTTCCCTTCTATGGCAACATCAAATTCTCACTCTAACAC
2735646 ATAGTTATGTACAATAACAACTTTTACCGATTAAACCGTTTTACTCATTTC
261 ATAGTTATGTACAATAACAACTTTTACCGATTAAACCGTTTTACTCATTTC
2735697 TTTCAATTTTTCTCCCATTCTAGATTCAAATCTCATTTTCCGGGATCTAAAACATCATATTTTAC
1 TTTCAATTTTTCTCCCATTCTAGATTCAAATCTCATTTTCCGGGATCTAAAACATCATATTTTAC
2735762 TTATTTAATTAATGTAATATTCAAAACAGTCCTTAACTCAAACTTTGGCAAAATTACAATTTTTC
66 TTATTTAATTAATGTAATATTCAAAACAGTCCTTAACTCAAACTTTGGCAAAATTACAATTTTTC
2735827 CCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAATTCATCCCTTATTC
131 CCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAATTCATCCCTTATTC
2735892 TTATGTTTTATGGAATGTTGATCAGTTTTCCCTTCTATGGCAACATCAAATTCTCACTCTAACAC
196 TTATGTTTTATGGAATGTTGATCAGTTTTCCCTTCTATGGCAACATCAAATTCTCACTCTAACAC
2735957 ATAGTTATGTACAATAACAACTTTTACCGATTAAACCGTTTTACTCATTT
261 ATAGTTATGTACAATAACAACTTTTACCGATTAAACCGTTTTACTCATTT
2736007 TTGCTTAAAA
Statistics
Matches: 310, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
311 310 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (311 bp):
TTTCAATTTTTCTCCCATTCTAGATTCAAATCTCATTTTCCGGGATCTAAAACATCATATTTTAC
TTATTTAATTAATGTAATATTCAAAACAGTCCTTAACTCAAACTTTGGCAAAATTACAATTTTTC
CCCTAAACTTTTGCATATTTACACTTTTGCCCCTAGGCTCGGGAATTAAAATTCATCCCTTATTC
TTATGTTTTATGGAATGTTGATCAGTTTTCCCTTCTATGGCAACATCAAATTCTCACTCTAACAC
ATAGTTATGTACAATAACAACTTTTACCGATTAAACCGTTTTACTCATTTC
Found at i:2738708 original size:43 final size:43
Alignment explanation
Indices: 2738624--2738709 Score: 104
Period size: 43 Copynumber: 2.0 Consensus size: 43
2738614 TATGTGATTC
* *
2738624 CGATATGTGTTTACGAGTAAGACCCTGTCTGGGAAAGTGGCAT
1 CGATATGTGGTTACGAGTAAGACCCTGTCTAGGAAAGTGGCAT
* *
2738667 CGATATGTGGTTAC-ATGTAAGACCAC-GTCTAGGACATTGGCAT
1 CGATATGTGGTTACGA-GTAAGACC-CTGTCTAGGAAAGTGGCAT
2738710 TGTACAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
42 1 0.03
43 35 0.95
44 1 0.03
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (43 bp):
CGATATGTGGTTACGAGTAAGACCCTGTCTAGGAAAGTGGCAT
Found at i:2743640 original size:41 final size:40
Alignment explanation
Indices: 2743480--2743640 Score: 252
Period size: 40 Copynumber: 4.0 Consensus size: 40
2743470 AAAAGGTCGT
2743480 TATAGATCGAGCATTAGCGGCGCTTTTTAAAAAACGCCGC
1 TATAGATCGAGCATTAGCGGCGCTTTTTAAAAAACGCCGC
* *
2743520 TATAGATCGAGTATTAGCGGCGCTTTTTAAAAAACACCGC
1 TATAGATCGAGCATTAGCGGCGCTTTTTAAAAAACGCCGC
*
2743560 TATAGATCTAGCATTAGCGGCGCTTTTTAAAAAACGCCGC
1 TATAGATCGAGCATTAGCGGCGCTTTTTAAAAAACGCCGC
* *
2743600 TATAGAATCGAGCATTA-CTGGCGCTTTCTAAAAAATGCCGC
1 TATAG-ATCGAGCATTAGC-GGCGCTTTTTAAAAAACGCCGC
2743641 AAAAAACATT
Statistics
Matches: 111, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 81 0.73
41 30 0.27
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
TATAGATCGAGCATTAGCGGCGCTTTTTAAAAAACGCCGC
Done.