Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 44 of 185
Found at i:12398032 original size:39 final size:39
Alignment explanation
Indices: 12397977--12398098 Score: 125
Period size: 39 Copynumber: 3.3 Consensus size: 39
12397967 TTGATACATT
*
12397977 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTAC
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTGTTAC
* ** *
12398016 TATGTGGTGTACTATTA---A-TT--ATGTAT-TTGGATA-
1 TATGTGGTGTAATATTATGCACTTGGA-CAATGTT-GTTAC
12398049 TATGTGGTGTAATATTATGCACTTGGACAATGTTGTTAC
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTGTTAC
12398088 TATGTGGTGTA
1 TATGTGGTGTA
12398099 CCATTAATTA
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
33 19 0.30
34 4 0.06
35 2 0.03
36 2 0.03
37 2 0.03
38 5 0.08
39 30 0.47
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.43
Consensus pattern (39 bp):
TATGTGGTGTAATATTATGCACTTGGACAATGTTGTTAC
Found at i:12398094 original size:72 final size:72
Alignment explanation
Indices: 12397977--12398120 Score: 270
Period size: 72 Copynumber: 2.0 Consensus size: 72
12397967 TTGATACATT
*
12397977 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACTATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
12398042 TTGGATA
66 TTGGATA
*
12398049 TATGTGGTGTAATATTATGCACTTGGACAATGTTGTTACTATGTGGTGTACCATTAATTATGTAT
1 TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
12398114 TTGGATA
66 TTGGATA
12398121 ATATTATTAT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.26, C:0.08, G:0.22, T:0.44
Consensus pattern (72 bp):
TATGTGGTGTAATATTATGCACTTGGACAATGTTCTTACTATGTGGTGTACCATTAATTATGTAT
TTGGATA
Found at i:12398331 original size:14 final size:14
Alignment explanation
Indices: 12398312--12398339 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12398302 ACAATTTTTT
12398312 AATATATATTAATA
1 AATATATATTAATA
12398326 AATATATATTAATA
1 AATATATATTAATA
12398340 TATGTAAAAT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATATATATTAATA
Found at i:12398413 original size:32 final size:33
Alignment explanation
Indices: 12398372--12398456 Score: 102
Period size: 32 Copynumber: 2.6 Consensus size: 33
12398362 AACTTTTCCG
* *
12398372 GAAAATATTTT-CAGGAAATCTGCCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACAGCA
* *
12398404 GAAAATATTTTACA-CAGATTTACCAAACAGCA
1 GAAAATATTTTACAGCAAATCTACCAAACAGCA
* *
12398436 GAAAATATTTTCCAGTAAATC
1 GAAAATATTTTACAGCAAATC
12398457 ATTTTACAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
32 38 0.88
33 5 0.12
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.26
Consensus pattern (33 bp):
GAAAATATTTTACAGCAAATCTACCAAACAGCA
Found at i:12398474 original size:20 final size:20
Alignment explanation
Indices: 12398449--12398488 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
12398439 AATATTTTCC
*
12398449 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
12398469 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
12398489 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:12398494 original size:34 final size:35
Alignment explanation
Indices: 12398437--12398503 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
12398427 CAAACAGCAG
*
12398437 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
12398472 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
12398504 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:12398495 original size:14 final size:14
Alignment explanation
Indices: 12398472--12398511 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12398462 ACAGAAAAGT
*
12398472 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
12398486 AAATCATTTTACGG
1 AAAACATTTTACAG
12398500 AAAACATTTTAC
1 AAAACATTTTAC
12398512 TGCCAAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:12399073 original size:41 final size:42
Alignment explanation
Indices: 12398983--12399082 Score: 109
Period size: 41 Copynumber: 2.4 Consensus size: 42
12398973 TTGCAATTTC
* * *
12398983 TCCACAGCTCGTATGAGCAACATCGTGTAGCTAACATCCTGA
1 TCCATAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGA
12399025 -CCTATAGCTCGTGTGAGCAGA-AT-GTATAGCTAACAT-CTCGA
1 TCC-ATAGCTCGTGTGAGCA-ACATCGTATAGCTAACATCCT-GA
*
12399066 TCCATAGCTTGTGTGAG
1 TCCATAGCTCGTGTGAG
12399083 AAGACCTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
40 2 0.04
41 29 0.58
42 18 0.36
43 1 0.02
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (42 bp):
TCCATAGCTCGTGTGAGCAACATCGTATAGCTAACATCCTGA
Found at i:12400002 original size:20 final size:22
Alignment explanation
Indices: 12399979--12400020 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
12399969 TTTGGTGTTT
12399979 TGAAA-GTGCTTTTAAC-CATG
1 TGAAATGTGCTTTTAACACATG
12399999 TGAAATGTGCTTTTAACACATG
1 TGAAATGTGCTTTTAACACATG
12400021 GGCACCCCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.25
21 11 0.55
22 4 0.20
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (22 bp):
TGAAATGTGCTTTTAACACATG
Found at i:12401528 original size:19 final size:20
Alignment explanation
Indices: 12401506--12401551 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
12401496 TTAATTTAAG
*
12401506 TAATTTAGTTTAATT-ACCT
1 TAATTTAGCTTAATTAACCT
* *
12401525 TAATTTCGCTTAATTAACTT
1 TAATTTAGCTTAATTAACCT
12401545 TAATTTA
1 TAATTTA
12401552 ATTTTTAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (20 bp):
TAATTTAGCTTAATTAACCT
Found at i:12409275 original size:45 final size:45
Alignment explanation
Indices: 12409174--12409357 Score: 212
Period size: 45 Copynumber: 4.1 Consensus size: 45
12409164 AATAATAACA
* * * *
12409174 GATACACGGTGG-ATCAGCACATAGC-ACCACCCTTATAGTCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
* ** * * *
12409217 GATACTCAATGGAATCAGCACATAGTAACCACCTTCATAATCAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
12409262 -AGTACCCGGTGGAATCAACACACAGCAACCACCTTTATAATCAAT
1 GA-TACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
* *
12409307 GATACCTGGTGGAATCAGCACACAGCAACCACCTTTATAATAAAT
1 GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
*
12409352 GGTACC
1 GATACC
12409358 TGGTACACGT
Statistics
Matches: 119, Mismatches: 18, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
43 9 0.08
44 13 0.11
45 96 0.81
46 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.15, T:0.22
Consensus pattern (45 bp):
GATACCCGGTGGAATCAGCACACAGCAACCACCTTTATAATCAAT
Found at i:12415893 original size:28 final size:26
Alignment explanation
Indices: 12415869--12415949 Score: 67
Period size: 27 Copynumber: 3.0 Consensus size: 26
12415859 TTGTAAAACT
12415869 TAATAA-AAAATCATAGAAATATAAAAA
1 TAATAACAAAAT-ATAGAAA-ATAAAAA
*
12415896 TCATAACAAAATATAGAAAATAAGATAA
1 TAATAACAAAATATAGAAAATAA-A-AA
* * * *
12415924 AAATTACAAAA-AAAGATAATAAAAA
1 TAATAACAAAATATAGAAAATAAAAA
12415949 T
1 T
12415950 TATTTATGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
25 2 0.05
26 5 0.11
27 22 0.50
28 15 0.34
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (26 bp):
TAATAACAAAATATAGAAAATAAAAA
Found at i:12417200 original size:31 final size:31
Alignment explanation
Indices: 12417136--12417200 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
12417126 AAAAAAATAT
* *
12417136 ATTTTTTTCATAATTTTCTATATTTTTTGTA
1 ATTTTTTTCATAATTTTCTATATTATTTATA
* *
12417167 ATTTTTTTTATCATTTT-TATAATTATTTATA
1 ATTTTTTTCATAATTTTCTAT-ATTATTTATA
12417198 ATT
1 ATT
12417201 ATTATTATGA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.68
Consensus pattern (31 bp):
ATTTTTTTCATAATTTTCTATATTATTTATA
Found at i:12417369 original size:27 final size:25
Alignment explanation
Indices: 12417329--12417405 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 25
12417319 AGTTTTTCTG
* *
12417329 ATTTTTTATTAATTTTTATATTTAT
1 ATTTTCTAATAATTTTTATATTTAT
*
12417354 AATTTTCTAAATAATTTTTATAATGGTAT
1 -ATTTTCT-AATAATTTTTAT-AT-TTAT
* *
12417383 GTTTTCTATTAATTTTTATATTT
1 ATTTTCTAATAATTTTTATATTT
12417406 TTTTAAAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 1 0.02
26 8 0.19
27 22 0.52
28 8 0.19
29 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (25 bp):
ATTTTCTAATAATTTTTATATTTAT
Found at i:12419123 original size:24 final size:21
Alignment explanation
Indices: 12419086--12419142 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
12419076 TATTTATAAA
12419086 ATTTTTTTAT-AATTTTGTATGT
1 ATTTTTTTATAAATTTTG--TGT
12419108 ATTTTTTTATAGAATTTTGTGT
1 ATTTTTTTATA-AATTTTGTGT
*
12419130 ATTTTTATATAAA
1 ATTTTTTTATAAA
12419143 AAAAGCTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.06
22 23 0.72
24 7 0.22
ACGTcount: A:0.28, C:0.00, G:0.09, T:0.63
Consensus pattern (21 bp):
ATTTTTTTATAAATTTTGTGT
Found at i:12436710 original size:16 final size:17
Alignment explanation
Indices: 12436689--12436729 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
12436679 TTAATTTTAT
12436689 ATAAAAATTA-TAAAAA
1 ATAAAAATTATTAAAAA
12436705 ATAAAAATTATTTAAAAA
1 ATAAAAATTA-TTAAAAA
12436723 ATAAAAA
1 ATAAAAA
12436730 GTTCTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 10 0.43
18 13 0.57
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
ATAAAAATTATTAAAAA
Found at i:12436742 original size:19 final size:18
Alignment explanation
Indices: 12436689--12436744 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
12436679 TTAATTTTAT
12436689 ATAAAAA-T-TATAAAAA
1 ATAAAAATTATATAAAAA
*
12436705 ATAAAAATTATTTAAAAA
1 ATAAAAATTATATAAAAA
*
12436723 ATAAAAAGTTCTATATAAAA
1 ATAAAAA-TTATATA-AAAA
12436743 AT
1 AT
12436745 TCTAGAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.21
17 1 0.03
18 14 0.42
19 5 0.15
20 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAAAAATTATATAAAAA
Found at i:12444403 original size:20 final size:20
Alignment explanation
Indices: 12444349--12444404 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
12444339 TGAAAAAATC
** *
12444349 AAAGTATCGATACCCTTAGT
1 AAAGTATCGATACTTTTAAT
* * *
12444369 TAAGTATTGACACTTTTAAT
1 AAAGTATCGATACTTTTAAT
12444389 AAAGTATCGATACTTT
1 AAAGTATCGATACTTT
12444405 ATCAGGGTAT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (20 bp):
AAAGTATCGATACTTTTAAT
Found at i:12445290 original size:28 final size:28
Alignment explanation
Indices: 12445246--12445315 Score: 97
Period size: 28 Copynumber: 2.5 Consensus size: 28
12445236 AGAGGGCACT
*
12445246 GAAGTGCATTAACAGAATAGAACAACACC
1 GAAGTGC-TTATCAGAATAGAACAACACC
*
12445275 -AATGTGCTTATCAGAATAGAGCAACACC
1 GAA-GTGCTTATCAGAATAGAACAACACC
12445303 GAAGTGCTTATCA
1 GAAGTGCTTATCA
12445316 AAACAGAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
28 31 0.84
29 6 0.16
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (28 bp):
GAAGTGCTTATCAGAATAGAACAACACC
Found at i:12445323 original size:28 final size:28
Alignment explanation
Indices: 12445268--12445323 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
12445258 CAGAATAGAA
* *
12445268 CAACACCAATGTGCTTATCAGAATAGAG
1 CAACACCAATGTGCTTATCAAAACAGAG
12445296 CAACACCGAA-GTGCTTATCAAAACAGAG
1 CAACACC-AATGTGCTTATCAAAACAGAG
12445324 AGCTCATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 23 0.92
29 2 0.08
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (28 bp):
CAACACCAATGTGCTTATCAAAACAGAG
Found at i:12447372 original size:6 final size:6
Alignment explanation
Indices: 12447363--12447391 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12447353 ACATCTTATA
12447363 TGAATC TGAATC TGAATC TGAATC TGAAT
1 TGAATC TGAATC TGAATC TGAATC TGAAT
12447392 TCTGGGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (6 bp):
TGAATC
Found at i:12450303 original size:28 final size:28
Alignment explanation
Indices: 12450239--12450292 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
12450229 CGATGTGCTA
* *
12450239 AAACCACC-AATAATCAATAATGCAATG
1 AAACTACCAAATAATAAATAATGCAATG
12450266 AAACTACCAAATAATAAATAATGCAAT
1 AAACTACCAAATAATAAATAATGCAAT
12450293 ATAATCGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 7 0.29
28 17 0.71
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.20
Consensus pattern (28 bp):
AAACTACCAAATAATAAATAATGCAATG
Found at i:12451833 original size:25 final size:25
Alignment explanation
Indices: 12451805--12451854 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
12451795 TTTTACAACC
* *
12451805 TTAGAAAACATACCCCATTTAGAGA
1 TTAGAAAACATAACACATTTAGAGA
**
12451830 TTAGAACTCATAACACATTTAGAGA
1 TTAGAAAACATAACACATTTAGAGA
12451855 ATTTTGTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.12, T:0.26
Consensus pattern (25 bp):
TTAGAAAACATAACACATTTAGAGA
Found at i:12460584 original size:19 final size:20
Alignment explanation
Indices: 12460560--12460599 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
12460550 TAATAGGGAC
12460560 TTTTGGAGGGGCTA-AATAT
1 TTTTGGAGGGGCTAGAATAT
12460579 TTTTGGAGGGGCTAGAATAT
1 TTTTGGAGGGGCTAGAATAT
12460599 T
1 T
12460600 CAGCTGTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.25, C:0.05, G:0.33, T:0.38
Consensus pattern (20 bp):
TTTTGGAGGGGCTAGAATAT
Found at i:12461256 original size:37 final size:37
Alignment explanation
Indices: 12461152--12461256 Score: 122
Period size: 37 Copynumber: 2.8 Consensus size: 37
12461142 TGTTTTCGGT
* * *
12461152 TGGACTAGCTCTT-CAGAGCAATTGGCATGATATCGAG
1 TGGATTAGCTCTTAC-GAGCAATTGGCATGTTATCGAA
* * *
12461189 TGGATTAGCTCTTATGAGCAACTGGTATGTTATCGAA
1 TGGATTAGCTCTTACGAGCAATTGGCATGTTATCGAA
**
12461226 TGGATTAGCTCTTACGAGTGATTGGCATGTT
1 TGGATTAGCTCTTACGAGCAATTGGCATGTT
12461257 TTGGTTGGAA
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (37 bp):
TGGATTAGCTCTTACGAGCAATTGGCATGTTATCGAA
Found at i:12468348 original size:24 final size:24
Alignment explanation
Indices: 12468302--12468348 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
12468292 TTTTAATTAC
* *
12468302 ACCATGAGAAATTTGAATGATTTT
1 ACCATGAAAAATTTGAATAATTTT
12468326 ACCATGAAAAA-TTGTAATAATTT
1 ACCATGAAAAATTTG-AATAATTT
12468349 GATTGTGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.36
Consensus pattern (24 bp):
ACCATGAAAAATTTGAATAATTTT
Found at i:12475654 original size:6 final size:6
Alignment explanation
Indices: 12475643--12475671 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
12475633 TAGTTTCCAA
12475643 AAATGG AAATGG AAATGG AAATGG AAATG
1 AAATGG AAATGG AAATGG AAATGG AAATG
12475672 ATTCATTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.31, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:12477483 original size:12 final size:12
Alignment explanation
Indices: 12477458--12477494 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
12477448 ATCATCATCA
12477458 TCTTC-TCCTCC
1 TCTTCTTCCTCC
*
12477469 TCTTCTTCTTCC
1 TCTTCTTCCTCC
12477481 TCTTCTTCCTCC
1 TCTTCTTCCTCC
12477493 TC
1 TC
12477495 CTCCTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 5 0.22
12 18 0.78
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (12 bp):
TCTTCTTCCTCC
Found at i:12484594 original size:35 final size:35
Alignment explanation
Indices: 12484553--12484625 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
12484543 TACATAATTA
12484553 ACTAAATTACATAGTATTTACTACAAATTATTTAT
1 ACTAAATTACATAGTATTTACTACAAATTATTTAT
* * * **
12484588 ACTAAATTATATAGTGTTTATTATTAATTATTTAT
1 ACTAAATTACATAGTATTTACTACAAATTATTTAT
12484623 ACT
1 ACT
12484626 TGGTAAATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (35 bp):
ACTAAATTACATAGTATTTACTACAAATTATTTAT
Found at i:12490264 original size:4 final size:4
Alignment explanation
Indices: 12490255--12490296 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
12490245 AAGCAAAATA
12490255 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
12490297 ATATTTCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:12492998 original size:23 final size:23
Alignment explanation
Indices: 12492972--12493015 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
12492962 TGTCAAATTG
*
12492972 GATTTCTTAATGGGATGAGAATA
1 GATTTCTTAATGGGAAGAGAATA
12492995 GATTTCTTAATGGGAAGAGAA
1 GATTTCTTAATGGGAAGAGAA
12493016 ATGGATAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (23 bp):
GATTTCTTAATGGGAAGAGAATA
Found at i:12493881 original size:28 final size:27
Alignment explanation
Indices: 12493850--12493962 Score: 95
Period size: 28 Copynumber: 4.1 Consensus size: 27
12493840 TTTTAATAAA
*
12493850 TTTATATTTTTTATAATTTATTAGATTT
1 TTTATATTTTTTATAATTTATAAG-TTT
*
12493878 TTTATATTTTATA-ATATTTATAAGTTT
1 TTTATATTTTTTATA-ATTTATAAGTTT
* * *
12493905 TTAACT-TTTTTTATAAGTTTATATGCTT
1 TTTA-TATTTTTTATAA-TTTATAAGTTT
* ** *
12493933 TTAATATTTTTTATTTTTTATAAATTT
1 TTTATATTTTTTATAATTTATAAGTTT
12493960 TTT
1 TTT
12493963 TCTGATTTTT
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
27 25 0.37
28 43 0.63
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (27 bp):
TTTATATTTTTTATAATTTATAAGTTT
Found at i:12493896 original size:19 final size:19
Alignment explanation
Indices: 12493853--12493896 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
12493843 TAATAAATTT
*
12493853 ATATTTTTTATAATTTATT
1 ATATTTTTTATAATTTATA
* *
12493872 AGATTTTTTATATTTTATA
1 ATATTTTTTATAATTTATA
12493891 ATATTT
1 ATATTT
12493897 ATAAGTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
ATATTTTTTATAATTTATA
Found at i:12496090 original size:40 final size:38
Alignment explanation
Indices: 12496046--12496128 Score: 112
Period size: 38 Copynumber: 2.1 Consensus size: 38
12496036 TTAAAAATAT
* * *
12496046 TTATAGTAAAAACATTACCATAAATATAATAAATGTTTTA
1 TTATAGTAAAAACA-CA-AATAAATATAATAAATATTTTA
*
12496086 TTATATTAAAAACACAAATAAATATAATAAATATTTTA
1 TTATAGTAAAAACACAAATAAATATAATAAATATTTTA
12496124 TTATA
1 TTATA
12496129 TTACATACAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 25 0.64
39 1 0.03
40 13 0.33
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (38 bp):
TTATAGTAAAAACACAAATAAATATAATAAATATTTTA
Found at i:12499819 original size:102 final size:101
Alignment explanation
Indices: 12499637--12499940 Score: 374
Period size: 102 Copynumber: 2.9 Consensus size: 101
12499627 AGGTGAAAAG
* *
12499637 GCTCGATTCCGATGACATGAGCTCCTTCACCTTCACCTTCGTCTACTTCAGGATCCATCGTGTTG
1 GCTCGATTCCGATGAGATGAGCTCCTTCA---T---CTTCGTCTA-TTCAGGCTCCATCGTGTTG
*
12499702 CCATGGCCACCATCCTCCGCTCCAGCGTTAATATAGTTATAAA
59 CCATGGCCACCATCCTCTGCTCCAGCGTTAATATAGTTATAAA
* * *
12499745 GCTCGATTCCGATGAGATGAGCTCCTTCATCTTCCTCTATTACAGGCTCCCTCGTGTTTCCATGG
1 GCTCGATTCCGATGAGATGAGCTCCTTCATCTTCGTCTATT-CAGGCTCCATCGTGTTGCCATGG
* * * *
12499810 CCGCCATCCTCTACACCTGCGTTAATATAGTTATAAA
65 CCACCATCCTCTGCTCCAGCGTTAATATAGTTATAAA
* * * * **
12499847 GCGCGATTCCGATGAGCTCAACTCCTTCATCTTCGTCTATTTCAGGCTCTGTCGTGTTGCCATGG
1 GCTCGATTCCGATGAGATGAGCTCCTTCATCTTCGTCTA-TTCAGGCTCCATCGTGTTGCCATGG
*
12499912 CCACCATCCTCTGCTCCATCGTTAATATA
65 CCACCATCCTCTGCTCCAGCGTTAATATA
12499941 ATTAGGGATG
Statistics
Matches: 171, Mismatches: 23, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
101 2 0.01
102 138 0.81
103 2 0.01
105 1 0.01
108 28 0.16
ACGTcount: A:0.20, C:0.32, G:0.17, T:0.32
Consensus pattern (101 bp):
GCTCGATTCCGATGAGATGAGCTCCTTCATCTTCGTCTATTCAGGCTCCATCGTGTTGCCATGGC
CACCATCCTCTGCTCCAGCGTTAATATAGTTATAAA
Found at i:12504880 original size:51 final size:52
Alignment explanation
Indices: 12504828--12504927 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 52
12504818 AAAAATCAAT
*
12504828 TTTTATATATTATTTTAA-TTTTCTAAATTT-TA-TATTTATATATTATAGAA
1 TTTTATA-ATTATTTTAATTTTTCTAAATTTGAATTATTTATATATTATAGAA
* *
12504878 TTTTATAATTTTTTTAATTTTTTTTAAATTTGAATTATTTATATATTATA
1 TTTTATAATTATTTTAA-TTTTTCTAAATTTGAATTATTTATATATTATA
12504928 TATGATTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
49 9 0.21
50 7 0.16
51 11 0.26
52 1 0.02
53 15 0.35
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.63
Consensus pattern (52 bp):
TTTTATAATTATTTTAATTTTTCTAAATTTGAATTATTTATATATTATAGAA
Found at i:12504956 original size:87 final size:85
Alignment explanation
Indices: 12504801--12504961 Score: 196
Period size: 87 Copynumber: 1.9 Consensus size: 85
12504791 TCAAATACCT
* * **
12504801 TTTTTTTAATTTTTTATAAAAATCAATTTTTATATATTATTTTAATTTTCTAAATTTTATATTTA
1 TTTTTTTAATTTTTTATAAAAATCAATTTTTATATATTATTATAATTTTCTAAATTTTAAATCAA
*
12504866 TATATTATAGAATTTTATAA
66 TATAATATAGAATTTTATAA
* ** * * * *
12504886 TTTTTTTAATTTTTTTTAAATTTGAATTATTTATATATTATATATGATTTTTTACATTTTAAATC
1 TTTTTTTAATTTTTTATAAAAATCAATT-TTTATATATTAT-TATAATTTTCTAAATTTTAAATC
12504951 AATATAATATA
64 AATATAATATA
12504962 TGATATTTAA
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
85 24 0.39
86 12 0.19
87 26 0.42
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (85 bp):
TTTTTTTAATTTTTTATAAAAATCAATTTTTATATATTATTATAATTTTCTAAATTTTAAATCAA
TATAATATAGAATTTTATAA
Found at i:12530690 original size:23 final size:23
Alignment explanation
Indices: 12530664--12530707 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12530654 ACGCCAGAGA
*
12530664 GTGTAACAAGACAGCATCAAAAT
1 GTGTAACAAGACAGCACCAAAAT
*
12530687 GTGTAACAGGACAGCACCAAA
1 GTGTAACAAGACAGCACCAAA
12530708 GTGCGTAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (23 bp):
GTGTAACAAGACAGCACCAAAAT
Found at i:12530715 original size:23 final size:23
Alignment explanation
Indices: 12530666--12530715 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
12530656 GCCAGAGAGT
* *
12530666 GTAACAAGACAGCATCAAAATGT
1 GTAACAAGACAGCACCAAAATGC
* *
12530689 GTAACAGGACAGCACCAAAGTGC
1 GTAACAAGACAGCACCAAAATGC
12530712 GTAA
1 GTAA
12530716 ATAGATAGCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (23 bp):
GTAACAAGACAGCACCAAAATGC
Found at i:12540372 original size:21 final size:21
Alignment explanation
Indices: 12540305--12540372 Score: 50
Period size: 21 Copynumber: 3.2 Consensus size: 21
12540295 AAAAATACAT
*
12540305 AAAAGAGAAAAAGAAAAAAATAC
1 AAAA-AGAAAAAG-AAAAATTAC
** * *
12540328 -AAATTAAAAAG-AAATTTTC
1 AAAAAGAAAAAGAAAAATTAC
12540347 AAAAAAGAAAAAGAAAAATTAC
1 -AAAAAGAAAAAGAAAAATTAC
12540369 AAAA
1 AAAA
12540373 TAATATAGAT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 5 0.15
21 19 0.58
22 9 0.27
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (21 bp):
AAAAAGAAAAAGAAAAATTAC
Found at i:12541733 original size:16 final size:15
Alignment explanation
Indices: 12541712--12541759 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 15
12541702 CTTTTATGAC
12541712 AATTTTTAATTTTTGA
1 AATTTTTAATTTTT-A
12541728 AATTTTATATATTTTTA
1 AATTTT-TA-ATTTTTA
*
12541745 ATTTTTTTAATTTTT
1 A-ATTTTTAATTTTT
12541760 TTATTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 12 0.43
17 6 0.21
18 10 0.36
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (15 bp):
AATTTTTAATTTTTA
Found at i:12541756 original size:25 final size:24
Alignment explanation
Indices: 12541713--12541766 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
12541703 TTTTATGACA
12541713 ATTTTTAATTTTTGAAATTTTATAT
1 ATTTTTAATTTTTGAAATTTT-TAT
** *
12541738 ATTTTTAATTTTTTTAATTTTTTT
1 ATTTTTAATTTTTGAAATTTTTAT
12541762 ATTTT
1 ATTTT
12541767 ATTTTCCCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (24 bp):
ATTTTTAATTTTTGAAATTTTTAT
Found at i:12542432 original size:11 final size:11
Alignment explanation
Indices: 12542391--12542450 Score: 86
Period size: 11 Copynumber: 5.5 Consensus size: 11
12542381 AACTAAATCC
12542391 TTTCTCTC-AA
1 TTTCTCTCAAA
*
12542401 TTTCTCTCTAA
1 TTTCTCTCAAA
12542412 TATTCTCTCAAA
1 T-TTCTCTCAAA
*
12542424 TTCCTCTCAAA
1 TTTCTCTCAAA
12542435 TTTCTCTCAAA
1 TTTCTCTCAAA
12542446 TTTCT
1 TTTCT
12542451 ATTTAAAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
10 8 0.18
11 27 0.60
12 10 0.22
ACGTcount: A:0.23, C:0.28, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:12544300 original size:18 final size:18
Alignment explanation
Indices: 12544277--12544319 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12544267 TGCCAGGTCC
* *
12544277 GTATCCTAGCCCTTTTAT
1 GTATCCTAACCCTTATAT
12544295 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
12544313 GTTTCCT
1 GTATCCT
12544320 TTTTCTAGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:12544793 original size:49 final size:49
Alignment explanation
Indices: 12544740--12545007 Score: 464
Period size: 49 Copynumber: 5.5 Consensus size: 49
12544730 GTTTATATTA
* *
12544740 ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGGTATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
12544789 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
12544838 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
12544887 ATGTAATAAAATACAAAATAGTTTATTTTAAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
12544936 ATTTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
12544985 ATTTAATAAAATACAAAGTAGTT
1 ATGTAATAAAATACAAAATAGTT
12545008 AATATTCTTA
Statistics
Matches: 212, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 212 1.00
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:12548194 original size:124 final size:124
Alignment explanation
Indices: 12547792--12548204 Score: 709
Period size: 126 Copynumber: 3.3 Consensus size: 124
12547782 CCCAAACATG
** * * *
12547792 CTACTGTAGCAAAAATGCATCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCACCCGGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
*
12547857 TTGAAGCATTTTATATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAAGAC
66 TTGAAGCATTTT-TATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
12547917 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* * *
12547982 TTAAAGCCTTTTTTTATACTATTTGCTCAGAAACGTGAACTCGAAATTATTTTTTCAGGAC
66 TTGAAG-C-ATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
12548043 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
*
12548108 TTGAAGCATTTTTATACTATTTGCTCAGAAATGTCAACTCGAAATTATTTTTTCAGGAC
66 TTGAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
12548167 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
12548205 CTTAATAAAT
Statistics
Matches: 273, Mismatches: 13, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
124 87 0.32
125 66 0.24
126 116 0.42
127 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
Found at i:12548401 original size:13 final size:13
Alignment explanation
Indices: 12548383--12548416 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
12548373 AAATCCTAAA
*
12548383 AACCCTAAACCTT
1 AACCCTAAACCCT
12548396 AACCCT-AACCCT
1 AACCCTAAACCCT
12548408 AACCCTAAA
1 AACCCTAAA
12548417 AACCCAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.41, G:0.00, T:0.18
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:12558247 original size:18 final size:18
Alignment explanation
Indices: 12558224--12558261 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
12558214 AAAATTCACT
12558224 TAACAA-AATACTTATAAA
1 TAACAACAATACTTA-AAA
12558242 TAACAACTAATACTTAAAA
1 TAACAAC-AATACTTAAAA
12558261 T
1 T
12558262 TCATCATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 4 0.22
20 8 0.44
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (18 bp):
TAACAACAATACTTAAAA
Found at i:12561132 original size:28 final size:30
Alignment explanation
Indices: 12561100--12561171 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 30
12561090 CTGGATGGGT
12561100 AACC-TAATATAA-GTCAACTTGTGTGAAC
1 AACCTTAATATAATGTCAACTTGTGTGAAC
* * * *
12561128 AACCTTTATATAATTTCAGCTTGTGTGAGC
1 AACCTTAATATAATGTCAACTTGTGTGAAC
* *
12561158 AACATTGATATAAT
1 AACCTTAATATAAT
12561172 TTAAGATTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 4 0.11
29 7 0.19
30 25 0.69
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (30 bp):
AACCTTAATATAATGTCAACTTGTGTGAAC
Found at i:12561153 original size:30 final size:30
Alignment explanation
Indices: 12561117--12561173 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
12561107 TATAAGTCAA
* *
12561117 CTTGTGTGAACAACCTTTATATAATTTCAG
1 CTTGTGTGAACAACATTGATATAATTTCAG
*
12561147 CTTGTGTGAGCAACATTGATATAATTT
1 CTTGTGTGAACAACATTGATATAATTT
12561174 AAGATTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (30 bp):
CTTGTGTGAACAACATTGATATAATTTCAG
Found at i:12561869 original size:22 final size:22
Alignment explanation
Indices: 12561839--12561881 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12561829 ACACCAAAAC
*
12561839 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
12561861 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
12561882 AGCGCCGCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:12562091 original size:43 final size:43
Alignment explanation
Indices: 12561942--12562211 Score: 312
Period size: 43 Copynumber: 6.3 Consensus size: 43
12561932 TTTTAGAAAT
* *
12561942 AAACGCCGCTAAAGACCATGACCTTTAGCGGCGC-TTTCCCAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
12561984 AAACGCCACTAAAGACCAAGACCTTCAACGGCGCTTTTCCCA-
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * *
12562026 AAATGCCGCTAAAGACCAAGACCTTCAGCGACGCTATCCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * *
12562069 AAACGCCGCTAAAGACCAAGACCTTTAACGGCACTTTTACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* *
12562112 AAACGCCGCTATAA-ACCATGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTA-AAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
* * * * * *
12562155 AAACGCCGCTATAGGCCATGACCTTTAGCGACGCTTTTCCTAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
*
12562198 AAACGCCACTAAAG
1 AAACGCCGCTAAAG
12562212 GCACTTCTAC
Statistics
Matches: 193, Mismatches: 31, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
42 67 0.35
43 124 0.64
44 2 0.01
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.19
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCCCAC
Found at i:12563667 original size:41 final size:41
Alignment explanation
Indices: 12563609--12563758 Score: 264
Period size: 41 Copynumber: 3.6 Consensus size: 41
12563599 CTTAATTTAA
* * *
12563609 CAGATTCACCGGCACTTAGCTTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
12563651 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
12563692 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
12563733 CAGATCACCGGCACTTAGCCTGCTAG
1 CAGATCACCGGCACTTAGCCTGCTAG
12563759 ACGTATAGTC
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 101 0.96
42 4 0.04
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT
Found at i:12563787 original size:82 final size:82
Alignment explanation
Indices: 12563613--12563788 Score: 235
Period size: 82 Copynumber: 2.1 Consensus size: 82
12563603 ATTTAACAGA
* * *
12563613 TTCACCGGCACTTAGCTTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGA
** * *
12563678 TTTATAACCTGATTCAG
66 CGTATAACCTGAATAAG
* *
12563695 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGA
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGA
** *
12563760 CGTATAGTCTGAATAAT
66 CGTATAACCTGAATAAG
*
12563777 TTCACTGGCACT
1 TTCACCGGCACT
12563789 AAATCCGATT
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.30
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGA
CGTATAACCTGAATAAG
Found at i:12568823 original size:13 final size:13
Alignment explanation
Indices: 12568790--12568834 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
12568780 CCTTTATAAG
**
12568790 GGATTCAACTCTT
1 GGATTCAACTCCA
12568803 GGATTTCAACTCCA
1 GGA-TTCAACTCCA
*
12568817 GGATTCAACTCCC
1 GGATTCAACTCCA
12568830 GGATT
1 GGATT
12568835 TCGTATATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (13 bp):
GGATTCAACTCCA
Found at i:12569442 original size:22 final size:22
Alignment explanation
Indices: 12569417--12569459 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
12569407 GGAGACCAAT
12569417 TTTAGGGGGGAAAATTAGGGGG
1 TTTAGGGGGGAAAATTAGGGGG
*
12569439 TTTAGGGGGGAAATTTAGGGG
1 TTTAGGGGGGAAAATTAGGGG
12569460 AAAAAAAGGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.49, T:0.26
Consensus pattern (22 bp):
TTTAGGGGGGAAAATTAGGGGG
Found at i:12569920 original size:7 final size:7
Alignment explanation
Indices: 12569910--12570028 Score: 80
Period size: 7 Copynumber: 16.7 Consensus size: 7
12569900 TTATAAAACA
12569910 TAAACCC
1 TAAACCC
12569917 TAAACCCC
1 TAAA-CCC
12569925 T-AACCC
1 TAAACCC
*
12569931 TAAATCC
1 TAAACCC
*
12569938 TAAATCC
1 TAAACCC
* *
12569945 TAAATCT
1 TAAACCC
12569952 TAAACCCC
1 TAAA-CCC
*
12569960 TAAACCT
1 TAAACCC
12569967 TAAA-CC
1 TAAACCC
*
12569973 TCAACCC
1 TAAACCC
*
12569980 TTAAACCA
1 -TAAACCC
*
12569988 TAAACCA
1 TAAACCC
**
12569995 TAAACAA
1 TAAACCC
*
12570002 TAATCCC
1 TAAACCC
12570009 TAAACCC
1 TAAACCC
*
12570016 ATAATCCC
1 -TAAACCC
12570024 TAAAC
1 TAAAC
12570029 TATAATGATA
Statistics
Matches: 90, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
6 8 0.09
7 62 0.69
8 20 0.22
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:12569963 original size:15 final size:15
Alignment explanation
Indices: 12569928--12569972 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
12569918 AAACCCCTAA
*
12569928 CCCTAAATCCTAAA-
1 CCCTAAATCTTAAAC
*
12569942 TCCTAAATCTTAAAC
1 CCCTAAATCTTAAAC
*
12569957 CCCTAAACCTTAAAC
1 CCCTAAATCTTAAAC
12569972 C
1 C
12569973 TCAACCCTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.40, C:0.36, G:0.00, T:0.24
Consensus pattern (15 bp):
CCCTAAATCTTAAAC
Found at i:12570012 original size:14 final size:14
Alignment explanation
Indices: 12569981--12570034 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
12569971 CCTCAACCCT
* *
12569981 TAAACCATAAACCA
1 TAAACCATAATCCC
*
12569995 TAAACAATAATCCC
1 TAAACCATAATCCC
12570009 TAAACCCATAATCCC
1 TAAA-CCATAATCCC
*
12570024 TAAACTATAAT
1 TAAACCATAAT
12570035 GATAATTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 21 0.62
15 13 0.38
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:12571047 original size:41 final size:40
Alignment explanation
Indices: 12570981--12571306 Score: 314
Period size: 41 Copynumber: 7.7 Consensus size: 40
12570971 AATATTTTTT
* * *
12570981 GCGGCGCTTTTTCAAAAATGTCGCTAAAGACCAAAGCATTA
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAGACCAGAGCATTA
* * **
12571022 GTGGCGCTTCTTAAAAAACGCCGCTAAA-AATAGAGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTAAAGACCAGAGCATTA
12571062 GCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGACCAGAGCATTA
* *
12571103 GCGACGCTTTTCCAAAAACGCCGCTAAAGACCAAAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCTAAAGACCAGAGCATTA
*
12571144 GCGGCGCTTTTCCAAAAACGCTGCTAAAGCCCAGAGCAAGCCTAGAGCATTA
1 GCGGCGCTTTT-CAAAAACGCCGCT--A----A-AG--A-CC-AGAGCATTA
*
12571196 GCGGTGCTTCTTCAAAAACGCCGCTAAAGACCAGAGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTAAAGACCAGAGCATTA
* *
12571237 GCGGCGCTTCTTCAAAAACACCGCTAAAGCCCCA-AGCATTA
1 GCGGCGCTT-TTCAAAAACGCCGCTAAAG-ACCAGAGCATTA
* * *
12571278 GTGGCACTTTTTAAAAAACGCCGCTAAAG
1 GCGGCGC-TTTTCAAAAACGCCGCTAAAG
12571307 GCTCAAAAAC
Statistics
Matches: 243, Mismatches: 25, Indels: 34
0.80 0.08 0.11
Matches are distributed among these distances:
39 2 0.01
40 34 0.14
41 158 0.65
42 7 0.03
43 2 0.01
45 2 0.01
46 1 0.00
47 1 0.00
48 2 0.01
50 2 0.01
51 2 0.01
52 28 0.12
53 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.20
Consensus pattern (40 bp):
GCGGCGCTTTTCAAAAACGCCGCTAAAGACCAGAGCATTA
Found at i:12571253 original size:93 final size:93
Alignment explanation
Indices: 12571094--12571268 Score: 273
Period size: 93 Copynumber: 1.9 Consensus size: 93
12571084 GCTAAAGACC
12571094 AGAGCATTAGCGACGCTTTTCCAAAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTTTTCCAA
1 AGAGCATTAGCGACGCTTTTCCAAAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTTTTCCAA
* *
12571159 AAACGCTGCTAAAGCCCAGAGCAAGCCT
66 AAACACCGCTAAAGCCCAGAGCAAGCCT
** *
12571187 AGAGCATTAGCGGTGCTTCTT-CAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTCTT-C
1 AGAGCATTAGCGACGCTT-TTCCAAAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTT-TTCC
12571250 AAAAACACCGCTAAAGCCC
64 AAAAACACCGCTAAAGCCC
12571269 CAAGCATTAG
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
93 71 0.95
94 4 0.05
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.18
Consensus pattern (93 bp):
AGAGCATTAGCGACGCTTTTCCAAAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTTTTCCAA
AAACACCGCTAAAGCCCAGAGCAAGCCT
Found at i:12571295 original size:134 final size:134
Alignment explanation
Indices: 12571052--12571306 Score: 388
Period size: 134 Copynumber: 1.9 Consensus size: 134
12571042 CCGCTAAAAA
12571052 TAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGACGCTTTTCCA
1 TAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGACGCTTTTCCA
* * * *
12571117 AAAACGCCGCTAAAGACCAAAGCATTAGCGGCGCTTTTCCAAAAACGCTGCTAAAGCCCAGAGCA
66 AAAACACCGCTAAAGACCAAAGCATTAGCGGCACTTTTCAAAAAACGCCGCTAAAGCCCAGAGCA
12571182 AGCC
131 AGCC
* *
12571186 TAGAGCATTAGCGGTGCTTCTT-CAAAAACGCCGCTAAAGACCAGAGCATTAGCGGCGCTTCTT-
1 TAGAGCATTAGCGGCGCTT-TTCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGACGCTT-TTC
* * * *
12571249 CAAAAACACCGCTAAAGCCCCAAGCATTAGTGGCACTTTTTAAAAAACGCCGCTAAAG
64 CAAAAACACCGCTAAAGACCAAAGCATTAGCGGCACTTTTCAAAAAACGCCGCTAAAG
12571307 GCTCAAAAAC
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
134 105 0.96
135 4 0.04
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (134 bp):
TAGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGACCAGAGCATTAGCGACGCTTTTCCA
AAAACACCGCTAAAGACCAAAGCATTAGCGGCACTTTTCAAAAAACGCCGCTAAAGCCCAGAGCA
AGCC
Found at i:12585076 original size:17 final size:17
Alignment explanation
Indices: 12585051--12585083 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
12585041 TAATGATTAA
12585051 AAATCATTAAAAATTATC
1 AAATCATT-AAAATTATC
12585069 AAAT-ATTAAAATTAT
1 AAATCATTAAAATTAT
12585084 ATAAACTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.53
17 3 0.20
18 4 0.27
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATCATTAAAATTATC
Found at i:12585088 original size:10 final size:10
Alignment explanation
Indices: 12585075--12585159 Score: 61
Period size: 10 Copynumber: 8.5 Consensus size: 10
12585065 TATCAAATAT
12585075 TAAAATTATA
1 TAAAATTATA
*
12585085 TAAACTTATA
1 TAAAATTATA
*
12585095 -AAAATTATTT
1 TAAAATTA-TA
*
12585105 TAAAA-AATA
1 TAAAATTATA
12585114 TAATAAATTATA
1 T-A-AAATTATA
12585126 -AAAATTA-A
1 TAAAATTATA
*
12585134 TAAAATATATT
1 TAAAAT-TATA
*
12585145 TAAAATTTTA
1 TAAAATTATA
12585155 TAAAA
1 TAAAA
12585160 AAATAGTATA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
8 1 0.02
9 19 0.33
10 22 0.38
11 13 0.22
12 3 0.05
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (10 bp):
TAAAATTATA
Found at i:12585139 original size:40 final size:40
Alignment explanation
Indices: 12585069--12585149 Score: 96
Period size: 40 Copynumber: 2.0 Consensus size: 40
12585059 AAAAATTATC
* *
12585069 AAATATTAAAATTATATAAACTTATAAAAAT-TATTTTAAA
1 AAATATAAAAATTATATAAAATTATAAAAATATA-TTTAAA
12585109 AAATATAATAAATTATA-AAAATTA-ATAAAATATATTTAAA
1 AAATATAA-AAATTATATAAAATTATA-AAAATATATTTAAA
12585149 A
1 A
12585150 TTTTATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
39 1 0.03
40 25 0.69
41 10 0.28
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (40 bp):
AAATATAAAAATTATATAAAATTATAAAAATATATTTAAA
Found at i:12585191 original size:10 final size:10
Alignment explanation
Indices: 12585076--12585193 Score: 57
Period size: 10 Copynumber: 11.4 Consensus size: 10
12585066 ATCAAATATT
12585076 AAAA-TTATA
1 AAAATTTATA
* *
12585085 TAAACTTATA
1 AAAATTTATA
*
12585095 AAAATTATTTTA
1 AAAA-T-TTATA
*
12585107 AAAA-ATATA
1 AAAATTTATA
12585116 ATAAA-TTATA
1 A-AAATTTATA
*
12585126 AAAATTAATA
1 AAAATTTATA
12585136 AAATATATT-TA
1 AAA-AT-TTATA
*
12585147 AAATTTTATAAA
1 AAAATTTAT--A
*
12585159 AAAATAGTATA
1 AAAAT-TTATA
12585170 AAAATTCT-TA
1 AAAATT-TATA
12585180 AAAATTTATA
1 AAAATTTATA
12585190 AAAA
1 AAAA
12585194 AATCATAAAA
Statistics
Matches: 83, Mismatches: 13, Indels: 25
0.69 0.11 0.21
Matches are distributed among these distances:
9 13 0.16
10 39 0.47
11 14 0.17
12 14 0.17
13 3 0.04
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (10 bp):
AAAATTTATA
Found at i:12588693 original size:25 final size:24
Alignment explanation
Indices: 12588644--12588694 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
12588634 AATGAAAAAT
*
12588644 AAAGAAAGAAAAAAAGATAAGTTA
1 AAAGAAAGAAAAAAAGAAAAGTTA
*
12588668 AAAGAATAGAAAAGAAA-AAAATTTA
1 AAAGAA-AGAAAA-AAAGAAAAGTTA
12588693 AA
1 AA
12588695 TTGCTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 6 0.26
25 14 0.61
26 3 0.13
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (24 bp):
AAAGAAAGAAAAAAAGAAAAGTTA
Found at i:12599661 original size:45 final size:43
Alignment explanation
Indices: 12599573--12599664 Score: 114
Period size: 45 Copynumber: 2.1 Consensus size: 43
12599563 ATTACAACAT
* *
12599573 CATTCTATTCAACCAAACACAATATACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACAATATACTATTACAATTCTATTC
* *
12599616 CATTCCATTCAACCAAACA-ATTGAATTACTATTATAATTCTATTC
1 CATTCCATTCAACCAAACACAAT--A-TACTATTACAATTCTATTC
12599661 CATT
1 CATT
12599665 ACAGCTTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
42 2 0.05
43 18 0.43
44 1 0.02
45 21 0.50
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (43 bp):
CATTCCATTCAACCAAACACAATATACTATTACAATTCTATTC
Found at i:12599675 original size:16 final size:16
Alignment explanation
Indices: 12599654--12599697 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
12599644 CTATTATAAT
12599654 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
* **
12599670 TTTATTAAATTACAGC
1 TCTATTCCATTACAGC
12599686 TCTATTCCATTA
1 TCTATTCCATTA
12599698 TAGTGAACCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.43
Consensus pattern (16 bp):
TCTATTCCATTACAGC
Found at i:12600605 original size:24 final size:24
Alignment explanation
Indices: 12600578--12600645 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
12600568 TCATAATCAG
**
12600578 ATACAGATGCAAATTTAGATTCAA
1 ATACAGATGCAAACGTAGATTCAA
* * * *
12600602 ATACAAATGTAGACGTAGATTCAG
1 ATACAGATGCAAACGTAGATTCAA
* *
12600626 ATACAGATGCAGACATAGAT
1 ATACAGATGCAAACGTAGAT
12600646 CCTACCTCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.44, C:0.13, G:0.18, T:0.25
Consensus pattern (24 bp):
ATACAGATGCAAACGTAGATTCAA
Found at i:12603090 original size:57 final size:57
Alignment explanation
Indices: 12603023--12603146 Score: 203
Period size: 57 Copynumber: 2.2 Consensus size: 57
12603013 ATTTTCATTT
*
12603023 TATGGAGCATGCCCAAGACCTATTTTTATCACACTGTCCTTCTAGGACATATACTTA
1 TATGGAGCATGCCCAAGACCTATTTTTATCACACTGTCCTTCTAAGACATATACTTA
* * *
12603080 TATGGAGCATGCCCAAGACTTATTTTTATCACATTGTCCTTCTAAGACATATACTTT
1 TATGGAGCATGCCCAAGACCTATTTTTATCACACTGTCCTTCTAAGACATATACTTA
*
12603137 TTTGGAGCAT
1 TATGGAGCAT
12603147 TTTAGTTGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 62 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (57 bp):
TATGGAGCATGCCCAAGACCTATTTTTATCACACTGTCCTTCTAAGACATATACTTA
Found at i:12608964 original size:39 final size:38
Alignment explanation
Indices: 12608899--12608972 Score: 87
Period size: 39 Copynumber: 1.9 Consensus size: 38
12608889 CTTAGATATT
* * *
12608899 TATATTATTTATTTATATAATATATAATTAATTATAAAG
1 TATATTATTAAATTATATAATATATAAAT-ATTATAAAG
*
12608938 TATATTATTAAATTA-ATTATATTATAAATATTATA
1 TATATTATTAAATTATATAATA-TATAAATATTATA
12608973 TTAAGAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
38 11 0.37
39 19 0.63
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (38 bp):
TATATTATTAAATTATATAATATATAAATATTATAAAG
Found at i:12608970 original size:14 final size:17
Alignment explanation
Indices: 12608938--12608975 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
12608928 AATTATAAAG
12608938 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
12608955 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
12608969 TATATTA
1 TATATTA
12608976 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:12609210 original size:15 final size:17
Alignment explanation
Indices: 12609192--12609223 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12609182 CATAATAGAA
12609192 AGAA-CAAA-GAAACAG
1 AGAAGCAAACGAAACAG
12609207 AGAAGCAAACGAAACAG
1 AGAAGCAAACGAAACAG
12609224 GGGAAGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 4 0.27
17 7 0.47
ACGTcount: A:0.62, C:0.16, G:0.22, T:0.00
Consensus pattern (17 bp):
AGAAGCAAACGAAACAG
Found at i:12610139 original size:43 final size:43
Alignment explanation
Indices: 12610073--12610242 Score: 202
Period size: 43 Copynumber: 4.0 Consensus size: 43
12610063 GTTTTTAGAT
* **
12610073 ACCAAGACCTTTAGCGGCTCTTTTTCCACAAATACCGCTAAAG
1 ACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAG
* *
12610116 ACCAAGACCTTTAGCGGCGCTTTTCCCACAAACGTCGCTAAAG
1 ACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAG
*
12610159 ACCAAGACCTTTAGCGACGCTTTTAT-CACAAACGCCGCTAAAG
1 ACCAAGACCTTTAGCGGCGCTTTT-TCCACAAACGCCGCTAAAG
** * * *
12610202 AATAA-ACCTTTAGCGGTGC-TTCTCACAAAAACGCCGCTAAA
1 ACCAAGACCTTTAGCGGCGCTTTTTC-CACAAACGCCGCTAAA
12610243 AACATAACCT
Statistics
Matches: 110, Mismatches: 14, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 2 0.02
42 27 0.25
43 80 0.73
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (43 bp):
ACCAAGACCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAG
Found at i:12615091 original size:14 final size:14
Alignment explanation
Indices: 12615072--12615135 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
12615062 ACCCTTAAAT
12615072 CCCTAAATCCTAAC
1 CCCTAAATCCTAAC
12615086 CCCTAAATCCCTAA-
1 CCCTAAAT-CCTAAC
* * *
12615100 CTCTTAACCCTTAAC
1 CCCTAAATCC-TAAC
* *
12615115 CCCTAACTACTAAC
1 CCCTAAATCCTAAC
12615129 CCCTAAA
1 CCCTAAA
12615136 CCTTTAAATC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
13 2 0.05
14 26 0.68
15 10 0.26
ACGTcount: A:0.34, C:0.42, G:0.00, T:0.23
Consensus pattern (14 bp):
CCCTAAATCCTAAC
Found at i:12615092 original size:22 final size:22
Alignment explanation
Indices: 12615062--12615157 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 22
12615052 CCCTAACCCG
*
12615062 ACCCTTAAATCCCTAAATCCTA
1 ACCCCTAAATCCCTAAATCCTA
* *
12615084 ACCCCTAAATCCCTAACTCTTA
1 ACCCCTAAATCCCTAAATCCTA
* * * *
12615106 A-CCCTTAACCCCTAACTACTA
1 ACCCCTAAATCCCTAAATCCTA
* *
12615127 ACCCCTAAA-CCTTTAAATCCCA
1 ACCCCTAAATCC-CTAAATCCTA
*
12615149 ACCCTTAAA
1 ACCCCTAAA
12615158 CCATAATCCC
Statistics
Matches: 59, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
21 19 0.32
22 40 0.68
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (22 bp):
ACCCCTAAATCCCTAAATCCTA
Found at i:12615377 original size:16 final size:16
Alignment explanation
Indices: 12615349--12615381 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
12615339 TCTTTTTTAC
12615349 AATTATATAATAAATT
1 AATTATATAATAAATT
12615365 AATTA-ATATATAAATT
1 AATTATATA-ATAAATT
12615381 A
1 A
12615382 GAAAACACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTATATAATAAATT
Found at i:12615834 original size:73 final size:73
Alignment explanation
Indices: 12615742--12615915 Score: 296
Period size: 73 Copynumber: 2.4 Consensus size: 73
12615732 CTAAGCATTA
* *
12615742 GCGGCGC-TTCTTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTT
1 GCGGCGCTTTCTT-GAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTAGCTT
12615806 AGGTTCTTT
65 AGGTTCTTT
**
12615815 GCGGCGCTTTCTTGAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTTTTAGCTTA
1 GCGGCGCTTTCTTGAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTAGCTTA
12615880 GGTTCTTT
66 GGTTCTTT
12615888 GCGGCGCTTTCTTGAAAACGCCGCTAAA
1 GCGGCGCTTTCTTGAAAACGCCGCTAAA
12615916 GCCCTGAGCA
Statistics
Matches: 96, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
73 91 0.95
74 5 0.05
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (73 bp):
GCGGCGCTTTCTTGAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTAGCTTA
GGTTCTTT
Found at i:12616017 original size:111 final size:113
Alignment explanation
Indices: 12615815--12616026 Score: 320
Period size: 111 Copynumber: 1.9 Consensus size: 113
12615805 TAGGTTCTTT
*
12615815 GCGGCGCTTTCTTGAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTTTTAGCTTA
1 GCGGCGCTTTCTTGAAAAC-ACGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTTTTAGCTTA
* **
12615880 GGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTA
65 GGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* * * *
12615929 GCGGCGCTTTCTT-AAAA-ACGCTAAATCCCCGAAAGCTCACAGAACGGCGTTGTTTTGGCTTAG
1 GCGGCGCTTTCTTGAAAACACGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTTTTAGCTTAG
*
12615992 GTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAA
66 GTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAA
12616027 TCCCCCAAAG
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
111 72 0.81
113 4 0.04
114 13 0.15
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (113 bp):
GCGGCGCTTTCTTGAAAACACGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTTTTAGCTTAG
GTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:12616055 original size:184 final size:185
Alignment explanation
Indices: 12615725--12616099 Score: 565
Period size: 184 Copynumber: 2.0 Consensus size: 185
12615715 TAAATTATTT
*
12615725 TAAATCCCTAAGCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAAC
1 TAAAGCCCTAAGCATTAGCGGCGCTTCTTCAAAAA--CCGCTAAATCCCCCAAAGCTCACAAAAC
* **
12615790 AACGTCGTTTTGGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAATCCCCCAAAGCT
64 AACGTCGTTTTGGCTTAGGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCT
** **
12615855 CACAAAACGGCGTCGTTTTAGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGC
129 CACAAAACAACGTCGTTTTAGCTTAGGTTCTTTGCGGCGCTTTCTCAAAAACGCCGC
* * * *
12615912 TAAAGCCCTGAGCATTAGCGGCGCTTTCTT-AAAAA-CGCTAAATCCCCGAAAGCTCACAGAACG
1 TAAAGCCCTAAGCATTAGCGGCGC-TTCTTCAAAAACCGCTAAATCCCCCAAAGCTCACAAAACA
* * *
12615975 GCGTTGTTTTGGCTTAGGTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTC
65 ACGTCGTTTTGGCTTAGGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTC
*
12616040 ACAAAACAACGTCGTTTTGGCTTAGGTTCTTTGCGGCGCTTTCTCAAAAACGCCGC
130 ACAAAACAACGTCGTTTTAGCTTAGGTTCTTTGCGGCGCTTTCTCAAAAACGCCGC
12616096 TAAA
1 TAAA
12616100 TCCCCCAAAG
Statistics
Matches: 171, Mismatches: 16, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
184 139 0.81
187 27 0.16
188 5 0.03
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.26
Consensus pattern (185 bp):
TAAAGCCCTAAGCATTAGCGGCGCTTCTTCAAAAACCGCTAAATCCCCCAAAGCTCACAAAACAA
CGTCGTTTTGGCTTAGGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCA
CAAAACAACGTCGTTTTAGCTTAGGTTCTTTGCGGCGCTTTCTCAAAAACGCCGC
Found at i:12616057 original size:73 final size:73
Alignment explanation
Indices: 12615929--12616172 Score: 359
Period size: 73 Copynumber: 3.4 Consensus size: 73
12615919 CTGAGCATTA
* * * * *
12615929 GCGGCGCTTTCTTAAAAA---CGCTAAATCCCCGAAAGCTCACAGAACGGCGTTGTTTTGGCTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTA
*
12615991 GGTTTTTT
66 GGTTCTTT
* *
12615999 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTA
12616064 GGTTCTTT
66 GGTTCTTT
* *
12616072 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAAACGACGTCGTTTTGACTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTA
12616137 GGTTCTTT
66 GGTTCTTT
**
12616145 GCGGCGCTTTCTTGAAAACGCCGCTAAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAA
12616173 GCCCTGAGCA
Statistics
Matches: 157, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
70 16 0.10
73 141 0.90
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.26
Consensus pattern (73 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGACGTCGTTTTGGCTTA
GGTTCTTT
Found at i:12616246 original size:187 final size:186
Alignment explanation
Indices: 12615999--12616365 Score: 599
Period size: 187 Copynumber: 2.0 Consensus size: 186
12615989 TAGGTTTTTT
12615999 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
*
12616064 GGTTCTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAAACGACGTCGTT
66 GGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCACAC-AAACGACGTCGTT
*
12616129 TTGACTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTA
130 TTGACTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCCAAAGCCCTGAGCATTA
* * ** * * *
12616186 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAATCTCACAAAACGACGTTGTTTTGGCTTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
* * *
12616251 GGTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAACGATGTCGTTT
66 GGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAACGACGTCGTTT
* *
12616316 TGGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCCAAATCCCTGA
131 TGACTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCCAAAGCCCTGA
12616366 AAGCTCACAA
Statistics
Matches: 166, Mismatches: 14, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
186 60 0.36
187 106 0.64
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (186 bp):
GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
GGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAACGACGTCGTTT
TGACTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCCAAAGCCCTGAGCATTA
Found at i:12616277 original size:114 final size:114
Alignment explanation
Indices: 12616072--12616286 Score: 331
Period size: 114 Copynumber: 1.9 Consensus size: 114
12616062 TAGGTTCTTT
12616072 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAAACGACGTCGTTTTGACTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAAACGACGTCGTTTTGACTTA
* **
12616137 GGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTA
66 GGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
* ** * * * *
12616186 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAATCTCACAAAACGACGTTGTTTTGGCTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAAACGACGTCGTTTTGACTTA
*
12616251 GGTTTTTTGCGGCGCTTCCTCAAAAACGCCGCTAAA
66 GGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAA
12616287 TCCCCCAAAG
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
114 90 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (114 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAAACGACGTCGTTTTGACTTA
GGTTCTTTGCGGCGCTTCCTCAAAAACGCCGCTAAAGCCCTGAGCATTA
Found at i:12616349 original size:72 final size:73
Alignment explanation
Indices: 12616186--12616438 Score: 382
Period size: 73 Copynumber: 3.5 Consensus size: 73
12616176 CTGAGCATTA
*
12616186 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAATCTCACAAAACGACGTTGTTTTGGCTTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGACGTTGTTTTGGCTTA
12616251 GGTTTTTT
66 GGTTTTTT
* * ** * *
12616259 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCAC-AAACGATGTCGTTTTGGCTTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGACGTTGTTTTGGCTTA
*
12616323 GGTTCTTT
66 GGTTTTTT
* * *
12616331 GCGGCGCTTTCTTGAAAACGCCGCCAAATCCCTGAAAGCTCACAAAACGGCGTTGTTTTGGCTTA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGACGTTGTTTTGGCTTA
12616396 GGTTTTTT
66 GGTTTTTT
* *
12616404 GTGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGA
1 GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGA
12616439 GCATTAGCAG
Statistics
Matches: 157, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
72 63 0.40
73 94 0.60
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (73 bp):
GCGGCGCTTTCTTAAAAACGCCGCTAAATCCCTGAAAGCTCACAAAACGACGTTGTTTTGGCTTA
GGTTTTTT
Found at i:12616424 original size:259 final size:260
Alignment explanation
Indices: 12615742--12616619 Score: 1399
Period size: 259 Copynumber: 3.4 Consensus size: 260
12615732 CTAAGCATTA
*
12615742 GCGGCGCTTCTTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
*
12615807 GGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTT
66 GGTTCTTTGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTT
*
12615872 TTAGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT
131 TTGGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT
12615937 TTCTTAAAAA---CGCTAAATCCCCGAAAGCTCACAGAACGGCGTTGTTTTGGCTTAGGTTTTTT
196 TTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAGAACGGCGTTGTTTTGGCTTAGGTTTTTT
12615999 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
* * *
12616064 GGTTCTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCAAAGCACACAAAACGACGTCGTT
66 GGTTCTTTGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTT
*
12616129 TTGACTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT
131 TTGGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT
* * * *
12616194 TTCTTAAAAACGCCGCTAAATCCCTGAAATCTCACAAAACGACGTTGTTTTGGCTTAGGTTTTTT
196 TTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAGAACGGCGTTGTTTTGGCTTAGGTTTTTT
* *
12616259 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCAC-AAACGATGTCGTTTTGGCTTA
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
* * ** *
12616323 GGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCCAAATCCCTGAAAGCTCACAAAACGGCGTTGTT
66 GGTTCTTTGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTT
* * * *
12616388 TTGGCTTAGGTTTTTTGTGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCGCT
131 TTGGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT
* * * *
12616453 TTCCTT-AAAGCGCCGCTAAATCCCCGAAAGCTCATAGAACGGCGTCGTTTTTGCTTAGGTTTTT
196 TT-CTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAGAACGGCGTTGTTTTGGCTTAGGTTTTT
12616517 T
260 T
** * *
12616518 GCGGCGCTTTTTCAAAAACGCCGCTAAATCCCCCAAATCTCACAAAA-ATGACGTCGTTTTGGTT
1 GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACA--ACGTCGTTTTGGCT
* *
12616582 TAGGTTCTTTGTGGCGCTTTCTTAAAAATGCCGCTAAA
64 TAGGTTCTTTGCGGCGCTTTCTTAAAAACGCCGCTAAA
12616620 GCTTATTGTT
Statistics
Matches: 570, Mismatches: 44, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
257 198 0.35
259 229 0.40
260 97 0.17
261 46 0.08
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.28
Consensus pattern (260 bp):
GCGGCGCTTCCTCAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACAACGTCGTTTTGGCTTA
GGTTCTTTGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCACAAAACGGCGTCGTT
TTGGCTTAGGTTCTTTGCGGCGCTTTCTTGAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCT
TTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCACAGAACGGCGTTGTTTTGGCTTAGGTTTTTT
Found at i:12616535 original size:114 final size:114
Alignment explanation
Indices: 12616334--12616545 Score: 320
Period size: 114 Copynumber: 1.9 Consensus size: 114
12616324 GTTCTTTGCG
* *
12616334 GCGCTTTCTTGAAAACGCCGCCAAATCCCTGAAAGCTCACAAAACGGCGTTGTTTTGGCTTAGGT
1 GCGCTTTCTTGAAAACGCCGCCAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAGGT
*
12616399 TTTTTGTGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
66 TTTTTGCGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
* * * * *
12616448 GCGCTTTCCTT-AAAGCGCCGCTAAATCCCCGAAAGCTCATAGAACGGCGTCGTTTTTGCTTAGG
1 GCGCTTT-CTTGAAAACGCCGCCAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAGG
12616512 TTTTTTGCGGCGCTTT-TTCAAAAACGCCGCTAAA
65 TTTTTTGCGGCGCTTTCTT-AAAAACGCCGCTAAA
12616546 TCCCCCAAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
113 2 0.02
114 83 0.94
115 3 0.03
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.29
Consensus pattern (114 bp):
GCGCTTTCTTGAAAACGCCGCCAAATCCCCGAAAGCTCACAAAACGGCGTCGTTTTGGCTTAGGT
TTTTTGCGGCGCTTTCTTAAAAACGCCGCTAAAGCCCTGAGCATTAGCA
Found at i:12616600 original size:74 final size:73
Alignment explanation
Indices: 12616448--12616619 Score: 195
Period size: 74 Copynumber: 2.3 Consensus size: 73
12616438 AGCATTAGCA
* * * * * *
12616448 GCGCTTTCCTT-AAAGCGCCGCTAAATCCCCGAAAGCTCATAGAACGGCGTCGTTTTTGCTTAGG
1 GCGCTTT-CTTAAAAACGCCGCTAAATCCCCCAAAGCTCAAAAAACGACGTCGTTTTGGCTTAGG
*
12616512 TTTTTTGCG
65 TTCTTTGCG
* * *
12616521 GCGCTTT-TTCAAAAACGCCGCTAAATCCCCCAAATCTCACAAAAATGACGTCGTTTTGGTTTAG
1 GCGCTTTCTT-AAAAACGCCGCTAAATCCCCCAAAGCTCA-AAAAACGACGTCGTTTTGGCTTAG
*
12616585 GTTCTTTGTG
64 GTTCTTTGCG
*
12616595 GCGCTTTCTTAAAAATGCCGCTAAA
1 GCGCTTTCTTAAAAACGCCGCTAAA
12616620 GCTTATTGTT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
71 2 0.02
73 32 0.39
74 47 0.57
75 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (73 bp):
GCGCTTTCTTAAAAACGCCGCTAAATCCCCCAAAGCTCAAAAAACGACGTCGTTTTGGCTTAGGT
TCTTTGCG
Found at i:12616860 original size:24 final size:27
Alignment explanation
Indices: 12616823--12616886 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
12616813 AATTGCGGAT
*
12616823 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
12616847 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
12616873 TTGTGATTGAATTG
1 TAATGATTGAATTG
12616887 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:12623141 original size:20 final size:23
Alignment explanation
Indices: 12623118--12623166 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
12623108 ATTATTTATC
12623118 TATATA-ATA-TA-TAAATTAAT
1 TATATAGATATTATTAAATTAAT
*
12623138 TATAAAGTATATTATTAAATTAAT
1 TATATAG-ATATTATTAAATTAAT
12623162 TATAT
1 TATAT
12623167 TATAAATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.22
22 3 0.13
23 2 0.09
24 13 0.57
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATATAGATATTATTAAATTAAT
Found at i:12623151 original size:12 final size:11
Alignment explanation
Indices: 12623122--12623165 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
12623112 TTTATCTATA
12623122 TAATATATAAAT
1 TAAT-TATAAAT
*
12623134 TAATTATAAAG
1 TAATTATAAAT
12623145 TATATTATTAAAT
1 TA-ATTA-TAAAT
12623158 TAATTATA
1 TAATTATA
12623166 TTATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:12623177 original size:14 final size:17
Alignment explanation
Indices: 12623145--12623182 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
12623135 AATTATAAAG
12623145 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
12623162 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
12623176 TATATTA
1 TATATTA
12623183 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:12623396 original size:6 final size:5
Alignment explanation
Indices: 12623355--12623430 Score: 50
Period size: 5 Copynumber: 14.6 Consensus size: 5
12623345 TAAAGTAAAT
* *
12623355 AAAAG -AAAG TAAAG AAATA- AAAAG AAAAG AAAAG AAACAG AATAG -AAAG
1 AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG
*
12623404 AACAAAG AAACAG AGAAG CAAAAG AAA
1 -A-AAAG AAA-AG AAAAG -AAAAG AAA
12623431 CGAGGGAAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
4 8 0.14
5 31 0.54
6 14 0.25
7 4 0.07
ACGTcount: A:0.72, C:0.05, G:0.18, T:0.04
Consensus pattern (5 bp):
AAAAG
Found at i:12623412 original size:16 final size:16
Alignment explanation
Indices: 12623360--12623430 Score: 56
Period size: 16 Copynumber: 4.4 Consensus size: 16
12623350 TAAATAAAAG
* *
12623360 AAAGTAAAG-AAATAA
1 AAAGAAAAGAAAAGAA
12623375 AAAGAAAAGAAAAGAA
1 AAAGAAAAGAAAAGAA
* *
12623391 ACAGAATAG-AAAGAA
1 AAAGAAAAGAAAAGAA
* *
12623406 CAAAGAAACAGAGAAGCA
1 -AAAGAAA-AGAAAAGAA
12623424 AAAGAAA
1 AAAGAAA
12623431 CGAGGGAAGA
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
15 14 0.32
16 17 0.39
17 9 0.20
18 4 0.09
ACGTcount: A:0.72, C:0.06, G:0.18, T:0.04
Consensus pattern (16 bp):
AAAGAAAAGAAAAGAA
Found at i:12624326 original size:24 final size:27
Alignment explanation
Indices: 12624289--12624352 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
12624279 AATTGCGGAT
*
12624289 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
12624313 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
12624339 TTGTGATTGAATTG
1 TAATGATTGAATTG
12624353 GGATTATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:12630541 original size:27 final size:27
Alignment explanation
Indices: 12630471--12630541 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
12630461 GGTCGAGGGT
* * *
12630471 CTGCCACATGCGGCACCAAAGGTGCTA
1 CTGCCACAGGCGACACCAAAGGTGCCA
* * * *
12630498 GTGGCAGAGGCGGCACCAAAGGTGCCA
1 CTGCCACAGGCGACACCAAAGGTGCCA
*
12630525 CTGCCACAGGTGACACC
1 CTGCCACAGGCGACACC
12630542 TGTGCCATGT
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.25, C:0.32, G:0.31, T:0.11
Consensus pattern (27 bp):
CTGCCACAGGCGACACCAAAGGTGCCA
Found at i:12630644 original size:3 final size:3
Alignment explanation
Indices: 12630636--12630673 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
12630626 AAATGAAAGG
*
12630636 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
12630674 GAGAGGGTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:12630839 original size:24 final size:24
Alignment explanation
Indices: 12630785--12630842 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
12630775 AAAGATTATC
12630785 TTGTTATTATGTTTTTTTGTATAT
1 TTGTTATTATGTTTTTTTGTATAT
* *
12630809 TTTTTATTGT-TTTTTTTGT-TAGT
1 TTGTTATTATGTTTTTTTGTATA-T
12630832 TTAGTTATTAT
1 TT-GTTATTAT
12630843 TGTTAGTTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 2 0.07
23 12 0.43
24 14 0.50
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (24 bp):
TTGTTATTATGTTTTTTTGTATAT
Found at i:12631055 original size:23 final size:23
Alignment explanation
Indices: 12631015--12631061 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
12631005 CTAATTATTA
12631015 TTTTACTTAGTATGATTGTTAGT
1 TTTTACTTAGTATGATTGTTAGT
*
12631038 TTTTACATTA-TATTATTGTTAGT
1 TTTTAC-TTAGTATGATTGTTAGT
12631061 T
1 T
12631062 ATTATTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.23, C:0.04, G:0.13, T:0.60
Consensus pattern (23 bp):
TTTTACTTAGTATGATTGTTAGT
Found at i:12631128 original size:76 final size:77
Alignment explanation
Indices: 12630923--12631146 Score: 231
Period size: 76 Copynumber: 2.9 Consensus size: 77
12630913 GTTTAGTTAT
* *
12630923 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTAATATTATTATTATGGTAAGTTAT
1 TAATTATTATTGTTACTTAGTATTATTGTTAGTAAAAAAC---TATTATTA-T-T-GTTAGTTAT
**
12630988 TAAGATTAGTAAAAACCC
60 TATTATTAGTAAAAACCC
* *** * * *
12631006 TAATTATTATT-TTACTTAGTATGATTGTTAGTTTTTACATTA-TATTATTGTTAGTTATTATTT
1 TAATTATTATTGTTACTTAGTATTATTGTTAG-TAAAAAACTATTATTATTGTTAGTTATTATTA
12631069 TTAGT-AAAACCC
65 TTAGTAAAAACCC
* * *
12631081 TAATTATTATTGTTAGTTAGTATTATTTTTAGTAAAAAACTATTATTATTATTA-TTATTATTAT
1 TAATTATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTAGTTATTATTAT
12631145 TA
66 TA
12631147 TTATTATTAT
Statistics
Matches: 117, Mismatches: 21, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
75 34 0.29
76 42 0.36
77 1 0.01
78 1 0.01
79 5 0.04
80 2 0.02
82 19 0.16
83 13 0.11
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (77 bp):
TAATTATTATTGTTACTTAGTATTATTGTTAGTAAAAAACTATTATTATTGTTAGTTATTATTAT
TAGTAAAAACCC
Found at i:12631129 original size:3 final size:3
Alignment explanation
Indices: 12631121--12631167 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
12631111 AGTAAAAAAC
12631121 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
12631168 GTGGTTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:12633992 original size:8 final size:8
Alignment explanation
Indices: 12633964--12634005 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
12633954 GAGCTTATGC
*
12633964 TGTAAAGT
1 TGTAATGT
*
12633972 TGTTATG-
1 TGTAATGT
12633979 TGTAATGT
1 TGTAATGT
12633987 TGTAATGT
1 TGTAATGT
12633995 TGTAATGT
1 TGTAATGT
12634003 TGT
1 TGT
12634006 TGTAACACCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.24, C:0.00, G:0.26, T:0.50
Consensus pattern (8 bp):
TGTAATGT
Found at i:12636961 original size:158 final size:158
Alignment explanation
Indices: 12636415--12637107 Score: 1131
Period size: 159 Copynumber: 4.4 Consensus size: 158
12636405 TAATTTCAAT
*
12636415 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* *
12636480 TATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAG
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTG-TTTTTTATATAAATTTAG
*
12636545 TAAAAAACCCTTATTTTGGCCATTTGTTC
130 TAAAAAACCCTTATTTTGGCCCTTTGTTC
*
12636574 GTATTTTTCTTATTTTCGGATTTTATTACTTTTAAAAAATATACTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
12636639 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGA
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAG-
* *
12636704 AAAAAAACCCTTATTTTGGCCCTTTGTTA
130 TAAAAAACCCTTATTTTGGCCCTTTGTTC
* * *
12636733 ATATTTTTCTTATTTTCGGATTTTATTACTTT-AAAAGAAAATACTATTTTTGTATTTTATTATT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAA-AATATACTATTTTCGTATTTTATTATT
* *
12636797 TTATATTATTTTAGTACATAATGTTTAAAATGTATTATTTTAGTGTGTTTTTCATATAAATTTAG
65 TTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAG
*
12636862 TAAAAAACCCTTATTTTGGCTCTTTGTTC
130 TAAAAAACCCTTATTTTGGCCCTTTGTTC
* * *
12636891 GGATTTTTCTTATTTTCAGATTTTATTTCTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
* *
12636956 CATATTATTTTAGTACATAATGTTTGAAATATATTATTTTAGTGTG-TTTTTATATAAATTTAGT
66 TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGT
*
12637020 AAAAAACCATTATTTTGGCCCTTTGTTC
131 AAAAAACCCTTATTTTGGCCCTTTGTTC
** * *
12637048 GTATTTTTCTT-TTTTCGGATTTTATTACTTTCAGTAAATATACTATTTTCATTTTTTATT
1 GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATT
12637108 TCTTTTCGTA
Statistics
Matches: 497, Mismatches: 34, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
156 43 0.09
157 53 0.11
158 145 0.29
159 256 0.52
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (158 bp):
GTATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATACTATTTTCGTATTTTATTATTT
TATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTTATATAAATTTAGT
AAAAAACCCTTATTTTGGCCCTTTGTTC
Found at i:12636993 original size:317 final size:316
Alignment explanation
Indices: 12636416--12637107 Score: 1122
Period size: 317 Copynumber: 2.2 Consensus size: 316
12636406 AATTTCAATG
* *
12636416 TATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAATATATTATTTTCGTATTTTATTATTTT
1 TATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAAAATACTATTTTCGTATTTTATTATTTT
* *
12636481 ATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTTTTTTTATATAAATTTAGT
66 ATATTATTTTAGTACATAAAGTTTAAAATGTATTAATTTAGTGTGTTTTTTCATATAAATTTAGT
* * *
12636546 AAAAAACCCTTATTTTGGCCATTTGTTCGTATTTTTCTTATTTTCGGATTTTATTACTTTTAAAA
131 AAAAAACCCTTATTTTGGCCATTTGTTCGGATTTTTCTTATTTTCAGATTTTATTACTTTCAAAA
* *
12636611 AATATACTATTTTCGTATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTAT
196 AATATACTATTTTCGTATTTTATTATTTCATATTATTTTAGTACATAATGTTTGAAATATATTAT
*
12636676 TTTAGTGTGTTTTTTATATAAATTTAGAAAAAAAACCCTTATTTTGGCCCTTTGTTAA
261 TTTAGTGTG-TTTTTATATAAATTTAG-AAAAAAACCATTATTTTGGCCCTTTGTTAA
*
12636734 TATTTTTCTTATTTTCGGATTTTATTACTTT-AAAAGAAAATACTATTTTTGTATTTTATTATTT
1 TATTTTTCTTATTTTCGGATTTTATTACTTTCAAAA-AAAATACTATTTTCGTATTTTATTATTT
* *
12636798 TATATTATTTTAGTACATAATGTTTAAAATGTATTATTTTAGTGTG-TTTTTCATATAAATTTAG
65 TATATTATTTTAGTACATAAAGTTTAAAATGTATTAATTTAGTGTGTTTTTTCATATAAATTTAG
*
12636862 TAAAAAACCCTTATTTTGGCTC-TTTGTTCGGATTTTTCTTATTTTCAGATTTTATTTCTTTCAA
130 TAAAAAACCCTTATTTTGGC-CATTTGTTCGGATTTTTCTTATTTTCAGATTTTATTACTTTCAA
12636926 AAAATATACTATTTTCGTATTTTATTATTTCATATTATTTTAGTACATAATGTTTGAAATATATT
194 AAAATATACTATTTTCGTATTTTATTATTTCATATTATTTTAGTACATAATGTTTGAAATATATT
* **
12636991 ATTTTAGTGTGTTTTTATATAAATTTAGTAAAAAACCATTATTTTGGCCCTTTGTTCG
259 ATTTTAGTGTGTTTTTATATAAATTTAGAAAAAAACCATTATTTTGGCCCTTTGTTAA
** * * *
12637049 TATTTTTCTT-TTTTCGGATTTTATTACTTTCAGTAAATATACTATTTTCATTTTTTATT
1 TATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAAAATACTATTTTCGTATTTTATT
12637108 TCTTTTCGTA
Statistics
Matches: 348, Mismatches: 23, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
314 40 0.11
315 38 0.11
316 17 0.05
317 153 0.44
318 100 0.29
ACGTcount: A:0.29, C:0.08, G:0.09, T:0.54
Consensus pattern (316 bp):
TATTTTTCTTATTTTCGGATTTTATTACTTTCAAAAAAAATACTATTTTCGTATTTTATTATTTT
ATATTATTTTAGTACATAAAGTTTAAAATGTATTAATTTAGTGTGTTTTTTCATATAAATTTAGT
AAAAAACCCTTATTTTGGCCATTTGTTCGGATTTTTCTTATTTTCAGATTTTATTACTTTCAAAA
AATATACTATTTTCGTATTTTATTATTTCATATTATTTTAGTACATAATGTTTGAAATATATTAT
TTTAGTGTGTTTTTATATAAATTTAGAAAAAAACCATTATTTTGGCCCTTTGTTAA
Found at i:12637292 original size:30 final size:30
Alignment explanation
Indices: 12637258--12637380 Score: 147
Period size: 30 Copynumber: 4.4 Consensus size: 30
12637248 AAATTAAATA
12637258 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
12637288 AAATAATAAAACATA-AA--TA-AT---A-
1 AAATAATAAAACATAGAATGTACATAACAT
* * *
12637310 AAATAATAAGACATAGTATGTACATAAAAT
1 AAATAATAAAACATAGAATGTACATAACAT
12637340 AAATAATAAAACATAGAATGTACATAACAT
1 AAATAATAAAACATAGAATGTACATAACAT
12637370 AAA-AATTAAAA
1 AAATAA-TAAAA
12637381 TTAAATTATG
Statistics
Matches: 79, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
22 14 0.18
23 2 0.03
25 2 0.03
26 4 0.05
27 2 0.03
29 5 0.06
30 50 0.63
ACGTcount: A:0.63, C:0.07, G:0.06, T:0.24
Consensus pattern (30 bp):
AAATAATAAAACATAGAATGTACATAACAT
Found at i:12637302 original size:14 final size:14
Alignment explanation
Indices: 12637258--12637312 Score: 67
Period size: 14 Copynumber: 3.8 Consensus size: 14
12637248 AAATTAAATA
12637258 AAATAATAAAACAT
1 AAATAATAAAACAT
*
12637272 AGAAT-GTACATAACAT
1 A-AATAATA-A-AACAT
12637288 AAATAATAAAACAT
1 AAATAATAAAACAT
12637302 AAATAATAAAA
1 AAATAATAAAA
12637313 TAATAAGACA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
14 19 0.54
15 8 0.23
16 8 0.23
ACGTcount: A:0.67, C:0.07, G:0.04, T:0.22
Consensus pattern (14 bp):
AAATAATAAAACAT
Found at i:12637317 original size:52 final size:52
Alignment explanation
Indices: 12637254--12637354 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
12637244 AAATAAATTA
*
12637254 AATAAAATAATAAAACATAGAATGTACATAACATAAATAATAAAACATAAAT
1 AATAAAATAATAAAACATAGAATGTACATAAAATAAATAATAAAACATAAAT
* *
12637306 AATAAAATAATAAGACATAGTATGTACATAAAATAAATAATAAAACATA
1 AATAAAATAATAAAACATAGAATGTACATAAAATAAATAATAAAACATA
12637355 GAATGTACAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (52 bp):
AATAAAATAATAAAACATAGAATGTACATAAAATAAATAATAAAACATAAAT
Found at i:12637674 original size:3 final size:3
Alignment explanation
Indices: 12637666--12637718 Score: 67
Period size: 3 Copynumber: 18.0 Consensus size: 3
12637656 CCTCCTTCCC
12637666 CTT CTT CTT CTT CTT C-T CTT C-T CTT CTT CTT -TT CTT CTT CTCT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT-T
12637709 CATT CTT CTT
1 C-TT CTT CTT
12637719 TCCTGCAGCT
Statistics
Matches: 45, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.13
3 34 0.76
4 4 0.09
5 1 0.02
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:12637687 original size:8 final size:8
Alignment explanation
Indices: 12637666--12637708 Score: 52
Period size: 8 Copynumber: 5.2 Consensus size: 8
12637656 CCTCCTTCCC
12637666 CTTCTTCTT
1 CTTCTTC-T
12637675 CTTCTTCT
1 CTTCTTCT
12637683 CTTC-TCTT
1 CTTCTTC-T
*
12637691 CTTCTTTT
1 CTTCTTCT
12637699 CTTCTTCT
1 CTTCTTCT
12637707 CT
1 CT
12637709 CATTCTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
7 2 0.07
8 20 0.67
9 8 0.27
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (8 bp):
CTTCTTCT
Found at i:12637687 original size:11 final size:11
Alignment explanation
Indices: 12637666--12637718 Score: 65
Period size: 11 Copynumber: 4.8 Consensus size: 11
12637656 CCTCCTTCCC
12637666 CTTCTTCTTCTT
1 CTTCTTCTTC-T
12637678 CTTC-TCTTCT
1 CTTCTTCTTCT
*
12637688 CTTCTTCTTTT
1 CTTCTTCTTCT
12637699 CTTCTTC-TCT
1 CTTCTTCTTCT
12637709 CATTCTTCTT
1 C-TTCTTCTT
12637719 TCCTGCAGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 8 0.22
11 23 0.64
12 5 0.14
ACGTcount: A:0.02, C:0.34, G:0.00, T:0.64
Consensus pattern (11 bp):
CTTCTTCTTCT
Found at i:12637692 original size:19 final size:20
Alignment explanation
Indices: 12637668--12637718 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
12637658 TCCTTCCCCT
12637668 TCTTCTTCTTCTTC-TCTTC
1 TCTTCTTCTTCTTCTTCTTC
12637687 TCTTCTTCTT-TTCTTCTTC
1 TCTTCTTCTTCTTCTTCTTC
12637706 TC-TCATTCTTCTT
1 TCTTC-TTCTTCTT
12637719 TCCTGCAGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.17
19 22 0.76
20 2 0.07
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (20 bp):
TCTTCTTCTTCTTCTTCTTC
Found at i:12641244 original size:6 final size:6
Alignment explanation
Indices: 12641233--12641263 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
12641223 CAAAATTCTG
12641233 CAGATC CAGATC CAGATC CAGATC CAGATC C
1 CAGATC CAGATC CAGATC CAGATC CAGATC C
12641264 CTTCAAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.35, G:0.16, T:0.16
Consensus pattern (6 bp):
CAGATC
Found at i:12645968 original size:24 final size:24
Alignment explanation
Indices: 12645941--12645986 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
12645931 TTTAAACCCA
*
12645941 AATACCCATTGAA-ATTTAAAACTC
1 AATACACATT-AATATTTAAAACTC
12645965 AATACACATTAATATTTAAAAC
1 AATACACATTAATATTTAAAAC
12645987 CCAAATTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.30
Consensus pattern (24 bp):
AATACACATTAATATTTAAAACTC
Found at i:12646144 original size:27 final size:27
Alignment explanation
Indices: 12646106--12646171 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
12646096 GTCAGTTCGA
12646106 TTTATTCGGTTTACATAGATAACTCAG
1 TTTATTCGGTTTACATAGATAACTCAG
*
12646133 TTTATTCGGTTTACATAGATAGCTCAG
1 TTTATTCGGTTTACATAGATAACTCAG
*
12646160 TTTATTCAGTTT
1 TTTATTCGGTTT
12646172 TTGGTATAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (27 bp):
TTTATTCGGTTTACATAGATAACTCAG
Found at i:12648517 original size:28 final size:28
Alignment explanation
Indices: 12648459--12648524 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
12648449 TCGGTTAATA
*
12648459 GGTCGGTTAACCGAATTAATTCAATCGG
1 GGTCGGTTAACCGAATTAATTCAATCAG
* **
12648487 GGTTGGTTAACCGAATTAATTCGGTCAG
1 GGTCGGTTAACCGAATTAATTCAATCAG
12648515 GGTCGGTTAA
1 GGTCGGTTAA
12648525 TAATTTTTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.30
Consensus pattern (28 bp):
GGTCGGTTAACCGAATTAATTCAATCAG
Found at i:12652376 original size:40 final size:40
Alignment explanation
Indices: 12652309--12652421 Score: 156
Period size: 40 Copynumber: 2.9 Consensus size: 40
12652299 CGATTGAAAT
* * **
12652309 TACCGAAGTATAAATA-GGGCACGTATGTGCAATCAGGGG
1 TACCGAAGTACAAACAGGGGCACGTATGTGCAATCAGAAG
*
12652348 TACCGAAGTACAAACAGGGGCACATATGTGCAATCAGAAG
1 TACCGAAGTACAAACAGGGGCACGTATGTGCAATCAGAAG
* *
12652388 TATCGAAGTACAAACAGGGGCACGTATGTACAAT
1 TACCGAAGTACAAACAGGGGCACGTATGTGCAAT
12652422 TAGGTATAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 14 0.22
40 51 0.78
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.19
Consensus pattern (40 bp):
TACCGAAGTACAAACAGGGGCACGTATGTGCAATCAGAAG
Found at i:12652420 original size:20 final size:20
Alignment explanation
Indices: 12652325--12652420 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
12652315 AGTATAAATA
* *
12652325 GGGCACGTATGTGCAATCAG
1 GGGCACGTATGTACAAACAG
* *
12652345 GGGTACCG-AAGTACAAACAG
1 GGGCA-CGTATGTACAAACAG
* * *
12652365 GGGCACATATGTGCAATCAG
1 GGGCACGTATGTACAAACAG
** * *
12652385 AAGTATCG-AAGTACAAACAG
1 GGGCA-CGTATGTACAAACAG
12652405 GGGCACGTATGTACAA
1 GGGCACGTATGTACAA
12652421 TTAGGTATAA
Statistics
Matches: 52, Mismatches: 20, Indels: 8
0.65 0.25 0.10
Matches are distributed among these distances:
19 3 0.06
20 46 0.88
21 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.17
Consensus pattern (20 bp):
GGGCACGTATGTACAAACAG
Found at i:12674436 original size:16 final size:16
Alignment explanation
Indices: 12674415--12674451 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
12674405 TTGGTTCGTT
12674415 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
12674431 GTAATGGATTAGAGGC
1 GTAATGGAATAGAGGC
12674447 GTAAT
1 GTAAT
12674452 AGCAATTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.35, T:0.24
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:12674495 original size:45 final size:44
Alignment explanation
Indices: 12674431--12674527 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
12674421 GAATAGAGGC
*
12674431 GTAATGGATTAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AATTC-ATGTGTTTGGTTGAAT
* *
12674476 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
*
12674520 GGAATGGA
1 GTAATGGA
12674528 GGTGTAATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.51
45 22 0.47
ACGTcount: A:0.30, C:0.05, G:0.30, T:0.35
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAATTCATGTGTTTGGTTGAAT
Found at i:12674705 original size:18 final size:17
Alignment explanation
Indices: 12674684--12674718 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12674674 TTATTATTAA
*
12674684 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
12674702 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
12674719 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Done.