Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008241.1 Hibiscus syriacus cultivar Beakdansim tig00110889_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1355325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:614770 original size:20 final size:20
Alignment explanation
Indices: 614745--614811 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
614735 TTGCAGCCTT
614745 GATGCATGGCAGGATGCATC
1 GATGCATGGCAGGATGCATC
**
614765 GATGCATGGCCTTGATGCATC
1 GATGCATGG-CAGGATGCATC
** *
614786 GATGCACAGAAGGATGCATC
1 GATGCATGGCAGGATGCATC
614806 GATGCA
1 GATGCA
614812 CTAATTGCAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 23 0.59
21 16 0.41
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (20 bp):
GATGCATGGCAGGATGCATC
Found at i:615011 original size:29 final size:29
Alignment explanation
Indices: 614990--615047 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
614980 AAACTTTGAA
614990 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
615019 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
615048 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:615037 original size:30 final size:30
Alignment explanation
Indices: 614990--615049 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
614980 AAACTTTGAA
614990 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
615019 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
615050 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:618410 original size:21 final size:20
Alignment explanation
Indices: 618342--618439 Score: 99
Period size: 21 Copynumber: 4.7 Consensus size: 20
618332 GGTGTTTGAG
* * *
618342 TGCATGGATGTACTGTATGA
1 TGCATGGATGCACTGCAGGA
*
618362 TGCATCGATGCACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
618384 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
618405 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
618426 TGCATAGATGCACT
1 TGCATGGATGCACT
618440 TTGACACCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 34 0.51
22 12 0.18
23 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:618550 original size:29 final size:31
Alignment explanation
Indices: 618518--618577 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
618508 AAACTTTGAA
618518 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
618547 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
618578 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:621819 original size:12 final size:12
Alignment explanation
Indices: 621802--621883 Score: 128
Period size: 12 Copynumber: 6.7 Consensus size: 12
621792 TTGATGCATG
621802 GATGCATGGCAA
1 GATGCATGGCAA
621814 GATGCATGGCAA
1 GATGCATGGCAA
*
621826 GATGCATGGCATT
1 GATGCATGGCA-A
621839 GATGCATGGCAA
1 GATGCATGGCAA
*
621851 GATGCATGGCATT
1 GATGCATGGCA-A
621864 GATGCATGGCAA
1 GATGCATGGCAA
621876 GATGCATG
1 GATGCATG
621884 CCTTGATGCA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
12 42 0.66
13 22 0.34
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (12 bp):
GATGCATGGCAA
Found at i:621848 original size:25 final size:25
Alignment explanation
Indices: 621802--621894 Score: 154
Period size: 25 Copynumber: 3.8 Consensus size: 25
621792 TTGATGCATG
*
621802 GATGCATGGCA-AGATGCATGGCAA
1 GATGCATGGCATTGATGCATGGCAA
621826 GATGCATGGCATTGATGCATGGCAA
1 GATGCATGGCATTGATGCATGGCAA
621851 GATGCATGGCATTGATGCATGGCAA
1 GATGCATGGCATTGATGCATGGCAA
*
621876 GATGCAT-GCCTTGATGCAT
1 GATGCATGGCATTGATGCAT
621895 CGATGCACAG
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
24 22 0.33
25 44 0.67
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (25 bp):
GATGCATGGCATTGATGCATGGCAA
Found at i:621852 original size:37 final size:38
Alignment explanation
Indices: 621797--621883 Score: 133
Period size: 37 Copynumber: 2.3 Consensus size: 38
621787 CAGCCTTGAT
*
621797 GCATGGATGCATGGCAAGATGCATGGCA-AGATGCATG
1 GCATAGATGCATGGCAAGATGCATGGCATAGATGCATG
* *
621834 GCATTGATGCATGGCAAGATGCATGGCATTGATGCATG
1 GCATAGATGCATGGCAAGATGCATGGCATAGATGCATG
621872 GCA-AGATGCATG
1 GCATAGATGCATG
621884 CCTTGATGCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 35 0.76
38 11 0.24
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (38 bp):
GCATAGATGCATGGCAAGATGCATGGCATAGATGCATG
Found at i:622012 original size:21 final size:20
Alignment explanation
Indices: 621944--622041 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 20
621934 GGTGTTTGAG
*
621944 TGCATGGATGCACTGCATGA
1 TGCATGGATGCACTGCAGGA
*
621964 TGCATCGATGCACTAGTGCAGG-
1 TGCATGGATGCAC---TGCAGGA
621986 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
*
622007 TGCATGGATACACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
622028 TGCATGGATGCACT
1 TGCATGGATGCACT
622042 TTGACACGCT
Statistics
Matches: 68, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.21
21 33 0.49
22 12 0.18
23 5 0.07
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.22
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:622142 original size:29 final size:29
Alignment explanation
Indices: 622121--622178 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
622111 AAACTTTGAA
622121 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
622150 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
622179 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:622168 original size:30 final size:30
Alignment explanation
Indices: 622121--622180 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
622111 AAACTTTGAA
622121 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
622150 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
622181 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:622606 original size:21 final size:21
Alignment explanation
Indices: 622582--622640 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
622572 GTTTCGGTGG
* * *
622582 CATCGGAAATGGTTGCGATGC
1 CATCTGAAATGGTTGCAATGA
* *
622603 CATCTAAAATGGCTGCAATGA
1 CATCTGAAATGGTTGCAATGA
622624 CATCTGAAATGGTTGCA
1 CATCTGAAATGGTTGCA
622641 GAATATAAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (21 bp):
CATCTGAAATGGTTGCAATGA
Found at i:623378 original size:19 final size:19
Alignment explanation
Indices: 623350--623392 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
623340 GATTTTTCCT
623350 TATACCTAAAAATTCA-TTA
1 TATACCTAAAAATT-ATTTA
*
623369 TATACTTAAAAATTATTTA
1 TATACCTAAAAATTATTTA
623388 TATAC
1 TATAC
623393 GAACTCAGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 1 0.05
19 21 0.95
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (19 bp):
TATACCTAAAAATTATTTA
Found at i:624360 original size:13 final size:13
Alignment explanation
Indices: 624342--624367 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
624332 AATAATAAAC
624342 TATTTATAGGGGA
1 TATTTATAGGGGA
624355 TATTTATAGGGGA
1 TATTTATAGGGGA
624368 GGGAGAGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (13 bp):
TATTTATAGGGGA
Found at i:625366 original size:17 final size:16
Alignment explanation
Indices: 625333--625363 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
625323 TAATTTTGAT
625333 TTTTAAGTATAAATTA
1 TTTTAAGTATAAATTA
*
625349 TTTTATGTATAAATT
1 TTTTAAGTATAAATT
625364 TATCGCTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (16 bp):
TTTTAAGTATAAATTA
Found at i:625705 original size:7 final size:8
Alignment explanation
Indices: 625668--625714 Score: 51
Period size: 8 Copynumber: 5.8 Consensus size: 8
625658 AACAGTCGTC
*
625668 ATTTTAAA
1 ATTTTAAT
*
625676 ATTTTCAT
1 ATTTTAAT
625684 ATTATTATAT
1 ATT-TTA-AT
625694 ATTTTAAT
1 ATTTTAAT
625702 -TTTTAAT
1 ATTTTAAT
625709 ATTTTA
1 ATTTTA
625715 GTGTAATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
7 7 0.21
8 16 0.48
9 5 0.15
10 5 0.15
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (8 bp):
ATTTTAAT
Found at i:626316 original size:35 final size:35
Alignment explanation
Indices: 626277--626344 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
626267 TTGCAAATGA
626277 ACATATAAATAAACATTAAACGAACATGTTCGTAT
1 ACATATAAATAAACATTAAACGAACATGTTCGTAT
* **
626312 ACATATAAATGAACATTAATTGAACATGTTCGT
1 ACATATAAATAAACATTAAACGAACATGTTCGT
626345 GAATATGTCC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
ACATATAAATAAACATTAAACGAACATGTTCGTAT
Found at i:626591 original size:2 final size:2
Alignment explanation
Indices: 626584--626625 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
626574 TTAGCACTGA
626584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
626626 TATTTCCTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:634497 original size:20 final size:19
Alignment explanation
Indices: 634453--634507 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
634443 GAATGCAATA
*
634453 AGTGCATCGATTCATAGGC
1 AGTGCATCGATACATAGGC
634472 AGTGCATCGATACACTATGG-
1 AGTGCATCGATACA-TA-GGC
634492 AGTGCATCGATACATA
1 AGTGCATCGATACATA
634508 AGGACCAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 15 0.45
20 16 0.48
21 2 0.06
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (19 bp):
AGTGCATCGATACATAGGC
Found at i:634890 original size:59 final size:60
Alignment explanation
Indices: 634827--635504 Score: 540
Period size: 59 Copynumber: 11.5 Consensus size: 60
634817 TTACCAAATG
* * *
634827 GCACT-ATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCTATATGGA
1 GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * * *
634886 GCACTGA-GTGTGCTAAAATGATAAGGAAATTATATTGAGTGTATGAATTTCCATATGGA
1 GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * * * *
634945 GCACTGA-GTGTGCTAAAATGATAAAGAAATCAGATTGAATATATGGATTTCCAGATAGG-
1 GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGA
* * * *
635004 GCA-TTATATGTGCTAAAATGGTAAGGGAAT-ATACTGAGTGTATGAATTTCCAGATGGA
1 GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * * * * *
635062 GTACTGA-GTGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGAT-AA
1 GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * *
635120 GGCA-TTATATGTGCTAAAATGGTAA-GAGAATCATACTGAGTGTATGTATTTCCATATGGA
1 -GCACTGATATGTGCTAAAATGATAAGGA-AATCATACTGAGTGTATGGATTTCCAGATGGA
* * * * * *
635180 GCACTGA-GTGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTACAGATAGG-
1 GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGAT-GGA
* * * * *
635239 GCA-TTATATGTGCTAAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCATATGGA
1 GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * * *
635298 GCACTGAGT-T-TGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATGGG
1 GCACTGA-TATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
* * * *
635357 GCA-TTATATGTGCTAAAATGGTAA-GAGAATCATACT-AATGGTATGGATTCTCGCATA-GG-
1 GCACTGATATGTGCTAAAATGATAAGGA-AATCATACTGAGT-GTATGGATT-TC-CAGATGGA
* * ** * * * **
635416 GCACT--TCGTGTGCTAAAATAAGGAGGAAATCATATTAAGTATAT-GATATTCCAGATAAA
1 GCACTGAT-ATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGAT-TTCCAGATGGA
* * *
635475 GCACTGAGA-GTGCTAATATTATAAGGAAAT
1 GCACTGATATGTGCTAAAATGATAAGGAAAT
635505 TATATGAATT
Statistics
Matches: 490, Mismatches: 97, Indels: 64
0.75 0.15 0.10
Matches are distributed among these distances:
57 6 0.01
58 66 0.13
59 392 0.80
60 22 0.04
61 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (60 bp):
GCACTGATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATGGA
Found at i:634967 original size:118 final size:118
Alignment explanation
Indices: 634835--635472 Score: 819
Period size: 118 Copynumber: 5.4 Consensus size: 118
634825 TGGCACTATA
* * * * * * * * *
634835 TGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCTATAT-GGAGCACTGA-GTGTG
1 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGG-GCA-TTATATGTG
* * *
634898 CTAAAATGATAAGGAAATTATATTGAGTGTATGAATTTCCATATGGAGCACTGAG
64 CTAAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
* * *
634953 TGTGCTAAAATGATAAAGAAATCAGATTGAATATATGGATTTCCAGATAGGGCATTATATGTGCT
1 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTATATGTGCT
* * *
635018 AAAATGGTAAGGGAAT-ATACTGAGTGTATGAATTTCCAGATGGAGTACTGAG
66 AAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
*
635070 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAAGGCATTATATGTGCT
1 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTATATGTGCT
*
635135 AAAATGGTAA-GAGAATCATACTGAGTGTATGTATTTCCATATGGAGCACTGAG
66 AAAATGGTAAGGA-AATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
*
635188 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTACAGATAGGGCATTATATGTGCT
1 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTATATGTGCT
* * *
635253 AAAATGGTAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTGAG
66 AAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
* *
635306 TTTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATGGGGCATTATATGTGCT
1 TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTATATGTGCT
* * **
635371 AAAATGGTAA-GAGAATCATACT-AATGGTATGGATTCTCGCATA-GG-GCACTTCG
66 AAAATGGTAAGGA-AATCATACTGAGT-GTATGAATT-TC-CATATGGAGCACTGAG
* * **
635424 TGTGCTAAAATAAGGAGGAAATCATATT-AAGTATAT-GATATTCCAGATA
1 TGTGCTAAAGTGATAAGGAAATCATATTGAA-TATATGGAT-TTCCAGATA
635473 AAGCACTGAG
Statistics
Matches: 468, Mismatches: 41, Indels: 22
0.88 0.08 0.04
Matches are distributed among these distances:
116 1 0.00
117 117 0.25
118 339 0.72
119 7 0.01
120 4 0.01
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.31
Consensus pattern (118 bp):
TGTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATAGGGCATTATATGTGCT
AAAATGGTAAGGAAATCATACTGAGTGTATGAATTTCCATATGGAGCACTGAG
Found at i:635449 original size:177 final size:177
Alignment explanation
Indices: 634826--635513 Score: 625
Period size: 177 Copynumber: 3.9 Consensus size: 177
634816 ATTACCAAAT
* * *
634826 GGCACTATATGTGCTAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCTATATGGAGCACT
1 GGCATTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCATATGGAGCACT
* * * * * * *
634891 GAGTGTGCTAAAATGATAAGGAAATTATATTGAGTGTATGAATTTCCATATGGAGCACTGAGTGT
66 GAGTGTGCTAAAATGAGAAGGAAATCATATTAAGTATATGGATTTCCAGATGAAGCACTGAGTGT
* * *
634956 GCTAAAATGATAAAGAAATCAGATTGAATATATGGATTTCCAGATAG
131 GCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATGG
* * * * *
635003 GGCATTATATGTGCTAAAATGGTAAGGGAAT-ATACTGAGTGTATGAATTTCCAGATGGAGTACT
1 GGCATTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCATATGGAGCACT
* * * *
635067 GAGTGTGCTAAAGTGATAAGGAAATCATATTGAA-TATATGGATTTCCAGAT-AAGGCA-TTATA
66 GAGTGTGCTAAAATGAGAAGGAAATCATATT-AAGTATATGGATTTCCAGATGAA-GCACTGA-G
* * * * * *
635129 TGTGCTAAAATGGTAA-GAGAATCATACTGAGTGTATGTATTTCCATATGG
128 TGTGCTAAAATGATAAGGA-AATCATATTGAATATATGGATTTCCAGATGG
* * * * * * * * *
635179 AGCACTGA-GTGTGCTAAAGTGATAAGGAAATCATATTGAA-TATATGGATTTACAGATAGG-GC
1 GGCA-TTATATGTGCTAAAATGATAAGGAAATCATACT-AAGTGTATGAATTTCCATAT-GGAGC
* * * * * * *
635241 A-TTATATGTGCTAAAATG-GTAAGGGAATCATACTAAGTGTATGGATTTCCATATGGAGCACTG
63 ACTGA-GTGTGCTAAAATGAG-AAGGAAATCATATTAAGTATATGGATTTCCAGATGAAGCACTG
* *
635304 AGTTTGCTAAAGTGATAAGGAAATCATATTGAATATATGGATTTCCAGATGG
126 AGTGTGCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATGG
* *
635356 GGCATTATATGTGCTAAAATGGTAA-GAGAATCATACTAA-TGGTATGGATTCTCGCATA-GG-G
1 GGCATTATATGTGCTAAAATGATAAGGA-AATCATACTAAGT-GTATGAATT-TC-CATATGGAG
** * * *
635417 CACTTCGTGTGCTAAAATAAGGAGGAAATCATATTAAGTATAT-GATATTCCAGATAAAGCACTG
62 CACTGAGTGTGCTAAAATGAGAAGGAAATCATATTAAGTATATGGAT-TTCCAGATGAAGCACTG
* * * *
635481 AGAGTGCTAATATTATAAGGAAATTATA-TGAAT
126 AGTGTGCTAAAATGATAAGGAAATCATATTGAAT
635514 TGTACAAATT
Statistics
Matches: 410, Mismatches: 79, Indels: 45
0.77 0.15 0.08
Matches are distributed among these distances:
175 5 0.01
176 156 0.38
177 234 0.57
178 12 0.03
179 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (177 bp):
GGCATTATATGTGCTAAAATGATAAGGAAATCATACTAAGTGTATGAATTTCCATATGGAGCACT
GAGTGTGCTAAAATGAGAAGGAAATCATATTAAGTATATGGATTTCCAGATGAAGCACTGAGTGT
GCTAAAATGATAAGGAAATCATATTGAATATATGGATTTCCAGATGG
Found at i:635650 original size:44 final size:44
Alignment explanation
Indices: 635586--635759 Score: 246
Period size: 44 Copynumber: 4.0 Consensus size: 44
635576 TTAGTGATGT
*
635586 AAATTATAGTAAGTATATTGATAACATAAGCTTACGAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
* * *
635630 AAATTATAGTAAGTAGATTGATAACATAAGCTTACAAGCTTATG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
*
635674 AAATTATAGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATTG
1 AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTA-TG
* *
635719 -AATAATCA--AAGTATATTGGTAAAATAAGCTTACGAGCTTAT
1 AAATTAT-AGTAAGTATATTGATAAAATAAGCTTACGAGCTTAT
635760 AGATTAAATG
Statistics
Matches: 121, Mismatches: 7, Indels: 6
0.90 0.05 0.04
Matches are distributed among these distances:
42 1 0.01
43 32 0.26
44 85 0.70
45 3 0.02
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (44 bp):
AAATTATAGTAAGTATATTGATAAAATAAGCTTACGAGCTTATG
Found at i:637719 original size:24 final size:24
Alignment explanation
Indices: 637640--637728 Score: 96
Period size: 23 Copynumber: 3.8 Consensus size: 24
637630 ACATATGATA
*
637640 TGGCACTACGGTGC-AATTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
*
637663 TGGCACTTCGGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAAATTCTACG
* *
637686 CGGTC-TTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAAATTCTACG
637710 TGGCACTTCGGTGCAAATT
1 TGGCACTTCGGTGCAAATT
637729 TTTATGAGCT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
22 1 0.02
23 30 0.56
24 22 0.41
25 1 0.02
ACGTcount: A:0.19, C:0.25, G:0.26, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAAATTCTACG
Found at i:638316 original size:22 final size:22
Alignment explanation
Indices: 638288--638333 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
638278 TGTAGTAGTA
638288 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
*
638310 CTGTAGCAGGGGAATTGGTTCC
1 CTGTAGCAGGGGAATCGGTTCC
638332 CT
1 CT
638334 ATTTGCATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.35, T:0.26
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGTTCC
Found at i:642377 original size:26 final size:26
Alignment explanation
Indices: 642346--642400 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
642336 TCCGTTCTTG
642346 TCACCGCCTAGCCCAATCGAAGCGCC
1 TCACCGCCTAGCCCAATCGAAGCGCC
642372 TCACCGCCTAGCCCAATCGAAGCGCC
1 TCACCGCCTAGCCCAATCGAAGCGCC
642398 TCA
1 TCA
642401 TTGCCATGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.18, T:0.13
Consensus pattern (26 bp):
TCACCGCCTAGCCCAATCGAAGCGCC
Found at i:642811 original size:26 final size:26
Alignment explanation
Indices: 642775--642830 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
642765 TCCGTTCTTG
642775 TCACTGCCTAGCCCAATCGAAGCACC
1 TCACTGCCTAGCCCAATCGAAGCACC
*
642801 TCACTGCCTAGCCCAATCGAAGCGCC
1 TCACTGCCTAGCCCAATCGAAGCACC
642827 TCAC
1 TCAC
642831 CGCCATGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.43, G:0.16, T:0.16
Consensus pattern (26 bp):
TCACTGCCTAGCCCAATCGAAGCACC
Found at i:643056 original size:430 final size:428
Alignment explanation
Indices: 642233--643093 Score: 1427
Period size: 430 Copynumber: 2.0 Consensus size: 428
642223 CATTAATTTC
* * *
642233 AATGATTTTTATTCCAAAAAAACACATTAATTTTGAAATAATTTCAAGACTTTAAAAACCTTTAT
1 AATGATTTTTATTCCAAAAAAACACATTAATTTCGAAATAATTTCAAAACTTTAAAAACCTTCAT
* *
642298 TTCAACCCCTAAACCCACATTGACCGCCGCCGCGCTCATCCGTTCTTGTCACCGCCTAGCCCAAT
66 TTCAACCCATAAACCCACACTGACCGCCGCCGCGCTCATCCGTTCTTGTCACCGCCTAGCCCAAT
* **
642363 CGAAGCGCCTCACCGCCTAGCCCAATCGAAGCGCCTCATTGCCATGATCAAAACCCCAAAACAAT
131 CGAAGCACCTCACCGCCTAGCCCAATCGAAGCGCCTCACCGCCATGATCAAAACCCCAAAACAAT
642428 TCGTGGATAGCCATCGTCGTTCGCCATAATCGAACCCTTGAAGTTTCGCCCAAAACCCACACCGA
196 TCGTGGATAGCCATCGTCGTTCGCCATAATCGAACCCTTGAAGTTTCGCCCAAAACCCACACCGA
* * * *
642493 CTCCTCGAATTTTGGACTATTCCGACTACCTCGGAGCTCCGTTCGCCTCACTGCCACTATATTTA
261 CTCCTCGAATTTTGGACGATTCCGACTACCTCAGACCTCCGTTCGCCTCACCGCCACTATATTTA
*
642558 GTTTCCTCGTCGCTGTCCGCTCAAAACCCAACCGGTAGGTCACGTCGTAGTCATCGTCCCCCGTC
326 GTTTCCTCGTCGCTGTCCGCTCAAAACCCAACCGGTAGGTCACGTCGTAGTCATCGTCCACCGTC
*
642623 GTGGGTAAGCTTCAGTGTTAGGATTTGGG-TTTTTTTT
391 GTGGGTAAGCTTCAGTGTTAGGATTTGGGCTTTTTTGT
*
642660 AATGATTTTTATTCCAACAAAAACACATTAATTTCGAAATAATTTCAAAACTTTGAAAACCTTCA
1 AATGATTTTTATTCCAA-AAAAACACATTAATTTCGAAATAATTTCAAAACTTTAAAAACCTTCA
* *
642725 TTTCAACCCATAAACCCACACTGATCGCCGCCGCCGCTCATCCGTTCTTGTCACTGCCTAGCCCA
65 TTTCAACCCATAAACCCACACTGACCGCCGCCG-CGCTCATCCGTTCTTGTCACCGCCTAGCCCA
* *
642790 ATCGAAGCACCTCACTGCCTAGCCCAATCGAAGCGCCTCACCGCCATGATTAAAACCCCCAAAAC
129 ATCGAAGCACCTCACCGCCTAGCCCAATCGAAGCGCCTCACCGCCATGATCAAAA-CCCCAAAAC
* *
642855 AATTCGTGGATAGCCGTCGTCGTTCGCCATAATCGAACCCTTGAAGTTTCGCCCAGAACCCACAC
193 AATTCGTGGATAGCCATCGTCGTTCGCCATAATCGAACCCTTGAAGTTTCGCCCAAAACCCACAC
* *
642920 CGACTCCTCGAATTTTGGACGATTCCGGCTGCCTCAGACCTCCGTTCGCCTCACCGCCACTATAT
258 CGACTCCTCGAATTTTGGACGATTCCGACTACCTCAGACCTCCGTTCGCCTCACCGCCACTATAT
* * * * *
642985 TTAGTTTCCTCGTTGTTGTCCGCTCAAAACCCAACCGGTGGGTCACGTCGTAGTCGTCGTCCACT
323 TTAGTTTCCTCGTCGCTGTCCGCTCAAAACCCAACCGGTAGGTCACGTCGTAGTCATCGTCCACC
*
643050 GTCGTGGGTAAGCTTCGGTGTTAGGATTTGGGCTTTTTTGT
388 GTCGTGGGTAAGCTTCAGTGTTAGGATTTGGGCTTTTTTGT
643091 AAT
1 AAT
643094 TTAAAAGAAA
Statistics
Matches: 401, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
427 17 0.04
428 73 0.18
429 80 0.20
430 221 0.55
431 10 0.02
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (428 bp):
AATGATTTTTATTCCAAAAAAACACATTAATTTCGAAATAATTTCAAAACTTTAAAAACCTTCAT
TTCAACCCATAAACCCACACTGACCGCCGCCGCGCTCATCCGTTCTTGTCACCGCCTAGCCCAAT
CGAAGCACCTCACCGCCTAGCCCAATCGAAGCGCCTCACCGCCATGATCAAAACCCCAAAACAAT
TCGTGGATAGCCATCGTCGTTCGCCATAATCGAACCCTTGAAGTTTCGCCCAAAACCCACACCGA
CTCCTCGAATTTTGGACGATTCCGACTACCTCAGACCTCCGTTCGCCTCACCGCCACTATATTTA
GTTTCCTCGTCGCTGTCCGCTCAAAACCCAACCGGTAGGTCACGTCGTAGTCATCGTCCACCGTC
GTGGGTAAGCTTCAGTGTTAGGATTTGGGCTTTTTTGT
Found at i:646717 original size:2 final size:2
Alignment explanation
Indices: 646710--646734 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
646700 TCCTCCATTT
646710 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
646735 TTATATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:654554 original size:41 final size:41
Alignment explanation
Indices: 654482--654559 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
654472 TTCCAAGGAT
*
654482 TTTTTGCTCAAAGGATCGATCCCCTAGAAAAATGATCGATC
1 TTTTTGCTCAAAGGATCGATCCCCTAGAAAAAGGATCGATC
* **
654523 TTTTTG-TCCAAATGATCGATCCCCTTTAAAAAGGATC
1 TTTTTGCT-CAAAGGATCGATCCCCTAGAAAAAGGATC
654560 ATTCCTTGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.03
41 31 0.97
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (41 bp):
TTTTTGCTCAAAGGATCGATCCCCTAGAAAAAGGATCGATC
Found at i:661742 original size:22 final size:22
Alignment explanation
Indices: 661706--661756 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
661696 CACAACATAA
* *
661706 ATTTGATTAATAAT-ATACTTT
1 ATTTTATTAATAATAAGACTTT
*
661727 ATTTTATTAAATAATAAGATTTT
1 ATTTTATT-AATAATAAGACTTT
661750 ATTTTAT
1 ATTTTAT
661757 ATATCATAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.28
22 6 0.24
23 12 0.48
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (22 bp):
ATTTTATTAATAATAAGACTTT
Found at i:664877 original size:2 final size:2
Alignment explanation
Indices: 664870--664898 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
664860 GCAGCTTAAG
664870 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
664899 GCATACATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:676084 original size:21 final size:21
Alignment explanation
Indices: 676060--676107 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
676050 GTTATGAAAC
*
676060 TATGAACTTTGAA-CATGTGAA
1 TATGAACTTCGAATCA-GTGAA
676081 TATGAACTTCGAATCAGTGAA
1 TATGAACTTCGAATCAGTGAA
*
676102 TGTGAA
1 TATGAA
676108 TATACTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (21 bp):
TATGAACTTCGAATCAGTGAA
Found at i:679824 original size:23 final size:23
Alignment explanation
Indices: 679793--679840 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
679783 TCACCACAGC
*
679793 CCGCGTAGAAATGCACCAAAGTG
1 CCGCATAGAAATGCACCAAAGTG
679816 CCGCATAGAAATGCACCAAAGTG
1 CCGCATAGAAATGCACCAAAGTG
679839 CC
1 CC
679841 ATATAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.23, T:0.12
Consensus pattern (23 bp):
CCGCATAGAAATGCACCAAAGTG
Found at i:680185 original size:22 final size:22
Alignment explanation
Indices: 680146--680187 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
680136 TATTGTAATG
*
680146 CATATCATATGAGTTCATGTCA
1 CATATCATATCAGTTCATGTCA
680168 CATATCATATCA-TATCATGT
1 CATATCATATCAGT-TCATGT
680188 AATGTAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (22 bp):
CATATCATATCAGTTCATGTCA
Found at i:680310 original size:2 final size:2
Alignment explanation
Indices: 680303--680331 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
680293 CATATCACAC
680303 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
680332 CAAGTGTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:680681 original size:20 final size:21
Alignment explanation
Indices: 680656--680710 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
680646 TATTTCCAAA
*
680656 ATGGTATCGATACCT-GCCTT
1 ATGGTATCGATACCTACCCTT
*
680676 ATGGTACCGATA-CTACCCTT
1 ATGGTATCGATACCTACCCTT
680696 -TCGGTATCGATACCT
1 AT-GGTATCGATACCT
680711 CATGAAGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 3 0.10
20 24 0.83
21 2 0.07
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (21 bp):
ATGGTATCGATACCTACCCTT
Found at i:682839 original size:8 final size:7
Alignment explanation
Indices: 682820--682872 Score: 52
Period size: 8 Copynumber: 7.0 Consensus size: 7
682810 TTAAAATAAC
*
682820 TAATACA
1 TAATATA
682827 TACATATA
1 TA-ATATA
682835 TACATATA
1 TA-ATATA
682843 TATATATA
1 TA-ATATA
*
682851 TATTATA
1 TAATATA
682858 TATATATA
1 TA-ATATA
682866 TAATATA
1 TAATATA
682873 AACTAGATAG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
7 13 0.32
8 27 0.68
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (7 bp):
TAATATA
Found at i:682859 original size:15 final size:15
Alignment explanation
Indices: 682830--682929 Score: 64
Period size: 15 Copynumber: 6.6 Consensus size: 15
682820 TAATACATAC
*
682830 ATATATACA-TATAT
1 ATATATATATTATAT
682844 ATATATATATTATAT
1 ATATATATATTATAT
* *
682859 ATATATATAATATAA
1 ATATATATATTATAT
*
682874 ACTAGATAGT-TTATAT
1 A-TATATA-TATTATAT
* *
682890 ATAAAGAGT-TTATAT
1 ATATATA-TATTATAT
*
682905 ATAAAGTATATGTAT-T
1 ATATA-TATAT-TATAT
682921 ATATATATA
1 ATATATATA
682930 AACTATATAG
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
14 8 0.11
15 41 0.59
16 17 0.24
17 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (15 bp):
ATATATATATTATAT
Found at i:682892 original size:2 final size:2
Alignment explanation
Indices: 682830--682872 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
682820 TAATACATAC
*
682830 AT AT AT AC AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
682870 AT A
1 AT A
682873 AACTAGATAG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:682950 original size:22 final size:21
Alignment explanation
Indices: 682856--682951 Score: 66
Period size: 22 Copynumber: 4.9 Consensus size: 21
682846 ATATATATTA
*
682856 TATATA-TATATAATATAAAC
1 TATATAGTTTATAATATAAAC
*
682876 TAGATAGTTTAT-ATAT--A-
1 TATATAGTTTATAATATAAAC
* *
682893 -A-AGAGTTTAT-ATATAAAG
1 TATATAGTTTATAATATAAAC
682911 TATAT-GTATTATATATATAAAC
1 TATATAGT-TTATA-ATATAAAC
682933 TATATAGTTTATCAATATA
1 TATATAGTTTAT-AATATA
682952 TTATGTATAA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
15 12 0.20
16 1 0.02
17 1 0.02
18 1 0.02
19 3 0.05
20 14 0.23
21 4 0.07
22 21 0.35
23 3 0.05
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (21 bp):
TATATAGTTTATAATATAAAC
Found at i:683218 original size:51 final size:50
Alignment explanation
Indices: 683162--683287 Score: 119
Period size: 51 Copynumber: 2.4 Consensus size: 50
683152 CCCTAAACCA
* * * *
683162 TATATATATATATAAACTATATAGTTTATTAATTATAGTTTACATATGAAC
1 TATATATATATATAAACTATATA-TATATGAACTATAGTTTACATATAAAC
** *
683213 TATATATACTATAGTTGA-TATTTATATATGAACTATAGTTTACATATAAAC
1 TATATATA-TATA-TAAACTATATATATATGAACTATAGTTTACATATAAAC
*
683264 TATATAGTTTATATAGTAACTATA
1 TATATA-TATATATA--AACTATA
683288 GTTGATATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
50 1 0.02
51 41 0.71
52 11 0.19
53 5 0.09
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.44
Consensus pattern (50 bp):
TATATATATATATAAACTATATATATATGAACTATAGTTTACATATAAAC
Found at i:683296 original size:62 final size:60
Alignment explanation
Indices: 683213--683331 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 60
683203 ACATATGAAC
*
683213 TATATATACTATAGTTGATATTTATATATGAACTATAGTTTACATATAAACTATATAGTT
1 TATATATACTATAGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATAGTT
* *
683273 TATATAGTAACTATAGTTGATATTTACATATGAACTATATTTTACATATTAACTATATA
1 TATATA-T-ACTATAGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATA
683332 TATAAACTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 6 0.11
61 1 0.02
62 47 0.87
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.45
Consensus pattern (60 bp):
TATATATACTATAGTTGATATTTACATATGAACTATAGTTTACATATAAACTATATAGTT
Found at i:683302 original size:95 final size:94
Alignment explanation
Indices: 683200--683451 Score: 236
Period size: 95 Copynumber: 2.7 Consensus size: 94
683190 TTAATTATAG
* *
683200 TTTACATATGAACTATA-TATACTATAGTTGATA-TTTATATATGAAC-TATAGTTTACATATAA
1 TTTACATATGAACTATATTATAC-ATA-TT-A-ACTATATATATAAACATATAGTTTACATATAA
*
683262 ACTATATAGT-T-TATATAGTA-ACTATAGTTGATA
62 ACTATAT-CTCTCTATATA-TATA-TATAGTTGATA
* *
683295 TTTACATATGAACTATATTTTACATATTAACTATATATATAAACTATATAGTTTACATGTAAACT
1 TTTACATATGAACTATATTATACATATTAACTATATATATAAAC-ATATAGTTTACATATAAACT
* *
683360 CTCTCTCTCTATATATATATATAGTTGATA
65 ATATCTCTCTATATATATATATAGTTGATA
* * *
683390 TTTATATATGAACTACAGTT-TACAT-TTAAACTATATATTTATATAC-TA-AGTTTACATATAA
1 TTTACATATGAACTATA-TTATACATATT-AACTATATA--TATAAACATATAGTTTACATATAA
683451 A
62 A
683452 ATAGTTGATT
Statistics
Matches: 135, Mismatches: 11, Indels: 23
0.80 0.07 0.14
Matches are distributed among these distances:
92 1 0.01
93 12 0.09
94 18 0.13
95 85 0.63
96 13 0.10
97 6 0.04
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.44
Consensus pattern (94 bp):
TTTACATATGAACTATATTATACATATTAACTATATATATAAACATATAGTTTACATATAAACTA
TATCTCTCTATATATATATATAGTTGATA
Found at i:683318 original size:18 final size:18
Alignment explanation
Indices: 683195--683330 Score: 66
Period size: 18 Copynumber: 7.3 Consensus size: 18
683185 GTTTATTAAT
*
683195 TATAGTTTACATATGAAC
1 TATATTTTACATATGAAC
* **
683213 TATA-TATAC-TAT-AGT
1 TATATTTTACATATGAAC
*
683228 TGATA-TTTATATATGAAC
1 T-ATATTTTACATATGAAC
* *
683246 TATAGTTTACATATAAAC
1 TATATTTTACATATGAAC
*
683264 TATATAGTTTATATA-GTAAC
1 TATAT--TTTACATATG-AAC
683284 TATAGTTGATATTTACATATGAAC
1 --TA--T-AT-TTTACATATGAAC
*
683308 TATATTTTACATATTAAC
1 TATATTTTACATATGAAC
683326 TATAT
1 TATAT
683331 ATATAAACTA
Statistics
Matches: 90, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
15 2 0.02
16 9 0.10
17 10 0.11
18 38 0.42
19 2 0.02
20 11 0.12
22 4 0.04
24 11 0.12
25 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
TATATTTTACATATGAAC
Found at i:683605 original size:20 final size:20
Alignment explanation
Indices: 683557--683645 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 20
683547 ATAAACTATT
*
683557 TATATAATATATACTATATATA
1 TATATACTATATA-T-TATATA
* * *
683579 AACATACTATAGT-TTATATT
1 TATATACTATA-TATTATATA
683599 TATATACTATATATTATATA
1 TATATACTATATATTATATA
*
683619 TATAAACTATATA-TACTATA
1 TATATACTATATATTA-TATA
683639 TAGTATA
1 TA-TATA
683646 ATTTATGAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
19 3 0.06
20 38 0.70
21 4 0.07
22 8 0.15
23 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (20 bp):
TATATACTATATATTATATA
Found at i:683639 original size:42 final size:40
Alignment explanation
Indices: 683541--683639 Score: 98
Period size: 44 Copynumber: 2.4 Consensus size: 40
683531 GTTATTAGTG
*
683541 AACTATATAAAC--TATTTATATAATATATACTATATATA
1 AACTATATATACTATATTTATATAATATATACTATATATA
*
683579 AAC-ATACTATAGTTTATATTTATATACTATATATTA-TATATATA
1 AACTATA-TATA--CTATATTTATATA--ATATA-TACTATATATA
683623 AACTATATATACTATAT
1 AACTATATATACTATAT
683640 AGTATAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
37 3 0.06
38 6 0.12
42 15 0.31
44 20 0.41
45 5 0.10
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (40 bp):
AACTATATATACTATATTTATATAATATATACTATATATA
Found at i:683660 original size:29 final size:28
Alignment explanation
Indices: 683599--683664 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
683589 AGTTTATATT
*
683599 TATATACTATATATTATATATATAAACTA
1 TATATACTATATAGTATATATATAAAC-A
*
683628 TATATACTATATAGTATAATTTATGAAACTA
1 TATATACTATATAGTAT-ATATAT-AAAC-A
683659 TATATA
1 TATATA
683665 AAAACCATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 16 0.48
30 5 0.15
31 12 0.36
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (28 bp):
TATATACTATATAGTATATATATAAACA
Found at i:683664 original size:2 final size:2
Alignment explanation
Indices: 683557--683645 Score: 56
Period size: 2 Copynumber: 42.0 Consensus size: 2
683547 ATAAACTATT
* * * *
683557 TA TA TA -A TA TA TA CTA TA TA TA AA CA TA CTA TA GTT TA TA TT
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA -TA TA TA TA
*
683599 TA TA TA CTA TA TA T- TA TA TA TA TA AA CTA TA TA TA CTA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA TA
683641 GTA TA
1 -TA TA
683646 ATTTATGAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
1 2 0.03
2 55 0.80
3 12 0.17
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:683703 original size:44 final size:43
Alignment explanation
Indices: 683606--683704 Score: 119
Period size: 44 Copynumber: 2.3 Consensus size: 43
683596 ATTTATATAC
* * * *
683606 TATATATTATATATATAAACTATATATACTATATAGTATAATT
1 TATATACTATATATAAAAACCATATAAACTATATAGTATAATT
*
683649 TATGAAACTATATATAAAAACCATATAAACTATATAGT-TGATATT
1 TAT-ATACTATATATAAAAACCATATAAACTATATAGTAT-A-ATT
683694 TATATACTATA
1 TATATACTATA
683705 AAATAATTTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
43 4 0.09
44 37 0.79
45 6 0.13
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.41
Consensus pattern (43 bp):
TATATACTATATATAAAAACCATATAAACTATATAGTATAATT
Found at i:683762 original size:18 final size:18
Alignment explanation
Indices: 683718--683957 Score: 103
Period size: 18 Copynumber: 13.2 Consensus size: 18
683708 TAATTTATAC
683718 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
* *
683736 TATGGTATATATAAATTA
1 TATAGTATATATAAACTA
**
683754 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
683770 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
**
683787 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
*
683803 T-TAGTATATATAACCTA
1 TATAGTATATATAAACTA
683820 TATAGTATATGGTATATACAAGCTA
1 TATAG--TA---TATATA-AA-CTA
* *
683845 TATATTATATAGTGCATTACTA
1 TATAGTATATA-T--A-AACTA
* *
683867 TATA-TA-ACCTATATAGTA
1 TATAGTATA--TATAAACTA
* *
683885 TATGGTATATACAAACTA
1 TATAGTATATATAAACTA
**
683903 TATA-T-TATAT-AGTTCA
1 TATAGTATATATAAACT-A
683919 T-TAGTATATATAAACTA
1 TATAGTATATATAAACTA
683936 TATAGTATATATAAACTA
1 TATAGTATATATAAACTA
683954 TATA
1 TATA
683958 TTGAAAAGTT
Statistics
Matches: 168, Mismatches: 25, Indels: 58
0.67 0.10 0.23
Matches are distributed among these distances:
15 13 0.08
16 23 0.14
17 24 0.14
18 66 0.39
19 3 0.02
20 8 0.05
21 4 0.02
22 9 0.05
23 10 0.06
24 1 0.01
25 7 0.04
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:683782 original size:33 final size:33
Alignment explanation
Indices: 683740--683946 Score: 203
Period size: 33 Copynumber: 6.8 Consensus size: 33
683730 AAACTATATG
*
683740 GTATATATAAATTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
683773 GTATATATAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
* *
683806 GTATATATAACCTATATAGTATAT-G-------
1 GTATATATAAACTATATATTATATAGTTCATTA
* * *
683831 GTATATACAAGCTATATATTATATAGTGCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
* * *
683864 CTATATATAACCTATATAGTATAT-G-------
1 GTATATATAAACTATATATTATATAGTTCATTA
*
683889 GTATATACAAACTATATATTATATAGTTCATTA
1 GTATATATAAACTATATATTATATAGTTCATTA
*
683922 GTATATATAAACTATATAGTATATA
1 GTATATATAAACTATATATTATATA
683947 TAAACTATAT
Statistics
Matches: 142, Mismatches: 16, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
25 41 0.29
26 2 0.01
32 2 0.01
33 97 0.68
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (33 bp):
GTATATATAAACTATATATTATATAGTTCATTA
Found at i:683826 original size:51 final size:51
Alignment explanation
Indices: 683718--683991 Score: 259
Period size: 58 Copynumber: 5.1 Consensus size: 51
683708 TAATTTATAC
** ** **
683718 TATAGTATATATAAACTATATGGTATATA-TAAATTA-TATATTATATAGTTCA
1 TATAGTATATATAAACTATATATTATATAGTTCATTAGTATA-TATA-ACCT-A
683770 T-TAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTA
1 TATAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTA
* *
683820 TATAGTATATGGTATATACAAGCTATATATTATATAGTGCATTACTATATATAACCTA
1 TATAG--TA---TATATA-AA-CTATATATTATATAGTTCATTAGTATATATAACCTA
*
683878 TATAGTATATGGTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTA
1 TATAG--TA---TATAT--AAACTATATATTATATAGTTCATTAGTATATATAACCTA
*
683936 TATAGTATATATAAACTATATATTGA-AAAGTTCATTAGTATATTATAACCTA
1 TATAGTATATATAAACTATATATT-ATATAGTTCATTAGTATA-TATAACCTA
683988 TATA
1 TATA
683992 TTAATTTATT
Statistics
Matches: 195, Mismatches: 13, Indels: 28
0.83 0.06 0.12
Matches are distributed among these distances:
50 2 0.01
51 57 0.29
52 23 0.12
53 11 0.06
56 8 0.04
57 2 0.01
58 89 0.46
59 2 0.01
60 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.08, T:0.42
Consensus pattern (51 bp):
TATAGTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTA
Found at i:683835 original size:58 final size:58
Alignment explanation
Indices: 683773--683991 Score: 310
Period size: 58 Copynumber: 3.9 Consensus size: 58
683763 TAGTTCATTA
*
683773 GTATATATAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
* * *
683831 GTATATACAAGCTATATATTATATAGTGCATTACTATATATAACCTATATAGTATATG
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
*
683889 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAAACTATATAG--TA--
1 GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
*
683943 -TATAT--AAACTATATATTGA-AAAGTTCATTAGTATATTATAACCTATATA
1 GTATATACAAACTATATATT-ATATAGTTCATTAGTATA-TATAACCTATATA
683992 TTAATTTATT
Statistics
Matches: 149, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
51 27 0.18
52 13 0.09
53 5 0.03
56 2 0.01
58 102 0.68
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.41
Consensus pattern (58 bp):
GTATATACAAACTATATATTATATAGTTCATTAGTATATATAACCTATATAGTATATG
Found at i:683845 original size:25 final size:25
Alignment explanation
Indices: 683806--683854 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
683796 TAGTTCATTA
*
683806 GTATATATAACCTATATAGTATATG
1 GTATATACAACCTATATAGTATATG
* *
683831 GTATATACAAGCTATATATTATAT
1 GTATATACAACCTATATAGTATAT
683855 AGTGCATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (25 bp):
GTATATACAACCTATATAGTATATG
Found at i:683903 original size:25 final size:25
Alignment explanation
Indices: 683865--683912 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
683855 AGTGCATTAC
* *
683865 TATATATAACCTATATAGTATATGG
1 TATATACAAACTATATAGTATATGG
*
683890 TATATACAAACTATATATTATAT
1 TATATACAAACTATATAGTATAT
683913 AGTTCATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (25 bp):
TATATACAAACTATATAGTATATGG
Found at i:684132 original size:61 final size:61
Alignment explanation
Indices: 684051--684180 Score: 190
Period size: 61 Copynumber: 2.1 Consensus size: 61
684041 TATAATGATC
* * * *
684051 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAATTGTAAT-ATTAAATTTGGACT
1 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATTG-AATCATTAAATCTGGACT
* *
684112 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATATATTGCATCATTAAATCTGGACT
1 AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATTGAATCATTAAATCTGGACT
684173 AAATTGAA
1 AAATTGAA
684181 CAAATTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
60 2 0.03
61 60 0.97
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.35
Consensus pattern (61 bp):
AAATTGAAAAAAGTTGAAATATGAAGCTTAAATTAATAAATTGAATCATTAAATCTGGACT
Found at i:684323 original size:18 final size:17
Alignment explanation
Indices: 684302--684335 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
684292 TTTTCAGCAT
684302 TTTCCTTAGTTTTTCTCA
1 TTTCCTTA-TTTTTCTCA
*
684320 TTTCGTTATTTTTCTC
1 TTTCCTTATTTTTCTC
684336 TCTCTAACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.09, C:0.21, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTCCTTATTTTTCTCA
Found at i:684357 original size:18 final size:20
Alignment explanation
Indices: 684334--684378 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
684324 GTTATTTTTC
*
684334 TCTCTCTAACT-CTCTG-AT
1 TCTCTCTAAATCCTCTGCAT
684352 TCTCTC-AAATCCTCTGCAT
1 TCTCTCTAAATCCTCTGCAT
684371 TCTCTCTA
1 TCTCTCTA
684379 GAAAATTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 11 0.48
19 8 0.35
20 1 0.04
ACGTcount: A:0.18, C:0.36, G:0.04, T:0.42
Consensus pattern (20 bp):
TCTCTCTAAATCCTCTGCAT
Found at i:684596 original size:123 final size:123
Alignment explanation
Indices: 684393--684767 Score: 538
Period size: 123 Copynumber: 3.0 Consensus size: 123
684383 ATTAACCGTG
*
684393 TTCATTTTTTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCAA
1 TTCA-TTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCAA
* *
684458 AACATTTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCTTCCGTGTTC
65 ACCA-TTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATCCGTGTTC
* * *
684518 TTCATTTGTTCGTCCCAGTTCTTCCCCAAAA-CCTTATTTGATCTTCAAAAACACCTAAACACAA
1 TTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAAC-CAA
* * * *
684582 ACCATTTCGTGTTTTTTTCGATCAAACACCCAAATTTTCTTCGGTGTTCATCTGTGTTC
65 ACCATTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATCCGTGTTC
* * * *
684641 TTCATTTGTTCATCCCAATTCTTCCCCAAAACCCTCATTTAATATTCAAAAACACCGAAACCAAA
1 TTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCAAA
* * *
684706 CCATTTCGTGTTGTTTTCTATCAAACACCCACAA-ATTCATCCATTGTTCATCCGTGTTC
66 CCATTTCGTGTTTTTTTCGATCAAACACCCA-AATATTCATCC-GTGTTCATCCGTGTTC
684765 TTC
1 TTC
684768 CCTAAATCCT
Statistics
Matches: 223, Mismatches: 23, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
123 144 0.65
124 75 0.34
125 4 0.02
ACGTcount: A:0.27, C:0.29, G:0.08, T:0.37
Consensus pattern (123 bp):
TTCATTTGTTCATCCCAGTTCTTCCCCAAAACCCTCATTTGATCTTCAAAAACACCAAAACCAAA
CCATTTCGTGTTTTTTTCGATCAAACACCCAAATATTCATCCGTGTTCATCCGTGTTC
Found at i:684945 original size:30 final size:29
Alignment explanation
Indices: 684903--684997 Score: 102
Period size: 30 Copynumber: 3.2 Consensus size: 29
684893 ATCCAAACAC
* *
684903 TAACCCAGACCCTAACCCAGACCCAAACCT
1 TAACCCATACCCTAACCCA-ACCCTAACCT
* *
684933 TAATCTATACCCTAACCCTAACCCTAACCT
1 TAACCCATACCCTAACCC-AACCCTAACCT
*
684963 TAACCCATACCC-ATACCCATACCCTAACCC
1 TAACCCATACCCTA-ACCCA-ACCCTAACCT
684993 TAACC
1 TAACC
684998 TGAACCCAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 2 0.04
30 52 0.95
31 1 0.02
ACGTcount: A:0.35, C:0.45, G:0.02, T:0.18
Consensus pattern (29 bp):
TAACCCATACCCTAACCCAACCCTAACCT
Found at i:685003 original size:12 final size:11
Alignment explanation
Indices: 684941--685020 Score: 56
Period size: 12 Copynumber: 6.8 Consensus size: 11
684931 CTTAATCTAT
684941 ACCCTAACCCTA
1 ACCCTAA-CCTA
684953 ACCCTAACCTTA
1 ACCCTAACC-TA
*
684965 ACCC-ATACCCA
1 ACCCTA-ACCTA
*
684976 TACCCATACCCTA
1 -ACCC-TAACCTA
684989 ACCCTAACCTGA
1 ACCCTAACCT-A
685001 ACCC-AACCTGA
1 ACCCTAACCT-A
*
685012 ACCCAAACC
1 ACCCTAACC
685021 CAGGTATTTC
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
11 20 0.35
12 33 0.58
13 3 0.05
14 1 0.02
ACGTcount: A:0.35, C:0.47, G:0.03, T:0.15
Consensus pattern (11 bp):
ACCCTAACCTA
Found at i:685010 original size:11 final size:11
Alignment explanation
Indices: 684988--685017 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
684978 CCCATACCCT
684988 AACCCTAACCTG
1 AACCC-AACCTG
685000 AACCCAACCTG
1 AACCCAACCTG
685011 AACCCAA
1 AACCCAA
685018 ACCCAGGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.40, C:0.43, G:0.07, T:0.10
Consensus pattern (11 bp):
AACCCAACCTG
Found at i:685020 original size:6 final size:6
Alignment explanation
Indices: 684902--684997 Score: 60
Period size: 6 Copynumber: 16.0 Consensus size: 6
684892 AATCCAAACA
* * *
684902 CTAACC C-AGACC CTAACC C-AGACC CAAACC TTAA-T CTATACC CTAACC
1 CTAACC CTA-ACC CTAACC CTA-ACC CTAACC CTAACC CTA-ACC CTAACC
*
684950 CTAACC CTAACC TTAACC C-ATACC C-ATACC C-ATACC CTAACC CTAACC
1 CTAACC CTAACC CTAACC CTA-ACC CTA-ACC CTA-ACC CTAACC CTAACC
684998 TGAACCCAAC
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
5 5 0.07
6 64 0.85
7 6 0.08
ACGTcount: A:0.34, C:0.46, G:0.02, T:0.18
Consensus pattern (6 bp):
CTAACC
Found at i:685233 original size:31 final size:31
Alignment explanation
Indices: 685192--685281 Score: 137
Period size: 31 Copynumber: 2.9 Consensus size: 31
685182 ATATATATAT
685192 ATATACTGGTTTATTGTTGTTGATGTAAATG
1 ATATACTGGTTTATTGTTGTTGATGTAAATG
* *
685223 ATGTACTGGTTTATTGCTGTTGATGTAAATG
1 ATATACTGGTTTATTGTTGTTGATGTAAATG
* *
685254 ATATACTGATTTATTGTTG-TAATGTAAA
1 ATATACTGGTTTATTGTTGTTGATGTAAA
685282 CTAACCATGG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 8 0.15
31 45 0.85
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.47
Consensus pattern (31 bp):
ATATACTGGTTTATTGTTGTTGATGTAAATG
Found at i:686778 original size:133 final size:133
Alignment explanation
Indices: 686540--686807 Score: 536
Period size: 133 Copynumber: 2.0 Consensus size: 133
686530 TAATGCTCAT
686540 AATGATCCATGTGAAGGTATTTCTGCAATGGCTAGACCCATGCTTGAACTATTTGAGAAATATTG
1 AATGATCCATGTGAAGGTATTTCTGCAATGGCTAGACCCATGCTTGAACTATTTGAGAAATATTG
686605 GTCTGATCACTCAATGATTCAGTTTTTTTGTATTTTACTTGATCCTCGATATAAATTACAACTTC
66 GTCTGATCACTCAATGATTCAGTTTTTTTGTATTTTACTTGATCCTCGATATAAATTACAACTTC
686670 TGA
131 TGA
686673 AATGATCCATGTGAAGGTATTTCTGCAATGGCTAGACCCATGCTTGAACTATTTGAGAAATATTG
1 AATGATCCATGTGAAGGTATTTCTGCAATGGCTAGACCCATGCTTGAACTATTTGAGAAATATTG
686738 GTCTGATCACTCAATGATTCAGTTTTTTTGTATTTTACTTGATCCTCGATATAAATTACAACTTC
66 GTCTGATCACTCAATGATTCAGTTTTTTTGTATTTTACTTGATCCTCGATATAAATTACAACTTC
686803 TGA
131 TGA
686806 AA
1 AA
686808 GAGTTGTACA
Statistics
Matches: 135, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
133 135 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (133 bp):
AATGATCCATGTGAAGGTATTTCTGCAATGGCTAGACCCATGCTTGAACTATTTGAGAAATATTG
GTCTGATCACTCAATGATTCAGTTTTTTTGTATTTTACTTGATCCTCGATATAAATTACAACTTC
TGA
Found at i:687775 original size:20 final size:20
Alignment explanation
Indices: 687752--687816 Score: 96
Period size: 20 Copynumber: 3.2 Consensus size: 20
687742 ATTCTGTTTT
687752 ATATTGTTTGCTTCTATTTG
1 ATATTGTTTGCTTCTATTTG
*
687772 ATATTGCTTGCTTCTATTTG
1 ATATTGTTTGCTTCTATTTG
*
687792 ATATTGCTTT-CTTCTACTTG
1 ATATTG-TTTGCTTCTATTTG
687812 ATATT
1 ATATT
687817 TGTAAGGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.14, G:0.12, T:0.57
Consensus pattern (20 bp):
ATATTGTTTGCTTCTATTTG
Found at i:687781 original size:40 final size:40
Alignment explanation
Indices: 687737--687816 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
687727 AATACTTAGA
* * *
687737 GCTTGATTCTGTTTTATATTG-TTTGCTTCTATTTGATATT
1 GCTTGATTCTATTTGATATTGCTTT-CTTCTACTTGATATT
*
687777 GCTTGCTTCTATTTGATATTGCTTTCTTCTACTTGATATT
1 GCTTGATTCTATTTGATATTGCTTTCTTCTACTTGATATT
687817 TGTAAGGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.91
41 3 0.09
ACGTcount: A:0.15, C:0.14, G:0.14, T:0.57
Consensus pattern (40 bp):
GCTTGATTCTATTTGATATTGCTTTCTTCTACTTGATATT
Found at i:688684 original size:51 final size:48
Alignment explanation
Indices: 688628--688756 Score: 168
Period size: 51 Copynumber: 2.6 Consensus size: 48
688618 AATATAAAAC
*
688628 TAAATTTCAAAAAGTAATCATATTAATTTGATTATCATAATAATTTATGA
1 TAAATTTCAAAAAGTAATCATATTAATTTAATTATCAT-A-AATTTATGA
*
688678 TAAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAATTTATTA
1 T-AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAATTTATGA
* * *
688727 TAAATTTAAAATAACATAATTATATTAATT
1 TAAATTTCAAA-AA-GTAATCATATTAATT
688757 GTAACTTCAC
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
48 9 0.13
49 11 0.15
50 15 0.21
51 36 0.51
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (48 bp):
TAAATTTCAAAAAGTAATCATATTAATTTAATTATCATAAATTTATGA
Found at i:690650 original size:20 final size:20
Alignment explanation
Indices: 690627--690678 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
690617 AACGCGATCC
690627 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
690647 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
690667 CCAAAATCGCAA
1 CCAGAATCGCAA
690679 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:690759 original size:20 final size:20
Alignment explanation
Indices: 690734--690927 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
690724 GATTTTCCAT
* *
690734 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
690754 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
690774 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
690794 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
690814 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
690834 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
690854 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
690874 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
690895 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
690915 AATCGCAACGCGA
1 AATCGCAACGCGA
690928 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:690779 original size:40 final size:39
Alignment explanation
Indices: 690730--690927 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
690720 TTGCGATTTT
* ** *
690730 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
690768 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
690809 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
690849 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
690888 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
690928 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:690817 original size:60 final size:60
Alignment explanation
Indices: 690734--690926 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
690724 GATTTTCCAT
* ** * *
690734 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
690794 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
690854 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
690915 AATCGCAACGCG
1 AATCGCAACGCG
690927 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:691345 original size:33 final size:33
Alignment explanation
Indices: 691306--691376 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
691296 TTCACTTAGA
*
691306 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
691339 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
691372 TTTCA
1 TTTCA
691377 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:691480 original size:19 final size:19
Alignment explanation
Indices: 691456--691538 Score: 86
Period size: 19 Copynumber: 4.6 Consensus size: 19
691446 TGCAGAAGAG
691456 TCGCAACGAGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
***
691475 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGA-AATGAAAA
691495 TCGCAACGAG--A-G--AA
1 TCGCAACGAGAAATGAAAA
*
691509 TCGCAACGCGAAATGAAAA
1 TCGCAACGAGAAATGAAAA
691528 TCGCAACGAGA
1 TCGCAACGAGA
691539 GAATCGCAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 9 0.18
16 2 0.04
17 2 0.04
19 23 0.45
20 15 0.29
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.11
Consensus pattern (19 bp):
TCGCAACGAGAAATGAAAA
Found at i:691498 original size:20 final size:20
Alignment explanation
Indices: 691454--691509 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
691444 TTTGCAGAAG
691454 AGTCGCAACGAGA-AATGAA
1 AGTCGCAACGAGAGAATGAA
* *
691473 AATCGCAACGAGAGAATGAC
1 AGTCGCAACGAGAGAATGAA
*
691493 TGTCGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
691510 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 12 0.38
20 20 0.62
ACGTcount: A:0.43, C:0.18, G:0.27, T:0.12
Consensus pattern (20 bp):
AGTCGCAACGAGAGAATGAA
Found at i:691514 original size:14 final size:14
Alignment explanation
Indices: 691495--691549 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
691485 AGAATGACTG
691495 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
691509 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
691528 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
691542 TCGCAACG
1 TCGCAACG
691550 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:691532 original size:33 final size:33
Alignment explanation
Indices: 691495--691565 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
691485 AGAATGACTG
**
691495 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
691528 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
691561 TCGCA
1 TCGCA
691566 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:691583 original size:19 final size:19
Alignment explanation
Indices: 691561--691657 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
691551 GAAACCAAAA
*
691561 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
691580 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
691594 TC-CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
691612 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
691626 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
691645 TCGCGTTGCGATT
1 TCGCGTTGCGATT
691658 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 4, Indels: 22
0.71 0.04 0.25
Matches are distributed among these distances:
13 8 0.13
14 12 0.19
15 3 0.05
16 2 0.03
17 6 0.10
18 2 0.03
19 30 0.48
ACGTcount: A:0.10, C:0.25, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:691634 original size:14 final size:14
Alignment explanation
Indices: 691583--691671 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
691573 TTTCATTTCG
691583 CGTTGCGATTCTC-
1 CGTTGCGATTCTCT
*
691596 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
691615 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
691629 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
691646 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
691662 CGTTGCGATT
1 CGTTGCGATT
691672 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 1, Indels: 21
0.74 0.01 0.24
Matches are distributed among these distances:
13 8 0.12
14 20 0.31
15 4 0.06
16 5 0.08
17 8 0.12
18 3 0.05
19 16 0.25
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:691638 original size:33 final size:33
Alignment explanation
Indices: 691566--691679 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
691556 CAAAATCGCA
691566 TTGCGATTTTCATTTCGCGTTGCGATTCTC-CG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
691598 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
691631 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
691664 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
691680 AACCAAAAGA
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 30 0.39
33 47 0.61
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:693687 original size:181 final size:184
Alignment explanation
Indices: 693367--693826 Score: 872
Period size: 181 Copynumber: 2.5 Consensus size: 184
693357 TAGATTGCTT
*
693367 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693432 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
693497 GTATATTCTTTAACACTGTGAAATATATTTG-TTT-TTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGCTTTGTTTTGTCTTTTGGTTGAA
693549 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693613 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
693678 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTG-CTTTGTTTTGTCTTTTGGTTGAA
693733 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693798 TTTGTCTTTGTTTTGTCTTTTGGTTGAAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAA
693827 ATCGCAACGA
Statistics
Matches: 272, Mismatches: 2, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
181 152 0.56
182 6 0.02
183 3 0.01
184 24 0.09
185 87 0.32
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (184 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGCTTTGTTTTGTCTTTTGGTTGAA
Found at i:693711 original size:92 final size:93
Alignment explanation
Indices: 693367--693826 Score: 860
Period size: 93 Copynumber: 5.0 Consensus size: 93
693357 TAGATTGCTT
*
693367 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693432 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
693460 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693524 TTTG--TTT-TTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
693549 AGTAAA-TTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693613 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
693641 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693705 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
693733 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
693798 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
693826 A
1 A
693827 ATCGCAACGA
Statistics
Matches: 358, Mismatches: 3, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
88 54 0.15
89 30 0.08
90 3 0.01
91 3 0.01
92 122 0.34
93 146 0.41
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:693864 original size:19 final size:19
Alignment explanation
Indices: 693840--693898 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
693830 GCAACGACAG
693840 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
693859 AATCGCAA--CG--A-CAA
1 AATCGCAACGCGAAACCAA
*
693873 GATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACCAA
693892 AATCGCA
1 AATCGCA
693899 TTGCGATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.31, G:0.17, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACCAA
Found at i:693866 original size:33 final size:33
Alignment explanation
Indices: 693824--693898 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
693814 CTTTTGGTTG
693824 AAAATCGCAACGAC-AGAATCGCAACGCGAAACC
1 AAAATCGCAACGACAAG-ATCGCAACGCGAAACC
693857 AAAATCGCAACGACAAGATCGCAACGCGAAACC
1 AAAATCGCAACGACAAGATCGCAACGCGAAACC
693890 AAAATCGCA
1 AAAATCGCA
693899 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 39 0.95
34 2 0.05
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGACAAGATCGCAACGCGAAACC
Found at i:693935 original size:14 final size:14
Alignment explanation
Indices: 693916--693971 Score: 58
Period size: 14 Copynumber: 3.7 Consensus size: 14
693906 TTTCATTTCG
693916 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
*
693930 CGTTGCGATTTTCATT
1 CGTTGCGA--TTCTTT
*
693946 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
693962 CGTTGCGATT
1 CGTTGCGATT
693972 TTCATTTCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 16 0.46
16 13 0.37
18 6 0.17
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:693954 original size:32 final size:33
Alignment explanation
Indices: 693899--694026 Score: 159
Period size: 32 Copynumber: 3.8 Consensus size: 33
693889 CAAAATCGCA
*
693899 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
693932 TTGCGATTTTCA-TTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
693964 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTCGCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCT-G-T--CG
* *
694001 TTGCGATTTTAAGTTTCGTGTTGCGA
1 TTGCGATTTTCA-TTTCGCGTTGCGA
694027 AAGTAAACTA
Statistics
Matches: 83, Mismatches: 6, Indels: 7
0.86 0.06 0.07
Matches are distributed among these distances:
32 30 0.36
33 26 0.31
34 1 0.01
35 1 0.01
37 13 0.16
38 12 0.14
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:695921 original size:14 final size:14
Alignment explanation
Indices: 695902--695937 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
695892 ATTGTTTAAT
695902 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
695916 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
695930 TGATTTGT
1 TGATTTGT
695938 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:696059 original size:19 final size:19
Alignment explanation
Indices: 696043--696144 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
696033 AAAAATGACT
696043 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
696062 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
696081 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
696095 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
696114 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
696134 ATCGCAATGCG
1 ATCGCAATGCG
696145 TTTATAATTC
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:696196 original size:19 final size:19
Alignment explanation
Indices: 696172--696481 Score: 403
Period size: 19 Copynumber: 17.4 Consensus size: 19
696162 GATTATCTCG
696172 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
696191 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
696210 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
696224 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
696243 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
696262 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
696281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
696300 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
696318 TTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCA
*
696337 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
696356 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
696370 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
696389 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
696408 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
696422 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
696442 TTGCGA-TTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
696455 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
696474 TTGCGATT
1 TTGCGATT
696482 GTATTTTCCG
Statistics
Matches: 258, Mismatches: 10, Indels: 46
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.02
14 23 0.09
15 1 0.00
16 23 0.09
17 21 0.08
18 20 0.08
19 159 0.62
20 6 0.02
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:696353 original size:146 final size:139
Alignment explanation
Indices: 696152--696481 Score: 481
Period size: 146 Copynumber: 2.4 Consensus size: 139
696142 GCGTTTATAA
* *
696152 TTCGCATTGCGA-TT-ATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 TTCGCATTGCGATTTCATCTCGTTGCGATTTTCATTCCGCATTGCGATTTTAATTTCGCATTGCG
* *
696215 ATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGC
66 ATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
696280 ATTGCGATTTTCAT
127 -TTGCGATTTTCAT
*
696294 TTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTCCGCATTGCGATTTTAATTTCGCATTG
1 TTCGCATTGCGATTTCATCTCG--TTGCGATTTTCATTCCGCATTGCGATTTTAATTTCGCATTG
696359 CGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
64 CGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTT
696424 GCGATTTTCAT
129 GCGATTTTCAT
* * *
696435 TTCCGCATTGCGATTTCA--T-GTTGGGATTTTCATTTCGCGTTGCGATT
1 TT-CGCATTGCGATTTCATCTCGTTGCGATTTTCATTCCGCATTGCGATT
696482 GTATTTTCCG
Statistics
Matches: 175, Mismatches: 8, Indels: 15
0.88 0.04 0.08
Matches are distributed among these distances:
137 24 0.14
139 1 0.01
140 1 0.01
141 15 0.09
142 27 0.15
143 6 0.03
144 8 0.05
146 93 0.53
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (139 bp):
TTCGCATTGCGATTTCATCTCGTTGCGATTTTCATTCCGCATTGCGATTTTAATTTCGCATTGCG
ATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGC
GATTTTCAT
Found at i:696453 original size:52 final size:55
Alignment explanation
Indices: 696172--696450 Score: 391
Period size: 52 Copynumber: 5.2 Consensus size: 55
696162 GATTATCTCG
696172 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
696224 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGCA
*
696281 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCATTGCGATTTTCATTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCG-ATTGCGATTTTCATTTCGCA
* *
696337 TTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
*
696389 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTT-CGCA
696442 TTGCGATTT
1 TTGCGATTT
696451 CATGTTGGGA
Statistics
Matches: 215, Mismatches: 6, Indels: 11
0.93 0.03 0.05
Matches are distributed among these distances:
52 108 0.50
53 13 0.06
54 7 0.03
55 8 0.04
56 54 0.25
57 25 0.12
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (55 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGCA
Found at i:696476 original size:52 final size:50
Alignment explanation
Indices: 696250--696481 Score: 234
Period size: 52 Copynumber: 4.4 Consensus size: 50
696240 GCATTGCGAT
*
696250 TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
1 TTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT--C---G-GA
* * * *
696306 TTTCATTTCGCATTGCGATTTTCATTCCGCATTGCGATTTTAATTTCGCA
1 TTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGGA
* *
696356 TTGCGA-TTCTGTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTTC-ATTTC-G-CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGGA
* * *
696408 TTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA-TTTCATGTTGGGA
1 TTTC-ATT-TCGCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT-TTCGGA
696461 TTTTCATTTCGCGTTGCGATT
1 -TTTCATTTCGCGTTGCGATT
696482 GTATTTTCCG
Statistics
Matches: 156, Mismatches: 12, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
50 7 0.04
51 3 0.02
52 78 0.50
53 18 0.12
54 6 0.04
56 44 0.28
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (50 bp):
TTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGGA
Found at i:698973 original size:24 final size:24
Alignment explanation
Indices: 698939--698985 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
698929 CTGAAACATC
698939 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
698963 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
698986 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:699694 original size:20 final size:20
Alignment explanation
Indices: 699666--700034 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
699656 AAATTTAAGT
* * * *
699666 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
699686 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
699706 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
699726 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
699746 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
699766 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
699786 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
699806 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
699826 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
699846 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
699866 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
699886 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
699906 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
699926 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
699946 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
699966 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
699986 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
700006 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
700026 GTTGCGATT
1 GTTGCGATT
700035 ATGTAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:708803 original size:9 final size:9
Alignment explanation
Indices: 708789--708822 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
708779 AAATAAACAG
708789 TATTAATAA
1 TATTAATAA
708798 TATTAATAA
1 TATTAATAA
708807 TA-TAATAA
1 TATTAATAA
*
708815 TAATAATA
1 TATTAATA
708823 TAATTATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
TATTAATAA
Found at i:708813 original size:14 final size:14
Alignment explanation
Indices: 708794--708831 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
708784 AACAGTATTA
708794 ATAATATTAATAAT
1 ATAATATTAATAAT
*
708808 ATAATAATAATAAT
1 ATAATATTAATAAT
708822 ATAATTATTA
1 ATAA-TATTA
708832 TATCCCGGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATATTAATAAT
Found at i:714796 original size:21 final size:20
Alignment explanation
Indices: 714772--714866 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 20
714762 TCGACGGTTC
*
714772 TATGCGGTCTTTCGAGACATA
1 TATGTGGTCTTTCGA-ACATA
* *
714793 TATGTGATCCTTTGGAACATA
1 TATGTGGT-CTTTCGAACATA
*
714814 TATGTGTTCTTTCGAGACATA
1 TATGTGGTCTTTCGA-ACATA
* *
714835 TATTTGGTCATTTGGAACATA
1 TATGTGGTC-TTTCGAACATA
714856 TATGTGGTCTT
1 TATGTGGTCTT
714867 ACAAGACAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.13
21 43 0.69
22 11 0.18
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (20 bp):
TATGTGGTCTTTCGAACATA
Found at i:714874 original size:42 final size:42
Alignment explanation
Indices: 714772--714866 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
714762 TCGACGGTTC
* *
714772 TATGCGGTCTTTCGAGACATATATGTGATCCTTTGGAACATA
1 TATGTGGTCTTTCGAGACATATATGTGATCATTTGGAACATA
* * *
714814 TATGTGTTCTTTCGAGACATATATTTGGTCATTTGGAACATA
1 TATGTGGTCTTTCGAGACATATATGTGATCATTTGGAACATA
714856 TATGTGGTCTT
1 TATGTGGTCTT
714867 ACAAGACAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (42 bp):
TATGTGGTCTTTCGAGACATATATGTGATCATTTGGAACATA
Found at i:714968 original size:23 final size:23
Alignment explanation
Indices: 714921--714968 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
714911 ATTCGGGACA
* *
714921 TTCTATGTGGCACTTCGATGTAT
1 TTCTACGTGGCACTTCGATGCAT
*
714944 TTCTACGTGGCACTTCGGTGCAT
1 TTCTACGTGGCACTTCGATGCAT
714967 TT
1 TT
714969 TATACGTGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (23 bp):
TTCTACGTGGCACTTCGATGCAT
Found at i:716003 original size:20 final size:22
Alignment explanation
Indices: 715947--716005 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 22
715937 CAATACCTAG
*
715947 GGGGTACCGATACCTCAGTTGA
1 GGGGTACCGATACCTCAATTGA
*
715969 GGGATGTATCGATACC-CAATTGA
1 GGG--GTACCGATACCTCAATTGA
715992 -GGGTACCGATACCT
1 GGGGTACCGATACCT
716006 ACTTTAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 10 0.32
22 5 0.16
23 6 0.19
24 10 0.32
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.24
Consensus pattern (22 bp):
GGGGTACCGATACCTCAATTGA
Found at i:722668 original size:22 final size:20
Alignment explanation
Indices: 722638--722695 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
722628 TGGTGCAGGA
* *
722638 GGAATCGATACCCCTTTGAAGG
1 GGAACCGATACCCC-CTGAA-G
* *
722660 GGAACCGATTCCCCCTGGAG
1 GGAACCGATACCCCCTGAAG
722680 GGAACCGATACCCCCT
1 GGAACCGATACCCCCT
722696 ACGGGGTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 16 0.52
21 3 0.10
22 12 0.39
ACGTcount: A:0.24, C:0.33, G:0.26, T:0.17
Consensus pattern (20 bp):
GGAACCGATACCCCCTGAAG
Found at i:729332 original size:46 final size:46
Alignment explanation
Indices: 729279--729367 Score: 160
Period size: 46 Copynumber: 1.9 Consensus size: 46
729269 TGCTACTTGG
* *
729279 ATAACTATTATTTTGATTATCATGGCTTTGTTGTATAGTCATTAGC
1 ATAACTATTATTTTGATTATCATGGCTTTGATGTATAGCCATTAGC
729325 ATAACTATTATTTTGATTATCATGGCTTTGATGTATAGCCATT
1 ATAACTATTATTTTGATTATCATGGCTTTGATGTATAGCCATT
729368 CTTTTGTCCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.11, G:0.15, T:0.47
Consensus pattern (46 bp):
ATAACTATTATTTTGATTATCATGGCTTTGATGTATAGCCATTAGC
Found at i:729835 original size:44 final size:45
Alignment explanation
Indices: 729785--729872 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 45
729775 ACACCCTAAG
*
729785 AAGCTTACATCCATAAATCACAAAAAGCTTACATCCACC-ATTAC
1 AAGCTTACATCCAGAAATCACAAAAAGCTTACATCCACCTATTAC
* * *
729829 AAGCTTACATCTAGAAATCACAATAAGCTTTCATCCACCTATTA
1 AAGCTTACATCCAGAAATCACAAAAAGCTTACATCCACCTATTA
729873 TTTAATTACC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 35 0.90
45 4 0.10
ACGTcount: A:0.41, C:0.27, G:0.06, T:0.26
Consensus pattern (45 bp):
AAGCTTACATCCAGAAATCACAAAAAGCTTACATCCACCTATTAC
Found at i:730857 original size:18 final size:20
Alignment explanation
Indices: 730811--730860 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
730801 TAGTTTACGT
* *
730811 AATGTAAGATTACTAGCGGG
1 AATGTAAGATTACCAGCGAG
730831 AATGTAAGATTACCAGCGAG
1 AATGTAAGATTACCAGCGAG
730851 -A-GTAAGATTA
1 AATGTAAGATTA
730861 TTGGAAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 9 0.32
19 1 0.04
20 18 0.64
ACGTcount: A:0.40, C:0.10, G:0.26, T:0.24
Consensus pattern (20 bp):
AATGTAAGATTACCAGCGAG
Found at i:731082 original size:36 final size:37
Alignment explanation
Indices: 731011--731082 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 37
731001 CTATAATTAA
**
731011 TTTATATATTTTCTTTAAAAAATTTAAATTCATAAAG
1 TTTATATATTTTCTTTAAAAAATTTAAAAACATAAAG
* *
731048 TTTATATAATTTT-TTTACAAAA-TTAAAAAGATAAA
1 TTTATAT-ATTTTCTTTAAAAAATTTAAAAACATAAA
731083 TAAATTTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
36 10 0.33
37 15 0.50
38 5 0.17
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (37 bp):
TTTATATATTTTCTTTAAAAAATTTAAAAACATAAAG
Found at i:733025 original size:51 final size:51
Alignment explanation
Indices: 732970--733188 Score: 156
Period size: 51 Copynumber: 4.3 Consensus size: 51
732960 CAGCCTTTCG
*
732970 GCCATACCCAGATCCGTA-TCCAGATTC-GGATTCCCCATACTCGGGTTTCCT
1 GCCATACCCAGATCCGTAGT-CAGATCCTGG-TTCCCCATACTCGGGTTTCCT
* * * * *
733021 GCCATATCCGGATCCGTAGTCGGATCCTTGTTCCCCATACTTGGGTTTCCT
1 GCCATACCCAGATCCGTAGTCAGATCCTGGTTCCCCATACTCGGGTTTCCT
* * * * * * * * * * *
733072 GTCATATCCGGATTCGTATTCGGATCCTTGCTCCCCAGAGTCGGTTTTCCT
1 GCCATACCCAGATCCGTAGTCAGATCCTGGTTCCCCATACTCGGGTTTCCT
** * * * * **
733123 TTCATATCCGGATCCGTATTCAGATCCTTGTTCCCCATACTCAAGTCTTCC-
1 GCCATACCCAGATCCGTAGTCAGATCCTGGTTCCCCATACTCGGGT-TTCCT
*
733174 ACCATACCCAGATCC
1 GCCATACCCAGATCC
733189 AAATTCAGGA
Statistics
Matches: 138, Mismatches: 27, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
51 132 0.96
52 6 0.04
ACGTcount: A:0.18, C:0.33, G:0.17, T:0.32
Consensus pattern (51 bp):
GCCATACCCAGATCCGTAGTCAGATCCTGGTTCCCCATACTCGGGTTTCCT
Found at i:735454 original size:30 final size:30
Alignment explanation
Indices: 735411--735497 Score: 138
Period size: 30 Copynumber: 2.9 Consensus size: 30
735401 ACGACGGCGA
* *
735411 GGCGGTGTTTTCTTCATGTTGAAGAACCAC
1 GGCGGCGTGTTCTTCATGTTGAAGAACCAC
* *
735441 GGCGGCGTGTTCTTCATGCTGAAGAATCAC
1 GGCGGCGTGTTCTTCATGTTGAAGAACCAC
735471 GGCGGCGTGTTCTTCATGTTGAAGAAC
1 GGCGGCGTGTTCTTCATGTTGAAGAAC
735498 ACGCGAGAGA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (30 bp):
GGCGGCGTGTTCTTCATGTTGAAGAACCAC
Found at i:736162 original size:3 final size:3
Alignment explanation
Indices: 736144--736198 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
736134 AATTTGAATG
* * * *
736144 ATT ACT ATT ATT -TT ATT ATT ATT ACT ATT ATA AGT ATT ATT ATT -TT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
736190 ATT ATT ATT
1 ATT ATT ATT
736199 TTTACCTAAC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:736165 original size:11 final size:11
Alignment explanation
Indices: 736149--736200 Score: 54
Period size: 11 Copynumber: 4.8 Consensus size: 11
736139 GAATGATTAC
736149 TATTATTTTAT
1 TATTATTTTAT
*
736160 TATTA--TTAC
1 TATTATTTTAT
**
736169 TATTATAAGTAT
1 TATTAT-TTTAT
736181 TATTATTTTAT
1 TATTATTTTAT
736192 TATTATTTT
1 TATTATTTT
736201 TACCTAACTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
9 8 0.24
11 17 0.52
12 8 0.24
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:739927 original size:23 final size:23
Alignment explanation
Indices: 739884--739927 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
739874 AGACCACAAG
* *
739884 AAAACTCTTCTGCTGTCAAAGGA
1 AAAACTCATCTGCTATCAAAGGA
739907 AAAACATCATCTGCTAT-AAAG
1 AAAAC-TCATCTGCTATCAAAG
739928 ATGCAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 9 0.50
24 9 0.50
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (23 bp):
AAAACTCATCTGCTATCAAAGGA
Found at i:746574 original size:75 final size:74
Alignment explanation
Indices: 746446--746584 Score: 172
Period size: 75 Copynumber: 1.9 Consensus size: 74
746436 AATACTTCGC
* * * *
746446 TTAGGATGAAAACCCGAAAAGGCGTCCTAAGTCGAAAAAAGGAAAAAGAAGAAAAACAACAAAGA
1 TTAGGATGAAAACCCGAAAAGGAGCCCTAAATCAAAAAAAGGAAAAAGAAGAAAAACAA-AAAGA
746511 GTGAAAATGT
65 GTGAAAATGT
* * * * *
746521 TTAGGGTGAAAACCCGAAAGGGAGCCCTAAATTAAAAAAATTGAAAAAG-AGAAAAAGAAAAAGA
1 TTAGGATGAAAACCCGAAAAGGAGCCCTAAATCAAAAAAA-GGAAAAAGAAGAAAAACAAAAAGA
746585 ACAAAAATAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
74 5 0.09
75 42 0.78
76 7 0.13
ACGTcount: A:0.55, C:0.11, G:0.22, T:0.12
Consensus pattern (74 bp):
TTAGGATGAAAACCCGAAAAGGAGCCCTAAATCAAAAAAAGGAAAAAGAAGAAAAACAAAAAGAG
TGAAAATGT
Found at i:747416 original size:43 final size:43
Alignment explanation
Indices: 747359--747464 Score: 185
Period size: 43 Copynumber: 2.5 Consensus size: 43
747349 TAGCTCGAAA
**
747359 TACGATTTCAACTCCACGATGGAGGATATCGTACCCACACATC
1 TACGATTTCAACTCCACGACAGAGGATATCGTACCCACACATC
*
747402 TGCGATTTCAACTCCACGACAGAGGATATCGTACCCACACATC
1 TACGATTTCAACTCCACGACAGAGGATATCGTACCCACACATC
747445 TACGATTTCAACTCCACGAC
1 TACGATTTCAACTCCACGAC
747465 GAAGGGAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.30, C:0.32, G:0.15, T:0.23
Consensus pattern (43 bp):
TACGATTTCAACTCCACGACAGAGGATATCGTACCCACACATC
Found at i:747476 original size:43 final size:43
Alignment explanation
Indices: 747359--747476 Score: 170
Period size: 43 Copynumber: 2.7 Consensus size: 43
747349 TAGCTCGAAA
*
747359 TACGATTTCAACTCCACGATG-GAGGATATCGTACCCACACATC
1 TACGATTTCAACTCCACGACGAG-GGATATCGTACCCACACATC
*
747402 TGCGATTTCAACTCCACGAC-AGAGGATATCGTACCCACACATC
1 TACGATTTCAACTCCACGACGAG-GGATATCGTACCCACACATC
747445 TACGATTTCAACTCCACGACGAAGGGA-ATCGT
1 TACGATTTCAACTCCACGACG-AGGGATATCGT
747477 GCATACAAAC
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
43 64 0.93
44 3 0.04
45 2 0.03
ACGTcount: A:0.31, C:0.30, G:0.18, T:0.22
Consensus pattern (43 bp):
TACGATTTCAACTCCACGACGAGGGATATCGTACCCACACATC
Found at i:748043 original size:161 final size:161
Alignment explanation
Indices: 747722--748046 Score: 609
Period size: 159 Copynumber: 2.0 Consensus size: 161
747712 CACCAAAGTC
747722 TTTAGGTCAAGTTTCACCTTCACGACGAAGTGTCTTGAGACAGAAGACGATTCGGAGGCCACTAA
1 TTTAGGTCAAGTTTCACCTTCACGACGAAG-GTCTTGAGACAGAAGACGATTCGGAGGCCACTAA
747787 CCAAAAGCTTTGAGTTCGATTTCAACTTCACGACGAAGGATATCGTGCTCATAAGCTTCCAGTTC
65 CCAAAAGCTTTGAGTTCGATTTCAACTTCACGACGAAGGATATCGTGCTCATAAGCTTCCAGTTC
747852 ACTCGACCTCCGACGAGGGAGTCATTCGATAT
130 ACTCGACCTCCGACGAGGGAGTCATTCGATAT
747884 TTTAGGTC-AGTTTCACCTTCACGACGAA-GTCTTGAGACAGAAGACGATTCGGAGGCCACTAAC
1 TTTAGGTCAAGTTTCACCTTCACGACGAAGGTCTTGAGACAGAAGACGATTCGGAGGCCACTAAC
747947 CAAAAGCTTTGAGTTCGATTTCAACTTCACGACGAAGGATATCGTGCTCATAAGCTTCCAGTTCA
66 CAAAAGCTTTGAGTTCGATTTCAACTTCACGACGAAGGATATCGTGCTCATAAGCTTCCAGTTC-
748012 ACTCGACCTCACGACGAGGGAGTCATTCGATAT
130 ACTCGACCTC-CGACGAGGGAGTCATTCGATAT
748045 TT
1 TT
748047 CAATCCATAT
Statistics
Matches: 161, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
159 99 0.61
160 10 0.06
161 44 0.27
162 8 0.05
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (161 bp):
TTTAGGTCAAGTTTCACCTTCACGACGAAGGTCTTGAGACAGAAGACGATTCGGAGGCCACTAAC
CAAAAGCTTTGAGTTCGATTTCAACTTCACGACGAAGGATATCGTGCTCATAAGCTTCCAGTTCA
CTCGACCTCCGACGAGGGAGTCATTCGATAT
Found at i:749506 original size:2 final size:2
Alignment explanation
Indices: 749499--749549 Score: 72
Period size: 2 Copynumber: 26.5 Consensus size: 2
749489 ATTTCCTATG
749499 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
749539 CTA T- TA TA TA T
1 -TA TA TA TA TA T
749550 CTAACCTAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.07
2 40 0.89
3 2 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:754067 original size:18 final size:19
Alignment explanation
Indices: 754034--754074 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
754024 AGTTTTCATG
754034 AAAACAACATAATTAAATCA
1 AAAACAACA-AATTAAATCA
754054 AAAACAAC-AATTAAATCA
1 AAAACAACAAATTAAATCA
754072 AAA
1 AAA
754075 CAATAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAACAACAAATTAAATCA
Found at i:754082 original size:17 final size:18
Alignment explanation
Indices: 754042--754082 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
754032 TGAAAACAAC
754042 ATAATTAAATCAAAAACA
1 ATAATTAAATCAAAAACA
*
754060 ACAATTAAATC-AAAACA
1 ATAATTAAATCAAAAACA
754077 ATAATT
1 ATAATT
754083 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAATTAAATCAAAAACA
Found at i:758430 original size:20 final size:20
Alignment explanation
Indices: 758405--758458 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
758395 GACCAACAAA
758405 TTCGCAACGCGAATTCCAAT
1 TTCGCAACGCGAATTCCAAT
* *
758425 TTCGCAAC-CCAGTTTCCAAT
1 TTCGCAACGCGA-ATTCCAAT
758445 TTCGCAACGCGAAT
1 TTCGCAACGCGAAT
758459 ATGTAATTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 24 0.86
21 2 0.07
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
TTCGCAACGCGAATTCCAAT
Found at i:758507 original size:20 final size:20
Alignment explanation
Indices: 758482--758573 Score: 71
Period size: 19 Copynumber: 4.7 Consensus size: 20
758472 TGCGATTTTC
* * *
758482 CAAATTTGCAATGCGATAGT
1 CAAATTCGCAACGCGAAAGT
758502 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * * **
758522 TAAATTCACAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
* **
758541 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAAAGT
758560 CAAATTCGCAACGC
1 CAAATTCGCAACGC
758574 CAATTTAATT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
19 33 0.55
20 27 0.45
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Done.