Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 109 of 378
Found at i:30236223 original size:2 final size:2
Alignment explanation
Indices: 30236216--30236254 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
30236206 TTTGGTTGCG
30236216 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30236255 GCAAATGGCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30239576 original size:25 final size:25
Alignment explanation
Indices: 30239547--30239597 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
30239537 TAATTTTGTC
30239547 ATTGCCATCTTCATTTCTAGATTCT
1 ATTGCCATCTTCATTTCTAGATTCT
30239572 ATTGCCATCTTCATTTCTAGATTCT
1 ATTGCCATCTTCATTTCTAGATTCT
30239597 A
1 A
30239598 ACATTGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.08, T:0.47
Consensus pattern (25 bp):
ATTGCCATCTTCATTTCTAGATTCT
Found at i:30241268 original size:58 final size:59
Alignment explanation
Indices: 30241150--30241311 Score: 195
Period size: 58 Copynumber: 2.8 Consensus size: 59
30241140 GTGACGAGAT
* *
30241150 TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGC-ATGCTGGAAAAATA
1 TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
***
30241208 TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGA-GCTCGAAGGGTA
1 TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
* ** * **
30241266 TGGCACTGTGTGTGCGGGCT-TAAATCGCATGGCACTAAGTGTGCGA
1 TGGCACTGAGTGTGCATGCTGGAAAT-ATATGGCACTAAGTGTGCGA
30241312 AATCGAGTAT
Statistics
Matches: 91, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
57 4 0.04
58 86 0.95
59 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (59 bp):
TGGCACTGAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCGATGCTCGAAAAATA
Found at i:30241272 original size:29 final size:29
Alignment explanation
Indices: 30241150--30241251 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
30241140 GTGACGAGAT
30241150 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
30241179 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
30241208 TGGCACTGAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
30241237 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
30241252 GAGCTCGAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 69 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:30246554 original size:15 final size:15
Alignment explanation
Indices: 30246534--30246572 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
30246524 TGGATTCAGT
*
30246534 GGATCATTCAGATCA
1 GGATCATTCAAATCA
*
30246549 GGATCATTTAAATCA
1 GGATCATTCAAATCA
30246564 GGATCATTC
1 GGATCATTC
30246573 CCTTTCCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (15 bp):
GGATCATTCAAATCA
Found at i:30251630 original size:48 final size:48
Alignment explanation
Indices: 30251505--30251642 Score: 204
Period size: 48 Copynumber: 2.9 Consensus size: 48
30251495 TGTCTCATAT
* ** *
30251505 CAATGCCATGTCCCAGACATGGTCTTACACGAAATCACATATCGATGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGATGC
* * *
30251553 CAATGCCATATCCTAGATATGGTCTTACATGGGATCTCATATCGATGC
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGATGC
*
30251601 CAATGCCATGTCCCAGACATGGTCTTACATGGGATATCATAT
1 CAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATAT
30251643 AACCCTAATG
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 79 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (48 bp):
CAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCATATCGATGC
Found at i:30253212 original size:37 final size:37
Alignment explanation
Indices: 30253091--30253199 Score: 191
Period size: 37 Copynumber: 2.9 Consensus size: 37
30253081 TTATTACGAA
*
30253091 GTCTTACCCGGACATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
30253128 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
* *
30253165 GTCTTACCCGGTCAAAATCTCCGCACGTAGTCATC
1 GTCTTACCCGGTCATAATCTCCACACGTAGTCATC
30253200 AGATCTCACC
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 69 1.00
ACGTcount: A:0.23, C:0.33, G:0.18, T:0.26
Consensus pattern (37 bp):
GTCTTACCCGGTCATAATCTCCACACGTAGTCATCGG
Found at i:30253320 original size:49 final size:49
Alignment explanation
Indices: 30253267--30253499 Score: 358
Period size: 49 Copynumber: 4.8 Consensus size: 49
30253257 ATTCACATTT
* * * *
30253267 GCCATTCGGCTTTACCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
* *
30253316 GCCATTAGGCCTTATCACATATATATACACTTTCGCATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
* **
30253365 GCCATTAGGCCTTATCACATATACGTACACCATCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
*
30253414 GCCATTAGGCCTTATCACATATACATACACCTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
* *
30253463 GCCATTAGGCCTTATCACATATATATACATTTTCACA
1 GCCATTAGGCCTTATCACATATACATACACTTTCACA
30253500 AATTTTAATA
Statistics
Matches: 168, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 168 1.00
ACGTcount: A:0.30, C:0.31, G:0.09, T:0.30
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
Found at i:30256896 original size:38 final size:38
Alignment explanation
Indices: 30256810--30256961 Score: 196
Period size: 38 Copynumber: 3.9 Consensus size: 38
30256800 GAATTTGGTC
* * * * *
30256810 ACCAGCACAAAACTTGCGGGACTTTAAGCTCGAATATAAT
1 ACCAGCACTAAGCCTGCGGGA-TTTAA-CCCGGATATAAT
*
30256850 ACCAGCACTAAGCCTGCGGGATTTAACCCTGATATAAT
1 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
*
30256888 ACCGGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
1 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
* * *
30256926 ACCAGTACGAAGCCTGCGGGATTTAACTCGGATATA
1 ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATA
30256962 CATCAAATAT
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
38 77 0.77
39 5 0.05
40 18 0.18
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (38 bp):
ACCAGCACTAAGCCTGCGGGATTTAACCCGGATATAAT
Found at i:30259330 original size:13 final size:13
Alignment explanation
Indices: 30259312--30259337 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30259302 ATATTATAAT
30259312 TATTTTATGTTAA
1 TATTTTATGTTAA
30259325 TATTTTATGTTAA
1 TATTTTATGTTAA
30259338 AAATAAAAAT
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:0.08, T:0.62
Consensus pattern (13 bp):
TATTTTATGTTAA
Found at i:30268021 original size:2 final size:2
Alignment explanation
Indices: 30268014--30268044 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
30268004 AGGCACAAAC
30268014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30268045 CTCCTAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30269339 original size:46 final size:46
Alignment explanation
Indices: 30269286--30269461 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
30269276 TATTTGGGCA
30269286 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
30269332 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
* *
30269379 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * *
30269425 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
30269462 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 32 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:30269441 original size:93 final size:93
Alignment explanation
Indices: 30269282--30269454 Score: 310
Period size: 93 Copynumber: 1.9 Consensus size: 93
30269272 GGGATATTTG
* *
30269282 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
30269347 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
30269375 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
30269440 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
30269455 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.31, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:30280444 original size:27 final size:26
Alignment explanation
Indices: 30280414--30280509 Score: 111
Period size: 27 Copynumber: 3.6 Consensus size: 26
30280404 GTGACGAAGT
30280414 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGA-ACAGATATTGTGGCAGAGC
* *
30280441 CACCAGAACAGATATATGTGGTAGAAC
1 CACCAGAACAGATAT-TGTGGCAGAGC
* * * *
30280468 CGCCAGATCAGATAATCGTGGCATAGC
1 CACCAGAACAGAT-ATTGTGGCAGAGC
30280495 CACCAGAACAGATAT
1 CACCAGAACAGATAT
30280510 ATTGTAACAC
Statistics
Matches: 57, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
26 10 0.18
27 45 0.79
28 2 0.04
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
CACCAGAACAGATATTGTGGCAGAGC
Found at i:30281272 original size:31 final size:32
Alignment explanation
Indices: 30281197--30281281 Score: 102
Period size: 31 Copynumber: 2.6 Consensus size: 32
30281187 CTCAAACATG
*
30281197 TACTGGGCC-ATAGCCCTTTTCATATTTCATATT
1 TACTGGGCCGA-AG-CCTTTTCAAATTTCATATT
30281230 TAACACTGGGCCGAAGCCTTTTCAAATTTCATA-T
1 T---ACTGGGCCGAAGCCTTTTCAAATTTCATATT
30281264 TACTGGGCCGAAGCCTTT
1 TACTGGGCCGAAGCCTTT
30281282 ACGGTAAACG
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
31 17 0.36
33 1 0.02
34 2 0.04
35 16 0.34
36 10 0.21
37 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (32 bp):
TACTGGGCCGAAGCCTTTTCAAATTTCATATT
Found at i:30281521 original size:24 final size:24
Alignment explanation
Indices: 30281475--30281648 Score: 244
Period size: 24 Copynumber: 7.2 Consensus size: 24
30281465 GCTTTATCAT
* *
30281475 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* * *
30281500 ATAACTGAGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTG
30281524 ATAACTGGGGCATAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
30281547 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
30281571 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
30281595 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
*
30281619 ATAACTGGGGTATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
30281643 ATAACT
1 ATAACT
30281649 TCCTCCATTC
Statistics
Matches: 135, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
23 21 0.16
24 103 0.76
25 11 0.08
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:30281576 original size:71 final size:72
Alignment explanation
Indices: 30281475--30281648 Score: 244
Period size: 71 Copynumber: 2.4 Consensus size: 72
30281465 GCTTTATCAT
* * *
30281475 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGAGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGAGGCAAAAGCCCTTTTGATAACTGGGGCATAA
*
30281539 GCCC-TTTG
64 GCCCTTTTA
* * *
30281547 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGAGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
30281612 CCTTTTA
66 CCTTTTA
*
30281619 ATAACTGGGGTATAAGCCCTTTTGATAACT
1 ATAACTGGGGCATAAGCCCTTTTGATAACT
30281649 TCCTCCATTC
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
71 49 0.53
72 43 0.47
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGAGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTTA
Found at i:30281716 original size:9 final size:9
Alignment explanation
Indices: 30281702--30281758 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
30281692 ATCTCGTGTG
30281702 CATATCATA
1 CATATCATA
*
30281711 CATATCATGTG
1 CATATCA--TA
30281722 CATATCATA
1 CATATCATA
* *
30281731 CATGTCATGTG
1 CATATCA--TA
30281742 CATATCATA
1 CATATCATA
30281751 CATATCAT
1 CATATCAT
30281759 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:30281721 original size:20 final size:20
Alignment explanation
Indices: 30281698--30281760 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
30281688 GAACATCTCG
30281698 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
30281718 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
30281738 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
30281758 TGT
1 TGT
30281761 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:30281836 original size:25 final size:25
Alignment explanation
Indices: 30281797--30281844 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
30281787 ATATATAAAC
* * *
30281797 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
30281822 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
30281845 CATATTATAA
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:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:30287643 original size:40 final size:39
Alignment explanation
Indices: 30287475--30287645 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
30287465 AGAAATTGAA
* *
30287475 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
30287515 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
30287555 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
30287595 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
30287635 TGATATCCGGG
1 TGATATCCGGG
30287646 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:30291879 original size:25 final size:25
Alignment explanation
Indices: 30291839--30291898 Score: 102
Period size: 25 Copynumber: 2.3 Consensus size: 25
30291829 CGGCCATGGG
30291839 AGGTAAGAATGTTGAAAAGTCAACATT
1 AGGTAAG--TGTTGAAAAGTCAACATT
30291866 AGGTAAGTGTTGAAAAGTCAACATT
1 AGGTAAGTGTTGAAAAGTCAACATT
30291891 AGGTAAGT
1 AGGTAAGT
30291899 TAATGACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
25 26 0.79
27 7 0.21
ACGTcount: A:0.42, C:0.07, G:0.25, T:0.27
Consensus pattern (25 bp):
AGGTAAGTGTTGAAAAGTCAACATT
Found at i:30292851 original size:46 final size:45
Alignment explanation
Indices: 30292793--30293018 Score: 180
Period size: 44 Copynumber: 5.0 Consensus size: 45
30292783 TCACTTGTGT
* * *
30292793 GAGCTAGAGTAAGACATGTCTGGGACATGCATTGG-ATACATTATGA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-CA-GATGA
* *
30292839 GAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGAGATGA
1 GAGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA-TCAGATGA
* * *
30292887 GTGCTAGTGTAAGACATGTCTGGAACATGCATCGGCCTCAAGAT-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATC-AGATGA
* * *
30292932 -AGCTAGTATAAGACATGTTTGGGACATGCATCGAC-TACGAGAT-A
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCAT-C-AGATGA
* *
30292976 -TG-TCAGTGTAAGACCATGTCTGGGACATGGCATTGGCA-CAGAT
1 GAGCT-AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCAGAT
30293019 ATACTATAAC
Statistics
Matches: 149, Mismatches: 21, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
43 2 0.01
44 49 0.33
45 16 0.11
46 31 0.21
47 25 0.17
48 23 0.15
49 2 0.01
50 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (45 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCAGATGA
Found at i:30295374 original size:46 final size:46
Alignment explanation
Indices: 30295298--30295414 Score: 132
Period size: 46 Copynumber: 2.5 Consensus size: 46
30295288 GACGAGTGCT
*
30295298 AGTGTAAGACATGTTTGGGACATGTATCGGCCT-CAAGACG-TAAGCC
1 AGTGTAAGACATGTCTGGGACATGTATCGG-CTACAAGACGAT-AGCC
* * *
30295344 AGTGTAAGACATGTCTGGGACAT-TCGTCGGCTACAAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGT-ATCGGCTACAAGACGATAGCC
*
30295390 AGTGTAAGACCATGTCTGCGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
30295415 GCTTCAACTT
Statistics
Matches: 61, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
45 3 0.05
46 44 0.72
47 14 0.23
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGTATCGGCTACAAGACGATAGCC
Found at i:30296458 original size:28 final size:28
Alignment explanation
Indices: 30296418--30296483 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
30296408 CACAAGGGCT
*
30296418 AGGACACGAGTGTGTCATGGCCGTGTGA
1 AGGACACGAGTGTGTCATGGCCATGTGA
30296446 AGGACACGAGTGTGTCATGGCCATGTGA
1 AGGACACGAGTGTGTCATGGCCATGTGA
30296474 AGGACACGAG
1 AGGACACGAG
30296484 CCAGGGACAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.26, C:0.18, G:0.38, T:0.18
Consensus pattern (28 bp):
AGGACACGAGTGTGTCATGGCCATGTGA
Found at i:30308640 original size:4 final size:4
Alignment explanation
Indices: 30308631--30308655 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
30308621 AGTGTAGGTG
30308631 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
30308656 GTATAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:30309606 original size:29 final size:29
Alignment explanation
Indices: 30309563--30309677 Score: 135
Period size: 29 Copynumber: 4.0 Consensus size: 29
30309553 GCGAGCATGA
* *
30309563 ATATGAATGTTATTTGGGCCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
*
30309592 ATATAAATGTGATTTGGGTCTGATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
* * * *
30309621 ATATAAATGTAAATTAGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
* *
30309650 ATACAAATGTGA-TTGGGCCAG-TGGGCC
1 ATATAAATGTGATTTGGGCCTGATGGGCC
30309677 A
1 A
30309678 GATACAGGTA
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
27 7 0.10
28 6 0.08
29 60 0.82
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.30
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTGATGGGCC
Found at i:30310005 original size:27 final size:26
Alignment explanation
Indices: 30309958--30310012 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
30309948 AAACCCGTAA
* * * *
30309958 TAAAGGAAAAATTATCGAAATGCCCC
1 TAAAGGAAAAATGACCAAAATACCCC
30309984 TAAAGGCAAAAATGACCAAAATACCCC
1 TAAAGG-AAAAATGACCAAAATACCCC
30310011 TA
1 TA
30310013 TATGTTGAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.49, C:0.22, G:0.13, T:0.16
Consensus pattern (26 bp):
TAAAGGAAAAATGACCAAAATACCCC
Found at i:30313338 original size:46 final size:46
Alignment explanation
Indices: 30313247--30313372 Score: 137
Period size: 46 Copynumber: 2.7 Consensus size: 46
30313237 CATTTGTGAG
* * *
30313247 AGCTAGTGTAAGACCATGTCTGCGACGTGGCATCAGAATTGAGACG-A
1 AGCTAGTGTAAGA-CATGTCTGAGACAT-GCATCAGAATCGAGACGTA
* **
30313294 GTGCTAGTGTAAGACATGTCTGAGACATGCATCAGCCTCGAGACGTA
1 -AGCTAGTGTAAGACATGTCTGAGACATGCATCAGAATCGAGACGTA
* * *
30313341 AGCCAGTGTAAGACATGTCCGGGACATGCATC
1 AGCTAGTGTAAGACATGTCTGAGACATGCATC
30313373 GACTACAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
46 42 0.63
47 13 0.19
48 12 0.18
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (46 bp):
AGCTAGTGTAAGACATGTCTGAGACATGCATCAGAATCGAGACGTA
Found at i:30313394 original size:46 final size:46
Alignment explanation
Indices: 30313299--30313415 Score: 139
Period size: 46 Copynumber: 2.5 Consensus size: 46
30313289 GACGAGTGCT
* * *
30313299 AGTGTAAGACATGTCTGAGACATGCATCAGCCTCGAGACGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGACTCAAGACGTAAGCC
* * *
30313345 AGTGTAAGACATGTCCGGGACATGCATC-GACTACAAGATGGT-AGTC
1 AGTGTAAGACATGTCTGGGACATGCATCAGACT-CAAGA-CGTAAGCC
30313391 AGTGTAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
30313416 GCTTTGACTT
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
45 3 0.05
46 42 0.69
47 16 0.26
ACGTcount: A:0.30, C:0.21, G:0.28, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGACTCAAGACGTAAGCC
Found at i:30313632 original size:13 final size:13
Alignment explanation
Indices: 30313614--30313639 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30313604 TAAAATGTGA
30313614 GCCACATTATATG
1 GCCACATTATATG
30313627 GCCACATTATATG
1 GCCACATTATATG
30313640 CTATATGATG
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:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
GCCACATTATATG
Found at i:30316181 original size:22 final size:21
Alignment explanation
Indices: 30316137--30316179 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
30316127 TACAATCTAG
30316137 TAGCGGAAAAGTGATTTTTTT
1 TAGCGGAAAAGTGATTTTTTT
30316158 TAGCGGAAAAGTGATTTTTTT
1 TAGCGGAAAAGTGATTTTTTT
30316179 T
1 T
30316180 TACTTTGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.44
Consensus pattern (21 bp):
TAGCGGAAAAGTGATTTTTTT
Found at i:30316824 original size:45 final size:45
Alignment explanation
Indices: 30316773--30317000 Score: 239
Period size: 45 Copynumber: 5.1 Consensus size: 45
30316763 ATAGATAAAA
* * *
30316773 ACTAGGCTGTGGATGCACAACAAAA-ATTCAG-AGATGAAACCTGTC
1 ACTAGGCTGTGGATACACAACAAAATA-TC-GCAGATAAAACCTGCC
* * **
30316818 ACTAGGCTGTGGGTACACAGCAAAATATCGCAGATAAAATTTGCC
1 ACTAGGCTGTGGATACACAACAAAATATCGCAGATAAAACCTGCC
* * **
30316863 ACTAGGCTGTGGGTACACAGCAAAATATCGCAGATAAAATTTGCC
1 ACTAGGCTGTGGATACACAACAAAATATCGCAGATAAAACCTGCC
* * *
30316908 ACTAGGCTGTGAATACACAACAAAA-ATTCGCAGATGAAACCTGTC
1 ACTAGGCTGTGGATACACAACAAAATA-TCGCAGATAAAACCTGCC
* * * *
30316953 ACT-GGCTGTGGGTACACAGCAAAATATCACAGATAAAATCTGCC
1 ACTAGGCTGTGGATACACAACAAAATATCGCAGATAAAACCTGCC
30316997 ACTA
1 ACTA
30317001 CATTGTAGAT
Statistics
Matches: 157, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
44 37 0.24
45 119 0.76
46 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (45 bp):
ACTAGGCTGTGGATACACAACAAAATATCGCAGATAAAACCTGCC
Found at i:30316987 original size:89 final size:90
Alignment explanation
Indices: 30316773--30317000 Score: 273
Period size: 90 Copynumber: 2.5 Consensus size: 90
30316763 ATAGATAAAA
* * * * * * * **
30316773 ACTAGGCTGTGGATGCACAACAAAA-ATTCAGAGATGAAACCTGTCACTAGGCTGTGGGTACACA
1 ACTAGGCTGTGGGTACACAGCAAAATA-TCACAGATAAAATCTGCCACTAGGCTGTGAATACACA
* **
30316837 GCAAAATATCGCAGATAAAATTTGCC
65 ACAAAATATCGCAGATAAAACCTGCC
* *
30316863 ACTAGGCTGTGGGTACACAGCAAAATATCGCAGATAAAATTTGCCACTAGGCTGTGAATACACAA
1 ACTAGGCTGTGGGTACACAGCAAAATATCACAGATAAAATCTGCCACTAGGCTGTGAATACACAA
* *
30316928 CAAAA-ATTCGCAGATGAAACCTGTC
66 CAAAATA-TCGCAGATAAAACCTGCC
30316953 ACT-GGCTGTGGGTACACAGCAAAATATCACAGATAAAATCTGCCACTA
1 ACTAGGCTGTGGGTACACAGCAAAATATCACAGATAAAATCTGCCACTA
30317001 CATTGTAGAT
Statistics
Matches: 118, Mismatches: 18, Indels: 5
0.84 0.13 0.04
Matches are distributed among these distances:
89 44 0.37
90 73 0.62
91 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (90 bp):
ACTAGGCTGTGGGTACACAGCAAAATATCACAGATAAAATCTGCCACTAGGCTGTGAATACACAA
CAAAATATCGCAGATAAAACCTGCC
Found at i:30317580 original size:28 final size:28
Alignment explanation
Indices: 30317549--30317665 Score: 121
Period size: 28 Copynumber: 4.1 Consensus size: 28
30317539 TAAAATTTGG
*
30317549 AAAATAAAGG-AAAATTTGTAAAATCTAA
1 AAAATAAAGGCAAAA-TTATAAAATCTAA
* * *
30317577 AAAAT-AGGGAAAAAACTATAAAATCTAAA
1 AAAATAAAGG-CAAAATTATAAAATCT-AA
* *
30317606 AAAATATAGGCAAAATTATAAAATCCAA
1 AAAATAAAGGCAAAATTATAAAATCTAA
**
30317634 AAAATAGGGGCAAAATTATAAAATCTAA
1 AAAATAAAGGCAAAATTATAAAATCTAA
30317662 AAAA
1 AAAA
30317666 CAAGAAACAC
Statistics
Matches: 74, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
27 3 0.04
28 45 0.61
29 24 0.32
30 2 0.03
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (28 bp):
AAAATAAAGGCAAAATTATAAAATCTAA
Found at i:30317610 original size:57 final size:57
Alignment explanation
Indices: 30317549--30317665 Score: 164
Period size: 57 Copynumber: 2.1 Consensus size: 57
30317539 TAAAATTTGG
* *
30317549 AAAATAAAGG-AAAATTTGTAAAATCTAAAAAATAGGGAAAAAACTATAAAATCTAAA
1 AAAATAAAGGCAAAA-TTATAAAATCCAAAAAATAGGGAAAAAACTATAAAATCTAAA
* ** *
30317606 AAAATATAGGCAAAATTATAAAATCCAAAAAATAGGGGCAAAATTATAAAATCTAAA
1 AAAATAAAGGCAAAATTATAAAATCCAAAAAATAGGGAAAAAACTATAAAATCTAAA
30317663 AAA
1 AAA
30317666 CAAGAAACAC
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 49 0.92
58 4 0.08
ACGTcount: A:0.62, C:0.07, G:0.10, T:0.21
Consensus pattern (57 bp):
AAAATAAAGGCAAAATTATAAAATCCAAAAAATAGGGAAAAAACTATAAAATCTAAA
Found at i:30319016 original size:38 final size:38
Alignment explanation
Indices: 30318965--30319041 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
30318955 ACAAAAATGG
*
30318965 TAAATTTTCAAAAATTTGACAGTATTATGAATTAGTAC
1 TAAATTTTCAAAAATTTGACAGTATTATAAATTAGTAC
30319003 TAAATTTTCAAAAATTTGACAGTATTATAAATTAGTAC
1 TAAATTTTCAAAAATTTGACAGTATTATAAATTAGTAC
30319041 T
1 T
30319042 TGGGCTAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (38 bp):
TAAATTTTCAAAAATTTGACAGTATTATAAATTAGTAC
Found at i:30320434 original size:2 final size:2
Alignment explanation
Indices: 30320427--30320451 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
30320417 CTCGTATGTA
30320427 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
30320452 GGTTTTAATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30324326 original size:34 final size:34
Alignment explanation
Indices: 30324274--30324354 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
30324264 TTAGCCCCTC
30324274 TTTCAGTAGCAGTAACAGTCTGGG-CTTGAGCCCA
1 TTTCAGTAGCAGTAACAGTCTGGGCCTT-AGCCCA
** * *
30324308 TTTCAGTATTAGTGACAGTTTGGGCCTTAGCCCA
1 TTTCAGTAGCAGTAACAGTCTGGGCCTTAGCCCA
30324342 TTTCAGTA-CAGTA
1 TTTCAGTAGCAGTA
30324355 TGCAAACACA
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
33 3 0.08
34 34 0.85
35 3 0.08
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (34 bp):
TTTCAGTAGCAGTAACAGTCTGGGCCTTAGCCCA
Found at i:30334720 original size:171 final size:171
Alignment explanation
Indices: 30334418--30334751 Score: 450
Period size: 171 Copynumber: 1.9 Consensus size: 171
30334408 TTTTGTAAGG
* * *
30334418 CATTTTCCAACTCTCACTAATCTTTCCTCCTTGCGCCGTTCTTCATCTTCCTTCTTCATCATCCA
1 CATTTTCCAACTCTCACCAATCTTT-CTCCTTGAGCCGTACTTCATCTTCCTTCTTCATCATCCA
* * *
30334483 GGTACTTTCCTCCTACTTCTTCTGTTCTTCATCTTTTAATTTTCTTTTTTCCTTAGCTTTTCGCA
65 GGTACTTTCCTCCTACTTCTTCTATTCGTCATCTTTTAATTTTCTGTTTTCCTTAGCTTTTCGCA
30334548 TATCTTCTCTTCTCAGGGCTGCTGTTTCGTTTCGCTCTGTAA
130 TATCTTCTCTTCTCAGGGCTGCTGTTTCGTTTCGCTCTGTAA
*
30334590 CATTTTCCAACTCTCACCAATC-TT-TCC-T-AGCCGTACTTCATCTTCCTTCTTC-TCCATCTA
1 CATTTTCCAACTCTCACCAATCTTTCTCCTTGAGCCGTACTTCATCTTCCTTCTTCAT-CATCCA
*
30334650 GGTAACTTTTTTCCTTCTACTTCTTCTATTCGTCATCTTTT-ATTTTC-GTTTTCCTTAG-TGTC
65 GGT-AC---TTTCCTCCTACTTCTTCTATTCGTCATCTTTTAATTTTCTGTTTTCCTTAGCT-T-
*
30334712 TGTCGCATATCTTCTCTTCTCAGGGCTGTTGTTTCGTTTC
124 T-TCGCATATCTTCTCTTCTCAGGGCTGCTGTTTCGTTTC
30334752 ACTTAAATCT
Statistics
Matches: 145, Mismatches: 9, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
166 1 0.01
167 30 0.21
168 4 0.03
169 14 0.10
170 7 0.05
171 68 0.47
172 21 0.14
ACGTcount: A:0.13, C:0.30, G:0.10, T:0.48
Consensus pattern (171 bp):
CATTTTCCAACTCTCACCAATCTTTCTCCTTGAGCCGTACTTCATCTTCCTTCTTCATCATCCAG
GTACTTTCCTCCTACTTCTTCTATTCGTCATCTTTTAATTTTCTGTTTTCCTTAGCTTTTCGCAT
ATCTTCTCTTCTCAGGGCTGCTGTTTCGTTTCGCTCTGTAA
Found at i:30337771 original size:28 final size:28
Alignment explanation
Indices: 30337739--30337865 Score: 204
Period size: 28 Copynumber: 4.5 Consensus size: 28
30337729 ACAGTAAGTC
30337739 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATT-AAACT
30337767 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATT-AAACT
*
30337796 CGCACACTTAGTGCTATGCAATTAAACT
1 CGCACACTTAGTGCTATACAATTAAACT
30337824 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATTAAACT
30337852 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30337866 CAATCTCATT
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
28 61 0.64
29 33 0.35
30 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATTAAACT
Found at i:30337823 original size:57 final size:56
Alignment explanation
Indices: 30337739--30337865 Score: 204
Period size: 57 Copynumber: 2.2 Consensus size: 56
30337729 ACAGTAAGTC
30337739 CGCACACTTAGTGCTTAATATTCAAACTCGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTTAATATTCAAACTCGCACACTTAGTGCTATACAATT-AAACT
*
30337796 CGCACACTTAGTGCTATGCA-ATT-AAACTCGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCT-T-AATATTCAAACTCGCACACTTAGTGCTATACAATTAAACT
30337852 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30337866 CAATCTCATT
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
56 19 0.28
57 43 0.64
58 4 0.06
59 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (56 bp):
CGCACACTTAGTGCTTAATATTCAAACTCGCACACTTAGTGCTATACAATTAAACT
Found at i:30338988 original size:17 final size:18
Alignment explanation
Indices: 30338951--30338988 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
30338941 CACTTTTTTT
30338951 TTCCTTTGTTTTCATCATA
1 TTCCTTTGTTTTCAT-ATA
*
30338970 TTCCTTTTTTTTCAT-TA
1 TTCCTTTGTTTTCATATA
30338987 TT
1 TT
30338989 TTATTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.66
Consensus pattern (18 bp):
TTCCTTTGTTTTCATATA
Found at i:30345470 original size:28 final size:28
Alignment explanation
Indices: 30345438--30345564 Score: 204
Period size: 28 Copynumber: 4.5 Consensus size: 28
30345428 TACAGTAGTC
30345438 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATT-AAACT
30345466 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATT-AAACT
*
30345495 CGCACACTTAGTGCTATGCAATTAAACT
1 CGCACACTTAGTGCTATACAATTAAACT
30345523 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATTAAACT
30345551 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30345565 CAATCTCATT
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
28 61 0.64
29 33 0.35
30 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATTAAACT
Found at i:30345522 original size:57 final size:56
Alignment explanation
Indices: 30345438--30345564 Score: 204
Period size: 57 Copynumber: 2.2 Consensus size: 56
30345428 TACAGTAGTC
30345438 CGCACACTTAGTGCTTAATATTCAAACTCGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTTAATATTCAAACTCGCACACTTAGTGCTATACAATT-AAACT
*
30345495 CGCACACTTAGTGCTATGCA-ATT-AAACTCGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCT-T-AATATTCAAACTCGCACACTTAGTGCTATACAATTAAACT
30345551 CGCACACTTAGTGC
1 CGCACACTTAGTGC
30345565 CAATCTCATT
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
56 19 0.28
57 43 0.64
58 4 0.06
59 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.13, T:0.28
Consensus pattern (56 bp):
CGCACACTTAGTGCTTAATATTCAAACTCGCACACTTAGTGCTATACAATTAAACT
Found at i:30346689 original size:17 final size:18
Alignment explanation
Indices: 30346652--30346689 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
30346642 CACTTTTTTT
30346652 TTCCTTTGTTTTCATCATA
1 TTCCTTTGTTTTCAT-ATA
*
30346671 TTCCTTTTTTTTCAT-TA
1 TTCCTTTGTTTTCATATA
30346688 TT
1 TT
30346690 TTATTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
19 14 0.78
ACGTcount: A:0.13, C:0.18, G:0.03, T:0.66
Consensus pattern (18 bp):
TTCCTTTGTTTTCATATA
Found at i:30349280 original size:21 final size:21
Alignment explanation
Indices: 30349256--30349331 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 21
30349246 GTCTTGAATT
30349256 TGTTAGATATTGAATTTTTTA
1 TGTTAGATATTGAATTTTTTA
* * * *
30349277 TGTTTTAAGCTTGTTAAATTTATTA
1 TG--TT-AG-ATATTGAATTTTTTA
30349302 TGTTAGATATTGAATTTATTTA
1 TGTTAGATATTGAATTT-TTTA
*
30349324 -GTTGGATA
1 TGTTAGATA
30349332 ATGATATTGA
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 17 0.41
22 5 0.12
23 4 0.10
24 2 0.05
25 13 0.32
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.54
Consensus pattern (21 bp):
TGTTAGATATTGAATTTTTTA
Found at i:30350618 original size:20 final size:20
Alignment explanation
Indices: 30350575--30350618 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
30350565 TTTAAAATAT
*
30350575 AAATTTATTAATACATATAT
1 AAATTTATTAATACATATAA
* *
30350595 AAATTTATTAATATATGTAA
1 AAATTTATTAATACATATAA
30350615 AAAT
1 AAAT
30350619 AGCTTTTCCG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATTTATTAATACATATAA
Found at i:30350702 original size:34 final size:33
Alignment explanation
Indices: 30350629--30350702 Score: 78
Period size: 34 Copynumber: 2.2 Consensus size: 33
30350619 AGCTTTTCCG
*
30350629 AAAAATATTTTCAAGAAATCTGCCAAATAACAA
1 AAAAATATTTTCAAGAAATCTGCCAAACAACAA
* * * *
30350662 ATAAATATTTTACACAG-ATTCTTCCAAACACCAA
1 AAAAATATTTT-CA-AGAAATCTGCCAAACAACAA
30350696 AAAAATA
1 AAAAATA
30350703 AATTATTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 10 0.30
34 21 0.64
35 2 0.06
ACGTcount: A:0.53, C:0.18, G:0.04, T:0.26
Consensus pattern (33 bp):
AAAAATATTTTCAAGAAATCTGCCAAACAACAA
Found at i:30367499 original size:161 final size:161
Alignment explanation
Indices: 30367294--30367607 Score: 493
Period size: 161 Copynumber: 2.0 Consensus size: 161
30367284 CTTTATCTTG
* *
30367294 TTAGGATTATACAGTAATAGTTAAAATTTAGTTTTAGTCCTTATCTTATATTCAACTTAAAATTT
1 TTAGGATTATAAAGTAATAGTTAAAATTCAGTTTTAGTCCTTATCTTATATTCAACTTAAAATTT
* * * *
30367359 ATTTTTTATATATTAATTTTTTATAATATCATTAATTAATTTAAATATTTTATTTTAATTAAAAT
66 ATTCTTTATACATTAATTTTTTACAATATCATTAATCAATTTAAATATTTTATTTTAATTAAAAT
*
30367424 ACTAACATGAATTTTTTAAATTTGCATTTTC
131 AATAACATGAATTTTTTAAATTTGCATTTTC
* * * * *
30367455 TTAGGATTATAAAGTAATCGTTACAATTCAGTTTTAGTCCTTATCTTATATTTAATTTAAATTTT
1 TTAGGATTATAAAGTAATAGTTAAAATTCAGTTTTAGTCCTTATCTTATATTCAACTTAAAATTT
* *
30367520 ATTCTTTATACATTAATTTTTTACAATGTCATTAATCAATTTAAATATTTTATTTTGATTAAAAT
66 ATTCTTTATACATTAATTTTTTACAATATCATTAATCAATTTAAATATTTTATTTTAATTAAAAT
*
30367585 AATAACATGAATTTTTTTAATTT
131 AATAACATGAATTTTTTAAATTT
30367608 ATTAATATCA
Statistics
Matches: 138, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
161 138 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.51
Consensus pattern (161 bp):
TTAGGATTATAAAGTAATAGTTAAAATTCAGTTTTAGTCCTTATCTTATATTCAACTTAAAATTT
ATTCTTTATACATTAATTTTTTACAATATCATTAATCAATTTAAATATTTTATTTTAATTAAAAT
AATAACATGAATTTTTTAAATTTGCATTTTC
Found at i:30374093 original size:128 final size:128
Alignment explanation
Indices: 30373873--30374382 Score: 693
Period size: 128 Copynumber: 4.0 Consensus size: 128
30373863 TAATATGAAT
* * * * * *
30373873 AAATCTATTTATATGATACACATGACAGACAATAATTAAAGAAATCTAAATTTGTCATACTCTTT
1 AAATCCATTTATGTGATACACATGACAGACAATAATCAAAGAAATCCAAACTTGCCATACTCTTT
* * *
30373938 GATACAAACAATAATCATATTTTAACAAATAAATTCAAACCTACCATACACTTTAATACAAAT
66 GATACAAATAATAATCATATTTCAACAAATAAATTCAAACCTACCATACACTTTAATACAAAC
** ** * *
30374001 AAATCCATTTATGTGATGTACATGACAGACAATAGCCAAAGAAATCCGAACATGCCATACTCTTT
1 AAATCCATTTATGTGATACACATGACAGACAATAATCAAAGAAATCCAAACTTGCCATACTCTTT
* * *
30374066 GATACAAAAAAAAATCATATTTCAACAAATAAATTCAAACCTGCCATACACTTTAATACAAAC
66 GATACAAATAATAATCATATTTCAACAAATAAATTCAAACCTACCATACACTTTAATACAAAC
* * *
30374129 AAATCCATTTATTTGATACACATGACAGACAATAATCAAAGAAATCTAAACTTGCCTTACTCTTT
1 AAATCCATTTATGTGATACACATGACAGACAATAATCAAAGAAATCCAAACTTGCCATACTCTTT
* *
30374194 GATACAAATAATAATCATATTTCAACAAATAAATTCAAACCTGCCATACACTTTAACACAAAC
66 GATACAAATAATAATCATATTTCAACAAATAAATTCAAACCTACCATACACTTTAATACAAAC
* * * * * *
30374257 AAATCCATTTATGTGATGCACGTGATAGACAATAA-CAAA-AAATTCCAAACCTACCGTACTCTT
1 AAATCCATTTATGTGATACACATGACAGACAATAATCAAAGAAA-TCCAAACTTGCCATACTCTT
* * *
30374320 TAATACAAATAATAATCATATTTCAACAAATAAA-TCTAAACCTATCATATACTTTAATACAAA
65 TGATACAAATAATAATCATATTTCAACAAATAAATTC-AAACCTACCATACACTTTAATACAAA
30374383 AAAGAATCAT
Statistics
Matches: 338, Mismatches: 42, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
126 5 0.01
127 75 0.22
128 258 0.76
ACGTcount: A:0.46, C:0.19, G:0.06, T:0.29
Consensus pattern (128 bp):
AAATCCATTTATGTGATACACATGACAGACAATAATCAAAGAAATCCAAACTTGCCATACTCTTT
GATACAAATAATAATCATATTTCAACAAATAAATTCAAACCTACCATACACTTTAATACAAAC
Found at i:30375193 original size:17 final size:16
Alignment explanation
Indices: 30375168--30375215 Score: 78
Period size: 17 Copynumber: 2.9 Consensus size: 16
30375158 GAAAAAGAAT
30375168 TATTTTTTAATTTTAA
1 TATTTTTTAATTTTAA
30375184 TATATTTTTAATATTTAA
1 TAT-TTTTTAAT-TTTAA
30375202 TATTTTTTAATTTT
1 TATTTTTTAATTTT
30375216 TAAAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.20
17 16 0.53
18 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATTTTTTAATTTTAA
Found at i:30385309 original size:39 final size:39
Alignment explanation
Indices: 30385263--30385480 Score: 310
Period size: 39 Copynumber: 5.6 Consensus size: 39
30385253 GCTCTGGTGA
* *
30385263 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTCTGT
1 GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTATGT
* *
30385302 GCTTCAGTCAACCTTCGGGCTTCCGTTTAGCACTTCTGT
1 GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTATGT
*** *
30385341 GCTTCAGTCGGCCTTCGGGCTTCCGTTTAGCACTTGTGT
1 GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTATGT
* *
30385380 GCTTCAGTTAGCCTCCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTATGT
* *
30385419 GCTTCAGCTAAACTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTATGT
* *
30385458 GCTTCAGCTAAACTTCGGGCTTC
1 GCTTCAGTTAACCTTCGGGCTTC
30385481 AGATCACGAA
Statistics
Matches: 166, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 166 1.00
ACGTcount: A:0.13, C:0.28, G:0.23, T:0.36
Consensus pattern (39 bp):
GCTTCAGTTAACCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:30385481 original size:18 final size:18
Alignment explanation
Indices: 30385419--30385482 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
30385409 GCACTTATGT
30385419 GCTTCAGCTAAACTTCGG
1 GCTTCAGCTAAACTTCGG
* * * * *
30385437 GCTTCCGTTTAGCACTTATGT
1 GCTTCAG-CTA-AACTT-CGG
30385458 GCTTCAGCTAAACTTCGG
1 GCTTCAGCTAAACTTCGG
30385476 GCTTCAG
1 GCTTCAG
30385483 ATCACGAAGG
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
18 14 0.42
19 6 0.18
20 6 0.18
21 7 0.21
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.33
Consensus pattern (18 bp):
GCTTCAGCTAAACTTCGG
Found at i:30390581 original size:14 final size:14
Alignment explanation
Indices: 30390562--30390589 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30390552 GATTAGACGA
30390562 GCTGTTGGAAAGCT
1 GCTGTTGGAAAGCT
30390576 GCTGTTGGAAAGCT
1 GCTGTTGGAAAGCT
30390590 TTAATTACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.36, T:0.29
Consensus pattern (14 bp):
GCTGTTGGAAAGCT
Found at i:30392010 original size:17 final size:17
Alignment explanation
Indices: 30391988--30392053 Score: 62
Period size: 17 Copynumber: 3.7 Consensus size: 17
30391978 TAAAAATTTA
*
30391988 TTCTTTTCTTTCTCTCT
1 TTCTTTTCTTTTTCTCT
*
30392005 TTCTTTTTTTTTTCTCT
1 TTCTTTTCTTTTTCTCT
*
30392022 CTT-TTTGCTTTTTCTTCCT
1 -TTCTTTTCTTTTTC-T-CT
30392041 TTCTTCTTCTTTT
1 TTCTT-TTCTTTT
30392054 ATAGTGTCGG
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 24 0.62
18 5 0.13
19 4 0.10
20 6 0.15
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (17 bp):
TTCTTTTCTTTTTCTCT
Found at i:30392015 original size:21 final size:21
Alignment explanation
Indices: 30391991--30392053 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
30391981 AAATTTATTC
30391991 TTTTCTTTCTCTCTTTCTTTT
1 TTTTCTTTCTCTCTTTCTTTT
*
30392012 TTTT-TTCTCTCTTTTTGCTTTT
1 TTTTCTT-TCTCTCTTT-CTTTT
*
30392034 TCTTCCTTTCT-TC-TTCTTTT
1 T-TTTCTTTCTCTCTTTCTTTT
30392054 ATAGTGTCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
20 7 0.20
21 14 0.40
22 7 0.20
23 5 0.14
24 2 0.06
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (21 bp):
TTTTCTTTCTCTCTTTCTTTT
Found at i:30392033 original size:19 final size:19
Alignment explanation
Indices: 30391988--30392053 Score: 66
Period size: 19 Copynumber: 3.5 Consensus size: 19
30391978 TAAAAATTTA
30391988 TTCTTTTCTTTCTCTCTTTC
1 TTCTTTT-TTTCTCTCTTTC
*
30392008 TTTTTTTTTTCTCTCTTT-
1 TTCTTTTTTTCTCTCTTTC
*
30392026 TTGCTTTTTCT-TC-CTTTC
1 TT-CTTTTTTTCTCTCTTTC
30392044 TTCTTCTTTT
1 TTCTT-TTTT
30392054 ATAGTGTCGG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
17 7 0.18
18 9 0.23
19 17 0.44
20 6 0.15
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.74
Consensus pattern (19 bp):
TTCTTTTTTTCTCTCTTTC
Found at i:30392851 original size:33 final size:30
Alignment explanation
Indices: 30392771--30392855 Score: 91
Period size: 30 Copynumber: 2.7 Consensus size: 30
30392761 CCAACTTCGG
** *
30392771 AAAAATATAGTTTAAGTACCACTTATGACAA
1 AAAAATATAGTTTAAGTACCA-AGATGAAAA
*
30392802 AAAAAT-TATTTTAAGTACCAAGATGAAAGA
1 AAAAATATAGTTTAAGTACCAAGATGAAA-A
30392832 AAGAGAATATAGTTTAAGTACCAA
1 AA-A-AATATAGTTTAAGTACCAA
30392856 TTTATGGGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 5 0.11
30 16 0.36
31 7 0.16
32 3 0.07
33 14 0.31
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (30 bp):
AAAAATATAGTTTAAGTACCAAGATGAAAA
Found at i:30394482 original size:127 final size:127
Alignment explanation
Indices: 30394349--30394665 Score: 411
Period size: 127 Copynumber: 2.5 Consensus size: 127
30394339 CAAGAAATCA
* *
30394349 AAACCCAACACATTAGGGCACGATTTCCT-GAATTGCCAAACATCAATCATCGCTTTTGTTTTAA
1 AAACCCAACACATTAGGGCACGA-TTCCTCGAATTGCCAAACATCAAACATCGCCTTTGTTTTAA
* * * * *
30394413 AGTTTAATAAATGCGAACGAAGTTTAAAAGGGAAATCTGAGTATTTAGACAAACGAAAGATCG
65 AGTTTAAAAAACGCGAACAAAATTTAAAAGGGAAATCTGAGTATTTAAACAAACGAAAGATCG
* * * * *
30394476 AAACCCAGCACATTAGGGTACGATTCCTCGAATTTCTAAACATCAAACATCGCCTTTGTTTTAAG
1 AAACCCAACACATTAGGGCACGATTCCTCGAATTGCCAAACATCAAACATCGCCTTTGTTTTAAA
* * * *
30394541 GTTTAAAAAACGCGGACAAAATTTTAAAGGGAAATTTGATTATTTAAACAAACGAAAGATCG
66 GTTTAAAAAACGCGAACAAAATTTAAAAGGGAAATCTGAGTATTTAAACAAACGAAAGATCG
* * * * * * *
30394603 AAACCCAACACATTAGGGCACGGTCCCTCGAATTTCTAAACATCAAACTTCACCTTTTTTTTA
1 AAACCCAACACATTAGGGCACGATTCCTCGAATTGCCAAACATCAAACATCGCCTTTGTTTTA
30394666 CAAAGTCACC
Statistics
Matches: 166, Mismatches: 23, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
126 5 0.03
127 161 0.97
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (127 bp):
AAACCCAACACATTAGGGCACGATTCCTCGAATTGCCAAACATCAAACATCGCCTTTGTTTTAAA
GTTTAAAAAACGCGAACAAAATTTAAAAGGGAAATCTGAGTATTTAAACAAACGAAAGATCG
Found at i:30395390 original size:27 final size:26
Alignment explanation
Indices: 30395358--30395455 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 26
30395348 ATATATATAT
30395358 ATATAATAATTTAAAATACAA-AGATAC
1 ATATAATAATTTAAAATA-AATA-ATAC
* *
30395385 ATATAAAAATTTCAAAATAAATACTAC
1 ATATAATAATTT-AAAATAAATAATAC
* * *
30395412 ATATGATAATTTAAAAGAAATAATAT
1 ATATAATAATTTAAAATAAATAATAC
* *
30395438 ATGTAAAATATTTAAAAT
1 ATATAATA-ATTTAAAAT
30395456 TGATAATAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
26 16 0.28
27 34 0.60
28 7 0.12
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (26 bp):
ATATAATAATTTAAAATAAATAATAC
Found at i:30395617 original size:3 final size:3
Alignment explanation
Indices: 30395599--30395755 Score: 74
Period size: 3 Copynumber: 52.7 Consensus size: 3
30395589 AGATGATAGC
* * * *
30395599 AAT AGT AAT AAT -AT AAT AAA AAT AA- AGT AAA AAT AAT AAT AAT ACATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T
* * * * * * * *
30395647 AAT AAG AAT AAT AAT AGT -GT ATT GAT AAC AAC AAT AAT AGAA AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT
* * * * *
30395692 AAT GAT AA- AAT AAT AAT AAT AA- ACT AAGG AAT AAT AAT ACT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
30395736 AAT AAT -AT AAAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AA
30395756 AAACAACAAG
Statistics
Matches: 114, Mismatches: 29, Indels: 22
0.69 0.18 0.13
Matches are distributed among these distances:
2 10 0.09
3 94 0.82
4 8 0.07
5 2 0.02
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:30395674 original size:23 final size:23
Alignment explanation
Indices: 30395630--30395686 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
30395620 ATAAAGTAAA
* *
30395630 AATAATAATAATACATTAATAAG
1 AATAATAATAGTACATTAATAAC
** *
30395653 AATAATAATAGTGTATTGATAAC
1 AATAATAATAGTACATTAATAAC
*
30395676 AACAATAATAG
1 AATAATAATAG
30395687 AAAATAATGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (23 bp):
AATAATAATAGTACATTAATAAC
Found at i:30395771 original size:24 final size:24
Alignment explanation
Indices: 30395721--30395772 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
30395711 TAAACTAAGG
** * * *
30395721 AATAATAATACTAACAATAATATA
1 AATAATAATAAAAACAACAAGAGA
30395745 AATAATAATAAAAACAACAAGAGA
1 AATAATAATAAAAACAACAAGAGA
30395769 AATA
1 AATA
30395773 GCAACAACAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.21
Consensus pattern (24 bp):
AATAATAATAAAAACAACAAGAGA
Found at i:30397483 original size:44 final size:45
Alignment explanation
Indices: 30397378--30397586 Score: 192
Period size: 44 Copynumber: 4.7 Consensus size: 45
30397368 TGTAATTTAG
* * * *
30397378 CTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGA-TTTACTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGA-TAT
* * * *
30397423 CTTCAGTCTGCCCCACTGCAACTTCGGGGAGATAAGA-TTGGTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATAT
* * * *
30397467 CTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTTGAAAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATAT
* * * *
30397512 -TTCAACCTGCTCCACTGCAACTTCAGGGAGATAAG-GTTTATAG
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATAT
* * * * *
30397555 CTTTAATCTGTTCCATTGTAATTTCAGGGAGA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGA
30397587 AGAGCTTTGT
Statistics
Matches: 134, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
43 4 0.03
44 92 0.69
45 38 0.28
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGATAT
Found at i:30397503 original size:89 final size:88
Alignment explanation
Indices: 30397378--30397546 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 88
30397368 TGTAATTTAG
* * * * * * **
30397378 CTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGA-TTTACTATCTTCAGTCTGCCCCACTGC
1 CTTCAATCTGCTCCACTACAACTTCAGAGAAATAAGACTTGA-AAT-TTCAACCTGCCCCACTGC
*
30397442 AACTTCGGGGAGATAAGATTGGTAT
64 AACTTCAGGGAGATAAGATTGGTAT
* * *
30397467 CTTCAGTCTGCTCCACTACAACTTCAGAGAGATAAGACTTGAAATTTCAACCTGCTCCACTGCAA
1 CTTCAATCTGCTCCACTACAACTTCAGAGAAATAAGACTTGAAATTTCAACCTGCCCCACTGCAA
30397532 CTTCAGGGAGATAAG
66 CTTCAGGGAGATAAG
30397547 GTTTATAGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
88 31 0.46
89 33 0.49
90 3 0.04
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.28
Consensus pattern (88 bp):
CTTCAATCTGCTCCACTACAACTTCAGAGAAATAAGACTTGAAATTTCAACCTGCCCCACTGCAA
CTTCAGGGAGATAAGATTGGTAT
Found at i:30397648 original size:44 final size:44
Alignment explanation
Indices: 30397593--30397728 Score: 114
Period size: 44 Copynumber: 3.1 Consensus size: 44
30397583 GAGAAGAGCT
*
30397593 TTGTAGCTTCGATCTACTCCGCAGGAACTTCAAGGAGATACGAA
1 TTGTAGCTTCGATCTACTCCGCAGGAAATTCAAGGAGATACGAA
* * ** * * * * * * *
30397637 TTGTGGCTTCGAGCCGCT-C-TAGTGCCATTTCAGGGAGAAAAGAT
1 TTGTAGCTTCGATCTACTCCGCAG-G-AAATTCAAGGAGATACGAA
* *
30397681 TTGTAGCCTCGATCTACTCCGCTGGAAATTCAAGGAGATACGAA
1 TTGTAGCTTCGATCTACTCCGCAGGAAATTCAAGGAGATACGAA
30397725 TTGT
1 TTGT
30397729 TGATTTCAAC
Statistics
Matches: 64, Mismatches: 24, Indels: 8
0.67 0.25 0.08
Matches are distributed among these distances:
42 2 0.03
43 2 0.03
44 57 0.89
45 2 0.03
46 1 0.02
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (44 bp):
TTGTAGCTTCGATCTACTCCGCAGGAAATTCAAGGAGATACGAA
Found at i:30397760 original size:88 final size:88
Alignment explanation
Indices: 30397577--30397762 Score: 230
Period size: 88 Copynumber: 2.1 Consensus size: 88
30397567 CCATTGTAAT
* * * *
30397577 TTCAGGGAGAAGAGCTTTGTAGCTTCGATCTACTCCGCAGGAACTTCAAGGAGATACGAATTGTG
1 TTCAGGGAGAAAAGATTTGTAGCCTCGATCTACTCCGCAGGAAATTCAAGGAGATACGAATTGTG
* * * * * * *
30397642 GCTTCGAGCCGCTCTAGTGCCAT
66 ACTTCAACCCGCTCCACTACCAC
*
30397665 TTCAGGGAGAAAAGATTTGTAGCCTCGATCTACTCCGCTGGAAATTCAAGGAGATACGAATTGTT
1 TTCAGGGAGAAAAGATTTGTAGCCTCGATCTACTCCGCAGGAAATTCAAGGAGATACGAATTG-T
* *
30397730 GATTTCAACCCGCTCCACTACTAC
65 GACTTCAACCCGCTCCACTACCAC
30397754 TT-AGGGAGA
1 TTCAGGGAGA
30397763 TCAGATAATG
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
88 65 0.78
89 18 0.22
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.26
Consensus pattern (88 bp):
TTCAGGGAGAAAAGATTTGTAGCCTCGATCTACTCCGCAGGAAATTCAAGGAGATACGAATTGTG
ACTTCAACCCGCTCCACTACCAC
Found at i:30398025 original size:64 final size:64
Alignment explanation
Indices: 30397924--30398044 Score: 215
Period size: 64 Copynumber: 1.9 Consensus size: 64
30397914 TCATGTATCT
* *
30397924 ATGCTTATGCCAAATGATTAGGATGCTATGATCGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACTAGATGTG
*
30397988 ATGCTTATGTCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACT
1 ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACT
30398045 GAATGATATA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 54 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATGATCGAAATAAATCAAATGCTCCTAACTAGATGTG
Found at i:30399662 original size:4 final size:4
Alignment explanation
Indices: 30399644--30399677 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
30399634 TTTTTGTTTT
*
30399644 TTTC TTTC TCT- TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
30399678 TTTTTTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 25 0.93
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:30399670 original size:12 final size:11
Alignment explanation
Indices: 30399641--30399680 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
30399631 TTGTTTTTGT
30399641 TTTTTTCTTTC
1 TTTTTTCTTTC
*
30399652 TCTTTTCTTTC
1 TTTTTTCTTTC
30399663 TTTCTTTCTTTC
1 TTT-TTTCTTTC
30399675 TTTTTT
1 TTTTTT
30399681 TTTATTGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:30405624 original size:48 final size:48
Alignment explanation
Indices: 30405555--30406334 Score: 1173
Period size: 48 Copynumber: 16.0 Consensus size: 48
30405545 AGATAAATAT
* *
30405555 ATATATGTTTGATATGTATATGTGGTAAAGCCGAATGGTGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
*
30405603 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
*
30405651 ATATATGTGTGAAATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
* ** *
30405699 ATACATACGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
*
30405747 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
*
30405795 ATATATGTGTGAAATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
30405843 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
30405891 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAAT---G-G-C-----G--AATGTGAA
*
30405951 ATATATGTGTGAAATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
30405999 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
* *
30406047 ATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
*
30406095 ATATATGTGTGAAATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
* * * *
30406143 ATATATATGAGATATGTATATGTCGTAAAGTCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
* * * *
30406191 ATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
* * * *
30406239 ATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
* * * * *
30406287 ATATGTATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
30406335 GGTTGTAACA
Statistics
Matches: 685, Mismatches: 35, Indels: 24
0.92 0.05 0.03
Matches are distributed among these distances:
48 634 0.93
50 1 0.00
51 1 0.00
52 1 0.00
53 1 0.00
55 1 0.00
56 1 0.00
57 1 0.00
58 1 0.00
60 43 0.06
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
Found at i:30405938 original size:60 final size:60
Alignment explanation
Indices: 30405871--30406039 Score: 236
Period size: 60 Copynumber: 3.0 Consensus size: 60
30405861 TATGTGGTAA
30405871 AGCCGAATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCG
1 AGCCGAATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCG
* *
30405931 AGCCGAATGGCTAATGTGAAATATATGTGTGAAATGTATATGTGGT-------AA-----
1 AGCCGAATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCG
30405979 AGCCGAATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCG
1 AGCCGAATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCG
30406039 A
1 A
30406040 ATGTGAAATA
Statistics
Matches: 93, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
48 44 0.47
53 2 0.02
55 2 0.02
60 45 0.48
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (60 bp):
AGCCGAATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCG
Found at i:30408654 original size:127 final size:127
Alignment explanation
Indices: 30408301--30408660 Score: 404
Period size: 127 Copynumber: 2.8 Consensus size: 127
30408291 ATGTGGACGG
** * * * * *
30408301 AATTTTAAAGGGATGTTTGATTATTTGGATAAAC-AAGAAATTGAAACCCAACACATTAGGGTAC
1 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAA-AGATCGAAACCCAACACATTAGGGCAC
* * * * * * * * *
30408365 GATTTCTTGAATTGCCAAACATCAATCA-TCGCTTTTGTTTTAAAGTTTAATAAATGCGGACGA
65 GATTCCTCGAATTTCTAAACATCAA-AATTCGCCTTTGTTTTAAAGTTTAATAAACGCAGACAA
* * * * *
30408428 AGTTTAAAAGGGAAATCTGATTATTTAGACAAATGAAAGATCGAAACCCAGCACATTAGGGCACG
1 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAACACATTAGGGCACG
*
30408493 ATTCCTCGAATTTCTAAACATCAAACATT-GCCTTTGTTTTAAGGTTTAGA-AAACGCAGACAA
66 ATTCCTCGAATTTCTAAACATCAAA-ATTCGCCTTTGTTTTAAAGTTTA-ATAAACGCAGACAA
* *
30408555 AATTTTAAAGGGAAATTTGATTATTTAAACAAACGAAAGATCGAAACCCAACACATTAGGGCACA
1 AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAACACATTAGGGCACG
* * * *
30408620 ATCCCTCGAATTTCTAAACATCAAAGTTCACCTTTTTTTTA
66 ATTCCTCGAATTTCTAAACATCAAAATTCGCCTTTGTTTTA
30408661 CAAAGTCACC
Statistics
Matches: 195, Mismatches: 33, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
126 2 0.01
127 189 0.97
128 4 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (127 bp):
AATTTTAAAGGGAAATTTGATTATTTAGACAAACGAAAGATCGAAACCCAACACATTAGGGCACG
ATTCCTCGAATTTCTAAACATCAAAATTCGCCTTTGTTTTAAAGTTTAATAAACGCAGACAA
Found at i:30409398 original size:27 final size:26
Alignment explanation
Indices: 30409344--30409441 Score: 90
Period size: 27 Copynumber: 3.7 Consensus size: 26
30409334 ATATGTATAT
*
30409344 ATATAATAATTTAAAATACAA-AGATAC
1 ATATAAAAATTTAAAATA-AATA-ATAC
*
30409371 ATATAAAAATTTCAAAATAAATACTAC
1 ATATAAAAATTT-AAAATAAATAATAC
* * * *
30409398 ATATGATAATTTAAAAGAAATAATAT
1 ATATAAAAATTTAAAATAAATAATAC
*
30409424 ATGTAAAATATTTAAAAT
1 ATATAAAA-ATTTAAAAT
30409442 TGATAATAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
26 16 0.28
27 34 0.60
28 7 0.12
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (26 bp):
ATATAAAAATTTAAAATAAATAATAC
Found at i:30409625 original size:3 final size:3
Alignment explanation
Indices: 30409617--30409745 Score: 68
Period size: 3 Copynumber: 42.7 Consensus size: 3
30409607 TAAAGTCGAA
* * * * * *
30409617 AAT AAT AAT AAT ACATT AAT AAG AAT AAT AAT AGT -GT ATT GAT AAC
1 AAT AAT AAT AAT A-A-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
30409663 AAC AAT AAT AGAA AAT AAT GAT AA- AAT AAT AAT AAT AAT AA- ACT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
30409707 AAGG AAT AAT AAT ACT AAC AAT AAT -AT AAAT AAT AAT AA
1 AA-T AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AA
30409746 AAACAACAAG
Statistics
Matches: 96, Mismatches: 21, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
2 7 0.07
3 79 0.82
4 8 0.08
5 2 0.02
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:30409753 original size:27 final size:27
Alignment explanation
Indices: 30409660--30409754 Score: 75
Period size: 27 Copynumber: 3.3 Consensus size: 27
30409650 GTGTATTGAT
* *
30409660 AACAACAATAATAGAAAATAATGAT-AA
1 AACAACAATAATA-TAAATAATAATAAA
* * *
30409687 AATAATAATAATAATAAACTAAGGAATAATA
1 AACAACAATAAT-ATAAA-TAA-TAATAA-A
30409718 ATACTAACAATAATATAAATAATAATAAA
1 A-AC-AACAATAATATAAATAATAATAAA
30409747 AACAACAA
1 AACAACAA
30409755 GAGAAATAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 14
0.71 0.11 0.19
Matches are distributed among these distances:
27 18 0.34
28 6 0.11
29 4 0.08
30 6 0.11
31 5 0.09
32 6 0.11
33 8 0.15
ACGTcount: A:0.66, C:0.07, G:0.04, T:0.22
Consensus pattern (27 bp):
AACAACAATAATATAAATAATAATAAA
Found at i:30409761 original size:24 final size:24
Alignment explanation
Indices: 30409686--30409762 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
30409676 AATAATGATA
30409686 AAATAATAATAATAATA-AACTAAG-G
1 AAATAATAATAA-AA-ACAAC-AAGAG
** * * *
30409711 -AATAATAATACTAACAATAATAT
1 AAATAATAATAAAAACAACAAGAG
30409734 AAATAATAATAAAAACAACAAGAG
1 AAATAATAATAAAAACAACAAGAG
30409758 AAATA
1 AAATA
30409763 GCAACAACAA
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
22 3 0.08
23 3 0.08
24 33 0.85
ACGTcount: A:0.66, C:0.06, G:0.05, T:0.22
Consensus pattern (24 bp):
AAATAATAATAAAAACAACAAGAG
Found at i:30411130 original size:3 final size:3
Alignment explanation
Indices: 30411122--30411173 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
30411112 ACTAACACTT
30411122 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30411170 ATA A
1 ATA A
30411174 AAAATAAAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30414579 original size:25 final size:25
Alignment explanation
Indices: 30414464--30414573 Score: 195
Period size: 25 Copynumber: 4.4 Consensus size: 25
30414454 ACACGGGAAC
30414464 AATGCTCACACAAGCTATGATAGTA
1 AATGCTCACACAAGCTATGATAGTA
30414489 AATGCTCACACAAGCTATGATAGTA
1 AATGCTCACACAAGCTATGATAGTA
30414514 AATGCTCACACAAGCTATGATAGTA
1 AATGCTCACACAAGCTATGATAGTA
*
30414539 AATGCTCACACGAGCTATGACT-GTA
1 AATGCTCACACAAGCTATGA-TAGTA
30414564 AATGCTCACA
1 AATGCTCACA
30414574 TGAGCTGTGA
Statistics
Matches: 83, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
25 82 0.99
26 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (25 bp):
AATGCTCACACAAGCTATGATAGTA
Found at i:30415297 original size:67 final size:66
Alignment explanation
Indices: 30415185--30415314 Score: 242
Period size: 67 Copynumber: 2.0 Consensus size: 66
30415175 CTAACTTATT
30415185 TTCCACCTCATTGGTTAATATGGAACTATCGAACGGGTGCATGACAAGATTACCTTCTGGTCTAT
1 TTCCACCTCATTGGTTAATATGGAACTATCGAACGGGTGCATGACAAGATTACCTTCTGGTCTAT
30415250 C
66 C
*
30415251 TTCCGACCTCATTGGTTAATATGGAACTATCGAACGGGTGCGTGACAAGATTACCTTCTGGTCT
1 TTCC-ACCTCATTGGTTAATATGGAACTATCGAACGGGTGCATGACAAGATTACCTTCTGGTCT
30415315 TACTTTATCT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
66 4 0.06
67 58 0.94
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (66 bp):
TTCCACCTCATTGGTTAATATGGAACTATCGAACGGGTGCATGACAAGATTACCTTCTGGTCTAT
C
Found at i:30418414 original size:40 final size:40
Alignment explanation
Indices: 30418333--30418473 Score: 198
Period size: 40 Copynumber: 3.6 Consensus size: 40
30418323 AAACCAAGTA
** * *
30418333 CCTTCGGGGTTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGTTATAG-TAACTCGCACAAATG
*
30418372 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAATTG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
*
30418412 CCTTCGGGACTTGGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
30418452 CCTTCGGG-CTTAGCCCGGTTAT
1 CCTTCGGGACTTAGCCCGGTTAT
30418474 CAATCCGAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
39 26 0.28
40 66 0.72
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
Found at i:30419072 original size:2 final size:2
Alignment explanation
Indices: 30419065--30419094 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
30419055 TTAAAATACC
30419065 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
30419095 TCATAAGTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30423787 original size:27 final size:27
Alignment explanation
Indices: 30423735--30423789 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
30423725 ATAAAGTAAA
* *
30423735 TAAAAGAAACTAAAGAAAGAAAAGAAG
1 TAAAAGAAACAAAAGAAACAAAAGAAG
*
30423762 TAAAAGAAACAAAA-AGAACAACAGAAG
1 TAAAAGAAACAAAAGA-AACAAAAGAAG
30423789 T
1 T
30423790 CATTCAAACG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.69, C:0.07, G:0.16, T:0.07
Consensus pattern (27 bp):
TAAAAGAAACAAAAGAAACAAAAGAAG
Found at i:30424807 original size:47 final size:47
Alignment explanation
Indices: 30424709--30424810 Score: 125
Period size: 47 Copynumber: 2.2 Consensus size: 47
30424699 ACCTTGTGTT
** * * *
30424709 TCGTACTGTTACTGTTACTTCGGTTTAATCCAATGAGGTATTAAGTA
1 TCGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTAAGTA
* *
30424756 TCGTACTGTTACTGTTTACTTCGG-CAAAGCCAATGAGGCACTGAGTG
1 TCGTACTGTTACTG-TTACTTCGGTCAAAGCCAATGAGGCACTAAGTA
30424803 TCGTACTG
1 TCGTACTG
30424811 GTGTGTTGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
47 38 0.81
48 9 0.19
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (47 bp):
TCGTACTGTTACTGTTACTTCGGTCAAAGCCAATGAGGCACTAAGTA
Found at i:30427285 original size:53 final size:53
Alignment explanation
Indices: 30427204--30427354 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
30427194 CTTACACGGT
* *
30427204 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
30427259 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
30427312 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
30427355 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:30434790 original size:53 final size:53
Alignment explanation
Indices: 30434709--30434859 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
30434699 CTTACACGGT
* *
30434709 TCACATATCATACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTA
1 TCACAT-T-ATACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTA
*
30434764 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAGTCACATTA
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
** *
30434817 TCACATTGCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGG
30434860 GCACACTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (53 bp):
TCACATTATACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTA
Found at i:30438815 original size:26 final size:26
Alignment explanation
Indices: 30438779--30438914 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
30438769 TGATACAAAT
30438779 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
30438805 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
30438831 TGATAATAGGTTAAGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
30438857 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
30438883 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
30438909 TGATAA
1 TGATAA
30438915 GAATTTCATG
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 105 1.00
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:30440102 original size:8 final size:8
Alignment explanation
Indices: 30440089--30440120 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
30440079 CTAGATTGGC
30440089 AAAAGCCG
1 AAAAGCCG
30440097 AAAAGCCG
1 AAAAGCCG
*
30440105 AAATGCCG
1 AAAAGCCG
30440113 AAAAGCCG
1 AAAAGCCG
30440121 GTATTTTGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.47, C:0.25, G:0.25, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:30440573 original size:27 final size:27
Alignment explanation
Indices: 30440532--30440629 Score: 151
Period size: 27 Copynumber: 3.6 Consensus size: 27
30440522 GAGGAAGAGT
*
30440532 TCTGGTGGCTATGCCACAAATATCTAA
1 TCTGGTGGCTCTGCCACAAATATCTAA
*
30440559 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTAA
* *
30440586 TCTGGTGGCTCTGCCACATATATCTAT
1 TCTGGTGGCTCTGCCACAAATATCTAA
*
30440613 TCTGGTCGCTCTGCCAC
1 TCTGGTGGCTCTGCCAC
30440630 GATTATCTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 65 1.00
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.32
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTAA
Found at i:30440617 original size:54 final size:55
Alignment explanation
Indices: 30440532--30440670 Score: 167
Period size: 54 Copynumber: 2.6 Consensus size: 55
30440522 GAGGAAGAGT
* * * *
30440532 TCTGGTGGCTATGCCACAAATATCTAATCTGGTGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTATTCTGGTCGCTCTGCCACAAATATCTGTA
* *
30440586 TCTGGTGGCTCTGCCACATATATCTATTCTGGTCGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTATTCTGGTCGCTCTGCCACAAATATCTGTA
* * * *
30440641 TCTAGT-GATCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTATTCTGG
30440671 CAGCCATGCT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
53 11 0.15
54 57 0.77
55 6 0.08
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.35
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTATTCTGGTCGCTCTGCCACAAATATCTGTA
Found at i:30442165 original size:15 final size:15
Alignment explanation
Indices: 30442145--30442176 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
30442135 TATGCATGCA
30442145 AAATATAAAAGACAT
1 AAATATAAAAGACAT
30442160 AAATATAAAAGACAT
1 AAATATAAAAGACAT
30442175 AA
1 AA
30442177 CAGTGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:30443338 original size:14 final size:17
Alignment explanation
Indices: 30443301--30443340 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 17
30443291 AAAGAAAGGG
30443301 AATTAAATATGAATATA
1 AATTAAATATGAATATA
*
30443318 AAATAAATA-G-A-ATA
1 AATTAAATATGAATATA
30443332 AATTAAATA
1 AATTAAATA
30443341 AAAATAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 11 0.52
15 1 0.05
16 1 0.05
17 8 0.38
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (17 bp):
AATTAAATATGAATATA
Found at i:30444355 original size:17 final size:17
Alignment explanation
Indices: 30444308--30444355 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
30444298 TATATATAAT
30444308 TTAAAATAATAAT-ACC
1 TTAAAATAATAATAACC
*
30444324 TAAAACATAATAATAACAC
1 TTAAA-ATAATAATAAC-C
30444343 TTAAAATAA-AATA
1 TTAAAATAATAATA
30444356 TAATGATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 4 0.15
17 12 0.44
18 6 0.22
19 5 0.19
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAAATAATAATAACC
Found at i:30444355 original size:20 final size:20
Alignment explanation
Indices: 30444309--30444355 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
30444299 ATATATAATT
*
30444309 TAAAATAATAATACCTAAAA
1 TAAAATAATAACACCTAAAA
* * *
30444329 CATAATAATAACACTTAAAA
1 TAAAATAATAACACCTAAAA
30444349 TAAAATA
1 TAAAATA
30444356 TAATGATTAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.11, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAAATAATAACACCTAAAA
Found at i:30453097 original size:44 final size:44
Alignment explanation
Indices: 30453046--30453134 Score: 126
Period size: 44 Copynumber: 2.0 Consensus size: 44
30453036 AAAATTATAA
* **
30453046 ATTAAATTATAA-TTATTTAAAAATGTTTAATTATCACAACTTCT
1 ATTAAATTAAAATTTATTT-AAAATGCATAATTATCACAACTTCT
*
30453090 ATTAAATTAAAATTTATTTAAAATGCATAATTATCACAATTTCT
1 ATTAAATTAAAATTTATTTAAAATGCATAATTATCACAACTTCT
30453134 A
1 A
30453135 CTTTATTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 34 0.85
45 6 0.15
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (44 bp):
ATTAAATTAAAATTTATTTAAAATGCATAATTATCACAACTTCT
Found at i:30454664 original size:20 final size:21
Alignment explanation
Indices: 30454641--30454687 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
30454631 TTTCACATCA
*
30454641 ATTTAATAT-TAAAGAATAAT
1 ATTTAATATCAAAAGAATAAT
*
30454661 ATTTTATATCAAAAGAATAAT
1 ATTTAATATCAAAAGAATAAT
30454682 ATTTAA
1 ATTTAA
30454688 ATATATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (21 bp):
ATTTAATATCAAAAGAATAAT
Found at i:30454747 original size:28 final size:29
Alignment explanation
Indices: 30454691--30454807 Score: 107
Period size: 30 Copynumber: 4.0 Consensus size: 29
30454681 TATTTAAATA
**
30454691 TATATTAAAATATTT-TTAT-TTTTACTTT
1 TATATTAAAATATTTAAAATATTTTA-TTT
30454719 TATATTAAAATATTTAAAATATTTT-TTT
1 TATATTAAAATATTTAAAATATTTTATTT
* **
30454747 TATATTTAATAAAATTTAAAA-ATAATATTT
1 TATA-TTAA-AATATTTAAAATATTTTATTT
* *
30454777 TATATTAAATTATATTAAAAGATTTTATTT
1 TATATTAAAATAT-TTAAAATATTTTATTT
30454807 T
1 T
30454808 GTTATTCAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
28 25 0.34
29 19 0.26
30 29 0.40
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (29 bp):
TATATTAAAATATTTAAAATATTTTATTT
Found at i:30454769 original size:40 final size:43
Alignment explanation
Indices: 30454676--30454775 Score: 108
Period size: 37 Copynumber: 2.5 Consensus size: 43
30454666 ATATCAAAAG
* *
30454676 AATAATATTTAAATATATATTAAAATATTTTTATTTTTACTTT
1 AATAATATTTAAAAATATATTAAAATATTTTTATTTATACTTT
30454719 --T-ATA-TT-AAAATAT-TTAAAATATTTTT-TTTATA-TTT
1 AATAATATTTAAAAATATATTAAAATATTTTTATTTATACTTT
*
30454754 AATAAAATTTAAAAATAATATT
1 AATAATATTTAAAAAT-ATATT
30454776 TTATATTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
35 3 0.06
36 5 0.11
37 14 0.30
38 8 0.17
39 4 0.09
40 8 0.17
41 3 0.06
42 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (43 bp):
AATAATATTTAAAAATATATTAAAATATTTTTATTTATACTTT
Found at i:30455340 original size:17 final size:17
Alignment explanation
Indices: 30455311--30455345 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
30455301 TAAATTATGA
30455311 AAAATCTTTTTAAAAAT
1 AAAATCTTTTTAAAAAT
30455328 AAAAT-TTTATTAAAAAT
1 AAAATCTTT-TTAAAAAT
30455345 A
1 A
30455346 TAAAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.18
17 14 0.82
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATCTTTTTAAAAAT
Found at i:30476525 original size:20 final size:20
Alignment explanation
Indices: 30476481--30476531 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
30476471 TGTGTCTCTC
* *
30476481 TGTGTGTGTGTGTGCGTGCA
1 TGTGTATGTGTGTGCATGCA
* *
30476501 CGTGTATGTGTGTGCATGTA
1 TGTGTATGTGTGTGCATGCA
30476521 TGTGTATGTGT
1 TGTGTATGTGT
30476532 CTTTATTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.10, C:0.08, G:0.39, T:0.43
Consensus pattern (20 bp):
TGTGTATGTGTGTGCATGCA
Found at i:30478754 original size:2 final size:2
Alignment explanation
Indices: 30478747--30478787 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
30478737 TCTAATCTCC
30478747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30478788 GGAGTATAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:30479206 original size:16 final size:16
Alignment explanation
Indices: 30479185--30479218 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
30479175 CTTAAATATG
*
30479185 TATATCTTTCATAACA
1 TATATCATTCATAACA
*
30479201 TATATCATTCATATCA
1 TATATCATTCATAACA
30479217 TA
1 TA
30479219 GCTACATTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (16 bp):
TATATCATTCATAACA
Found at i:30481307 original size:5 final size:5
Alignment explanation
Indices: 30481297--30481328 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
30481287 TTATTTATTT
30481297 TTTTC TTTTC --TTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
30481329 TTGCTTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
3 3 0.12
5 22 0.88
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:30481315 original size:13 final size:13
Alignment explanation
Indices: 30481297--30481321 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
30481287 TTATTTATTT
30481297 TTTTCTTTTCTTC
1 TTTTCTTTTCTTC
30481310 TTTTCTTTTCTT
1 TTTTCTTTTCTT
30481322 TTCTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTTTCTTC
Found at i:30481320 original size:18 final size:17
Alignment explanation
Indices: 30481297--30481330 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
30481287 TTATTTATTT
30481297 TTTTCTTTTCTTCTTTTC
1 TTTTCTTTTCTT-TTTTC
30481315 TTTTCTTTTCTTTTTT
1 TTTTCTTTTCTTTTTT
30481331 GCTTGTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTCTTTTTTC
Found at i:30482878 original size:22 final size:24
Alignment explanation
Indices: 30482845--30482900 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
30482835 GTTAAGAATA
* *
30482845 TCTGCATCTGAATCTAAAA-TG-T
1 TCTGCATATGAAACTAAAATTGTT
*
30482867 TCTGTATATGAAACTAAAATTGTT
1 TCTGCATATGAAACTAAAATTGTT
30482891 TCTGCATATG
1 TCTGCATATG
30482901 TAATTAATCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 16 0.57
23 2 0.07
24 10 0.36
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (24 bp):
TCTGCATATGAAACTAAAATTGTT
Found at i:30485049 original size:19 final size:20
Alignment explanation
Indices: 30485006--30485051 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
30484996 ATTAGGCCTT
30485006 GCCCATATTAACATAGTTGG
1 GCCCATATTAACATAGTTGG
* *
30485026 GCCCATTTTAATATAGTT-G
1 GCCCATATTAACATAGTTGG
30485045 GCCCATA
1 GCCCATA
30485052 ACAAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (20 bp):
GCCCATATTAACATAGTTGG
Found at i:30487590 original size:30 final size:30
Alignment explanation
Indices: 30487555--30487613 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
30487545 GGTACAGACC
* *
30487555 GTGTGTGACACATGGTCTAGACACACGCCT
1 GTGTGTCACACACGGTCTAGACACACGCCT
* *
30487585 GTGTGTCACACACGGTTTAGACATACGCC
1 GTGTGTCACACACGGTCTAGACACACGCC
30487614 CCTGTGCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (30 bp):
GTGTGTCACACACGGTCTAGACACACGCCT
Found at i:30488778 original size:48 final size:48
Alignment explanation
Indices: 30488694--30488833 Score: 228
Period size: 48 Copynumber: 2.9 Consensus size: 48
30488684 ACGATGTCTG
* *
30488694 ATATAGATGCCAATGCCATAT-CCAGATATGGTCTTACATGGGATCAC
1 ATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAC
*
30488741 ATATTGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAC
1 ATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAC
* *
30488789 ATATCGATGCCAATGCCATGTCCCAGACATGATCTTACATGGGAT
1 ATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGAT
30488834 TACACATAAC
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
47 19 0.22
48 68 0.78
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (48 bp):
ATATAGATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCAC
Found at i:30491476 original size:33 final size:32
Alignment explanation
Indices: 30491439--30491513 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
30491429 CCTTGCCATT
*
30491439 GTCTTACACTTAT-AATGCCATAACCCAGTTATG
1 GTCTTACA-TT-TGAATGCCATAACCCAGCTATG
* * *
30491472 GTCTTATCATTTGAATGCCTTAGCCTAGCTATG
1 GTCTTA-CATTTGAATGCCATAACCCAGCTATG
30491505 GTCTTACAT
1 GTCTTACAT
30491514 ACAAATATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 4 0.11
33 30 0.83
34 2 0.06
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (32 bp):
GTCTTACATTTGAATGCCATAACCCAGCTATG
Found at i:30493291 original size:40 final size:40
Alignment explanation
Indices: 30493236--30493378 Score: 227
Period size: 40 Copynumber: 3.6 Consensus size: 40
30493226 GATGATAACG
*
30493236 GGGCTAAGTCCCGAAGGCATTTGTACTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
30493276 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
30493316 GGGCTAAGTCCCGAAGGCATTTGTGCGAACT-ACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-TAGTGACTAAT-TCC
30493356 GGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
30493379 AGCGAGTAGC
Statistics
Matches: 98, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
39 2 0.02
40 94 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
Found at i:30501093 original size:40 final size:40
Alignment explanation
Indices: 30501038--30501300 Score: 370
Period size: 40 Copynumber: 6.6 Consensus size: 40
30501028 GATGATAACG
30501038 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
*
30501078 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
30501118 GGGCTAAGTCCCAAAGGCATTTGTGCTAGTGACTAATTTC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* * * *
30501158 GGGCTAAGTCCCTAAGGCATTTGTGCGAGTTACTAATTCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
* *
30501198 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-TCC
* * *
30501238 GGGCTAAGTCCTGAAGGCATTTGTGCGAACT-ACT-ATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGC-TAGTGACTAAT-TCC
30501278 GGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
30501301 AGCGAGTAGC
Statistics
Matches: 208, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
39 2 0.01
40 204 0.98
41 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCC
Found at i:30513343 original size:25 final size:25
Alignment explanation
Indices: 30513311--30513358 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
30513301 CTATAACATG
* * *
30513311 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
30513336 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
30513359 GTTTATGTAT
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:30513442 original size:11 final size:11
Alignment explanation
Indices: 30513406--30513461 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
30513396 CATGGTATGT
30513406 ATGATATGCAC
1 ATGATATGCAC
* *
30513417 ATGACATG--T
1 ATGATATGCAC
30513426 ATGATATGCAC
1 ATGATATGCAC
*
30513437 ATGATATG--T
1 ATGATATGCAC
30513446 ATGATATGCAC
1 ATGATATGCAC
30513457 ATGAT
1 ATGAT
30513462 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:30513461 original size:20 final size:20
Alignment explanation
Indices: 30513395--30513461 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
30513385 ATTTTGATAA
*
30513395 ACATGGTATGTATGATATGC
1 ACATGATATGTATGATATGC
*
30513415 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
30513435 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
30513455 ACATGAT
1 ACATGAT
30513462 GTAATCATAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:30513541 original size:23 final size:24
Alignment explanation
Indices: 30513510--30513661 Score: 236
Period size: 24 Copynumber: 6.4 Consensus size: 24
30513500 GAGGAAGTGA
30513510 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
30513533 TAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
* *
30513557 AAAAGGGCTTATGCCCTAGTTATA
1 AAAAGGGCTTATGCCCCAGTTATC
30513581 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
30513605 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
* *
30513628 TAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
30513652 AAAAGAGGCT
1 AAAAG-GGCT
30513662 AGGCCTCCAG
Statistics
Matches: 118, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 44 0.37
24 70 0.59
25 4 0.03
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:30513603 original size:48 final size:47
Alignment explanation
Indices: 30513510--30513661 Score: 259
Period size: 47 Copynumber: 3.2 Consensus size: 47
30513500 GAGGAAGTGA
30513510 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
* *
30513557 AAAAGGGCTTATGCCCTAGTTATAAAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTAT-TAAAGGGCTTATGCCCCAGTTATC
*
30513605 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
30513652 AAAAGAGGCT
1 AAAAG-GGCT
30513662 AGGCCTCCAG
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
47 49 0.50
48 49 0.50
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATC
Found at i:30513903 original size:31 final size:31
Alignment explanation
Indices: 30513868--30513928 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
30513858 CGTTTACAGT
30513868 AAAGGCTTCGGCCCAGTAATATGAAATATGG
1 AAAGGCTTCGGCCCAGTAATATGAAATATGG
**
30513899 AAAGGCTTCGGCCCAGTGTTATGAAATATG
1 AAAGGCTTCGGCCCAGTAATATGAAATATG
30513929 AAATATGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGG
Found at i:30520495 original size:32 final size:32
Alignment explanation
Indices: 30520459--30520522 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
30520449 ATTTCATTTC
30520459 AACACATATAATTTGCATTTAATTAAAATTAA
1 AACACATATAATTTGCATTTAATTAAAATTAA
30520491 AACACATATAATTTGCATTTAATTAAAATTAA
1 AACACATATAATTTGCATTTAATTAAAATTAA
30520523 GTACATCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (32 bp):
AACACATATAATTTGCATTTAATTAAAATTAA
Done.