Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001836.1 Hibiscus syriacus cultivar Beakdansim tig00003715_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: 2428596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 12
Found at i:379780 original size:27 final size:29
Alignment explanation
Indices: 379750--379803 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
379740 TCCCTCTAAA
*
379750 TTCTCAATTT-TCT-TATATTCTCAAAAT
1 TTCTCAATTTCTCTCTAAATTCTCAAAAT
379777 TTCTCAATTTCTCTCTAAATTCTCAAA
1 TTCTCAATTTCTCTCTAAATTCTCAAA
379804 TAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 10 0.42
28 3 0.12
29 11 0.46
ACGTcount: A:0.30, C:0.22, G:0.00, T:0.48
Consensus pattern (29 bp):
TTCTCAATTTCTCTCTAAATTCTCAAAAT
Found at i:379965 original size:13 final size:13
Alignment explanation
Indices: 379949--380003 Score: 56
Period size: 13 Copynumber: 4.1 Consensus size: 13
379939 TAGTTTATAC
379949 ATATATAATTTAT
1 ATATATAATTTAT
*
379962 ATATATAGTTCATAT
1 ATATATAATT--TAT
* *
379977 AAACATAATTTAT
1 ATATATAATTTAT
*
379990 ATATATAACTTAT
1 ATATATAATTTAT
380003 A
1 A
380004 ATAATTATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
13 23 0.70
15 10 0.30
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.45
Consensus pattern (13 bp):
ATATATAATTTAT
Found at i:379966 original size:26 final size:26
Alignment explanation
Indices: 379911--379994 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
379901 TAATATAAAT
* *
379911 TATAGTTTATAAACTATAT-ATTTTTT
1 TATAGTTTATAAA-TATATAATTTATA
*
379937 TATAGTTTATACATATATAATTTATATA
1 TATAGTTTATAAATATATAA-TT-TATA
* *
379965 TATAGTTCATATAA-ACATAATTTATA
1 TATAGTTTATA-AATATATAATTTATA
379991 TATA
1 TATA
379995 TAACTTATAA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
25 5 0.10
26 21 0.44
27 4 0.08
28 17 0.35
29 1 0.02
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.50
Consensus pattern (26 bp):
TATAGTTTATAAATATATAATTTATA
Found at i:379977 original size:15 final size:15
Alignment explanation
Indices: 379937--380070 Score: 55
Period size: 13 Copynumber: 8.8 Consensus size: 15
379927 TATATTTTTT
* *
379937 TATAGTTTATACATA
1 TATAATTTATATATA
379952 TATAA-TT-TATATA
1 TATAATTTATATATA
* * *
379965 TATAGTTCATATAAA
1 TATAATTTATATATA
*
379980 CATAA-TT-TATATA
1 TATAATTTATATATA
*
379993 TATAACTTATAATAATTA
1 TATAATTTAT-AT-A-TA
*
380011 TATAGTTTATA-ATA
1 TATAATTTATATATA
* *
380025 TA-AATATAGTTTATA
1 TATAATTTA-TATATA
*
380040 TATAGACTTATATATTA
1 TATA-ATTTATATA-TA
380057 TATATATATTATAT
1 TATA-AT-TTATAT
380071 TTTTTTCAAT
Statistics
Matches: 86, Mismatches: 20, Indels: 23
0.67 0.16 0.18
Matches are distributed among these distances:
13 22 0.26
14 11 0.13
15 19 0.22
16 6 0.07
17 12 0.14
18 16 0.19
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (15 bp):
TATAATTTATATATA
Found at i:380031 original size:18 final size:17
Alignment explanation
Indices: 380010--380043 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
380000 TATAATAATT
380010 ATATAGTTTATAATATAA
1 ATATAGTTTAT-ATATAA
380028 ATATAGTTTATATATA
1 ATATAGTTTATATATA
380044 GACTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATATAGTTTATATATAA
Found at i:392073 original size:21 final size:22
Alignment explanation
Indices: 392049--392089 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
392039 CTTCGAGTTT
*
392049 CAAGA-TTCAAACTTTTCCAAA
1 CAAGACTTCAAAATTTTCCAAA
*
392070 CAAGACTTGAAAATTTTCCA
1 CAAGACTTCAAAATTTTCCA
392090 CTACAGCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (22 bp):
CAAGACTTCAAAATTTTCCAAA
Found at i:393151 original size:24 final size:24
Alignment explanation
Indices: 393122--393177 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
393112 CTATTCTTTT
393122 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
*
393146 GTTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTGAGCTCAAATTTTAG
393170 GCTTCAAT
1 GCTTCAAT
393178 CGAACTTCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (24 bp):
GCTTCAATTGAGCTCAAATTTTAG
Found at i:397366 original size:2 final size:2
Alignment explanation
Indices: 397361--397397 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
397351 ACACACACAC
397361 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 A
397398 CCAACCCTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:399573 original size:2 final size:2
Alignment explanation
Indices: 399561--399606 Score: 58
Period size: 2 Copynumber: 22.5 Consensus size: 2
399551 TATTATATTT
*
399561 TA TA GTA TA TA TA TA TA TA TA TA TA TA T- TA TA TA GTA TA AA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
399604 TA T
1 TA T
399607 GTATGGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
1 1 0.03
2 34 0.87
3 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:399618 original size:30 final size:30
Alignment explanation
Indices: 399554--399620 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
399544 GGTTTCCTAT
* * *
399554 TATATTTTATAGTATATATATATATATATA
1 TATATTATATAGTATAAATATATATATAGA
* * *
399584 TATATTATATAGTATAAATATATGTATGGG
1 TATATTATATAGTATAAATATATATATAGA
399614 TATATTA
1 TATATTA
399621 AAATATAGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (30 bp):
TATATTATATAGTATAAATATATATATAGA
Found at i:399673 original size:35 final size:36
Alignment explanation
Indices: 399629--399736 Score: 118
Period size: 35 Copynumber: 3.0 Consensus size: 36
399619 TAAAATATAG
399629 TATAGTTTTGAAAACAATTATTATATATATATATTA
1 TATAGTTTTGAAAACAATTATTATATATATATATTA
* *
399665 TAT-TTTTTGGAAAA-AAATATTATATATAT-TATATA
1 TATAGTTTT-GAAAACAATTATTATATATATATAT-TA
*
399700 TTATAGTTTTGAAAACGATTATTAT-TAT-TATTATTA
1 -TATAGTTTTGAAAACAATTATTATATATATA-TATTA
399736 T
1 T
399737 TATAATTGTA
Statistics
Matches: 60, Mismatches: 5, Indels: 15
0.75 0.06 0.19
Matches are distributed among these distances:
34 3 0.05
35 22 0.37
36 21 0.35
37 14 0.23
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.50
Consensus pattern (36 bp):
TATAGTTTTGAAAACAATTATTATATATATATATTA
Found at i:399738 original size:36 final size:36
Alignment explanation
Indices: 399614--399740 Score: 136
Period size: 36 Copynumber: 3.5 Consensus size: 36
399604 TATGTATGGG
** *
399614 TATATTAAAATATAGTATAGTTTTGAAAACAATTAT
1 TATATTATTATATATTATAGTTTTGAAAACAATTAT
* *
399650 TATA-TA-TATATATTATATTTTTTGGAAAA-AAATAT
1 TATATTATTATATATTATA-GTTTT-GAAAACAATTAT
*
399685 TATATATATTATATATTATAGTTTTGAAAACGATTAT
1 TATAT-TATTATATATTATAGTTTTGAAAACAATTAT
399722 TATTATTATTAT-TATTATA
1 TA-TATTATTATATATTATA
399741 ATTGTAGACA
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
34 9 0.12
35 15 0.19
36 21 0.27
37 18 0.23
38 14 0.18
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (36 bp):
TATATTATTATATATTATAGTTTTGAAAACAATTAT
Found at i:399808 original size:15 final size:15
Alignment explanation
Indices: 399785--399817 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
399775 AATATCGTAG
399785 TTTTTGAAAT-ATTT
1 TTTTTGAAATCATTT
399799 TTTTTAGAAATCATTT
1 TTTTT-GAAATCATTT
399815 TTT
1 TTT
399818 GAATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 5 0.29
16 7 0.41
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTGAAATCATTT
Found at i:399896 original size:37 final size:36
Alignment explanation
Indices: 399814--400021 Score: 231
Period size: 37 Copynumber: 5.4 Consensus size: 36
399804 AGAAATCATT
* *
399814 TTTTGAATATATATATATATAATATAGTTTTTAAAATCGTT
1 TTTTGAAAATATATATA-AT-ATATAGTTTTTAAAA-C--A
399855 TTTTGAAAATATATATTAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATA-TAATATATAGTTTTTAAAACA
399892 TTTTGAAAACT-TATATAATATATAGTTTTTTAAAA-A
1 TTTTGAAAA-TATATATAATATATAG-TTTTTAAAACA
* *
399928 TATTTGAAAATATATGTAATATATAGTTTTTAAAAACG
1 T-TTTGAAAATATATATAATATATAGTTTTT-AAAACA
399966 TTTTGAATATATATATATATATAATATAGTTTTTAAAACA
1 TTTTGAA-A-ATATATATA-AT-ATATAGTTTTTAAAACA
400006 TTTTTGAAAATATATA
1 -TTTTGAAAATATATA
400022 GGTTTTGAAA
Statistics
Matches: 149, Mismatches: 6, Indels: 26
0.82 0.03 0.14
Matches are distributed among these distances:
36 18 0.12
37 53 0.36
38 3 0.02
39 16 0.11
40 23 0.15
41 34 0.23
42 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:400022 original size:28 final size:28
Alignment explanation
Indices: 399989--400049 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
399979 TATATATATA
*
399989 ATATA-GTTTTTAAAACATTTTTGAAAAT
1 ATATAGGTTTTGAAAACATTTTT-AAAAT
* *
400017 ATATAGGTTTTGAAAACGTTTTTAATAT
1 ATATAGGTTTTGAAAACATTTTTAAAAT
400045 ATATA
1 ATATA
400050 ATTATTAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (28 bp):
ATATAGGTTTTGAAAACATTTTTAAAAT
Found at i:401614 original size:2 final size:2
Alignment explanation
Indices: 401607--401648 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
401597 ACGCTTCGAC
401607 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
401649 ATTTTGGGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:401704 original size:20 final size:20
Alignment explanation
Indices: 401676--401723 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
401666 TATATCTATC
*
401676 ATATAATATCATTTTAAAA-A
1 ATATAATAT-ATATTAAAATA
*
401696 ATATTATATATATTAAAATA
1 ATATAATATATATTAAAATA
401716 ATATAATA
1 ATATAATA
401724 AGTATCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (20 bp):
ATATAATATATATTAAAATA
Found at i:403444 original size:2 final size:2
Alignment explanation
Indices: 403405--403430 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
403395 ATACTTTTTG
403405 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
403431 TTAATTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:406304 original size:15 final size:15
Alignment explanation
Indices: 406284--406313 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
406274 AACATGCCAA
406284 TAACAATGCTTTTAT
1 TAACAATGCTTTTAT
406299 TAACAATGCTTTTAT
1 TAACAATGCTTTTAT
406314 ATGTTACTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
TAACAATGCTTTTAT
Found at i:411208 original size:95 final size:97
Alignment explanation
Indices: 411024--411219 Score: 360
Period size: 95 Copynumber: 2.0 Consensus size: 97
411014 TGCACAAAAC
411024 ATATGTTTGATTTTCTCCTTGGGGGAAAGATGTGGACCTACTCCAAACTAAGGTCAGATATTTTC
1 ATATGTTTGATTTTCTCCTTGGGGGAAAGATGTGGACCTACTCCAAACTAAGGT-A-ATATTTTC
411089 TCCCACATTTTACCTCTAAATTTTGTCCAACTTT
64 TCCCACATTTTACCTCTAAATTTTGTCCAACTTT
411123 ATATGTTTGATTTTCTCCTT-GGGGAAAGATGTGGACCTACTCCAAACTAAGGT-ATATTTTCTC
1 ATATGTTTGATTTTCTCCTTGGGGGAAAGATGTGGACCTACTCCAAACTAAGGTAATATTTTCTC
411186 CCACATTTTACCTCTAAATTTTGTCCAACTTT
66 CCACATTTTACCTCTAAATTTTGTCCAACTTT
411218 AT
1 AT
411220 TATTTATTTA
Statistics
Matches: 97, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
95 44 0.45
98 33 0.34
99 20 0.21
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (97 bp):
ATATGTTTGATTTTCTCCTTGGGGGAAAGATGTGGACCTACTCCAAACTAAGGTAATATTTTCTC
CCACATTTTACCTCTAAATTTTGTCCAACTTT
Found at i:411550 original size:2 final size:2
Alignment explanation
Indices: 411543--411571 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
411533 GAATACGAGA
411543 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 A
411572 ATTAAAGAGG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:418948 original size:18 final size:18
Alignment explanation
Indices: 418925--418965 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
418915 TCATTCCCAA
418925 CTCATCTTAGCTCATTAG
1 CTCATCTTAGCTCATTAG
*
418943 CTCATCTTAGCTCATTTG
1 CTCATCTTAGCTCATTAG
418961 CTCAT
1 CTCAT
418966 TTGTATGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.29, G:0.10, T:0.41
Consensus pattern (18 bp):
CTCATCTTAGCTCATTAG
Found at i:418952 original size:10 final size:9
Alignment explanation
Indices: 418925--418967 Score: 54
Period size: 8 Copynumber: 4.8 Consensus size: 9
418915 TCATTCCCAA
418925 CTCATCTTAG
1 CTCAT-TTAG
418935 CTCA-TTAG
1 CTCATTTAG
418943 CTCATCTTAG
1 CTCAT-TTAG
418953 CTCATTT-G
1 CTCATTTAG
418961 CTCATTT
1 CTCATTT
418968 GTATGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
8 16 0.52
9 2 0.06
10 13 0.42
ACGTcount: A:0.19, C:0.28, G:0.09, T:0.44
Consensus pattern (9 bp):
CTCATTTAG
Found at i:419173 original size:21 final size:21
Alignment explanation
Indices: 419147--419194 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
419137 ATAAGTAGTT
419147 GAATGAAGTTGAACGAGAGCA
1 GAATGAAGTTGAACGAGAGCA
419168 GAATGAAGTTGAACGAGAGCA
1 GAATGAAGTTGAACGAGAGCA
419189 GAATGA
1 GAATGA
419195 GCTGAATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.33, T:0.15
Consensus pattern (21 bp):
GAATGAAGTTGAACGAGAGCA
Found at i:419213 original size:11 final size:11
Alignment explanation
Indices: 419143--419213 Score: 51
Period size: 11 Copynumber: 6.8 Consensus size: 11
419133 ATGGATAAGT
419143 AGTTGAATGA-
1 AGTTGAATGAG
*
419153 AGTTGAACGAG
1 AGTTGAATGAG
**
419164 AGCAGAATGA-
1 AGTTGAATGAG
*
419174 AGTTGAACGAG
1 AGTTGAATGAG
**
419185 AGCAGAAT--G
1 AGTTGAATGAG
*
419194 AGCTGAATGAG
1 AGTTGAATGAG
419205 AGTTGAATG
1 AGTTGAATG
419214 TGTCACTAAC
Statistics
Matches: 45, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
9 8 0.18
10 16 0.36
11 21 0.47
ACGTcount: A:0.39, C:0.07, G:0.34, T:0.20
Consensus pattern (11 bp):
AGTTGAATGAG
Found at i:424373 original size:17 final size:17
Alignment explanation
Indices: 424353--424391 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
424343 GAAAGTCAAC
*
424353 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGCCG
*
424370 GGTCAACGGTCGGGCCG
1 GGTCAACAGTCGGGCCG
424387 GGTCA
1 GGTCA
424392 GGTTGGTCGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.44, T:0.15
Consensus pattern (17 bp):
GGTCAACAGTCGGGCCG
Found at i:424418 original size:19 final size:18
Alignment explanation
Indices: 424361--424418 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
424351 ACGGTCAACA
424361 GTCGGGTCGGGTCA-ACG
1 GTCGGGTCGGGTCAGACG
* **
424378 GTCGGGCCGGGTCAGGTTG
1 GTCGGGTCGGGTCA-GACG
424397 GTCGGGTCGGGTCAGACCG
1 GTCGGGTCGGGTCAGA-CG
424416 GTC
1 GTC
424419 AAACCGGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
17 13 0.41
18 1 0.03
19 18 0.56
ACGTcount: A:0.09, C:0.24, G:0.48, T:0.19
Consensus pattern (18 bp):
GTCGGGTCGGGTCAGACG
Found at i:431646 original size:14 final size:15
Alignment explanation
Indices: 431617--431649 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
431607 AATAGTCAGC
431617 GGTCGGCTCAGGTCG
1 GGTCGGCTCAGGTCG
*
431632 GGTCGGGTC-GGTCG
1 GGTCGGCTCAGGTCG
431646 GGTC
1 GGTC
431650 AGACCGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.03, C:0.24, G:0.52, T:0.21
Consensus pattern (15 bp):
GGTCGGCTCAGGTCG
Found at i:431674 original size:10 final size:9
Alignment explanation
Indices: 431646--431715 Score: 86
Period size: 9 Copynumber: 7.3 Consensus size: 9
431636 GGGTCGGTCG
*
431646 GGTCAGACC
1 GGTCAAACC
431655 GGTCAAACC
1 GGTCAAACC
431664 GGTCGAAACC
1 GGTC-AAACC
431674 GGTCAAACC
1 GGTCAAACC
*
431683 GGTCAAAACA
1 GGTC-AAACC
431693 GGTTCAAAACC
1 GG-TC-AAACC
431704 GGTCAAACC
1 GGTCAAACC
431713 GGT
1 GGT
431716 TTTCCAGCTG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
9 29 0.53
10 17 0.31
11 9 0.16
ACGTcount: A:0.33, C:0.29, G:0.26, T:0.13
Consensus pattern (9 bp):
GGTCAAACC
Found at i:431676 original size:19 final size:18
Alignment explanation
Indices: 431646--431715 Score: 86
Period size: 19 Copynumber: 3.7 Consensus size: 18
431636 GGGTCGGTCG
*
431646 GGTCAGACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
431664 GGTCGAAACCGGTCAAACC
1 GGTC-AAACCGGTCAAACC
*
431683 GGTCAAAACAGGTTCAAAACC
1 GGTC-AAACCGG-TC-AAACC
431704 GGTCAAACCGGT
1 GGTCAAACCGGT
431716 TTTCCAGCTG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 4 0.09
19 24 0.53
20 8 0.18
21 9 0.20
ACGTcount: A:0.33, C:0.29, G:0.26, T:0.13
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:434651 original size:2 final size:2
Alignment explanation
Indices: 434646--434675 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
434636 AGGATTTTTT
434646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
434676 AATCAATGCT
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):
TA
Found at i:435865 original size:16 final size:16
Alignment explanation
Indices: 435844--435897 Score: 90
Period size: 16 Copynumber: 3.4 Consensus size: 16
435834 ATAGTCGATT
435844 AATTGATTGTCTTTGC
1 AATTGATTGTCTTTGC
435860 AATTGATTGTCTTTGC
1 AATTGATTGTCTTTGC
* *
435876 AATTGATTGTTTTTTC
1 AATTGATTGTCTTTGC
435892 AATTGA
1 AATTGA
435898 AAGTTATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.22, C:0.09, G:0.17, T:0.52
Consensus pattern (16 bp):
AATTGATTGTCTTTGC
Found at i:437345 original size:22 final size:23
Alignment explanation
Indices: 437302--437353 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
437292 ATATGCATCA
* *
437302 TTTTATTATTTTTTGCAATGCAT
1 TTTTATTATTTCTTACAATGCAT
*
437325 TTTTATT-TTTCTTACACTGCA-
1 TTTTATTATTTCTTACAATGCAT
*
437346 CTTTATTA
1 TTTTATTA
437354 ATTCATAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 6 0.25
22 11 0.46
23 7 0.29
ACGTcount: A:0.21, C:0.13, G:0.06, T:0.60
Consensus pattern (23 bp):
TTTTATTATTTCTTACAATGCAT
Found at i:439628 original size:19 final size:19
Alignment explanation
Indices: 439604--439650 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
439594 ATAGATTATA
439604 CGCTAAAGCTGAGCTATTC
1 CGCTAAAGCTGAGCTATTC
439623 CGCTAAAGCTGAGCTATTC
1 CGCTAAAGCTGAGCTATTC
*
439642 CGCTTAAGC
1 CGCTAAAGC
439651 AATTGGTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (19 bp):
CGCTAAAGCTGAGCTATTC
Found at i:440948 original size:77 final size:76
Alignment explanation
Indices: 440851--441029 Score: 202
Period size: 76 Copynumber: 2.3 Consensus size: 76
440841 TAATACATAG
* ** *
440851 GATTTATCTCACTTGAGATTGTTTTTTCTTAAAAC-AGAATTTGTCTCACTTGAGACAG-TTTTT
1 GATTTATTTCACTCAAGATTGTTTTTTCTTAAAACAAG-ATTTATCTCACTTGAGA-AGATTTTT
440914 ACTCGAAATAAAAA
64 ACTCGAAA-AAAAA
* *
440928 GATTTATTTCACTCAAGATTG-TTTTTCTTAAAACAAGATTTATCTCGCTTGAGATGATTTTTAC
1 GATTTATTTCACTCAAGATTGTTTTTTCTTAAAACAAGATTTATCTCACTTGAGAAGATTTTTAC
* **
440992 TCGAAAGAAGT
66 TCGAAAAAAAA
* *
441003 CATTTCATTTCACTCAAGATTATTTTT
1 GATTT-ATTTCACTCAAGATTGTTTTT
441030 AAAGAAGATT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
75 7 0.08
76 56 0.64
77 24 0.28
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (76 bp):
GATTTATTTCACTCAAGATTGTTTTTTCTTAAAACAAGATTTATCTCACTTGAGAAGATTTTTAC
TCGAAAAAAAA
Found at i:441178 original size:117 final size:118
Alignment explanation
Indices: 441032--441257 Score: 373
Period size: 117 Copynumber: 1.9 Consensus size: 118
441022 TTATTTTTAA
*
441032 AGAAGATTTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTGTCTCACTTGAGATA
1 AGAAGATTTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTATCTCACTTGAGATA
* *
441097 GTTTCACTTGAAACATAAGATTTTATCTCGTTTGAGATAGTTTCCCTTGAAAC
66 GTTTCACTTGAAACAGAAGATTTTATATCGTTTGAGATAGTTTCCCTTGAAAC
* * * *
441150 AGAAGA-TTTTATCTCGCTTTAGATAGTTTCTCTTAAAACAGAAGATTTTATCTCGCTTGAGATA
1 AGAAGATTTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTATCTCACTTGAGATA
*
441214 GTTTCACTTGAAACAGAAGATTTTGTATCGTTTGAGATAGTTTC
66 GTTTCACTTGAAACAGAAGATTTTATATCGTTTGAGATAGTTTC
441258 GCTCTAAACA
Statistics
Matches: 100, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 94 0.94
118 6 0.06
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (118 bp):
AGAAGATTTTTATCTCGCTTGAGATAGTTTCCCTCAAAACAGAAGATTTTATCTCACTTGAGATA
GTTTCACTTGAAACAGAAGATTTTATATCGTTTGAGATAGTTTCCCTTGAAAC
Found at i:441267 original size:39 final size:39
Alignment explanation
Indices: 441032--441257 Score: 317
Period size: 39 Copynumber: 5.8 Consensus size: 39
441022 TTATTTTTAA
* **
441032 AGAAGATTTTTATCTCGCTTGAGATAGTTTCCCTCAAAAC
1 AGAAGA-TTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* *
441072 AGAAGATTTTGTCTCACTTGAGATAGTTTCACTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* * *
441111 ATAAGATTTTATCTCGTTTGAGATAGTTTCCCTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* * *
441150 AGAAGATTTTATCTCGCTTTAGATAGTTTCTCTTAAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
441189 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
* * *
441228 AGAAGATTTTGTATCGTTTGAGATAGTTTC
1 AGAAGATTTTATCTCGCTTGAGATAGTTTC
441258 GCTCTAAACA
Statistics
Matches: 165, Mismatches: 21, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 159 0.96
40 6 0.04
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (39 bp):
AGAAGATTTTATCTCGCTTGAGATAGTTTCACTTGAAAC
Found at i:441585 original size:90 final size:89
Alignment explanation
Indices: 441414--441607 Score: 284
Period size: 90 Copynumber: 2.1 Consensus size: 89
441404 AGCATGATGC
* *
441414 GTAAGTTCTTCGGGCCATCCATAAGACCTTCAGTGCATGATGATTTAAAATGAGATTTATAGAAA
1 GTAAG-TCTTCGGGCCATCCATAAGACCTTCAGTACACGATGATTTAAAATGAGATTTATAGAAA
441479 CTAAGCCTCAGGGGTTTCTTGATTT
65 CTAAGCCTCAGGGGTTTCTTGATTT
* *
441504 GTAAGTCATTCGGGCCATCCATAAGACCTTCAGTACACGATGTTTTCAAATGAGA-TTATAGAAA
1 GTAAGTC-TTCGGGCCATCCATAAGACCTTCAGTACACGATGATTTAAAATGAGATTTATAGAAA
441568 CTAAGCCTTC-GGAGGTTTCTTGATTT
65 CTAAGCC-TCAGG-GGTTTCTTGATTT
*
441594 GTAAATCCTTCGGG
1 GTAAGT-CTTCGGG
441608 TTATCTGTAA
Statistics
Matches: 95, Mismatches: 5, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
89 20 0.21
90 74 0.78
91 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.32
Consensus pattern (89 bp):
GTAAGTCTTCGGGCCATCCATAAGACCTTCAGTACACGATGATTTAAAATGAGATTTATAGAAAC
TAAGCCTCAGGGGTTTCTTGATTT
Found at i:442182 original size:2 final size:2
Alignment explanation
Indices: 442177--442208 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
442167 TTTTATATTT
442177 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
442209 AATGTTTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:447254 original size:19 final size:19
Alignment explanation
Indices: 447222--447269 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
447212 AAAGATGTTC
*
447222 GCTACAAGGTACGGTTGGTA
1 GCTA-AAGGCACGGTTGGTA
447242 GCTAAAGGCACGGTTGGTA
1 GCTAAAGGCACGGTTGGTA
447261 GCTAAAGGC
1 GCTAAAGGC
447270 TACGCTCAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.21
Consensus pattern (19 bp):
GCTAAAGGCACGGTTGGTA
Found at i:451984 original size:18 final size:19
Alignment explanation
Indices: 451949--451991 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
451939 GTTTGTTGGT
451949 ATATATCGATACAAATAAAA
1 ATATATCGATAC-AATAAAA
451969 ATATATCGATAC-ATAAAA
1 ATATATCGATACAATAAAA
451987 ATATA
1 ATATA
451992 ACAGGTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 11 0.48
20 12 0.52
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (19 bp):
ATATATCGATACAATAAAA
Found at i:453364 original size:17 final size:17
Alignment explanation
Indices: 453342--453375 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
453332 ATTAGATGAT
453342 TCAAAAAAAAATTAACA
1 TCAAAAAAAAATTAACA
*
453359 TCAAAAAAAATTTAACA
1 TCAAAAAAAAATTAACA
453376 CATTTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (17 bp):
TCAAAAAAAAATTAACA
Found at i:456756 original size:38 final size:37
Alignment explanation
Indices: 456711--456828 Score: 146
Period size: 38 Copynumber: 3.4 Consensus size: 37
456701 AAAATAAAGC
*
456711 AATATATTTTATAAAATTATTATCTATAACTTTACTTT
1 AATATATTTTATAAAATTATTATTTATAACTTTAC-TT
456749 AATATATTTTATAAAATTATTATTTATAACTTTAC--
1 AATATATTTTATAAAATTATTATTTATAACTTTACTT
456784 AA-A-A---TAT--AATTATTATTTATAACTTTACTT
1 AATATATTTTATAAAATTATTATTTATAACTTTACTT
456814 AAATATATTTTATAA
1 -AATATATTTTATAA
456829 TATTTAAAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 20
0.77 0.01 0.22
Matches are distributed among these distances:
28 21 0.30
30 3 0.04
31 2 0.03
32 1 0.01
33 2 0.03
34 1 0.01
35 2 0.03
36 3 0.04
38 34 0.49
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (37 bp):
AATATATTTTATAAAATTATTATTTATAACTTTACTT
Found at i:456800 original size:28 final size:29
Alignment explanation
Indices: 456763--456820 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
456753 TATTTTATAA
456763 AATTATTATTTATAACTTTAC-AAAATAT
1 AATTATTATTTATAACTTTACTAAAATAT
*
456791 AATTATTATTTATAACTTTACTTAAATAT
1 AATTATTATTTATAACTTTACTAAAATAT
456820 A
1 A
456821 TTTTATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (29 bp):
AATTATTATTTATAACTTTACTAAAATAT
Found at i:457532 original size:19 final size:18
Alignment explanation
Indices: 457508--457552 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
457498 ATCAAGAATC
*
457508 AAATTAATATTTAATCAAA
1 AAATTAATATTAAAT-AAA
*
457527 AAATTAAATATTAAATTAA
1 AAATT-AATATTAAATAAA
457546 AAATTAA
1 AAATTAA
457553 CTTATTTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 12 0.52
20 9 0.39
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTAATATTAAATAAA
Found at i:457686 original size:2 final size:2
Alignment explanation
Indices: 457679--457737 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
457669 AATCAAAAAG
457679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
457721 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
457738 TAAATTTGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:462156 original size:30 final size:28
Alignment explanation
Indices: 462117--462205 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 28
462107 AACATAAAAA
*
462117 AAATGAAAAAATGAAGAAAAGTAAATAAAT
1 AAATAAAAAAAT-AAGAAAAG-AAATAAAT
462147 GAAATAAAAAAACTAAAGAAAA-AAATAAAT
1 -AAATAAAAAAA-T-AAGAAAAGAAATAAAT
* *
462177 AGATAAATAAATAAGATAAAGAAAATAAA
1 AAATAAAAAAATAAGA-AAAG-AAATAAA
462206 GGCAAAAATG
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
27 4 0.08
28 4 0.08
29 9 0.18
30 15 0.30
31 10 0.20
32 8 0.16
ACGTcount: A:0.73, C:0.01, G:0.10, T:0.16
Consensus pattern (28 bp):
AAATAAAAAAATAAGAAAAGAAATAAAT
Found at i:462169 original size:42 final size:46
Alignment explanation
Indices: 462123--462216 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 46
462113 AAAAAAATGA
462123 AAAAATGAAGAAA-AG-TAAATAAATGAA-ATAAA-AAAACTAAA-G-
1 AAAAATGAAGAAATAGATAAATAAAT-AAGATAAAGAAAA-TAAAGGC
*
462165 AAAAA--AATAAATAGATAAATAAATAAGATAAAGAAAATAAAGGC
1 AAAAATGAAGAAATAGATAAATAAATAAGATAAAGAAAATAAAGGC
462209 AAAAATGA
1 AAAAATGA
462217 CAAAATGAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
40 5 0.12
41 4 0.09
42 23 0.53
43 5 0.12
44 5 0.12
46 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.12, T:0.15
Consensus pattern (46 bp):
AAAAATGAAGAAATAGATAAATAAATAAGATAAAGAAAATAAAGGC
Found at i:462186 original size:4 final size:4
Alignment explanation
Indices: 462138--462196 Score: 55
Period size: 4 Copynumber: 14.0 Consensus size: 4
462128 TGAAGAAAAG
* * * *
462138 TAAA TAAA TGAAA TAAA AAAA CTAAA GAAA AAAA TAAA TAGA TAAA TAAA
1 TAAA TAAA T-AAA TAAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA
462188 TAAGA TAAA
1 TAA-A TAAA
462197 GAAAATAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 34 0.76
5 11 0.24
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.19
Consensus pattern (4 bp):
TAAA
Found at i:462345 original size:13 final size:12
Alignment explanation
Indices: 462317--462376 Score: 50
Period size: 12 Copynumber: 4.7 Consensus size: 12
462307 ATGTACATAT
462317 AAATAAAATGTAAA
1 AAATAAAA--TAAA
462331 AAATAATAAT-AA
1 AAATAA-AATAAA
*
462343 AAATAAATTAAA
1 AAATAAAATAAA
462355 AAATAAAAGATAAA
1 AAAT-AAA-ATAAA
*
462369 AGATAAAA
1 AAATAAAA
462377 AACAATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 2 0.05
12 15 0.38
13 7 0.18
14 13 0.33
15 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.20
Consensus pattern (12 bp):
AAATAAAATAAA
Found at i:462347 original size:6 final size:6
Alignment explanation
Indices: 462329--462499 Score: 50
Period size: 6 Copynumber: 27.2 Consensus size: 6
462319 ATAAAATGTA
* *
462329 AAAAAT AATAAT AAAAAT -AAATT AAAAAAT AAAAGAT AAAAGAT -AAAA-
1 AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAA-AT AAAA-AT AAAAAT
* * * **
462377 AACAAT AAAACAT ATAAACTAT AATAAT AATAAT GAAGTATAAT AGTAAT
1 AAAAAT AAAA-AT A-AAA--AT AAAAAT AAAAAT -AA--A-AAT AAAAAT
* *
462427 AATAAAT AAATGAA- AAAAAT AAAAAG AAAAA- GAAAAT -AAAAT -AAAAT
1 AA-AAAT AAA--AAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* **
462474 AAAAAG AAGTAT AAAAAAT AAAAAT A
1 AAAAAT AAAAAT -AAAAAT AAAAAT A
462500 TATAAGTAAA
Statistics
Matches: 125, Mismatches: 21, Indels: 38
0.68 0.11 0.21
Matches are distributed among these distances:
5 24 0.19
6 57 0.46
7 30 0.24
8 7 0.06
9 4 0.03
10 3 0.02
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.20
Consensus pattern (6 bp):
AAAAAT
Found at i:462570 original size:25 final size:24
Alignment explanation
Indices: 462541--462594 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
462531 AAAAATGATG
462541 TATAAA-AATACATAATAGAAT-AAAA
1 TATAAAGAATA-ATAAT--AATGAAAA
462566 TATAAAGAATAATAATAATGAAAA
1 TATAAAGAATAATAATAATGAAAA
462590 TATAA
1 TATAA
462595 TTAAACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.11
24 9 0.33
25 11 0.41
26 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.26
Consensus pattern (24 bp):
TATAAAGAATAATAATAATGAAAA
Found at i:465656 original size:22 final size:22
Alignment explanation
Indices: 465628--465670 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
465618 TACCTTCTTT
465628 TTCTTTTCCTCTTTTTCTTTTG
1 TTCTTTTCCTCTTTTTCTTTTG
* *
465650 TTCTTTTTCTCTTTTTTTTTT
1 TTCTTTTCCTCTTTTTCTTTT
465671 AATTTAGGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (22 bp):
TTCTTTTCCTCTTTTTCTTTTG
Found at i:465670 original size:14 final size:14
Alignment explanation
Indices: 465622--465659 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
465612 TGAACCTACC
*
465622 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTG
*
465636 CTCTTTTTCTTTTG
1 TTCTTTTTCTTTTG
465650 TTCTTTTTCT
1 TTCTTTTTCT
465660 CTTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
TTCTTTTTCTTTTG
Found at i:472142 original size:38 final size:38
Alignment explanation
Indices: 472091--472166 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
472081 TCATTTCCCC
472091 CATATCCTATCATCATCTAACAGAACATAGTGATGTGG
1 CATATCCTATCATCATCTAACAGAACATAGTGATGTGG
472129 CATATCCTATCATCATCTAACAGAACATAGTGATGTGG
1 CATATCCTATCATCATCTAACAGAACATAGTGATGTGG
472167 GCTGAGGGGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (38 bp):
CATATCCTATCATCATCTAACAGAACATAGTGATGTGG
Found at i:476062 original size:50 final size:51
Alignment explanation
Indices: 476002--476099 Score: 130
Period size: 51 Copynumber: 1.9 Consensus size: 51
475992 AAAAAACGTA
476002 AATGAATAAAATAAAG-AAAATAAAAAAATAG-AATAAAGCAAAAATAAAAAT
1 AATGAATAAAATAAAGAAAAATAAAAAAA-AGAAATAAAG-AAAAATAAAAAT
* * *
476053 AATG-ATAAAATGAAGAAAAATAAATAAAAGAAATAAAGTAAAATAAA
1 AATGAATAAAATAAAGAAAAATAAAAAAAAGAAATAAAGAAAAATAAA
476100 GGAAAAAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
50 20 0.48
51 22 0.52
ACGTcount: A:0.73, C:0.01, G:0.09, T:0.16
Consensus pattern (51 bp):
AATGAATAAAATAAAGAAAAATAAAAAAAAGAAATAAAGAAAAATAAAAAT
Found at i:476089 original size:28 final size:29
Alignment explanation
Indices: 476019--476094 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 29
476009 AAAATAAAGA
*
476019 AAATAAAA-AAATAGAATAAAGCAAAAAT
1 AAATAAAAGAAATAAAATAAAGCAAAAAT
*
476047 AAA-AATAATG--ATAAAATGAAG-AAAAAT
1 AAATAA-AA-GAAATAAAATAAAGCAAAAAT
*
476074 AAATAAAAGAAATAAAGTAAA
1 AAATAAAAGAAATAAAATAAA
476095 ATAAAGGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
26 1 0.03
27 13 0.34
28 24 0.63
ACGTcount: A:0.74, C:0.01, G:0.09, T:0.16
Consensus pattern (29 bp):
AAATAAAAGAAATAAAATAAAGCAAAAAT
Found at i:476096 original size:19 final size:18
Alignment explanation
Indices: 476074--476117 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
476064 GAAGAAAAAT
**
476074 AAATAAAAGAAATAAAGTA
1 AAATAAAAGAAA-AAAACA
*
476093 AAATAAAGGAAAAAAACA
1 AAATAAAAGAAAAAAACA
476111 AAATAAA
1 AAATAAA
476118 TAGGTAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (18 bp):
AAATAAAAGAAAAAAACA
Found at i:476117 original size:23 final size:23
Alignment explanation
Indices: 476069--476117 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
476059 AAAATGAAGA
* * *
476069 AAAATAAATAAAAGAAATAAAGT
1 AAAATAAAGAAAAGAAACAAAAT
476092 AAAATAAAGGAAAA-AAACAAAAT
1 AAAATAAA-GAAAAGAAACAAAAT
476115 AAA
1 AAA
476118 TAGGTAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.78, C:0.02, G:0.08, T:0.12
Consensus pattern (23 bp):
AAAATAAAGAAAAGAAACAAAAT
Found at i:486495 original size:3 final size:3
Alignment explanation
Indices: 486487--486512 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
486477 GGGTCGGCTC
486487 GTG GTG GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GT
486513 AATACGTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.65, T:0.35
Consensus pattern (3 bp):
GTG
Found at i:486707 original size:22 final size:22
Alignment explanation
Indices: 486677--486731 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
486667 TCAGGAGTTA
* *
486677 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
486699 CAGGGGTTAAATGATATAATTT
1 CAGGAGTTATATGATATAATTC
486721 CAGGAGTTATA
1 CAGGAGTTATA
486732 ACAGCTGAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.07, G:0.22, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:492259 original size:32 final size:32
Alignment explanation
Indices: 492218--492283 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
492208 TCCTTGTTGA
*
492218 GTGATAGAGAACAAGGGGGACTCTCGCACACC
1 GTGATAGAGAACAAGGGGGACTATCGCACACC
*
492250 GTGATAGAGAACAAGGGGGACTATCGCGCACC
1 GTGATAGAGAACAAGGGGGACTATCGCACACC
492282 GT
1 GT
492284 CGCCGCCGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.30, C:0.23, G:0.33, T:0.14
Consensus pattern (32 bp):
GTGATAGAGAACAAGGGGGACTATCGCACACC
Found at i:495832 original size:43 final size:43
Alignment explanation
Indices: 495784--495871 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
495774 TTTATTAGCA
495784 TTCTTTTAGTTAAGTTTTAGAAATACATTGGGTGAAAAACCTT
1 TTCTTTTAGTTAAGTTTTAGAAATACATTGGGTGAAAAACCTT
495827 TTCTTTTAGTTAAGTTTTAGAAATACATTGGGTGAAAAACCTT
1 TTCTTTTAGTTAAGTTTTAGAAATACATTGGGTGAAAAACCTT
495870 TT
1 TT
495872 TTGTTCAAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (43 bp):
TTCTTTTAGTTAAGTTTTAGAAATACATTGGGTGAAAAACCTT
Found at i:502586 original size:21 final size:21
Alignment explanation
Indices: 502562--502610 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
502552 TAAAAAATAT
502562 ATATATTTTA-GTCTTAAATTC
1 ATAT-TTTTATGTCTTAAATTC
* *
502583 ATATTTTTATTTTTTAAATTC
1 ATATTTTTATGTCTTAAATTC
502604 ATATTTT
1 ATATTTT
502611 AAATTCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (21 bp):
ATATTTTTATGTCTTAAATTC
Found at i:502612 original size:13 final size:13
Alignment explanation
Indices: 502594--502694 Score: 92
Period size: 13 Copynumber: 8.3 Consensus size: 13
502584 TATTTTTATT
502594 TTTTAAATTCATA
1 TTTTAAATTCATA
502607 TTTTAAATTCATAA
1 TTTTAAATTCAT-A
502621 TTTT--ATT--T-
1 TTTTAAATTCATA
502629 TTTTAAATTCATA
1 TTTTAAATTCATA
*
502642 TTTTAGATTCATA
1 TTTTAAATTCATA
* *
502655 TTTT---TTTATT
1 TTTTAAATTCATA
*
502665 TTTTAAATCCATA
1 TTTTAAATTCATA
*
502678 TCTTAAATTCATA
1 TTTTAAATTCATA
502691 TTTT
1 TTTT
502695 TCATATTTTT
Statistics
Matches: 70, Mismatches: 9, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
8 4 0.06
10 12 0.17
12 4 0.06
13 45 0.64
14 5 0.07
ACGTcount: A:0.32, C:0.08, G:0.01, T:0.59
Consensus pattern (13 bp):
TTTTAAATTCATA
Found at i:502667 original size:36 final size:36
Alignment explanation
Indices: 502575--502706 Score: 189
Period size: 35 Copynumber: 3.7 Consensus size: 36
502565 TATTTTAGTC
502575 TTAAATTCATA-TTTT-TATTTTTTAAATTCATATT
1 TTAAATTCATATTTTTATATTTTTTAAATTCATATT
*
502609 TTAAATTCATAATTTTAT-TTTTTTAAATTCATATT
1 TTAAATTCATATTTTTATATTTTTTAAATTCATATT
* * * *
502644 TTAGATTCATATTTTTTTATTTTTTAAATCCATATC
1 TTAAATTCATATTTTTATATTTTTTAAATTCATATT
502680 TTAAATTCATATTTTTCATATTTTTTA
1 TTAAATTCATATTTTT-ATATTTTTTA
502707 TTTTTATGTC
Statistics
Matches: 87, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
34 11 0.13
35 36 0.41
36 31 0.36
37 9 0.10
ACGTcount: A:0.31, C:0.08, G:0.01, T:0.61
Consensus pattern (36 bp):
TTAAATTCATATTTTTATATTTTTTAAATTCATATT
Found at i:502740 original size:14 final size:14
Alignment explanation
Indices: 502721--502749 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
502711 TATGTCTTAG
502721 ATTAGTATATTTAA
1 ATTAGTATATTTAA
502735 ATTAGTATATTTAA
1 ATTAGTATATTTAA
502749 A
1 A
502750 ATATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
ATTAGTATATTTAA
Found at i:502755 original size:25 final size:23
Alignment explanation
Indices: 502726--502791 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
502716 CTTAGATTAG
502726 TATATTTAAATTAGTATATTTAAAA
1 TATATTTAAATT--TATATTTAAAA
** *
502751 TATATTTTTATTTTTATTTAAAA
1 TATATTTAAATTTATATTTAAAA
*
502774 TATATTTAAA-ATATATTT
1 TATATTTAAATTTATATTT
502792 TTATTTTTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 6 0.18
23 18 0.53
25 10 0.29
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TATATTTAAATTTATATTTAAAA
Found at i:502756 original size:11 final size:11
Alignment explanation
Indices: 502726--502791 Score: 60
Period size: 11 Copynumber: 5.6 Consensus size: 11
502716 CTTAGATTAG
502726 TATATTTAAATTA
1 TATATTTAAA--A
502739 GTATATTTAAAA
1 -TATATTTAAAA
* **
502751 TATATTTTTATT
1 TATA-TTTAAAA
*
502763 TTTATTTAAAA
1 TATATTTAAAA
502774 TATATTTAAAA
1 TATATTTAAAA
502785 TATATTT
1 TATATTT
502792 TTATTTTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
11 25 0.58
12 8 0.19
14 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TATATTTAAAA
Found at i:502769 original size:37 final size:36
Alignment explanation
Indices: 502728--502900 Score: 180
Period size: 37 Copynumber: 4.8 Consensus size: 36
502718 TAGATTAGTA
502728 TATTTAAATTAGTATATTTAAAATATATTTTTATTTT
1 TATTTAAATTA-TATATTTAAAATATATTTTTATTTT
502765 TATTTAAA--ATATATTTAAAATATATTTTTA--TT
1 TATTTAAATTATATATTTAAAATATATTTTTATTTT
** * *
502797 T-TTTATCTTA-ACATTAAAAATATA-TTTTATTTT
1 TATTTAAATTATATATTTAAAATATATTTTTATTTT
502830 TATCTTAAATTAGTATATTTAAAATATATTTTTATTTT
1 TAT-TTAAATTA-TATATTTAAAATATATTTTTATTTT
* **
502868 TATATATTTTTATATATTTAAATATTATATTTT
1 TATTTA-AATTATATATTTAAA-A-TATATTTT
502901 AAAAAATAAA
Statistics
Matches: 113, Mismatches: 11, Indels: 22
0.77 0.08 0.15
Matches are distributed among these distances:
31 9 0.08
32 15 0.13
33 4 0.04
34 22 0.19
35 7 0.06
37 32 0.28
38 16 0.14
39 8 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (36 bp):
TATTTAAATTATATATTTAAAATATATTTTTATTTT
Found at i:502783 original size:34 final size:35
Alignment explanation
Indices: 502740--502870 Score: 175
Period size: 34 Copynumber: 3.8 Consensus size: 35
502730 TTTAAATTAG
502740 TATATTTAAAATATATTTTTATTTTTAT-TTAAAA
1 TATATTTAAAATATATTTTTATTTTTATCTTAAAA
*
502774 TATATTTAAAATATATTTTTATTTTTTATCTTAACA
1 TATATTTAAAATATATTTTTA-TTTTTATCTTAAAA
502810 T-TA---AAAATATA-TTTTATTTTTATCTTAAATTA
1 TATATTTAAAATATATTTTTATTTTTATCTTAAA--A
502842 GTATATTTAAAATATATTTTTATTTTTAT
1 -TATATTTAAAATATATTTTTATTTTTAT
502871 ATATTTTTAT
Statistics
Matches: 85, Mismatches: 2, Indels: 16
0.83 0.02 0.16
Matches are distributed among these distances:
30 12 0.14
31 5 0.06
32 9 0.11
33 1 0.01
34 23 0.27
35 9 0.11
36 6 0.07
37 8 0.09
38 12 0.14
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (35 bp):
TATATTTAAAATATATTTTTATTTTTATCTTAAAA
Found at i:502877 original size:10 final size:10
Alignment explanation
Indices: 502862--502886 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
502852 AATATATTTT
502862 TATTTTTATA
1 TATTTTTATA
502872 TATTTTTATA
1 TATTTTTATA
502882 TATTT
1 TATTT
502887 AAATATTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TATTTTTATA
Found at i:502901 original size:38 final size:37
Alignment explanation
Indices: 502726--502872 Score: 152
Period size: 34 Copynumber: 4.1 Consensus size: 37
502716 CTTAGATTAG
502726 TATATTTAAATTAGTATATTTAAAATATATTTTTATTTT
1 TATA-TTAAATTAGTATATTTAAAATATA-TTTTATTTT
502765 TAT-TTAAA--A-TATATTTAAAATATATTTTTATTTT
1 TATATTAAATTAGTATATTTAAAATATA-TTTTATTTT
* * *
502799 T-TA-T--CTTA--ACATTAAAAATATATTTTATTTT
1 TATATTAAATTAGTATATTTAAAATATATTTTATTTT
*
502830 TATCTTAAATTAGTATATTTAAAATATATTTTTATTTT
1 TATATTAAATTAGTATATTTAAAATATA-TTTTATTTT
502868 TATAT
1 TATAT
502873 ATTTTTATAT
Statistics
Matches: 90, Mismatches: 8, Indels: 21
0.76 0.07 0.18
Matches are distributed among these distances:
31 10 0.11
32 13 0.14
33 4 0.04
34 26 0.29
35 4 0.04
37 17 0.19
38 13 0.14
39 3 0.03
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (37 bp):
TATATTAAATTAGTATATTTAAAATATATTTTATTTT
Found at i:502951 original size:51 final size:50
Alignment explanation
Indices: 502896--502992 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
502886 TAAATATTAT
* *
502896 ATTTTAAAAAATAAAATATATTAAATTAATATATGAATTTAAAAAAAATAC
1 ATTTTAAAAAATAAAA-ATATGAAATTAAGATATGAATTTAAAAAAAATAC
* * *
502947 ATTTTAAAATATAAAAATATGAATTTAAGATATGAATTTTAAAAAA
1 ATTTTAAAAAATAAAAATATGAAATTAAGATATGAATTTAAAAAAA
502993 TAAAAATATG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
50 26 0.63
51 15 0.37
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (50 bp):
ATTTTAAAAAATAAAAATATGAAATTAAGATATGAATTTAAAAAAAATAC
Found at i:502967 original size:37 final size:35
Alignment explanation
Indices: 502926--503007 Score: 103
Period size: 35 Copynumber: 2.3 Consensus size: 35
502916 TTAAATTAAT
*
502926 ATATGAATTTAAAAAAAAT-ACATTTTAAAATATAAAA
1 ATATGAATTT--AAAAAATGA-ATTTTAAAAAATAAAA
* *
502963 ATATGAATTTAAGATATGAATTTTAAAAAATAAAA
1 ATATGAATTTAAAAAATGAATTTTAAAAAATAAAA
502998 ATATGAATTT
1 ATATGAATTT
503008 GAGACTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
35 30 0.73
36 1 0.02
37 10 0.24
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.35
Consensus pattern (35 bp):
ATATGAATTTAAAAAATGAATTTTAAAAAATAAAA
Found at i:503022 original size:2 final size:2
Alignment explanation
Indices: 503015--503040 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
503005 TTTGAGACTA
503015 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
503041 TATTTTAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:504045 original size:17 final size:19
Alignment explanation
Indices: 504024--504079 Score: 71
Period size: 21 Copynumber: 2.9 Consensus size: 19
504014 TATATTTTCC
504024 AACAATTGGTAT-TTTTTT
1 AACAATTGGTATCTTTTTT
*
504042 -ACAATTGATATCATTTTGTT
1 AACAATTGGTATC-TTTT-TT
504062 AACAATTGGTATCTTTTT
1 AACAATTGGTATCTTTTT
504080 CATTAAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 10 0.31
19 5 0.16
20 6 0.19
21 11 0.34
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.52
Consensus pattern (19 bp):
AACAATTGGTATCTTTTTT
Found at i:504500 original size:21 final size:21
Alignment explanation
Indices: 504474--504535 Score: 106
Period size: 21 Copynumber: 3.0 Consensus size: 21
504464 TTTGAATTTA
504474 ATGAAGGTGTACCGATACCCT
1 ATGAAGGTGTACCGATACCCT
504495 ATGAAGGTGTACCGATACCCT
1 ATGAAGGTGTACCGATACCCT
* *
504516 ATGAAGGGGTACCAATACCC
1 ATGAAGGTGTACCGATACCC
504536 CTTGTTATGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (21 bp):
ATGAAGGTGTACCGATACCCT
Found at i:504593 original size:21 final size:21
Alignment explanation
Indices: 504564--504603 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
504554 GTTTTGTAGA
504564 AAAATCATCTCCAAACGGCTCC
1 AAAATCATC-CCAAACGGCTCC
*
504586 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCAAACGGCT
504604 AGAAACGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 4 0.24
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCAAACGGCTCC
Found at i:505360 original size:32 final size:31
Alignment explanation
Indices: 505318--505393 Score: 84
Period size: 32 Copynumber: 2.4 Consensus size: 31
505308 AGGCACAAAA
*
505318 ACAAATATAAAAAAATATATATA-AATAA-AAT
1 ACAAAAATAAAAAAATA-ATA-ACAATAACAAT
*
505349 ACATAAAATAAAGAAGATAATAACAATAACAAT
1 ACA-AAAATAAA-AAAATAATAACAATAACAAT
505382 ACAAAAATAAAA
1 ACAAAAATAAAA
505394 TAAAATAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
31 5 0.13
32 23 0.59
33 11 0.28
ACGTcount: A:0.71, C:0.07, G:0.03, T:0.20
Consensus pattern (31 bp):
ACAAAAATAAAAAAATAATAACAATAACAAT
Found at i:505449 original size:16 final size:17
Alignment explanation
Indices: 505428--505493 Score: 72
Period size: 16 Copynumber: 4.1 Consensus size: 17
505418 AGATAAAATG
505428 AAATATATA-AAATAAT
1 AAATATATATAAATAAT
505444 AAATATATATAACAT-AT
1 AAATATATATAA-ATAAT
505461 -AAT-TATAGT-AATAA-
1 AAATATATA-TAAATAAT
505475 AAATATATATAAATAAT
1 AAATATATATAAATAAT
505492 AA
1 AA
505494 TGATATATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 15
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.05
15 10 0.24
16 22 0.52
17 6 0.14
18 2 0.05
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (17 bp):
AAATATATATAAATAAT
Found at i:508577 original size:18 final size:18
Alignment explanation
Indices: 508554--508588 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
508544 CCTTGTGATA
508554 ATTTTAATTTTTTATATG
1 ATTTTAATTTTTTATATG
508572 ATTTTAATTTTTTATAT
1 ATTTTAATTTTTTATAT
508589 TTTCAATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
ATTTTAATTTTTTATATG
Found at i:508596 original size:16 final size:15
Alignment explanation
Indices: 508554--508596 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 15
508544 CCTTGTGATA
508554 ATTTTAATTTTTTATAT
1 ATTTTAA-TTTTT-TAT
508571 GATTTTAATTTTTTAT
1 -ATTTTAATTTTTTAT
508587 ATTTTCAATT
1 ATTTT-AATT
508597 CATTAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.21
16 7 0.29
17 5 0.21
18 7 0.29
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (15 bp):
ATTTTAATTTTTTAT
Found at i:511764 original size:4 final size:4
Alignment explanation
Indices: 511747--511779 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
511737 GGTTGAACAC
*
511747 ACAT ACAT AAAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
511780 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:514828 original size:17 final size:17
Alignment explanation
Indices: 514803--514846 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
514793 TGGATACTCG
* * *
514803 AAATACGGGTAGCTGCA
1 AAATCCGGGTACCTACA
514820 AAATCCGGGTACCTACA
1 AAATCCGGGTACCTACA
*
514837 ACATCCGGGT
1 AAATCCGGGT
514847 CGGGACACGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.18
Consensus pattern (17 bp):
AAATCCGGGTACCTACA
Found at i:527609 original size:19 final size:19
Alignment explanation
Indices: 527587--527635 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
527577 GTGTGTGTAA
527587 AAGCAATGTGCCCCCTGAT
1 AAGCAATGTGCCCCCTGAT
*
527606 AAGCAATGTGCCCCCTGCT
1 AAGCAATGTGCCCCCTGAT
527625 AAGCAATGTGC
1 AAGCAATGTGC
527636 TCCTACTTCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (19 bp):
AAGCAATGTGCCCCCTGAT
Found at i:527916 original size:29 final size:29
Alignment explanation
Indices: 527874--527933 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
527864 TGCTTTTTAT
527874 ATATATATATAATCGAGCTATTTCAAATG
1 ATATATATATAATCGAGCTATTTCAAATG
527903 ATATATATATAATCGAGCTATTTCAAATG
1 ATATATATATAATCGAGCTATTTCAAATG
527932 AT
1 AT
527934 CGACCGAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
ATATATATATAATCGAGCTATTTCAAATG
Found at i:538396 original size:12 final size:12
Alignment explanation
Indices: 538379--538446 Score: 120
Period size: 12 Copynumber: 5.8 Consensus size: 12
538369 AACAATCCTC
538379 CACCTAACTCTT
1 CACCTAACTCTT
538391 CACCTAACTC-T
1 CACCTAACTCTT
538402 CACCTAACTCTT
1 CACCTAACTCTT
*
538414 CACCTAATTCTT
1 CACCTAACTCTT
538426 CACCTAACTCTT
1 CACCTAACTCTT
538438 CACCTAACT
1 CACCTAACT
538447 AAATTGATGT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
11 11 0.21
12 42 0.79
ACGTcount: A:0.26, C:0.41, G:0.00, T:0.32
Consensus pattern (12 bp):
CACCTAACTCTT
Found at i:538426 original size:35 final size:36
Alignment explanation
Indices: 538379--538446 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
538369 AACAATCCTC
538379 CACCTAACTCTTCACCTAACTC-TCACCTAACTCTT
1 CACCTAACTCTTCACCTAACTCTTCACCTAACTCTT
*
538414 CACCTAATTCTTCACCTAACTCTTCACCTAACT
1 CACCTAACTCTTCACCTAACTCTTCACCTAACT
538447 AAATTGATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.26, C:0.41, G:0.00, T:0.32
Consensus pattern (36 bp):
CACCTAACTCTTCACCTAACTCTTCACCTAACTCTT
Found at i:545153 original size:12 final size:12
Alignment explanation
Indices: 545125--545177 Score: 72
Period size: 12 Copynumber: 4.5 Consensus size: 12
545115 ATATACAAAT
545125 ACCTAACTCTT-
1 ACCTAACTCTTC
*
545136 ACCTAAATCTTC
1 ACCTAACTCTTC
*
545148 ACCTAATTCTTC
1 ACCTAACTCTTC
*
545160 ACCCAACTCTTC
1 ACCTAACTCTTC
545172 ACCTAA
1 ACCTAA
545178 TTAAATTGAT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.30, C:0.38, G:0.00, T:0.32
Consensus pattern (12 bp):
ACCTAACTCTTC
Found at i:551340 original size:13 final size:13
Alignment explanation
Indices: 551318--551351 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
551308 GAATGGAAAC
*
551318 TTTATATCACTCA
1 TTTATCTCACTCA
551331 TTTATCTCACTCA
1 TTTATCTCACTCA
551344 TTTATCTC
1 TTTATCTC
551352 CTTCCCTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTATCTCACTCA
Found at i:573042 original size:24 final size:25
Alignment explanation
Indices: 572989--573042 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
572979 AACAACTAAG
**
572989 GATAAAATCCTAAAAATATTCATAT
1 GATAAAATCCTAAAAATAAACATAT
*
573014 AATAAAATCCT-AAAATAAACA-AGT
1 GATAAAATCCTAAAAATAAACATA-T
573038 GATAA
1 GATAA
573043 TTCCCAAATT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
23 1 0.04
24 13 0.54
25 10 0.42
ACGTcount: A:0.57, C:0.11, G:0.06, T:0.26
Consensus pattern (25 bp):
GATAAAATCCTAAAAATAAACATAT
Found at i:573537 original size:28 final size:28
Alignment explanation
Indices: 573506--573606 Score: 107
Period size: 28 Copynumber: 3.6 Consensus size: 28
573496 ACGGGGATAC
* *
573506 AATCCCATGCAGGAAT-AGGATGGGATCA
1 AATCCCATGCA-GAATCAGGACGAGATCA
* *
573534 AATCCAATGTAGAATCAGGACGAGATCA
1 AATCCCATGCAGAATCAGGACGAGATCA
* * *
573562 AATCCCATGGAGAATCAAGAC-ATGATCC
1 AATCCCATGCAGAATCAGGACGA-GATCA
573590 AATCCCATGCAGAATCA
1 AATCCCATGCAGAATCA
573607 AGACTTGGAT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 5 0.08
28 57 0.92
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.18
Consensus pattern (28 bp):
AATCCCATGCAGAATCAGGACGAGATCA
Found at i:573607 original size:28 final size:28
Alignment explanation
Indices: 573529--573642 Score: 122
Period size: 28 Copynumber: 4.0 Consensus size: 28
573519 AATAGGATGG
* *
573529 GATCAAATCCAATGTAGAATCAGGACGA-
1 GATCAAATCCCATGTAGAATCAAGAC-AT
*
573557 GATCAAATCCCATGGAGAATCAAGACAT
1 GATCAAATCCCATGTAGAATCAAGACAT
* * *
573585 GATCCAATCCCATGCAGAATCAAGACTT
1 GATCAAATCCCATGTAGAATCAAGACAT
* **
573613 GGATCTAATCTTATGTAGAATCAAGACAT
1 -GATCAAATCCCATGTAGAATCAAGACAT
573642 G
1 G
573643 GATTATGCCC
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
27 1 0.01
28 49 0.67
29 23 0.32
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (28 bp):
GATCAAATCCCATGTAGAATCAAGACAT
Found at i:573632 original size:29 final size:29
Alignment explanation
Indices: 573557--573645 Score: 108
Period size: 29 Copynumber: 3.1 Consensus size: 29
573547 ATCAGGACGA
* *
573557 GATCAAATCCCATGGAGAATCAAGACAT-
1 GATCCAATCCCATGCAGAATCAAGACATG
*
573585 GATCCAATCCCATGCAGAATCAAGACTTG
1 GATCCAATCCCATGCAGAATCAAGACATG
* ** *
573614 GATCTAATCTTATGTAGAATCAAGACATG
1 GATCCAATCCCATGCAGAATCAAGACATG
573643 GAT
1 GAT
573646 TATGCCCTCC
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 25 0.48
29 27 0.52
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (29 bp):
GATCCAATCCCATGCAGAATCAAGACATG
Found at i:573858 original size:16 final size:16
Alignment explanation
Indices: 573837--573871 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
573827 TCAAGGGAAC
573837 ACACCTATACCAACTA
1 ACACCTATACCAACTA
573853 ACACCTATACCAACTA
1 ACACCTATACCAACTA
573869 ACA
1 ACA
573872 TATATCGACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.37, G:0.00, T:0.17
Consensus pattern (16 bp):
ACACCTATACCAACTA
Found at i:574339 original size:23 final size:23
Alignment explanation
Indices: 574305--574361 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
574295 TTCAGGTTGG
574305 TCAAAGTT-AACGGGTTAGGTCAA
1 TCAAA-TTCAACGGGTTAGGTCAA
* *
574328 TTAAATTCAACGGGTTGGGTCAA
1 TCAAATTCAACGGGTTAGGTCAA
574351 TCAAATTCAAC
1 TCAAATTCAAC
574362 TCGGTCAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.28
Consensus pattern (23 bp):
TCAAATTCAACGGGTTAGGTCAA
Found at i:577704 original size:15 final size:17
Alignment explanation
Indices: 577684--577715 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
577674 ATGGATTTCC
577684 TTAA-TTTGCAT-ATTA
1 TTAATTTTGCATCATTA
577699 TTAATTTTGCATCATTA
1 TTAATTTTGCATCATTA
577716 GATACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.27
16 7 0.47
17 4 0.27
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.53
Consensus pattern (17 bp):
TTAATTTTGCATCATTA
Found at i:582602 original size:20 final size:20
Alignment explanation
Indices: 582573--582614 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
582563 TTCATCACAC
* *
582573 CAAATCCTCTCAACTTCTCT
1 CAAATACTCTCAAATTCTCT
*
582593 CAAATACTCTTAAATTCTCT
1 CAAATACTCTCAAATTCTCT
582613 CA
1 CA
582615 TAGTTTTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (20 bp):
CAAATACTCTCAAATTCTCT
Found at i:582650 original size:17 final size:18
Alignment explanation
Indices: 582628--582661 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
582618 TTTTTAAGGT
582628 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
582645 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
582662 TATTTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:582693 original size:29 final size:30
Alignment explanation
Indices: 582628--582698 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 30
582618 TTTTTAAGGT
582628 ATATTTTA-TT-ATATTTAATATTTTGTTA
1 ATATTTTATTTAATATTTAATATTTTGTTA
*
582656 GTATTTTATTTAACTATTTAA-ATTTT-TTA
1 ATATTTTATTTAA-TATTTAATATTTTGTTA
582685 ATATTTTATTTAAT
1 ATATTTTATTTAAT
582699 TAAATTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 8 0.21
29 17 0.45
30 6 0.16
31 7 0.18
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (30 bp):
ATATTTTATTTAATATTTAATATTTTGTTA
Found at i:588210 original size:12 final size:12
Alignment explanation
Indices: 588193--588217 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
588183 TCATATATAA
588193 TTATAAAAAAAT
1 TTATAAAAAAAT
588205 TTATAAAAAAAT
1 TTATAAAAAAAT
588217 T
1 T
588218 ACCTTATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTATAAAAAAAT
Found at i:590852 original size:2 final size:2
Alignment explanation
Indices: 590847--590878 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
590837 ACACACACAC
590847 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
590879 GAATATGTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:591556 original size:23 final size:23
Alignment explanation
Indices: 591507--591598 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
591497 ATAAGTTCAT
*
591507 GAACACGTTTGTGAACATATAAAC
1 GAACACGTTCGTGAACAT-TAAAC
*
591531 GAACACGTTCGCGAACATTAAAC
1 GAACACGTTCGTGAACATTAAAC
* *
591554 GAACACGTTCGTGAACATTGAAT
1 GAACACGTTCGTGAACATTAAAC
* *
591577 GAACATGTTCGTGAACAATAAA
1 GAACACGTTCGTGAACATTAAA
591599 TAAACAAACA
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
23 44 0.73
24 16 0.27
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.23
Consensus pattern (23 bp):
GAACACGTTCGTGAACATTAAAC
Found at i:592658 original size:20 final size:21
Alignment explanation
Indices: 592633--592684 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
592623 TTTTCCCAAT
*
592633 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
592653 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
592674 TCGCAATGCGA
1 TCGCAATGCGA
592685 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:593323 original size:19 final size:19
Alignment explanation
Indices: 593263--593343 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
593253 TTCGAGAATG
593263 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
** *
593283 ACTATCGCAA--CGAGAT-
1 AAAATCGCAACGCGAAATA
593299 --AATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
593316 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
593335 AAAATCGCA
1 AAAATCGCA
593344 TTGCGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
14 7 0.14
16 5 0.10
17 4 0.08
18 1 0.02
19 24 0.49
20 8 0.16
ACGTcount: A:0.47, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:593361 original size:19 final size:19
Alignment explanation
Indices: 593339--593523 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
593329 GAAACCAAAA
*
593339 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
593358 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
593377 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
593396 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
593416 TCGCGGTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
593432 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
593449 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
593463 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
593482 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
593502 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
593522 TC
1 TC
593524 AACCAAAAAA
Statistics
Matches: 135, Mismatches: 18, Indels: 26
0.75 0.10 0.15
Matches are distributed among these distances:
14 18 0.13
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 59 0.44
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:593416 original size:39 final size:38
Alignment explanation
Indices: 593339--593523 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
593329 GAAACCAAAA
*
593339 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
593377 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
593416 TCGCGGTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* * **
593449 TTGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
593482 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
593522 TC
1 TC
593524 AACCAAAAAA
Statistics
Matches: 120, Mismatches: 17, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
31 3 0.03
33 36 0.30
34 9 0.08
35 1 0.01
36 3 0.03
38 21 0.17
39 29 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:593500 original size:20 final size:20
Alignment explanation
Indices: 593466--593523 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
593456 GCGATTCTCT
**
593466 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
593486 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
593506 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
593524 AACCAAAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:595585 original size:42 final size:42
Alignment explanation
Indices: 595525--595647 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
595515 GCCCGACTCG
* * *
595525 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
595567 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
595609 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
595648 CCTAATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:595605 original size:21 final size:21
Alignment explanation
Indices: 595581--595647 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
595571 TCATTCCTCG
595581 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
595602 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
595623 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
595644 AGAG
1 AGAG
595648 CCTAATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:597025 original size:14 final size:14
Alignment explanation
Indices: 597006--597041 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
596996 ATTGTTTAAT
597006 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
597020 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
597034 TGATTTGT
1 TGATTTGT
597042 TTAATTGATG
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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:597192 original size:19 final size:19
Alignment explanation
Indices: 597168--597226 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
597158 GAAATTAGCG
597168 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
597187 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
597201 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
597220 TTGCGAT
1 TTGCGAT
597227 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:597192 original size:33 final size:34
Alignment explanation
Indices: 597149--597225 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
597139 AAAAGTACTA
*
597149 TCGCAATGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
* **
597182 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
597215 TCGCATTGCGA
1 TCGCATTGCGA
597226 TAGTAATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
Found at i:599536 original size:12 final size:12
Alignment explanation
Indices: 599519--599543 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
599509 TCTTCGGGGA
599519 CTTTTTCTTCTT
1 CTTTTTCTTCTT
599531 CTTTTTCTTCTT
1 CTTTTTCTTCTT
599543 C
1 C
599544 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:599752 original size:24 final size:24
Alignment explanation
Indices: 599718--599771 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
599708 CTGAAACATC
* *
599718 ATCAAAATCCGTGTATTAACCAAT
1 ATCAAAATCCGGGTATTAACCAAG
* *
599742 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTAACCAAG
599766 ATCAAA
1 ATCAAA
599772 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTAACCAAG
Found at i:600860 original size:20 final size:20
Alignment explanation
Indices: 600831--600888 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
600821 ATTCATTTGA
*
600831 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATAG
*
600851 CTATCACAACGCGAAAATAG
1 CTATCGCAACGCGAAAATAG
* *
600871 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
600889 CGCAATGCGA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATAG
Found at i:600931 original size:14 final size:16
Alignment explanation
Indices: 600911--600984 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
600901 TGAAAATCGC
600911 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
600926 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
600943 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
600962 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
600978 -TTGCGAT
1 ATTGCGAT
600985 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:600948 original size:19 final size:19
Alignment explanation
Indices: 600907--600974 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
600897 GAAATGAAAA
600907 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
600923 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
600940 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
600959 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
600975 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:600950 original size:52 final size:52
Alignment explanation
Indices: 600888--601002 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
600878 AACGAGAAAA
* ***
600888 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
600940 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
600992 TCGCGTTGCGA
1 TCGCATTGCGA
601003 TAGTCTATTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Done.