Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007735.1 Hibiscus syriacus cultivar Beakdansim tig00109992_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: 534668
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:346885 original size:22 final size:22
Alignment explanation
Indices: 346819--346899 Score: 92
Period size: 23 Copynumber: 3.7 Consensus size: 22
346809 CAGAACCCTA
* *
346819 GGGGTATCGATTCCCCTAC-AG
1 GGGGAATCGATTCCCCTTCAAG
* *
346840 GGGGAATCGGTTCCCGTTCAAAG
1 GGGGAATCGATTCCCCTTC-AAG
*
346863 GGGGAATCGGTTCCCCTTCAAG
1 GGGGAATCGATTCCCCTTCAAG
*
346885 GGGGTATCGATTCCC
1 GGGGAATCGATTCCC
346900 TCTACACTAA
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 15 0.29
22 16 0.31
23 20 0.39
ACGTcount: A:0.19, C:0.26, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGAATCGATTCCCCTTCAAG
Found at i:350740 original size:22 final size:21
Alignment explanation
Indices: 350698--350737 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
350688 GAGTTTATTT
*
350698 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
350719 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
350738 ACAATTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:354435 original size:14 final size:14
Alignment explanation
Indices: 354416--354443 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
354406 TAGTCACTTC
354416 TCCACATCTTTCTG
1 TCCACATCTTTCTG
354430 TCCACATCTTTCTG
1 TCCACATCTTTCTG
354444 CTGAAGATGG
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:0.14, C:0.36, G:0.07, T:0.43
Consensus pattern (14 bp):
TCCACATCTTTCTG
Found at i:358843 original size:29 final size:30
Alignment explanation
Indices: 358796--358857 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 30
358786 TATACGTTTG
* * * *
358796 GTTCTAGTTTAGTGTCTAATGTTT-ATTTC
1 GTTCAAGTTTAGTGCCTAACGTTTCATTCC
*
358825 GTTCAAGTTTGGTGCCTAACGTTTCATTCC
1 GTTCAAGTTTAGTGCCTAACGTTTCATTCC
358855 GTT
1 GTT
358858 ACTCATTTAG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.48
Consensus pattern (30 bp):
GTTCAAGTTTAGTGCCTAACGTTTCATTCC
Found at i:363167 original size:9 final size:9
Alignment explanation
Indices: 363155--363206 Score: 56
Period size: 9 Copynumber: 6.1 Consensus size: 9
363145 TAATATTTTA
363155 TATTTAATT
1 TATTTAATT
*
363164 TATTTAA-G
1 TATTTAATT
363172 TATTTAATT
1 TATTTAATT
363181 TATTTAA--
1 TATTTAATT
*
363188 TATTTAACT
1 TATTTAATT
*
363197 TAATTAATT
1 TATTTAATT
363206 T
1 T
363207 TTTTGCATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 22 0.61
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
TATTTAATT
Found at i:363177 original size:17 final size:16
Alignment explanation
Indices: 363148--363204 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
363138 ATATTTTTAA
*
363148 TATTTTATATTTAATT
1 TATTTAATATTTAATT
363164 TATTTAAGTATTTAATT
1 TATTTAA-TATTTAATT
*
363181 TATTTAATATTTAACT
1 TATTTAATATTTAATT
*
363197 TAATTAAT
1 TATTTAAT
363205 TTTTTTGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 21 0.57
17 16 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (16 bp):
TATTTAATATTTAATT
Found at i:364988 original size:33 final size:33
Alignment explanation
Indices: 364941--365004 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
364931 TACCAGATGT
* * *
364941 CGCCGCCGCCTTCACATAGTTTTATGACCCCGC
1 CGCCGCCACATTCACAGAGTTTTATGACCCCGC
364974 CGCCGCCACATTCACAGAGTTTTATGACCCC
1 CGCCGCCACATTCACAGAGTTTTATGACCCC
365005 TCCTGGAGGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.19, C:0.41, G:0.17, T:0.23
Consensus pattern (33 bp):
CGCCGCCACATTCACAGAGTTTTATGACCCCGC
Found at i:365275 original size:3 final size:3
Alignment explanation
Indices: 365267--365298 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
365257 AGCTGCTCAG
*
365267 GAC GAC GAC GAC GAT GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
365299 TGATGATGAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.28, G:0.34, T:0.03
Consensus pattern (3 bp):
GAC
Found at i:365287 original size:12 final size:12
Alignment explanation
Indices: 365270--365310 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
365260 TGCTCAGGAC
365270 GACGACGACGAT
1 GACGACGACGAT
*
365282 GACGACGACGAC
1 GACGACGACGAT
* *
365294 GACGATGATGAT
1 GACGACGACGAT
365306 GACGA
1 GACGA
365311 TGGTGATGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.34, C:0.22, G:0.34, T:0.10
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:365473 original size:13 final size:13
Alignment explanation
Indices: 365453--365499 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
365443 TATTTAGTAC
*
365453 TTTTTATTGTAGT
1 TTTTTATTGTAAT
* * *
365466 TGTTTATTGGACT
1 TTTTTATTGTAAT
365479 TTTTTATTGTAAT
1 TTTTTATTGTAAT
365492 TTTTTATT
1 TTTTTATT
365500 ATTTATCATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.17, C:0.02, G:0.13, T:0.68
Consensus pattern (13 bp):
TTTTTATTGTAAT
Found at i:369665 original size:21 final size:20
Alignment explanation
Indices: 369639--369817 Score: 157
Period size: 21 Copynumber: 8.7 Consensus size: 20
369629 GTTTCCAGAT
*
369639 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAA-TTCGACTA
*
369660 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
*
369681 TCGCAATGCGAATAT-GTA-AA
1 TCGCAATGCGAAT-TCG-ACTA
*
369701 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTCGACTA
** *
369722 TCGCAATGCGAATATATA-AA
1 TCGCAATGCGAAT-TCGACTA
*
369742 TCGCAATGCGATAGTCGACTA
1 TCGCAATGCGA-ATTCGACTA
*
369763 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
* *
369784 TCTCAATGCGAATTTGGACTA
1 TCGCAATGCGAA-TTCGACTA
369805 TCGCAATGCGAAT
1 TCGCAATGCGAAT
369818 ATGTGTTGCG
Statistics
Matches: 131, Mismatches: 18, Indels: 19
0.78 0.11 0.11
Matches are distributed among these distances:
20 33 0.25
21 98 0.75
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATTCGACTA
Found at i:369704 original size:41 final size:41
Alignment explanation
Indices: 369659--369821 Score: 197
Period size: 41 Copynumber: 4.0 Consensus size: 41
369649 AACTTCGACT
* *
369659 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGTAA
*
369700 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATATAA
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
* *
369741 ATCGCAATGCGATAGTCGACTATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGATAGTCGACTATCGCAATGCGAA-TATGTA-A
* * *
369783 ATCTCAATGCGA-ATTTGGACTATCGCAATGCGAATATGT
1 ATCGCAATGCGATA-GTCGACTATCGCAATGCGAATATGT
369822 GTTGCGATTT
Statistics
Matches: 107, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
41 74 0.69
42 33 0.31
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.26
Consensus pattern (41 bp):
ATCGCAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
Found at i:369705 original size:20 final size:20
Alignment explanation
Indices: 369680--369752 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
369670 AACTTGGACT
369680 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
369700 ATCGCAATGCG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
*
369721 ATCGCAATGCGAATATATAA
1 ATCGCAATGCGAATATGTAA
369741 ATCGCAATGCGA
1 ATCGCAATGCGA
369753 TAGTCGACTA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.04
19 3 0.07
20 24 0.53
21 12 0.27
22 3 0.07
23 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:369960 original size:6 final size:6
Alignment explanation
Indices: 369949--369981 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
369939 GACACGTATT
369949 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
369982 CGAGACGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:370638 original size:21 final size:20
Alignment explanation
Indices: 370586--370642 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
370576 CGTTGCGATT
370586 TTGGACTATCGCAA-CGAAC
1 TTGGACTATCGCAACCGAAC
*
370605 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAAC-CGAAC
*
370628 TTTGACTATCGCAAC
1 TTGGACTATCGCAAC
370643 AAATTTGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 6 0.19
21 15 0.48
23 10 0.32
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (20 bp):
TTGGACTATCGCAACCGAAC
Found at i:372208 original size:106 final size:106
Alignment explanation
Indices: 372023--372339 Score: 584
Period size: 105 Copynumber: 3.0 Consensus size: 106
372013 TAGTGTTGCG
*
372023 ATCCAACATCATAATTTCATACTTTAATGTTAATTTGTTAAAAGATAACTG-CAACTATAATAAT
1 ATCCAACATCATAATTTCATACTTTAATGTTAATTTGTTAAAAGATAAC-GACAAGTATAATAAT
372087 CACCCAACAAAAGAAACATCAATATTTTACATGATTTTTTTT
65 CACCCAACAAAAGAAACATCAATATTTTACATGATTTTTTTT
372129 ATCCAACATCATAATTTCATACTTTAATGTTAATTTGTTAAAAGATAACGACAAGTATAATAATC
1 ATCCAACATCATAATTTCATACTTTAATGTTAATTTGTTAAAAGATAACGACAAGTATAATAATC
372194 ACCCAACAAAAGAAACATCAATATTTTACATGA-TTTTTTT
66 ACCCAACAAAAGAAACATCAATATTTTACATGATTTTTTTT
*
372234 ATCCAACATCATAATTTCATACTTTAATGTTAATTTGTTAAAAGATAACAACAAGTATAATAATC
1 ATCCAACATCATAATTTCATACTTTAATGTTAATTTGTTAAAAGATAACGACAAGTATAATAATC
*
372299 ACCCAACAAAAGAAACACCAATATTTTACATGATTTTTTTT
66 ACCCAACAAAAGAAACATCAATATTTTACATGATTTTTTTT
372340 CCAGAAAAAT
Statistics
Matches: 206, Mismatches: 3, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
105 104 0.50
106 102 0.50
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.36
Consensus pattern (106 bp):
ATCCAACATCATAATTTCATACTTTAATGTTAATTTGTTAAAAGATAACGACAAGTATAATAATC
ACCCAACAAAAGAAACATCAATATTTTACATGATTTTTTTT
Found at i:383818 original size:20 final size:20
Alignment explanation
Indices: 383781--383823 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
383771 ATTCCACCAC
* *
383781 ATGCAACTATATGTTCCTAA
1 ATGCAACTACATGGTCCTAA
*
383801 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGGTCCTAA
383821 ATG
1 ATG
383824 AGATCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTACATGGTCCTAA
Found at i:403557 original size:18 final size:18
Alignment explanation
Indices: 403534--403571 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
403524 CGTGAGGATT
403534 GGGCAGTGGTCCAGCATG
1 GGGCAGTGGTCCAGCATG
*
403552 GGGCAGTGGTCCAGTATG
1 GGGCAGTGGTCCAGCATG
403570 GG
1 GG
403572 CATATGGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.18
Consensus pattern (18 bp):
GGGCAGTGGTCCAGCATG
Found at i:403961 original size:20 final size:20
Alignment explanation
Indices: 403924--403966 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
403914 ATTCCACCAC
* *
403924 ATGCAACTATATGTTCCTAA
1 ATGCAACTACATGGTCCTAA
*
403944 ATGCATCTACATGGTCCTAA
1 ATGCAACTACATGGTCCTAA
403964 ATG
1 ATG
403967 AGATCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTACATGGTCCTAA
Found at i:407859 original size:60 final size:60
Alignment explanation
Indices: 407713--407865 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 60
407703 TTAATATTGA
* *
407713 TCCTTAAACTTTTGAATATTT-CAATTTCATCCCTAAACTATGACTCTCATTCTAAACTAG
1 TCCTCAAACTTTTGAAT-TTTCCAATTTCATCCCTAAAATATGACTCTCATTCTAAACTAG
* * * ** * * * *
407773 TCCTTAAATTTTTAAACATTCTAATTTCATCCCTAAAATATGAC-CTTCTTTCTAAATTGG
1 TCCTCAAACTTTTGAATTTTCCAATTTCATCCCTAAAATATGACTC-TCATTCTAAACTAG
*
407833 TTCC-CAAACTTTTGAATTTTCCAATTTTATCCC
1 -TCCTCAAACTTTTGAATTTTCCAATTTCATCCC
407866 CAAATTCATC
Statistics
Matches: 74, Mismatches: 16, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
59 3 0.04
60 68 0.92
61 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (60 bp):
TCCTCAAACTTTTGAATTTTCCAATTTCATCCCTAAAATATGACTCTCATTCTAAACTAG
Found at i:417578 original size:2 final size:2
Alignment explanation
Indices: 417571--417608 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
417561 TTTTATTCGA
417571 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
417609 TATGGTATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:419329 original size:32 final size:31
Alignment explanation
Indices: 419289--419381 Score: 159
Period size: 32 Copynumber: 2.9 Consensus size: 31
419279 GAACGGAAGG
419289 AAAAGGGTAAATTACACCATGAGTCATTAGA
1 AAAAGGGTAAATTACACCATGAGTCATTAGA
*
419320 AAAATGGGTAAATTACACCATGATTCATTAGAA
1 AAAA-GGGTAAATTACACCATGAGTCATTAG-A
419353 AAAAGGGTAAATTACACCATGAGTCATTA
1 AAAAGGGTAAATTACACCATGAGTCATTA
419382 AACTTTACTC
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
31 4 0.07
32 49 0.84
33 5 0.09
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (31 bp):
AAAAGGGTAAATTACACCATGAGTCATTAGA
Found at i:420210 original size:106 final size:106
Alignment explanation
Indices: 420057--420253 Score: 242
Period size: 106 Copynumber: 1.9 Consensus size: 106
420047 CACTAATAAC
* * *
420057 AAATATTAAAAAAACTAAATTTTAAGAGTATAGTCATAATAATAAATATCT-AAAAATTGAACCT
1 AAATATTAAAAAAACTAAATTTTAAAAGTATAGTCATAATAACAAATAT-TAAAAAAATGAACC-
420121 CC-AATAAAAAGTACT-AAAAAATTGGATTCATAACAACAAAT
64 CCTAATAAAAAGTACTGAAAAAATTGGATTCATAACAACAAAT
* * *
420162 AAATATTAGAAAAAATTGAATTTTAAAAGTAT-GCCTC-TAATAACAAATATTAAAAAAATGGAC
1 AAATATTA-AAAAAACTAAATTTTAAAAGTATAG--TCATAATAACAAATATTAAAAAAATGAAC
* *
420225 CCCTAATAACAAGTATTGAAAAAATTGGA
63 CCCTAATAAAAAGTACTGAAAAAATTGGA
420254 CATTTAATAA
Statistics
Matches: 78, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
105 12 0.15
106 53 0.68
107 13 0.17
ACGTcount: A:0.54, C:0.10, G:0.09, T:0.27
Consensus pattern (106 bp):
AAATATTAAAAAAACTAAATTTTAAAAGTATAGTCATAATAACAAATATTAAAAAAATGAACCCC
TAATAAAAAGTACTGAAAAAATTGGATTCATAACAACAAAT
Found at i:420254 original size:30 final size:29
Alignment explanation
Indices: 420198--420279 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 29
420188 AAGTATGCCT
420198 CTAATAACAAATATTAAAAAAATGGACCC
1 CTAATAACAAATATTAAAAAAATGGACCC
* * **
420227 CTAATAACAAGTATTGAAAAAATTGGACAT
1 CTAATAACAAATATT-AAAAAAATGGACCC
* *
420257 TTAATAACAAATGTTAGAAAAAA
1 CTAATAACAAATATTA-AAAAAA
420280 ATATTGGCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
29 15 0.35
30 28 0.65
ACGTcount: A:0.55, C:0.11, G:0.10, T:0.24
Consensus pattern (29 bp):
CTAATAACAAATATTAAAAAAATGGACCC
Found at i:420338 original size:45 final size:45
Alignment explanation
Indices: 420238--420325 Score: 112
Period size: 43 Copynumber: 2.0 Consensus size: 45
420228 TAATAACAAG
* *
420238 TATT-GAAAAA-ATTGGACATTTAATAACAAATGTTAGAAAAAAA
1 TATTAGAAAAATATTGGACACTTAATAACAAATATTAGAAAAAAA
* *
420281 TATTGGCAAAATATTGGACACTT-AT-ACAAATATTAGAAAAAAA
1 TATTAGAAAAATATTGGACACTTAATAACAAATATTAGAAAAAAA
420324 TA
1 TA
420326 AATTATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
43 23 0.57
44 7 0.17
45 10 0.25
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.28
Consensus pattern (45 bp):
TATTAGAAAAATATTGGACACTTAATAACAAATATTAGAAAAAAA
Found at i:423160 original size:18 final size:17
Alignment explanation
Indices: 423134--423167 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
423124 ACCATTTTTT
*
423134 TATATATTTATGACCAAA
1 TATACATTTAT-ACCAAA
423152 TATACATTTATACCAA
1 TATACATTTATACCAA
423168 GTTTTTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.44, C:0.15, G:0.03, T:0.38
Consensus pattern (17 bp):
TATACATTTATACCAAA
Found at i:424541 original size:20 final size:20
Alignment explanation
Indices: 424512--424573 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
424502 GTTGAACGCA
*
424512 ATTTTCCATTTCGCGTTGCG
1 ATTTTTCATTTCGCGTTGCG
424532 ATTTTTCATTTCGCGTTGCG
1 ATTTTTCATTTCGCGTTGCG
424552 ATTTTTCATTTCGCGTTGCG
1 ATTTTTCATTTCGCGTTGCG
424572 AT
1 AT
424574 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.48
Consensus pattern (20 bp):
ATTTTTCATTTCGCGTTGCG
Found at i:424593 original size:22 final size:22
Alignment explanation
Indices: 424565--424636 Score: 87
Period size: 22 Copynumber: 3.4 Consensus size: 22
424555 TTTCATTTCG
424565 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
** * *
424587 CGTTGCGATTTTCCA-AATT-T
1 CGTTGCGATAGTCTACAGTTGT
424607 -GTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
424628 CGTTGCGAT
1 CGTTGCGAT
424637 TTTCCAAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.28
20 4 0.10
21 4 0.10
22 20 0.51
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:424611 original size:41 final size:41
Alignment explanation
Indices: 424565--424658 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
424555 TTTCATTTCG
424565 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
*
424606 TGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
424647 CGTTGCGATAGT
1 CGTTGCGATAGT
424659 TAAAAAAAAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
Found at i:424612 original size:19 final size:19
Alignment explanation
Indices: 424588--424655 Score: 64
Period size: 19 Copynumber: 3.4 Consensus size: 19
424578 TACAGTTGTC
424588 GTTGCGATTTTCCAAATTT
1 GTTGCGATTTTCCAAATTT
** * *
424607 GTTGCGATAGTCTACAGTTGT
1 GTTGCGATTTTCCA-AATT-T
*
424628 CGTTGCGATTTTCCAAATTC
1 -GTTGCGATTTTCCAAATTT
424648 GTTGCGAT
1 GTTGCGAT
424656 AGTTAAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 19 0.51
20 3 0.08
21 4 0.11
22 11 0.30
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (19 bp):
GTTGCGATTTTCCAAATTT
Found at i:424746 original size:6 final size:6
Alignment explanation
Indices: 424735--424804 Score: 105
Period size: 6 Copynumber: 12.5 Consensus size: 6
424725 GACACGTATT
424735 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCA-G
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
424782 ACCA-G ACCA-G ACCA-G ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
424805 CGAGACGAGA
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
5 23 0.37
6 40 0.63
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:426934 original size:34 final size:36
Alignment explanation
Indices: 426876--426971 Score: 124
Period size: 35 Copynumber: 2.6 Consensus size: 36
426866 TAATAATATA
*
426876 AAAAATATTTTCCCAAAACCTATATAATATATAC-TTTT
1 AAAAATATTTT--CAAAA-TTATATAATATATACTTTTT
*
426914 AAAAATATTTT-AAAATTATATATTATATACTTTTT
1 AAAAATATTTTCAAAATTATATAATATATACTTTTT
*
426949 AAAAATGTTTTCAAAATTATATA
1 AAAAATATTTTCAAAATTATATA
426972 GTTTTTAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 13 0.25
35 18 0.34
36 11 0.21
38 11 0.21
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (36 bp):
AAAAATATTTTCAAAATTATATAATATATACTTTTT
Found at i:426965 original size:36 final size:35
Alignment explanation
Indices: 426889--427337 Score: 266
Period size: 35 Copynumber: 12.6 Consensus size: 35
426879 AATATTTTCC
* * *
426889 CAAAACCTATATAATATATACTTTTAAAAATATTTT
1 CAAAA-CTATATATTATATATTTTTAAAAATGTTTT
*
426925 -AAAATTATATATTATATACTTTTTAAAAATGTTTT
1 CAAAACTATATATTATATA-TTTTTAAAAATGTTTT
*
426960 C-AAA--AT-TA-TATA-GTTTTTAAAAATGTTTT
1 CAAAACTATATATTATATATTTTTAAAAATGTTTT
* * * *
426989 TAAAACTATATATTATAT-GTTTTCAAAATGATTT
1 CAAAACTATATATTATATATTTTTAAAAATGTTTT
* *
427023 CAAAAACTATATAATATATTTATGTTTTCAAAATGTTTTTT
1 C-AAAACTATAT-AT-TATATAT-TTTTAAAAATG--TTTT
* *
427064 TAAAA--A-CTA-TATATATTTTT-AAAATGTTTT
1 CAAAACTATATATTATATATTTTTAAAAATGTTTT
* ** * *
427094 AAAAACTATATAACATGTATTTTCAAAAATGTTTT
1 CAAAACTATATATTATATATTTTTAAAAATGTTTT
* * *
427129 AAAAACTATATATTATATTAATTTTCAAAATGTTTTTTT
1 CAAAACTATATATTATA-TATTTTTAAAAATG---TTTT
* * *
427168 AAAAACTATGTAATATATATATTTTCAAAAATGTTTT
1 CAAAACTATAT-AT-TATATATTTTTAAAAATGTTTT
* * * * *
427205 GAAAACCATATATTATATTAATTTTCAAAATGTCTT
1 CAAAACTATATATTATA-TATTTTTAAAAATGTTTT
* *
427241 -AAGAACTATATAATATATAAATGTTTTCAAACATGCTTTT
1 CAA-AACTATAT-AT-TATATAT-TTTT-AAAAATG-TTTT
427281 CAAAA-T-TATATTATATATATATATTAAAAATGTTTT
1 CAAAACTATATATTATATAT-T-T-TTAAAAATGTTTT
427317 C-AAACTATATACTGTATATAT
1 CAAAACTATATA-T-TATATAT
427338 ATATATATAG
Statistics
Matches: 326, Mismatches: 47, Indels: 77
0.72 0.10 0.17
Matches are distributed among these distances:
29 16 0.05
30 11 0.03
31 4 0.01
32 11 0.03
33 10 0.03
34 43 0.13
35 64 0.20
36 50 0.15
37 33 0.10
38 15 0.05
39 38 0.12
40 22 0.07
41 9 0.03
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.45
Consensus pattern (35 bp):
CAAAACTATATATTATATATTTTTAAAAATGTTTT
Found at i:426977 original size:29 final size:29
Alignment explanation
Indices: 426935--427000 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
426925 AAAATTATAT
426935 ATTATATACTTTTTAAAAATGTTTTCAAA
1 ATTATATACTTTTTAAAAATGTTTTCAAA
* *
426964 ATTATATAGTTTTTAAAAATGTTTTTAAA
1 ATTATATACTTTTTAAAAATGTTTTCAAA
*
426993 ACTATATA
1 ATTATATA
427001 TTATATGTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (29 bp):
ATTATATACTTTTTAAAAATGTTTTCAAA
Found at i:427210 original size:76 final size:73
Alignment explanation
Indices: 426966--427337 Score: 324
Period size: 76 Copynumber: 5.1 Consensus size: 73
426956 TTTTCAAAAT
* * *
426966 TATATAGTTTTTAAAAATGTTTTTAAAACTATATATTATA-T-GTTTTCAAAATGATTTCAAAAA
1 TATATA-TTTTCAAAAATGTTTTTAAAACTATATATTATATTAATTTTCAAAATG-TTTTAAAAA
427029 CTATATAATA
64 CTATATAATA
*
427039 TATTTATGTTTTC-AAAATGTTTTTTTAAAA--ACTATA-TATA-T--TTTT-AAAATGTTTTAA
1 TA--TATATTTTCAAAAATG--TTTTTAAAACTA-TATATTATATTAATTTTCAAAATGTTTTAA
427096 AAACTATAT-A-A
61 AAACTATATAATA
* * *
427107 CATGTATTTTCAAAAATGTTTTAAAAACTATATATTATATTAATTTTCAAAATGTTTTTTTAAAA
1 TATATATTTTCAAAAATGTTTTTAAAACTATATATTATATTAATTTTCAAAATG---TTTTAAAA
*
427172 ACTATGTAATA
63 ACTATATAATA
* * * *
427183 TATATATTTTCAAAAATGTTTTGAAAACCATATATTATATTAATTTTCAAAATGTCTTAAGAACT
1 TATATATTTTCAAAAATGTTTTTAAAACTATATATTATATTAATTTTCAAAATGTTTTAAAAACT
427248 ATATAATA
66 ATATAATA
* * * * * *
427256 TATAAATGTTTTCAAACATGCTTTTCAAAA-T-TATATTATATATATATATTAAAAATGTTTT-C
1 TAT--ATATTTTCAAAAATG-TTTTTAAAACTATATATTATAT-TA-ATTTTCAAAATGTTTTAA
* *
427318 AAACTATATACTG
61 AAACTATATAATA
427331 TATATAT
1 TATATAT
427338 ATATATATAG
Statistics
Matches: 249, Mismatches: 27, Indels: 46
0.77 0.08 0.14
Matches are distributed among these distances:
65 8 0.03
66 11 0.04
67 11 0.04
68 3 0.01
69 1 0.00
70 18 0.07
71 12 0.05
72 4 0.02
73 36 0.14
74 32 0.13
75 41 0.16
76 72 0.29
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.46
Consensus pattern (73 bp):
TATATATTTTCAAAAATGTTTTTAAAACTATATATTATATTAATTTTCAAAATGTTTTAAAAACT
ATATAATA
Found at i:427617 original size:6 final size:6
Alignment explanation
Indices: 427606--427656 Score: 93
Period size: 6 Copynumber: 8.5 Consensus size: 6
427596 TCTCGTCTCG
*
427606 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT TGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
427654 GGT
1 GGT
427657 AATACGTGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
GGTCGT
Found at i:427803 original size:20 final size:20
Alignment explanation
Indices: 427778--427841 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
427768 ATTGTAGACT
427778 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** ** *
427798 ATCGCAACACGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
427819 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
427839 ATC
1 ATC
427842 ACTCGCATTG
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:427820 original size:41 final size:41
Alignment explanation
Indices: 427729--427841 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 41
427719 AAATCTTTTT
*
427729 TTTTAACTATCGCAA--CGAATTTGGAAAATCGCAACGACAA
1 TTTTAACTATCGCAACGCGAA-ATGGAAAATCGCAACGACAA
* *
427769 TTGTAGACTATCGCAACGCGAAATGGAAAATCGCAAC-ACGA
1 TTTTA-ACTATCGCAACGCGAAATGGAAAATCGCAACGACAA
427810 TTTTCAACTATCGCAACGCGAAATGGAAAATC
1 TTTT-AACTATCGCAACGCGAAATGGAAAATC
427842 ACTCGCATTG
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
40 4 0.06
41 42 0.65
42 15 0.23
43 4 0.06
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.22
Consensus pattern (41 bp):
TTTTAACTATCGCAACGCGAAATGGAAAATCGCAACGACAA
Found at i:428165 original size:2 final size:2
Alignment explanation
Indices: 428158--428196 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
428148 TCTTAAAATA
428158 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 A
428197 AGTATAATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:434848 original size:31 final size:31
Alignment explanation
Indices: 434812--434871 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
434802 AACTTAAAAG
* * *
434812 AGTTTTGCAATATTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
434843 AGTTTTACAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
434872 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:435008 original size:22 final size:22
Alignment explanation
Indices: 434935--435008 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
434925 AAATTATTTA
*
434935 AAATAAATCAATCCATACAACTACA
1 AAATAAATCAATCCATACAA--A-T
***
434960 ATAATAAATCAATCCATA-TTTT
1 A-AATAAATCAATCCATACAAAT
434982 AAAATAAATCAATCCATACAAAT
1 -AAATAAATCAATCCATACAAAT
435005 AAAT
1 AAAT
435009 TATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 9
0.71 0.13 0.16
Matches are distributed among these distances:
22 20 0.51
23 2 0.05
25 1 0.03
26 16 0.41
ACGTcount: A:0.55, C:0.18, G:0.00, T:0.27
Consensus pattern (22 bp):
AAATAAATCAATCCATACAAAT
Found at i:435018 original size:32 final size:32
Alignment explanation
Indices: 434979--435175 Score: 210
Period size: 32 Copynumber: 6.7 Consensus size: 32
434969 CAATCCATAT
434979 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
435011 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
435043 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACAAATAAATTA
*
435065 TTTAAAGTAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
** * *
435097 TTTAAAATAAATCAATATATACAACTACA--A
1 TTTAAAATAAATCAATCCATACAAATAAATTA
* *
435127 --T--AATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTA
435155 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
435176 TTTTAAAATA
Statistics
Matches: 137, Mismatches: 12, Indels: 32
0.76 0.07 0.18
Matches are distributed among these distances:
22 15 0.11
23 2 0.01
24 1 0.01
26 23 0.17
28 5 0.04
30 3 0.02
31 2 0.01
32 86 0.63
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.33
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACAAATAAATTA
Found at i:435069 original size:22 final size:22
Alignment explanation
Indices: 435043--435085 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
435033 TAATAAATTA
435043 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
*
435065 TTTAAAGTAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
435086 CAAATAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.14, G:0.02, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:435069 original size:54 final size:54
Alignment explanation
Indices: 435011--435188 Score: 248
Period size: 54 Copynumber: 3.2 Consensus size: 54
435001 AAATAAATTA
435011 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
* * ** *
435065 TTTAAAGTAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACAAC
1 TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCAT---AT
** *
435122 TACAATAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCCATAT
1 TTTAA-AATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
435177 TTTAAAATAAAT
1 TTTAAAATAAAT
435189 ATGTATTTAT
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
54 55 0.52
55 4 0.04
57 4 0.04
58 42 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (54 bp):
TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATCCATAT
Found at i:435080 original size:86 final size:80
Alignment explanation
Indices: 434895--435139 Score: 330
Period size: 86 Copynumber: 2.9 Consensus size: 80
434885 TAATAAATTA
* *
434895 TTTAAAATAAATCAATCCATATTTTAAAATAAATTATTTAAAATAAATCAATCCATACAACTACA
1 TTTAAAATAAATCAATCCATA----CAAATAAATTATTTAAAATAAATCAATCCATACAACTAAA
434960 ATAATAAATCAATCCATAT
62 ATAATAAATCAATCCATAT
434979 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACTAA-TAAATTA
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATAC-AACTAAA--A
435043 TTTAAAATAAATCAATCCATAT
63 --T--AATAAATCAATCCATAT
* ** *
435065 TTTAAAGTAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATATATACAACTACAATAA
1 TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
435130 TAAATCAATC
66 TAAATCAATC
435140 TATACTAATA
Statistics
Matches: 147, Mismatches: 6, Indels: 20
0.85 0.03 0.12
Matches are distributed among these distances:
80 47 0.32
81 2 0.01
82 2 0.01
84 23 0.16
85 2 0.01
86 71 0.48
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (80 bp):
TTTAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCCATACAACTAAAATAA
TAAATCAATCCATAT
Found at i:435409 original size:33 final size:30
Alignment explanation
Indices: 435367--435511 Score: 137
Period size: 30 Copynumber: 4.5 Consensus size: 30
435357 TGTTGTTGTA
435367 TATTTTAAAATAAATCAATCCATACTAATAAAT
1 TATTTTAAAATAAAT-AAT-CATA-TAATAAAT
*
435400 TATTTTAAAATAAATCAATCCATATTTTATAATAATT
1 TATTTTAAAATAAAT-AAT-C--A---TATAATAAAT
* **
435437 TATTTTAAAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATAATCATATAATAAAT
* **
435467 TATTTTAAAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAATAATCATATAATAAAT
435497 TATTTTAAAATAAAT
1 TATTTTAAAATAAAT
435512 TATTTTAAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
30 54 0.53
33 21 0.21
35 1 0.01
36 2 0.02
37 22 0.22
38 2 0.02
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
TATTTTAAAATAAATAATCATATAATAAAT
Found at i:435413 original size:15 final size:15
Alignment explanation
Indices: 435393--435526 Score: 169
Period size: 15 Copynumber: 8.5 Consensus size: 15
435383 AATCCATACT
435393 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
435408 AATAAATCAATCCATATTTTAT
1 AATAAAT---T--AT--TTTAA
*
435430 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
435445 AATAAATTATTTTAT
1 AATAAATTATTTTAA
435460 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
435475 AATAAATTATTTTAT
1 AATAAATTATTTTAA
435490 AATAAATTATTTTAA
1 AATAAATTATTTTAA
435505 AATAAATTATTTTAA
1 AATAAATTATTTTAA
435520 AATAAAT
1 AATAAAT
435527 AACCTTATTA
Statistics
Matches: 104, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
15 88 0.85
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
22 10 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:435458 original size:30 final size:30
Alignment explanation
Indices: 435422--435526 Score: 192
Period size: 30 Copynumber: 3.5 Consensus size: 30
435412 AATCAATCCA
*
435422 TATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
435452 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
435482 TATTTTATAATAAATTATTTTAAAATAAAT
1 TATTTTATAATAAATTATTTTAAAATAAAT
*
435512 TATTTTAAAATAAAT
1 TATTTTATAATAAAT
435527 AACCTTATTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 73 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
TATTTTATAATAAATTATTTTAAAATAAAT
Found at i:448262 original size:21 final size:24
Alignment explanation
Indices: 448238--448289 Score: 74
Period size: 21 Copynumber: 2.3 Consensus size: 24
448228 AGAGAATCGA
448238 TCCCCCCTTG-A-GGGAACCGA-T
1 TCCCCCCTTGAAGGGGAACCGATT
*
448259 TCCCCCTTTGAAGGGGAACCGATT
1 TCCCCCCTTGAAGGGGAACCGATT
448283 TCCCCCC
1 TCCCCCC
448290 CCCCCCACAG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 9 0.35
22 1 0.04
23 9 0.35
24 7 0.27
ACGTcount: A:0.17, C:0.40, G:0.21, T:0.21
Consensus pattern (24 bp):
TCCCCCCTTGAAGGGGAACCGATT
Found at i:455268 original size:15 final size:15
Alignment explanation
Indices: 455248--455279 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
455238 GTATGAACTC
455248 TTTTCAAGTACTGAA
1 TTTTCAAGTACTGAA
455263 TTTTCAAGTACTGAA
1 TTTTCAAGTACTGAA
455278 TT
1 TT
455280 GTTACGAAAT
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:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (15 bp):
TTTTCAAGTACTGAA
Found at i:456069 original size:20 final size:20
Alignment explanation
Indices: 456046--456083 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
456036 AAATCAAATT
456046 TATAAAAAAATCATTAAAGA
1 TATAAAAAAATCATTAAAGA
* *
456066 TATAAAAATATTATTAAA
1 TATAAAAAAATCATTAAA
456084 ATTAGAAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
TATAAAAAAATCATTAAAGA
Found at i:461455 original size:20 final size:20
Alignment explanation
Indices: 461432--461493 Score: 124
Period size: 20 Copynumber: 3.1 Consensus size: 20
461422 ACACGGGCAT
461432 GCATATGTTGAAACAACAGG
1 GCATATGTTGAAACAACAGG
461452 GCATATGTTGAAACAACAGG
1 GCATATGTTGAAACAACAGG
461472 GCATATGTTGAAACAACAGG
1 GCATATGTTGAAACAACAGG
461492 GC
1 GC
461494 TTGATACGTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.19
Consensus pattern (20 bp):
GCATATGTTGAAACAACAGG
Found at i:464141 original size:20 final size:20
Alignment explanation
Indices: 464116--464244 Score: 100
Period size: 20 Copynumber: 6.3 Consensus size: 20
464106 TTTTCCCAAT
*
464116 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
464136 TCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAG-AAAA
*
464157 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
464177 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
* **
464198 TCGCAATGCG-ATACTGACTA
1 TCGCAATGCGAATA-AGAAAA
464218 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCG--AATAAGAAAA
464239 TCGCAA
1 TCGCAA
464245 CGAGATACTT
Statistics
Matches: 83, Mismatches: 20, Indels: 11
0.73 0.18 0.10
Matches are distributed among these distances:
19 1 0.01
20 41 0.49
21 38 0.46
23 3 0.04
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:464159 original size:21 final size:20
Alignment explanation
Indices: 464133--464208 Score: 89
Period size: 21 Copynumber: 3.7 Consensus size: 20
464123 GCGAATAAGT
464133 AAATCGCAACGCGAATTGGAA
1 AAATCGCAACGCGAATTGG-A
* ** *
464154 AAATCGCAATGCGAATAAGT
1 AAATCGCAACGCGAATTGGA
464174 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATT-GGA
*
464195 AAATCGCAATGCGA
1 AAATCGCAACGCGA
464209 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (20 bp):
AAATCGCAACGCGAATTGGA
Found at i:464161 original size:41 final size:41
Alignment explanation
Indices: 464116--464208 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
464106 TTTTCCCAAT
464116 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
*
464157 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
464198 TCGCAATGCGA
1 TCGCAATGCGA
464209 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGAAAAA
Found at i:464221 original size:41 final size:41
Alignment explanation
Indices: 464135--464269 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
464125 GAATAAGTAA
* *
464135 ATCGCAACGCGAATTGGAAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCG-ATACTG-ACT
*
464176 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
* * * * * *
464217 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGAAAAATCGCAATGCGATACTGACT
*
464258 TTCGCAACGCGA
1 ATCGCAACGCGA
464270 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGAAAAATCGCAATGCGATACTGACT
Found at i:464264 original size:20 final size:20
Alignment explanation
Indices: 464239--464291 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
464229 TAATAAAAAA
* *
464239 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
464259 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
464279 TCGCAACGCGATA
1 TCGCAACGCGATA
464292 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:464507 original size:22 final size:22
Alignment explanation
Indices: 464479--464522 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
464469 CACTCTCTCA
464479 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
464501 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
464523 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:464811 original size:20 final size:20
Alignment explanation
Indices: 464786--464823 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
464776 TGATTCTCTC
464786 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
464806 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
464824 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:466164 original size:18 final size:18
Alignment explanation
Indices: 466143--466187 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
466133 TCCACTTCGG
*
466143 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
466161 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
466179 GAGCCATCA
1 GAGCCATCA
466188 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:466714 original size:19 final size:20
Alignment explanation
Indices: 466660--466726 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
466650 TAGTTTACTT
* *
466660 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
466680 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
466700 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
466719 TCGCAACG
1 TCGCAACG
466727 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:466734 original size:14 final size:14
Alignment explanation
Indices: 466715--466772 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
466705 ATGCGAAATG
466715 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
466729 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
*
466745 ATGAAACCGCAACGAC
1 A--AAATCGCAACGAC
466761 AAAATCGCAACG
1 AAAATCGCAACG
466773 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:466741 original size:33 final size:33
Alignment explanation
Indices: 466699--466789 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
466689 GGAAATGGCT
466699 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
466732 ATCGCAATGCGAAATG-AAACCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
466764 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
466790 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:466825 original size:14 final size:14
Alignment explanation
Indices: 466806--466863 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
466796 TTGTGTTTCG
466806 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
466820 CGTTGCGGTTTCATTT
1 CGTTGCGATTT--TGT
466836 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
466852 CGTTGCGATTTT
1 CGTTGCGATTTT
466864 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.61
16 4 0.11
18 10 0.28
ACGTcount: A:0.07, C:0.17, G:0.28, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:466842 original size:32 final size:33
Alignment explanation
Indices: 466801--466879 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
466791 GCGATTTGTG
466801 TTTCGCGTTGCGATTTTGTCGTTGCG-GTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAGTTTCA
*
466833 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGAGTTTCA
*
466866 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
466880 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.09, C:0.19, G:0.25, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGAGTTTCA
Found at i:466878 original size:19 final size:19
Alignment explanation
Indices: 466852--466918 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
466842 GCGATTTTGT
**
466852 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
466871 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
466891 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
466910 CGTTGCGAT
1 CGTTGCGAT
466919 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:466898 original size:20 final size:19
Alignment explanation
Indices: 466864--466918 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
466854 TTGCGATTTT
*
466864 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
466883 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
466903 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
466919 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:468945 original size:14 final size:14
Alignment explanation
Indices: 468926--468979 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
468916 CGAAATGGCT
468926 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
468940 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
468959 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
468973 ATCGCAA
1 ATCGCAA
468980 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:468997 original size:33 final size:33
Alignment explanation
Indices: 468907--468984 Score: 129
Period size: 33 Copynumber: 2.4 Consensus size: 33
468897 AAAACATACT
***
468907 ATCGCAATGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
468940 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
468973 ATCGCAATGCGA
1 ATCGCAATGCGA
468985 TTTTCATTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:469053 original size:39 final size:38
Alignment explanation
Indices: 469005--469078 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
468995 GCATTGCGAT
* *
469005 TTTCTCGTTGCGATAACCATTTTCGCGTTGCGATAGCCA
1 TTTCGCGTTGCGATAACCA-TTTCACGTTGCGATAGCCA
**
469044 TTTCGCGTTGCGATAGTCATTTCACGTTGCGATAG
1 TTTCGCGTTGCGATAACCATTTCACGTTGCGATAG
469079 TCAAATGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 15 0.48
39 16 0.52
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (38 bp):
TTTCGCGTTGCGATAACCATTTCACGTTGCGATAGCCA
Found at i:469081 original size:19 final size:19
Alignment explanation
Indices: 469005--469078 Score: 103
Period size: 19 Copynumber: 3.8 Consensus size: 19
468995 GCATTGCGAT
* *
469005 TTTCTCGTTGCGATAACCA
1 TTTCGCGTTGCGATAGCCA
469024 TTTTCGCGTTGCGATAGCCA
1 -TTTCGCGTTGCGATAGCCA
*
469044 TTTCGCGTTGCGATAGTCA
1 TTTCGCGTTGCGATAGCCA
*
469063 TTTCACGTTGCGATAG
1 TTTCGCGTTGCGATAG
469079 TCAAATGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 33 0.66
20 17 0.34
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGCCA
Found at i:470165 original size:24 final size:24
Alignment explanation
Indices: 470138--470191 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
470128 GTATTCGAAA
* *
470138 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
470162 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
470186 TTTGAT
1 TTTGAT
470192 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:470383 original size:12 final size:12
Alignment explanation
Indices: 470366--470390 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
470356 ATATAATCCT
470366 GAAGAAGAAAAA
1 GAAGAAGAAAAA
470378 GAAGAAGAAAAA
1 GAAGAAGAAAAA
470390 G
1 G
470391 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:472705 original size:19 final size:19
Alignment explanation
Indices: 472683--472832 Score: 123
Period size: 19 Copynumber: 8.7 Consensus size: 19
472673 GGAAATTACT
472683 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
472702 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
472716 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
472735 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
472749 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
472768 ATCGCAA--C--AA-GGGA
1 ATCGCAATGCGAAATGAAA
472782 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
472801 ATCGTAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
472820 ATCGCAACGCGAA
1 ATCGCAATGCGAA
472833 TTTAATTTCG
Statistics
Matches: 101, Mismatches: 15, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
14 27 0.27
15 4 0.04
16 5 0.05
17 5 0.05
18 4 0.04
19 56 0.55
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:472725 original size:33 final size:33
Alignment explanation
Indices: 472683--472804 Score: 183
Period size: 33 Copynumber: 3.7 Consensus size: 33
472673 GGAAATTACT
472683 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
472716 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
472748 TTTCGCAATGCGAAATGAAAATCGCAACAAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
472782 ATCGCAATGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
472805 TAATGCGAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
32 1 0.01
33 77 0.97
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:472850 original size:19 final size:20
Alignment explanation
Indices: 472828--472870 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
472818 AAATCGCAAC
472828 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
472847 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
472867 GCGA
1 GCGA
472871 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:472855 original size:14 final size:14
Alignment explanation
Indices: 472856--472889 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
472846 TGCGATTTTC
472856 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
472870 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
472884 ATTTTC
1 ATTTTC
472890 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:474456 original size:21 final size:21
Alignment explanation
Indices: 474390--474456 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
474380 GTGAATCGGG
*
474390 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
474410 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
474432 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
474453 CTCT
1 CTCT
474457 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:474475 original size:42 final size:41
Alignment explanation
Indices: 474390--474512 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
474380 GTGAATCGGG
* * * * *
474390 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
474432 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
474474 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
474513 CGAGTCGAGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:476588 original size:33 final size:33
Alignment explanation
Indices: 476531--476629 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
476521 ACGAGATAAT
476531 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* *
476565 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* **
476598 GACAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
476630 CGAAATGAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:476623 original size:19 final size:19
Alignment explanation
Indices: 476506--476651 Score: 114
Period size: 19 Copynumber: 8.1 Consensus size: 19
476496 TCTTTTGGTT
*
476506 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
476525 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
476545 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
476563 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
476579 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
476597 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
476612 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
476631 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
476650 GA
1 GA
476652 TTTTGGTTTC
Statistics
Matches: 102, Mismatches: 13, Indels: 24
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.19
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.04
19 44 0.43
20 27 0.26
21 2 0.02
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:476680 original size:19 final size:19
Alignment explanation
Indices: 476647--476713 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
476637 AAAATCGCAA
**
476647 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
476666 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
476685 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
476705 TGCGATTTT
1 TGCGATTTT
476714 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:477282 original size:20 final size:20
Alignment explanation
Indices: 477232--477283 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
477222 CGCTATGTAA
* *
477232 ATCGCGTTGCAAAAGTCAGT
1 ATCGCGTTGCGAAAGTAAGT
477252 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTAAGT
*
477272 ATCTCGTTGCGA
1 ATCGCGTTGCGA
477284 TTTTTTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTAAGT
Found at i:477317 original size:20 final size:20
Alignment explanation
Indices: 477245--477325 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
477235 GCGTTGCAAA
* *
477245 AGTCAGTATCGCGTTGCGAA
1 AGTCAGTATCGCATTGCGAT
* * *
477265 AGTAAGTATCTCGTTGCGATT
1 AGTCAGTATCGCATTGCGA-T
** * *
477286 TTTTATTATCGCATTGCGAT
1 AGTCAGTATCGCATTGCGAT
*
477306 AGTCAGTATCGCATTACGAT
1 AGTCAGTATCGCATTGCGAT
477326 TTTCCCAATT
Statistics
Matches: 46, Mismatches: 14, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 33 0.72
21 13 0.28
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (20 bp):
AGTCAGTATCGCATTGCGAT
Found at i:477326 original size:41 final size:41
Alignment explanation
Indices: 477251--477328 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
477241 CAAAAGTCAG
* * * *
477251 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTAT
* *
477292 TATCGCATTGCGATAGTCAGTATCGCATTACGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTT
477329 CCCAATTCGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTACGATTTTTTAT
Found at i:477344 original size:41 final size:41
Alignment explanation
Indices: 477294--477386 Score: 118
Period size: 41 Copynumber: 2.3 Consensus size: 41
477284 TTTTTTATTA
477294 TCGCATTGCGATAGTCA-GTA-TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGAT--TCACGTATTCGCATTACGATTTTCCCAAT
* * * *
477335 TCGCGTTGCGATTTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTCACGTATTCGCATTACGATTTTCCCAAT
477376 TCGCATTGCGA
1 TCGCATTGCGA
477387 ATTGGGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
39 2 0.04
40 2 0.04
41 41 0.91
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (41 bp):
TCGCATTGCGATTCACGTATTCGCATTACGATTTTCCCAAT
Found at i:477346 original size:21 final size:21
Alignment explanation
Indices: 477314--477386 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
477304 ATAGTCAGTA
*
477314 TCGCATTACGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
477335 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
477355 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
477376 TCGCATTGCGA
1 TCGCATTGCGA
477387 ATTGGGAAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 16 0.38
21 26 0.62
ACGTcount: A:0.19, C:0.26, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:480498 original size:2 final size:2
Alignment explanation
Indices: 480491--480523 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
480481 GTGTACACTT
480491 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 T
480524 TTGCAACAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:480748 original size:62 final size:65
Alignment explanation
Indices: 480665--480825 Score: 175
Period size: 73 Copynumber: 2.4 Consensus size: 65
480655 TTAAGAACAT
* *
480665 AGATATTCATCACTCTACTGATTCTA-AT-G-GTCAGAATTTAGAATGCAGTTGCATCACGGACA
1 AGAT-TTCATCACTCTACTGATTCTACATGGAGACAGAATTTAGAATGCAGCTGCATCACGGACA
480727 C
65 C
*
480728 AGATTTCATCACTCTACTGATACTATGCATGGGAGAACAGACAGAATTTAGAATGCAGCTGCATC
1 AGATTTCATCACTCTACTGATTCTA--CAT--G-G---AGACAGAATTTAGAATGCAGCTGCATC
* *
480793 ACGGGCAT
58 ACGGACAC
480801 AGATTTCATCACTCTACTGATTCTA
1 AGATTTCATCACTCTACTGATTCTA
480826 TGGACTATGC
Statistics
Matches: 81, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
62 20 0.25
63 4 0.05
65 2 0.02
69 1 0.01
73 54 0.67
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (65 bp):
AGATTTCATCACTCTACTGATTCTACATGGAGACAGAATTTAGAATGCAGCTGCATCACGGACAC
Found at i:480783 original size:73 final size:72
Alignment explanation
Indices: 480690--480996 Score: 306
Period size: 73 Copynumber: 4.2 Consensus size: 72
480680 TACTGATTCT
* *
480690 AATGGTCAGAATTTAGAATGCAGTTGCATCACGGACACAGATTTCATCACTCTACTGATACTATG
1 AATGGACAGAATTTAGAATGCAGTTGCATCACGGACATAGATTTCATCACTCTACTGATACTATG
480755 CATGGGAG
66 CATGGG-G
** * * *
480763 AACAGACAGAATTTAGAATGCAGCTGCATCACGGGCATAGATTTCATCACTCTACTGATTCTATG
1 AATGGACAGAATTTAGAATGCAGTTGCATCACGGACATAGATTTCATCACTCTACTGATACTAT-
480828 GACTATGCATGGG
65 G-C-ATG---GGG
* * * * * *
480841 AATGGAC-G--TGT-GAATGCAGAATG-ATTAGGGACATAGATATTTA-CTACTCTACTAATACT
1 AATGGACAGAATTTAGAATGCAG-TTGCATCACGGACATAGAT-TTCATC-ACTCTACTGATACT
*
480900 ATGCAT-AGG
63 ATGCATGGGG
* * * *
480909 AGTGGACAGAACTTAGAATGCAGTTACATCACGGACATAGATTTCATCACTCTACTGATTCTATG
1 AATGGACAGAATTTAGAATGCAGTTGCATCACGGACATAGATTTCATCACTCTACTGATACTATG
480974 CAT-GGG
66 CATGGGG
480980 AATGGACAGAATTTAGA
1 AATGGACAGAATTTAGA
480997 TTGCGGCAAA
Statistics
Matches: 188, Mismatches: 31, Indels: 32
0.75 0.12 0.13
Matches are distributed among these distances:
68 8 0.04
69 1 0.01
71 40 0.21
72 24 0.13
73 58 0.31
74 23 0.12
75 22 0.12
76 3 0.02
77 1 0.01
78 6 0.03
79 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.28
Consensus pattern (72 bp):
AATGGACAGAATTTAGAATGCAGTTGCATCACGGACATAGATTTCATCACTCTACTGATACTATG
CATGGGG
Found at i:488326 original size:31 final size:31
Alignment explanation
Indices: 488291--488380 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 31
488281 AAAGTGAATG
* *
488291 TTATTTGAGTACCCGGTGTTTACTTTTTATT
1 TTATTTTAGTACCCGGAGTTTACTTTTTATT
* *
488322 TTATTTTAGTACCCGGAGTTTACTTATTGTT
1 TTATTTTAGTACCCGGAGTTTACTTTTTATT
* *
488353 TTATTTTAGTGCCCAGAGTTTACTTTTT
1 TTATTTTAGTACCCGGAGTTTACTTTTT
488381 GTTTCTTAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (31 bp):
TTATTTTAGTACCCGGAGTTTACTTTTTATT
Found at i:488793 original size:17 final size:17
Alignment explanation
Indices: 488771--488809 Score: 64
Period size: 15 Copynumber: 2.4 Consensus size: 17
488761 AAAAATATTT
488771 TTTTTGAGATTATTCAA
1 TTTTTGAGATTATTCAA
488788 TTTTT--GATTATTCAA
1 TTTTTGAGATTATTCAA
488803 TTTTTGA
1 TTTTTGA
488810 TCATCTCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 15 0.75
17 5 0.25
ACGTcount: A:0.26, C:0.05, G:0.10, T:0.59
Consensus pattern (17 bp):
TTTTTGAGATTATTCAA
Found at i:488796 original size:15 final size:15
Alignment explanation
Indices: 488778--488810 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
488768 TTTTTTTTGA
488778 GATTATTCAATTTTT
1 GATTATTCAATTTTT
488793 GATTATTCAATTTTT
1 GATTATTCAATTTTT
488808 GAT
1 GAT
488811 CATCTCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (15 bp):
GATTATTCAATTTTT
Found at i:494737 original size:43 final size:43
Alignment explanation
Indices: 494657--494743 Score: 147
Period size: 43 Copynumber: 2.0 Consensus size: 43
494647 ATATTCTGAC
* *
494657 GCTGATAGAACAACGATTGGGGATTCAATAGCCATCAATGAAT
1 GCTGATAGAACAACGATTGGGGATTCAATAGCAATCAAAGAAT
*
494700 GCTGATAGAACAACGATTGGGGATTCAATAGTAATCAAAGAAT
1 GCTGATAGAACAACGATTGGGGATTCAATAGCAATCAAAGAAT
494743 G
1 G
494744 AAGGTACACA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.23
Consensus pattern (43 bp):
GCTGATAGAACAACGATTGGGGATTCAATAGCAATCAAAGAAT
Found at i:497233 original size:33 final size:34
Alignment explanation
Indices: 497179--497242 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 34
497169 AAAACATTAG
*
497179 ACACTTTGACCCAAAAAAAAAACTTTAGGCACCA
1 ACACTTTGACCAAAAAAAAAAACTTTAGGCACCA
497213 ACACTTTGA-CAAAAAAAAAAACTTTAGGCA
1 ACACTTTGACCAAAAAAAAAAACTTTAGGCA
497243 TAAGAGGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 20 0.69
34 9 0.31
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.19
Consensus pattern (34 bp):
ACACTTTGACCAAAAAAAAAAACTTTAGGCACCA
Found at i:498375 original size:18 final size:18
Alignment explanation
Indices: 498352--498394 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
498342 TACACCGTAT
*
498352 ATCATTTAACTTTAGGTG
1 ATCATTAAACTTTAGGTG
498370 ATCATTAAACTTTAGGTG
1 ATCATTAAACTTTAGGTG
498388 ATGCATT
1 AT-CATT
498395 CTTTATGCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (18 bp):
ATCATTAAACTTTAGGTG
Found at i:500381 original size:82 final size:81
Alignment explanation
Indices: 500146--500381 Score: 258
Period size: 82 Copynumber: 2.9 Consensus size: 81
500136 GTGTTTCTTA
* * *
500146 AACAAACGCCGCGATAGAGTAGTACTTTAGCGGCGTTTTTATATAAATGTTGCAATAGGGTTCGT
1 AACAAACGTCGCGAAAG-GTAGTACTTTAGCGGCGTTTTTATACAAATGTTGCAATAGGGTTCG-
*
500211 TTATAGTATCGTTTTTCC
64 TTATAGTAGCGTTTTTCC
* * * **** * *
500229 AACAAACGTTGCGATAAAG-AGTACTTTAGCGGTGTTTTTATACAAATGCCAAAATAAGATTCGT
1 AACAAACGTCGCGA-AAGGTAGTACTTTAGCGGCGTTTTTATACAAATGTTGCAATAGGGTTCGT
500293 TCATAGTAGCGTTTTTCC
65 T-ATAGTAGCGTTTTTCC
* * * * *
500311 AACAAACGTCGCGACAAGGTAGTACTTTAACAGCATTTATATACAAACGTTGCAATAGGGTTCGT
1 AACAAACGTCGCGA-AAGGTAGTACTTTAGCGGCGTTTTTATACAAATGTTGCAATAGGGTTCGT
500376 TATAGT
65 TATAGT
500382 GTCTTTTTTC
Statistics
Matches: 122, Mismatches: 28, Indels: 7
0.78 0.18 0.04
Matches are distributed among these distances:
81 2 0.02
82 72 0.59
83 47 0.39
84 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (81 bp):
AACAAACGTCGCGAAAGGTAGTACTTTAGCGGCGTTTTTATACAAATGTTGCAATAGGGTTCGTT
ATAGTAGCGTTTTTCC
Found at i:501844 original size:20 final size:22
Alignment explanation
Indices: 501799--501856 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
501789 GCATGGGTAG
501799 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
501823 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
501843 TGTATCGATGCACT
1 TGCATCGATGCACT
501857 TCAAAGGGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:503371 original size:6 final size:6
Alignment explanation
Indices: 503360--503409 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
503350 CTTGATCCTT
503360 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
503408 TG
1 TG
503410 GTTCTTAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
TGTATA
Found at i:503521 original size:23 final size:23
Alignment explanation
Indices: 503453--503513 Score: 104
Period size: 23 Copynumber: 2.7 Consensus size: 23
503443 ACATTTTATA
503453 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
503476 CGGTACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
503499 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
503514 TTTATACGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:506854 original size:20 final size:22
Alignment explanation
Indices: 506809--506866 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 22
506799 GCATGGGTAG
506809 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
506833 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
* *
506853 TGTATCGACGCACT
1 TGCATCGATGCACT
506867 TCAAATGGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 2 0.06
24 13 0.41
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:508468 original size:23 final size:23
Alignment explanation
Indices: 508424--508468 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
508414 CATTTGATAT
*
508424 GGCACTTCAGTGCAATTCTACGC
1 GGCACTTCAGTGCAATTATACGC
** *
508447 GGCACTTTGGTGCATTTATACG
1 GGCACTTCAGTGCAATTATACG
508469 AGCTGTGGTG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTATACGC
Found at i:511884 original size:17 final size:17
Alignment explanation
Indices: 511862--511894 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
511852 TTGAAGCCAT
511862 GGGCGAAGAGAGTGTTA
1 GGGCGAAGAGAGTGTTA
511879 GGGCGAAGAGAGTGTT
1 GGGCGAAGAGAGTGTT
511895 GGAACGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.06, G:0.48, T:0.18
Consensus pattern (17 bp):
GGGCGAAGAGAGTGTTA
Found at i:511902 original size:17 final size:17
Alignment explanation
Indices: 511865--511903 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
511855 AAGCCATGGG
*
511865 CGAAGAGAGTGTTAGGG
1 CGAAGAGAGTGTTAGGA
511882 CGAAGAGAGTGTT-GGAA
1 CGAAGAGAGTGTTAGG-A
511899 CGAAG
1 CGAAG
511904 GAAAGTCAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.33, C:0.08, G:0.44, T:0.15
Consensus pattern (17 bp):
CGAAGAGAGTGTTAGGA
Found at i:513453 original size:21 final size:21
Alignment explanation
Indices: 513429--513470 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
513419 GTGGGAGATT
*
513429 GTTGGAAGTCAAAATTGGGGG
1 GTTGGAAATCAAAATTGGGGG
513450 GTTGGAAATCAAAATTGGGGG
1 GTTGGAAATCAAAATTGGGGG
513471 CACCAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.05, G:0.40, T:0.24
Consensus pattern (21 bp):
GTTGGAAATCAAAATTGGGGG
Found at i:515927 original size:29 final size:32
Alignment explanation
Indices: 515894--515956 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
515884 GTGATTATTG
*
515894 TTATTG-TT-GTTTATGTTCGT-TTATTTCAT
1 TTATTGATTCGTTTATGTTCGTGTTAATTCAT
*
515923 TTATTGTATTCGTTTATGTTTGTGTTAATTCAT
1 TTATTG-ATTCGTTTATGTTCGTGTTAATTCAT
515956 T
1 T
515957 ATTTCGGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 6 0.21
31 2 0.07
32 11 0.39
33 9 0.32
ACGTcount: A:0.16, C:0.06, G:0.14, T:0.63
Consensus pattern (32 bp):
TTATTGATTCGTTTATGTTCGTGTTAATTCAT
Found at i:517447 original size:40 final size:37
Alignment explanation
Indices: 517362--517447 Score: 84
Period size: 39 Copynumber: 2.2 Consensus size: 37
517352 TTATTTTTTA
*
517362 TAACATTTTAGATTCAACTAAAAATGTTATAAAAAAG
1 TAACATTTTAGATTCAACTAAAAATATTATAAAAAAG
* * * *
517399 AAATATTTTCGATTGTCAAC-AGAAAATATTATGAAAAAGG
1 TAACATTTTAGA-T-TCAACTA-AAAATATTAT-AAAAAAG
517439 TAACATTTT
1 TAACATTTT
517448 TTATTGAACC
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
37 9 0.24
38 2 0.05
39 14 0.37
40 13 0.34
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.34
Consensus pattern (37 bp):
TAACATTTTAGATTCAACTAAAAATATTATAAAAAAG
Found at i:525953 original size:61 final size:59
Alignment explanation
Indices: 525880--526002 Score: 194
Period size: 61 Copynumber: 2.1 Consensus size: 59
525870 TAAACCCGAA
* *
525880 CCGACTGAAATATCACACTTAAAAAACCCCGACCCGACCTGAATATCACACTTAAAAAAAC
1 CCGACTGAAATATCACACTTAAAAAA-CCCGACCCGACCCGAAT-TCAAACTTAAAAAAAC
525941 CCGACTCG-AATATCACACTTAAAAAACCCGACCCGACCCGAATTCAAACTTAAAAAAAC
1 CCGACT-GAAATATCACACTTAAAAAACCCGACCCGACCCGAATTCAAACTTAAAAAAAC
526000 CCG
1 CCG
526003 TCCGACCCGA
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
59 18 0.31
60 16 0.27
61 24 0.41
62 1 0.02
ACGTcount: A:0.43, C:0.33, G:0.09, T:0.15
Consensus pattern (59 bp):
CCGACTGAAATATCACACTTAAAAAACCCGACCCGACCCGAATTCAAACTTAAAAAAAC
Found at i:525972 original size:27 final size:28
Alignment explanation
Indices: 525880--526002 Score: 108
Period size: 28 Copynumber: 4.1 Consensus size: 28
525870 TAAACCCGAA
525880 CCGA-CTGAAATATCACACTTAAAAAACCCCGAC
1 CCGACCTG-AATATCACACTTAAAAAA-----AC
525913 CCGACCTGAATATCACACTTAAAAAAAC
1 CCGACCTGAATATCACACTTAAAAAAAC
525941 CCGA-CTCGAATATCACACTTAAAAAACCCGAC
1 CCGACCT-GAATATCACACTTAAAAAA----AC
* *
525973 CCGACCCGAAT-TCAAACTTAAAAAAAC
1 CCGACCTGAATATCACACTTAAAAAAAC
526000 CCG
1 CCG
526003 TCCGACCCGA
Statistics
Matches: 81, Mismatches: 2, Indels: 20
0.79 0.02 0.19
Matches are distributed among these distances:
27 7 0.09
28 25 0.31
31 13 0.16
32 10 0.12
33 23 0.28
34 3 0.04
ACGTcount: A:0.43, C:0.33, G:0.09, T:0.15
Consensus pattern (28 bp):
CCGACCTGAATATCACACTTAAAAAAAC
Found at i:525995 original size:31 final size:32
Alignment explanation
Indices: 525871--526013 Score: 156
Period size: 33 Copynumber: 4.6 Consensus size: 32
525861 TTTTCACCAT
* *
525871 AAACCCGAACCGA-CTGAAATATCACACTTAAA
1 AAACCCGACCCGACCCG-AATATCACACTTAAA
*
525903 AAACCCCGACCCGACCTGAATATCACACTTAAA
1 AAA-CCCGACCCGACCCGAATATCACACTTAAA
*
525936 AAA----ACCCGACTCGAATATCACACTTAAA
1 AAACCCGACCCGACCCGAATATCACACTTAAA
*
525964 AAACCCGACCCGACCCGAAT-TCAAACTTAAAA
1 AAACCCGACCCGACCCGAATATCACACTT-AAA
*
525996 AAACCCG-TCCGACCCGAA
1 AAACCCGACCCGACCCGAA
526014 CCTGAAATTT
Statistics
Matches: 98, Mismatches: 6, Indels: 15
0.82 0.05 0.13
Matches are distributed among these distances:
28 26 0.27
31 17 0.17
32 25 0.26
33 27 0.28
34 3 0.03
ACGTcount: A:0.43, C:0.34, G:0.10, T:0.14
Consensus pattern (32 bp):
AAACCCGACCCGACCCGAATATCACACTTAAA
Found at i:526029 original size:32 final size:32
Alignment explanation
Indices: 525959--526030 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
525949 AATATCACAC
*
525959 TTAAAAAACCCGACCCGACCCGAATTCAAACT
1 TTAAAAAACCCGACCCGACCCGAACTCAAACT
* * * *
525991 TAAAAAAACCCG-TCCGACCCGAACCTGAAATT
1 TTAAAAAACCCGACCCGACCCGAA-CTCAAACT
526023 TTAAAAAA
1 TTAAAAAA
526031 AAAATCCGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.44, C:0.29, G:0.10, T:0.17
Consensus pattern (32 bp):
TTAAAAAACCCGACCCGACCCGAACTCAAACT
Found at i:526498 original size:16 final size:16
Alignment explanation
Indices: 526477--526517 Score: 82
Period size: 16 Copynumber: 2.6 Consensus size: 16
526467 AATCAAACTT
526477 AAAATAATTACAAAAG
1 AAAATAATTACAAAAG
526493 AAAATAATTACAAAAG
1 AAAATAATTACAAAAG
526509 AAAATAATT
1 AAAATAATT
526518 CGGATTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.68, C:0.05, G:0.05, T:0.22
Consensus pattern (16 bp):
AAAATAATTACAAAAG
Done.