Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008342.1 Hibiscus syriacus cultivar Beakdansim tig00111069_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: 1228932
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:330395 original size:64 final size:63
Alignment explanation
Indices: 330212--330398 Score: 204
Period size: 64 Copynumber: 3.0 Consensus size: 63
330202 AACCTCGGCA
* * * * *
330212 ACTGTCCATAGGTCCCG-AAGAACCTAGGTAA-ACTGTCCATATGTTCCT-TAGAACATAGATAT
1 ACTGTCCATATGTCTCGAAAG-ACATAGGTAATTCTGTCCATATGTT-CTGTAGAACATAGGTAT
* * * *
330274 AATGTCCATATGTCTCAAAAGACATAGGTAATTCTGTCCATAT-ATCTCG-AAAGACATAGGTAA
1 ACTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCT-GTAGA-ACATAGGT-A
330337 T
63 T
*
330338 TCTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCTGTAGAACATAGGT
1 ACTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCTGTAGAACATAGGT
330399 CTCGACTCTT
Statistics
Matches: 103, Mismatches: 14, Indels: 14
0.79 0.11 0.11
Matches are distributed among these distances:
61 2 0.02
62 25 0.24
63 20 0.19
64 51 0.50
65 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (63 bp):
ACTGTCCATATGTCTCGAAAGACATAGGTAATTCTGTCCATATGTTCTGTAGAACATAGGTAT
Found at i:330968 original size:2 final size:2
Alignment explanation
Indices: 330961--330986 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
330951 TCACATAAAC
330961 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
330987 CACATGGCAC
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:333133 original size:3 final size:3
Alignment explanation
Indices: 333120--333148 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
333110 GAAAAATACT
333120 AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
333149 GTTGGTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:340109 original size:7 final size:7
Alignment explanation
Indices: 340099--340128 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
340089 TTGACTCTTG
340099 AAAGGAA
1 AAAGGAA
340106 AAAGGAA
1 AAAGGAA
340113 AAAGGAA
1 AAAGGAA
340120 AAAGGAA
1 AAAGGAA
340127 AA
1 AA
340129 TACTAGCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (7 bp):
AAAGGAA
Found at i:340559 original size:13 final size:12
Alignment explanation
Indices: 340541--340570 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
340531 TTATTTATTT
340541 AAAAAATTAAATA
1 AAAAAATT-AATA
340554 AAAAAATTAATA
1 AAAAAATTAATA
340566 AAAAA
1 AAAAA
340571 CAGTTCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (12 bp):
AAAAAATTAATA
Found at i:346941 original size:26 final size:28
Alignment explanation
Indices: 346866--346925 Score: 111
Period size: 28 Copynumber: 2.1 Consensus size: 28
346856 GAAGGCTAAA
*
346866 ATTGGGGGTGGGGGAGGAGGAGAGACAT
1 ATTGGGGGTGGGGGAAGAGGAGAGACAT
346894 ATTGGGGGTGGGGGAAGAGGAGAGACAT
1 ATTGGGGGTGGGGGAAGAGGAGAGACAT
346922 ATTG
1 ATTG
346926 TTGTTTGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.53, T:0.17
Consensus pattern (28 bp):
ATTGGGGGTGGGGGAAGAGGAGAGACAT
Found at i:357683 original size:17 final size:17
Alignment explanation
Indices: 357663--357701 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
357653 TTAATAAAGT
*
357663 GATTTTAGTAATTAAGA
1 GATTTTAGTAATCAAGA
357680 GATTTTAGTAATCAAGA
1 GATTTTAGTAATCAAGA
357697 GATTT
1 GATTT
357702 ATTATTATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
GATTTTAGTAATCAAGA
Found at i:357809 original size:16 final size:16
Alignment explanation
Indices: 357788--357829 Score: 52
Period size: 14 Copynumber: 2.7 Consensus size: 16
357778 TATTTTAAAT
*
357788 ATATATATTTTATTAA
1 ATATATATTTTATCAA
357804 ATATATA--TTATCAA
1 ATATATATTTTATCAA
357818 ATATAATATTTT
1 ATAT-ATATTTT
357830 TAATAGATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
14 10 0.45
15 3 0.14
16 7 0.32
17 2 0.09
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATATATTTTATCAA
Found at i:357834 original size:14 final size:15
Alignment explanation
Indices: 357777--357840 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
357767 ATGATTGAGA
357777 ATATTTTAAATATAT
1 ATATTTTAAATATAT
357792 ATATTTTATTAA-ATAT
1 ATATTTTA--AATATAT
*
357808 ATATTATCAAATATA-
1 ATATT-TTAAATATAT
* *
357823 ATATTTTTAATAGAT
1 ATATTTTAAATATAT
357838 ATA
1 ATA
357841 ATAGAGGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 6 0.15
15 18 0.45
16 12 0.30
17 4 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
ATATTTTAAATATAT
Found at i:362506 original size:20 final size:20
Alignment explanation
Indices: 362483--362520 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
362473 TCATAAAGGT
362483 AGAGAACATATCACAAAGAC
1 AGAGAACATATCACAAAGAC
362503 AGAGAACATATCACAAAG
1 AGAGAACATATCACAAAG
362521 GCATAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.18, G:0.16, T:0.11
Consensus pattern (20 bp):
AGAGAACATATCACAAAGAC
Found at i:367682 original size:20 final size:20
Alignment explanation
Indices: 367657--367695 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
367647 CTTGACAATC
367657 TTACATTCTC-ACTTGTAATA
1 TTACATTC-CGACTTGTAATA
367677 TTACATTCCGACTTGTAAT
1 TTACATTCCGACTTGTAAT
367696 CTTATATTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.44
Consensus pattern (20 bp):
TTACATTCCGACTTGTAATA
Found at i:367782 original size:14 final size:13
Alignment explanation
Indices: 367764--367788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
367754 ATGCGTATCT
367764 TTTTTTATTTGTA
1 TTTTTTATTTGTA
367777 TTTTTTATTTGT
1 TTTTTTATTTGT
367789 CTAATAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.00, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTTATTTGTA
Found at i:368718 original size:4 final size:4
Alignment explanation
Indices: 368709--368733 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
368699 ACATTTATAA
368709 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
368734 TCGTCTACGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:369002 original size:74 final size:74
Alignment explanation
Indices: 368899--369047 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
368889 TTTTATTATT
368899 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
1 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
368964 TAATCGCAA
66 TAATCGCAA
368973 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
1 TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
*
369038 TAGTCGCAA
66 TAATCGCAA
369047 T
1 T
369048 AAAAATAAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (74 bp):
TTATAAATTATAAAATGTTAAATTTATATTTGAAATTAATAATAATAGTTAGTTTTATCATAATT
TAATCGCAA
Found at i:370349 original size:25 final size:25
Alignment explanation
Indices: 370316--370365 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
370306 ACTTACTCCA
370316 CCAGATTAATAAATAAATATATAAT
1 CCAGATTAATAAATAAATATATAAT
370341 CCAGATTAATAAATAAATATATAAT
1 CCAGATTAATAAATAAATATATAAT
370366 TAAAATATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (25 bp):
CCAGATTAATAAATAAATATATAAT
Found at i:372117 original size:119 final size:120
Alignment explanation
Indices: 371891--372173 Score: 374
Period size: 119 Copynumber: 2.4 Consensus size: 120
371881 AGTTTTGAAC
* * * * * *
371891 AAAATTGAAAGTTTATGAACTAAAACATATTAAAACTGATAGTTTATGTACTAAATGCGTTAAGT
1 AAAATTAAAAGTTTAGGTACTAAAACAAATCAAAACTGATA-TTTATGCACTAAATGCGTTAAGT
* * * *
371956 TTTTAACGGATGTTACTAAAATGAAACAAAAACTAAATGTTAAATATAATTTTTAA
65 TTTTAACGAAAGTTACTAAAATGAAACAAAAACTAAACGTTAAATATAATTTTAAA
* * *
372012 AAAATTAAAAGTTTAGGTACTAAAACAGATCAAAACTAATATTTATGCACTAAATGTGTTTAA-T
1 AAAATTAAAAGTTTAGGTACTAAAACAAATCAAAACTGATATTTATGCACTAAATGCG-TTAAGT
* *
372076 TTTTAATGAAAG-TACTAAAATGAAACAAAAACTAAACGTTAAATATGATTTTAAA
65 TTTTAACGAAAGTTACTAAAATGAAACAAAAACTAAACGTTAAATATAATTTTAAA
* *
372131 AAAATTAAAA-TTTAGATACTAAAATAAATCAAAACTGATATTT
1 AAAATTAAAAGTTTAGGTACTAAAACAAATCAAAACTGATATTT
372174 TAAGTACTAA
Statistics
Matches: 143, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
118 29 0.20
119 50 0.35
120 25 0.17
121 39 0.27
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.33
Consensus pattern (120 bp):
AAAATTAAAAGTTTAGGTACTAAAACAAATCAAAACTGATATTTATGCACTAAATGCGTTAAGTT
TTTAACGAAAGTTACTAAAATGAAACAAAAACTAAACGTTAAATATAATTTTAAA
Found at i:377060 original size:23 final size:24
Alignment explanation
Indices: 377034--377121 Score: 74
Period size: 24 Copynumber: 3.8 Consensus size: 24
377024 TTTATGTTAA
377034 TTTA-TTGTGTTCGTTTACGTTCG
1 TTTACTTGTGTTCGTTTACGTTCG
* *
377057 TTTA-TTGTGTTTGCTTATC-TTCG
1 TTTACTTGTGTTCGTTTA-CGTTCG
* ** *
377080 TTTACATCCGTTCGTTTATGTTCG
1 TTTACTTGTGTTCGTTTACGTTCG
* *
377104 TTCATTTGTGTTCGTTTA
1 TTTACTTGTGTTCGTTTA
377122 TCATTTAAAT
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
23 23 0.47
24 26 0.53
ACGTcount: A:0.10, C:0.15, G:0.18, T:0.57
Consensus pattern (24 bp):
TTTACTTGTGTTCGTTTACGTTCG
Found at i:377116 original size:24 final size:23
Alignment explanation
Indices: 377023--377122 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
377013 GTTTACGTTT
**
377023 GTTTATGTTAATTTATTGTGTTC
1 GTTTATGTTCGTTTATTGTGTTC
* *
377046 GTTTACGTTCGTTTATTGTGTTT
1 GTTTATGTTCGTTTATTGTGTTC
* * * **
377069 GCTTATCTTCGTTTACATCCGTTC
1 GTTTATGTTCGTTTA-TTGTGTTC
*
377093 GTTTATGTTCGTTCATTTGTGTTC
1 GTTTATGTTCGTTTA-TTGTGTTC
377117 GTTTAT
1 GTTTAT
377123 CATTTAAATG
Statistics
Matches: 58, Mismatches: 18, Indels: 1
0.75 0.23 0.01
Matches are distributed among these distances:
23 31 0.53
24 27 0.47
ACGTcount: A:0.12, C:0.13, G:0.18, T:0.57
Consensus pattern (23 bp):
GTTTATGTTCGTTTATTGTGTTC
Found at i:377169 original size:31 final size:31
Alignment explanation
Indices: 377132--377210 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
377122 TCATTTAAAT
*
377132 GAACGAACATGAACAAGCTACATTCCTTAAC
1 GAACGAACACGAACAAGCTACATTCCTTAAC
377163 GAACGAACACGAACAAGCTACATTCCTTAAC
1 GAACGAACACGAACAAGCTACATTCCTTAAC
377194 GAACGAACACGAACAAG
1 GAACGAACACGAACAAG
377211 AATTTTTTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.14
Consensus pattern (31 bp):
GAACGAACACGAACAAGCTACATTCCTTAAC
Found at i:379402 original size:29 final size:29
Alignment explanation
Indices: 379370--379433 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
379360 GCCTTCCAGG
*
379370 CGACTTTGTAGGTCG-CGATACACTCCGGA
1 CGACCTTGTAGGTCGTC-ATACACTCCGGA
* *
379399 CGACCTTGTAGGTCGTCATGCACTCCGGG
1 CGACCTTGTAGGTCGTCATACACTCCGGA
379428 CGACCT
1 CGACCT
379434 ACCCTTACTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 30 0.97
30 1 0.03
ACGTcount: A:0.17, C:0.31, G:0.28, T:0.23
Consensus pattern (29 bp):
CGACCTTGTAGGTCGTCATACACTCCGGA
Found at i:379525 original size:29 final size:29
Alignment explanation
Indices: 379492--379576 Score: 136
Period size: 29 Copynumber: 2.9 Consensus size: 29
379482 TCCCAACACA
*
379492 TAGGTCGCCATGCCCTCCGGGAGACCTTG
1 TAGGTCGCCATGCACTCCGGGAGACCTTG
379521 TAGGTCGCCATGCACTCC-GGACGACCTTG
1 TAGGTCGCCATGCACTCCGGGA-GACCTTG
*
379550 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGAGACCT
379577 ACCCTCGCTC
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
28 3 0.06
29 47 0.90
30 2 0.04
ACGTcount: A:0.15, C:0.35, G:0.29, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGAGACCTTG
Found at i:379623 original size:23 final size:23
Alignment explanation
Indices: 379594--379652 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
379584 CTCGGCTGCC
*
379594 CTCGGAT-TCCCTCGCATAGCTCG
1 CTCGGATGT-CCTCGCATAACTCG
379617 CTCGGATGTCCTCGCATAACTCG
1 CTCGGATGTCCTCGCATAACTCG
* *
379640 TTCGGATGGCCTC
1 CTCGGATGTCCTC
379653 TGATGCTCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 31 0.97
24 1 0.03
ACGTcount: A:0.14, C:0.36, G:0.24, T:0.27
Consensus pattern (23 bp):
CTCGGATGTCCTCGCATAACTCG
Found at i:381482 original size:21 final size:21
Alignment explanation
Indices: 381456--381632 Score: 164
Period size: 21 Copynumber: 8.5 Consensus size: 21
381446 GTTTCCAGAT
* *
381456 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
381477 TCGCAATACGAGCTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
381498 TCGCAATGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
* *
381519 TCGCAATACGAATTTGGACTA
1 TCGCAATGCGAACTTGGACTA
381540 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * *
381561 TCACAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* * * *
381581 TCGCATTACGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
* *
381602 TCGCAATGCGAACTTGTA-AA
1 TCGCAATGCGAACTTGGACTA
381622 TCGCAATGCGA
1 TCGCAATGCGA
381633 TAGTCGAAGT
Statistics
Matches: 124, Mismatches: 28, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
20 25 0.20
21 99 0.80
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:381509 original size:42 final size:42
Alignment explanation
Indices: 381456--381632 Score: 182
Period size: 42 Copynumber: 4.3 Consensus size: 42
381446 GTTTCCAGAT
* *
381456 TCGCAACGCGAACTTCGACTATCGCAATACGAGCTTGGACTA
1 TCGCAATGCGAACTTCGACTATCGCAATACGAACTTGGACTA
*
381498 TCGCAATGCGAACTTCGACTATCGCAATACGAATTTGGACTA
1 TCGCAATGCGAACTTCGACTATCGCAATACGAACTTGGACTA
* * * * *
381540 TCGCAATGCGAACTTGGACTATCACAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACTTCGACTATCGCAATACGAACT-TGGACTA
* * * * * *
381581 TCGCATTACGATA-GTCGACTATCGCAATGCGAACTTGTA-AA
1 TCGCAATGCGA-ACTTCGACTATCGCAATACGAACTTGGACTA
381622 TCGCAATGCGA
1 TCGCAATGCGA
381633 TAGTCGAAGT
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
41 43 0.37
42 74 0.63
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (42 bp):
TCGCAATGCGAACTTCGACTATCGCAATACGAACTTGGACTA
Found at i:381647 original size:41 final size:41
Alignment explanation
Indices: 381512--381639 Score: 125
Period size: 41 Copynumber: 3.1 Consensus size: 41
381502 AATGCGAACT
* * * * * *
381512 TCGACTATCGCAATACGAATTTGGACTATCGCAATGCGA-ACT
1 TCGACTATCGCAATGCGAATATGTA-AATCGCAATACGATA-G
* * *
381554 TGGACTATCACAATGCGAATATGTAAATCGCATTACGATAG
1 TCGACTATCGCAATGCGAATATGTAAATCGCAATACGATAG
*
381595 TCGACTATCGCAATGCGAACT-TGTAAATCGCAATGCGATAG
1 TCGACTATCGCAATGCGAA-TATGTAAATCGCAATACGATAG
381636 TCGA
1 TCGA
381640 AGTTCGCATT
Statistics
Matches: 71, Mismatches: 13, Indels: 5
0.80 0.15 0.06
Matches are distributed among these distances:
41 49 0.69
42 22 0.31
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
TCGACTATCGCAATGCGAATATGTAAATCGCAATACGATAG
Found at i:381652 original size:21 final size:21
Alignment explanation
Indices: 381622--381717 Score: 140
Period size: 21 Copynumber: 4.6 Consensus size: 21
381612 AACTTGTAAA
*
381622 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
381643 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
381664 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
381685 TCGCATTGCGATAGTCG-ACT
1 TCGCATTGCGATAGTCGAAGT
381705 ATCGCATTGCGAT
1 -TCGCATTGCGAT
381718 TTACAGAACT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
20 2 0.03
21 66 0.97
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:381653 original size:41 final size:40
Alignment explanation
Indices: 381567--381695 Score: 118
Period size: 41 Copynumber: 3.1 Consensus size: 40
381557 ACTATCACAA
* * *
381567 TGCGAATATGTAAATCGCATTACGATAGTCG-ACTATCGCAA
1 TGCGAAT-TGTAAATCGCATTGCGATAGTCGAAGT-TCGCAT
*
381608 TGCGAACTTGTAAATCGCAATGCGATAGTCGAAGTTCGCAT
1 TGCGAA-TTGTAAATCGCATTGCGATAGTCGAAGTTCGCAT
* * * *
381649 TGCG-ATAGTCGAAGTTCGCGTTGCGATAGTCCAAGTTCGCAT
1 TGCGAATTGT--AA-ATCGCATTGCGATAGTCGAAGTTCGCAT
381691 TGCGA
1 TGCGA
381696 TAGTCGACTA
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
39 3 0.04
40 1 0.01
41 38 0.52
42 31 0.42
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (40 bp):
TGCGAATTGTAAATCGCATTGCGATAGTCGAAGTTCGCAT
Found at i:381787 original size:21 final size:21
Alignment explanation
Indices: 381761--381836 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
381751 TAAATCGCAA
*
381761 TGCGATAGTCGAAGTTCACGT
1 TGCGATAGTCCAAGTTCACGT
*
381782 TGCGATAGTCCAAGTTCGCGT
1 TGCGATAGTCCAAGTTCACGT
* *
381803 TGCGATTTATTCCAAATTCA--T
1 TGCGA--TAGTCCAAGTTCACGT
381824 TGCGATAGTCCAA
1 TGCGATAGTCCAA
381837 AATCGCAACG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 7 0.15
21 30 0.64
23 10 0.21
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (21 bp):
TGCGATAGTCCAAGTTCACGT
Found at i:381842 original size:133 final size:132
Alignment explanation
Indices: 381597--381843 Score: 372
Period size: 133 Copynumber: 1.9 Consensus size: 132
381587 TACGATAGTC
* *
381597 GACTATCGCAATGCGAACTTGTAAATCGCAATGCGATAGTCGAAGTTCGCATTGCGATAGTCGAA
1 GACTATCGCAATGCGAACTTGTAAATCGCAATGCGATAGTCGAAGTTCACATTGCGATAGTCCAA
* * **
381662 GTTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACAGAAC
66 GTTCGCGTTGCGATAGTCCAAATTC-CATTGCGATAGTCCAAAATCGCATTGCGATTTACAGAAC
381727 TTG
130 TTG
*
381730 GACTATCGCAATGCGAA-TATGTAAATCGCAATGCGATAGTCGAAGTTCACGTTGCGATAGTCCA
1 GACTATCGCAATGCGAACT-TGTAAATCGCAATGCGATAGTCGAAGTTCACATTGCGATAGTCCA
*
381794 AGTTCGCGTTGCGATTTATTCCAAATT-CATTGCGATAGTCCAAAATCGCA
65 AGTTCGCGTTGCGA--TAGTCCAAATTCCATTGCGATAGTCCAAAATCGCA
381844 ACGACTGGTG
Statistics
Matches: 103, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
132 1 0.01
133 93 0.90
135 9 0.09
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (132 bp):
GACTATCGCAATGCGAACTTGTAAATCGCAATGCGATAGTCGAAGTTCACATTGCGATAGTCCAA
GTTCGCGTTGCGATAGTCCAAATTCCATTGCGATAGTCCAAAATCGCATTGCGATTTACAGAACT
TG
Found at i:381937 original size:6 final size:6
Alignment explanation
Indices: 381926--381950 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
381916 GACACGTATT
381926 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
381951 GACGGACGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:382466 original size:6 final size:6
Alignment explanation
Indices: 382445--382481 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
382435 TCTCGTCTCG
382445 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
382482 AATAGTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:382489 original size:6 final size:6
Alignment explanation
Indices: 382480--382521 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
382470 CGTGGTCGTG
382480 GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA
1 GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA GTAATA
382522 CGTGTCTTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
GTAATA
Found at i:384340 original size:20 final size:20
Alignment explanation
Indices: 384296--384334 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
384286 AGAACTTTAA
*
384296 ATTATTTTTATATTATATAT
1 ATTAATTTTATATTATATAT
384316 ATTAATTTTATATT-TATAT
1 ATTAATTTTATATTATATAT
384335 CTTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTAATTTTATATTATATAT
Found at i:384596 original size:2 final size:2
Alignment explanation
Indices: 384589--384614 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
384579 GACATTTTAA
384589 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
384615 GTTTAATTTA
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:385324 original size:60 final size:60
Alignment explanation
Indices: 385217--385365 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
385207 ATACATATAA
* * * *
385217 TTTG-GGATGAACTTAAAATGGTCAAAAAGTTTGGGGACCAATTTAGAATGAAAATCATAG
1 TTTGAGGATGAAATTAAAAT-GTTAAAAAGTTTGAGGACCAATCTAGAATGAAAATCATAG
* * * * *
385277 TTTGAGGATGAAATTGAAATGTTAAAAAGTTTGATGACTAATCTAGAATGATAGTCATAG
1 TTTGAGGATGAAATTAAAATGTTAAAAAGTTTGAGGACCAATCTAGAATGAAAATCATAG
* * *
385337 TTTAAGGATGAAATTAAAATATTTAAAAG
1 TTTGAGGATGAAATTAAAATGTTAAAAAG
385366 CTTAGGGACT
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
60 62 0.83
61 13 0.17
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (60 bp):
TTTGAGGATGAAATTAAAATGTTAAAAAGTTTGAGGACCAATCTAGAATGAAAATCATAG
Found at i:385395 original size:60 final size:60
Alignment explanation
Indices: 385269--385395 Score: 130
Period size: 60 Copynumber: 2.1 Consensus size: 60
385259 TTAGAATGAA
* * * * * * * *
385269 AATCATAGTTTGAGGATGAAATTGAAATGTTAAAAAGTTTGATGACTAATCTAGAATGAT
1 AATCATAGTTTAAGGATGAAATTAAAATATTAAAAAGTTAGAGGACTAATCTAAAATAAG
* * * *
385329 AGTCATAGTTTAAGGATGAAATTAAAATATTTAAAAGCTTAG-GGACTAGTTTAAAATAAG
1 AATCATAGTTTAAGGATGAAATTAAAATATTAAAAAG-TTAGAGGACTAATCTAAAATAAG
385389 AATCATA
1 AATCATA
385396 TATAAAGGAT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
60 50 0.94
61 3 0.06
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (60 bp):
AATCATAGTTTAAGGATGAAATTAAAATATTAAAAAGTTAGAGGACTAATCTAAAATAAG
Found at i:387307 original size:13 final size:13
Alignment explanation
Indices: 387289--387313 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
387279 ACAGATGCGT
387289 ATATGAAGACTGC
1 ATATGAAGACTGC
387302 ATATGAAGACTG
1 ATATGAAGACTG
387314 TTCAACTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.24, T:0.24
Consensus pattern (13 bp):
ATATGAAGACTGC
Found at i:388545 original size:54 final size:53
Alignment explanation
Indices: 388453--388555 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
388443 CACGAAAAAC
388453 CGAATCCGAATAACATAGTTGTAATATCTCTAAAACCCGAATGACCGAACAAT
1 CGAATCCGAATAACATAGTTGTAATATCTCTAAAACCCGAATGACCGAACAAT
* * *
388506 CGAAT-CGAAATAACATAGGTTGTGATATCTCTAAGACCCGAATGGCCGAA
1 CGAATCCG-AATAACATA-GTTGTAATATCTCTAAAACCCGAATGACCGAA
388556 GTACCCATGT
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 2 0.04
53 14 0.31
54 29 0.64
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.22
Consensus pattern (53 bp):
CGAATCCGAATAACATAGTTGTAATATCTCTAAAACCCGAATGACCGAACAAT
Found at i:392784 original size:132 final size:132
Alignment explanation
Indices: 392547--392806 Score: 475
Period size: 132 Copynumber: 2.0 Consensus size: 132
392537 ATAAAAAAAA
* *
392547 TTACGTACTAAAACGGATCAAAACTTATAGTTTATGTACTAAACGCATAATTTACCCAAATTATT
1 TTACGTACTAAAACGGATCAAAACTTATAATTTAAGTACTAAACGCATAATTTACCCAAATTATT
*
392612 TTGACAATTGATACAAGGGTCTTCTAGATTAATTTTCAAGAGTAATCAAAACTAAATCTTCGTAA
66 TTGACAATTAATACAAGGGTCTTCTAGATTAATTTTCAAGAGTAATCAAAACTAAATCTTCGTAA
392677 CT
131 CT
*
392679 TTACGTAGTAAAACGGATCAAAACTTATAATTTAAGTACTAAACGCATAATTTACCCAAATTATT
1 TTACGTACTAAAACGGATCAAAACTTATAATTTAAGTACTAAACGCATAATTTACCCAAATTATT
*
392744 TTGACAATTAATACAAGGGTCTTCTAGATTAATTTTCAAGAGTAATCAAAACTAAGTCTTCGT
66 TTGACAATTAATACAAGGGTCTTCTAGATTAATTTTCAAGAGTAATCAAAACTAAATCTTCGT
392807 TACGAATTTG
Statistics
Matches: 123, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
132 123 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (132 bp):
TTACGTACTAAAACGGATCAAAACTTATAATTTAAGTACTAAACGCATAATTTACCCAAATTATT
TTGACAATTAATACAAGGGTCTTCTAGATTAATTTTCAAGAGTAATCAAAACTAAATCTTCGTAA
CT
Found at i:393938 original size:16 final size:18
Alignment explanation
Indices: 393911--393943 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
393901 ACGCCCAACC
393911 TAAAATAAATA-TATTTA
1 TAAAATAAATATTATTTA
393928 TAAAA-AAATATTATTT
1 TAAAATAAATATTATTT
393944 TGATTCACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATAAATATTATTTA
Found at i:397710 original size:650 final size:649
Alignment explanation
Indices: 396470--397770 Score: 2566
Period size: 650 Copynumber: 2.0 Consensus size: 649
396460 AATCAACTGG
396470 ATTATGAACTATGGTTACCTGAAATGTGTTATATGGTTTCCTGTTTTCACTGGAAAATATGATCG
1 ATTATGAACTATGGTTACCTGAAATGTGTTATATGGTTTCCTGTTTTCACTGGAAAATATGATCG
*
396535 TTCCTGATTTATGGATCATGAAATATGCTGTTACTACTTGAACTGTTTATTGGGATATTATCTGG
66 TTCCTGATTTATAGATCATGAAATATGCTGTTACTACTTGAACTGTTTATTGGGATATTATCTGG
*
396600 GTAGGCTGGAGTATGGAGGTTCAGTTCTGATCAAGCTGGTAAATCCTTACAAACTTAAGGTGACC
131 GTAGGCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAATCCTTACAAACTTAAGGTGACC
396665 CTTGGGTAAGCTCTGAGGCTCCGAGAAACTTTATTGGGCAGGTTCTCAAGCCCCAAGGCATTCCC
196 CTTGGGTAAGCTCTGAGGCTCCGAGAAACTTTATTGGGCAGGTTCTCAAGCCCCAAGGCATTCCC
396730 CTTGGGTTAATTATGGAACTACATATGGTGTACGGATGAAGGACATTTATATGATTTATTTTATT
261 CTTGGGTTAATTATGGAACTACATATGGTGTACGGATGAAGGACATTTATATGATTTATTTTATT
396795 GTCACGTTTATGAGATTTTACTGGATCACGATCCATATATTACGGTTTACTATTAAATCTGATTT
326 GTCACGTTTATGAGATTTTACTGGATCACGATCCATATATTACGGTTTACTATTAAATCTGATTT
396860 CTATGTATATTGTATGAGTAGGATTCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAATC
391 CTATGTATATTGTATGAGTAGGATTCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAATC
396925 CTTGAAGACCTAAGGTGACCCTTGGGTAGGCCCTTAGGCCCCAATGCATTCCCTTAGGGTGGCTC
456 CTTGAAGACCTAAGGTGACCCTTGGGTAGGCCCTTAGGCCCCAATGCATTCCCTTAGGGTGGCTC
396990 ATTTGTTGTGTGCTTAGAGGTTGTTTGGTTCGGGGAATGTGGGATTCCCATGGGAATGAAATCCA
521 ATTTGTTGTGTGCTTAGAGGTTGTTTGGTTCGGGGAATGTGGGATTCCCATGGGAATGAAATCCA
397055 CATTCCTCCGTTTGGTTAGCCGGTAATCTCATTCCCGATAATGTAACAGTGAATTTTTTAGGGT
586 CATTCCTCCGTTTGGTTAGCCGGTAATCTCATTCCCGATAATGTAACAGTGAATTTTTTAGGGT
397119 ATTATGAACTATGGTTACCTGAAATGTGTTATATGGTTTCCTGTTTTCACTGGAAAATATGATCG
1 ATTATGAACTATGGTTACCTGAAATGTGTTATATGGTTTCCTGTTTTCACTGGAAAATATGATCG
397184 TTCCTGATTTATAGATCATGAAATATGCTGTTACTACTTGAACTGTTTTATTGGGATATTATCTG
66 TTCCTGATTTATAGATCATGAAATATGCTGTTACTACTTGAACTG-TTTATTGGGATATTATCTG
397249 GGTAGGCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAATCCTTACAAACTTAAGGTGAC
130 GGTAGGCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAATCCTTACAAACTTAAGGTGAC
*
397314 CCTTGGGTAAGCTCTGAGGCTCCGAGAAACTTTATTGGGTAGGTTCTCAAGCCCCAAGGCATTCC
195 CCTTGGGTAAGCTCTGAGGCTCCGAGAAACTTTATTGGGCAGGTTCTCAAGCCCCAAGGCATTCC
397379 CCTTGGGTTAATTATGGAACTACATATGGTGTACGGATGAAGGACATTTATATGATTTATTTTAT
260 CCTTGGGTTAATTATGGAACTACATATGGTGTACGGATGAAGGACATTTATATGATTTATTTTAT
397444 TGTCACGTTTATGAGATTTTACTGGATCACGATCCATATATTACGGTTTACTATTAAATCTGATT
325 TGTCACGTTTATGAGATTTTACTGGATCACGATCCATATATTACGGTTTACTATTAAATCTGATT
397509 TCTATGTATATTGTATGAGTAGGATTCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAAT
390 TCTATGTATATTGTATGAGTAGGATTCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAAT
397574 CCTTGAAGACCTAAGGTGACCCTTGGGTAGGCCCTTAGGCCCCAATGCATTCCCTTAGGGTGGCT
455 CCTTGAAGACCTAAGGTGACCCTTGGGTAGGCCCTTAGGCCCCAATGCATTCCCTTAGGGTGGCT
397639 CATTTGTTGTGTGCTTAGAGGTTGTTTGGTTCGGGGAATGTGGGATTCCCATGGGAATGAAATCC
520 CATTTGTTGTGTGCTTAGAGGTTGTTTGGTTCGGGGAATGTGGGATTCCCATGGGAATGAAATCC
397704 ACATTCCTCCGTTTGGTTAGCCGGTAATCTCATTCCCGATAATGTAACAGTGAATTTTTTAGGGT
585 ACATTCCTCCGTTTGGTTAGCCGGTAATCTCATTCCCGATAATGTAACAGTGAATTTTTTAGGGT
397769 AT
1 AT
397771 ATTATCGGGA
Statistics
Matches: 648, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
649 109 0.17
650 539 0.83
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (649 bp):
ATTATGAACTATGGTTACCTGAAATGTGTTATATGGTTTCCTGTTTTCACTGGAAAATATGATCG
TTCCTGATTTATAGATCATGAAATATGCTGTTACTACTTGAACTGTTTATTGGGATATTATCTGG
GTAGGCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAATCCTTACAAACTTAAGGTGACC
CTTGGGTAAGCTCTGAGGCTCCGAGAAACTTTATTGGGCAGGTTCTCAAGCCCCAAGGCATTCCC
CTTGGGTTAATTATGGAACTACATATGGTGTACGGATGAAGGACATTTATATGATTTATTTTATT
GTCACGTTTATGAGATTTTACTGGATCACGATCCATATATTACGGTTTACTATTAAATCTGATTT
CTATGTATATTGTATGAGTAGGATTCTGGAGTATGGAGGTTCAGCTCTGATCAAGCTGGTAAATC
CTTGAAGACCTAAGGTGACCCTTGGGTAGGCCCTTAGGCCCCAATGCATTCCCTTAGGGTGGCTC
ATTTGTTGTGTGCTTAGAGGTTGTTTGGTTCGGGGAATGTGGGATTCCCATGGGAATGAAATCCA
CATTCCTCCGTTTGGTTAGCCGGTAATCTCATTCCCGATAATGTAACAGTGAATTTTTTAGGGT
Found at i:403382 original size:50 final size:52
Alignment explanation
Indices: 403305--403437 Score: 180
Period size: 50 Copynumber: 2.5 Consensus size: 52
403295 ATCAATCGAG
*
403305 AGATCAATCGATATAAGACCAACTGATAAAATGTGACCTAA-C-ATCTTGTT
1 AGATCAATCGAGATAAGACCAACTGATAAAATGTGACCTAACCTATCTTGTT
* *
403355 AGATCAATTGAGATAAGACCAATTGATAAAATGTGACCTAACGTCTTATCTTGTT
1 AGATCAATCGAGATAAGACCAACTGATAAAATGTGACCTAAC--C-TATCTTGTT
* *
403410 AGATCAATCGAGATAAGATCAAGTGATA
1 AGATCAATCGAGATAAGACCAACTGATA
403438 GCCGGTATTT
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
50 38 0.53
53 1 0.01
55 33 0.46
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (52 bp):
AGATCAATCGAGATAAGACCAACTGATAAAATGTGACCTAACCTATCTTGTT
Found at i:406905 original size:21 final size:21
Alignment explanation
Indices: 406862--406913 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
406852 CAGAAAGTTT
* * *
406862 GGGATCGATCTTTTTGGTTGA
1 GGGATCAATCTTTTTGCTCGA
*
406883 GGGATCAATCTTTTTTCTCGA
1 GGGATCAATCTTTTTGCTCGA
406904 GGGATCAATC
1 GGGATCAATC
406914 CTATGCACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.15, G:0.27, T:0.38
Consensus pattern (21 bp):
GGGATCAATCTTTTTGCTCGA
Found at i:406987 original size:68 final size:68
Alignment explanation
Indices: 406830--407036 Score: 290
Period size: 68 Copynumber: 3.0 Consensus size: 68
406820 CAAAACAACG
* * * * *
406830 AAGGGATCAATCCTTTGCACAACAGAAAGTTTGGGATCGATCTTTTTGGTTGAGGGATC-AATCT
1 AAGGGATCAATCCTATGCACAACAGAAAGTTTGGTATCGATC--CTT--TCGAGGGATCGAACCT
406894 TTTTTCTC
62 TTTTT-TC
*
406902 GAGGGATCAATCCTATGCACAACAGAAAGTTTGGTATCGATCCTTTCGAGGGATCGAACCTTTTT
1 AAGGGATCAATCCTATGCACAACAGAAAGTTTGGTATCGATCCTTTCGAGGGATCGAACCTTTTT
406967 TTC
66 TTC
* *
406970 AAGGGATCAATCCTATGCACAACAGAAAGTTTGGTATCGATCCTTTCGAGGGATCGATCATTTTT
1 AAGGGATCAATCCTATGCACAACAGAAAGTTTGGTATCGATCCTTTCGAGGGATCGAACCTTTTT
407035 TT
66 TT
407037 GGGAATAACT
Statistics
Matches: 125, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
68 75 0.60
69 9 0.07
70 2 0.02
72 39 0.31
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (68 bp):
AAGGGATCAATCCTATGCACAACAGAAAGTTTGGTATCGATCCTTTCGAGGGATCGAACCTTTTT
TTC
Found at i:407700 original size:13 final size:13
Alignment explanation
Indices: 407682--407711 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
407672 TTGAGTTGAG
407682 AGAAAGAGAAGGA
1 AGAAAGAGAAGGA
*
407695 AGAAAGTGAAGGA
1 AGAAAGAGAAGGA
407708 AGAA
1 AGAA
407712 GGGAAGATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.37, T:0.03
Consensus pattern (13 bp):
AGAAAGAGAAGGA
Found at i:418947 original size:39 final size:39
Alignment explanation
Indices: 418893--418976 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
418883 TTTTTGGAGA
* *
418893 CCCTGCGCGGTCGCGCAGTTTGCGTCGCCCGAGCCATGG
1 CCCTGCGCGGTCGCGCAGTTTGCGCCGCCCCAGCCATGG
418932 CCCTGCGCGGTCGCGCAGTTTGCGCCGCCCCAGCCATGG
1 CCCTGCGCGGTCGCGCAGTTTGCGCCGCCCCAGCCATGG
418971 CCCTGC
1 CCCTGC
418977 ACATACACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.07, C:0.43, G:0.33, T:0.17
Consensus pattern (39 bp):
CCCTGCGCGGTCGCGCAGTTTGCGCCGCCCCAGCCATGG
Found at i:420477 original size:18 final size:17
Alignment explanation
Indices: 420444--420507 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 17
420434 GTATATTTAT
*
420444 TAAAAAATA-AAAATAA
1 TAAAAAATATAGAATAA
420460 TAAAAAATATAGATATAA
1 TAAAAAATATAGA-ATAA
*
420478 TATAAAAGGATGTAAGAATAA
1 TA-AAAA--ATAT-AGAATAA
420499 TAAAAAATA
1 TAAAAAATA
420508 CCGACGATCG
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 9 0.23
17 2 0.05
18 8 0.21
19 4 0.10
20 4 0.10
21 9 0.23
22 3 0.08
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (17 bp):
TAAAAAATATAGAATAA
Found at i:421209 original size:53 final size:52
Alignment explanation
Indices: 421063--421216 Score: 179
Period size: 50 Copynumber: 3.0 Consensus size: 52
421053 CTACAAAAAG
* * *
421063 TATAGCACTTAACACATATTTACATCGGTGTAAGTGAATAAAATAAACAAGTA
1 TATAGCAATTAACACATA-TTACATCGGTGTAAGTGAATAAAATAAAAAAATA
* * *
421116 TA-A-CAATTAACACATACTACATCAGTATAAGTGAATAAAATAAAAAAATA
1 TATAGCAATTAACACATATTACATCGGTGTAAGTGAATAAAATAAAAAAATA
* * *
421166 TATAGCATTTAACGCATAGTTACA-CTGGTGTAAGTAAATAAAATAAAAAAA
1 TATAGCAATTAACACATA-TTACATC-GGTGTAAGTGAATAAAATAAAAAAA
421217 GAACAACACT
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
50 31 0.36
51 13 0.15
52 13 0.15
53 28 0.33
ACGTcount: A:0.51, C:0.12, G:0.11, T:0.27
Consensus pattern (52 bp):
TATAGCAATTAACACATATTACATCGGTGTAAGTGAATAAAATAAAAAAATA
Found at i:421241 original size:52 final size:53
Alignment explanation
Indices: 421068--421253 Score: 141
Period size: 52 Copynumber: 3.6 Consensus size: 53
421058 AAAAGTATAG
* * * * * * *
421068 CACTTAACACATATTTACATCGGTGTAAGTGAATAAAAT-AAACAAG-TATAA
1 CACTTAACGCATAGTTACACCGATGTAAGTAAATAAAATAAAAAAAGATACAA
* * * * * * * * *
421119 CAATTAACACATA-CTACATC-AGTATAAGTGAATAAAATAAAAAAATATATAG
1 CACTTAACGCATAGTTACACCGA-TGTAAGTAAATAAAATAAAAAAAGATACAA
* * *
421171 CATTTAACGCATAGTTACACTGGTGTAAGTAAATAAAATAAAAAAAGA-ACAA
1 CACTTAACGCATAGTTACACCGATGTAAGTAAATAAAATAAAAAAAGATACAA
421223 CACTTAACGCAT-GCTTACACCGATGTAAGTA
1 CACTTAACGCATAG-TTACACCGATGTAAGTA
421254 TGTACATCTC
Statistics
Matches: 108, Mismatches: 21, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
50 21 0.19
51 18 0.17
52 43 0.40
53 26 0.24
ACGTcount: A:0.48, C:0.15, G:0.12, T:0.25
Consensus pattern (53 bp):
CACTTAACGCATAGTTACACCGATGTAAGTAAATAAAATAAAAAAAGATACAA
Found at i:423091 original size:41 final size:41
Alignment explanation
Indices: 423037--423117 Score: 162
Period size: 41 Copynumber: 2.0 Consensus size: 41
423027 CCTGACCTTG
423037 CTTAAAAAAATCTAATTCCTCGTCCAACTAGATCAACAGAC
1 CTTAAAAAAATCTAATTCCTCGTCCAACTAGATCAACAGAC
423078 CTTAAAAAAATCTAATTCCTCGTCCAACTAGATCAACAGA
1 CTTAAAAAAATCTAATTCCTCGTCCAACTAGATCAACAGA
423118 TTGTTGGTAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.42, C:0.26, G:0.07, T:0.25
Consensus pattern (41 bp):
CTTAAAAAAATCTAATTCCTCGTCCAACTAGATCAACAGAC
Found at i:429348 original size:2 final size:2
Alignment explanation
Indices: 429341--429394 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
429331 ACCATCCACG
429341 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
429383 TA TA TA TA TA TA
1 TA TA TA TA TA TA
429395 AAATTTTGAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:429478 original size:22 final size:22
Alignment explanation
Indices: 429453--429495 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
429443 AAATTAAAAA
429453 ATATATAAATA-AAAAATAATTT
1 ATAT-TAAATATAAAAATAATTT
*
429475 ATATTTAATATAAAAATAATT
1 ATATTAAATATAAAAATAATT
429496 AATCTCAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATATTAAATATAAAAATAATTT
Found at i:442862 original size:3 final size:3
Alignment explanation
Indices: 442854--442879 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
442844 AAAAACTAAA
442854 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
442880 AATCATATTC
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:442969 original size:51 final size:51
Alignment explanation
Indices: 442893--442995 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
442883 CATATTCTCA
442893 TATATAATATATAACGGGGGTAAGGGAGGTAGGGTAGTACACAAATTCATG
1 TATATAATATATAACGGGGGTAAGGGAGGTAGGGTAGTACACAAATTCATG
442944 TATATAATATATAACGGGGGTAAGGGAGGTAGGGTAGTACACAAATTCATG
1 TATATAATATATAACGGGGGTAAGGGAGGTAGGGTAGTACACAAATTCATG
442995 T
1 T
442996 TGAAAGCAGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.37, C:0.08, G:0.29, T:0.26
Consensus pattern (51 bp):
TATATAATATATAACGGGGGTAAGGGAGGTAGGGTAGTACACAAATTCATG
Found at i:444692 original size:21 final size:21
Alignment explanation
Indices: 444666--444707 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
444656 AATAATTAAT
*
444666 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
444687 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
444708 TAATAATTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:444699 original size:26 final size:26
Alignment explanation
Indices: 444614--444699 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
444604 ATAATTTTTT
* * * *
444614 TAATTTTTATTT-AAAAACTATTTTA
1 TAATATTTATTTAAAAAAATAATTAA
*
444639 TGATATTTATTTAAAAAAATAATTAA
1 TAATATTTATTTAAAAAAATAATTAA
* * *
444665 TATTATTTATTATAAAAAATTAATTAT
1 TAATATTTATT-TAAAAAAATAATTAA
444692 TAAT-TTTA
1 TAATATTTA
444700 AAATATTATA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
25 10 0.20
26 23 0.47
27 16 0.33
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
TAATATTTATTTAAAAAAATAATTAA
Found at i:455952 original size:30 final size:30
Alignment explanation
Indices: 455916--455978 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
455906 GTCAGAATAG
455916 TTCCTTGCATAATCACTATTAGTTATAAAA
1 TTCCTTGCATAATCACTATTAGTTATAAAA
455946 TTCCTTGCATAATCACTATTAGTTATAAAA
1 TTCCTTGCATAATCACTATTAGTTATAAAA
455976 TTC
1 TTC
455979 TCTCTTTAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.41
Consensus pattern (30 bp):
TTCCTTGCATAATCACTATTAGTTATAAAA
Found at i:457435 original size:33 final size:35
Alignment explanation
Indices: 457362--457446 Score: 122
Period size: 33 Copynumber: 2.5 Consensus size: 35
457352 TGGGGCAAAC
* *
457362 CAGACAGTAACTAAATT-TAATAAACATAAAAAAT
1 CAGACAGTGACTAAATTGTAATAAACACAAAAAAT
*
457396 CTGACAGTGACTAAATTGT-ATAAAC-CAAAAAAT
1 CAGACAGTGACTAAATTGTAATAAACACAAAAAAT
457429 CAGACAGTGACTAAATTG
1 CAGACAGTGACTAAATTG
457447 AATGAAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
33 24 0.52
34 21 0.46
35 1 0.02
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (35 bp):
CAGACAGTGACTAAATTGTAATAAACACAAAAAAT
Found at i:457684 original size:2 final size:2
Alignment explanation
Indices: 457677--457718 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
457667 CCTAAATTAA
457677 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
457719 TTAACTCTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:457850 original size:24 final size:25
Alignment explanation
Indices: 457816--457862 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
457806 TATTTTAATC
* *
457816 CAATTCAATTTTGTTCATTTATTCT
1 CAATTCAATTTTCTTCATATATTCT
457841 CAATTC-ATTTTCTTCATATATT
1 CAATTCAATTTTCTTCATATATT
457863 TTAGTCCCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.26, C:0.17, G:0.02, T:0.55
Consensus pattern (25 bp):
CAATTCAATTTTCTTCATATATTCT
Found at i:458039 original size:31 final size:31
Alignment explanation
Indices: 458004--458076 Score: 146
Period size: 31 Copynumber: 2.4 Consensus size: 31
457994 CAAACTCAAA
458004 GGATGACTTTGGCTAACAAGTAGTTATTTGG
1 GGATGACTTTGGCTAACAAGTAGTTATTTGG
458035 GGATGACTTTGGCTAACAAGTAGTTATTTGG
1 GGATGACTTTGGCTAACAAGTAGTTATTTGG
458066 GGATGACTTTG
1 GGATGACTTTG
458077 TCAAACACTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.36
Consensus pattern (31 bp):
GGATGACTTTGGCTAACAAGTAGTTATTTGG
Found at i:458361 original size:25 final size:25
Alignment explanation
Indices: 458333--458394 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
458323 GAAACTTGAT
* *
458333 GTGTCTGGCACTTGGATCCTTGCCC
1 GTGTCTGACACCTGGATCCTTGCCC
458358 GTGTCTGACACCTGGATCCTTGCCC
1 GTGTCTGACACCTGGATCCTTGCCC
458383 GTGTCTGACACC
1 GTGTCTGACACC
458395 GTGTCCTGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.11, C:0.34, G:0.26, T:0.29
Consensus pattern (25 bp):
GTGTCTGACACCTGGATCCTTGCCC
Found at i:464536 original size:24 final size:25
Alignment explanation
Indices: 464499--464549 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
464489 AATTTATTCC
*
464499 ATTTATTATCTATTCTAAATACA-AA
1 ATTTATTATATATT-TAAATACATAA
464524 ATTT-TTATATATTTAAATACATAA
1 ATTTATTATATATTTAAATACATAA
464548 AT
1 AT
464550 ATAAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 8 0.33
24 12 0.50
25 4 0.17
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTTATTATATATTTAAATACATAA
Found at i:466892 original size:23 final size:23
Alignment explanation
Indices: 466854--466897 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
466844 TTTACAATTC
466854 TTTTATCTTTTCTTT-ATCTTTT
1 TTTTATCTTTTCTTTAATCTTTT
466876 TTTTAATCTTATT-TTTAATCTT
1 TTTT-ATCTT-TTCTTTAATCTT
466898 GTTTCCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.21
23 8 0.42
24 7 0.37
ACGTcount: A:0.16, C:0.11, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTATCTTTTCTTTAATCTTTT
Found at i:467250 original size:11 final size:11
Alignment explanation
Indices: 467232--467269 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
467222 CTTTTTTTTT
467232 CAAAAAAAAAA
1 CAAAAAAAAAA
*
467243 -ACAAAAAAAA
1 CAAAAAAAAAA
467253 CAAAAAAAAAA
1 CAAAAAAAAAA
467264 CAAAAA
1 CAAAAA
467270 TGCCAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:467269 original size:9 final size:9
Alignment explanation
Indices: 467236--467261 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
467226 TTTTTTCAAA
467236 AAAAAAAAC
1 AAAAAAAAC
467245 AAAAAAAAC
1 AAAAAAAAC
467254 AAAAAAAA
1 AAAAAAAA
467262 AACAAAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:471607 original size:12 final size:11
Alignment explanation
Indices: 471576--471614 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
471566 CAATTCCTTT
471576 ATCTTTTCTTT-
1 ATCTTTT-TTTA
471587 ATCTTTTTTTA
1 ATCTTTTTTTA
471598 ATCTTATTTTTA
1 ATCTT-TTTTTA
471610 ATCTT
1 ATCTT
471615 GTTTCCAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 3 0.12
11 12 0.46
12 11 0.42
ACGTcount: A:0.18, C:0.13, G:0.00, T:0.69
Consensus pattern (11 bp):
ATCTTTTTTTA
Found at i:473945 original size:14 final size:15
Alignment explanation
Indices: 473926--473956 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
473916 GTTAACAATA
473926 TTAAATTA-TGTTAT
1 TTAAATTATTGTTAT
473940 TTAAATTATTGTTAT
1 TTAAATTATTGTTAT
473955 TT
1 TT
473957 TTTTGTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.61
Consensus pattern (15 bp):
TTAAATTATTGTTAT
Found at i:477170 original size:23 final size:23
Alignment explanation
Indices: 477139--477199 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
477129 AAGTGAAAAT
*
477139 TAAATAAAAACATTATAAACTAAA
1 TAAATAAAAACATTAAAAAC-AAA
* *
477163 T-AATAAAAACAATAAAAACAAT
1 TAAATAAAAACATTAAAAACAAA
*
477185 TAAATACAAACATTA
1 TAAATAAAAACATTA
477200 CAATTCAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 3 0.10
23 27 0.87
24 1 0.03
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (23 bp):
TAAATAAAAACATTAAAAACAAA
Found at i:477333 original size:25 final size:25
Alignment explanation
Indices: 477305--477383 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
477295 AAAGTTCAAT
477305 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
* *
477330 TAAATAAAAA-ATCT-----A-TAAT
1 TAAATAAAAACAT-TAAGAAACAAAA
477349 TAAATAAAAACATTAAGAAACAAAA
1 TAAATAAAAACATTAAGAAACAAAA
477374 TAAATAAAAA
1 TAAATAAAAA
477384 GTCCATAATT
Statistics
Matches: 42, Mismatches: 4, Indels: 16
0.68 0.06 0.26
Matches are distributed among these distances:
19 13 0.31
20 3 0.07
24 3 0.07
25 23 0.55
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (25 bp):
TAAATAAAAACATTAAGAAACAAAA
Found at i:477365 original size:44 final size:44
Alignment explanation
Indices: 477218--477420 Score: 297
Period size: 44 Copynumber: 4.6 Consensus size: 44
477208 AAAATTAAAT
477218 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATT--A
* *
477264 TAATAAAAACATCAAGAAACAAAATAAATAAAAAGTTC--AATTA
1 -AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
* *
477307 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCTATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
477351 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
*
477395 AATAAAAA-ATTAATAATA-AAAATAAA
1 AATAAAAACATTAAGAA-ACAAAATAAA
477421 AATAAGTGTA
Statistics
Matches: 144, Mismatches: 9, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
42 33 0.23
43 16 0.11
44 56 0.39
45 4 0.03
47 35 0.24
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.21
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTA
Found at i:477410 original size:19 final size:20
Alignment explanation
Indices: 477373--477422 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
477363 AAGAAACAAA
* *
477373 ATAAATAAAAAGTCCATAAT
1 ATAAATAAAAAATCAATAAT
*
477393 -TAAATAAAAAATTAATAAT
1 ATAAATAAAAAATCAATAAT
*
477412 AAAAATAAAAA
1 ATAAATAAAAA
477423 TAAGTGTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
ATAAATAAAAAATCAATAAT
Found at i:477425 original size:89 final size:88
Alignment explanation
Indices: 477218--477420 Score: 297
Period size: 89 Copynumber: 2.3 Consensus size: 88
477208 AAAATTAAAT
*
477218 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCCATAATTAAATAATAAAAACATCAAGAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATT-AATAATAAAAACATCAAGAAA
*
477283 CAAAATAAATAAAAAGTTCAATTA
65 CAAAATAAATAAAAAGTCCAATTA
* *
477307 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCTATAATT-A-AATAAAAACATTAAGAAAC
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTAATAATAAAAACATCAAGAAAC
477370 AAAATAAATAAAAAGTCCATAATTA
66 AAAATAAATAAAAAGTCC--AATTA
*
477395 AATAAAAA-ATTAATAATA-AAAATAAA
1 AATAAAAACATTAAGAA-ACAAAATAAA
477421 AATAAGTGTA
Statistics
Matches: 106, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
86 35 0.33
87 16 0.15
88 14 0.13
89 41 0.39
ACGTcount: A:0.68, C:0.07, G:0.03, T:0.21
Consensus pattern (88 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAATCCATAATTAATAATAAAAACATCAAGAAAC
AAAATAAATAAAAAGTCCAATTA
Found at i:478617 original size:21 final size:21
Alignment explanation
Indices: 478578--478617 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
478568 TATTCAGTGT
*
478578 AAAAAAATTCATTATATACTC
1 AAAAAAATTCATTAAATACTC
478599 AAAAAAATT-ATTTAAATAC
1 AAAAAAATTCA-TTAAATAC
478618 AAACTCATTA
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:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAAATTCATTAAATACTC
Found at i:490107 original size:20 final size:20
Alignment explanation
Indices: 490082--490122 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
490072 TAGGCTCCCC
*
490082 AAATATAATAGAAGGTTATG
1 AAATATAATAGAAGATTATG
* *
490102 AAATATATTGGAAGATTATG
1 AAATATAATAGAAGATTATG
490122 A
1 A
490123 GAGATTTCAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.32
Consensus pattern (20 bp):
AAATATAATAGAAGATTATG
Found at i:492563 original size:14 final size:14
Alignment explanation
Indices: 492546--492585 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
492536 AGGTTTAGGG
492546 TTTAAAATTTATAA
1 TTTAAAATTTATAA
* *
492560 TTTAAAATTTAGAG
1 TTTAAAATTTATAA
*
492574 TTTAAGATTTAT
1 TTTAAAATTTAT
492586 TACAAAAACG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
TTTAAAATTTATAA
Found at i:497992 original size:2 final size:2
Alignment explanation
Indices: 497985--498032 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
497975 ACAAACCATT
497985 AG AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
498026 AG AG AG A
1 AG AG AG A
498033 AGAAGGCTCA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:507411 original size:21 final size:21
Alignment explanation
Indices: 507385--507424 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
507375 TCATCGAAGG
*
507385 TACTATTACGGCCGTCGTGAA
1 TACTATTACAGCCGTCGTGAA
507406 TACTATTACAGCCGTCGTG
1 TACTATTACAGCCGTCGTG
507425 GGTAACTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.30
Consensus pattern (21 bp):
TACTATTACAGCCGTCGTGAA
Found at i:512029 original size:22 final size:22
Alignment explanation
Indices: 512004--512055 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
511994 TCTGAATCAT
*
512004 TTGATTTTAAATATTTACACTC
1 TTGATATTAAATATTTACACTC
512026 TTGATATTAAATATTTACACTC
1 TTGATATTAAATATTTACACTC
512048 TTGATATT
1 TTGATATT
512056 TCTGATGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.12, G:0.06, T:0.50
Consensus pattern (22 bp):
TTGATATTAAATATTTACACTC
Found at i:512480 original size:22 final size:21
Alignment explanation
Indices: 512454--512503 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 21
512444 AGTATCCAAT
512454 AATAATAAAACCGATAGAAAAA
1 AATAATAAAACCGATAG-AAAA
* *
512476 AATAACAAAACCGATAGAAAT
1 AATAATAAAACCGATAGAAAA
512497 AATAATA
1 AATAATA
512504 TTTCCAGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.66, C:0.10, G:0.08, T:0.16
Consensus pattern (21 bp):
AATAATAAAACCGATAGAAAA
Found at i:513459 original size:36 final size:36
Alignment explanation
Indices: 513407--513479 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
513397 TTTTATTATT
**
513407 TCGGATCGGGTTTCTATGTCATATATTTGGGTCGGG
1 TCGGATCGGGTTTCTATGTCATATATTCAGGTCGGG
*
513443 TCGGGTCGGGTTTCTATGTCATATATTCAGGTCGGG
1 TCGGATCGGGTTTCTATGTCATATATTCAGGTCGGG
513479 T
1 T
513480 GGAGGCTCTC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.14, C:0.15, G:0.33, T:0.38
Consensus pattern (36 bp):
TCGGATCGGGTTTCTATGTCATATATTCAGGTCGGG
Found at i:513654 original size:15 final size:15
Alignment explanation
Indices: 513636--513685 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
513626 CCGGAAAATA
513636 AATTACTGGAATTTG
1 AATTACTGGAATTTG
*
513651 AATTGCTGGAATTTG
1 AATTACTGGAATTTG
**
513666 AATT-CTGGAAAATG
1 AATTACTGGAATTTG
513680 AATTAC
1 AATTAC
513686 ATTTCTGGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (15 bp):
AATTACTGGAATTTG
Found at i:513681 original size:14 final size:15
Alignment explanation
Indices: 513628--513685 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
513618 TTGGTTTTCC
*
513628 GGAAAATAAATTACT
1 GGAAAATGAATTACT
** *
513643 GGAATTTGAATTGCT
1 GGAAAATGAATTACT
**
513658 GGAATTTGAATT-CT
1 GGAAAATGAATTACT
513672 GGAAAATGAATTAC
1 GGAAAATGAATTAC
513686 ATTTCTGGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
14 12 0.33
15 24 0.67
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.33
Consensus pattern (15 bp):
GGAAAATGAATTACT
Found at i:513726 original size:14 final size:14
Alignment explanation
Indices: 513687--513727 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
513677 ATGAATTACA
* *
513687 TTTCTGGAAAACGT
1 TTTCCGGAAAATGT
513701 TTTCCGGAAAATGT
1 TTTCCGGAAAATGT
*
513715 TTTCCGTAAAATG
1 TTTCCGGAAAATG
513728 AATTACATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.37
Consensus pattern (14 bp):
TTTCCGGAAAATGT
Found at i:514061 original size:23 final size:23
Alignment explanation
Indices: 514012--514074 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
514002 GTGTTATATT
* **
514012 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAATATATTAATTAAA
* *
514035 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATATTAATTAAA
514058 ATATTATTTAAATATAT
1 ATA-T-TTTAAATATAT
514075 AAATAATATT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
23 21 0.66
24 1 0.03
25 10 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAATATATTAATTAAA
Found at i:514102 original size:19 final size:20
Alignment explanation
Indices: 514050--514124 Score: 59
Period size: 20 Copynumber: 3.9 Consensus size: 20
514040 TTAAATATCT
514050 TTATTAAA-ATATTATTTAA
1 TTATTAAATATATTATTTAA
* *
514069 ATATATAAATAATATTA-TTCA
1 TTAT-TAAAT-ATATTATTTAA
* **
514090 TTATTAAATATATAATTTTT
1 TTATTAAATATATTATTTAA
514110 TTATT--ATATATTATT
1 TTATTAAATATATTATT
514125 AAAATAAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
18 9 0.20
19 8 0.18
20 16 0.36
21 6 0.13
22 6 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTAAATATATTATTTAA
Found at i:514121 original size:59 final size:56
Alignment explanation
Indices: 514049--514213 Score: 146
Period size: 59 Copynumber: 2.9 Consensus size: 56
514039 TTTAAATATC
*
514049 TTTATTAAAATATTATTTAAATATATAAATAATATTATTCATTATTAAATATATAATTT-T
1 TTTATT-ATATATTA-TTAAA-ATATAAATAATATTATT-ATTATTAAA-ATATAATTTAT
* *
514109 TTTATTATATATTATTAAAATAAAAATATCATATCT-TATATTATTATAATATAATTTAT
1 TTTATTATATATTATTAAAATATAAATA--ATAT-TAT-TATTATTAAAATATAATTTAT
*
514168 TATT-TTATATAATATTAAAA-AT--ATAATATTA-TATTATTATAAATAT
1 T-TTATTATATATTATTAAAATATAAATAATATTATTATTATTA-AAATAT
514214 TAATAAATTA
Statistics
Matches: 91, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
52 8 0.09
53 6 0.07
54 4 0.04
56 3 0.03
57 8 0.09
58 15 0.16
59 37 0.41
60 10 0.11
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (56 bp):
TTTATTATATATTATTAAAATATAAATAATATTATTATTATTAAAATATAATTTAT
Found at i:514200 original size:22 final size:23
Alignment explanation
Indices: 514175--514218 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
514165 TATTATTTTA
514175 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
514197 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
514219 AATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:514226 original size:31 final size:33
Alignment explanation
Indices: 514146--514226 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 33
514136 ATCATATCTT
*
514146 ATATTATTATAATATAAT-TTATTATTTTATATA
1 ATATTAATA-AATATAATATTATTATTTTATATA
514179 ATATTAA-AAATATAATATTA-TATTATTATA-A
1 ATATTAATAAATATAATATTATTATT-TTATATA
514210 ATATTAATAAAT-TAATA
1 ATATTAATAAATATAATA
514227 AATAATGTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
31 25 0.57
32 13 0.30
33 6 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (33 bp):
ATATTAATAAATATAATATTATTATTTTATATA
Found at i:514509 original size:42 final size:43
Alignment explanation
Indices: 514410--514525 Score: 150
Period size: 42 Copynumber: 2.8 Consensus size: 43
514400 ATGAATTACG
514410 TTCCGGAAAA-AGAATTACGTGAAAC-AACAC-AGGAAAACATT
1 TTCCGGAAAACA-AATTACGTGAAACAAACACGAGGAAAACATT
** * *
514451 TTCCGGAAAATGAATTACGTGAAACAAATACGA-GAAAATATT
1 TTCCGGAAAACAAATTACGTGAAACAAACACGAGGAAAACATT
*
514493 TTCCGGATAACAAATTACGTGAAACAAACACGA
1 TTCCGGAAAACAAATTACGTGAAACAAACACGA
514526 AAATTCAGGG
Statistics
Matches: 65, Mismatches: 7, Indels: 5
0.84 0.09 0.06
Matches are distributed among these distances:
41 23 0.35
42 41 0.63
43 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.20
Consensus pattern (43 bp):
TTCCGGAAAACAAATTACGTGAAACAAACACGAGGAAAACATT
Found at i:516159 original size:2 final size:2
Alignment explanation
Indices: 516154--516191 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
516144 AAAATTACAT
*
516154 TA TA TA AA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
516192 TTGTTCTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:516983 original size:31 final size:31
Alignment explanation
Indices: 516947--517008 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
516937 TTTCATCCAT
516947 TGGCATATATAATTTCATATTGTTGTTGTTG
1 TGGCATATATAATTTCATATTGTTGTTGTTG
516978 TGGCATATATAATTTCATATTGTTGTTGTTG
1 TGGCATATATAATTTCATATTGTTGTTGTTG
517009 AATTAGACTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.06, G:0.19, T:0.52
Consensus pattern (31 bp):
TGGCATATATAATTTCATATTGTTGTTGTTG
Found at i:517543 original size:20 final size:20
Alignment explanation
Indices: 517520--517643 Score: 189
Period size: 20 Copynumber: 6.3 Consensus size: 20
517510 AATTTATAAA
517520 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
*
517540 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
517560 TCACAACAC--AAGTTAAAT
1 TCGCAACACAGAAGTCAAAT
517578 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
* *
517598 TCGCAATACAAAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
517618 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAGAAGTCAAAT
517638 TCGCAA
1 TCGCAA
517644 AGCGCGTTTA
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
18 16 0.17
20 77 0.83
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.17
Consensus pattern (20 bp):
TCGCAACACAGAAGTCAAAT
Found at i:517587 original size:58 final size:59
Alignment explanation
Indices: 517516--517643 Score: 206
Period size: 58 Copynumber: 2.2 Consensus size: 59
517506 CGCGAATTTA
517516 TAAA-TCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACAC-AAGT
1 TAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACACAAAGT
* *
517573 TAAATTCGCAACACAGAAGTCAAATTCGCAATACAAAAGTCAAATTCGCAACACAGAAGT
1 TAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACACA-AAGT
*
517633 CAAATTCGCAA
1 TAAATTCGCAA
517644 AGCGCGTTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
57 4 0.06
58 47 0.72
60 14 0.22
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.17
Consensus pattern (59 bp):
TAAATTCGCAACACAGAAGTCAAATTCGCAACACAAAAGTCAAATTCACAACACAAAGT
Found at i:517823 original size:22 final size:22
Alignment explanation
Indices: 517798--517848 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
517788 CTACGGCGAC
517798 ATCCGTCCCCATCTCCGACGAA
1 ATCCGTCCCCATCTCCGACGAA
* * *
517820 ATCCTTTCCCATCTCCGGCGAA
1 ATCCGTCCCCATCTCCGACGAA
517842 ATCCGTC
1 ATCCGTC
517849 TATCTCCATC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.20, C:0.43, G:0.14, T:0.24
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCGACGAA
Found at i:518232 original size:20 final size:20
Alignment explanation
Indices: 518199--518356 Score: 150
Period size: 20 Copynumber: 8.2 Consensus size: 20
518189 AAATCGCAAC
*
518199 GCGA-TTTTAGTTTCGCGTT
1 GCGATTTTTATTTTCGCGTT
*
518218 GCGATTTTTATTTTCGTGTT
1 GCGATTTTTATTTTCGCGTT
* * *
518238 GCGATTTTCATGTTCGCATT
1 GCGATTTTTATTTTCGCGTT
518258 GCGA----TA-TTT-GCGTT
1 GCGATTTTTATTTTCGCGTT
*
518272 GCGATTTTCTAGTTTCGCGTT
1 GCGATTTT-TATTTTCGCGTT
*
518293 GCGATTTTAATTTTCGCGTT
1 GCGATTTTTATTTTCGCGTT
* *
518313 GCGATTTTCATGTTCGCGTT
1 GCGATTTTTATTTTCGCGTT
* * *
518333 GTGATTTTCATTTTCGCATT
1 GCGATTTTTATTTTCGCGTT
518353 GCGA
1 GCGA
518357 ATTTAAGTTT
Statistics
Matches: 114, Mismatches: 17, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
14 8 0.07
15 2 0.02
16 1 0.01
19 6 0.05
20 84 0.74
21 13 0.11
ACGTcount: A:0.13, C:0.16, G:0.23, T:0.48
Consensus pattern (20 bp):
GCGATTTTTATTTTCGCGTT
Found at i:518297 original size:55 final size:54
Alignment explanation
Indices: 518213--518317 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 54
518203 TTTTAGTTTC
* * *
518213 GCGTTGCGATTTTTATTTTCGTGTTGCGATTTTCATGTTCGCATTGCGATATTT
1 GCGTTGCGATTTTTAGTTTCGCGTTGCGATTTTAATGTTCGCATTGCGATATTT
* *
518267 GCGTTGCGATTTTCTAGTTTCGCGTTGCGATTTTAATTTTCGCGTTGCGAT
1 GCGTTGCGATTTT-TAGTTTCGCGTTGCGATTTTAATGTTCGCATTGCGAT
518318 TTTCATGTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 13 0.29
55 32 0.71
ACGTcount: A:0.12, C:0.16, G:0.24, T:0.48
Consensus pattern (54 bp):
GCGTTGCGATTTTTAGTTTCGCGTTGCGATTTTAATGTTCGCATTGCGATATTT
Found at i:521649 original size:3 final size:3
Alignment explanation
Indices: 521641--521697 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
521631 TATTTATTTG
521641 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
521686 TAA TAA TAA TAA
1 TAA TAA TAA TAA
521698 ACAAAAAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:521707 original size:17 final size:17
Alignment explanation
Indices: 521648--521724 Score: 52
Period size: 19 Copynumber: 4.3 Consensus size: 17
521638 TTGTAATAAT
*
521648 AATAAT-AATAATAATAAT
1 AATAATAAATAA-AA-AAA
521666 AATAATAAATAATAATATAA
1 AATAATAAATAA-AA-A-AA
521686 TAATAAT-AATAAACAAAA
1 -AATAATAAATAAA-AAAA
*
521704 AAT-ATAAATAAAATAA
1 AATAATAAATAAAAAAA
521720 AATAA
1 AATAA
521725 ATGGATGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
16 8 0.16
17 10 0.20
18 8 0.16
19 12 0.24
20 7 0.14
21 6 0.12
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAAATAAAAAAA
Found at i:521712 original size:6 final size:5
Alignment explanation
Indices: 521645--521725 Score: 54
Period size: 6 Copynumber: 14.2 Consensus size: 5
521635 TATTTGTAAT
*
521645 AATAA TAATAA TAATAA TAATAA TAATAAA TAATAA TATAA TAATAA TAATAA
1 AATAA -AATAA -AATAA -AATAA -AAT-AA -AATAA AATAA -AATAA -AATAA
*
521698 ACAAAA AATATA AATAA AATAA AATAA A
1 A-ATAA AATA-A AATAA AATAA AATAA A
521726 TGGATGAAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
5 19 0.28
6 42 0.63
7 6 0.09
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (5 bp):
AATAA
Found at i:521724 original size:30 final size:30
Alignment explanation
Indices: 521642--521724 Score: 98
Period size: 31 Copynumber: 2.7 Consensus size: 30
521632 ATTTATTTGT
* *
521642 AATAATAATAATAATAATAATAATAATAATA
1 AATAATAATAA-AATAATAATAATAACAAAA
*
521673 AATAATAATATAATAATAATAATAAACAAAA
1 AATAATAATAAAATAATAATAAT-AACAAAA
521704 AAT-ATAAATAAAATAA-AATAA
1 AATAAT-AATAAAATAATAATAA
521725 ATGGATGAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
30 19 0.41
31 27 0.59
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (30 bp):
AATAATAATAAAATAATAATAATAACAAAA
Found at i:521726 original size:9 final size:10
Alignment explanation
Indices: 521641--521720 Score: 79
Period size: 9 Copynumber: 8.7 Consensus size: 10
521631 TATTTATTTG
521641 TAAT-AATAA
1 TAATAAATAA
521650 TAAT-AATAA
1 TAATAAATAA
521659 TAAT-AATAA
1 TAATAAATAA
521668 TAATAAATAA
1 TAATAAATAA
521678 TAATATAATAA
1 TAATA-AATAA
521689 TAAT-AATAA
1 TAATAAATAA
521698 -ACA-AAA-AA
1 TA-ATAAATAA
521706 T-ATAAATAA
1 TAATAAATAA
521715 -AATAAA
1 TAATAAA
521721 ATAAATGGAT
Statistics
Matches: 63, Mismatches: 0, Indels: 16
0.80 0.00 0.20
Matches are distributed among these distances:
7 1 0.02
8 6 0.10
9 37 0.59
10 10 0.16
11 9 0.14
ACGTcount: A:0.70, C:0.01, G:0.00, T:0.29
Consensus pattern (10 bp):
TAATAAATAA
Found at i:522165 original size:19 final size:19
Alignment explanation
Indices: 522143--522276 Score: 72
Period size: 19 Copynumber: 7.2 Consensus size: 19
522133 AGATGACGAA
*
522143 TTCTTCTCATTATAAACTC
1 TTCTTCTCATTATGAACTC
*
522162 TTCTTCTTCAGATGATGAA---
1 TTCTTC-TC--ATTATGAACTC
522181 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
* **
522200 TTCTTCTTCA-GATG-ACGAG
1 TTCTTC-TCATTATGAAC-TC
*
522219 TTCTTCTCATTATGAACTTA
1 TTCTTCTCATTATGAAC-TC
*
522239 TTCTTCTTCA-GATGAA---
1 TTCTTC-TCATTATGAACTC
522255 TTCTTCTCATTATGAACT-
1 TTCTTCTCATTATGAACTC
522273 TTCT
1 TTCT
522277 CTGGAAATGT
Statistics
Matches: 89, Mismatches: 12, Indels: 29
0.68 0.09 0.22
Matches are distributed among these distances:
15 3 0.03
16 18 0.20
18 11 0.12
19 30 0.34
20 18 0.20
21 3 0.03
22 6 0.07
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (19 bp):
TTCTTCTCATTATGAACTC
Found at i:522175 original size:38 final size:38
Alignment explanation
Indices: 522124--522276 Score: 224
Period size: 38 Copynumber: 4.1 Consensus size: 38
522114 AACAAATTCT
* *
522124 TTCTTCTTAAGATGACGAATTCTTCTCATTATAAACTC
1 TTCTTCTTCAGATGACGAATTCTTCTCATTATGAACTC
*
522162 TTCTTCTTCAGATGATGAATTCTTCTCATTATGAACTC
1 TTCTTCTTCAGATGACGAATTCTTCTCATTATGAACTC
* *
522200 TTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTTA
1 TTCTTCTTCAGATGACGAATTCTTCTCATTATGAAC-TC
522239 TTCTTCTTCAGAT---GAATTCTTCTCATTATGAACT-
1 TTCTTCTTCAGATGACGAATTCTTCTCATTATGAACTC
522273 TTCT
1 TTCT
522277 CTGGAAATGT
Statistics
Matches: 107, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
34 4 0.04
35 1 0.01
36 19 0.18
38 69 0.64
39 14 0.13
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.45
Consensus pattern (38 bp):
TTCTTCTTCAGATGACGAATTCTTCTCATTATGAACTC
Found at i:522388 original size:113 final size:112
Alignment explanation
Indices: 522219--523059 Score: 1152
Period size: 112 Copynumber: 7.5 Consensus size: 112
522209 AGATGACGAG
* *
522219 TTCTTCTCATTATGAA---CTTATT-CTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * ** *
522280 GAAATGTCAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAG
66 GAAAAGT-AATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
*
522328 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAAC-TT-TCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
522391 GAAAAGATAATCCATCAAGTGATGGATTTGAGACAAAAGGTTGATCAAA
66 GAAAAG-TAATCCATCAAGTGAT-GAATTCAGACAAAAGGTTGAACAAA
522440 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
522504 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
66 G-AAAAGTAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
522552 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
522616 GAAAAGATAATCCATCAAGTGATGGATTTGAGACAAAAGGTTGATCAAA
66 GAAAAG-TAATCCATCAAGTGAT-GAATTCAGACAAAAGGTTGAACAAA
522665 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
522729 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAAGTTGAACAAG
66 G-AAAAGTAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
* * **
522777 TTCTTCTCATTATGAACTT-TCTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACT
1 TTCTTCTCATTATGAACTTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * * * * *
522840 GGTAATGATGATCCATCAAATGATGAATTTA-AGCAAAAAGTTGAACAAG
65 GGAAAAG-TAATCCATCAAGTGATGAATTCAGA-CAAAAGGTTGAACAAA
*
522889 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
522954 GAAATGCTGATCCATCGAA-TGATGGATT-TGAGCAAAAGGTTGAACAAA
66 GAAAAG-TAATCCATC-AAGTGATGAATTCAGA-CAAAAGGTTGAACAAA
*
523002 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
523060 CGACCTGGAA
Statistics
Matches: 663, Mismatches: 48, Indels: 38
0.89 0.06 0.05
Matches are distributed among these distances:
109 16 0.02
111 61 0.09
112 294 0.44
113 282 0.43
114 10 0.02
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (112 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGTAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAA
Found at i:522644 original size:225 final size:225
Alignment explanation
Indices: 522219--523059 Score: 1256
Period size: 225 Copynumber: 3.8 Consensus size: 225
522209 AGATGACGAG
* *
522219 TTCTTCTCATTATGAA---CTTATT-CTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
** * ** *
522280 GAAATGTCAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAAC
66 GAAAAAT-AATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
522345 TTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAAC-TTTCTGGAAAAGATAATCCATCAA
130 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGATAATCCATCAA
522409 GTGATGGATTTGAGACAAAAGGTTGATCAAA
195 GTGATGGATTTGAGACAAAAGGTTGATCAAA
522440 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
522504 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 G-AAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
522569 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGATAATCCATCAA
130 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGATAATCCATCAA
522634 GTGATGGATTTGAGACAAAAGGTTGATCAAA
195 GTGATGGATTTGAGACAAAAGGTTGATCAAA
522665 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
522729 GCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAAGTTGAACAAGTTCTTCTCATTATGAAC
66 G-AAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* ** * * *
522794 TT-TCTCTT-CTTCTTCAAATGAGTTCTTCTCATTATGAACTCTAACTGGTAATGATGATCCATC
130 TTCT-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTTCTGGAAAAGATAATCCATC
* * * * * *
522857 AAATGATGAATTTAAG-CAAAAAGTTGAACAAG
193 AAGTGATGGATTTGAGACAAAAGGTTGATCAAA
*
522889 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
** * * *
522954 GAAATGCTGATCCATCGAA-TGATGGATT-TGAGCAAAAGGTTGAACAAATTCTTCTCATTATGA
66 GAAA-AATAATCCATC-AAGTGATGAATTCAGA-CAAAAGGTTGAACAAATTCTTCTCATTATGA
*
523017 ATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
128 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
523060 CGACCTGGAA
Statistics
Matches: 573, Mismatches: 33, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
221 16 0.03
224 212 0.37
225 311 0.54
226 34 0.06
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (225 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAACT
TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTTCTGGAAAAGATAATCCATCAAG
TGATGGATTTGAGACAAAAGGTTGATCAAA
Found at i:522656 original size:337 final size:334
Alignment explanation
Indices: 522219--523059 Score: 1236
Period size: 337 Copynumber: 2.5 Consensus size: 334
522209 AGATGACGAG
* *
522219 TTCTTCTCATTATGAA---CTTATT-CTTCTTCAGATGAATTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
522280 GAAATGTCAATCCATCAATTGAT-GAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAA
66 GAAATGT-AATCCATCAA-TGATGGATTTGA-GCAAAAGGTTGAACAAATTCTTCTCATTATGAA
*
522344 CTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTT-TCTGG-AAAAGATAATCCATC
128 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGCAAAA-ATAATCCATC
* * * *
522407 AAGTGATGGATTTGAGACAAAAGGTTGATCAAATTCTTCTCATTATGAAC-TTCTTCTTCCTTCT
192 AAGTGAT-GAATTCAGACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTTC-TCTT-CTTCT
* *
522471 TCAGATGAGTTCTTCTCATTATGAACTTCT-CTGGCAAAAATAATCCATCAAGTGATGAATTC-A
254 TCAAATGAGTTCTTCTCATTATGAAC-TCTACTGGCAAAAATAATCCATCAAATGATGAATTCAA
*
522534 GACAAAAGGTTGAACAAA
318 G-CAAAAAGTTGAACAAA
522552 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-TCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
522616 GAAAAGATAATCCATCAAGTGATGGATTTGAGACAAAAGGTTGATCAAATTCTTCTCATTATGAA
66 GAAATG-TAATCCATCAA-TGATGGATTTGAG-CAAAAGGTTGAACAAATTCTTCTCATTATGAA
522681 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGCAAAAATAATCCATCA
128 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGCAAAAATAATCCATCA
*
522746 AGTGATGAATTCAGACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTTCTCTTCTTCTTCAA
193 AGTGATGAATTCAGACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTTCTCTTCTTCTTCAA
* ** * *
522811 ATGAGTTCTTCTCATTATGAACTCTAACTGGTAATGATGATCCATCAAATGATGAATTTAAGCAA
258 ATGAGTTCTTCTCATTATGAACTCT-ACTGGCAAAAATAATCCATCAAATGATGAATTCAAGCAA
*
522876 AAAGTTGAACAAG
322 AAAGTTGAACAAA
*
522889 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTA
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
522954 GAAATGCTGATCCATCGAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAT
66 GAAATG-TAATCCATC-AATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAAC
523019 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
129 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
523060 CGACCTGGAA
Statistics
Matches: 463, Mismatches: 30, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
333 16 0.03
335 3 0.01
336 59 0.13
337 323 0.70
338 56 0.12
339 6 0.01
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (334 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAATGTAATCCATCAATGATGGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTCTCTGGCAAAAATAATCCATCAAGT
GATGAATTCAGACAAAAAGTTGAACAAATTCTTCTCATTATGAACTTTCTCTTCTTCTTCAAATG
AGTTCTTCTCATTATGAACTCTACTGGCAAAAATAATCCATCAAATGATGAATTCAAGCAAAAAG
TTGAACAAA
Found at i:523521 original size:22 final size:22
Alignment explanation
Indices: 523496--523550 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
523486 CATAAAGTTT
**
523496 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCCA
*
523518 TCATCTTTAAAAAGAGAATCCA
1 TCATCTTTGAAAAGAGAATCCA
523540 TCATCTTTGAA
1 TCATCTTTGAA
523551 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCCA
Found at i:524015 original size:54 final size:53
Alignment explanation
Indices: 523891--524091 Score: 232
Period size: 54 Copynumber: 3.8 Consensus size: 53
523881 CACTGGTTCA
* * *
523891 TAAAACATTTGACAATACATTCAT-CTTTTCCTGTGGTTTCTG-TC-GAG-ATG
1 TAAAACATTTGACAACACATTCATCCTTTT-CTGTGGCTTCTGCTCAGAGTTTG
*
523941 TAAAACACTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA-GTTTG
* * **
523995 TAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCA
1 TAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGA-GTTTG
* * *
524049 TAAAGCGTTTGACAACACATTCATCATTTTCTGTGGCTTCTGC
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
524092 CAAGATTTCT
Statistics
Matches: 129, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
50 33 0.26
51 7 0.05
52 2 0.02
53 5 0.04
54 78 0.60
55 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (53 bp):
TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAGTTTG
Found at i:524089 original size:108 final size:104
Alignment explanation
Indices: 523891--524091 Score: 278
Period size: 104 Copynumber: 1.9 Consensus size: 104
523881 CACTGGTTCA
* * *
523891 TAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTTGACAA
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
*
523956 CACATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
66 CACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTTG
* * **
523995 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTC-AGACGTTCATAAAGCGTTT
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTG-TCGAGACG-T-A-AAA-CACTT
524059 GACAACACATTCATCATTTTCTGTGGCTTCTGC
61 GACAACACATTCATCATTTTCTGTGGCTTCTGC
524092 CAAGATTTCT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
104 42 0.50
105 3 0.04
106 1 0.01
107 3 0.04
108 35 0.42
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (104 bp):
TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
CACATTCATCATTTTCTGTGGCTTCTGCTCAGATGTTTG
Found at i:526522 original size:115 final size:114
Alignment explanation
Indices: 526208--526548 Score: 574
Period size: 114 Copynumber: 3.0 Consensus size: 114
526198 GATCATGCAG
* * * * * *
526208 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
526273 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
* *
526322 TTCATTTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
526387 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
526436 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
526501 AACACTTCCAGAAAATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
526549 CGTGGCACTT
Statistics
Matches: 214, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
114 128 0.60
115 86 0.40
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:528827 original size:10 final size:9
Alignment explanation
Indices: 528801--528826 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
528791 ATTTTCCTTC
528801 TTTTTTTTA
1 TTTTTTTTA
528810 TTTTTTTTA
1 TTTTTTTTA
528819 TTTTTTTT
1 TTTTTTTT
528827 TTCTTTGCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:529132 original size:2 final size:2
Alignment explanation
Indices: 529125--529155 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
529115 ATAATAAAGG
529125 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
529156 AGGATAAATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:532180 original size:14 final size:14
Alignment explanation
Indices: 532142--532195 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
532132 CATAAAAATA
* *
532142 CAAATGCAAAGATG
1 CAAATGTAAATATG
532156 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
532171 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
532185 TAAATGTAAAT
1 CAAATGTAAAT
532196 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:533805 original size:15 final size:17
Alignment explanation
Indices: 533772--533813 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
533762 TTAATACCTG
*
533772 AATAAAAACAATATTAAT
1 AATAAAAATAATA-TAAT
533790 -ATAAAAATAATA-AAT
1 AATAAAAATAATATAAT
533805 AATAAAAAT
1 AATAAAAAT
533814 TTGAAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 8 0.36
17 11 0.50
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAAAATAATATAAT
Found at i:535883 original size:3 final size:3
Alignment explanation
Indices: 535875--535925 Score: 86
Period size: 3 Copynumber: 17.0 Consensus size: 3
535865 TATTTATTTG
535875 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
535920 TAA TAA
1 TAA TAA
535926 ACAAAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:535935 original size:17 final size:17
Alignment explanation
Indices: 535876--535952 Score: 52
Period size: 19 Copynumber: 4.3 Consensus size: 17
535866 ATTTATTTGT
*
535876 AATAAT-AATAATAATAAT
1 AATAATAAATAA-AA-AAA
535894 AATAATAAATAATAATATAA
1 AATAATAAATAA-AA-A-AA
535914 TAATAAT-AATAAACAAAA
1 -AATAATAAATAAA-AAAA
*
535932 AAT-ATAAATAAAATAA
1 AATAATAAATAAAAAAA
535948 AATAA
1 AATAA
535953 ATGGATGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
16 8 0.16
17 10 0.20
18 8 0.16
19 12 0.24
20 7 0.14
21 6 0.12
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAATAAATAAAAAAA
Found at i:535940 original size:6 final size:5
Alignment explanation
Indices: 535879--535953 Score: 51
Period size: 6 Copynumber: 13.2 Consensus size: 5
535869 TATTTGTAAT
* *
535879 AATAA TAATAA TAATAA TAATAAA TAATAA TATAA TAATAA TAATAA ACAAAA
1 AATAA -AATAA -AATAA -AAT-AA -AATAA AATAA -AATAA -AATAA A-ATAA
535932 AATATA AATAA AATAA AATAA A
1 AATA-A AATAA AATAA AATAA A
535954 TGGATGAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
5 19 0.31
6 36 0.59
7 6 0.10
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (5 bp):
AATAA
Found at i:535952 original size:30 final size:30
Alignment explanation
Indices: 535875--535952 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
535865 TATTTATTTG
* *
535875 TAATAATAATAATAATAATAATAATAAATAA
1 TAATAA-AATAATAATAATAACAAAAAATAA
*
535906 TAATATAATAATAATAATAAACAAAAAAT-A
1 TAATAAAATAATAATAAT-AACAAAAAATAA
535936 TAAATAAAATAA-AATAA
1 T-AATAAAATAATAATAA
535953 ATGGATGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 19 0.46
31 22 0.54
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.28
Consensus pattern (30 bp):
TAATAAAATAATAATAATAACAAAAAATAA
Found at i:536774 original size:21 final size:21
Alignment explanation
Indices: 536678--536776 Score: 94
Period size: 21 Copynumber: 4.7 Consensus size: 21
536668 AATTCACCTA
*
536678 TCATCATTCAAGAGGCACCTC
1 TCATCATTCAAGAGGCCCCTC
* *
536699 -CTATCGTTCAAGAGGCCTCTC
1 TC-ATCATTCAAGAGGCCCCTC
*
536720 TCATCA-TCGAAGAGGTCCCTC
1 TCATCATTC-AAGAGGCCCCTC
* * *
536741 TCACCATTTAAGAGGCCCCTG
1 TCATCATTCAAGAGGCCCCTC
*
536762 TCATCGTTCAAGAGG
1 TCATCATTCAAGAGG
536777 TCCCGTTAGC
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
20 3 0.05
21 56 0.92
22 2 0.03
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (21 bp):
TCATCATTCAAGAGGCCCCTC
Done.