Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008353.1 Hibiscus syriacus cultivar Beakdansim tig00111088_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: 2583621
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 13
Found at i:282884 original size:6 final size:6
Alignment explanation
Indices: 282875--282907 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
282865 CATTACCATT
282875 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
282908 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:282884 original size:18 final size:18
Alignment explanation
Indices: 282848--282884 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
282838 GAAGACACGT
**
282848 ATTACCATTACCATTACC
1 ATTACCATTACCACGACC
282866 ATTACCATTACCACGACC
1 ATTACCATTACCACGACC
282884 A
1 A
282885 CGACCACGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.35, G:0.03, T:0.27
Consensus pattern (18 bp):
ATTACCATTACCACGACC
Found at i:283434 original size:29 final size:29
Alignment explanation
Indices: 283397--283464 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
283387 CTCGTCTCGG
*
283397 GTCGGGGTCGGGGTCG-GGTCGTGGTCGTG
1 GTCGTGGTCGGGGTCGTGGTCG-GGTCGTG
*
283426 GTCGTGGTCGGGGTTGTGGTCGGGTCGTG
1 GTCGTGGTCGGGGTCGTGGTCGGGTCGTG
283455 GTCGTGGTCG
1 GTCGTGGTCG
283465 TGGTAATACG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 31 0.86
30 5 0.14
ACGTcount: A:0.00, C:0.16, G:0.56, T:0.28
Consensus pattern (29 bp):
GTCGTGGTCGGGGTCGTGGTCGGGTCGTG
Found at i:283447 original size:35 final size:35
Alignment explanation
Indices: 283396--283468 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
283386 TCTCGTCTCG
283396 GGTCGGGGTCGGGGTCGGGTCGTGGTCGTGGTCGT
1 GGTCGGGGTCGGGGTCGGGTCGTGGTCGTGGTCGT
* *
283431 GGTCGGGGTTGTGGTCGGGTCGTGGTCGTGGTCGT
1 GGTCGGGGTCGGGGTCGGGTCGTGGTCGTGGTCGT
283466 GGT
1 GGT
283469 AATACGTATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.29
Consensus pattern (35 bp):
GGTCGGGGTCGGGGTCGGGTCGTGGTCGTGGTCGT
Found at i:283465 original size:6 final size:6
Alignment explanation
Indices: 283396--283468 Score: 96
Period size: 6 Copynumber: 12.5 Consensus size: 6
283386 TCTCGTCTCG
* * * *
283396 GGTCGG GGTCGG GGTCG- GGTCGT GGTCGT GGTCGT GGTCGG GGTTGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
283443 GGTCG- GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
283469 AATACGTATC
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
5 10 0.16
6 51 0.84
ACGTcount: A:0.00, C:0.15, G:0.56, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:283581 original size:19 final size:19
Alignment explanation
Indices: 283557--283623 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
283547 TCGTTGCGAT
283557 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
* * *
283576 TTTGGAATAAATCACAACGCGAC
1 TTTGGACT--ATCGCAA--CGAA
* *
283599 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
283618 TTTGGA
1 TTTGGA
283624 AAATCACAAC
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
19 14 0.41
21 12 0.35
23 8 0.24
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:284020 original size:2 final size:2
Alignment explanation
Indices: 284013--284038 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
284003 TGAATTTTAA
284013 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
284039 TCATTTTGTA
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:284342 original size:31 final size:31
Alignment explanation
Indices: 284304--284365 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
284294 GGGTATATCG
284304 CACTGACTACAGTACGTCTTCACTCCCATGA
1 CACTGACTACAGTACGTCTTCACTCCCATGA
*
284335 CACTGACTACAGTGCGTCTTCACTCCCATGA
1 CACTGACTACAGTACGTCTTCACTCCCATGA
284366 GTGTGTCGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (31 bp):
CACTGACTACAGTACGTCTTCACTCCCATGA
Found at i:288888 original size:6 final size:6
Alignment explanation
Indices: 288877--288901 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
288867 TCAGTCGGTG
288877 ATGCAC ATGCAC ATGCAC ATGCAC A
1 ATGCAC ATGCAC ATGCAC ATGCAC A
288902 ATCAGAGGTG
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:0.32, G:0.16, T:0.16
Consensus pattern (6 bp):
ATGCAC
Found at i:291417 original size:17 final size:17
Alignment explanation
Indices: 291395--291435 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
291385 CCGATTCTAC
291395 TTTTCCAGTCATTGTCT
1 TTTTCCAGTCATTGTCT
291412 TTTTCCAGTCATTGTCT
1 TTTTCCAGTCATTGTCT
291429 TTTTCCA
1 TTTTCCA
291436 CGGTGGGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.10, T:0.54
Consensus pattern (17 bp):
TTTTCCAGTCATTGTCT
Found at i:292395 original size:21 final size:21
Alignment explanation
Indices: 292371--292411 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
292361 ATTGATCGTG
292371 ATATTAATATGATAATCTATA
1 ATATTAATATGATAATCTATA
*
292392 ATATTAATATGATAGTCTAT
1 ATATTAATATGATAATCTAT
292412 TATTATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (21 bp):
ATATTAATATGATAATCTATA
Found at i:292810 original size:29 final size:29
Alignment explanation
Indices: 292768--292823 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
292758 GTCCCCATAT
292768 AGGTCGCCATGCACGCCCAGCGACCTACC
1 AGGTCGCCATGCACGCCCAGCGACCTACC
292797 AGGTCGCCATGCACGCCCAGCGACCTA
1 AGGTCGCCATGCACGCCCAGCGACCTA
292824 GGTAAGTCGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.43, G:0.25, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCAGCGACCTACC
Found at i:292835 original size:30 final size:29
Alignment explanation
Indices: 292770--292839 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
292760 CCCCATATAG
*
292770 GTCGCCATGCACGCCCAGCGACCTACCAG
1 GTCGCCATGCACGCCCAGCGACCTACCAA
**
292799 GTCGCCATGCACGCCCAGCGACCTAGGTAA
1 GTCGCCATGCACGCCCAGCGACCTA-CCAA
292829 GTCGCCATGCA
1 GTCGCCATGCA
292840 ATCCATGCAG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 25 0.68
30 12 0.32
ACGTcount: A:0.21, C:0.40, G:0.26, T:0.13
Consensus pattern (29 bp):
GTCGCCATGCACGCCCAGCGACCTACCAA
Found at i:292900 original size:10 final size:10
Alignment explanation
Indices: 292887--292943 Score: 82
Period size: 10 Copynumber: 5.7 Consensus size: 10
292877 ACACGCTGGG
292887 CATCCGAGGC
1 CATCCGAGGC
292897 CATCCGAGAG-
1 CATCCGAG-GC
292907 CATCCGAGGC
1 CATCCGAGGC
292917 CATCCGAGAG-
1 CATCCGAG-GC
292927 CATCCGAGGC
1 CATCCGAGGC
292937 CATCCGA
1 CATCCGA
292944 ACGAGCTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
9 2 0.05
10 39 0.91
11 2 0.05
ACGTcount: A:0.25, C:0.37, G:0.28, T:0.11
Consensus pattern (10 bp):
CATCCGAGGC
Found at i:292911 original size:20 final size:20
Alignment explanation
Indices: 292886--292943 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
292876 AACACGCTGG
292886 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
292906 GCATCCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAGA
292926 GCATCCGAGGCCATCCGA
1 GCATCCGAGGCCATCCGA
292944 ACGAGCTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.24, C:0.36, G:0.29, T:0.10
Consensus pattern (20 bp):
GCATCCGAGGCCATCCGAGA
Found at i:292982 original size:33 final size:32
Alignment explanation
Indices: 292921--293012 Score: 105
Period size: 33 Copynumber: 2.8 Consensus size: 32
292911 CGAGGCCATC
* * * *
292921 CGAGAGCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGGGCATCC-AGGGCAACCGAGCGAGCTATG
292954 CGAGGGCATCCAAGGGCAACCGAGCGAGCTATG
1 CGAGGGCATCC-AGGGCAACCGAGCGAGCTATG
* *
292987 CGAGGGAATCC-GAGCAACCGAGCGAG
1 CGAGGGCATCCAGGGCAACCGAGCGAG
293013 GGTAGGTCGC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
31 14 0.27
33 38 0.73
ACGTcount: A:0.28, C:0.28, G:0.35, T:0.09
Consensus pattern (32 bp):
CGAGGGCATCCAGGGCAACCGAGCGAGCTATG
Found at i:293118 original size:23 final size:23
Alignment explanation
Indices: 293059--293118 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
293049 CTCGGTTGCC
* *
293059 CTCGGATTCCCTCACATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
293082 CTCGGATGCCCTCGCATAGCTCG
1 CTCGGATGCCCTCGCATAGCTCG
* *
293105 TTCGGATGGCCTCG
1 CTCGGATGCCCTCG
293119 GTCGGATGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.13, C:0.37, G:0.25, T:0.25
Consensus pattern (23 bp):
CTCGGATGCCCTCGCATAGCTCG
Found at i:296714 original size:2 final size:2
Alignment explanation
Indices: 296697--296731 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
296687 GTTATCAAAT
* *
296697 TA TA CA TA TA TC TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
296732 TATGGAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:301991 original size:13 final size:13
Alignment explanation
Indices: 301973--301997 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
301963 CTTAGTTGCG
301973 AAAATTTAAATTT
1 AAAATTTAAATTT
301986 AAAATTTAAATT
1 AAAATTTAAATT
301998 CAAATTATTC
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:302172 original size:19 final size:19
Alignment explanation
Indices: 302150--302216 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 19
302140 AAAAACAACG
302150 AATAAAAAGGAAAAAAAAA
1 AATAAAAAGGAAAAAAAAA
* * *
302169 AATATAATAA-TAAGAAAATA
1 AATA-AA-AAGGAAAAAAAAA
*
302189 AATCAAAAAGGAGAAAAAGAA
1 AAT-AAAAAGGA-AAAAAAAA
302210 AATAAAA
1 AATAAAA
302217 TAAACCAAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 9
0.69 0.13 0.17
Matches are distributed among these distances:
19 6 0.17
20 19 0.53
21 11 0.31
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.12
Consensus pattern (19 bp):
AATAAAAAGGAAAAAAAAA
Found at i:302906 original size:19 final size:18
Alignment explanation
Indices: 302867--302909 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
302857 TGCTTGGCTC
*
302867 TTTGTTGTTTTTTGTATT
1 TTTGTTGTTTTTTGTAGT
302885 TTTGTGTGTTTTTATG-AGT
1 TTTGT-TGTTTTT-TGTAGT
302904 TTTGTT
1 TTTGTT
302910 TTGGCCTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 6 0.27
19 14 0.64
20 2 0.09
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.72
Consensus pattern (18 bp):
TTTGTTGTTTTTTGTAGT
Found at i:303514 original size:19 final size:21
Alignment explanation
Indices: 303484--303522 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
303474 ATCAGACCTA
303484 AAATGAAATAAACAA-AAAAG
1 AAATGAAATAAACAATAAAAG
303504 AAATG-AATAAACAATAAAA
1 AAATGAAATAAACAATAAAA
303523 ATAATACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.74, C:0.05, G:0.08, T:0.13
Consensus pattern (21 bp):
AAATGAAATAAACAATAAAAG
Found at i:303679 original size:38 final size:36
Alignment explanation
Indices: 303627--303891 Score: 166
Period size: 37 Copynumber: 7.2 Consensus size: 36
303617 TCAAATAATA
*
303627 TTTTAAAATTATATATTATATATATTTTTTAAAAATG
1 TTTTAAAATCATATATTATATATA-TTTTTAAAAATG
* *
303664 TTTTCAAAATCATATA-T-TATATAGTTTTCAAAATG
1 TTTT-AAAATCATATATTATATATATTTTTAAAAATG
* * * *
303699 TTTTAAAAAC-TATA-CAT-TATACATTTTCAAAATG
1 TTTTAAAATCATATATTATATATA-TTTTTAAAAATG
*
303733 TTTTTAAAAACCATATATTATATATA-TTTTAAAAATG
1 -TTTT-AAAATCATATATTATATATATTTTTAAAAATG
** ** **
303770 TTTTTAAAAAAAATCATATTATATATATTTCAAAAAAAA
1 -TTTT-AAAATCAT-ATATTATATATATTTTTAAAAATG
** * * *
303809 AATTAAACT-ATATAATATATATATTTTTTTAAAATATT
1 TTTTAAAATCATAT-AT-TATATATATTTTTAAAA-ATG
** * *
303847 TTTTAAACCCATATATTATATATATTTTCAAAAATA
1 TTTTAAAATCATATATTATATATATTTTTAAAAATG
303883 TTTTCAAAA
1 TTTT-AAAA
303892 ACTATACACT
Statistics
Matches: 182, Mismatches: 31, Indels: 30
0.75 0.13 0.12
Matches are distributed among these distances:
33 8 0.04
34 17 0.09
35 20 0.11
36 21 0.12
37 66 0.36
38 35 0.19
39 15 0.08
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (36 bp):
TTTTAAAATCATATATTATATATATTTTTAAAAATG
Found at i:303718 original size:35 final size:35
Alignment explanation
Indices: 303643--303805 Score: 161
Period size: 35 Copynumber: 4.6 Consensus size: 35
303633 AATTATATAT
* * *
303643 TATA-TATATTTTTTAAAAATGTTTTCAAAATC-A
1 TATATTATATATTTTAAAAATGTTTTTAAAAACTA
*
303676 TATATTATATAGTTTTCAAAATG-TTTTAAAAACTA
1 TATATTATATA-TTTTAAAAATGTTTTTAAAAACTA
* * * *
303711 TACATTATACATTTTCAAAATGTTTTTAAAAACCA
1 TATATTATATATTTTAAAAATGTTTTTAAAAACTA
**
303746 TATATTATATATATTTTAAAAATGTTTTTAAAAAAAA
1 TATA-T-TATATATTTTAAAAATGTTTTTAAAAACTA
303783 TCATATTATATATATTTCAAAAA
1 T-ATATTATATAT-TTT-AAAAA
303806 AAAAATTAAA
Statistics
Matches: 109, Mismatches: 12, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
33 4 0.04
34 24 0.22
35 34 0.31
36 8 0.07
37 31 0.28
38 8 0.07
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (35 bp):
TATATTATATATTTTAAAAATGTTTTTAAAAACTA
Found at i:303885 original size:12 final size:12
Alignment explanation
Indices: 303868--303921 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 12
303858 TATATTATAT
303868 ATATTTTCAAAA
1 ATATTTTCAAAA
303880 ATATTTTCAAAA
1 ATATTTTCAAAA
*
303892 ACTATACACTTTTAAAA
1 A-TAT----TTTCAAAA
303909 ATATTTTCAAAA
1 ATATTTTCAAAA
303921 A
1 A
303922 ACTATATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
12 21 0.60
13 3 0.09
16 3 0.09
17 8 0.23
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (12 bp):
ATATTTTCAAAA
Found at i:303924 original size:30 final size:30
Alignment explanation
Indices: 303871--303927 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
303861 ATTATATATA
303871 TTTTCAAAAATATTTTCAAAAACTATACAC
1 TTTTCAAAAATATTTTCAAAAACTATACAC
303901 TTTT-AAAAATATTTTCAAAAAACTATA
1 TTTTCAAAAATATTTTC-AAAAACTATA
303928 TTATATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTTCAAAAATATTTTCAAAAACTATACAC
Found at i:312138 original size:25 final size:25
Alignment explanation
Indices: 312104--312161 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
312094 TACTAAGGCA
*
312104 GTTCTACAAGTTTCCATTGCTCATT
1 GTTCTACAAGTTTCCATTGCCCATT
*
312129 GTTCTACAAGTTTCCATTGCCCCTT
1 GTTCTACAAGTTTCCATTGCCCATT
312154 GTTCTACA
1 GTTCTACA
312162 GATATAATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.19, C:0.28, G:0.12, T:0.41
Consensus pattern (25 bp):
GTTCTACAAGTTTCCATTGCCCATT
Found at i:316755 original size:7 final size:7
Alignment explanation
Indices: 316737--316771 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
316727 TTTAAATATA
316737 TATATATT
1 TATAT-TT
316745 TATATTT
1 TATATTT
316752 TATATTTT
1 TATA-TTT
316760 TATATTT
1 TATATTT
316767 TATAT
1 TATAT
316772 CATCTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 14 0.54
8 12 0.46
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TATATTT
Found at i:316761 original size:15 final size:15
Alignment explanation
Indices: 316737--316785 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
316727 TTTAAATATA
316737 TATATATTTATATTT
1 TATATATTTATATTT
*
316752 TATATTTTTATATTT
1 TATATATTTATATTT
316767 TATATCATCTT-TATTT
1 TATAT-AT-TTATATTT
316783 TAT
1 TAT
316786 TTGTCACGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 19 0.63
16 9 0.30
17 2 0.07
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATATTTATATTT
Found at i:322714 original size:17 final size:16
Alignment explanation
Indices: 322692--322725 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
322682 TTAATCGCAG
322692 TAATTCATACATACACA
1 TAATTCAT-CATACACA
*
322709 TAATTCATCATTCACA
1 TAATTCATCATACACA
322725 T
1 T
322726 GTTATCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTCATCATACACA
Found at i:322972 original size:21 final size:22
Alignment explanation
Indices: 322915--322980 Score: 107
Period size: 21 Copynumber: 3.0 Consensus size: 22
322905 CTCGTATAAA
322915 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
322938 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
322960 TGCA-CGTAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
322981 GTCCATAAGG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
21 16 0.38
22 14 0.33
23 12 0.29
ACGTcount: A:0.26, C:0.27, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:324650 original size:21 final size:21
Alignment explanation
Indices: 324626--324670 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
324616 TCTTGTTCGT
* *
324626 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
324647 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
324668 TTG
1 TTG
324671 CCCAGAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:327673 original size:17 final size:16
Alignment explanation
Indices: 327651--327684 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
327641 TTAATCGCAG
327651 TAATTCATACATACACA
1 TAATTCAT-CATACACA
*
327668 TAATTCATCATTCACA
1 TAATTCATCATACACA
327684 T
1 T
327685 GTTATCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.41, C:0.24, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATTCATCATACACA
Found at i:327937 original size:23 final size:22
Alignment explanation
Indices: 327876--327939 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 22
327866 CTCGTATAAA
327876 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
327899 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
327921 TGCACCCGTAGTGCCCGTA
1 TGCA-CCGAAGTGCCCGTA
327940 AATGATGTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
22 14 0.36
23 25 0.64
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:329493 original size:21 final size:20
Alignment explanation
Indices: 329463--329506 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
329453 TTCTTGTTCG
* *
329463 TTGAAGGGTATCGGTTCCCC
1 TTGAAGGGTACCGATTCCCC
329483 TTGAATGGGTACCGATTCCCC
1 TTGAA-GGGTACCGATTCCCC
329504 TTG
1 TTG
329507 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (20 bp):
TTGAAGGGTACCGATTCCCC
Found at i:337240 original size:24 final size:23
Alignment explanation
Indices: 337199--337244 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
337189 TTTTAGAGAC
*
337199 TAATTTATAAATTTTAATATTATA
1 TAATTTATAAATTATAAT-TTATA
337223 TAATTTATAACA-TATAATTTAT
1 TAATTTATAA-ATTATAATTTAT
337245 CCAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 15 0.75
25 1 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TAATTTATAAATTATAATTTATA
Found at i:339886 original size:280 final size:274
Alignment explanation
Indices: 339354--339855 Score: 672
Period size: 280 Copynumber: 1.8 Consensus size: 274
339344 ATTTTTATTC
* *
339354 AATATATGAATTAGAAACCCGACACGACACAAAATAATAAAAAAAAATTATTCAATAAAAATATT
1 AATATATGAATTAGAAACCCGACACGACACAAAATAATAAAAAAAAATTATTCAATAAAAACAGT
* * *
339419 GACTTAATTGAAAAAATATATATAGGGGTATTATTGTAATTATTCTTAAATATTTAAGGTAAAAT
66 GACTTAATTGAAAAAATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAAT
* * *
339484 TATATATTTTCTCCAGGTCGGTCCGATTTTTTTCACCCTAAACCCGAACCGACCTGAATATCACA
131 TATATATTTTCTCCAGGTCGG--CGATATTTTTCACCCTAAACCCGAACCGACCCGAAAATCACA
* * * *
339549 CTTAAAAAAACCCGACCTGACTCGACCCGAATATCACACTTAAAAAACCCGACCCGAACAAAATA
194 CTTAAAAAAACCCGACCCGACCCGACCCGAAAATCAAACTTAAAAAACCCGACCCGAA-AAAATA
339614 AAGTTTCACCCGACCAG
258 AAGTTTCACCCGACCAG
* * * * * *
339631 AATATATGAATTAGAAATCTGACCCGACCCGAAATAATAAAAAAATATTTTTATTCAATAAAAAC
1 AATATATGAATTAGAAACCCGACACGACACAAAATAATAAAAAAA-A--ATTATTCAATAAAAAC
339696 AGTGACTTAATTGAAAAAATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAA
63 AGTGACTTAATTGAAAAAATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAA
*
339761 AATTATATATATTT-T-CGGGTCGG-G-TATTTTTCACCCTAAACCCGAACTCGACCCGACCCGA
128 AATTATATAT-TTTCTCCAGGTCGGCGATATTTTTCACCCTAAACCCG-A----A-CCGACCCGA
*
339822 AAATCACACTTAAAAAAA-CTGACCCGACCCGACC
186 AAATCACACTTAAAAAAACCCGACCCGACCCGACC
339856 AAAATAAAGT
Statistics
Matches: 197, Mismatches: 18, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
275 19 0.10
276 2 0.01
277 40 0.20
278 1 0.01
279 7 0.04
280 100 0.51
281 28 0.14
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (274 bp):
AATATATGAATTAGAAACCCGACACGACACAAAATAATAAAAAAAAATTATTCAATAAAAACAGT
GACTTAATTGAAAAAATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAAT
TATATATTTTCTCCAGGTCGGCGATATTTTTCACCCTAAACCCGAACCGACCCGAAAATCACACT
TAAAAAAACCCGACCCGACCCGACCCGAAAATCAAACTTAAAAAACCCGACCCGAAAAAATAAAG
TTTCACCCGACCAG
Found at i:351814 original size:29 final size:29
Alignment explanation
Indices: 351779--351854 Score: 125
Period size: 29 Copynumber: 2.6 Consensus size: 29
351769 TCCCTAAGCA
* *
351779 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCAACCTTG
*
351808 TAGGTCGCCATACACTCCGGGCAACCTTG
1 TAGGTCGCCATGCACTCCGGGCAACCTTG
351837 TAGGTCGCCATGCACTCC
1 TAGGTCGCCATGCACTCC
351855 CTCCTGCTCC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.16, C:0.37, G:0.26, T:0.21
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCAACCTTG
Found at i:355112 original size:14 final size:14
Alignment explanation
Indices: 355088--355123 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
355078 CTATATGTGT
355088 AATTATAAAAATAAA
1 AATT-TAAAAATAAA
355103 AATTTAAAAATAAA
1 AATTTAAAAATAAA
355117 AATTTAA
1 AATTTAA
355124 TTTAAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AATTTAAAAATAAA
Found at i:355363 original size:21 final size:21
Alignment explanation
Indices: 355334--355380 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
355324 ATTCTGACTA
355334 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
355355 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
355376 TCGCA
1 TCGCA
355381 ATGTGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:355401 original size:20 final size:20
Alignment explanation
Indices: 355376--355467 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
355366 TTTTCCTAAT
*
355376 TCGCAATGTGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
355396 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
355417 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
355437 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
355457 TCGCAATGCGA
1 TCGCAATGCGA
355468 TTTACATAGC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 45 0.75
21 15 0.25
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:356062 original size:20 final size:20
Alignment explanation
Indices: 356037--356083 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
356027 CAACGAGTGA
356037 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
356057 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
356077 ATCGCAA
1 ATCGCAA
356084 CGAGAGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:356168 original size:20 final size:20
Alignment explanation
Indices: 356098--356184 Score: 95
Period size: 20 Copynumber: 4.4 Consensus size: 20
356088 AGAATCGCAA
356098 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
356117 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
356137 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
356157 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
356177 TGCGATTT
1 TGCGATTT
356185 AAAGTTTCAG
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 9 0.15
20 50 0.85
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:356192 original size:20 final size:20
Alignment explanation
Indices: 356149--356192 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
356139 CGATAGTCAT
** *
356149 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
356169 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
356189 TTTC
1 TTTC
356193 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:358087 original size:20 final size:20
Alignment explanation
Indices: 358062--358165 Score: 157
Period size: 20 Copynumber: 5.5 Consensus size: 20
358052 AGAATAGTTT
358062 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
358082 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
358098 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
358116 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
358136 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
358156 ACTATCGCAA
1 ACTATCGCAA
358166 CGAAAGAATC
Statistics
Matches: 76, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 7 0.09
16 4 0.05
17 4 0.05
18 4 0.05
20 57 0.75
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.18
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:358108 original size:34 final size:34
Alignment explanation
Indices: 358065--358186 Score: 172
Period size: 34 Copynumber: 3.4 Consensus size: 34
358055 ATAGTTTACT
*
358065 ATCGCAATGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
358099 ATCGCAATGCGAAAATGACTATCGCAATGCGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
358137 CTATCGCAATGCGAAAATGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
*
358173 ATCTCAATGCGAAA
1 ATCGCAATGCGAAA
358187 TGAAAATCGC
Statistics
Matches: 80, Mismatches: 2, Indels: 12
0.85 0.02 0.13
Matches are distributed among these distances:
34 40 0.50
36 4 0.05
37 5 0.06
38 4 0.05
40 27 0.34
ACGTcount: A:0.42, C:0.20, G:0.20, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:358183 original size:74 final size:73
Alignment explanation
Indices: 358062--358203 Score: 230
Period size: 74 Copynumber: 1.9 Consensus size: 73
358052 AGAATAGTTT
* **
358062 ACTATCGCAATGCGAAAATGACTATCGCAACGAGAGAATCGCAATGCGAAAATGACTATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCG-AAATGAAAATCGCAAT
358127 GCGAAAATG
65 GCGAAAATG
* *
358136 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCTCAATGCGAAATGAAAATCGCATTG
1 ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATG
358201 CGA
66 CGA
358204 TTCTCTCGTT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
73 17 0.27
74 46 0.73
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (73 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATG
CGAAAATG
Found at i:358237 original size:20 final size:20
Alignment explanation
Indices: 358212--358258 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
358202 GATTCTCTCG
358212 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
* ** *
358232 TTGCGAAAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
358252 TTGCGAT
1 TTGCGAT
358259 TTTGTTGTTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:358289 original size:33 final size:34
Alignment explanation
Indices: 358232--358325 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
358222 CAAATTCGCA
* * * *
358232 TTGCGAAAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
** *
358266 TTGCGATTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
358299 TTGCGATAGTCATTTTCGCGTTGCGAT
1 TTGCGATAGTCATTTTCGCGTTGCGAT
358326 AGTCATTTGC
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
33 27 0.55
34 22 0.45
ACGTcount: A:0.14, C:0.19, G:0.23, T:0.44
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCGTTGCGATTCTCTCG
Found at i:358900 original size:21 final size:21
Alignment explanation
Indices: 358809--358907 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
358799 GACTCACCTG
*
358809 TCATCGTTCAAGAGGCCTC-C
1 TCATCGTTCAAGAGGCCACTC
* * *
358829 CCTATCGTTCAAGAGGCCTCTA
1 TC-ATCGTTCAAGAGGCCACTC
** *
358851 TCATCCCTCAAGAGTCCACTC
1 TCATCGTTCAAGAGGCCACTC
* * *
358872 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCACTC
*
358893 TCATCGTTGAAGAGG
1 TCATCGTTCAAGAGG
358908 TCCCTCCCAA
Statistics
Matches: 60, Mismatches: 17, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 1 0.02
21 58 0.97
22 1 0.02
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCACTC
Found at i:358906 original size:42 final size:41
Alignment explanation
Indices: 358806--358916 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 41
358796 CCCGACTCAC
* * *
358806 CTGTCATCGTTCAAGAG-GCCTCCCCTATCGTTCAAGAGGCCT
1 CTGTCATCGTTCAAGAGTCCCT-CCC-ACCGTTCAAGAGGCCA
* **
358848 CTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCC-CTCCCACCGTTCAAGAGGCCA
*
358890 CTGTCATCGTTGAAGAGGTCCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCTCCCA
358917 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
42 46 0.82
43 8 0.14
44 2 0.04
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGTCCCTCCCACCGTTCAAGAGGCCA
Found at i:360289 original size:14 final size:14
Alignment explanation
Indices: 360270--360305 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
360260 ATTGTTTAAT
360270 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
360284 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
360298 TGATTTGT
1 TGATTTGT
360306 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:360502 original size:33 final size:33
Alignment explanation
Indices: 360440--360535 Score: 122
Period size: 33 Copynumber: 2.8 Consensus size: 33
360430 GCAAATTTCG
*
360440 CGTTGCGATTTTCATTTTCACATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
360474 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* *
360507 CGTTGCG-TTAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATT-TTCATTT-CGCATTGCGAT
360536 AGTCAATTCC
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 2 0.04
33 30 0.54
34 24 0.43
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:360532 original size:20 final size:20
Alignment explanation
Indices: 360507--360595 Score: 126
Period size: 20 Copynumber: 4.5 Consensus size: 20
360497 GCGATTCTCT
*
360507 CGTTGCGTTAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
360527 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
360547 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
360567 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
360587 CGTTGCGAT
1 CGTTGCGAT
360596 TTCCGCGTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 59 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:363067 original size:24 final size:24
Alignment explanation
Indices: 363040--363086 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
363030 CAAAATCCGA
363040 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
363064 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
363087 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:363095 original size:24 final size:24
Alignment explanation
Indices: 363044--363095 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
363034 ATCCGAGTAT
** *
363044 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
363068 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
363092 TGAC
1 TGAC
363096 TAGTATTTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:363882 original size:40 final size:38
Alignment explanation
Indices: 363837--363964 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 38
363827 GAAATTCAGT
363837 ATTGCGATAGTCAGAATCTCGTTGCGATTTACAG-ATTCGC
1 ATTGCGAT--TCAGAATCTCGTTGCGATTTAC-GTATTCGC
* * *
363877 ATTGCGATTTACGTAT-TCGCATTGCGATTTACGTAATCGC
1 ATTGCGATTCA-GAATCTCG--TTGCGATTTACGTATTCGC
*
363917 ATTGCGATTTTCCA-AATTCGCGTTGCGATTTACGTATTCGC
1 ATTGCGA--TT-CAGAA-TCTCGTTGCGATTTACGTATTCGC
363958 ATTGCGA
1 ATTGCGA
363965 ATTAGGAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 17
0.75 0.07 0.18
Matches are distributed among these distances:
38 5 0.07
39 4 0.06
40 31 0.43
41 26 0.36
42 3 0.04
43 3 0.04
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (38 bp):
ATTGCGATTCAGAATCTCGTTGCGATTTACGTATTCGC
Found at i:363948 original size:41 final size:40
Alignment explanation
Indices: 363856--363964 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 40
363846 GTCAGAATCT
**
363856 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCGCATTGCGATTTACAAATTCG
* * *
363896 CATTGCGATTTACGTAATCGCATTGCGATTTTCCAAATTCG
1 CGTTGCGATTTACGTATTCGCATTGCGA-TTTACAAATTCG
363937 CGTTGCGATTTACGTATTCGCATTGCGA
1 CGTTGCGATTTACGTATTCGCATTGCGA
363965 ATTAGGAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.02
40 24 0.40
41 35 0.58
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCATTGCGATTTACAAATTCG
Found at i:363957 original size:20 final size:20
Alignment explanation
Indices: 363858--363964 Score: 144
Period size: 20 Copynumber: 5.3 Consensus size: 20
363848 CAGAATCTCG
363858 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
363878 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
*
363898 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTATTCGCA
* ** *
363918 TTGCGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGTATTCGCA
363939 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
363959 TTGCGA
1 TTGCGA
363965 ATTAGGAAAA
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 1 0.01
20 59 0.79
21 15 0.20
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:363985 original size:21 final size:21
Alignment explanation
Indices: 363961--364006 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
363951 TATTCGCATT
363961 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
363982 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
364003 GCGA
1 GCGA
364007 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:364473 original size:15 final size:15
Alignment explanation
Indices: 364453--364492 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
364443 AAATGATTTG
*
364453 CTCTGATTTTCGCTT
1 CTCTGATTTTCGATT
364468 CTCTGATTTTCGATT
1 CTCTGATTTTCGATT
364483 CTCTGATTTT
1 CTCTGATTTT
364493 ATATTTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.23, G:0.12, T:0.55
Consensus pattern (15 bp):
CTCTGATTTTCGATT
Found at i:373797 original size:20 final size:20
Alignment explanation
Indices: 373772--373900 Score: 99
Period size: 20 Copynumber: 7.2 Consensus size: 20
373762 TTTTGGTTGA
*
373772 AATGAAAATTGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
373792 AATGAAAATCGCAACGCAGA-
1 AATGAAAATCGCAACG-AGAG
**
373812 AATGACTATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
*
373830 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
373845 AATGAAAATCGCAAC--GAG
1 AATGAAAATCGCAACGAGAG
*
373863 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
373878 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
373898 AAT
1 AAT
373901 CGTAACGCGA
Statistics
Matches: 88, Mismatches: 5, Indels: 32
0.70 0.04 0.26
Matches are distributed among these distances:
14 17 0.19
16 8 0.09
17 8 0.09
19 21 0.24
20 31 0.35
21 3 0.03
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:373838 original size:14 final size:14
Alignment explanation
Indices: 373819--373907 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
373809 AGAAATGACT
373819 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
373833 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
373852 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
373866 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
373885 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
373899 ATCGTAACG
1 ATCGCAACG
373908 CGAAATAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
14 28 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:373856 original size:19 final size:19
Alignment explanation
Indices: 373770--373929 Score: 107
Period size: 19 Copynumber: 9.1 Consensus size: 19
373760 TCTTTTGGTT
* *
373770 GAAATGAAAATTGCAACGA
1 GAAATGAAAATCGCAACGC
373789 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
373809 AGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
373827 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
373843 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
373860 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
373876 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
* *
373893 G--A-GAGAATCGTAACGC
1 GAAATGAAAATCGCAACGC
* *
373909 GAAATAAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
373928 GA
1 GA
373930 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
14 28 0.26
15 3 0.03
16 6 0.06
17 5 0.05
18 4 0.04
19 34 0.31
20 27 0.25
21 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:373856 original size:33 final size:33
Alignment explanation
Indices: 373798--373924 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
373788 AGAGAATGAA
**
373798 AATCGCAACGCAGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
373832 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
373865 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
373898 AATCGTAACGCGAAATAAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
373925 TGCGATTTTG
Statistics
Matches: 89, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
33 78 0.88
34 11 0.12
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:373958 original size:19 final size:19
Alignment explanation
Indices: 373925--374017 Score: 96
Period size: 19 Copynumber: 4.7 Consensus size: 19
373915 AAAATCGCAA
**
373925 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
373944 TGCGATTTTCATTTCTCGT
1 TGCGATTTTCATTTCGCGT
*
373963 TGCGATTTTCATTTCTCTCGT
1 TGCGATTTTCA-TT-TCGCGT
** *
373984 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCA-TTTCGCGT
374004 TGCGATTTTCATTT
1 TGCGATTTTCATTT
374018 TCATGTTGCA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
19 30 0.48
20 15 0.24
21 18 0.29
ACGTcount: A:0.11, C:0.18, G:0.20, T:0.51
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:374032 original size:20 final size:20
Alignment explanation
Indices: 373942--374026 Score: 95
Period size: 20 Copynumber: 4.2 Consensus size: 20
373932 TTGGTTTCGC
373942 GTTGCGATTTTCA-TTTC-T
1 GTTGCGATTTTCATTTTCAT
373960 CGTTGCGATTTTCATTTCTC-T
1 -GTTGCGATTTTCATTT-TCAT
** *
373981 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
374002 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
374022 GTTGC
1 GTTGC
374027 AGTTTTAAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
19 13 0.22
20 26 0.45
21 19 0.33
ACGTcount: A:0.12, C:0.19, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:374619 original size:20 final size:19
Alignment explanation
Indices: 374594--374845 Score: 172
Period size: 20 Copynumber: 12.6 Consensus size: 19
374584 CTTTAAAAAT
374594 CGCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTAC-GATA
374614 CGCGTTGCGATTTTACG-TA
1 CGCGTTGCGA-TTTACGATA
* *
374633 TTGTTGTTGCGATTTACGGATA
1 -CG-CGTTGCGATTTAC-GATA
* *
374655 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACG-ATA
*
374675 CTCGTTGCGATTTACAGAT-
1 CGCGTTGCGATTTAC-GATA
* *
374694 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACG-ATA
*
374714 CTCGTTGCGATTTACAGAT-
1 CGCGTTGCGATTTAC-GATA
* *
374733 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACG-ATA
* *
374753 CGCATTGTGATTTACG-TAA
1 CGCGTTGCGATTTACGAT-A
374772 TCGCGTTGCGATTTTACG-TA
1 -CGCGTTGCGA-TTTACGATA
* *
374792 TTGTCATTGCGATTTACGGATA
1 -CG-CGTTGCGATTTAC-GATA
374814 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTAC-GATA
*
374835 CTCGTTGCGAT
1 CGCGTTGCGAT
374846 AGTCAGAATC
Statistics
Matches: 190, Mismatches: 23, Indels: 38
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.02
19 33 0.17
20 99 0.52
21 51 0.27
22 4 0.02
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (19 bp):
CGCGTTGCGATTTACGATA
Found at i:374843 original size:41 final size:40
Alignment explanation
Indices: 374596--374906 Score: 301
Period size: 41 Copynumber: 7.8 Consensus size: 40
374586 TTAAAAATCG
* *
374596 CGTTGCGATTTACAGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGATACGCATTGCGA-TTTACGTATTCT
* *
374637 TGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCT
374677 CGTTGCGATTTACAGAT-CGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCT
*
374716 CGTTGCGATTTACAGAT-CGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCT
* * * *
374755 CATTGTGATTTAC-G-TAATCGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACAGAT-A-CGCATTGCGA-TTTACGTATTCT
* * * * *
374796 CATTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACAGATACGCATTGCGA-TTTACGTATTCT
* * ** * *
374837 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGAT-TTACAGATA-CGCATTGCGATTTACGTATTCT
* * * *
374877 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACAGATACGCATTGCGATT
374907 ATGGAAAATC
Statistics
Matches: 232, Mismatches: 28, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 72 0.31
40 66 0.28
41 88 0.38
42 3 0.01
43 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACAGATACGCATTGCGATTTACGTATTCT
Found at i:374877 original size:20 final size:20
Alignment explanation
Indices: 374854--374906 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
374844 ATAGTCAGAA
*
374854 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
374874 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
374894 TCGCGTTGCGATT
1 TCGCGTTGCGATT
374907 ATGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:379490 original size:16 final size:17
Alignment explanation
Indices: 379449--379492 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
379439 AATAGTAAAA
*
379449 AATAAT-AATTTACTAT
1 AATAATAAATATACTAT
*
379465 AATAAAAAATATACTAT
1 AATAATAAATATACTAT
379482 -ATAATAAATAT
1 AATAATAAATAT
379493 GTATATATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAAATATACTAT
Found at i:379597 original size:18 final size:19
Alignment explanation
Indices: 379531--379629 Score: 60
Period size: 20 Copynumber: 5.2 Consensus size: 19
379521 CACTACGTAC
379531 TATATAATATAATATATATA
1 TATATAATATAATATATA-A
* ** *
379551 TGTATGCTATACCT-TATAA
1 TATATAATATA-ATATATAA
* *
379570 TATGT-TTATAATATATAA
1 TATATAATATAATATATAA
* **
379588 TATA-AATATACTATAGGA
1 TATATAATATAATATATAA
*
379606 TATAATAATATAATATATTA
1 TAT-ATAATATAATATATAA
379626 TATA
1 TATA
379630 CACAAGATCG
Statistics
Matches: 58, Mismatches: 16, Indels: 11
0.68 0.19 0.13
Matches are distributed among these distances:
17 1 0.02
18 24 0.41
19 6 0.10
20 26 0.45
21 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (19 bp):
TATATAATATAATATATAA
Found at i:380530 original size:24 final size:24
Alignment explanation
Indices: 380502--380574 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
380492 TAAAGAATGA
380502 TTGTAATATGTTAGTTTGGTGTAT
1 TTGTAATATGTTAGTTTGGTGTAT
* *
380526 TTGTAGAT-TGTTATTTTGGTATA-
1 TTGTA-ATATGTTAGTTTGGTGTAT
* * *
380549 AT-T-ATAGGTTAGTTTAGTGTAT
1 TTGTAATATGTTAGTTTGGTGTAT
380571 TTGT
1 TTGT
380575 GGATTATTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 9
0.69 0.15 0.17
Matches are distributed among these distances:
20 2 0.05
21 11 0.30
22 2 0.05
23 2 0.05
24 18 0.49
25 2 0.05
ACGTcount: A:0.22, C:0.00, G:0.23, T:0.55
Consensus pattern (24 bp):
TTGTAATATGTTAGTTTGGTGTAT
Found at i:389666 original size:180 final size:180
Alignment explanation
Indices: 389336--389684 Score: 655
Period size: 180 Copynumber: 1.9 Consensus size: 180
389326 TTGGGAGCTA
*
389336 AAGTTTTTAATTTCTTTAGCAATCATTTTAGACGAAAGAATGAGTGGGAAAAGGTGATCAATCTT
1 AAGTTTTTAATTTCTTTAGCAATCATTTTAGACGAAAGAAGGAGTGGGAAAAGGTGATCAATCTT
389401 CCGTTCAAACAACTTTCAAGGGCTGATGTTGAAGAGCTGGAAGCGAATTTTTGATTGAAGAAGTT
66 CCGTTCAAACAACTTTCAAGGGCTGATGTTGAAGAGCTGGAAGCGAATTTTTGATTGAAGAAGTT
*
389466 AAAGAAGCTGTGTGGAGTTGTGGTGAGGCAAGAGCACCGAGACTGGACTG
131 AAAGAAGCTGTGTGGAGTTGTGGTGAGACAAGAGCACCGAGACTGGACTG
*
389516 AAGTTTTTAATTTCTTTAGCAATCATTTTAGACGAAAGAAGGAGTGGGAAACGGTGATCAATCTT
1 AAGTTTTTAATTTCTTTAGCAATCATTTTAGACGAAAGAAGGAGTGGGAAAAGGTGATCAATCTT
389581 CCGTTCAAACAACTTTCAAGGGCTGATGTTGAAGAGCTGGAAGCGAATTTTTCGATTGAAGAAGT
66 CCGTTCAAACAACTTTCAAGGGCTGATGTTGAAGAGCTGGAAGCGAATTTTT-GATTGAAGAAGT
389646 TAAAGAAGCTGTGT-GAGTTGTGGTGAGACAAGAGCACCG
130 TAAAGAAGCTGTGTGGAGTTGTGGTGAGACAAGAGCACCG
389685 GGACCGGATG
Statistics
Matches: 165, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
180 139 0.84
181 26 0.16
ACGTcount: A:0.32, C:0.13, G:0.27, T:0.28
Consensus pattern (180 bp):
AAGTTTTTAATTTCTTTAGCAATCATTTTAGACGAAAGAAGGAGTGGGAAAAGGTGATCAATCTT
CCGTTCAAACAACTTTCAAGGGCTGATGTTGAAGAGCTGGAAGCGAATTTTTGATTGAAGAAGTT
AAAGAAGCTGTGTGGAGTTGTGGTGAGACAAGAGCACCGAGACTGGACTG
Found at i:391934 original size:10 final size:10
Alignment explanation
Indices: 391919--391958 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
391909 TAGTTGTAGC
*
391919 TTTTATTTTA
1 TTTTATTATA
391929 TTTTATTATA
1 TTTTATTATA
391939 TTTTATTATA
1 TTTTATTATA
*
391949 TATTA-TATA
1 TTTTATTATA
391958 T
1 T
391959 GAGATATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
9 5 0.18
10 23 0.82
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTATTATA
Found at i:391942 original size:15 final size:17
Alignment explanation
Indices: 391922--391956 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
391912 TTGTAGCTTT
391922 TATTTTATT-T-TATTA
1 TATTTTATTATATATTA
391937 TATTTTATTATATATTA
1 TATTTTATTATATATTA
391954 TAT
1 TAT
391957 ATGAGATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 1 0.06
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTATTATATATTA
Found at i:406059 original size:16 final size:16
Alignment explanation
Indices: 406040--406071 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
406030 TGTTTATTGT
406040 TATTAGAAAATTAATA
1 TATTAGAAAATTAATA
*
406056 TATTATAAAATTAATA
1 TATTAGAAAATTAATA
406072 ATAATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (16 bp):
TATTAGAAAATTAATA
Found at i:408688 original size:20 final size:20
Alignment explanation
Indices: 408594--408962 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
408584 GATTTTCCAT
* ** *
408594 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
408614 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
408634 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
408654 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
408674 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
408694 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
408714 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
408734 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
408754 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
408774 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
408794 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
408814 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
408834 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
408854 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
408874 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
408894 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
408914 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
408934 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
408954 AATCACAAC
1 AATCGCAAC
408963 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:409684 original size:24 final size:24
Alignment explanation
Indices: 409645--409691 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
409635 AAATTTGGTC
409645 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
409669 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
409692 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:409883 original size:12 final size:12
Alignment explanation
Indices: 409866--409890 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
409856 ATATAATCCT
409866 GAAGAAGAAAAA
1 GAAGAAGAAAAA
409878 GAAGAAGAAAAA
1 GAAGAAGAAAAA
409890 G
1 G
409891 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:412194 original size:19 final size:19
Alignment explanation
Indices: 412172--412445 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
412162 CGGAAAATAC
*
412172 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
412191 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
412205 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
412225 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
412239 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
412258 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
412277 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
412291 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
412310 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
412329 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
412348 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
412367 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
412386 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
412400 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
412419 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
412438 AATCGCAA
1 AATCGCAA
412446 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 38 0.17
15 1 0.00
16 14 0.06
17 12 0.05
18 2 0.01
19 146 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:412323 original size:71 final size:74
Alignment explanation
Indices: 412172--412467 Score: 314
Period size: 71 Copynumber: 4.2 Consensus size: 74
412162 CGGAAAATAC
* *
412172 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GC-GAAATG-AAATCGCA
*
412232 A--CG--A-GAG
63 ATGCGAAATGAA
*
412239 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACA-G-AATCGCAATG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
*
412301 CGAAATTAA
66 CGAAATGAA
412310 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
412375 TGCGAAATGAA
64 TGCGAAATGAA
412386 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCGAAATG-AAATCGCAA
*
412446 --CG--A-GAT
64 TGCGAAATGAA
412452 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
412468 TATAAACGCA
Statistics
Matches: 203, Mismatches: 8, Indels: 34
0.83 0.03 0.14
Matches are distributed among these distances:
66 18 0.09
67 26 0.13
68 8 0.04
69 6 0.03
70 2 0.01
71 93 0.46
72 13 0.06
73 5 0.02
74 6 0.03
76 26 0.13
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.15
Consensus pattern (74 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAAATGAAATCGCAATG
CGAAATGAA
Found at i:412371 original size:109 final size:104
Alignment explanation
Indices: 412200--412467 Score: 446
Period size: 109 Copynumber: 2.5 Consensus size: 104
412190 AAATCCCAAC
*
412200 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCA
*
412265 ATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
65 ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
412305 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAAAT
412370 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
61 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
412414 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAAT
412468 TATAAACGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 11
0.91 0.03 0.07
Matches are distributed among these distances:
104 34 0.22
105 16 0.10
106 2 0.01
107 2 0.01
108 1 0.01
109 98 0.64
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (104 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
TGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:412433 original size:161 final size:157
Alignment explanation
Indices: 412172--412483 Score: 502
Period size: 161 Copynumber: 2.0 Consensus size: 157
412162 CGGAAAATAC
*
412172 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
412237 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
412302 GAAATTA-AAATCGCAATGCGAAATGAA
131 GAAATTATAAA-CGCAATGCGAAATGAA
* *
412329 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCCCAA--C---ATGAAAATCGCAATGCGGAAATGAAAATCGCA
* *
412393 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGC
61 ACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGC
*
412458 AATGCGAAATTATAAACGCATTGCGA
126 AATGCGAAATTATAAACGCAATGCGA
412484 TTTTCATTTC
Statistics
Matches: 143, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
157 25 0.17
159 1 0.01
161 98 0.69
162 19 0.13
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (157 bp):
AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAA
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATTATAAACGCAATGCGAAATGAA
Found at i:412483 original size:52 final size:52
Alignment explanation
Indices: 412200--412467 Score: 437
Period size: 52 Copynumber: 5.0 Consensus size: 52
412190 AAATCCCAAC
412200 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
412253 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
412305 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
412362 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
412414 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
412466 AT
1 AT
412468 TATAAACGCA
Statistics
Matches: 201, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
52 133 0.66
53 17 0.08
54 2 0.01
55 2 0.01
56 1 0.00
57 46 0.23
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:412583 original size:19 final size:19
Alignment explanation
Indices: 412474--412575 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
412464 AAATTATAAA
412474 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
412493 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
412513 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
412529 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
412546 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
412565 CGCATTGCGAT
1 CGCATTGCGAT
412576 AGTCATTTTG
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:412700 original size:14 final size:14
Alignment explanation
Indices: 412681--412717 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
412671 CATCAATTAC
412681 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
412695 ACAAATCATCTTTT
1 ACAAATCAACTTTT
412709 ACAAATCAA
1 ACAAATCAA
412718 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:414168 original size:21 final size:21
Alignment explanation
Indices: 414101--414168 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
414091 GTGAATCGGC
*
414101 CTCTTGAACGGTAGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* * * ** * *
414122 CCTCTTCAATGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
414144 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
414165 CTCT
1 CTCT
414169 CGAGGAATGA
Statistics
Matches: 31, Mismatches: 15, Indels: 1
0.66 0.32 0.02
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:414697 original size:14 final size:14
Alignment explanation
Indices: 414678--414734 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
414668 GCGAAATGAA
*
414678 AATCGCAACGACAG
1 AATCGCAACGAAAG
414692 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
414709 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
414725 AATCGCAACG
1 AATCGCAACG
414735 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:414705 original size:33 final size:33
Alignment explanation
Indices: 414659--414751 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
414649 GCGAAACCAA
*
414659 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
414692 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
414725 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
414752 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:414716 original size:19 final size:19
Alignment explanation
Indices: 414622--414756 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
414612 TAGTTTACTT
* *
414622 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
414642 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
414661 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
414680 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
414694 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
414713 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
414727 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
414746 TCGCAATGCGA
1 TCGCAACGCGA
414757 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:414774 original size:19 final size:19
Alignment explanation
Indices: 414752--414880 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
414742 AAAATCGCAA
414752 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
414771 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
414785 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
414804 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
414818 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
414837 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
414856 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
414876 TGCGA
1 TGCGA
414881 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:414794 original size:33 final size:33
Alignment explanation
Indices: 414752--414843 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
414742 AAAATCGCAA
414752 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
414785 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
414818 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
414844 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:415215 original size:93 final size:93
Alignment explanation
Indices: 414924--415395 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
414914 TTGAATGGAT
414924 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
414989 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
415017 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
415081 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
415109 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
415174 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
415202 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
415266 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
415294 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
415359 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
415387 AAATTTACT
1 AAATTTACT
415396 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:415236 original size:185 final size:185
Alignment explanation
Indices: 414924--415395 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
414914 TTGAATGGAT
414924 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
414989 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
415054 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
415109 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
415174 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
415239 TATATTTCACAGTGTTAAAGAATATACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
415294 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
415359 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
415396 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:417121 original size:14 final size:14
Alignment explanation
Indices: 417102--417191 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
417092 TTGAAATGAA
417102 AATCGCAACGAGAG
1 AATCGCAACGAGAG
417116 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
417133 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
417149 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
417168 AATCGCAACGAGAG
1 AATCGCAACGAGAG
417182 AATCGCAACG
1 AATCGCAACG
417192 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:417139 original size:33 final size:33
Alignment explanation
Indices: 417094--417208 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
417084 TCTTTTGGTT
417094 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
417127 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
417160 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
417193 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
417209 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:417140 original size:19 final size:18
Alignment explanation
Indices: 417101--417213 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
417091 GTTGAAATGA
417101 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
417116 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
417133 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
417149 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
417166 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
417182 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
417199 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
417214 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:417244 original size:14 final size:14
Alignment explanation
Indices: 417225--417279 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
417215 TTTGGTTTCG
417225 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
417239 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
417258 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
417272 CGTTGCGA
1 CGTTGCGA
417280 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:417257 original size:33 final size:33
Alignment explanation
Indices: 417209--417279 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
417199 AAAATCGCAA
**
417209 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
417242 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
417275 TGCGA
1 TGCGA
417280 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:417287 original size:33 final size:33
Alignment explanation
Indices: 417220--417301 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
417210 GCGATTTTGG
***
417220 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
417253 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
417286 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
417302 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:417306 original size:20 final size:20
Alignment explanation
Indices: 417232--417320 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
417222 TCGCGTTGCG
417232 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
417252 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
417265 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
417285 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
417305 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
417321 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:417442 original size:33 final size:33
Alignment explanation
Indices: 417400--417470 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
417390 AATACTAACT
*
417400 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
417433 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
417466 TGAAA
1 TGAAA
417471 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:417703 original size:22 final size:22
Alignment explanation
Indices: 417651--417705 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
417641 TGGTTGTGAG
**
417651 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
417673 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
417695 GGATTTCTTCG
1 GGATTTCTTCG
417706 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:417876 original size:20 final size:20
Alignment explanation
Indices: 417851--418043 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
417841 CTTTAAATAT
417851 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
417871 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
417893 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
417912 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
417932 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
417952 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
417972 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
417992 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
418012 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
418032 CGCGTTGCGATT
1 CGCGTTGCGATT
418044 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:418038 original size:60 final size:60
Alignment explanation
Indices: 417851--418043 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
417841 CTTTAAATAT
**
417851 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
417912 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
417972 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
418032 CGCGTTGCGATT
1 CGCGTTGCGATT
418044 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:425545 original size:2 final size:2
Alignment explanation
Indices: 425538--425565 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
425528 GCATCCAAAC
425538 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
425566 TATTCATATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:428024 original size:13 final size:13
Alignment explanation
Indices: 428006--428031 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
427996 AGCTATGAGC
428006 TTATATGACATGT
1 TTATATGACATGT
428019 TTATATGACATGT
1 TTATATGACATGT
428032 GATATGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
TTATATGACATGT
Found at i:428292 original size:23 final size:23
Alignment explanation
Indices: 428262--428413 Score: 196
Period size: 23 Copynumber: 6.6 Consensus size: 23
428252 CATCTTATAT
428262 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
428285 GGCACTACGGTGCAATTTTAGGC
1 GGCACTACGGTGCAATTCTACGC
*
428308 GGCACTACGGTGCAATTCTAGGC
1 GGCACTACGGTGCAATTCTACGC
* * *
428331 GGCACTTCGATGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
428354 GGCATTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
428377 GACACTTCGATGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
428400 GACACTTCGGTGCA
1 GGCACTACGGTGCA
428414 TTTATACGAT
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 113 1.00
ACGTcount: A:0.22, C:0.27, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:434746 original size:2 final size:2
Alignment explanation
Indices: 434739--434769 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
434729 TCATACCAGC
434739 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
434770 AGACATGCTC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:440405 original size:43 final size:43
Alignment explanation
Indices: 440344--440464 Score: 215
Period size: 43 Copynumber: 2.8 Consensus size: 43
440334 AACCAAGTCC
*
440344 ATGGTTACCTTCATTAAGAAAGAAAACACACATATATATTAAT
1 ATGGTTACCATCATTAAGAAAGAAAACACACATATATATTAAT
440387 ATGGTTACCATCATTAAGAAAGAAAACACACATATATATTAAT
1 ATGGTTACCATCATTAAGAAAGAAAACACACATATATATTAAT
* *
440430 ATGGTTACCAACATTAAGAAAGAAAACACATATAT
1 ATGGTTACCATCATTAAGAAAGAAAACACACATAT
440465 TACTAAGGTG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 75 1.00
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (43 bp):
ATGGTTACCATCATTAAGAAAGAAAACACACATATATATTAAT
Found at i:441181 original size:18 final size:18
Alignment explanation
Indices: 441158--441202 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
441148 ACCATGCAAC
*
441158 TGCTGCCACCTCATGTGT
1 TGCTGCCACCCCATGTGT
*
441176 TGCTGCCCCCCCATGTGT
1 TGCTGCCACCCCATGTGT
441194 TGCTGCCAC
1 TGCTGCCAC
441203 GTTGAGCAAA
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:0.09, C:0.40, G:0.22, T:0.29
Consensus pattern (18 bp):
TGCTGCCACCCCATGTGT
Found at i:443323 original size:142 final size:142
Alignment explanation
Indices: 443066--443328 Score: 418
Period size: 142 Copynumber: 1.9 Consensus size: 142
443056 AGGGGTATGA
* *
443066 GTTAAACTTTTATCATTCAAATGTCAGCTACCTATTGTACCTACGTGAGTGGCATGCCATGCAAC
1 GTTAAACTTTTATCATTCAAATGCCAGCTACCTACTGTACCTACGTGAGTGGCATGCCATGCAAC
**
443131 TTTGCCAGCCACGAGAGGGGACCCCGAGGAGCCGCATGCGGCCACATGCAACCCAGCTCTCCTTG
66 TTTGCCAGCCACGAGAGGGGACCCCGAGGAAACGCATGCGGCCACATGCAACCCAGCTCTCCTTG
443196 GGAGACGCATGG
131 GGAGACGCATGG
* *
443208 GTTAAACTTTTATCATTCGAATGCCAGCTACCTACTGTACCTACGTGAGTGGCATGCCATGCGAC
1 GTTAAACTTTTATCATTCAAATGCCAGCTACCTACTGTACCTACGTGAGTGGCATGCCATGCAAC
* * * * * *
443273 TTTGCCGGCCATGCGAGGGGACCCTGATGAAACGCATGCGGCCACTTGCAACCCAG
66 TTTGCCAGCCACGAGAGGGGACCCCGAGGAAACGCATGCGGCCACATGCAACCCAG
443329 GCTAGGAGAG
Statistics
Matches: 109, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
142 109 1.00
ACGTcount: A:0.24, C:0.29, G:0.25, T:0.22
Consensus pattern (142 bp):
GTTAAACTTTTATCATTCAAATGCCAGCTACCTACTGTACCTACGTGAGTGGCATGCCATGCAAC
TTTGCCAGCCACGAGAGGGGACCCCGAGGAAACGCATGCGGCCACATGCAACCCAGCTCTCCTTG
GGAGACGCATGG
Found at i:444997 original size:18 final size:18
Alignment explanation
Indices: 444974--445011 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
444964 AGTTAAGTGT
444974 CACGTCAACAAAAACCAA
1 CACGTCAACAAAAACCAA
444992 CACGTCAACAAAAACCAA
1 CACGTCAACAAAAACCAA
445010 CA
1 CA
445012 TAGATAGCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.34, G:0.05, T:0.05
Consensus pattern (18 bp):
CACGTCAACAAAAACCAA
Found at i:449619 original size:31 final size:31
Alignment explanation
Indices: 449554--449630 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 31
449544 ATAAGATATT
* *
449554 AATTTAA-TTTTAAATTTTACTTACAATATT
1 AATTTAATTTTTAAATTTTACTTACAACATC
449584 AATTTAATTTTTAAATTTTA-TATGA-AACATC
1 AATTTAATTTTTAAATTTTACT-T-ACAACATC
* *
449615 AATTTGATTCTTAAAT
1 AATTTAATTTTTAAAT
449631 CTAATTAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 8 0.20
31 31 0.77
32 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (31 bp):
AATTTAATTTTTAAATTTTACTTACAACATC
Found at i:451831 original size:47 final size:48
Alignment explanation
Indices: 451762--451856 Score: 122
Period size: 47 Copynumber: 2.0 Consensus size: 48
451752 AGCGGCTTAA
* * * * *
451762 CGAGCGACTAGTCGAATTGAACAATGAATTTTTTTAAT-AGCATAAAT
1 CGAGCAACGAGTCGAATTGAACAACGAATTCTTTTAATGAACATAAAT
451809 CGAGCAACGAGTCG-ATTGGAACAACGAATTCTTTTAATGAACATAAAT
1 CGAGCAACGAGTCGAATT-GAACAACGAATTCTTTTAATGAACATAAAT
451857 TACGCATTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
46 3 0.07
47 30 0.73
48 8 0.20
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (48 bp):
CGAGCAACGAGTCGAATTGAACAACGAATTCTTTTAATGAACATAAAT
Found at i:452994 original size:34 final size:30
Alignment explanation
Indices: 452924--453023 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 30
452914 AAAGATAAAT
452924 TTATAATTTGAATTTAATTTTTTTATATGA
1 TTATAATTTGAATTTAATTTTTTTATATGA
* *
452954 TTATAATTTGAATCTTAATTTTTTCTTCTTCTGA
1 TTATAATTTGAAT-TTAA-TTTTT-TT-ATATGA
*
452988 TTATAATTTGAATATTAAATTATTTTTTTAATGA
1 TTATAATTTGAAT-TT-AATT-TTTTTAT-ATGA
453022 TT
1 TT
453024 TCATATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
30 13 0.22
31 4 0.07
32 5 0.08
33 4 0.07
34 28 0.47
35 5 0.08
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (30 bp):
TTATAATTTGAATTTAATTTTTTTATATGA
Found at i:456879 original size:20 final size:21
Alignment explanation
Indices: 456839--456879 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
456829 TTATTATAAC
*
456839 TATATTTTTAGTTTTTAGTTTT
1 TATATTTTTAG-TTATAGTTTT
456861 TATATTTTTA-TTATAGTTT
1 TATATTTTTAGTTATAGTTT
456880 AAACAGATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (21 bp):
TATATTTTTAGTTATAGTTTT
Found at i:465349 original size:30 final size:30
Alignment explanation
Indices: 465315--465371 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
465305 ATCTAGTGTC
* *
465315 TAGAAAATTCTAGAGCTTTCTGGAGAAGTG
1 TAGAAAATTCTAGAGCATTCTGAAGAAGTG
**
465345 TAGAATTTTCTAGAGCATTCTGAAGAA
1 TAGAAAATTCTAGAGCATTCTGAAGAA
465372 CTCTAGAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.32
Consensus pattern (30 bp):
TAGAAAATTCTAGAGCATTCTGAAGAAGTG
Found at i:469111 original size:14 final size:14
Alignment explanation
Indices: 469092--469118 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
469082 CTGAATATAC
469092 AAACATAAACAAAT
1 AAACATAAACAAAT
469106 AAACATAAACAAA
1 AAACATAAACAAA
469119 CATAAATGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.00, T:0.11
Consensus pattern (14 bp):
AAACATAAACAAAT
Done.