Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002158.1 Hibiscus syriacus cultivar Beakdansim tig00004406_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: 119257
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4856 original size:2 final size:2
Alignment explanation
Indices: 4849--4881 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4839 AGGAAACAGC
4849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4882 CTATTGGGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7476 original size:20 final size:22
Alignment explanation
Indices: 7453--7498 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
7443 GGATGTACAA
7453 ATATAATA-T-TAAATGTTAAT
1 ATATAATATTATAAATGTTAAT
**
7473 ATATTTTATTATAAATGTTAAT
1 ATATAATATTATAAATGTTAAT
7495 ATAT
1 ATAT
7499 GACGTTATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 1 0.05
22 15 0.68
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
ATATAATATTATAAATGTTAAT
Found at i:7506 original size:22 final size:22
Alignment explanation
Indices: 7462--7507 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
7452 AATATAATAT
***
7462 TAAATGTTAATATATTTTATTA
1 TAAATGTTAATATATGACATTA
*
7484 TAAATGTTAATATATGACGTTA
1 TAAATGTTAATATATGACATTA
7506 TA
1 TA
7508 CCGGTAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (22 bp):
TAAATGTTAATATATGACATTA
Found at i:11889 original size:13 final size:13
Alignment explanation
Indices: 11871--11909 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
11861 AATGGGCAAA
*
11871 TTTGAAAACTATT
1 TTTGAAAACTATG
*
11884 TTTGAAAACAATG
1 TTTGAAAACTATG
11897 TTTGAAAATCTAT
1 TTTGAAAA-CTAT
11910 ATGTAGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (13 bp):
TTTGAAAACTATG
Found at i:13147 original size:30 final size:30
Alignment explanation
Indices: 13088--13189 Score: 152
Period size: 30 Copynumber: 3.4 Consensus size: 30
13078 CCCGAAGGAC
* *
13088 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
13117 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
13147 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
13177 CTGTCCATAGGTC
1 CTATCCAGAGGTC
13190 CCGAAGAACC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
29 19 0.28
30 49 0.72
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:13206 original size:30 final size:30
Alignment explanation
Indices: 13091--13225 Score: 119
Period size: 30 Copynumber: 4.5 Consensus size: 30
13081 GAAGGACCTA
* * * *
13091 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCATAGGTCACGAAGATCCTCGGTAACTG
* **
13120 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACGAAGATCCTCGGTAACTG
* **
13150 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACGAAGATCCTCGGTAACTG
* * *
13180 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACGAAGATCCTCGGT-AACTG
* *
13211 TCCATATGTCTCGAA
1 TCCATAGGTCACGAA
13226 AGACATAGGT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
29 16 0.17
30 59 0.63
31 18 0.19
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
TCCATAGGTCACGAAGATCCTCGGTAACTG
Found at i:13206 original size:60 final size:60
Alignment explanation
Indices: 13091--13214 Score: 151
Period size: 60 Copynumber: 2.1 Consensus size: 60
13081 GAAGGACCTA
* * *
13091 TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCATAAAGATCCTCGGT-AACTG
1 TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAACTG
* * * * * *
13150 TCCAGAGGTCATAAAGATCCTCGGTAACTGTCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCAGAGGTCACAAAGA-CCCCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAACTG
13211 TCCA
1 TCCA
13215 TATGTCTCGA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 16 0.30
60 29 0.54
61 9 0.17
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (60 bp):
TCCAGAGGTCACAAAGACCCCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAACTG
Found at i:13213 original size:31 final size:31
Alignment explanation
Indices: 13175--13239 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
13165 GATCCTCGGT
*
13175 AACTGTCCATAGGTCCCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAG-ACATAGGTA
* *
13206 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAGACATAGGTA
13237 AAC
1 AAC
13240 CCTTGACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAGACATAGGTA
Found at i:13741 original size:20 final size:22
Alignment explanation
Indices: 13716--13773 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
13706 TTCCCCTTGA
13716 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
13736 AGTGCATCGATACATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
13759 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
13774 CTACCCATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:17255 original size:30 final size:30
Alignment explanation
Indices: 17192--17290 Score: 146
Period size: 30 Copynumber: 3.3 Consensus size: 30
17182 GAAGGACCTA
* * * *
17192 TCCAGAGGTCACAAAGA-CCCCGATAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
17221 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
17251 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
17281 TCCATAGGTC
1 TCCAGAGGTC
17291 CCGAAGAACC
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
29 16 0.25
30 48 0.75
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:17307 original size:30 final size:30
Alignment explanation
Indices: 17192--17326 Score: 110
Period size: 30 Copynumber: 4.5 Consensus size: 30
17182 GAAGGACCTA
* * * * *
17192 TCCAGAGGTCACAAAGA-CCCCGATAACTA
1 TCCATAGGTCACGAAGATCCTCGGTAACTG
* **
17221 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACGAAGATCCTCGGTAACTG
* **
17251 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCATAGGTCACGAAGATCCTCGGTAACTG
* * *
17281 TCCATAGGTCCCGAAGAACCTAGGTAAACTG
1 TCCATAGGTCACGAAGATCCTCGGT-AACTG
* *
17312 TCCATATGTCTCGAA
1 TCCATAGGTCACGAA
17327 AGACATAGGT
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
29 16 0.17
30 58 0.63
31 18 0.20
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
TCCATAGGTCACGAAGATCCTCGGTAACTG
Found at i:17314 original size:31 final size:31
Alignment explanation
Indices: 17276--17340 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
17266 GATCCTCGGT
*
17276 AACTGTCCATAGGTCCCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAG-ACATAGGTA
* *
17307 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAGACATAGGTA
17338 AAC
1 AAC
17341 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAGACATAGGTA
Found at i:17950 original size:19 final size:19
Alignment explanation
Indices: 17926--17976 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
17916 TTTTAAGGGG
17926 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
17945 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTT
17964 ATGCATCGATGCA
1 ATGCATCGATGCA
17977 TCAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTT
Found at i:18004 original size:83 final size:82
Alignment explanation
Indices: 17863--18021 Score: 198
Period size: 83 Copynumber: 1.9 Consensus size: 82
17853 CTTTAACATG
* * * *
17863 TGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGATGTTTTTATTTTAAGGGGAT
1 TGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTTACTTTAAAGAG-T
17928 GCATCGATGCACTCCTTA
65 GCATCGATGCACTCCTTA
* * *
17946 TGCATCGATGCACT-CCTTATGCATCGATGCATC-AATTGCATTCGATGTTTCTT-CTTTAAAGA
1 TGCATCGATGCACTACC-CATGCATCGATACA-CAAATTACATTCGATGTTT-TTACTTTAAAGA
18008 GTGCATCGATGCAC
63 GTGCATCGATGCAC
18022 ATTGAATATG
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
82 15 0.23
83 48 0.73
84 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (82 bp):
TGCATCGATGCACTACCCATGCATCGATACACAAATTACATTCGATGTTTTTACTTTAAAGAGTG
CATCGATGCACTCCTTA
Found at i:18840 original size:21 final size:20
Alignment explanation
Indices: 18789--18845 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
18779 AAACCCGATG
18789 AGTGTATCGATACACATTCA
1 AGTGTATCGATACACATTCA
*
18809 AGGAATGTATCGGTACACATTCA
1 A-G--TGTATCGATACACATTCA
18832 TAGTGTATC-ATACA
1 -AGTGTATCGATACA
18846 TAAGTATCGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 5 0.16
21 7 0.23
23 18 0.58
24 1 0.03
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (20 bp):
AGTGTATCGATACACATTCA
Found at i:22952 original size:117 final size:118
Alignment explanation
Indices: 22734--22954 Score: 304
Period size: 117 Copynumber: 1.9 Consensus size: 118
22724 TTTCAAATTG
* * *
22734 AAATTCTCTTTTTCAAAGCTTTCAAATTTTATTTTTGAGAGCTCTAAATCCTTCTTCAATATTTC
1 AAATTCTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTTC
* *
22799 ATTTTGATTTTCAAAATCCATTTTAGTTTCTTAAAGAAGTTTGTTTAATCCGA
66 ATTTTGATTTTCAAAATCCATTTTACTTTCTAAAAGAAGTTTGTTTAATCCGA
* * *
22852 AAATT-TCTTTTTCAAAGTTTTCAGATTTCATTTTTGAAAGCTCTAACTCCTT-TTACAAAATTT
1 AAATTCTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTT-CAAAATTT
* * *
22915 CATTTTGATTTTCCAAGTCTATTTTATCTTTC-AAAAGAAG
65 CATTTTGATTTTCAAAATCCATTTTA-CTTTCTAAAAGAAG
22955 ATCATTTTTA
Statistics
Matches: 90, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
116 2 0.02
117 79 0.88
118 9 0.10
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (118 bp):
AAATTCTCTTTTTCAAAGCTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAAATTTC
ATTTTGATTTTCAAAATCCATTTTACTTTCTAAAAGAAGTTTGTTTAATCCGA
Found at i:25445 original size:31 final size:32
Alignment explanation
Indices: 25385--25447 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
25375 TAGATTGACC
*
25385 TATTACGACGTTTTTTAAAAACACGCCATTAT
1 TATTACGACGTTTTTGAAAAACACGCCATTAT
*
25417 TATTACGAC-TTTATTGATAAA-ACGCCATTAT
1 TATTACGACGTTT-TTGAAAAACACGCCATTAT
25448 ATATGGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 13 0.46
32 15 0.54
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (32 bp):
TATTACGACGTTTTTGAAAAACACGCCATTAT
Found at i:26098 original size:2 final size:2
Alignment explanation
Indices: 26091--26118 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26081 TAATATTTTA
26091 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
26119 TCATTGAGTA
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:27507 original size:3 final size:3
Alignment explanation
Indices: 27499--27548 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
27489 TTCTTTTTTC
*
27499 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
27547 TA
1 TA
27549 ACCTAGGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:33054 original size:20 final size:23
Alignment explanation
Indices: 32997--33054 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 23
32987 ATGCAATTAG
*
32997 TGCATCGATGCACATGTTAAGGGA
1 TGCATCGATGCAC-TGTTAAGGAA
* *
33021 TGCATCGGTACACTG-T-A-GAA
1 TGCATCGATGCACTGTTAAGGAA
33041 TGCATCGATGCACT
1 TGCATCGATGCACT
33055 TCAAGGGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 1 0.03
23 2 0.07
24 11 0.38
ACGTcount: A:0.28, C:0.21, G:0.26, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCACTGTTAAGGAA
Found at i:33894 original size:30 final size:30
Alignment explanation
Indices: 33840--33912 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
33830 TTTCGAGACA
* * * *
33840 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTGCCGAAGTTCTTTAGGACC
*
33871 TATGGACAGTTGCCGAAGTTCTTTATGACC
1 TATGGACAGTTGCCGAAGTTCTTTAGGACC
* *
33901 TCTGGATAGTTG
1 TATGGACAGTTG
33913 TTGGGGTCTT
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.36
Consensus pattern (30 bp):
TATGGACAGTTGCCGAAGTTCTTTAGGACC
Found at i:35117 original size:21 final size:21
Alignment explanation
Indices: 35091--35143 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
35081 AGAATTTGTC
35091 CCGAAGGACCACGTAGATGTA
1 CCGAAGGACCACGTAGATGTA
*
35112 CCGAAGGACCACGTAGATGTC
1 CCGAAGGACCACGTAGATGTA
35133 CCGAAGGACCA
1 CCGAAGGACCA
35144 GTATGCTAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.28, T:0.11
Consensus pattern (21 bp):
CCGAAGGACCACGTAGATGTA
Found at i:36134 original size:21 final size:21
Alignment explanation
Indices: 36110--36165 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
36100 TATTTGAGAG
*
36110 TGCATCGATGCACATTGAAGA
1 TGCATCGATGCACATTAAAGA
36131 TGCATCGATGCACATTAAAGA
1 TGCATCGATGCACATTAAAGA
*
36152 TGCATTGATGCACA
1 TGCATCGATGCACA
36166 CAACCCAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (21 bp):
TGCATCGATGCACATTAAAGA
Found at i:36491 original size:31 final size:32
Alignment explanation
Indices: 36450--36520 Score: 126
Period size: 31 Copynumber: 2.2 Consensus size: 32
36440 TCCAGAATTC
36450 ATTTCTCAACCCTTAATCAAATTTCCTTTCTA
1 ATTTCTCAACCCTTAATCAAATTTCCTTTCTA
36482 ATTT-TCAACCCTTAATCAAATTTCCTTTCTA
1 ATTTCTCAACCCTTAATCAAATTTCCTTTCTA
36513 ATTCTCTC
1 ATT-TCTC
36521 CTTGTGGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
31 30 0.81
32 5 0.14
33 2 0.05
ACGTcount: A:0.27, C:0.28, G:0.00, T:0.45
Consensus pattern (32 bp):
ATTTCTCAACCCTTAATCAAATTTCCTTTCTA
Found at i:50569 original size:31 final size:31
Alignment explanation
Indices: 50534--50629 Score: 147
Period size: 31 Copynumber: 3.1 Consensus size: 31
50524 CGACCACATA
* * * *
50534 TTAATTAAATAAAAACGAAAATGATACTATC
1 TTAATTAAATATAAACGAAAGTGACAATATC
*
50565 TTAATTAAATATAAACGAAAGTGACAATACC
1 TTAATTAAATATAAACGAAAGTGACAATATC
50596 TTAATTAAATATAAACGAAAGTGACAATATC
1 TTAATTAAATATAAACGAAAGTGACAATATC
50627 TTA
1 TTA
50630 TTTTTTTTGA
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 59 1.00
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29
Consensus pattern (31 bp):
TTAATTAAATATAAACGAAAGTGACAATATC
Found at i:63301 original size:30 final size:29
Alignment explanation
Indices: 63260--63320 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 29
63250 TTCAGTTAAT
*
63260 ATATAAATATTTAATACTTTAAT-TAATAA
1 ATATAAATATTTAATA-TTTAATAGAATAA
63289 ATATAATATATTTAATATTTAATAGAATAA
1 ATATAA-ATATTTAATATTTAATAGAATAA
63319 AT
1 AT
63321 CCAACCGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATATAAATATTTAATATTTAATAGAATAA
Found at i:64033 original size:11 final size:11
Alignment explanation
Indices: 64012--64041 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
64002 AGTTTTGATG
64012 TATAT-ATATA
1 TATATAATATA
64022 TATATAATATA
1 TATATAATATA
64033 TATATAATA
1 TATATAATA
64042 CGATAGTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATATAATATA
Found at i:65862 original size:31 final size:30
Alignment explanation
Indices: 65812--65879 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
65802 AAAACAAAAC
*
65812 AAAATAATAATAATAAATAAAAGGGAAATAT
1 AAAAAAATAATAATAAATAAAA-GGAAATAT
* * *
65843 AATAAAATAATAA-ACAATAATAGTAAATAT
1 AAAAAAATAATAATA-AATAAAAGGAAATAT
65873 AAAAAAA
1 AAAAAAA
65880 GATGTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (30 bp):
AAAAAAATAATAATAAATAAAAGGAAATAT
Found at i:66941 original size:14 final size:14
Alignment explanation
Indices: 66919--66949 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
66909 AAAAAATAAC
66919 AAAAGAAATAAATA
1 AAAAGAAATAAATA
*
66933 AAAATAAATAAATA
1 AAAAGAAATAAATA
66947 AAA
1 AAA
66950 TGGTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (14 bp):
AAAAGAAATAAATA
Found at i:69193 original size:3 final size:3
Alignment explanation
Indices: 69185--69213 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
69175 TTTGCTTGCT
69185 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
69214 GGTTTTGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:72015 original size:41 final size:41
Alignment explanation
Indices: 71961--72257 Score: 326
Period size: 41 Copynumber: 7.2 Consensus size: 41
71951 GGTTCAGCCA
*
71961 TAGTGGCGTTTTTTAAACAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCG-TTTTTATACAAACGCCGCTAAAGACTCGTACTT
**
72003 TAGTGGCGTTTTTATACAAACGAAGCTAAAGACTCGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
72044 TAGTGGCGTTTTTATACAAACTCCGCTATACACTTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* *
72085 TAGTGGCGTTTGTGTTTAGAAACGCCGCTAAAGACTCGTACTT
1 TAGTGGCGTTT-T-TATACAAACGCCGCTAAAGACTCGTACTT
* * * * **
72128 TAGTGGCGTTTATATACAAACACCGCTATACACTTATACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
* * * *
72169 TAGTGGCGTTTTTATACAAACGTCACTATATG-CTTGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTA-AAGACTCGTACTT
* ** * * *
72210 TAGTGGCGTTTATATACTTACGCCACTATAGACTAGTACTT
1 TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
72251 TAGTGGC
1 TAGTGGC
72258 ACAAACGCCG
Statistics
Matches: 213, Mismatches: 38, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
40 1 0.00
41 169 0.79
42 9 0.04
43 34 0.16
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (41 bp):
TAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCGTACTT
Found at i:72122 original size:125 final size:125
Alignment explanation
Indices: 71979--72220 Score: 371
Period size: 125 Copynumber: 1.9 Consensus size: 125
71969 TTTTTTAAAC
* * *
71979 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGA-AGCTAAAGACTCGTACT
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTATATACAAAC-ACAGCTAAACACTCATACT
*
72043 TTAGTGGCGTTTTTATACAAAC-TCCGCTATACACTTGTACTTTAGTGGCGTTTGTGTTTAG
65 TTAGTGGCGTTTTTATACAAACGT-CACTATACACTTGTACTTTAGTGGCGTTTGTGTTTAG
* * *
72104 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTATATACAAACACCGCTATACACTTATACTT
1 AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTATATACAAACACAGCTAAACACTCATACTT
**
72169 TAGTGGCGTTTTTATACAAACGTCACTATATGCTTGTACTTTAGTGGCGTTT
66 TAGTGGCGTTTTTATACAAACGTCACTATACACTTGTACTTTAGTGGCGTTT
72221 ATATACTTAC
Statistics
Matches: 106, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
124 1 0.01
125 104 0.98
126 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.35
Consensus pattern (125 bp):
AAACGCCGCTAAAGACTCGTACTTTAGTGGCGTTTATATACAAACACAGCTAAACACTCATACTT
TAGTGGCGTTTTTATACAAACGTCACTATACACTTGTACTTTAGTGGCGTTTGTGTTTAG
Found at i:75519 original size:43 final size:43
Alignment explanation
Indices: 75458--75699 Score: 358
Period size: 43 Copynumber: 5.6 Consensus size: 43
75448 TGGTAATTAA
* *
75458 CGGCGTTTGTATCTAAAAACGCCGCTATAGATCTGACTTTTTG
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTG
*
75501 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTG
* *
75544 CGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTG
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTG
* * ** *
75587 CGACGTTTGTATCAAAAAACATCGCTATAGATCTAACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTG
* *
75630 CGGCGTTTGTATCCAAAAACGTCGCTATAGATATGACCTTTTG
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTG
* *
75673 CGGCGTTTGTATCAAAAAAAGCCGCTA
1 CGGCGTTTGTATCCAAAAACGCCGCTA
75700 AATCTCAACA
Statistics
Matches: 180, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 180 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (43 bp):
CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTG
Found at i:75605 original size:86 final size:86
Alignment explanation
Indices: 75458--75699 Score: 403
Period size: 86 Copynumber: 2.8 Consensus size: 86
75448 TGGTAATTAA
* * *
75458 CGGCGTTTGTATCTAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCCAAAAACGC
1 CGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAACGC
75523 CGCTATAGATCTAACCTTTTG
66 CGCTATAGATCTAACCTTTTG
* **
75544 CGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTGCGACGTTTGTATCAAAAAACAT
1 CGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAACGC
75609 CGCTATAGATCTAACCTTTTG
66 CGCTATAGATCTAACCTTTTG
* * *
75630 CGGCGTTTGTATCCAAAAACGTCGCTATAGATATGACCTTTTGCGGCGTTTGTATCAAAAAAAGC
1 CGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAACGC
75695 CGCTA
66 CGCTA
75700 AATCTCAACA
Statistics
Matches: 144, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 144 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (86 bp):
CGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAACGC
CGCTATAGATCTAACCTTTTG
Found at i:75734 original size:86 final size:86
Alignment explanation
Indices: 75458--75742 Score: 389
Period size: 86 Copynumber: 3.3 Consensus size: 86
75448 TGGTAATTAA
* * *
75458 CGGCGTTTGTATCTAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCCAAAAACGC
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAAAGC
75523 CGCTATAGATCTAACCTTTTG
66 CGCTATAGATCTAACCTTTTG
* *
75544 CGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTGCGACGTTTGTATCAAAAAACA-
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAA-AG
*
75608 TCGCTATAGATCTAACCTTTTG
65 CCGCTATAGATCTAACCTTTTG
* * *
75630 CGGCGTTTGTATCCAAAAACGTCGCTATAGATATGACCTTTTGCGGCGTTTGTATCAAAAAAAGC
1 CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAAAGC
*
75695 CGCTA-A-ATCTCAACACCTATTG
66 CGCTATAGATCT--A-ACCTTTTG
* **
75717 CGACGTTTGTA-GGAAAAACGCCGCTA
1 CGGCGTTTGTATCCAAAAACGCCGCTA
75743 AATCTCGTGA
Statistics
Matches: 179, Mismatches: 15, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
84 4 0.02
85 2 0.01
86 156 0.87
87 17 0.09
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (86 bp):
CGGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCAAAAAAAGC
CGCTATAGATCTAACCTTTTG
Found at i:75742 original size:129 final size:129
Alignment explanation
Indices: 75461--75742 Score: 372
Period size: 129 Copynumber: 2.2 Consensus size: 129
75451 TAATTAACGG
* * *
75461 CGTTTGTATCTAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTATCCAAAAACGCCGC
1 CGTTTGTATCAAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTATCCAAAAACGCCGC
* * * * * * *
75526 TATAGATCTAACCTTTTGCGGCGTTTGTATCCAAAAACGTCGCTATAGATCTGACTTTTTGCGA
66 TATAGATATAACCTTTTGCGGCGTTTGTATCAAAAAAAGCCGCTATAGATCTCACCTATTGCGA
** *
75590 CGTTTGTATCAAAAAACATCGCTATAGATCTAACCTTTTGCGGCGTTTGTATCCAAAAACGTCGC
1 CGTTTGTATCAAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTATCCAAAAACGCCGC
*
75655 TATAGATATGACCTTTTGCGGCGTTTGTATCAAAAAAAGCCGCTA-A-ATCTCAACACCTATTGC
66 TATAGATATAACCTTTTGCGGCGTTTGTATCAAAAAAAGCCGCTATAGATCT---CACCTATTGC
75718 GA
128 GA
**
75720 CGTTTGTA-GGAAAAACGCCGCTA
1 CGTTTGTATCAAAAAACGCCGCTA
75743 AATCTCGTGA
Statistics
Matches: 132, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
127 4 0.03
128 1 0.01
129 110 0.83
130 17 0.13
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (129 bp):
CGTTTGTATCAAAAAACGCCGCTATAGATCTAACCTTTTGCGGCGTTTGTATCCAAAAACGCCGC
TATAGATATAACCTTTTGCGGCGTTTGTATCAAAAAAAGCCGCTATAGATCTCACCTATTGCGA
Found at i:78051 original size:22 final size:21
Alignment explanation
Indices: 78010--78051 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
78000 CACGTACCAT
*
78010 TAAATAATTCGATGTCATATA
1 TAAATAATTCGAGGTCATATA
*
78031 TAAATAATTTGAAGGTCATAT
1 TAAATAATTCG-AGGTCATAT
78052 TAACTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (21 bp):
TAAATAATTCGAGGTCATATA
Found at i:80472 original size:15 final size:15
Alignment explanation
Indices: 80452--80489 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
80442 ACTGGCTGAG
80452 GTGGAGGTATTGGTA
1 GTGGAGGTATTGGTA
80467 GTGGAGGTATTGGTA
1 GTGGAGGTATTGGTA
*
80482 GGGGAGGT
1 GTGGAGGT
80490 GGTGCAACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.53, T:0.29
Consensus pattern (15 bp):
GTGGAGGTATTGGTA
Found at i:83254 original size:138 final size:139
Alignment explanation
Indices: 82906--83431 Score: 488
Period size: 138 Copynumber: 3.8 Consensus size: 139
82896 GGGAGCCCTG
* * * *
82906 AAGGAGTAGAGTGACTCGCACCTGAGCACCTAATCATA-TT-ATTCCGGGTGACTCGCACGAGAG
1 AAGGATTAGAGTGACTCACA-CGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAG
* * * * * * *
82969 TTCC-AAAAGATTAGATTGACCTGCACATA--A-TCACATAATCATA-TT-ATTCCAGTTGACTC
65 -CCCTGAAGGATTAGAGTGA-CT-CACAGAGGAGT-ACCTAATCATATTTAATTCCAGGTGACTC
*
83028 GCACGGGAG-CCCG
126 GCACGGGAGTCCCA
* * * * * *
83041 AAGGAGTAGAGTGACTCGCACGTGAGCACCTAATCATA-TT-ATTCCGGATGACTTGCACGGGAG
1 AAGGATTAGAGTGACTCACACG-GAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAG
**
83104 CCCTGAAGGATTATTGTGACTCGA-ACGA-GAGCT-CCTAATCATATTTAATTCCAGGTGACTCG
65 CCCTGAAGGATTAGAGTGACTC-ACA-GAGGAG-TACCTAATCATATTTAATTCCAGGTGACTCG
* *
83166 TACGGGAGTTCCA
127 CACGGGAGTCCCA
* * * * *
83179 AATGATTAGAGTGACTCATACGAAGCA-CTAATCATATTTAATTTCGGGTTACTCGCACGATAGC
1 AAGGATTAGAGTGACTCACACGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAGC
* *** *
83243 CTTGAAGGATTAGAGTGACTCACAGAGGAGTACCTAATCATATTTAATTATGGGTGATTCGCACG
66 CCTGAAGGATTAGAGTGACTCACAGAGGAGTACCTAATCATATTTAATTCCAGGTGACTCGCACG
*
83308 AGAGTCCCA
131 GGAGTCCCA
* * *
83317 AAGGATTAGAGTGACTCACACGGGAGCACCTAATCATATTTAATTTTGGGTGACTCGTATGAGAG
1 AAGGATTAGAGTGACTCACAC-GGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAG
** * * *
83382 CCCCAAAGGATTAGAGTGACTCGCAAAGGAGTACATAATCATATTTAATT
65 CCCTGAAGGATTAGAGTGACTCACAGAGGAGTACCTAATCATATTTAATT
83432 GCACGTCACT
Statistics
Matches: 323, Mismatches: 51, Indels: 29
0.80 0.13 0.07
Matches are distributed among these distances:
133 2 0.01
134 7 0.02
135 77 0.24
136 11 0.03
137 32 0.10
138 114 0.35
139 5 0.02
140 75 0.23
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (139 bp):
AAGGATTAGAGTGACTCACACGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAGC
CCTGAAGGATTAGAGTGACTCACAGAGGAGTACCTAATCATATTTAATTCCAGGTGACTCGCACG
GGAGTCCCA
Found at i:83421 original size:70 final size:70
Alignment explanation
Indices: 82906--83431 Score: 378
Period size: 70 Copynumber: 7.6 Consensus size: 70
82896 GGGAGCCCTG
* * *** *
82906 AAGGAGTAGAGTGACTCGCACCTGAGCACCTAATCATA-TT-ATTCCGGGTGACTCGCACGAGAG
1 AAGGATTAGAGTGACTCACAAAGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAG
**
82969 TTCCA
66 CCCCA
* * * * * * * * *
82974 AAAGATTAGATTGACCTGCACATA--ATCACATAATCATA-TT-ATTCCAGTTGACTCGCACGGG
1 AAGGATTAGAGTGA-CT-CACAAAGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAG
*
83035 AG-CCCG
64 AGCCCCA
* * * * * * *
83041 AAGGAGTAGAGTGACTCGC-ACGTGAGCACCTAATCATA-TT-ATTCCGGATGACTTGCACGGGA
1 AAGGATTAGAGTGACTCACAAAG-GAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGA
**
83103 GCCCTG
65 GCCCCA
** * * * * * * *
83109 AAGGATTATTGTGACTC-GAACGAGAGCTCCTAATCATATTTAATTCCAGGTGACTCGTACGGGA
1 AAGGATTAGAGTGACTCACAAAG-GAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGA
**
83173 GTTCCA
65 GCCCCA
* * * * * *
83179 AATGATTAGAGTGACTCA-TACGAAGCA-CTAATCATATTTAATTTCGGGTTACTCGCACGATAG
1 AAGGATTAGAGTGACTCACAAAGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAG
***
83242 CCTTG
66 CCCCA
* * *
83247 AAGGATTAGAGTGACTCACAGAGGAGTACCTAATCATATTTAATTAT-GGGTGATTCGCACGAGA
1 AAGGATTAGAGTGACTCACAAAGGAGCACCTAATCATATTTAATT-TCGGGTGACTCGCACGAGA
*
83311 GTCCCA
65 GCCCCA
** * * *
83317 AAGGATTAGAGTGACTCACACGGGAGCACCTAATCATATTTAATTTTGGGTGACTCGTATGAGAG
1 AAGGATTAGAGTGACTCACAAAGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAG
83382 CCCCA
66 CCCCA
* * *
83387 AAGGATTAGAGTGACTCGCAAAGGAGTACATAATCATATTTAATT
1 AAGGATTAGAGTGACTCACAAAGGAGCACCTAATCATATTTAATT
83432 GCACGTCACT
Statistics
Matches: 363, Mismatches: 81, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
65 2 0.01
66 2 0.01
67 47 0.13
68 126 0.35
69 12 0.03
70 173 0.48
71 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (70 bp):
AAGGATTAGAGTGACTCACAAAGGAGCACCTAATCATATTTAATTTCGGGTGACTCGCACGAGAG
CCCCA
Found at i:83508 original size:63 final size:63
Alignment explanation
Indices: 83409--83533 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
83399 GACTCGCAAA
83409 GGAGTACATAATCATATTTAATTGCACGTCACTTGCACAGAAGCCTGAAGGATCTAAGTGCAT
1 GGAGTACATAATCATATTTAATTGCACGTCACTTGCACAGAAGCCTGAAGGATCTAAGTGCAT
*
83472 GGAGTACATAATCATGTTTAATTGCACGTCACTTGCACAGAAGCCTGAAGGATCTAAGTGCA
1 GGAGTACATAATCATATTTAATTGCACGTCACTTGCACAGAAGCCTGAAGGATCTAAGTGCA
83534 CCCTACAAGA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (63 bp):
GGAGTACATAATCATATTTAATTGCACGTCACTTGCACAGAAGCCTGAAGGATCTAAGTGCAT
Found at i:93981 original size:23 final size:20
Alignment explanation
Indices: 93930--94009 Score: 60
Period size: 23 Copynumber: 4.0 Consensus size: 20
93920 GGGCTACTCA
93930 AATAAAAATTAAATAAAAAC
1 AATAAAAATTAAATAAAAAC
* *
93950 ATTACAAATTAAATAATAAAAAC
1 AATAAAAATT--A-AATAAAAAC
*
93973 AATAAAAA-T-AAT-TAAAC
1 AATAAAAATTAAATAAAAAC
* *
93990 -ATAAACATTAAATACAAAC
1 AATAAAAATTAAATAAAAAC
94009 A
1 A
94010 TTACAAGTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
16 6 0.13
17 5 0.11
18 6 0.13
19 4 0.09
20 8 0.17
22 2 0.04
23 15 0.33
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (20 bp):
AATAAAAATTAAATAAAAAC
Found at i:94171 original size:3 final size:3
Alignment explanation
Indices: 94163--94192 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
94153 CTCCTCACTC
94163 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
94193 GTAGCAGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:101736 original size:14 final size:14
Alignment explanation
Indices: 101717--101743 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
101707 TTATTAGAGC
101717 AGTACCGATACTCA
1 AGTACCGATACTCA
101731 AGTACCGATACTC
1 AGTACCGATACTC
101744 CCAGCTTGAG
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:0.33, C:0.30, G:0.15, T:0.22
Consensus pattern (14 bp):
AGTACCGATACTCA
Found at i:104569 original size:13 final size:14
Alignment explanation
Indices: 104548--104576 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
104538 AGATATGTTA
104548 TTAATTTTAATTAT
1 TTAATTTTAATTAT
104562 TTAA-TTTAATTAT
1 TTAATTTTAATTAT
104575 TT
1 TT
104577 CCAATTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTAATTTTAATTAT
Found at i:104881 original size:13 final size:14
Alignment explanation
Indices: 104863--104910 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
104853 ACATAATCAT
104863 TAAATTAT-TTTTA
1 TAAATTATATTTTA
104876 TAAATTATATTTT-
1 TAAATTATATTTTA
* *
104889 T-AATTTTATTTAA
1 TAAATTATATTTTA
104902 T-AATTATAT
1 TAAATTATAT
104911 AATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 9 0.30
13 17 0.57
14 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TAAATTATATTTTA
Found at i:105048 original size:20 final size:20
Alignment explanation
Indices: 105025--105063 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
105015 TTAATTTTTA
105025 ATTTTAAAAATATTAAATTT
1 ATTTTAAAAATATTAAATTT
* **
105045 ATTTTTATTATATTAAATT
1 ATTTTAAAAATATTAAATT
105064 ATTATTACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAAAAATATTAAATTT
Found at i:105070 original size:16 final size:15
Alignment explanation
Indices: 105049--105084 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
105039 AAATTTATTT
*
105049 TTATTATATTAAATTA
1 TTATTACATTAAA-TA
105065 TTATTACATTAAATA
1 TTATTACATTAAATA
105080 TTATT
1 TTATT
105085 TTAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (15 bp):
TTATTACATTAAATA
Found at i:106646 original size:30 final size:30
Alignment explanation
Indices: 106612--106676 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
106602 CTTATTAGTT
**
106612 ATTATAGGTATACTTTACCCTGATATTAAA
1 ATTATAGAAATACTTTACCCTGATATTAAA
**
106642 ATTATTTAAATACTTTACCCTGATATTAAA
1 ATTATAGAAATACTTTACCCTGATATTAAA
106672 ATTAT
1 ATTAT
106677 TTAAAAATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.43
Consensus pattern (30 bp):
ATTATAGAAATACTTTACCCTGATATTAAA
Found at i:106677 original size:30 final size:30
Alignment explanation
Indices: 106621--106681 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
106611 TATTATAGGT
106621 ATACTTTACCCTGATATTAAAATTATTTAA
1 ATACTTTACCCTGATATTAAAATTATTTAA
106651 ATACTTTACCCTGATATTAAAATTATTTAA
1 ATACTTTACCCTGATATTAAAATTATTTAA
106681 A
1 A
106682 AATTATGGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.41, C:0.13, G:0.03, T:0.43
Consensus pattern (30 bp):
ATACTTTACCCTGATATTAAAATTATTTAA
Found at i:118143 original size:13 final size:13
Alignment explanation
Indices: 118121--118153 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
118111 CTTACTTTTT
*
118121 TTTA-TTTATTTG
1 TTTATTTTATTTA
118133 TTTATTTTATTTA
1 TTTATTTTATTTA
118146 TTTATTTT
1 TTTATTTT
118154 TCTTTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTATTTTATTTA
Done.