Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002777.1 Hibiscus syriacus cultivar Beakdansim tig00005719_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: 227343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7211 original size:3 final size:3
Alignment explanation
Indices: 7205--7232 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7195 TGGTGGTGAA
7205 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
7233 GTGCATGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:10324 original size:31 final size:31
Alignment explanation
Indices: 10286--10395 Score: 130
Period size: 31 Copynumber: 3.5 Consensus size: 31
10276 AGAGTCGAGG
*
10286 GTTTACCTATGTTCTTTGAAACATATGGACT
1 GTTTACCTATGTTCTTCGAAACATATGGACT
* **
10317 GTTTACCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGAAACATATGGACT
** *
10348 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGAAACATATGGACT
** *
10379 GAATACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
10396 AGAATCTATG
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGAAACATATGGACT
Found at i:24700 original size:130 final size:129
Alignment explanation
Indices: 24382--24718 Score: 385
Period size: 131 Copynumber: 2.6 Consensus size: 129
24372 ATTATTTCTG
** *
24382 ATCGAGAATAAATGACCTCTTGTGCCTTAAAACATTCATTTATTACTCCAATTGAAATGAAGAGA
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAGCATT-ATTTATTACTCCAA-TGAAATGAAGAGA
* * * *
24447 TATCACTATTTCATCTTAAAATTCAATATCAATTCAAGTGAAAACAATAATATCTAATGATTTCC
64 TATCACTATTCCATCTTAAAAATCAATATCAATTCAAGAGAAAACAATAATATCAAATGATTTCC
24512 A
129 A
* * **
24513 ATCGAGAATAAAT-AACTGCTCATACCTTAAAGCAACCATTTATTACTCCAATCGAAATGAAGAG
1 ATCGAGAATAAATGACCT-CTCATGCCTTAAAGC-ATTATTTATTACTCCAAT-GAAATGAAGAG
* * * ** * * *
24577 ATGTCACTATTCCGTCTTAAAAATCAATAAT-GATTTGAGAGAAAATATTAATATCAAATTA-TT
63 ATATCACTATTCCATCTTAAAAATCAAT-ATCAATTCAAGAGAAAACAATAATATCAAATGATTT
24640 CCA
127 CCA
24643 ATCGAGAATAAATGACCTCTCATGCCTTAAAGCAGTTATTTATTACTCCAACTGAAATGATA-AG
1 ATCGAGAATAAATGACCTCTCATGCCTTAAAGCA-TTATTTATTACTCCAA-TGAAATGA-AGAG
*
24707 ATATTACTATTC
63 ATATCACTATTC
24719 TCAATATCAA
Statistics
Matches: 173, Mismatches: 25, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
129 1 0.01
130 69 0.40
131 100 0.58
132 3 0.02
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.32
Consensus pattern (129 bp):
ATCGAGAATAAATGACCTCTCATGCCTTAAAGCATTATTTATTACTCCAATGAAATGAAGAGATA
TCACTATTCCATCTTAAAAATCAATATCAATTCAAGAGAAAACAATAATATCAAATGATTTCCA
Found at i:26812 original size:3 final size:3
Alignment explanation
Indices: 26783--26828 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
26773 CTGTAAAATA
* * * *
26783 AAT AAA AAT AAT ATT AAT AAC ACT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
26829 GCGGGATGAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:27014 original size:16 final size:16
Alignment explanation
Indices: 26993--27025 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
26983 GATGCTAAAG
26993 GCCAAGTAGATATATA
1 GCCAAGTAGATATATA
27009 GCCAAGTAGATATATA
1 GCCAAGTAGATATATA
27025 G
1 G
27026 TCAAACATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (16 bp):
GCCAAGTAGATATATA
Found at i:29951 original size:15 final size:15
Alignment explanation
Indices: 29933--29966 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29923 TTTTCAACTT
*
29933 AACTCGATTCAAAAG
1 AACTCGACTCAAAAG
29948 AACTCGACTCAAAAG
1 AACTCGACTCAAAAG
29963 AACT
1 AACT
29967 TCAAGTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.47, C:0.24, G:0.12, T:0.18
Consensus pattern (15 bp):
AACTCGACTCAAAAG
Found at i:30140 original size:4 final size:4
Alignment explanation
Indices: 30131--30155 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
30121 ATTACATATA
30131 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
30156 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:30160 original size:2 final size:2
Alignment explanation
Indices: 30153--30220 Score: 77
Period size: 2 Copynumber: 33.5 Consensus size: 2
30143 AAATAAATAA
* *
30153 AT AT AT AT AT AT AT AT AT AT AT AT AT CA- AA AT CAT AC AT GA-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT -AT
30194 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 A
30221 ATGTATATTG
Statistics
Matches: 58, Mismatches: 3, Indels: 10
0.82 0.04 0.14
Matches are distributed among these distances:
1 2 0.03
2 52 0.90
3 4 0.07
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:30164 original size:8 final size:8
Alignment explanation
Indices: 30105--30220 Score: 78
Period size: 8 Copynumber: 14.5 Consensus size: 8
30095 CACTCAATTC
30105 TATATGATA
1 TATAT-ATA
*
30114 TATGTATA
1 TATATATA
*
30122 T-TACATA
1 TATATATA
*
30129 TA-AAATA
1 TATATATA
* *
30136 AATAAATA
1 TATATATA
* *
30144 AATAAATA
1 TATATATA
*
30152 AATATATA
1 TATATATA
30160 TATATATA
1 TATATATA
30168 TATATATA
1 TATATATA
*
30176 TATCA-AAA
1 TAT-ATATA
*
30184 TCATACATGA
1 T-ATATAT-A
30194 -ATATATA
1 TATATATA
30201 TATATATA
1 TATATATA
30209 TATATATA
1 TATATATA
30217 TATA
1 TATA
30221 ATGTATATTG
Statistics
Matches: 90, Mismatches: 10, Indels: 15
0.78 0.09 0.13
Matches are distributed among these distances:
7 11 0.12
8 70 0.78
9 8 0.09
10 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (8 bp):
TATATATA
Found at i:31449 original size:3 final size:3
Alignment explanation
Indices: 31443--31473 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
31433 ATTAAATAAA
31443 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31474 TTAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:33312 original size:229 final size:227
Alignment explanation
Indices: 32907--33355 Score: 799
Period size: 229 Copynumber: 2.0 Consensus size: 227
32897 GTAAATTATC
* * *
32907 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
**
32972 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
33037 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
131 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
33102 AAACATAAATTACATAACTTTCAAAAAAGTATA
196 AAACATAAATTACATAACTTT-AAAAAAGTATA
*
33135 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
33200 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATT
* *
33265 TTGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATT
33330 GAAACATAAATTACATAACTTTAAAA
195 GAAACATAAATTACATAACTTTAAAA
33356 GCAGTTTTAA
Statistics
Matches: 211, Mismatches: 9, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
228 40 0.19
229 171 0.81
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.39
Consensus pattern (227 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAAAATTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTACATAACTTTAAAAAAGTATA
Found at i:33443 original size:20 final size:20
Alignment explanation
Indices: 33420--33464 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
33410 CGATATACCA
33420 GGTAA-AAATATGATAAAACC
1 GGTAACAAA-ATGATAAAACC
33440 GGTAACAAAATGATAAAACC
1 GGTAACAAAATGATAAAACC
33460 GGTAA
1 GGTAA
33465 TTTAAAAGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (20 bp):
GGTAACAAAATGATAAAACC
Found at i:33609 original size:20 final size:19
Alignment explanation
Indices: 33586--33632 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
33576 CGATATAACA
33586 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
33606 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
33626 GGTAAAA
1 GGTAAAA
33633 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:33634 original size:17 final size:19
Alignment explanation
Indices: 33595--33637 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
33585 AGGTAAAAAT
33595 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
33615 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
33632 ATGATA
1 ATGATA
33638 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:35907 original size:21 final size:21
Alignment explanation
Indices: 35860--35924 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
35850 AAGACAATCA
* *
35860 AGAGTCGAAGAGAAACTTGATC
1 AGAGTCGAAGAGAAACTCGA-G
*
35882 A-AGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
* *
35902 AGAGTCGAAGATACACTCGAG
1 AGAGTCGAAGAGAAACTCGAG
35923 AG
1 AG
35925 GCATAAGGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.03
21 34 0.94
22 1 0.03
ACGTcount: A:0.40, C:0.15, G:0.29, T:0.15
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTCGAG
Found at i:35999 original size:33 final size:33
Alignment explanation
Indices: 35957--36022 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
35947 AAATAGATGG
*
35957 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
35990 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
36023 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:40421 original size:22 final size:20
Alignment explanation
Indices: 40387--40433 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
40377 ATAATTATTT
40387 AAAAAATTAAATAAAAATACA
1 AAAAAATTAAATAAAAA-ACA
*
40408 AAAAATATTTAATAAAAAACTA
1 AAAAA-ATTAAATAAAAAAC-A
40430 AAAA
1 AAAA
40434 CATTCCCACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAAAATTAAATAAAAAACA
Found at i:40433 original size:23 final size:21
Alignment explanation
Indices: 40387--40433 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40377 ATAATTATTT
40387 AAAAAATTAAATAAAAATACA
1 AAAAAATTAAATAAAAATACA
* *
40408 AAAAATATTTAATAAAAA-ACT
1 AAAAA-ATTAAATAAAAATACA
40429 AAAAA
1 AAAAA
40434 CATTCCCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACA
Found at i:41455 original size:25 final size:24
Alignment explanation
Indices: 41421--41484 Score: 94
Period size: 25 Copynumber: 2.6 Consensus size: 24
41411 TATGGTACCG
41421 AAATAACTATTATTAAATTTCAATA
1 AAATAACTATTATTAAATTTCAA-A
*
41446 AAATACCTATTATTAAATTTCAAA
1 AAATAACTATTATTAAATTTCAAA
41470 AAA-AATCTATTATTA
1 AAATAA-CTATTATTA
41485 GACTTGCCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 1 0.03
24 13 0.36
25 22 0.61
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (24 bp):
AAATAACTATTATTAAATTTCAAA
Found at i:42270 original size:42 final size:42
Alignment explanation
Indices: 42211--42294 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
42201 CTGCCTTTTT
*
42211 ATGTACTCATTTTGTATGGTAGTAAATAGAGTATAGTGGTGG
1 ATGTACGCATTTTGTATGGTAGTAAATAGAGTATAGTGGTGG
42253 ATGTACGCATTTTGTATGGTAGTAAATAGAGTATAGTGGTGG
1 ATGTACGCATTTTGTATGGTAGTAAATAGAGTATAGTGGTGG
42295 TTGGCTCTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.29, C:0.05, G:0.30, T:0.37
Consensus pattern (42 bp):
ATGTACGCATTTTGTATGGTAGTAAATAGAGTATAGTGGTGG
Found at i:43902 original size:135 final size:134
Alignment explanation
Indices: 43759--44014 Score: 397
Period size: 135 Copynumber: 1.9 Consensus size: 134
43749 TATGACTGAG
* * *
43759 AAAAAGTTGAATGATAC-AAGTTTATAATTGAGCCTTTAAATAATATTAACTTTAGAAAATTATG
1 AAAAAGTTGAATGATACTAA-TTTATAATTGAACCTTAAAATAATATCAACTTTAGAAAATTATG
** ** *
43823 TACCTATTTTTTTAAGATAATTTTAGAAAGAGGAAATAAAATGTTATTTTATGCAAAAATGAGTG
65 TACCTACCTTTAGAAGATAATTTTAG-AAGAGGAAATAAAATGCTATTTTATGCAAAAATGAGTG
43888 AGAAAA
129 AGAAAA
* *
43894 AAAAAGTTGAGTGATACTAATTTATAATTGAACCTTAAAATAATATCAACTTTAGAAAATTGTGT
1 AAAAAGTTGAATGATACTAATTTATAATTGAACCTTAAAATAATATCAACTTTAGAAAATTATGT
43959 ACCTACCTTTAGAAGATAATTTTAGAAGAGGAAATAAAATGCTATTTTATGCAAAA
66 ACCTACCTTTAGAAGATAATTTTAGAAGAGGAAATAAAATGCTATTTTATGCAAAA
44015 TGCTATTTTA
Statistics
Matches: 110, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
134 30 0.27
135 78 0.71
136 2 0.02
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (134 bp):
AAAAAGTTGAATGATACTAATTTATAATTGAACCTTAAAATAATATCAACTTTAGAAAATTATGT
ACCTACCTTTAGAAGATAATTTTAGAAGAGGAAATAAAATGCTATTTTATGCAAAAATGAGTGAG
AAAA
Found at i:44690 original size:2 final size:2
Alignment explanation
Indices: 44683--44722 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
44673 AAAACCCTAA
44683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44723 TTAGTTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45297 original size:20 final size:21
Alignment explanation
Indices: 45264--45308 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
45254 AAATAAAGGG
45264 TAAATTATGCA-TTTAGTACC
1 TAAATTATGCATTTTAGTACC
*
45284 TAAATTAT-CAATTTTAGTACT
1 TAAATTATGC-ATTTTAGTACC
45305 TAAA
1 TAAA
45309 CTCTTAGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.41
21 12 0.55
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (21 bp):
TAAATTATGCATTTTAGTACC
Found at i:47228 original size:43 final size:43
Alignment explanation
Indices: 47154--47267 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 43
47144 TTTGATAACA
* *** * *
47154 AAAAACGCCGCAATAGGTAAAGATATATAGCGGAGTTTGT-CC
1 AAAAACACCGCAATAGGTGTTGAGATTTAGCGGAGTTTGTCCC
* *
47196 AACAAACACTGCAATAGGTGTTGAGATTTAGCGGCGTTTGTCCC
1 AA-AAACACCGCAATAGGTGTTGAGATTTAGCGGAGTTTGTCCC
* *
47240 AAAAACACCGCAATATGTGTTGATATTT
1 AAAAACACCGCAATAGGTGTTGAGATTT
47268 TAGGGGCGAT
Statistics
Matches: 59, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 2 0.03
43 53 0.90
44 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (43 bp):
AAAAACACCGCAATAGGTGTTGAGATTTAGCGGAGTTTGTCCC
Found at i:47407 original size:45 final size:45
Alignment explanation
Indices: 47358--47443 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
47348 TTTAGCAGCA
47358 TTTTTCGGATACAAACGCCGCAAAAGGTCTGGTATATAGCGGCGC
1 TTTTTCGGATACAAACGCCGCAAAAGGTCTGGTATATAGCGGCGC
** * *
47403 TTTTTTTGATACAAACGCCGTAAAAGGTCTTGTATATAGCG
1 TTTTTCGGATACAAACGCCGCAAAAGGTCTGGTATATAGCG
47444 ACGTTGTCGT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (45 bp):
TTTTTCGGATACAAACGCCGCAAAAGGTCTGGTATATAGCGGCGC
Found at i:67175 original size:3 final size:3
Alignment explanation
Indices: 67169--67206 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
67159 AACATAATAT
*
67169 TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
67207 AATCACTCTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:70998 original size:31 final size:31
Alignment explanation
Indices: 70960--71038 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
70950 GTTTTTTTTG
70960 GTTCATGTTCGTTCATTAAAGAATATAGCTT
1 GTTCATGTTCGTTCATTAAAGAATATAGCTT
*
70991 GTTCATGTTCGTTCATTAAGGAATATAGCTT
1 GTTCATGTTCGTTCATTAAAGAATATAGCTT
71022 GTTCATGTTCGTTCATT
1 GTTCATGTTCGTTCATT
71039 TAATAAATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (31 bp):
GTTCATGTTCGTTCATTAAAGAATATAGCTT
Found at i:71112 original size:16 final size:16
Alignment explanation
Indices: 71049--71113 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
71039 TAATAAATAA
* *
71049 ACGAATATAAACGAAA
1 ACGAACATAAACGAAC
*
71065 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
71081 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
71097 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
71113 A
1 A
71114 TAAACGTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:71119 original size:26 final size:26
Alignment explanation
Indices: 71045--71111 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
71035 CATTTAATAA
*
71045 ATAAACGAATATAAACGAAAACGAAC
1 ATAAACGAACATAAACGAAAACGAAC
* *
71071 ATAAATGAACATGAAC-ATAAACGAAC
1 ATAAACGAACATAAACGA-AAACGAAC
71097 ----ACGAACATAAACGAA
1 ATAAACGAACATAAACGAA
71112 CATAAACGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
22 11 0.32
23 1 0.03
25 1 0.03
26 21 0.62
ACGTcount: A:0.60, C:0.16, G:0.12, T:0.12
Consensus pattern (26 bp):
ATAAACGAACATAAACGAAAACGAAC
Found at i:76516 original size:13 final size:13
Alignment explanation
Indices: 76498--76522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
76488 TAGTTTACCC
76498 TAAAATAAAAAAG
1 TAAAATAAAAAAG
76511 TAAAATAAAAAA
1 TAAAATAAAAAA
76523 TTATTAGAAT
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAAATAAAAAAG
Found at i:78573 original size:389 final size:389
Alignment explanation
Indices: 77856--78597 Score: 1466
Period size: 389 Copynumber: 1.9 Consensus size: 389
77846 CGTAGGAAGA
77856 AGAATATGGCATTCGTCATTGCGGAATGAAAAATGATGAGCCATATCAACGAATTGTTATTTATC
1 AGAATATGGCATTCGTCATTGCGGAATGAAAAATGATGAGCCATATCAACGAATTGTTATTTATC
77921 TACAACAATCTAGATTGTATCTTACCATATTTCTTCGTGGTTTTAGGGTGATGCATGCATGAATT
66 TACAACAATCTAGATTGTATCTTACCATATTTCTTCGTGGTTTTAGGGTGATGCATGCATGAATT
77986 TCGGTGTTGATTGTACATTGGAGACCCAAAACTCATATTTTTTGTTTTCTTAGTGGTGAAGCAGC
131 TCGGTGTTGATTGTACATTGGAGACCCAAAACTCATATTTTTTGTTTTCTTAGTGGTGAAGCAGC
*
78051 GATTACTTTGGAAGATATGGCTTATCAAGTTGGCGTTCTAATAAATGGTGTGACATTGGTAAGAC
196 GATTACTTTGAAAGATATGGCTTATCAAGTTGGCGTTCTAATAAATGGTGTGACATTGGTAAGAC
78116 AACAATTACAAGCGAGACTAGATTTGCCAGCAATTATTTGGAAAGGTACACTAAAAGATGTCACA
261 AACAATTACAAGCGAGACTAGATTTGCCAGCAATTATTTGGAAAGGTACACTAAAAGATGTCACA
78181 AATGGGCTTTAAATATTGATGACATAGTTGGAGAGTGAATCTTAAGTGGATGAGAGTTCTACCG
326 AATGGGCTTTAAATATTGATGACATAGTTGGAGAGTGAATCTTAAGTGGATGAGAGTTCTACCG
78245 AGAATATGGCATTCGTCATTGCGGAATGAAAAATGATGAGCCATATCAACGAATTGTTATTTATC
1 AGAATATGGCATTCGTCATTGCGGAATGAAAAATGATGAGCCATATCAACGAATTGTTATTTATC
*
78310 TACAACAATCTAGATTGTATCTTACCGTATTTCTTCGTGGTTTTAGGGTGATGCATGCATGAATT
66 TACAACAATCTAGATTGTATCTTACCATATTTCTTCGTGGTTTTAGGGTGATGCATGCATGAATT
78375 TCGGTGTTGATTGTACATTGGAGACCCAAAACTCATATTTTTTGTTTTCTTAGTGGTGAAGCAGC
131 TCGGTGTTGATTGTACATTGGAGACCCAAAACTCATATTTTTTGTTTTCTTAGTGGTGAAGCAGC
78440 GATTACTTTGAAAGATATGGCTTATCAAGTTGGCGTTCTAATAAATGGTGTGACATTGGTAAGAC
196 GATTACTTTGAAAGATATGGCTTATCAAGTTGGCGTTCTAATAAATGGTGTGACATTGGTAAGAC
78505 AACAATTACAAGCGAGACTAGATTTGCCAGCAATTATTTGGAAAGGTACACTAAAAGATGTCACA
261 AACAATTACAAGCGAGACTAGATTTGCCAGCAATTATTTGGAAAGGTACACTAAAAGATGTCACA
78570 AATGGGCTTTAAATATTGATGACATAGT
326 AATGGGCTTTAAATATTGATGACATAGT
78598 CTATGTATTC
Statistics
Matches: 351, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
389 351 1.00
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (389 bp):
AGAATATGGCATTCGTCATTGCGGAATGAAAAATGATGAGCCATATCAACGAATTGTTATTTATC
TACAACAATCTAGATTGTATCTTACCATATTTCTTCGTGGTTTTAGGGTGATGCATGCATGAATT
TCGGTGTTGATTGTACATTGGAGACCCAAAACTCATATTTTTTGTTTTCTTAGTGGTGAAGCAGC
GATTACTTTGAAAGATATGGCTTATCAAGTTGGCGTTCTAATAAATGGTGTGACATTGGTAAGAC
AACAATTACAAGCGAGACTAGATTTGCCAGCAATTATTTGGAAAGGTACACTAAAAGATGTCACA
AATGGGCTTTAAATATTGATGACATAGTTGGAGAGTGAATCTTAAGTGGATGAGAGTTCTACCG
Found at i:80921 original size:18 final size:19
Alignment explanation
Indices: 80892--80929 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
80882 TTAGGAAAAA
80892 TTATTATATTTTTTAATAT
1 TTATTATATTTTTTAATAT
80911 TTATT-TATTTTTTAATAT
1 TTATTATATTTTTTAATAT
80929 T
1 T
80930 GAAGCAAGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTATATTTTTTAATAT
Found at i:81020 original size:2 final size:2
Alignment explanation
Indices: 81013--81061 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
81003 AAAACCCTAA
81013 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81055 AT AT AT A
1 AT AT AT A
81062 CTTTAGTTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83894 original size:23 final size:23
Alignment explanation
Indices: 83868--83912 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
83858 CACCACAGCT
*
83868 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
83891 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
83913 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:84150 original size:149 final size:149
Alignment explanation
Indices: 83893--84194 Score: 559
Period size: 149 Copynumber: 2.0 Consensus size: 149
83883 AAGTGCCCCG
* *
83893 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
83958 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
84023 TATGTCCCGAAGAACCGCA
131 TATGTCCCGAAGAACCGCA
84042 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
84107 TATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
* *
84172 TATGTCTCGAAGAACCGCG
131 TATGTCCCGAAGAACCGCA
84191 TAGA
1 TAGA
84195 CCCTCGACTC
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCGCA
Found at i:85028 original size:18 final size:18
Alignment explanation
Indices: 85005--85039 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
84995 TCCCATCTAG
85005 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
85023 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
85040 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:85649 original size:21 final size:21
Alignment explanation
Indices: 85619--85662 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
85609 ATTCTGTCGT
* *
85619 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
85640 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
85661 TT
1 TT
85663 TCCCAGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:89170 original size:149 final size:149
Alignment explanation
Indices: 88900--89201 Score: 559
Period size: 149 Copynumber: 2.0 Consensus size: 149
88890 AAGTGCCCCG
* *
88900 TAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACGTAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
88965 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
89030 TATGTCCCGAAGAACCGCA
131 TATGTCCCGAAGAACCGCA
89049 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
1 TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
*
89114 TATACATATGCTAGGGATCAAGTATGTGTCTTTCTAGACTTCACACATGTTCCAAAGAATATACA
66 TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
* *
89179 TATGTCTCGAAGAACCGCG
131 TATGTCCCGAAGAACCGCA
89198 TAGA
1 TAGA
89202 CCCTCGACTC
Statistics
Matches: 148, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 148 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
TAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAATCA
TATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATACA
TATGTCCCGAAGAACCGCA
Found at i:90033 original size:18 final size:18
Alignment explanation
Indices: 90010--90044 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
90000 TCCCATCTAG
90010 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
90028 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
90045 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:90654 original size:21 final size:21
Alignment explanation
Indices: 90624--90668 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
90614 ATTCTGTCGT
* *
90624 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
90645 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
90666 TTG
1 TTG
90669 CCCAGAAATC
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:92312 original size:21 final size:21
Alignment explanation
Indices: 92287--92336 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
92277 TACTGATATG
*
92287 TTGCTTCTCTCTGTGCTTCCGC
1 TTGCTTCTCTCTCTGCTTCC-C
*
92309 -TGCTGCTCTCTCTGCTTCCC
1 TTGCTTCTCTCTCTGCTTCCC
92329 TTGCTTCT
1 TTGCTTCT
92337 TTTTCAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.00, C:0.38, G:0.16, T:0.46
Consensus pattern (21 bp):
TTGCTTCTCTCTCTGCTTCCC
Found at i:103291 original size:27 final size:27
Alignment explanation
Indices: 103261--103312 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
103251 TTTTCAAAAA
*
103261 CTATTATTTTCCTTTTCGAAAGCAGAT
1 CTATTATTTTCCTATTCGAAAGCAGAT
*
103288 CTATTATTTTTCTATTCGAAAGCAG
1 CTATTATTTTCCTATTCGAAAGCAG
103313 TAAACCAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.12, T:0.44
Consensus pattern (27 bp):
CTATTATTTTCCTATTCGAAAGCAGAT
Found at i:107021 original size:3 final size:3
Alignment explanation
Indices: 107013--107053 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
107003 AACATAATAT
*
107013 TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
107054 AATCACTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:107297 original size:23 final size:21
Alignment explanation
Indices: 107254--107317 Score: 60
Period size: 21 Copynumber: 3.0 Consensus size: 21
107244 ATTCTAATAA
*
107254 TAAATAA-TTAAAATATAAATT
1 TAAATAATTTAAAAAATAAA-T
107275 TAAGTATAATTTAAAAAAT-AAT
1 TAA--ATAATTTAAAAAATAAAT
*
107297 TAAATAATTATAAAAACTAAA
1 TAAATAATT-TAAAAAATAAA
107318 ATAGTATTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 6 0.17
21 10 0.28
22 6 0.17
23 6 0.17
24 8 0.22
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAATAATTTAAAAAATAAAT
Found at i:108061 original size:15 final size:15
Alignment explanation
Indices: 108041--108070 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
108031 GCAATACTCG
108041 AGCTCGACTCGGCTC
1 AGCTCGACTCGGCTC
*
108056 AGCTCGGCTCGGCTC
1 AGCTCGACTCGGCTC
108071 GTTTACACCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.40, G:0.30, T:0.20
Consensus pattern (15 bp):
AGCTCGACTCGGCTC
Found at i:110756 original size:31 final size:31
Alignment explanation
Indices: 110715--110793 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
110705 GTTTTTTTTG
*
110715 GTTCACGTTCGTTCATTAAAGAATATAGCTT
1 GTTCATGTTCGTTCATTAAAGAATATAGCTT
*
110746 GTTCATGTTCGTTCATTAAGGAATATAGCTT
1 GTTCATGTTCGTTCATTAAAGAATATAGCTT
110777 GTTCATGTTCGTTCATT
1 GTTCATGTTCGTTCATT
110794 TAATAAATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.43
Consensus pattern (31 bp):
GTTCATGTTCGTTCATTAAAGAATATAGCTT
Found at i:110839 original size:16 final size:16
Alignment explanation
Indices: 110810--110869 Score: 93
Period size: 16 Copynumber: 3.8 Consensus size: 16
110800 ATAAACGAAT
*
110810 ATAAACGAAAATGAAC
1 ATAAACGAACATGAAC
*
110826 ATAAATGAACATGAAC
1 ATAAACGAACATGAAC
*
110842 ATAAACGAACACGAAC
1 ATAAACGAACATGAAC
110858 ATAAACGAACAT
1 ATAAACGAACAT
110870 AAACGTTGGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.13
Consensus pattern (16 bp):
ATAAACGAACATGAAC
Found at i:113109 original size:2 final size:2
Alignment explanation
Indices: 113102--113152 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
113092 AATACGAAGC
113102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113144 AT AT AT AT A
1 AT AT AT AT A
113153 AAGACCTCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:116312 original size:13 final size:13
Alignment explanation
Indices: 116294--116318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116284 TAGTTTACCC
116294 TAAAATAAAAAAG
1 TAAAATAAAAAAG
116307 TAAAATAAAAAA
1 TAAAATAAAAAA
116319 TTATTAGAAT
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAAATAAAAAAG
Found at i:119602 original size:31 final size:31
Alignment explanation
Indices: 119567--119640 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
119557 TGATACTAAG
* *
119567 TACCAATACTATAGTGCAAATATTGTTGTAC
1 TACCAATACTATAGTGCAAATACTATTGTAC
* * ** *
119598 TACCAATACTAAAGTTCCGATACTATTGTAG
1 TACCAATACTATAGTGCAAATACTATTGTAC
119629 TACCAATACTAT
1 TACCAATACTAT
119641 TATAATATTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (31 bp):
TACCAATACTATAGTGCAAATACTATTGTAC
Found at i:122711 original size:21 final size:20
Alignment explanation
Indices: 122685--122732 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 20
122675 TCTTTTTCTA
122685 AAAAAATAATATTAAAATTAAT
1 AAAAAATAATA-TAAAA-TAAT
122707 AAAAAATAA-ATAAAATAAT
1 AAAAAATAATATAAAATAAT
122726 GAAAAAA
1 -AAAAAA
122733 ATAAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 1 0.04
22 9 0.36
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAAATAATATAAAATAAT
Found at i:122733 original size:21 final size:20
Alignment explanation
Indices: 122683--122744 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
122673 TTTCTTTTTC
122683 TAAAAAAATAATATTAAAATTAA
1 TAAAAAAATAA-A-TAAAA-TAA
122706 T-AAAAAATAAATAAAATAA
1 TAAAAAAATAAATAAAATAA
*
122725 TGAAAAAAATAAACAAAATA
1 T-AAAAAAATAAATAAAATA
122745 TTGCTATTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 17 0.47
22 9 0.25
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAAAAAATAAATAAAATAA
Found at i:126325 original size:31 final size:31
Alignment explanation
Indices: 126282--126360 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
126272 GTTTTTTTTG
126282 GTTCATGTTCGTTCATTAAAGAATATAGCTT
1 GTTCATGTTCGTTCATTAAAGAATATAGCTT
* *
126313 GTTCTTGTTCGTTCATTAAGGAATATAGCTT
1 GTTCATGTTCGTTCATTAAAGAATATAGCTT
126344 GTTCATGTTCGTTCATT
1 GTTCATGTTCGTTCATT
126361 TAATAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.23, C:0.14, G:0.18, T:0.46
Consensus pattern (31 bp):
GTTCATGTTCGTTCATTAAAGAATATAGCTT
Found at i:126434 original size:16 final size:16
Alignment explanation
Indices: 126371--126435 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
126361 TAATAAATAA
* *
126371 ACGAATATAAACGAAA
1 ACGAACATAAACGAAC
*
126387 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
126403 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
126419 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
126435 A
1 A
126436 TAAACGTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.58, C:0.18, G:0.12, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:126441 original size:26 final size:26
Alignment explanation
Indices: 126367--126433 Score: 63
Period size: 26 Copynumber: 2.7 Consensus size: 26
126357 CATTTAATAA
*
126367 ATAAACGAATATAAACGAAAACGAAC
1 ATAAACGAACATAAACGAAAACGAAC
* *
126393 ATAAATGAACATGAAC-ATAAACGAAC
1 ATAAACGAACATAAACGA-AAACGAAC
126419 ----ACGAACATAAACGAA
1 ATAAACGAACATAAACGAA
126434 CATAAACGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
22 11 0.32
23 1 0.03
25 1 0.03
26 21 0.62
ACGTcount: A:0.60, C:0.16, G:0.12, T:0.12
Consensus pattern (26 bp):
ATAAACGAACATAAACGAAAACGAAC
Found at i:127535 original size:14 final size:14
Alignment explanation
Indices: 127518--127559 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
127508 GATTGGGTTA
*
127518 AACATAAATGAACG
1 AACATAAACGAACG
*
127532 AACATAACCGAACG
1 AACATAAACGAACG
*
127546 AACATAACCGAACG
1 AACATAAACGAACG
127560 TTCACGAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:131847 original size:13 final size:13
Alignment explanation
Indices: 131829--131853 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
131819 TAGTTTACCC
131829 TAAAATAAAAAAG
1 TAAAATAAAAAAG
131842 TAAAATAAAAAA
1 TAAAATAAAAAA
131854 TTATTAGAAT
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:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
TAAAATAAAAAAG
Found at i:135140 original size:31 final size:31
Alignment explanation
Indices: 135105--135178 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
135095 TGATACTAAG
* *
135105 TACCAATACTATAGTGCAAATATTGTTGTAC
1 TACCAATACTATAGTGCAAATACTATTGTAC
* * * ** *
135136 TACCAATGCTAAAGTTCCGATACTATTGTAG
1 TACCAATACTATAGTGCAAATACTATTGTAC
135167 TACCAATACTAT
1 TACCAATACTAT
135179 TATAATATTA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (31 bp):
TACCAATACTATAGTGCAAATACTATTGTAC
Found at i:137382 original size:4 final size:4
Alignment explanation
Indices: 137373--137397 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
137363 TGTGACTACT
137373 TTCA TTCA TTCA TTCA TTCA TTCA T
1 TTCA TTCA TTCA TTCA TTCA TTCA T
137398 ATTATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (4 bp):
TTCA
Found at i:138248 original size:21 final size:20
Alignment explanation
Indices: 138222--138269 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 20
138212 TCTTTTTCTA
138222 AAAAAATAATATTAAAATTAAT
1 AAAAAATAATA-TAAAA-TAAT
138244 AAAAAATAA-ATAAAATAAT
1 AAAAAATAATATAAAATAAT
138263 GAAAAAA
1 -AAAAAA
138270 ATAAACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 1 0.04
22 9 0.36
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAAAATAATATAAAATAAT
Found at i:138270 original size:21 final size:20
Alignment explanation
Indices: 138220--138281 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
138210 TTTCTTTTTC
138220 TAAAAAAATAATATTAAAATTAA
1 TAAAAAAATAA-A-TAAAA-TAA
138243 T-AAAAAATAAATAAAATAA
1 TAAAAAAATAAATAAAATAA
*
138262 TGAAAAAAATAAACAAAATA
1 T-AAAAAAATAAATAAAATA
138282 TTGCTATTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 4 0.11
20 5 0.14
21 17 0.47
22 9 0.25
23 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
TAAAAAAATAAATAAAATAA
Found at i:141234 original size:33 final size:32
Alignment explanation
Indices: 141192--141257 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 32
141182 CATCGAAGGG
*
141192 ACTTCGAGTAAA-TGTTATTCACTTAGACTATAA
1 ACTTCGAGTAAAGT-TTATGCACTTAG-CTATAA
141225 ACTTCGAGTAAAGTTTATGCACTTAGCTATAA
1 ACTTCGAGTAAAGTTTATGCACTTAGCTATAA
141257 A
1 A
141258 ATGGTATTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
32 7 0.23
33 23 0.74
34 1 0.03
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (32 bp):
ACTTCGAGTAAAGTTTATGCACTTAGCTATAA
Found at i:142268 original size:55 final size:55
Alignment explanation
Indices: 142171--142316 Score: 136
Period size: 55 Copynumber: 2.6 Consensus size: 55
142161 CAGAAAGGGA
* * * ** *
142171 GGTACTGATACAGTCTTGGATGTATCGATATA-TTCCTAACATCGAATATAATTTG
1 GGTACCGATACACTCTT-GATGTATCGATACACCCCCTAACATCGAATACAATTTG
* *
142226 GGTACCGATACACTCTTCGATGTATCGATACACCCCCT-ACATCGAATGCATTTTG
1 GGTACCGATACACTCTT-GATGTATCGATACACCCCCTAACATCGAATACAATTTG
* * *
142281 TGTATCGATACACTGAC-TGATGTACCGATACACCCC
1 GGTACCGATACACT--CTTGATGTATCGATACACCCC
142317 TTACTCCGAG
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
55 71 0.93
56 4 0.05
57 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (55 bp):
GGTACCGATACACTCTTGATGTATCGATACACCCCCTAACATCGAATACAATTTG
Found at i:145518 original size:64 final size:64
Alignment explanation
Indices: 145410--145539 Score: 242
Period size: 64 Copynumber: 2.0 Consensus size: 64
145400 TTTTGGGCCA
145410 ATTAGAACGATTAGCTTGGGTGGAAAACAATATTGCTTTGTATTGGTAGATGACTATTCTAGAT
1 ATTAGAACGATTAGCTTGGGTGGAAAACAATATTGCTTTGTATTGGTAGATGACTATTCTAGAT
* *
145474 ATTAGAACGATTAGCTTGGGTGGAAAACAATATTTCTTTTTATTGGTAGATGACTATTCTAGAT
1 ATTAGAACGATTAGCTTGGGTGGAAAACAATATTGCTTTGTATTGGTAGATGACTATTCTAGAT
145538 AT
1 AT
145540 ACTTGGGTTA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.38
Consensus pattern (64 bp):
ATTAGAACGATTAGCTTGGGTGGAAAACAATATTGCTTTGTATTGGTAGATGACTATTCTAGAT
Found at i:150818 original size:55 final size:55
Alignment explanation
Indices: 150734--150880 Score: 163
Period size: 55 Copynumber: 2.7 Consensus size: 55
150724 TCACAAAGGG
* * *
150734 AGGTACTGATACACTCTTGGATGTATCGATATACCCCCAACATCGAATGTAATTT
1 AGGTACCGATACACTCTTCGATGTATCGATACACCCCCAACATCGAATGTAATTT
* * * *
150789 AGGTACCGATACACTCTTCGTTGTATCGATACACCCCCTACATTGAATG-CATTT
1 AGGTACCGATACACTCTTCGATGTATCGATACACCCCCAACATCGAATGTAATTT
* * * *
150843 TGTGTATCGATACACTGGTT-GATGTAGCGATACACCCC
1 AG-GTACCGATACACT-CTTCGATGTATCGATACACCCC
150881 TGGCTCCGAG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 5 0.06
55 71 0.91
56 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (55 bp):
AGGTACCGATACACTCTTCGATGTATCGATACACCCCCAACATCGAATGTAATTT
Found at i:157652 original size:28 final size:28
Alignment explanation
Indices: 157620--157688 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
157610 TTAGAAGTTA
157620 GTAATGAAAATAATACATGGACCAATAT
1 GTAATGAAAATAATACATGGACCAATAT
157648 GTAATGAAAATAATACATGGACCAATAT
1 GTAATGAAAATAATACATGGACCAATAT
*
157676 GTAACGAAAATAA
1 GTAATGAAAATAA
157689 AATTCAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.23
Consensus pattern (28 bp):
GTAATGAAAATAATACATGGACCAATAT
Found at i:162827 original size:17 final size:17
Alignment explanation
Indices: 162805--162876 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
162795 AATTAAGAGT
162805 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
162822 TAGTTTGATGAATCAAC
1 TAGTTTAATAAATGAAC
*
162839 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
162856 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
162874 TAG
1 TAG
162877 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:169122 original size:30 final size:29
Alignment explanation
Indices: 169065--169123 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
169055 AACTGCTCTC
* *
169065 AACTAACTACTCTTAACAAACACTTAACA
1 AACTAACAACTCTTAACAAACAATTAACA
* *
169094 AACTAACAACTTCTTAACTATCAATTAACA
1 AACTAACAAC-TCTTAACAAACAATTAACA
169124 GCCTGTGCCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.47, C:0.25, G:0.00, T:0.27
Consensus pattern (29 bp):
AACTAACAACTCTTAACAAACAATTAACA
Found at i:170858 original size:17 final size:17
Alignment explanation
Indices: 170836--170907 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
170826 AATTAAGAGT
170836 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
170853 TAGTTTGATGAATCAAC
1 TAGTTTAATAAATGAAC
*
170870 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
* * *
170887 TAACTTTATTCAATGAAC
1 T-AGTTTAATAAATGAAC
170905 TAG
1 TAG
170908 ATGCATGAAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
17 30 0.68
18 14 0.32
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:172890 original size:24 final size:24
Alignment explanation
Indices: 172858--172903 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
172848 GCATGATATG
172858 GTACATAGATGTTTTATACATCGT
1 GTACATAGATGTTTTATACATCGT
172882 GTACATAGATGTTTTATACATC
1 GTACATAGATGTTTTATACATC
172904 ATCTGGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (24 bp):
GTACATAGATGTTTTATACATCGT
Found at i:174096 original size:95 final size:96
Alignment explanation
Indices: 173922--174141 Score: 243
Period size: 95 Copynumber: 2.3 Consensus size: 96
173912 ATAGATTTGC
* * * * *
173922 TCTA-CTACTCTTCAGGGTAGCTCAAATATAAAGAAAAAAATGGAATTTGCTCTGTTGTTCTTAA
1 TCTATCTACTCTTCAAGGTAGCTAAAATATAAAGAAAAAAATGGAATCTGCTCTGGTGCTCTTAA
173986 GGGTAGGTCAAATTCAAAGAAA-AAGGGATCT
66 GGGTAGGTCAAATTCAAAGAAATAA-GGATCT
* * *
174017 TCT-TGCTACTCTTCAAGGTAGGTAAAATCTAAAG-AAAAATTGGAATCTGCT-TCGGTGCTCTT
1 TCTAT-CTACTCTTCAAGGTAGCTAAAATATAAAGAAAAAAATGGAATCTGCTCT-GGTGCTCTT
** *
174079 TGGGGTAGGTCAGATTCAAAGAAATAAGGATCT
64 AAGGGTAGGTCAAATTCAAAGAAATAAGGATCT
** *
174112 TCTCATCTACTCTTCATTGTAGCTCAAATA
1 TCT-ATCTACTCTTCAAGGTAGCTAAAATA
174142 GGAAAATAAA
Statistics
Matches: 103, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
94 1 0.01
95 55 0.53
96 46 0.45
97 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (96 bp):
TCTATCTACTCTTCAAGGTAGCTAAAATATAAAGAAAAAAATGGAATCTGCTCTGGTGCTCTTAA
GGGTAGGTCAAATTCAAAGAAATAAGGATCT
Found at i:175651 original size:20 final size:21
Alignment explanation
Indices: 175602--175651 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
175592 AAGTTCTTTC
175602 TCAATGTCT-TCTCAACATGAA
1 TCAATGT-TATCTCAACATGAA
* *
175623 TC-TTATTATCTCAACATG-A
1 TCAATGTTATCTCAACATGAA
175642 TCAATGTTAT
1 TCAATGTTAT
175652 TAGTAATGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 5
0.72 0.12 0.16
Matches are distributed among these distances:
19 4 0.17
20 17 0.74
21 2 0.09
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (21 bp):
TCAATGTTATCTCAACATGAA
Found at i:179408 original size:45 final size:45
Alignment explanation
Indices: 179369--179611 Score: 145
Period size: 45 Copynumber: 5.9 Consensus size: 45
179359 GCATTTTAGG
**
179369 TATAACATACATTT-ATGCTGATAATGCACCCATATGCATTTCAAC
1 TATAACATAC-TTTCATGCCAATAATGCACCCATATGCATTTCAAC
** *
179414 TATGGCATTCTTTCATGCCAATAATGCACCCATATGCA-TT--A-
1 TATAACATACTTTCATGCCAATAATGCACCCATATGCATTTCAAC
* * *
179455 T-T---AT--TTT-ATGCTAATAATGCACCTATATGCATTTCAGC
1 TATAACATACTTTCATGCCAATAATGCACCCATATGCATTTCAAC
** * *
179493 TATGGCATCCTTTCATGCCAATAATGCATCCATATGCA-TT--A-
1 TATAACATACTTTCATGCCAATAATGCACCCATATGCATTTCAAC
* *
179534 T-T--C-T--TTT-ATGCCGATAATGCACCCATATGTATTTCAAC
1 TATAACATACTTTCATGCCAATAATGCACCCATATGCATTTCAAC
** * * *
179572 TATGGCATCCTTTCATGCCAATAAAGCACCCATATACATT
1 TATAACATACTTTCATGCCAATAATGCACCCATATGCATT
179612 ATTCGTTTAT
Statistics
Matches: 156, Mismatches: 19, Indels: 46
0.71 0.09 0.21
Matches are distributed among these distances:
34 43 0.28
35 10 0.06
37 4 0.03
38 3 0.02
39 2 0.01
40 2 0.01
41 3 0.02
42 4 0.03
44 13 0.08
45 72 0.46
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (45 bp):
TATAACATACTTTCATGCCAATAATGCACCCATATGCATTTCAAC
Found at i:179453 original size:31 final size:31
Alignment explanation
Indices: 179418--179487 Score: 77
Period size: 34 Copynumber: 2.2 Consensus size: 31
179408 TTCAACTATG
*
179418 GCATTCTTTCATGCCAATAATGCACCCATAT
1 GCATTATTTCATGCCAATAATGCACCCATAT
* * *
179449 GCATTATTATTTTATGCTAATAATGCACCTATAT
1 GC---ATTATTTCATGCCAATAATGCACCCATAT
179483 GCATT
1 GCATT
179488 TCAGCTATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
31 5 0.16
34 27 0.84
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (31 bp):
GCATTATTTCATGCCAATAATGCACCCATAT
Found at i:179471 original size:34 final size:34
Alignment explanation
Indices: 179428--179639 Score: 127
Period size: 34 Copynumber: 5.6 Consensus size: 34
179418 GCATTCTTTC
179428 ATGCCAATAATGCACCCATATGCATTATTATTTT
1 ATGCCAATAATGCACCCATATGCATTATTATTTT
* *
179462 ATGCTAATAATGCACCTATATGCATTTCAGCTATGGCATCCTTT
1 ATGCCAATAATGCACCCATATGCA-TT-A--T-T---AT--TTT
* *
179506 CATGCCAATAATGCATCCATATGCATTATTCTTTT
1 -ATGCCAATAATGCACCCATATGCATTATTATTTT
* *
179541 ATGCCGATAATGCACCCATATGTATTTCAACTATGGCATCCTTT
1 ATGCCAATAATGCACCCATATGCA-TT--A-T-T---AT--TTT
* * **
179585 CATGCCAATAAAGCACCCATATACATTATTCGTTT
1 -ATGCCAATAATGCACCCATATGCATTATTATTTT
*
179620 ATGCCGATAATGCACCCATA
1 ATGCCAATAATGCACCCATA
179640 ATTTAAAGGA
Statistics
Matches: 138, Mismatches: 18, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
34 61 0.44
35 10 0.07
36 1 0.01
37 2 0.01
38 2 0.01
39 2 0.01
40 2 0.01
41 2 0.01
42 4 0.03
43 1 0.01
44 10 0.07
45 41 0.30
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (34 bp):
ATGCCAATAATGCACCCATATGCATTATTATTTT
Found at i:179511 original size:79 final size:79
Alignment explanation
Indices: 179380--179639 Score: 412
Period size: 79 Copynumber: 3.3 Consensus size: 79
179370 ATAACATACA
* *
179380 TTTATGCTGATAATGCACCCATATGCATTTCAACTATGGCATTCTTTCATGCCAATAATGCACCC
1 TTTATGCCGATAATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCC
*
179445 ATATGCATTATTAT
66 ATATGCATTATTCT
** * * *
179459 TTTATGCTAATAATGCACCTATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCATCC
1 TTTATGCCGATAATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCC
179524 ATATGCATTATTCT
66 ATATGCATTATTCT
* *
179538 TTTATGCCGATAATGCACCCATATGTATTTCAACTATGGCATCCTTTCATGCCAATAAAGCACCC
1 TTTATGCCGATAATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCC
* *
179603 ATATACATTATTCG
66 ATATGCATTATTCT
179617 TTTATGCCGATAATGCACCCATA
1 TTTATGCCGATAATGCACCCATA
179640 ATTTAAAGGA
Statistics
Matches: 166, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 166 1.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.35
Consensus pattern (79 bp):
TTTATGCCGATAATGCACCCATATGCATTTCAACTATGGCATCCTTTCATGCCAATAATGCACCC
ATATGCATTATTCT
Found at i:182265 original size:79 final size:79
Alignment explanation
Indices: 182138--182390 Score: 355
Period size: 79 Copynumber: 3.2 Consensus size: 79
182128 ATATTTATAC
* * *
182138 TGATAATGCACCCATATTCATTTCAGCTATGGCCTTCTTTCATGCCAATAATGCACTCATATGCA
1 TGATAATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACTCATATGCA
182203 TTATTCTTTTATGT
66 TTATTCTTTTATGT
* * * *
182217 TGATAATACACCTATATGCATTTCAGCTATGGCATCCTTTAATCCCAATAATGCA-TCCATATGC
1 TGATAATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACT-CATATGC
182281 ATTATTCTTTTATGT
65 ATTATTCTTTTATGT
* * * * *
182296 CGATAATGCACCCATATGCATTTCAGCTATGACATCCTTTCATGCTAATAATTCACCCATATGCA
1 TGATAATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACTCATATGCA
* *
182361 TTATTATTTTATGC
66 TTATTCTTTTATGT
*
182375 CGATAATGCACCCATA
1 TGATAATGCACCCATA
182391 ATTTAAAGGA
Statistics
Matches: 154, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
78 1 0.01
79 153 0.99
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (79 bp):
TGATAATGCACCCATATGCATTTCAGCTATGGCATCCTTTCATGCCAATAATGCACTCATATGCA
TTATTCTTTTATGT
Found at i:182463 original size:3 final size:3
Alignment explanation
Indices: 182455--182496 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
182445 ACACCAACGT
182455 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
182497 TTGTAGGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:184023 original size:16 final size:16
Alignment explanation
Indices: 184004--184034 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
183994 AATATGAATA
*
184004 AATTTTAAATGATATG
1 AATTTAAAATGATATG
184020 AATTTAAAATGATAT
1 AATTTAAAATGATAT
184035 TAACATGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (16 bp):
AATTTAAAATGATATG
Found at i:184610 original size:20 final size:21
Alignment explanation
Indices: 184585--184626 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
184575 TTTGTTTACT
184585 GCTGAATG-GAACCATTCAAC
1 GCTGAATGTGAACCATTCAAC
*
184605 GCTGAATGTTGAACCGTTCAAC
1 GCTGAATG-TGAACCATTCAAC
184627 ATTCAGCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
22 11 0.58
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (21 bp):
GCTGAATGTGAACCATTCAAC
Found at i:186489 original size:181 final size:182
Alignment explanation
Indices: 186074--186718 Score: 927
Period size: 182 Copynumber: 3.5 Consensus size: 182
186064 TACAAATTAA
* * * * *
186074 AAATGTATGGATCCATAGCAATATAACAGGTTAAAAATATGATAAAACCGGTGTC-ATTATGATA
1 AAATGTATCGATCCATAGCAATATAACAGG-TAAAAATATGACAAAACAGGTCTCGA-AATGATA
** *
186138 AAACCGGTAAACCGCTACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTT
64 AAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTT
*
186203 TGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
129 CGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* *
186257 AAATGTATCGATCCATAGCAATATAACATGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
** * * *
186322 ACCGGTAAAAAGATACCATAAATATTGAAAGTGTCGATACATTAGTATAAGTATCGACACTTTCG
66 ACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
* *
186387 TAATTTAAAAGAGAAGAAGTAATAGTG-CTAAAAAGTGTCGATACTTTATAC
131 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
* *
186438 AAATGTATCGATCTATAGCAATATAACAGGTAATAATATGACAAAACAGGTCTCGAAATGATAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
* *
186503 ACCAGTAAAAAGATATCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
66 ACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
* *
186568 TAATTTAAAAGAGAATAAATTATAGCGCCTAAAAAGTGTCGATACTTTATGA-
131 TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT-AC
* * * * * *
186620 AAACGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACCGGTATCGAAATGACAAA
1 AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
** * * *
186685 ACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGT
66 ACCGGTAAAAAGATACCGGATATATTGAAAGTGT
186719 TGGTACTTTA
Statistics
Matches: 413, Mismatches: 46, Indels: 7
0.89 0.10 0.02
Matches are distributed among these distances:
181 168 0.41
182 215 0.52
183 30 0.07
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.27
Consensus pattern (182 bp):
AAATGTATCGATCCATAGCAATATAACAGGTAAAAATATGACAAAACAGGTCTCGAAATGATAAA
ACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATATAAGTATCGACACTTTCG
TAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTATAC
Found at i:188624 original size:22 final size:22
Alignment explanation
Indices: 188573--188628 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
188563 ATGTTTTTTG
*
188573 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
188596 TAGTTATTATATAAAATGAT-TAA
1 T-TTTATTATATAAAATGATGT-A
188619 TTTTATTATA
1 TTTTATTATA
188629 AATGAAGGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 9 0.32
23 3 0.11
24 16 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:188878 original size:9 final size:9
Alignment explanation
Indices: 188866--188899 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
188856 TCAAGGACGT
188866 AGAGGAGGC
1 AGAGGAGGC
*
188875 AGAGAAGGC
1 AGAGGAGGC
188884 AGAGGAGGC
1 AGAGGAGGC
188893 AGAGGAG
1 AGAGGAG
188900 AGGGAAGAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.53, T:0.00
Consensus pattern (9 bp):
AGAGGAGGC
Found at i:188952 original size:15 final size:15
Alignment explanation
Indices: 188934--188970 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
188924 GTGGATGACG
188934 GTCAGGGGGATTACA
1 GTCAGGGGGATTACA
*
188949 GTCAGGGGGATTACG
1 GTCAGGGGGATTACA
188964 GTCAGGG
1 GTCAGGG
188971 AAAACAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.14, G:0.46, T:0.19
Consensus pattern (15 bp):
GTCAGGGGGATTACA
Found at i:189349 original size:18 final size:18
Alignment explanation
Indices: 189326--189364 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
189316 GAGAAAATTT
189326 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
189344 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
189362 GAA
1 GAA
189365 ATGAAGAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.05
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:189689 original size:17 final size:17
Alignment explanation
Indices: 189667--189702 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
189657 TTTAAATATT
189667 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
189684 TCATGAAAAGATATTAA
1 TCATGAAAAGATATTAA
189701 TC
1 TC
189703 CTAATGATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (17 bp):
TCATGAAAAGATATTAA
Found at i:190728 original size:23 final size:23
Alignment explanation
Indices: 190678--190722 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
190668 TGCCTATTTT
*
190678 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
190701 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
190723 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:190740 original size:87 final size:87
Alignment explanation
Indices: 190594--190756 Score: 299
Period size: 87 Copynumber: 1.9 Consensus size: 87
190584 AAATAGGTCA
*
190594 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
190659 CCGGTTAAATGCCTATTTTATT
66 CCGGTTAAATGCCTATTTTATT
* *
190681 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
190746 CCGGTTAAATG
66 CCGGTTAAATG
190757 ATATAACATA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 73 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTTAAATGCCTATTTTATT
Found at i:196078 original size:18 final size:18
Alignment explanation
Indices: 196055--196105 Score: 57
Period size: 19 Copynumber: 2.8 Consensus size: 18
196045 ACGACCTGAT
196055 CCGTTGACTTTGACCCAC
1 CCGTTGACTTTGACCCAC
* ** *
196073 CCGTTGTCTTTGATCTGAT
1 CCGTTGACTTTGA-CCCAC
196092 CCGTTGACTTTGAC
1 CCGTTGACTTTGAC
196106 TAGAGTTGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 13 0.48
19 14 0.52
ACGTcount: A:0.14, C:0.29, G:0.20, T:0.37
Consensus pattern (18 bp):
CCGTTGACTTTGACCCAC
Found at i:196097 original size:19 final size:18
Alignment explanation
Indices: 196050--196106 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
196040 TCAACACGAC
196050 CTGATCCGTTGACTTTGA
1 CTGATCCGTTGACTTTGA
** * *
196068 CCCACCCGTTGTCTTTGA
1 CTGATCCGTTGACTTTGA
196086 TCTGATCCGTTGACTTTGA
1 -CTGATCCGTTGACTTTGA
196105 CT
1 CT
196107 AGAGTTGACC
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
18 16 0.53
19 14 0.47
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (18 bp):
CTGATCCGTTGACTTTGA
Found at i:200118 original size:23 final size:23
Alignment explanation
Indices: 200065--200119 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 23
200055 CAACAATCTC
*
200065 AAACGTACCATAAAGGTAGAGAA
1 AAACGTATCATAAAGGTAGAGAA
* *
200088 AAA-ATATCATAAA-GTCATAGAA
1 AAACGTATCATAAAGGT-AGAGAA
200110 AAACGTATCA
1 AAACGTATCA
200120 CATAGATAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 16 0.62
23 8 0.31
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.18
Consensus pattern (23 bp):
AAACGTATCATAAAGGTAGAGAA
Found at i:220062 original size:15 final size:16
Alignment explanation
Indices: 220031--220066 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
220021 TTAAAGGTAA
*
220031 TTATTTTTTTCTTTTC
1 TTATTTTTTTCTCTTC
220047 TTATTTTTTTC-CTTC
1 TTATTTTTTTCTCTTC
220062 TTATT
1 TTATT
220067 GTTTCAATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (16 bp):
TTATTTTTTTCTCTTC
Found at i:223995 original size:16 final size:16
Alignment explanation
Indices: 223974--224005 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
223964 GGTTGTTTTC
223974 TTCTTTATTTTTTTAG
1 TTCTTTATTTTTTTAG
*
223990 TTCTTTGTTTTTTTAG
1 TTCTTTATTTTTTTAG
224006 ATTTTAGTTC
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:0.09, C:0.06, G:0.09, T:0.75
Consensus pattern (16 bp):
TTCTTTATTTTTTTAG
Found at i:227207 original size:23 final size:21
Alignment explanation
Indices: 227181--227225 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
227171 AGTGTGAATC
227181 TCTTAGTTTAAAGAGTTGTTTTA
1 TCTTAGTTTAAAG-GTT-TTTTA
*
227204 TCTTTGTTTAAAGGTTTTTTA
1 TCTTAGTTTAAAGGTTTTTTA
227225 T
1 T
227226 AAGATTAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 3 0.14
23 12 0.57
ACGTcount: A:0.22, C:0.04, G:0.16, T:0.58
Consensus pattern (21 bp):
TCTTAGTTTAAAGGTTTTTTA
Done.