Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004346.1 Hibiscus syriacus cultivar Beakdansim tig00009519_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: 84133
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:288 original size:27 final size:27
Alignment explanation
Indices: 250--307 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
240 ATATTTTTAA
** *
250 TTAATGTGGTATTTGAATCTAATATTT
1 TTAATGTGGTATTCAAATCTAATAATT
*
277 TTAATGTGGTATTCAAATTTAATAATT
1 TTAATGTGGTATTCAAATCTAATAATT
304 TTAA
1 TTAA
308 AATTTAATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.12, T:0.50
Consensus pattern (27 bp):
TTAATGTGGTATTCAAATCTAATAATT
Found at i:7546 original size:26 final size:26
Alignment explanation
Indices: 7517--7572 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
7507 TTTTATTATT
7517 TTTAATATAT-ATACTTTTTAATAAAA
1 TTTAATATATAAT-CTTTTTAATAAAA
* * *
7543 TTT-ATGTATAATTTTTTTTATAAAA
1 TTTAATATATAATCTTTTTAATAAAA
7568 TTTAA
1 TTTAA
7573 AAGATAAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (26 bp):
TTTAATATATAATCTTTTTAATAAAA
Found at i:12715 original size:19 final size:19
Alignment explanation
Indices: 12691--12727 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
12681 GTTTTGTTTC
12691 TTGCTTGAAGCTT-GTTATT
1 TTGCTTGAA-CTTAGTTATT
12710 TTGCTTGAACTTAGTTAT
1 TTGCTTGAACTTAGTTAT
12728 AATATTGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.19, C:0.11, G:0.19, T:0.51
Consensus pattern (19 bp):
TTGCTTGAACTTAGTTATT
Found at i:15038 original size:42 final size:42
Alignment explanation
Indices: 14991--15079 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
14981 ATAATAAAAT
* * * *
14991 AATATATTATTGATGATTTTTTATATGAATAATTTTTATTTA
1 AATATATTATCGATGAATTTGTATATAAATAATTTTTATTTA
15033 AATATATTATCGATGAATTTGTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTGTATATAAATAATTTTTATTTA
15075 AATAT
1 AATAT
15080 TTAAAATTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.39, C:0.01, G:0.07, T:0.53
Consensus pattern (42 bp):
AATATATTATCGATGAATTTGTATATAAATAATTTTTATTTA
Found at i:17692 original size:22 final size:23
Alignment explanation
Indices: 17655--17701 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
17645 AACCCTAAAC
17655 AAGCCCAAAAATCGTATCTGCTA
1 AAGCCCAAAAATCGTATCTGCTA
* *
17678 AAGCCC-AGAATCGTATCTTCTA
1 AAGCCCAAAAATCGTATCTGCTA
17700 AA
1 AA
17702 CTCACGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (23 bp):
AAGCCCAAAAATCGTATCTGCTA
Found at i:21034 original size:21 final size:20
Alignment explanation
Indices: 21010--21060 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
21000 AAAACGATAT
21010 ACCAGGTAAAAATATGATAAA
1 ACCAGGTAAAAA-ATGATAAA
21031 ACCA-GTAACAAAATGATAAA
1 ACCAGGTAA-AAAATGATAAA
21051 ACC-GGTAAAA
1 ACCAGGTAAAA
21061 CGTTACCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 2 0.07
20 19 0.68
21 7 0.25
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (20 bp):
ACCAGGTAAAAAATGATAAA
Found at i:21138 original size:181 final size:181
Alignment explanation
Indices: 20802--21212 Score: 599
Period size: 182 Copynumber: 2.3 Consensus size: 181
20792 GATCCAAATT
* * * * ***
20802 AAAAATATGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTAACAAAATGATA
* * *
20867 AAACCGGTAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * *
20932 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTTTCGATACTTTTA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTA
* *
20984 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCAGTAACAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTAACAAAATGATA
* * * *
21049 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATAC-TTCATATAAGGATCGACACTTT
66 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
21113 GTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAATGTGTCGATACTTTA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
*
21164 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAAC
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAAC
21213 TGGTAAAACG
Statistics
Matches: 204, Mismatches: 25, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
180 50 0.25
181 61 0.30
182 93 0.46
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (181 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCAGTAACAAAATGATA
AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
Found at i:23470 original size:21 final size:21
Alignment explanation
Indices: 23440--23504 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
23430 AAGACAATCA
* *
23440 AGAGTTGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
23461 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
23482 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
23503 AG
1 AG
23505 GCATAAGGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.42, C:0.09, G:0.31, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:23580 original size:33 final size:33
Alignment explanation
Indices: 23538--23603 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
23528 AAATAGATGG
*
23538 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
23571 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
23604 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:25410 original size:19 final size:19
Alignment explanation
Indices: 25386--25434 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
25376 AATGTAGGGT
25386 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
25405 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
25424 TAATTTTGTAT
1 TAATTTTGTAT
25435 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:26195 original size:201 final size:200
Alignment explanation
Indices: 25569--26691 Score: 1933
Period size: 200 Copynumber: 5.6 Consensus size: 200
25559 GTGCAACCAT
* * *
25569 AAAGTATCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
25634 TCGGTGCAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
* * *
25699 TGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTACAACCATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
25764 TATAA
196 TATAA
*
25769 AAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
25834 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
* *
25899 TGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTTGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
25964 TATAA
196 TATAA
25969 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
26034 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACAC-TTTTGTAGT
* *
26099 TTGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCAT
130 TTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCAT
26164 ATATAA
195 ATATAA
*
26170 AAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
26235 TCAGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
*
26300 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCTATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
26365 TATAA
196 TATAA
26370 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* *
26435 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACAC-TTTTGTAGT
* * *
26500 TTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGGAACAATAAAGTGTCGATCCAT
130 TTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCAT
26565 ATATAA
195 ATATAA
* *
26571 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * *
26636 CCGGTACAAGTATACCGGTTTTATGAGAGAATTGGTATATAAT-ATGTATCGACACT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTA-AATAATGTGTCGACACT
26692 GTTTAATGTT
Statistics
Matches: 876, Mismatches: 44, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
200 498 0.57
201 375 0.43
202 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (200 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATA
TATAA
Found at i:26710 original size:401 final size:401
Alignment explanation
Indices: 25569--26691 Score: 1991
Period size: 401 Copynumber: 2.8 Consensus size: 401
25559 GTGCAACCAT
* * *
25569 AAAGTATCGATCCCAAAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
* * * * *
25634 TCGGTGCAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACAC-TTTTGTAGT
66 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
*
25698 TTGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTACAACCATAAAGTGTCGATCCAT
131 TTGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCAT
25763 ATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
196 ATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
25828 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTT
261 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTT
25893 GTAGTTTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTTGA
326 GTAGTTTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTTGA
25958 TCCATATATAA
391 TCCATATATAA
25969 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
26034 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
66 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
26099 TTGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCAT
131 TTGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCAT
26164 ATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
196 ATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
* * *
26229 ATCTAATCAGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTT
261 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTT
*
26294 GTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCT-
326 GTAGTTTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGT-TG
26358 ATCCATATATAA
390 ATCCATATATAA
26370 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
26435 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
66 CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
* * * * *
26500 TTGTGTCGATATTTTTGGTCCATAATGAATGGCAAACAGGGTGGAACAATAAAGTGTCGATCCAT
131 TTGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCAT
* * *
26565 ATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCA
196 ATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
* * *
26630 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATTGGTATATAAT-ATGTATCGACACT
261 ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTA-AATAATGTGTCGACACT
26692 GTTTAATGTT
Statistics
Matches: 693, Mismatches: 27, Indels: 5
0.96 0.04 0.01
Matches are distributed among these distances:
400 113 0.16
401 576 0.83
402 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (401 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTAGT
TTGTGTCGATATTTCTGGTCCAGAATGAATGGCAAACAGGCTGCAACCATAAAGTGTCGATCCAT
ATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCA
ATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTT
GTAGTTTGTGTCGATATTTTTAGTCCAGAATGAATGGCAAACAGGGTGCAACCATAAAGTGTTGA
TCCATATATAA
Found at i:28184 original size:6 final size:6
Alignment explanation
Indices: 28173--28296 Score: 104
Period size: 6 Copynumber: 20.7 Consensus size: 6
28163 CAAGCGGTCA
* * * * * *
28173 ATGAAG ATGAAG CTGACG ATGAAG ATGACG ATGGAG ATGAGG ATGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * *
28221 ATGACG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * *
28269 ATGATG ACGATG ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGA
28297 TTATCCAAAC
Statistics
Matches: 95, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:28297 original size:12 final size:12
Alignment explanation
Indices: 28173--28296 Score: 149
Period size: 12 Copynumber: 10.3 Consensus size: 12
28163 CAAGCGGTCA
*
28173 ATGAAGATGAAG
1 ATGACGATGAAG
*
28185 CTGACGATGAAG
1 ATGACGATGAAG
*
28197 ATGACGATGGAG
1 ATGACGATGAAG
* *
28209 ATGAGGATGATG
1 ATGACGATGAAG
28221 ATGACGATGAAG
1 ATGACGATGAAG
*
28233 CTGACGATGAAG
1 ATGACGATGAAG
28245 ATGACGATGAAG
1 ATGACGATGAAG
28257 ATGACGATGAAG
1 ATGACGATGAAG
* * *
28269 ATGATGACGATG
1 ATGACGATGAAG
* *
28281 ATGATGATGATG
1 ATGACGATGAAG
28293 ATGA
1 ATGA
28297 TTATCCAAAC
Statistics
Matches: 97, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 97 1.00
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:30000 original size:183 final size:183
Alignment explanation
Indices: 29510--30084 Score: 951
Period size: 183 Copynumber: 3.1 Consensus size: 183
29500 CAAAGTTTTC
* *
29510 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCATT-
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACC-TTG
* *
29574 TCAAAAAGTGTCG--ATTGAAAAATCATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTA
65 TCAAAAAGTGTCGACATT--TACA-CATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTA
**
29637 ATATAACCGGTATAAATATACCGGTTTTATGAGCGAATATATCTACAACCTATATCG
127 ATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* * * *
29694 ACACTTTTT-TTCGCTTGCGTCGGTACTTTATGTCCAAATTGGAAGAAAAATGTGTCGATACCTT
1 ACACTTTTTAAT--ATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTT
29758 GTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAAT
64 GTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAAT
29823 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
129 ATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
29878 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
*
29943 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATATAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* *
30008 ATCCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
30061 ACACTTTTTAATATTGTGTCGGTA
1 ACACTTTTTAATATTGTGTCGGTA
30085 ATTTTAAGTA
Statistics
Matches: 368, Mismatches: 17, Indels: 13
0.92 0.04 0.03
Matches are distributed among these distances:
183 190 0.52
184 115 0.31
185 60 0.16
187 3 0.01
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:32964 original size:23 final size:23
Alignment explanation
Indices: 32933--33005 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
32923 ATAGGTAAAA
*
32933 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
32956 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
32979 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
33002 ATAT
1 ATAT
33006 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:33405 original size:22 final size:22
Alignment explanation
Indices: 33361--33405 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
33351 ATTACATAAC
*
33361 TTTAAAAAAAGTATCGATCCTT
1 TTTAAAAAAAGTATCGAACCTT
*
33383 TTTATAAAAAGTAT-GAACACTT
1 TTTAAAAAAAGTATCGAAC-CTT
33405 T
1 T
33406 CAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (22 bp):
TTTAAAAAAAGTATCGAACCTT
Found at i:33454 original size:23 final size:23
Alignment explanation
Indices: 33423--33495 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
33413 ATAGGTAAAA
*
33423 ATATGATGTAATAGGTAACGCTT
1 ATATAATGTAATAGGTAACGCTT
* *
33446 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAACGCTT
**
33469 ATATAATGTAATAGGTATTGCTT
1 ATATAATGTAATAGGTAACGCTT
33492 ATAT
1 ATAT
33496 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAACGCTT
Found at i:33946 original size:23 final size:23
Alignment explanation
Indices: 33915--33987 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
33905 ATAGGTAAAA
*
33915 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
33938 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
33961 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
33984 ATAT
1 ATAT
33988 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:34432 original size:21 final size:21
Alignment explanation
Indices: 34406--34476 Score: 88
Period size: 21 Copynumber: 3.3 Consensus size: 21
34396 TAAAAATATG
*
34406 ATGTAATAGGTAACGCTTATA
1 ATGTAATAGGTAGCGCTTATA
*
34427 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCG-CT-TATA
*
34450 ATGTAATAGGTAGTGCTTATA
1 ATGTAATAGGTAGCGCTTATA
*
34471 TTGTAA
1 ATGTAA
34477 AGTATCTATC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
21 23 0.53
22 2 0.05
23 18 0.42
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (21 bp):
ATGTAATAGGTAGCGCTTATA
Found at i:34453 original size:23 final size:22
Alignment explanation
Indices: 34401--34471 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
34391 ATAGGTAAAA
* * *
34401 ATATGATGTAATAGGTAACGCT
1 ATATAATGTAATAGGTAGCGTT
34423 -TATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCG-TT
*
34445 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCG-TT
34468 ATAT
1 ATAT
34472 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 17 0.40
22 1 0.02
23 24 0.57
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.38
Consensus pattern (22 bp):
ATATAATGTAATAGGTAGCGTT
Found at i:34913 original size:23 final size:23
Alignment explanation
Indices: 34887--34959 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
34877 ATAGGTAAAA
* *
34887 ATATGATGTAATAAGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
34910 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
34933 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
34956 ATAT
1 ATAT
34960 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:35049 original size:488 final size:490
Alignment explanation
Indices: 32585--35846 Score: 6066
Period size: 490 Copynumber: 6.7 Consensus size: 490
32575 AGGTATGTAC
32585 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
32650 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
* *
32715 TTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
*
32780 ATTTTTTGTGTAAATAAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAA
* * * *
32845 AAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATTGATCATTTTTGTAAAAAGTATGTA
260 AAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGA
32910 CACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
325 CACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGC
* *
32975 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTTTCCA
390 GTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCA
33040 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
455 TACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
33076 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
33141 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
*
33206 TTTGGTTAATATTATTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
*
33271 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGAAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
*
33336 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGAAC
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGAC
*
33401 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAACGCTTATATAATGTAATAGGTAGCG
326 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
*
33466 TTTATATAATGTAATAGGTATTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
391 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
* *
33531 ATTTTTTTCACTTTGGAAAACATTAATTTAAGGTT
456 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
33566 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
33631 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
* *
33696 TTTGGTTAATATTGTTAAATTTAAATACTAAATAATATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
33761 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT--AA
* * *
33826 AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATTGATCATTTTTATAAAAAGTATGT
259 AAAAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGG
33891 ACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAG
324 ACACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAG
33956 CGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCC
389 CGTTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCC
*
34021 ATACTTTTTTCACTGTGGAAAACATTAATTTAAAGTT
454 ATACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
34058 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
34123 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
*
34188 TTTGGTTAATATTATTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATC-AATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
34252 ATTTTTTGTGTAAATGAAATTATTAAATTAATA-TGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
34316 AAAATTGAAACATAAATTACATAACTTT-AAAAAAGTATCGATCC-TTTTATAAAAAGTATGGAC
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGAC
*
34379 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAACGC-T-TATAATGTAATAGGTAGCG
326 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
34442 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
391 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
*
34507 ATTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
34542 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
34607 GTTAC-A-ATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
34670 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
*
34735 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
*
34800 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCAATCCTTTTTATAAAAAGTATGGAC
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGAC
*
34865 ACTTTCAATATAATAGGTAAAAATATGATGTAATAAGTAGCGCTTATATAATGTAATAGGTAGCG
326 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
34930 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
391 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
34995 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
*
35030 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTGATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
35095 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
35160 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
*
35225 A-TTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
35288 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGAC
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGAC
35353 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
326 ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
*
35418 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCAT
391 TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
35483 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
456 ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
*
35518 ATCTTTTAAG-GAGTTTT-AGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
1 ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
*
35581 GTTACGATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
66 GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
35646 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
131 TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
*
35711 ATTTTTTGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT--AA
196 ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
* * *
35774 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCTTTTTTATAAAAAGTATAGAT
261 AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGAC
35839 ACTTTCAA
326 ACTTTCAA
35847 CATATTATAA
Statistics
Matches: 2708, Mismatches: 52, Indels: 27
0.97 0.02 0.01
Matches are distributed among these distances:
482 116 0.04
483 37 0.01
484 246 0.09
485 16 0.01
486 367 0.14
487 81 0.03
488 458 0.17
489 60 0.02
490 626 0.23
491 288 0.11
492 413 0.15
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.40
Consensus pattern (490 bp):
ATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGATTTATTTTTTAC
GTTACAATATATATTATTATTAAATTAAAAACAATAAACATATATATTACATATTTATTATTATC
TTTGGTTAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATA
ATTTTTTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAA
AAAATTGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGAC
ACTTTCAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCG
TTTATATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCAT
ACTTTTTTCACTGTGGAAAACATTAATTTAAGGTT
Found at i:35406 original size:23 final size:23
Alignment explanation
Indices: 35375--35447 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
35365 ATAGGTAAAA
*
35375 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
35398 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
35421 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
35444 ATAT
1 ATAT
35448 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:35824 original size:22 final size:23
Alignment explanation
Indices: 35799--35843 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
35789 ATTACATAAC
*
35799 TTTAAAAAAAGTATCGAT-CTTT
1 TTTAAAAAAAGTATAGATACTTT
*
35821 TTTATAAAAAGTATAGATACTTT
1 TTTAAAAAAAGTATAGATACTTT
35844 CAACATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.42, C:0.07, G:0.09, T:0.42
Consensus pattern (23 bp):
TTTAAAAAAAGTATAGATACTTT
Found at i:38912 original size:37 final size:37
Alignment explanation
Indices: 38871--38946 Score: 125
Period size: 37 Copynumber: 2.1 Consensus size: 37
38861 TCAATCAAAC
* *
38871 AATTTATTATTAACCCTACTTAAACTGAGAGTAGATT
1 AATTTATTATTAACCCTACTTAAACTAAGAATAGATT
*
38908 AATTTATTATTAACCCTAGTTAAACTAAGAATAGATT
1 AATTTATTATTAACCCTACTTAAACTAAGAATAGATT
38945 AA
1 AA
38947 GGCTTTCTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (37 bp):
AATTTATTATTAACCCTACTTAAACTAAGAATAGATT
Found at i:41265 original size:3 final size:3
Alignment explanation
Indices: 41257--41289 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
41247 ATATTTTATT
41257 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
41290 TGAAAACTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:45177 original size:37 final size:39
Alignment explanation
Indices: 45127--45209 Score: 125
Period size: 38 Copynumber: 2.2 Consensus size: 39
45117 TTTTGTTCGG
*
45127 GTCGGGTC-GGGTTTTTTAAGTGTAATATTCGGGTC-GA
1 GTCGGGTCAGGTTTTTTTAAGTGTAATATTCGGGTCAGA
*
45164 GTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGGTCAGA
1 GTCGGGTCAGGTTTTTTTAAGTGTAATATTCGGGTCAGA
*
45203 TTCGGGT
1 GTCGGGT
45210 TTAGGGTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
37 8 0.20
38 25 0.61
39 8 0.20
ACGTcount: A:0.16, C:0.11, G:0.35, T:0.39
Consensus pattern (39 bp):
GTCGGGTCAGGTTTTTTTAAGTGTAATATTCGGGTCAGA
Found at i:45362 original size:37 final size:37
Alignment explanation
Indices: 45312--45393 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
45302 ATTATTTCGG
45312 GTCGGGTCAGGTTTTTTAAGTGGGATATTCGGGTCGA
1 GTCGGGTCAGGTTTTTTAAGTGGGATATTCGGGTCGA
* * * *
45349 GTCGGGTCGGGTTTTTTAAGTGTGCTATTCGGGTCGG
1 GTCGGGTCAGGTTTTTTAAGTGGGATATTCGGGTCGA
45386 GTTCGGGT
1 G-TCGGGT
45394 TTAGGGTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 34 0.85
38 6 0.15
ACGTcount: A:0.11, C:0.12, G:0.40, T:0.37
Consensus pattern (37 bp):
GTCGGGTCAGGTTTTTTAAGTGGGATATTCGGGTCGA
Found at i:46121 original size:3 final size:3
Alignment explanation
Indices: 46113--46210 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
46103 GAGCACACAG
*
46113 GAA GAA GAA -AG GAA GAA GAA GAA -AA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
46159 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -AG GAA GAA GCA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
46206 GAA GA
1 GAA GA
46211 GTTCCAGATA
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
2 4 0.05
3 82 0.95
ACGTcount: A:0.65, C:0.01, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:46837 original size:58 final size:58
Alignment explanation
Indices: 46746--46884 Score: 192
Period size: 58 Copynumber: 2.4 Consensus size: 58
46736 GAAACTTCAG
* * **
46746 AAAATTAGACTTAGCTTCTTT-AAAATTCATTTGAAAACATTATGTCAAGAAA-CCCTA
1 AAAATTAGACTTAGTTTCTTTAAAAATGCATTTGAAAA-ACCATGTCAAGAAACCCCTA
*
46803 AAAATTAGACTTAGTTTCTTTAAAAATGCATTTGAAAAACCATGTCAAGAAACCCCTG
1 AAAATTAGACTTAGTTTCTTTAAAAATGCATTTGAAAAACCATGTCAAGAAACCCCTA
* *
46861 AAAATCAGACTTAGTTTCTCTAAA
1 AAAATTAGACTTAGTTTCTTTAAA
46885 GATATCATAT
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
57 32 0.44
58 41 0.56
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.32
Consensus pattern (58 bp):
AAAATTAGACTTAGTTTCTTTAAAAATGCATTTGAAAAACCATGTCAAGAAACCCCTA
Found at i:52504 original size:36 final size:36
Alignment explanation
Indices: 52464--52532 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
52454 GCGTTTCAAG
* **
52464 GGAAAACTATCTCAAGCGAGATGAATTTTGTTTTTA
1 GGAAAACAATCTCAAGCGAGACCAATTTTGTTTTTA
*
52500 GGAAAACAATCTCAAGTGAGACCAATTTTGTTT
1 GGAAAACAATCTCAAGCGAGACCAATTTTGTTT
52533 CAAGTGAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (36 bp):
GGAAAACAATCTCAAGCGAGACCAATTTTGTTTTTA
Found at i:52543 original size:102 final size:101
Alignment explanation
Indices: 52422--52700 Score: 382
Period size: 102 Copynumber: 2.7 Consensus size: 101
52412 GTGAGATATC
* * *
52422 ATTTTGTTTCGAGTGAAATAATTTCAAAATTTGCGTTTCAAGGGAAAACTATCTCAAGCGAGATG
1 ATTTTGTTTCAAGTGAAATAATTTCAAAATTTGCGTTTCAAGGGAAAACTGTCTCAAGCGATATG
52487 AATTTTGTTTTTAGGAAAACAATCTCAAGTGAGACCA
66 AA-TTTGTTTTTAGGAAAACAATCTCAAGTGAGACCA
* * *
52524 ATTTTGTTTCAAGTGAAATAATTTTAAAATTTGTGTTTCGAA-GGAAAACTGTCTCAAGAGATAC
1 ATTTTGTTTCAAGTGAAATAATTTCAAAATTTGCGTTTC-AAGGGAAAACTGTCTCAAGCGATA-
* *
52588 GGAATTTATTTTTAGGAAAACAATCTCAAGTGAGACCA
64 TGAATTTGTTTTTAGGAAAACAATCTCAAGTGAGACCA
* * * * *
52626 ATTTTGTTTCAAGTGAAACAACTTCAAAATTTGGGCTTCATGGG-AAACTGTCTCAAGCGATATG
1 ATTTTGTTTCAAGTGAAATAATTTCAAAATTTGCGTTTCAAGGGAAAACTGTCTCAAGCGATATG
52690 AAACTTTGTTT
66 -AA-TTTGTTT
52701 CAAGAGAAAC
Statistics
Matches: 155, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
100 1 0.01
101 20 0.13
102 129 0.83
103 5 0.03
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (101 bp):
ATTTTGTTTCAAGTGAAATAATTTCAAAATTTGCGTTTCAAGGGAAAACTGTCTCAAGCGATATG
AATTTGTTTTTAGGAAAACAATCTCAAGTGAGACCA
Found at i:52698 original size:66 final size:67
Alignment explanation
Indices: 52628--52939 Score: 247
Period size: 66 Copynumber: 4.7 Consensus size: 67
52618 TGAGACCAAT
* * * *
52628 TTTGTTTCAAGTGAAACAA-CTTCAAA-ATTTGGGCTTCATGGGAAACTGTCTCAAGCGATATGA
1 TTTGTTTCAAGAGAAACAATCTT-AAAGATTTAGGCTTCAAGGGAAACTGTCTCAAGCGAGATGA
52691 AAC
65 AAC
* * * * *
52694 TTTGTTTCAAGAGAAACAATCTTAAAGGTTTATGTTTCAAGTGAAACTGTCTCAAGTGAGATGAA
1 TTTGTTTCAAGAGAAACAATCTTAAAGATTTAGGCTTCAAGGGAAACTGTCTCAAGCGAGATGAA
52759 AC
66 AC
** * * * * * * * * * *
52761 TTTGTTTTGAGAGAAATAATCTCAAAGGTTTATGTTTCAAGAGAAGCTATCTCAAGCAAGA-CAA
1 TTTGTTTCAAGAGAAACAATCTTAAAGATTTAGGCTTCAAGGGAAACTGTCTCAAGCGAGATGAA
*
52825 AA
66 AC
* * * * * * * *
52827 TTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAGA
1 TTTGTTTCAAGAGAAACAATCTTAAAGATTTAGGCTTCAAGGGAAACTGTCTCAAGCGAGA-TGA
52892 AA-
65 AAC
* * * * * *
52894 -TTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAAC
1 TTTGTTTCAAGAGAAACAATCTTAAAGATTTAGGCTTCAAGGGAAAC
52940 AATCTCAAAG
Statistics
Matches: 217, Mismatches: 25, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
66 127 0.59
67 87 0.40
68 3 0.01
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.31
Consensus pattern (67 bp):
TTTGTTTCAAGAGAAACAATCTTAAAGATTTAGGCTTCAAGGGAAACTGTCTCAAGCGAGATGAA
AC
Found at i:52758 original size:67 final size:67
Alignment explanation
Indices: 52669--52947 Score: 393
Period size: 66 Copynumber: 4.2 Consensus size: 67
52659 GGCTTCATGG
* * * *
52669 GAAACTGTCTCAAGCGATATGAAACTTTGTTTCAAGAGAAACAATCTTAAAGGTTTATGTTTCAA
1 GAAACTATCTCAAGCGAGATGAAACTTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAA
*
52734 GT
66 GA
* * * *
52736 GAAACTGTCTCAAGTGAGATGAAACTTTGTTTTGAGAGAAATAATCTCAAAGGTTTATGTTTCAA
1 GAAACTATCTCAAGCGAGATGAAACTTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAA
52801 GA
66 GA
* * * *
52803 GAAGCTATCTCAAGCAAGA-CAAAATTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAA
1 GAAACTATCTCAAGCGAGATGAAACTTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAA
52867 GA
66 GA
*
52869 GAAACTATCTCAAGCGAGACAGAAA--TTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCA
1 GAAACTATCTCAAGCGAGA-TGAAACTTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCA
52932 AGA
65 AGA
*
52935 GAAACAATCTCAA
1 GAAACTATCTCAA
52948 AGGTTTTTGT
Statistics
Matches: 191, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
66 113 0.59
67 75 0.39
68 3 0.02
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (67 bp):
GAAACTATCTCAAGCGAGATGAAACTTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAA
GA
Found at i:52804 original size:30 final size:30
Alignment explanation
Indices: 52770--52969 Score: 129
Period size: 30 Copynumber: 6.3 Consensus size: 30
52760 CTTTGTTTTG
52770 AGAGAAATAATCTCAAAGGTTTATGTTTCA
1 AGAGAAATAATCTCAAAGGTTTATGTTTCA
* ** *
52800 AGAGAAGCT-ATCTCAAGCAAGACAAAATT-TGTTTTA
1 AGAGAA-ATAATCTC-A--AAG----GTTTATGTTTCA
*
52836 AGAGAAACAATCTCAAAGGTTTATGTTTCA
1 AGAGAAATAATCTCAAAGGTTTATGTTTCA
** *
52866 AGAGAAACT-ATCTCAAGCGAGACAG-AAATTGTTTTA
1 AGAGAAA-TAATCTCAA---AG---GTTTA-TGTTTCA
*
52902 AGAGAAACAATCTCAAAGGTTTATGTTTCA
1 AGAGAAATAATCTCAAAGGTTTATGTTTCA
* *
52932 AGAGAAACAATCTCAAAGGTTTTTGTTTCA
1 AGAGAAATAATCTCAAAGGTTTATGTTTCA
52962 AGAGAAAT
1 AGAGAAAT
52970 TGTCTTAAGG
Statistics
Matches: 131, Mismatches: 19, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
29 2 0.02
30 74 0.56
31 3 0.02
33 10 0.08
35 2 0.02
36 38 0.29
37 2 0.02
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (30 bp):
AGAGAAATAATCTCAAAGGTTTATGTTTCA
Found at i:52848 original size:133 final size:132
Alignment explanation
Indices: 52694--52947 Score: 393
Period size: 133 Copynumber: 1.9 Consensus size: 132
52684 GATATGAAAC
* * * * *
52694 TTTGTTTCAAGAGAAACAATCTTAAAGGTTTATGTTTCAAGTGAAACTGTCTCAAGTGAGA-TGA
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAGA
* * * *
52758 AACTTTGTTTTGAGAGAAATAATCTCAAAGGTTTATGTTTCAAGAGAAGCTATCTCAAGCAAGAC
66 AA--TTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAGCAAGAC
52823 AAAA
129 AAAA
*
52827 TTTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAGA
1 TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAGA
52892 AATTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAA
66 AATTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAA
52948 AGGTTTTTGT
Statistics
Matches: 110, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
132 50 0.45
133 56 0.51
134 4 0.04
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (132 bp):
TTTGTTTCAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACTATCTCAAGCGAGACAGA
AATTGTTTTAAGAGAAACAATCTCAAAGGTTTATGTTTCAAGAGAAACAATCTCAAGCAAGACAA
AA
Found at i:52906 original size:36 final size:35
Alignment explanation
Indices: 52793--52917 Score: 102
Period size: 36 Copynumber: 3.7 Consensus size: 35
52783 CAAAGGTTTA
* *
52793 TGTTTCAAGAGAAGCTATCTCAAGCAAGACA-AAATT
1 TGTTTCAAGAGAAACAATCTCAAGC-AGACAGAAA-T
* **
52829 TGTTTTAAGAGAAACAATCTCAA--AG---G-TTT
1 TGTTTCAAGAGAAACAATCTCAAGCAGACAGAAAT
*
52858 ATGTTTCAAGAGAAACTATCTCAAGCGAGACAGAAAT
1 -TGTTTCAAGAGAAACAATCTCAAGC-AGACAGAAAT
*
52895 TGTTTTAAGAGAAACAATCTCAA
1 TGTTTCAAGAGAAACAATCTCAA
52918 AGGTTTATGT
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
29 1 0.01
30 21 0.30
33 4 0.06
36 42 0.61
37 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (35 bp):
TGTTTCAAGAGAAACAATCTCAAGCAGACAGAAAT
Found at i:58579 original size:6 final size:7
Alignment explanation
Indices: 58548--58578 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
58538 ATTTAAATTG
58548 AAAAAT-
1 AAAAATA
58554 AAAAATA
1 AAAAATA
58561 AAAAATA
1 AAAAATA
58568 AAAAATA
1 AAAAATA
58575 AAAA
1 AAAA
58579 TGAAACAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.87, C:0.00, G:0.00, T:0.13
Consensus pattern (7 bp):
AAAAATA
Found at i:59924 original size:97 final size:97
Alignment explanation
Indices: 59757--59946 Score: 292
Period size: 97 Copynumber: 2.0 Consensus size: 97
59747 GAGTTGAGAT
* * *
59757 TCTGATCTCCTGAAGAGACTCCTCTATGAAATCTCATTCAAATTTTTCATACTCTTTCTCAAGGT
1 TCTGATCTCCCGAAGAGACTCCTCTATGAAAGCTCATTCAAATTTGTCATACTCTTTCTCAAGGT
59822 CCACCTTGATCACCATCCACGT-TTTCTTGGAG
66 CCACCTTGATCACCATCCAC-TCTTTCTTGGAG
* *
59854 TCTGATCTCCCGAAGAGTCTCCTCTGTGAAAGCTCATTCAAATTTGTCATACTCTTTCTCAAGGT
1 TCTGATCTCCCGAAGAGACTCCTCTATGAAAGCTCATTCAAATTTGTCATACTCTTTCTCAAGGT
* **
59919 TCACCTTGATTGCCATCCACTCTTTCTT
66 CCACCTTGATCACCATCCACTCTTTCTT
59947 ATAAGTTTTA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
96 1 0.01
97 83 0.99
ACGTcount: A:0.22, C:0.28, G:0.13, T:0.37
Consensus pattern (97 bp):
TCTGATCTCCCGAAGAGACTCCTCTATGAAAGCTCATTCAAATTTGTCATACTCTTTCTCAAGGT
CCACCTTGATCACCATCCACTCTTTCTTGGAG
Found at i:60935 original size:24 final size:24
Alignment explanation
Indices: 60891--60961 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
60881 TCGTATAAAT
* *
60891 TGCACCGAAA-TGCCGCTTAGAATA
1 TGCACC-AAAGTGCCACATAGAATA
60915 TGCACCAAAGTGCCACATAGAA-A
1 TGCACCAAAGTGCCACATAGAATA
*
60938 TGTC-CCAAAG-GACACATAG-ATA
1 TG-CACCAAAGTGCCACATAGAATA
60960 TG
1 TG
60962 TCCCGAAGGA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.02
22 11 0.27
23 12 0.29
24 17 0.41
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.18
Consensus pattern (24 bp):
TGCACCAAAGTGCCACATAGAATA
Found at i:60955 original size:22 final size:22
Alignment explanation
Indices: 60919--61008 Score: 99
Period size: 22 Copynumber: 4.0 Consensus size: 22
60909 AGAATATGCA
*
60919 CCAAAGTGCCACATAGAAATGTC
1 CCAAAG-GACACATAGAAATGTC
*
60942 CCAAAGGACACATAGATATGTC
1 CCAAAGGACACATAGAAATGTC
* *
60964 CCGAAGGACACATAGATATGTC
1 CCAAAGGACACATAGAAATGTC
* * *
60986 CCATAGGACCGCGTAGAAATGTC
1 CCAAAGGA-CACATAGAAATGTC
61009 TTGAAGGACC
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
22 41 0.71
23 17 0.29
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (22 bp):
CCAAAGGACACATAGAAATGTC
Found at i:61016 original size:23 final size:23
Alignment explanation
Indices: 60990--61046 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
60980 TATGTCCCAT
*
60990 AGGACCGCGTAGAAATGTCTTGA
1 AGGACCGCGTAGAAATGTCCTGA
* ** *
61013 AGGACCACACAGAATTGTCCTGA
1 AGGACCGCGTAGAAATGTCCTGA
61036 AGGACCGCGTA
1 AGGACCGCGTA
61047 AAACCCTCGA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.28, T:0.18
Consensus pattern (23 bp):
AGGACCGCGTAGAAATGTCCTGA
Found at i:63647 original size:36 final size:36
Alignment explanation
Indices: 63597--63672 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
63587 TTATAGCAAA
*
63597 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
63633 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
63669 AAAA
1 AAAA
63673 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:72354 original size:2 final size:2
Alignment explanation
Indices: 72347--72382 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
72337 AAGGAACATA
72347 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
72383 TAAAATTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75685 original size:61 final size:60
Alignment explanation
Indices: 75590--75706 Score: 180
Period size: 61 Copynumber: 1.9 Consensus size: 60
75580 GGATGCAGTT
* * *
75590 CTCCCAATTGACGACAAATTTGCTTAAGTTATTTTTCAGAGCTGACACGATAAGCCAGTGC
1 CTCCCAATTGACGACAAACTTGCTTAAGGTA-TTTTCAGAGCTGACACGACAAGCCAGTGC
* *
75651 CTCCCAATTGACGACAAACTTGCTTAAGGTATTTTCGGAGCTGTCACGACAAGCCA
1 CTCCCAATTGACGACAAACTTGCTTAAGGTATTTTCAGAGCTGACACGACAAGCCA
75707 AGGCTGTGTA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 22 0.43
61 29 0.57
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.27
Consensus pattern (60 bp):
CTCCCAATTGACGACAAACTTGCTTAAGGTATTTTCAGAGCTGACACGACAAGCCAGTGC
Found at i:80362 original size:19 final size:20
Alignment explanation
Indices: 80340--80380 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
80330 AAAAATATAT
80340 AATATA-TATAGTTTTTGAA
1 AATATAGTATAGTTTTTGAA
80359 AATATAGTATAGTTTTTGAA
1 AATATAGTATAGTTTTTGAA
80379 AA
1 AA
80381 CACGGTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (20 bp):
AATATAGTATAGTTTTTGAA
Found at i:80449 original size:42 final size:39
Alignment explanation
Indices: 80386--80531 Score: 143
Period size: 40 Copynumber: 3.7 Consensus size: 39
80376 GAAAACACGG
* * *
80386 TTTTGAAAGCATATAATATATAGTTTTCTTAAAAATTATT
1 TTTTTAAAACATATAATATATAGTTTT-TTAAAAAGTATT
* * *
80426 TTTTTAAAACATATATATAATATAGTCTTTGAAAACGTATT
1 TTTTTAAAACATATA-AT-ATATAGTTTTTTAAAAAGTATT
*
80467 TTTTTGAAAACATATAATATATAGTTTTTTAAAACG-A-T
1 TTTTT-AAAACATATAATATATAGTTTTTTAAAAAGTATT
* * * *
80505 TTTTGAACATATATAATATATAATTTT
1 TTTTTAAAACATATAATATATAGTTTT
80532 AAAAAAATGG
Statistics
Matches: 91, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
37 19 0.21
38 5 0.05
39 1 0.01
40 29 0.32
41 18 0.20
42 19 0.21
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (39 bp):
TTTTTAAAACATATAATATATAGTTTTTTAAAAAGTATT
Found at i:80469 original size:40 final size:39
Alignment explanation
Indices: 80386--80576 Score: 135
Period size: 40 Copynumber: 4.8 Consensus size: 39
80376 GAAAACACGG
* * * **
80386 TTTTGAAAGCATATAATATATAGTTTTCTTAAAAATTATTT
1 TTTTGAAAACATATAATATATAG-TCT-TTGAAAACGATTT
80427 TTTT-AAAACATATATATAATATAGTCTTTGAAAACGTATTT
1 TTTTGAAAACATATA-AT-ATATAGTCTTTGAAAACG-ATTT
* *
80468 TTTTGAAAACATATAATATATAGTTTTTTAAAACGA--T
1 TTTTGAAAACATATAATATATAGTCTTTGAAAACGATTT
* * * ** *
80505 TTTTGAACATATATAATATATAAT-TTT-AAAAAAATGGT
1 TTTTGAAAACATATAATATATAGTCTTTGAAAACGAT-TT
80543 TTTTGAAAAACATAT-ATAATATAGAT-TTTGAAAA
1 TTTTG-AAAACATATAAT-ATATAG-TCTTTGAAAA
80577 ATTATAATAT
Statistics
Matches: 124, Mismatches: 15, Indels: 22
0.77 0.09 0.14
Matches are distributed among these distances:
35 5 0.04
36 3 0.02
37 22 0.18
38 8 0.06
39 13 0.10
40 35 0.28
41 22 0.18
42 16 0.13
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (39 bp):
TTTTGAAAACATATAATATATAGTCTTTGAAAACGATTT
Found at i:80677 original size:70 final size:70
Alignment explanation
Indices: 80548--80719 Score: 188
Period size: 70 Copynumber: 2.6 Consensus size: 70
80538 ATGGTTTTTG
*
80548 AAAAACATATATAATATAGATTTTGAAAAATTATAATATAATTTTTGAAAACATATTATATAGTT
1 AAAAACATATATAATATAGATTTTGAAAAATTATAATATAATTTTTGAAAACATATTATATAATT
*
80613 TTTAA
66 TTGAA
* *
80618 AAAAACATATA-ACATATAGTTTTTG-AAAA-TATAGTATAATTTTT-AAAACATATTGTTATAT
1 AAAAACATATATA-ATATAGATTTTGAAAAATTATAATATAATTTTTGAAAACATA---TTATAT
80679 AATTTTG--
62 AATTTTGAA
80686 -AAAACATAT-T-ATAT-GATTTTG-AAAA-TATAATATA
1 AAAAACATATATAATATAGATTTTGAAAAATTATAATATA
80720 TTATATAGTT
Statistics
Matches: 91, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
64 18 0.20
65 4 0.04
67 17 0.19
68 14 0.15
69 5 0.05
70 33 0.36
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (70 bp):
AAAAACATATATAATATAGATTTTGAAAAATTATAATATAATTTTTGAAAACATATTATATAATT
TTGAA
Found at i:80713 original size:19 final size:21
Alignment explanation
Indices: 80543--80720 Score: 103
Period size: 24 Copynumber: 7.9 Consensus size: 21
80533 AAAAAATGGT
80543 TTTTGAAAAACATATATAATATAGA
1 TTTTG-AAAACATAT-T-ATATA-A
*
80568 TTTTGAAAA-ATTATAATATAA
1 TTTTGAAAACA-TATTATATAA
*
80589 TTTTTGAAAACATATTATATAGT
1 -TTTTGAAAACATATTATATA-A
* * *
80612 TTTTAAAAAAACATATAACATATAGT
1 TTTT--GAAAACATAT--TATATA-A
80638 TTTTG-AAA-ATA-TAGTATAA
1 TTTTGAAAACATATTA-TATAA
*
80657 TTTTTAAAACATATTGTTATATAA
1 TTTTGAAAACATA---TTATATAA
*
80681 TTTTGAAAACATATTATATGA
1 TTTTGAAAACATATTATATAA
* *
80702 TTTTGAAAATATAATATAT
1 TTTTGAAAACATATTATAT
80721 TATATAGTTT
Statistics
Matches: 125, Mismatches: 13, Indels: 34
0.73 0.08 0.20
Matches are distributed among these distances:
19 5 0.04
20 7 0.06
21 28 0.22
22 29 0.23
23 5 0.04
24 33 0.26
25 7 0.06
26 11 0.09
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (21 bp):
TTTTGAAAACATATTATATAA
Found at i:80797 original size:13 final size:13
Alignment explanation
Indices: 80761--80801 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
80751 TATATTAAGC
80761 TTATTAT-TATTA
1 TTATTATATATTA
*
80773 TTATTATTTATT-
1 TTATTATATATTA
80785 TTATATATATATTA
1 TTAT-TATATATTA
80799 TTA
1 TTA
80802 ATTTTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 11 0.44
13 11 0.44
14 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATATATTA
Found at i:82073 original size:25 final size:26
Alignment explanation
Indices: 82036--82090 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
82026 TTGTTTTCAA
*
82036 TTTAATCCTTTTTAATTTGAATTTCT
1 TTTAATCCTTTTTAATTTGAATTTAT
* * *
82062 TTTAATTC-TTTTATTTTTAATTTAT
1 TTTAATCCTTTTTAATTTGAATTTAT
82087 TTTA
1 TTTA
82091 TTTATTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTAATCCTTTTTAATTTGAATTTAT
Found at i:82091 original size:16 final size:15
Alignment explanation
Indices: 82061--82109 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
82051 TTTGAATTTC
*
82061 TTTTAATTCTTTTAT
1 TTTTAATTATTTTAT
82076 TTTTAATTTATTTTATT
1 TTTTAA-TTATTTTA-T
82093 TATTTAA-TATTTTAT
1 T-TTTAATTATTTTAT
82108 TT
1 TT
82110 ATTTATTGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 1 0.03
15 8 0.27
16 14 0.47
17 2 0.07
18 5 0.17
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTAATTATTTTAT
Found at i:82094 original size:20 final size:19
Alignment explanation
Indices: 82071--82121 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
82061 TTTTAATTCT
82071 TTTATTTTTAATTTATTTTA
1 TTTATTTTTAATTTA-TTTA
* *
82091 TTTATTTAATATTTTATTTA
1 TTTATTT-TTAATTTATTTA
*
82111 TTTATTGTTAA
1 TTTATTTTTAA
82122 CATTAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 17 0.68
21 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (19 bp):
TTTATTTTTAATTTATTTA
Found at i:82110 original size:16 final size:16
Alignment explanation
Indices: 82084--82114 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
82074 ATTTTTAATT
82084 TATTTTATTTATTTAA
1 TATTTTATTTATTTAA
82100 TATTTTATTTATTTA
1 TATTTTATTTATTTA
82115 TTGTTAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTATTTATTTAA
Done.