Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 27
Found at i:4560842 original size:10 final size:10
Alignment explanation
Indices: 4560827--4560867 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
4560817 TTTCACCACA
4560827 TCAAATTCTC
1 TCAAATTCTC
4560837 TCAAATTCTC
1 TCAAATTCTC
4560847 T-AAATTTCTC
1 TCAAA-TTCTC
*
4560857 TCAAATACTC
1 TCAAATTCTC
4560867 T
1 T
4560868 TTATTTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.27, G:0.00, T:0.41
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:4561186 original size:111 final size:111
Alignment explanation
Indices: 4560992--4561324 Score: 594
Period size: 111 Copynumber: 3.0 Consensus size: 111
4560982 TGGAAATCAT
* * *
4560992 ATATCTCTACACTTTGCTGATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACAATTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
4561057 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
*
4561103 ATATCTCGACATTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACAATTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
4561168 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
*
4561214 ATATCTCGACAATTTGCTGATGCGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACAATTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
4561279 TAATTAGTTGATTTATTTAATGTATGATTATTAGATTAAAAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
4561325 TTTTTGTAAT
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 214 1.00
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACAATTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAAAATTAA
Found at i:4562826 original size:14 final size:14
Alignment explanation
Indices: 4562807--4562841 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
4562797 CTCAGCTGCA
*
4562807 CCAGCAGGACCTTT
1 CCAGCAGGACCTTC
4562821 CCAGCAGGACCTTC
1 CCAGCAGGACCTTC
4562835 CCAGCAG
1 CCAGCAG
4562842 CCACCGCAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.40, G:0.23, T:0.14
Consensus pattern (14 bp):
CCAGCAGGACCTTC
Found at i:4562890 original size:27 final size:27
Alignment explanation
Indices: 4562860--4562918 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
4562850 GCCATATATG
*
4562860 ATGCCGCCATCGCCTTTCCATTACCAA
1 ATGCCGCCATCGCCTTTCAATTACCAA
*
4562887 ATGCCGCCATCGCCTTTCAATTACCAG
1 ATGCCGCCATCGCCTTTCAATTACCAA
4562914 ATGCC
1 ATGCC
4562919 ACTGCCGCCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.22, C:0.39, G:0.14, T:0.25
Consensus pattern (27 bp):
ATGCCGCCATCGCCTTTCAATTACCAA
Found at i:4562927 original size:27 final size:27
Alignment explanation
Indices: 4562860--4562929 Score: 68
Period size: 27 Copynumber: 2.6 Consensus size: 27
4562850 GCCATATATG
* * *
4562860 ATGCCGCCATCGCCTTTCCATTACCAA
1 ATGCCACCACCGCCTTTCAATTACCAA
* * *
4562887 ATGCCGCCATCGCCTTTCAATTACCAG
1 ATGCCACCACCGCCTTTCAATTACCAA
**
4562914 ATGCCACTGCCGCCTT
1 ATGCCACCACCGCCTT
4562930 CACCTGGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.20, C:0.40, G:0.14, T:0.26
Consensus pattern (27 bp):
ATGCCACCACCGCCTTTCAATTACCAA
Found at i:4563255 original size:21 final size:21
Alignment explanation
Indices: 4563225--4563285 Score: 95
Period size: 21 Copynumber: 2.9 Consensus size: 21
4563215 TACTCAGGAC
*
4563225 GACGAAGACGACGACGATGGT
1 GACGACGACGACGACGATGGT
*
4563246 GACGACGACGACGACTATGGT
1 GACGACGACGACGACGATGGT
*
4563267 GATGACGACGACGACGATG
1 GACGACGACGACGACGATG
4563286 ACAGCGAGGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.36, T:0.11
Consensus pattern (21 bp):
GACGACGACGACGACGATGGT
Found at i:4563258 original size:24 final size:24
Alignment explanation
Indices: 4563222--4563283 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
4563212 ACCTACTCAG
* *
4563222 GACGACGAAGACGACGACGATGGT
1 GACGACGACGACGACGACGATGAT
* * *
4563246 GACGACGACGACGACTATGGTGAT
1 GACGACGACGACGACGACGATGAT
4563270 GACGACGACGACGA
1 GACGACGACGACGA
4563284 TGACAGCGAG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.32, C:0.23, G:0.35, T:0.10
Consensus pattern (24 bp):
GACGACGACGACGACGACGATGAT
Found at i:4567243 original size:51 final size:51
Alignment explanation
Indices: 4567173--4567296 Score: 146
Period size: 51 Copynumber: 2.4 Consensus size: 51
4567163 CCCCTATGTG
* *
4567173 GCATATAGCGCAG-AGCAGGGGGCGCGCTATACCCCACGTGTAAC-CC-AGTCA
1 GCATATAGCGCGGTA-CAGGGGGCGCGCTATACCCCAC--GTAACGCCAAATCA
* * *
4567224 GCGTATAGCGCGGTACAGGGGGCGCGCTATACTCCACGTAGCGCCAAATCA
1 GCATATAGCGCGGTACAGGGGGCGCGCTATACCCCACGTAACGCCAAATCA
*
4567275 GCATATAGCGCGGTTCAGGGGG
1 GCATATAGCGCGGTACAGGGGG
4567297 TGTGCTTTAC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
49 4 0.06
50 2 0.03
51 56 0.89
52 1 0.02
ACGTcount: A:0.23, C:0.28, G:0.33, T:0.15
Consensus pattern (51 bp):
GCATATAGCGCGGTACAGGGGGCGCGCTATACCCCACGTAACGCCAAATCA
Found at i:4571431 original size:16 final size:16
Alignment explanation
Indices: 4571398--4571442 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4571388 CCCTACTTGA
*
4571398 TTAAATATTTAATAAAT
1 TTAAATATTT-TTAAAT
**
4571415 TTTTATATTTTTAAAT
1 TTAAATATTTTTAAAT
4571431 TTAAATATTTTT
1 TTAAATATTTTT
4571443 TTGCATGAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATATTTTTAAAT
Found at i:4573506 original size:21 final size:21
Alignment explanation
Indices: 4573464--4573506 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4573454 TTTCTGGGTG
* * *
4573464 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
4573485 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
4573506 A
1 A
4573507 CGAAATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:4573564 original size:68 final size:68
Alignment explanation
Indices: 4573486--4573638 Score: 231
Period size: 68 Copynumber: 2.2 Consensus size: 68
4573476 ACCCATTCAA
*
4573486 GGGGAACCGATACCCCCTCAACG-A-AATAAATTTCCAGAATG-TTAGAGGGGAATCGATACCCC
1 GGGGAACCGATACCCCCTCAACGTATAAGAAA-TTCCAGAATGCTT-GAGGGGAATCGATACCCC
4573548 CAGGGG
64 CA-GGG
*
4573554 GGGGAACCGATACCCCCTCATCGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
4573619 GGG
66 GGG
*
4573622 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
4573639 ATGAGAAAAA
Statistics
Matches: 79, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
68 41 0.52
69 31 0.39
70 7 0.09
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
GGG
Found at i:4574063 original size:30 final size:30
Alignment explanation
Indices: 4574005--4574063 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4573995 GTTATATGGG
* *
4574005 CTATGTGATAAAGGTATGAAATTGATATGT
1 CTATGTGATAAAGGTATGAAAATAATATGT
4574035 CTATGTGATAAAGGTATGAAAATAATATG
1 CTATGTGATAAAGGTATGAAAATAATATG
4574064 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGAAAATAATATGT
Found at i:4574302 original size:22 final size:22
Alignment explanation
Indices: 4574274--4574341 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
4574264 TCCTTATGGA
4574274 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
4574296 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
*
4574318 CAATTCTACGAGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
4574340 CA
1 CA
4574342 TTTATACGAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:4574349 original size:22 final size:22
Alignment explanation
Indices: 4574274--4574352 Score: 122
Period size: 22 Copynumber: 3.6 Consensus size: 22
4574264 TCCTTATGGA
*
4574274 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGAGCACTTCGGTG
*
4574296 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGAGCACTTCGGTG
4574318 CAATTCTACGAGCACTTCGGTG
1 CAATTCTACGAGCACTTCGGTG
* *
4574340 CATTTATACGAGC
1 CAATTCTACGAGC
4574353 TGTGGTGACA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.28
Consensus pattern (22 bp):
CAATTCTACGAGCACTTCGGTG
Found at i:4580419 original size:21 final size:21
Alignment explanation
Indices: 4580377--4580419 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4580367 TTTCTGGGTG
* * *
4580377 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
4580398 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
4580419 A
1 A
4580420 CGAAATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:4580477 original size:68 final size:67
Alignment explanation
Indices: 4580399--4580550 Score: 220
Period size: 69 Copynumber: 2.3 Consensus size: 67
4580389 ACCCATTCAA
*
4580399 GGGGAACCGATACCCCCTCAACG-A-AATAAATTTCCAGAATG-TTAGAGGGGAATCGATACCCC
1 GGGGAACCGATACCCCCTCAACGTATAAGAAA-TTCCAGAATGCTT-GAGGGGAATCGATACCCC
4580461 CAGGGG
64 CA--GG
*
4580467 GGGGAACCGATACCCCCTCATCGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
4580532 GG
66 GG
*
4580534 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
4580551 ATGAGAAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
67 18 0.23
68 22 0.28
69 31 0.40
70 7 0.09
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGTATAAGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
GG
Found at i:4580539 original size:20 final size:20
Alignment explanation
Indices: 4580514--4580551 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
4580504 GAATGCTTGA
*
4580514 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
4580534 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
4580552 TGAGAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:4580973 original size:30 final size:30
Alignment explanation
Indices: 4580915--4580973 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
4580905 GTTATATGGG
* *
4580915 CTATGTGATAAAGGTATGAAATTGATATGT
1 CTATGTGATAAAGGTATGAAAATAATATGT
4580945 CTATGTGATAAAGGTATGAAAATAATATG
1 CTATGTGATAAAGGTATGAAAATAATATG
4580974 ACTACGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.41, C:0.03, G:0.22, T:0.34
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGAAAATAATATGT
Found at i:4581257 original size:22 final size:22
Alignment explanation
Indices: 4581182--4581249 Score: 136
Period size: 22 Copynumber: 3.1 Consensus size: 22
4581172 TCCTTATGGA
4581182 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
4581204 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
4581226 CAATTCTACGGGCACTTCGGTG
1 CAATTCTACGGGCACTTCGGTG
4581248 CA
1 CA
4581250 TTTATACGAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (22 bp):
CAATTCTACGGGCACTTCGGTG
Found at i:4583188 original size:16 final size:15
Alignment explanation
Indices: 4583156--4583199 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
4583146 AAAAAATTGG
*
4583156 TAAAATAATTAAATA
1 TAAAATAAATAAATA
4583171 TAAAATAAATATAATA
1 TAAAATAAATA-AATA
*
4583187 TAATAAAAAATAA
1 TAA-AATAAATAA
4583200 TTTTACCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 10 0.40
16 8 0.32
17 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAATAAATAAATA
Found at i:4583816 original size:326 final size:326
Alignment explanation
Indices: 4583223--4583875 Score: 1288
Period size: 326 Copynumber: 2.0 Consensus size: 326
4583213 GAACTATAAC
4583223 AAAATCTACTTAGTTTGATAAAAGTAAGAATGTGAAAATAATTTTGGCGTGATTTGATGTTTGTA
1 AAAATCTACTTAGTTTGATAAAAGTAAGAATGTGAAAATAATTTTGGCGTGATTTGATGTTTGTA
*
4583288 TTCAGGGGTATTTATAAGGGAGGATAATGGATGAGTCGCTGAATCTGGAGTAATAATGTAACACT
66 TTCAGGGGTATTTATAAGGGAGGATAATGGATGAGTCGCTGAATCTCGAGTAATAATGTAACACT
4583353 CAATAATTCAAGGTGAATAATGGAAGGCGTGGATGGTAATTCGCGCTTTTATTGCGAGGCGCCAG
131 CAATAATTCAAGGTGAATAATGGAAGGCGTGGATGGTAATTCGCGCTTTTATTGCGAGGCGCCAG
4583418 CTCGAACGAAAACCTAGGAAAAACACAGATGATGATCCGCGCTTTACCTACGTGGCGCTAGTTCA
196 CTCGAACGAAAACCTAGGAAAAACACAGATGATGATCCGCGCTTTACCTACGTGGCGCTAGTTCA
*
4583483 AACGAAAATCGAGGAAAAGCTCACTTGATGATATGCGCCTTCCATCCATGTTAACAAATGTGTTT
261 AACGAAAATCGAGAAAAAGCTCACTTGATGATATGCGCCTTCCATCCATGTTAACAAATGTGTTT
4583548 T
326 T
4583549 AAAATCTACTTAGTTTGATAAAAGTAAGAATGTGAAAATAATTTTGGCGTGATTTGATGTTTGTA
1 AAAATCTACTTAGTTTGATAAAAGTAAGAATGTGAAAATAATTTTGGCGTGATTTGATGTTTGTA
4583614 TTCAGGGGTATTTATAAGGGAGGATAATGGATGAGTCGCTGAATCTCGAGTAATAATGTAACACT
66 TTCAGGGGTATTTATAAGGGAGGATAATGGATGAGTCGCTGAATCTCGAGTAATAATGTAACACT
4583679 CAATAATTCAAGGTGAATAATGGAAGGCGTGGATGGTAATTCGCGCTTTTATTGCGAGGCGCCAG
131 CAATAATTCAAGGTGAATAATGGAAGGCGTGGATGGTAATTCGCGCTTTTATTGCGAGGCGCCAG
4583744 CTCGAACGAAAACCTAGGAAAAACACAGATGATGATCCGCGCTTTACCTACGTGGCGCTAGTTCA
196 CTCGAACGAAAACCTAGGAAAAACACAGATGATGATCCGCGCTTTACCTACGTGGCGCTAGTTCA
4583809 AACGAAAATCGAGAAAAAGCTCACTTGATGATATGCGCCTTCCATCCATGTTAACAAATGTGTTT
261 AACGAAAATCGAGAAAAAGCTCACTTGATGATATGCGCCTTCCATCCATGTTAACAAATGTGTTT
4583874 T
326 T
4583875 A
1 A
4583876 GATCGGTAAA
Statistics
Matches: 325, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
326 325 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (326 bp):
AAAATCTACTTAGTTTGATAAAAGTAAGAATGTGAAAATAATTTTGGCGTGATTTGATGTTTGTA
TTCAGGGGTATTTATAAGGGAGGATAATGGATGAGTCGCTGAATCTCGAGTAATAATGTAACACT
CAATAATTCAAGGTGAATAATGGAAGGCGTGGATGGTAATTCGCGCTTTTATTGCGAGGCGCCAG
CTCGAACGAAAACCTAGGAAAAACACAGATGATGATCCGCGCTTTACCTACGTGGCGCTAGTTCA
AACGAAAATCGAGAAAAAGCTCACTTGATGATATGCGCCTTCCATCCATGTTAACAAATGTGTTT
T
Found at i:4597123 original size:2 final size:2
Alignment explanation
Indices: 4597116--4597140 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4597106 ATTATTAACG
4597116 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4597141 TCTTTGTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4597172 original size:50 final size:52
Alignment explanation
Indices: 4597077--4597176 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 52
4597067 TACGTATGTA
* *
4597077 ATATATATATTTTTTGTTTCCTTTTTATTATTATTAACGTATATATATATATAT
1 ATATATATATTCTTTGTTTCCTTTTTA-TATTATTAACATATATAT-TATATAT
4597131 ATATATATATTCTTTGTTT-C-TTTTA-ATTATTAA-ATATTATATTATA
1 ATATATATATTCTTTGTTTCCTTTTTATATTATTAACATA-TATATTATA
4597177 GGGGCCCATT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
49 6 0.14
50 13 0.30
52 5 0.12
53 1 0.02
54 18 0.42
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (52 bp):
ATATATATATTCTTTGTTTCCTTTTTATATTATTAACATATATATTATATAT
Found at i:4597386 original size:4 final size:4
Alignment explanation
Indices: 4597357--4597477 Score: 61
Period size: 4 Copynumber: 29.2 Consensus size: 4
4597347 TTACTTTTTC
* * * *
4597357 TTAT CTTAT CTTAT CTTAT CTAT TTAT TTAT TTAA TTAG TTAA TTA- TT-T
1 TTAT -TTAT -TTAT -TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
* * * *
4597406 TTAT TCTCT TTAT TT-T TCTAT TTCCT TTAT CT-T TGAT TTAT TTACT
1 TTAT T-TAT TTAT TTAT T-TAT TT-AT TTAT TTAT TTAT TTAT TTA-T
*
4597452 CATAT TTAT TTAT TTAT TTAT TTAT T
1 -TTAT TTAT TTAT TTAT TTAT TTAT T
4597478 CATGTATATA
Statistics
Matches: 92, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
3 7 0.08
4 59 0.64
5 24 0.26
6 2 0.02
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (4 bp):
TTAT
Found at i:4600009 original size:20 final size:20
Alignment explanation
Indices: 4599984--4600029 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
4599974 AAGGGAACTT
4599984 GAAGCTGAGCACTATCAGTG
1 GAAGCTGAGCACTATCAGTG
*
4600004 GAAGCTGAGCGCTATCAGTG
1 GAAGCTGAGCACTATCAGTG
4600024 GAAGCT
1 GAAGCT
4600030 AAATGTCGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.33, T:0.20
Consensus pattern (20 bp):
GAAGCTGAGCACTATCAGTG
Found at i:4609167 original size:106 final size:106
Alignment explanation
Indices: 4609038--4609465 Score: 689
Period size: 106 Copynumber: 4.0 Consensus size: 106
4609028 ATATCGTACC
* *
4609038 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
4609103 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
4609144 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTG-CTAATAAACAACTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-AATAAACAACTTCC
*
4609208 TAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
4609250 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
*
4609315 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
4609356 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
* * *
4609421 AGTTTCAGAGCCAATTTCAACTTTACAGC-AGATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGA-AGGATATTGG
4609462 ACTC
1 ACTC
4609466 GGAACAATAC
Statistics
Matches: 297, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
105 2 0.01
106 294 0.99
107 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:4609927 original size:7 final size:7
Alignment explanation
Indices: 4609915--4609939 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
4609905 TTTCGACCAC
4609915 ATAAATT
1 ATAAATT
4609922 ATAAATT
1 ATAAATT
4609929 ATAAATT
1 ATAAATT
4609936 ATAA
1 ATAA
4609940 TATGATATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATAAATT
Found at i:4611688 original size:4 final size:4
Alignment explanation
Indices: 4611669--4611796 Score: 84
Period size: 4 Copynumber: 31.5 Consensus size: 4
4611659 TTTCTTTACT
* * *
4611669 TTTA CTTA TCTTA TTTA TTTA TCTA TTTA TTTA ATTA TTTA TTTA TTT-
1 TTTA TTTA T-TTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * * * * *
4611717 TTCT- TCTC TTTA TTT- TTCTA TTTCC TTTA TCT- TTGA TTTA TTGA CTCATA
1 TT-TA TTTA TTTA TTTA TT-TA TTT-A TTTA TTTA TTTA TTTA TTTA -T-TTA
4611767 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
4611797 CATGTATATA
Statistics
Matches: 96, Mismatches: 19, Indels: 18
0.72 0.14 0.14
Matches are distributed among these distances:
3 6 0.06
4 78 0.81
5 11 0.11
6 1 0.01
ACGTcount: A:0.21, C:0.09, G:0.02, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:4612764 original size:28 final size:29
Alignment explanation
Indices: 4612728--4612854 Score: 96
Period size: 31 Copynumber: 4.1 Consensus size: 29
4612718 TATTAAAATA
** *
4612728 ATTTT-AAATAATTTA-ATAAGGTTATTT
1 ATTTTAAAATAATTTATATAAAATAATTT
4612755 ATTTTAAAATAATTTATTATAAAATAATTT
1 ATTTTAAAATAATTTA-TATAAAATAATTT
*
4612785 ATTTTTAAAATAAATTATTATAAAATATGAATTGATTT
1 A-TTTTAAAATAATTTA-TAT-AAA-AT--A---ATTT
* *
4612823 ATTTTAAAATAATTTATTTTAAATAATTT
1 ATTTTAAAATAATTTATATAAAATAATTT
4612852 ATT
1 ATT
4612855 AGTATGGATT
Statistics
Matches: 82, Mismatches: 7, Indels: 20
0.75 0.06 0.18
Matches are distributed among these distances:
27 5 0.06
28 10 0.12
29 7 0.09
30 10 0.12
31 18 0.22
32 4 0.05
33 2 0.02
34 2 0.02
35 3 0.04
36 2 0.02
37 14 0.17
38 5 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (29 bp):
ATTTTAAAATAATTTATATAAAATAATTT
Found at i:4612771 original size:15 final size:15
Alignment explanation
Indices: 4612751--4612854 Score: 102
Period size: 15 Copynumber: 6.5 Consensus size: 15
4612741 TAATAAGGTT
4612751 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
4612766 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
4612781 ATTTATTTTTAAAATA
1 ATTTA-TTTTAAAATA
* *
4612797 AATTATTATAAAATATGAA
1 ATTTATT-TTAAA-AT--A
4612816 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
4612834 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
4612848 ATTTATT
1 ATTTATT
4612855 AGTATGGATT
Statistics
Matches: 75, Mismatches: 6, Indels: 17
0.77 0.06 0.17
Matches are distributed among these distances:
14 12 0.16
15 30 0.40
16 17 0.23
17 2 0.03
18 1 0.01
19 1 0.01
20 2 0.03
21 4 0.05
22 6 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:4612829 original size:68 final size:69
Alignment explanation
Indices: 4612751--4612909 Score: 207
Period size: 68 Copynumber: 2.3 Consensus size: 69
4612741 TAATAAGGTT
*
4612751 ATTTATTTTAAAATAATTTATTATAAAATAATTTATT-TTTAAAATAAATTATTATAAAATATGA
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATATAAAATAAATTATTATAAAATATGA
4612815 ATTG
66 ATTG
* ** * * * *
4612819 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTA-TATAAAATAAATTATTATAAAATATG
*
4612883 GATTG
65 AATTG
4612888 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
4612910 GCATGAATTG
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
67 13 0.16
68 34 0.43
69 32 0.41
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.52
Consensus pattern (69 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATATAAAATAAATTATTATAAAATATGA
ATTG
Found at i:4612830 original size:22 final size:22
Alignment explanation
Indices: 4612799--4612899 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
4612789 TTAAAATAAA
*
4612799 TTATTATAAAATATGAATTGAT
1 TTATTTTAAAATATGAATTGAT
* * * *
4612821 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-A-TGAATTGAT
* * * * *
4612845 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGAATTGAT
*
4612868 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGAATTGAT
4612890 TTATTTTAAA
1 TTATTTTAAA
4612900 TAATTTATTA
Statistics
Matches: 58, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 33 0.57
23 11 0.19
24 12 0.21
25 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAATATGAATTGAT
Found at i:4612872 original size:32 final size:32
Alignment explanation
Indices: 4612834--4612985 Score: 137
Period size: 32 Copynumber: 5.4 Consensus size: 32
4612824 TTTTAAAATA
4612834 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4612866 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
* *
4612888 ATTTATTTTAAATAATTTATTAGCATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4612920 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
*
4612942 ATTTATTTTAAATAATTTATTAGTATGGGTTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
4612974 ATTTATTTTAAA
1 ATTTATTTTAAA
4612986 ATATGAATTG
Statistics
Matches: 95, Mismatches: 5, Indels: 40
0.68 0.04 0.29
Matches are distributed among these distances:
22 26 0.27
23 8 0.08
25 2 0.02
26 6 0.06
28 6 0.06
29 2 0.02
31 8 0.08
32 37 0.39
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.52
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:4612899 original size:54 final size:54
Alignment explanation
Indices: 4612834--4613553 Score: 442
Period size: 54 Copynumber: 13.4 Consensus size: 54
4612824 TTTTAAAATA
4612834 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
4612888 ATTTATTTTAAATAATTTATTAGCATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
4612942 ATTTATTTTAAATAATTTATTAGTATGGGTTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * **
4612996 ATTTA--TT--AT--TGTATTTGTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * **
4613045 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATAATTTATTAG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * *
4613099 TATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTTT-AAATA---ATTT
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * * ***
4613148 A-TTAGTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTA-TTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
* *
4613210 ATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
4613264 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * **
4613318 ATTTA--TT--AT--TGTAGTT-GTATAGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAAT-ATGGATT-G
** * ** * * * * *
4613367 TATGGA-TTGATTTATTTTA-AAATATGGATTAATTTATTTTAAAATATAGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * * * *
4613420 ATTTATTATT--GTAGTTGTATGT-GT-T-GATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATT-TTAAATAATT-TAT-TAGTATGGATTGA-TTT--AT--TTTA-AAATATGGATTG
*
4613478 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
4613532 ATTTATTTTAAATAATTTATTA
1 ATTTATTTTAAATAATTTATTA
4613554 TTGTAGTTGT
Statistics
Matches: 541, Mismatches: 74, Indels: 102
0.75 0.10 0.14
Matches are distributed among these distances:
47 9 0.02
48 55 0.10
49 13 0.02
50 13 0.02
51 2 0.00
52 16 0.03
53 11 0.02
54 319 0.59
55 19 0.04
56 4 0.01
57 11 0.02
58 35 0.06
59 10 0.02
60 7 0.01
62 14 0.03
63 3 0.01
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:4613031 original size:134 final size:133
Alignment explanation
Indices: 4612879--4613538 Score: 667
Period size: 134 Copynumber: 4.9 Consensus size: 133
4612869 TATTTTAAAA
4612879 TATGGATTGATTTATTTTAAATAATTTATTAGCATGAATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATT-G-ATG-ATTGATTTATTTTAAAATATGGATTGAT
* *
4612944 TTATTTTAAATAATTTATTAGTATGGGTTGATTTATTTTAAAATATGAATTGATTTATT-AT-TG
63 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTAATATT
*
4613007 TATTTG
128 TATTAG
4613013 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATT-G-AT-GATTGATTTATTTTAAAATATGGATTGAT
*
4613078 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAT
63 TTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTA--TT-AAT
4613143 AATTTATTAG
125 -ATTTATTAG
* * * * ***
4613153 TATGAATTGATTTATTTT-AA-AA--TATGGATTGATTTA-TTATTGTAGTTGTATGGATTGATT
1 TATGGATTGATTTATTTTAAATAATTTATTGA-TGATTGATTTATTTTA-AAATATGGATTGATT
*
4613213 TATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGAATTGATTTATTTTAAATA
64 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTA--TT-AAT-
4613278 ATTTATTAG
125 ATTTATTAG
** * *** *
4613287 TATGGATTGATTTATTTTAAA-ATATGAATTGAT--TT-A-TTATTGTAGTTGTATAGATTGATT
1 TATGGATTGATTTATTTTAAATA-ATTTATTGATGATTGATTTATTTTA-AAATATGGATTGATT
* *
4613347 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG----GATTAATTTAT-TTT
64 TATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTAATATTT
* *
4613407 A-AAA
129 ATTAG
* * * * * * *
4613411 TATAGATTGATTTATTATT--GTAGTTGTATGTGTTGATTTATTTTAAATAATTTATTAGTATGG
1 TATGGATTGATTTATT-TTAAATAATT-TAT-TGATGATTGA-TTT--AT--TTTA-AAATATGG
4613474 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
57 ATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
4613539 TTAAATAATT
Statistics
Matches: 462, Mismatches: 34, Indels: 56
0.84 0.06 0.10
Matches are distributed among these distances:
123 1 0.00
124 19 0.04
125 9 0.02
127 4 0.01
128 3 0.01
130 7 0.02
132 2 0.00
133 7 0.02
134 355 0.77
135 8 0.02
136 6 0.01
137 1 0.00
138 15 0.03
139 2 0.00
140 23 0.05
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (133 bp):
TATGGATTGATTTATTTTAAATAATTTATTGATGATTGATTTATTTTAAAATATGGATTGATTTA
TTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTAATATTTAT
TAG
Found at i:4613034 original size:188 final size:188
Alignment explanation
Indices: 4612834--4613324 Score: 901
Period size: 188 Copynumber: 2.6 Consensus size: 188
4612824 TTTTAAAATA
4612834 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
* *
4612899 ATAATTTATTAGCATGAATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
** *
4612964 GTATGGGTTGATTTATTTTAAAATATGAATTGATTTATTATTGTATTTGTATGGATTG
131 GTATGAATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGGATTG
4613022 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
4613087 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
*
4613152 GTATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
131 GTATGAATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGGATTG
* *
4613210 ATTTATTTTAAATAATTTATTAGTATGGATTAATTTATTTTAAAATATGAATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
*
4613275 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
66 ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
4613325 ATTGTAGTTG
Statistics
Matches: 294, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
188 294 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (188 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
ATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
GTATGAATTGATTTATTTTAAAATATGAATTGATTTATTATTGTAGTTGTATGGATTG
Found at i:4613048 original size:32 final size:32
Alignment explanation
Indices: 4613007--4613173 Score: 176
Period size: 32 Copynumber: 5.8 Consensus size: 32
4612997 TTTATTATTG
*
4613007 TATTTGTATGGATTGATTTATTTTAAATAATT
1 TATTAGTATGGATTGATTTATTTTAAATAATT
4613039 TATTAGTATGGATTGATTTA-TTT---TAA--
1 TATTAGTATGGATTGATTTATTTTAAATAATT
4613065 -A--A-TATGGATTGATTTATTTTAAATAATT
1 TATTAGTATGGATTGATTTATTTTAAATAATT
4613093 TATTAGTATGGATTGATTTA-TTT---TAA--
1 TATTAGTATGGATTGATTTATTTTAAATAATT
4613119 -A--A-TATGGATTGATTTATTTTAAATAATT
1 TATTAGTATGGATTGATTTATTTTAAATAATT
*
4613147 TATTAGTATGAATTGATTTATTTTAAA
1 TATTAGTATGGATTGATTTATTTTAAA
4613174 ATATGGATTG
Statistics
Matches: 113, Mismatches: 2, Indels: 40
0.73 0.01 0.26
Matches are distributed among these distances:
22 28 0.25
23 8 0.07
25 2 0.02
26 6 0.05
28 6 0.05
29 2 0.02
31 8 0.07
32 53 0.47
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
TATTAGTATGGATTGATTTATTTTAAATAATT
Found at i:4613070 original size:22 final size:22
Alignment explanation
Indices: 4613045--4613087 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4613035 AATTTATTAG
4613045 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4613067 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
4613088 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4613124 original size:22 final size:22
Alignment explanation
Indices: 4613099--4613141 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
4613089 AATTTATTAG
4613099 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
4613121 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
4613142 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4613246 original size:32 final size:32
Alignment explanation
Indices: 4613200--4613307 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
4613190 TATTGTAGTT
4613200 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
4613232 GTATGGATTAATTTATTTT-AA-AA--TA-T-
1 GTATGGATTGATTTATTTTAAATAATTTATTA
4613258 G-A---ATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
4613286 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
4613308 ATATGAATTG
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
22 12 0.19
23 2 0.03
24 2 0.03
25 1 0.02
26 3 0.05
27 2 0.03
28 3 0.05
29 1 0.02
30 2 0.03
31 2 0.03
32 34 0.53
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:4613258 original size:22 final size:22
Alignment explanation
Indices: 4613233--4613275 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4613223 AATTTATTAG
*
4613233 TATGGATTAATTTATTTTAAAA
1 TATGAATTAATTTATTTTAAAA
*
4613255 TATGAATTGATTTATTTTAAA
1 TATGAATTAATTTATTTTAAA
4613276 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGAATTAATTTATTTTAAAA
Found at i:4613380 original size:32 final size:32
Alignment explanation
Indices: 4613334--4613521 Score: 170
Period size: 32 Copynumber: 5.7 Consensus size: 32
4613324 TATTGTAGTT
*
4613334 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
4613366 GTATGGATTGATTTATTTTAAAATATGGATTAATTTA
1 GTATGGATTGATTTATTTT-AAATA---ATTTA-TTA
* * ** * *
4613403 TTTTAAAATATAGATTGA-TTT--ATTATTGTAGTT-
1 GTAT-GGAT-T-GATTTATTTTAAATAATT-TA-TTA
4613436 GTATGTG-TTGATTTATTTTAAATAATTTATTA
1 GTATG-GATTGATTTATTTTAAATAATTTATTA
4613468 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
4613500 GTATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
4613522 ATATGAATTG
Statistics
Matches: 125, Mismatches: 16, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
30 5 0.04
31 7 0.06
32 73 0.58
33 15 0.12
34 3 0.02
36 6 0.05
37 5 0.04
38 2 0.02
39 4 0.03
40 5 0.04
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:4613386 original size:214 final size:212
Alignment explanation
Indices: 4612834--4613538 Score: 574
Period size: 214 Copynumber: 3.3 Consensus size: 212
4612824 TTTTAAAATA
*
4612834 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATT-TTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATT-
* * * * * * *
4612898 AATAATT-TATTAGCATGAATTGATTTATTTTAAAATATGGATTGATTTA-TTTTAAATAATTTA
65 -GTAGTTGTA-T---A-G-ATTGATTTATTTT-AAATA---ATTTA-TTAGTATGAATTGATTTA
* * * * *
4612961 --TT--AGTATGGGTTGATTTATTTTAAAATAT-GAATTGATTTATTATTGTATTTGTATG-GAT
118 TTTTAAAATATGGATTAATTTATTTTAAAATATAG-ATTGATTTATTATTATAATTGTATGTG-T
* * * *
4613020 TGATTTATTTTAAATAATTTATTAGTATGGATTG
181 TGATTTAATTT-AAT-ATTTATAAATATGAATTG
** ** * ** * * * *
4613054 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGAATTGATTTATTA
*** *
4613114 TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATA
63 TTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATA
* *** *
4613177 TGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT-TTAAATAATT-TAT-TAGTATGGA
128 TGGATTAATTTA-T-TT-TA-AAATATAGATTGATTTATTATT--ATAATTGTATGT-GT-T-GA
4613239 -TTAATTT-AT-TTTA-AAATATGAATTG
184 TTTAATTTAATATTTATAAATATGAATTG
4613264 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTG
*
4613329 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
66 TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGG
* * *
4613394 ATTAATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGTGTTGATTTATTTTAAAT
131 ATTAATTTATTTTAAAATATAGATTGATTTATTATTATAATTGTATGTGTTGATTTAATTT-AAT
* * *
4613459 AATTTATTAGTATGGATTG
195 -ATTTATAAATATGAATTG
4613478 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATT
4613539 TTAAATAATT
Statistics
Matches: 393, Mismatches: 56, Indels: 78
0.75 0.11 0.15
Matches are distributed among these distances:
205 3 0.01
206 14 0.04
208 4 0.01
209 16 0.04
210 87 0.22
211 25 0.06
212 9 0.02
213 13 0.03
214 153 0.39
215 14 0.04
216 6 0.02
218 3 0.01
219 14 0.04
220 32 0.08
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.52
Consensus pattern (212 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGAATTGATTTATTATTG
TAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGG
ATTAATTTATTTTAAAATATAGATTGATTTATTATTATAATTGTATGTGTTGATTTAATTTAATA
TTTATAAATATGAATTG
Found at i:4613392 original size:22 final size:22
Alignment explanation
Indices: 4613367--4613426 Score: 102
Period size: 22 Copynumber: 2.7 Consensus size: 22
4613357 AATTTATTAG
4613367 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
4613389 TATGGATTAATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
*
4613411 TATAGATTGATTTATT
1 TATGGATTGATTTATT
4613427 ATTGTAGTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:4613483 original size:18 final size:18
Alignment explanation
Indices: 4613460--4613516 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
4613450 ATTTTAAATA
4613460 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
* * *
4613478 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGGATTG
4613492 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
4613510 ATTTATT
1 ATTTATT
4613517 TTAAAATATG
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
14 9 0.31
15 1 0.03
16 2 0.07
17 1 0.03
18 16 0.55
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:4613526 original size:22 final size:22
Alignment explanation
Indices: 4613501--4613543 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
4613491 AATTTATTAG
*
4613501 TATGGATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
4613523 TATGAATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
4613544 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:4613603 original size:31 final size:31
Alignment explanation
Indices: 4613568--4613626 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
4613558 AGTTGTATAG
* *
4613568 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
4613599 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
4613627 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:4616821 original size:17 final size:17
Alignment explanation
Indices: 4616799--4616831 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4616789 CGAGATCATA
4616799 ATATTAT-TTTTCATATT
1 ATATTATATTTT-ATATT
4616816 ATATTATATTTTATAT
1 ATATTATATTTTATAT
4616832 AAATAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:4616987 original size:22 final size:22
Alignment explanation
Indices: 4616935--4616996 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
4616925 TTAGATAGCG
4616935 TAATAATTAAAATATTTTATAATT
1 TAAT-ATTAAAATA-TTTATAATT
** *
4616959 TTTTATTCAAATATTTATAATT
1 TAATATTAAAATATTTATAATT
4616981 TAATATTAAAAT-TTTA
1 TAATATTAAAATATTTA
4616997 CTTGTTAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
21 4 0.12
22 18 0.56
23 8 0.25
24 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATATTAAAATATTTATAATT
Found at i:4632770 original size:22 final size:23
Alignment explanation
Indices: 4632725--4632778 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
4632715 TTATATTTTT
*
4632725 AATTTTGTAAAAAAAATTATATA
1 AATTTTTTAAAAAAAATTATATA
*
4632748 AATTTTTTAAAGAAAA-TATATA
1 AATTTTTTAAAAAAAATTATATA
4632770 AATATTTTT
1 AAT-TTTTT
4632779 CAACTTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 9 0.32
23 19 0.68
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
AATTTTTTAAAAAAAATTATATA
Found at i:4647345 original size:12 final size:12
Alignment explanation
Indices: 4647328--4647354 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4647318 GCGGGTTAGA
4647328 TGGTATATAATT
1 TGGTATATAATT
4647340 TGGTATATAATT
1 TGGTATATAATT
4647352 TGG
1 TGG
4647355 GGTGGGATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (12 bp):
TGGTATATAATT
Found at i:4647491 original size:21 final size:22
Alignment explanation
Indices: 4647458--4647502 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
4647448 TAGAGATTTT
4647458 TATTTTTATATTATT-AAAATA
1 TATTTTTATATTATTAAAAATA
4647479 TATTCTTTA-ATTATTAAAAATA
1 TATT-TTTATATTATTAAAAATA
4647501 TA
1 TA
4647503 ATAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATATTATTAAAAATA
Found at i:4647519 original size:31 final size:31
Alignment explanation
Indices: 4647472--4647555 Score: 93
Period size: 31 Copynumber: 2.7 Consensus size: 31
4647462 TTTATATTAT
*
4647472 TAAAATATATTCTTTAATTATTAAAAATATAA
1 TAAAA-ATATTATTTAATTATTAAAAATATAA
*
4647504 TAAAAATATTATTTAA-TAGTTTAAAATATAA
1 TAAAAATATTATTTAATTA-TTAAAAATATAA
*
4647535 TAAATA-ATTA-TTAATATATTA
1 TAAAAATATTATTTAAT-TATTA
4647556 TTGTAAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
29 4 0.09
30 8 0.18
31 28 0.62
32 5 0.11
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (31 bp):
TAAAAATATTATTTAATTATTAAAAATATAA
Found at i:4647543 original size:53 final size:59
Alignment explanation
Indices: 4647486--4647595 Score: 142
Period size: 58 Copynumber: 2.0 Consensus size: 59
4647476 ATATATTCTT
4647486 TAATTATTAA-A-AATATAATAAAA-ATATTA-TTTAA-TAGTTTAAAATA-TAATAAA
1 TAATTATTAATATAATATAATAAAATATATTATTTTAATTAGTTTAAAATATTAATAAA
* ** *
4647539 TAATTATTAATATATTATTGTAAAATATATTATTTTAATTATTTTAAAATATTAATA
1 TAATTATTAATATAATATAATAAAATATATTATTTTAATTAGTTTAAAATATTAATA
4647596 TATTCAGACC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 10 0.21
54 1 0.02
55 9 0.19
56 6 0.13
57 5 0.11
58 11 0.23
59 5 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (59 bp):
TAATTATTAATATAATATAATAAAATATATTATTTTAATTAGTTTAAAATATTAATAAA
Found at i:4654144 original size:6 final size:6
Alignment explanation
Indices: 4654133--4654193 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
4654123 GACACGTATT
* *
4654133 ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
4654181 ACCACG ACCACG A
1 ACCACG ACCACG A
4654194 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:4654201 original size:5 final size:5
Alignment explanation
Indices: 4654191--4654234 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
4654181 ACCACGACCA
* * *
4654191 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
4654235 ACGGACGGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.23, C:0.34, G:0.41, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:4659802 original size:22 final size:22
Alignment explanation
Indices: 4659754--4659804 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4659744 TTCAGCTGTT
* *
4659754 ATAACTCCCGAAATTATATCAT
1 ATAACTCCCGAAATTAAATCAA
* * *
4659776 GTAACTCCTGGAATTAAATCAA
1 ATAACTCCCGAAATTAAATCAA
4659798 ATAACTC
1 ATAACTC
4659805 ATGTAACTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.22, G:0.08, T:0.29
Consensus pattern (22 bp):
ATAACTCCCGAAATTAAATCAA
Found at i:4660087 original size:6 final size:6
Alignment explanation
Indices: 4660076--4660112 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
4660066 GACACGTGTT
4660076 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG A
4660113 GCCGAGCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.35, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:4660120 original size:5 final size:5
Alignment explanation
Indices: 4660110--4660153 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
4660100 ACCACGACCA
* * *
4660110 CGAGC CGAGC CGAGC CGAGC CGTGC CGACC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
4660154 ACGGACGGAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.20, C:0.39, G:0.39, T:0.02
Consensus pattern (5 bp):
CGAGC
Found at i:4660346 original size:27 final size:27
Alignment explanation
Indices: 4660308--4660374 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
4660298 TATCAATTTG
*
4660308 CATTTTCAATTTAATTTTTGAGTAGTA
1 CATTTTCAATTTAATTTTTGAGTAGAA
4660335 CATTTTCAATTTAATTTTTGAGTAGAA
1 CATTTTCAATTTAATTTTTGAGTAGAA
4660362 CATTTTCAATTTA
1 CATTTTCAATTTA
4660375 TATGAGTTAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (27 bp):
CATTTTCAATTTAATTTTTGAGTAGAA
Found at i:4662037 original size:177 final size:177
Alignment explanation
Indices: 4661741--4662096 Score: 687
Period size: 177 Copynumber: 2.0 Consensus size: 177
4661731 GAGGTTGCTG
*
4661741 CCCGAGATGCCTTGGCGACCTCCTATGTTGCCCGGAGTACATGACGACGTACGTTCTTACTGTAA
1 CCCGAGATGCCTTGACGACCTCCTATGTTGCCCGGAGTACATGACGACGTACGTTCTTACTGTAA
4661806 AGTTCACTCTAAATCAACAAGCAATTAATCCGATTATAGCATTATCTCGTGAATTAATTATTTTA
66 AGTTCACTCTAAATCAACAAGCAATTAATCCGATTATAGCATTATCTCGTGAATTAATTATTTTA
4661871 CGTCGCTCGGAGTACATGACGACCTACGTTCTTACTGTAGAATTCAC
131 CGTCGCTCGGAGTACATGACGACCTACGTTCTTACTGTAGAATTCAC
4661918 CCCGAGATGCCTTGACGACCTCCTATGTTGCCCGGAGTACATGACGACGTACGTTCTTACTGTAG
1 CCCGAGATGCCTTGACGACCTCCTATGTTGCCCGGAGTACATGACGACGTACGTTCTTACTGTA-
4661983 AA-TTCACTCTAAATCAACAAGCAATTAATCCGATTATAGCATTATCTCGTGAATTAATTATTTT
65 AAGTTCACTCTAAATCAACAAGCAATTAATCCGATTATAGCATTATCTCGTGAATTAATTATTTT
4662047 ACGTCGCTCGGAGTACATGACGACCTACGTTCTTACTGTAGAATTCAC
130 ACGTCGCTCGGAGTACATGACGACCTACGTTCTTACTGTAGAATTCAC
4662095 CC
1 CC
4662097 TAAATCAACA
Statistics
Matches: 177, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
177 175 0.99
178 2 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (177 bp):
CCCGAGATGCCTTGACGACCTCCTATGTTGCCCGGAGTACATGACGACGTACGTTCTTACTGTAA
AGTTCACTCTAAATCAACAAGCAATTAATCCGATTATAGCATTATCTCGTGAATTAATTATTTTA
CGTCGCTCGGAGTACATGACGACCTACGTTCTTACTGTAGAATTCAC
Found at i:4663130 original size:24 final size:24
Alignment explanation
Indices: 4663091--4663142 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
4663081 GGGAACCGTC
4663091 TACCCCCTCTCCTCTTCCTATAAA
1 TACCCCCTCTCCTCTTCCTATAAA
4663115 TACCCCCT-TCCTTCTTCCTATAAA
1 TACCCCCTCTCC-TCTTCCTATAAA
4663139 TACC
1 TACC
4663143 ATACCAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 3 0.11
24 24 0.89
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (24 bp):
TACCCCCTCTCCTCTTCCTATAAA
Found at i:4664754 original size:18 final size:18
Alignment explanation
Indices: 4664728--4664789 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 18
4664718 CCATTTATGT
4664728 GGATCATTACTCGGTTGC
1 GGATCATTACTCGGTTGC
* * ** * *
4664746 GGATGATTATTATG-AGT
1 GGATCATTACTCGGTTGC
4664763 GGATCATTACTCGGTTGC
1 GGATCATTACTCGGTTGC
*
4664781 GGATGATTA
1 GGATCATTA
4664790 TTATGAGTGG
Statistics
Matches: 30, Mismatches: 13, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
17 11 0.37
18 19 0.63
ACGTcount: A:0.23, C:0.13, G:0.29, T:0.35
Consensus pattern (18 bp):
GGATCATTACTCGGTTGC
Found at i:4664766 original size:35 final size:35
Alignment explanation
Indices: 4664726--4664803 Score: 156
Period size: 35 Copynumber: 2.2 Consensus size: 35
4664716 ACCCATTTAT
4664726 GTGGATCATTACTCGGTTGCGGATGATTATTATGA
1 GTGGATCATTACTCGGTTGCGGATGATTATTATGA
4664761 GTGGATCATTACTCGGTTGCGGATGATTATTATGA
1 GTGGATCATTACTCGGTTGCGGATGATTATTATGA
4664796 GTGGATCA
1 GTGGATCA
4664804 ACAAAAACGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.36
Consensus pattern (35 bp):
GTGGATCATTACTCGGTTGCGGATGATTATTATGA
Found at i:4668950 original size:18 final size:20
Alignment explanation
Indices: 4668924--4668960 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4668914 AAATTTATTC
4668924 AAATAATAATAT-ATAAAAT
1 AAATAATAATATAATAAAAT
4668943 AAAT-ATAATATAATAAAA
1 AAATAATAATATAATAAAA
4668961 AATAGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATAATAATATAATAAAAT
Found at i:4674370 original size:15 final size:15
Alignment explanation
Indices: 4674346--4674376 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4674336 GCACATAAGA
*
4674346 GCGGCGCATGAAATT
1 GCGGCCCATGAAATT
4674361 GCGGCCCATGAAATT
1 GCGGCCCATGAAATT
4674376 G
1 G
4674377 AAGAGGGCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.32, T:0.19
Consensus pattern (15 bp):
GCGGCCCATGAAATT
Found at i:4674522 original size:22 final size:22
Alignment explanation
Indices: 4674495--4674539 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4674485 GGTCAGTTAA
4674495 TCGGTCGATTAATGGTTAATGG
1 TCGGTCGATTAATGGTTAATGG
4674517 TCGGTCGATTAATGGTTAATGG
1 TCGGTCGATTAATGGTTAATGG
4674539 T
1 T
4674540 TTTTTTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.09, G:0.31, T:0.38
Consensus pattern (22 bp):
TCGGTCGATTAATGGTTAATGG
Found at i:4676225 original size:23 final size:23
Alignment explanation
Indices: 4676198--4676274 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
4676188 TATCTCATTC
*
4676198 TTTTTTCTTTAGAGTTTGTATCA
1 TTTTTTATTTAGAGTTTGTATCA
* *
4676221 TTTTTTATTT--A-TCT-CATTC-
1 TTTTTTATTTAGAGTTTGTA-TCA
*
4676240 TTTTTTCTTTAGAGTTTGTATCA
1 TTTTTTATTTAGAGTTTGTATCA
4676263 TTTTTTATTTAG
1 TTTTTTATTTAG
4676275 TCGACGTGAC
Statistics
Matches: 41, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
19 10 0.24
20 4 0.10
21 2 0.05
22 4 0.10
23 21 0.51
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.65
Consensus pattern (23 bp):
TTTTTTATTTAGAGTTTGTATCA
Found at i:4676240 original size:42 final size:42
Alignment explanation
Indices: 4676186--4676273 Score: 176
Period size: 42 Copynumber: 2.1 Consensus size: 42
4676176 TTGCCGCTAT
4676186 TTTATCTCATTCTTTTTTCTTTAGAGTTTGTATCATTTTTTA
1 TTTATCTCATTCTTTTTTCTTTAGAGTTTGTATCATTTTTTA
4676228 TTTATCTCATTCTTTTTTCTTTAGAGTTTGTATCATTTTTTA
1 TTTATCTCATTCTTTTTTCTTTAGAGTTTGTATCATTTTTTA
4676270 TTTA
1 TTTA
4676274 GTCGACGTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.17, C:0.11, G:0.07, T:0.65
Consensus pattern (42 bp):
TTTATCTCATTCTTTTTTCTTTAGAGTTTGTATCATTTTTTA
Found at i:4676769 original size:13 final size:13
Alignment explanation
Indices: 4676751--4676775 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4676741 AGTTCTTATA
4676751 GGCATGTTCGGGG
1 GGCATGTTCGGGG
4676764 GGCATGTTCGGG
1 GGCATGTTCGGG
4676776 TATTTAATCT
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:0.08, C:0.16, G:0.52, T:0.24
Consensus pattern (13 bp):
GGCATGTTCGGGG
Found at i:4677710 original size:259 final size:259
Alignment explanation
Indices: 4677250--4677772 Score: 712
Period size: 259 Copynumber: 2.0 Consensus size: 259
4677240 GAAGTCATGT
* ** *
4677250 CCACCACTGCCAGATCCACGTCACGAGCGATAAGTCGATAGGCCCACCTGAAGAGAATGTCTTCT
1 CCACCACTGCCAAATCCACGTCACGAGCGATAAGTCGATAGGCCCACCTGAAGAGAATACCTTAT
* ** * * * * * *
4677315 AAGAAACAATTAGTTTTCCGGGCGATTAGACGAGTGGCGGTGTGTCATTTGTTAAATCAGTATCT
66 AAGAAACAATTACTTTTCCAAGCAATTAGACAAGTGGCAGTGTGCCATTTGTCAAATCAGCATCT
* * * *
4677380 CGAGCGACAAAAGTCATATATGATGCCACCATAAGAGGATATCTTCGTAGAGTTTCCCAAGAAGA
131 CGAGCGACAAAAGCCATAAATGATGCCACCAGAAGAGGATACCTTCGTAGAGTTTCCCAAGAAGA
* * *
4677445 TCGGGTTACTCATGTTTAATCGACTTTACAAATATACCTTATAAAATAGAAGTA-TCAGAGGAAG
196 TCGGGTTACTCATGTTTAATCGACTTTACAAATATACCATATAAAAGACAAGTAGT-AGAGGAAG
*
4677509 CCACCACTTCCAAATCCACGTCACGAGCGATAAGTCGATAGAG-CCACCTGAAGAGAATACCTTA
1 CCACCACTGCCAAATCCACGTCACGAGCGATAAGTCGATAG-GCCCACCTGAAGAGAATACCTTA
* * * *
4677573 TTAGAAACAATTAC-TTTCTCAAGTAATTAGACAAGTGGTAGTGTGCCATTTGTCAAATCAGCGT
65 TAAGAAACAATTACTTTTC-CAAGCAATTAGACAAGTGGCAGTGTGCCATTTGTCAAATCAGCAT
* * *
4677637 CTCGAGCGAGAAAAGCCATAGAAT-ATGCCATCAGAAGAGGATGCCTTCGTAGAGTTTCCCAAGA
129 CTCGAGCGACAAAAGCCATA-AATGATGCCACCAGAAGAGGATACCTTCGTAGAGTTTCCCAAGA
* *
4677701 AGGTCGGGTTACTCATGTTTAATCGACTTTACAAATATATCATATAAAAGACAAGTAGTAGAGGA
193 AGATCGGGTTACTCATGTTTAATCGACTTTACAAATATACCATATAAAAGACAAGTAGTAGAGGA
4677766 AG
258 AG
4677768 CCACC
1 CCACC
4677773 CGAAGAGAAT
Statistics
Matches: 230, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
258 4 0.02
259 222 0.97
260 4 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (259 bp):
CCACCACTGCCAAATCCACGTCACGAGCGATAAGTCGATAGGCCCACCTGAAGAGAATACCTTAT
AAGAAACAATTACTTTTCCAAGCAATTAGACAAGTGGCAGTGTGCCATTTGTCAAATCAGCATCT
CGAGCGACAAAAGCCATAAATGATGCCACCAGAAGAGGATACCTTCGTAGAGTTTCCCAAGAAGA
TCGGGTTACTCATGTTTAATCGACTTTACAAATATACCATATAAAAGACAAGTAGTAGAGGAAG
Found at i:4678926 original size:26 final size:26
Alignment explanation
Indices: 4678867--4678928 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
4678857 AATTTTTCTA
** * * *
4678867 AACAAAAAAGAAAATGGAGTTCGATT
1 AACAAAAAAGAAAATACAATTCAAAT
4678893 AACTAAAAAAGAAAATACAATTCAAAT
1 AAC-AAAAAAGAAAATACAATTCAAAT
4678920 AACAAAAAA
1 AACAAAAAA
4678929 ATACAAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 9 0.30
27 21 0.70
ACGTcount: A:0.65, C:0.10, G:0.10, T:0.16
Consensus pattern (26 bp):
AACAAAAAAGAAAATACAATTCAAAT
Found at i:4679089 original size:18 final size:18
Alignment explanation
Indices: 4679068--4679104 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4679058 CCACCACCAC
*
4679068 CATCACCATTACCCTCAT
1 CATCACCATCACCCTCAT
*
4679086 CATCATCATCACCCTCAT
1 CATCACCATCACCCTCAT
4679104 C
1 C
4679105 TATATGGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.27, C:0.46, G:0.00, T:0.27
Consensus pattern (18 bp):
CATCACCATCACCCTCAT
Found at i:4679371 original size:27 final size:27
Alignment explanation
Indices: 4679333--4679408 Score: 127
Period size: 27 Copynumber: 2.8 Consensus size: 27
4679323 CCGTCAGTGG
*
4679333 CGCCATATGCTGAAATGATGACGGAGT
1 CGCCATATGCTGAAATGATGACAGAGT
4679360 CGCCATATGCTGAAATGATGACAGAGT
1 CGCCATATGCTGAAATGATGACAGAGT
4679387 CGCCATA-GACTGAAATGATGAC
1 CGCCATATG-CTGAAATGATGAC
4679409 TAAGTCGAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.33, C:0.20, G:0.26, T:0.21
Consensus pattern (27 bp):
CGCCATATGCTGAAATGATGACAGAGT
Found at i:4680624 original size:23 final size:22
Alignment explanation
Indices: 4680581--4680629 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
4680571 AAATTTATCG
4680581 TAAAAAATTACAATAACATAAA
1 TAAAAAATTACAATAACATAAA
**
4680603 CTAAAAAATTTA-AATATTATAAA
1 -TAAAAAA-TTACAATAACATAAA
4680626 TAAA
1 TAAA
4680630 TTAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 4 0.17
23 16 0.70
24 3 0.13
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAAAATTACAATAACATAAA
Found at i:4681123 original size:4 final size:4
Alignment explanation
Indices: 4681106--4681265 Score: 72
Period size: 4 Copynumber: 37.5 Consensus size: 4
4681096 ATTTCATAAC
* ** *
4681106 AAAT AAAC AAAT AAAT AAATT CGAAAT ACCT AAAT AAAT AAATT CAAGT
1 AAAT AAAT AAAT AAAT AAA-T --AAAT AAAT AAAT AAAT AAA-T -AAAT
* * * * * **
4681155 GGAAT AAAT AAAT -TAG AAAT AAAT GAAT ACAT AAAT TCA- AAAT AAAT
1 -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * *
4681202 AAAT CCAAATT AAAT AAAC AAAT AAAT CAGT AAAT AAATTT GAAAT AAAT
1 AAAT --AAA-T AAAT AAAT AAAT AAAT AAAT AAAT AAA--T -AAAT AAAT
4681252 AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AA
4681266 TTTCTTCAGT
Statistics
Matches: 114, Mismatches: 29, Indels: 26
0.67 0.17 0.15
Matches are distributed among these distances:
3 2 0.02
4 89 0.78
5 9 0.08
6 7 0.06
7 7 0.06
ACGTcount: A:0.63, C:0.07, G:0.05, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:4681132 original size:23 final size:22
Alignment explanation
Indices: 4681105--4681228 Score: 66
Period size: 23 Copynumber: 5.8 Consensus size: 22
4681095 GATTTCATAA
4681105 CAAATAAACAAATAAATAAATT
1 CAAATAAACAAATAAATAAATT
*
4681127 CGAAAT-ACCTAAATAAATAAATT
1 C-AAATAAAC-AAATAAATAAATT
* **
4681150 CAAGT---GGAATAAATAAATT
1 CAAATAAACAAATAAATAAATT
* ** *
4681169 AGAAATAAATGAATACATAAATT
1 -CAAATAAACAAATAAATAAATT
*
4681192 C--A-AAATAAATAAATCCAAATT
1 CAAATAAACAAATAAAT--AAATT
4681213 -AAATAAACAAATAAAT
1 CAAATAAACAAATAAAT
4681229 CAGTAAATAA
Statistics
Matches: 79, Mismatches: 12, Indels: 21
0.71 0.11 0.19
Matches are distributed among these distances:
19 22 0.28
20 4 0.05
21 5 0.06
22 7 0.09
23 41 0.52
ACGTcount: A:0.62, C:0.09, G:0.05, T:0.24
Consensus pattern (22 bp):
CAAATAAACAAATAAATAAATT
Found at i:4681161 original size:42 final size:42
Alignment explanation
Indices: 4681115--4681263 Score: 124
Period size: 42 Copynumber: 3.8 Consensus size: 42
4681105 CAAATAAACA
* **
4681115 AATAAATAAATTCGAAATACCTAAATAAATAAATTCAAGTGG
1 AATAAATAAATTAGAAATAAATAAATAAATAAATTCAAGTGG
* *
4681157 AATAAATAAATTAGAAATAAATGAATACATAAATTCAA----
1 AATAAATAAATTAGAAATAAATAAATAAATAAATTCAAGTGG
* * *
4681195 AATAAATAAATCCA-AATTAAATAAACAAATAAA-TC-A---G
1 AATAAATAAAT-TAGAAATAAATAAATAAATAAATTCAAGTGG
*
4681232 --TAAATAAATTTGAAATAAATAAATAAATAAAT
1 AATAAATAAATTAGAAATAAATAAATAAATAAAT
4681264 AATTTCTTCA
Statistics
Matches: 89, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
35 26 0.29
36 1 0.01
37 2 0.02
38 26 0.29
39 1 0.01
42 33 0.37
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (42 bp):
AATAAATAAATTAGAAATAAATAAATAAATAAATTCAAGTGG
Found at i:4681203 original size:15 final size:15
Alignment explanation
Indices: 4681180--4681219 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
4681170 GAAATAAATG
* *
4681180 AATACATAAATTCAA
1 AATAAATAAATCCAA
4681195 AATAAATAAATCCAA
1 AATAAATAAATCCAA
*
4681210 ATTAAATAAA
1 AATAAATAAA
4681220 CAAATAAATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.65, C:0.10, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAAATAAATCCAA
Found at i:4683324 original size:197 final size:197
Alignment explanation
Indices: 4682989--4683382 Score: 788
Period size: 197 Copynumber: 2.0 Consensus size: 197
4682979 ATGGCAACAC
4682989 CGCGTCCAGTTCAAGGGGAAGACATTCATCTGCAAATTTATTTGACCATATGGAGATGCCATCGA
1 CGCGTCCAGTTCAAGGGGAAGACATTCATCTGCAAATTTATTTGACCATATGGAGATGCCATCGA
4683054 CGCAACTATCTATGCAGTTTCCATTTGAAACGATGGCTTTAAGCTCCAGGGGGAGGCATTCGACT
66 CGCAACTATCTATGCAGTTTCCATTTGAAACGATGGCTTTAAGCTCCAGGGGGAGGCATTCGACT
4683119 GCGAGCTTTTTCGATCTCAATGTCAATATGCCTTCCAGTTCAAGGGGAAGGCGTGCAAGTAGTAG
131 GCGAGCTTTTTCGATCTCAATGTCAATATGCCTTCCAGTTCAAGGGGAAGGCGTGCAAGTAGTAG
4683184 GT
196 GT
4683186 CGCGTCCAGTTCAAGGGGAAGACATTCATCTGCAAATTTATTTGACCATATGGAGATGCCATCGA
1 CGCGTCCAGTTCAAGGGGAAGACATTCATCTGCAAATTTATTTGACCATATGGAGATGCCATCGA
4683251 CGCAACTATCTATGCAGTTTCCATTTGAAACGATGGCTTTAAGCTCCAGGGGGAGGCATTCGACT
66 CGCAACTATCTATGCAGTTTCCATTTGAAACGATGGCTTTAAGCTCCAGGGGGAGGCATTCGACT
4683316 GCGAGCTTTTTCGATCTCAATGTCAATATGCCTTCCAGTTCAAGGGGAAGGCGTGCAAGTAGTAG
131 GCGAGCTTTTTCGATCTCAATGTCAATATGCCTTCCAGTTCAAGGGGAAGGCGTGCAAGTAGTAG
4683381 GT
196 GT
4683383 TCTTCGACCT
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 197 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (197 bp):
CGCGTCCAGTTCAAGGGGAAGACATTCATCTGCAAATTTATTTGACCATATGGAGATGCCATCGA
CGCAACTATCTATGCAGTTTCCATTTGAAACGATGGCTTTAAGCTCCAGGGGGAGGCATTCGACT
GCGAGCTTTTTCGATCTCAATGTCAATATGCCTTCCAGTTCAAGGGGAAGGCGTGCAAGTAGTAG
GT
Found at i:4688066 original size:111 final size:111
Alignment explanation
Indices: 4687929--4688150 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
4687919 ATTACAAAAA
*
4687929 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
4687994 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
4688040 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
*
4688105 AATTAAAACGTTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
4688151 ATGATTTCCA
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGTAAAGTGTAGAGATAT
Found at i:4688500 original size:51 final size:50
Alignment explanation
Indices: 4688439--4688545 Score: 115
Period size: 50 Copynumber: 2.1 Consensus size: 50
4688429 AGATACCCAG
* * * *
4688439 GTATAGCGCGGATCAGGGGGGCGAGCTATACCCACGTGGCGCCAGATCACC
1 GTATAGCGCGGAGCA-GGGGACGAGCTATACCCACATGGCGCCAAATCACC
* * * * * *
4688490 GTATATCGCGGGGCAGGGGACGCGCTATACCTACATGGTGCCAAATCAGC
1 GTATAGCGCGGAGCAGGGGACGAGCTATACCCACATGGCGCCAAATCACC
4688540 GTATAG
1 GTATAG
4688546 TGCGATTCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
50 33 0.73
51 12 0.27
ACGTcount: A:0.23, C:0.26, G:0.34, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGAGCAGGGGACGAGCTATACCCACATGGCGCCAAATCACC
Found at i:4689263 original size:15 final size:15
Alignment explanation
Indices: 4689243--4689273 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4689233 TAATTCTAAA
4689243 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
4689258 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
4689273 T
1 T
4689274 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:4697439 original size:11 final size:11
Alignment explanation
Indices: 4697423--4697448 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4697413 TGTATATCAC
4697423 ATATGAAAAAA
1 ATATGAAAAAA
4697434 ATATGAAAAAA
1 ATATGAAAAAA
4697445 ATAT
1 ATAT
4697449 ACTTGTATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (11 bp):
ATATGAAAAAA
Found at i:4698505 original size:26 final size:26
Alignment explanation
Indices: 4698453--4698515 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
4698443 AGTTGGTAGT
* * *
4698453 TAATTTTAATAGTTGATTTGACCAAC
1 TAATTTTATTAGTTGACTTGACAAAC
* *
4698479 TGATTTTATTAGTTGACTTGAGAAAC
1 TAATTTTATTAGTTGACTTGACAAAC
*
4698505 TAATTTGATTA
1 TAATTTTATTA
4698516 ACTACTTATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.44
Consensus pattern (26 bp):
TAATTTTATTAGTTGACTTGACAAAC
Found at i:4700080 original size:23 final size:23
Alignment explanation
Indices: 4700036--4700083 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
4700026 ATTTATTTAA
*
4700036 TAAATTTTATTAAATATAAAAGT
1 TAAATTTTATAAAATATAAAAGT
*
4700059 TAAATTTTATAATAAT-TTAAAGT
1 TAAATTTTATAA-AATATAAAAGT
4700082 TA
1 TA
4700084 TATGAAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
TAAATTTTATAAAATATAAAAGT
Found at i:4706709 original size:4 final size:4
Alignment explanation
Indices: 4706702--4706733 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
4706692 AAAAGATCAA
*
4706702 AAAG AAAG AAAG AAAG AAAG AAAG AAAC AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
4706734 CAGATATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.75, C:0.03, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:4707474 original size:17 final size:17
Alignment explanation
Indices: 4707444--4707478 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4707434 CGACATCCGT
4707444 TCCTACATCCAACGACA
1 TCCTACATCCAACGACA
* *
4707461 TCCTATATCTAACGACA
1 TCCTACATCCAACGACA
4707478 T
1 T
4707479 TCTTCCCCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.34, G:0.06, T:0.26
Consensus pattern (17 bp):
TCCTACATCCAACGACA
Found at i:4708186 original size:24 final size:24
Alignment explanation
Indices: 4708129--4708188 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
4708119 TAGTCAGTAT
*
4708129 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
* * *
4708153 CCGGACTTTGATATTGGTCAATAC
1 TCGAAATTTGATATTGGTCAATAC
*
4708177 TCGAATTTTGAT
1 TCGAAATTTGAT
4708189 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.38
Consensus pattern (24 bp):
TCGAAATTTGATATTGGTCAATAC
Found at i:4708404 original size:14 final size:14
Alignment explanation
Indices: 4708375--4708411 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4708365 AGAAGAAGAA
4708375 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
4708390 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
4708404 GAAGAAAA
1 GAAGAAAA
4708412 TGCCACGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:4710465 original size:12 final size:12
Alignment explanation
Indices: 4710448--4710490 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
4710438 CAAGCAAAAG
4710448 GCAATCAAAATC
1 GCAATCAAAATC
4710460 GCAATCAAAATC
1 GCAATCAAAATC
**
4710472 AAAATCAAAATC
1 GCAATCAAAATC
*
4710484 CCAATCA
1 GCAATCA
4710491 CAACTGGCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.53, C:0.26, G:0.05, T:0.16
Consensus pattern (12 bp):
GCAATCAAAATC
Found at i:4710471 original size:6 final size:6
Alignment explanation
Indices: 4710450--4710483 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4710440 AGCAAAAGGC
**
4710450 AATCAA AATCGC AATCAA AATCAA AATCAA AATC
1 AATCAA AATCAA AATCAA AATCAA AATCAA AATC
4710484 CCAATCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.18
Consensus pattern (6 bp):
AATCAA
Found at i:4710686 original size:20 final size:20
Alignment explanation
Indices: 4710661--4710731 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 20
4710651 TTACACATTC
4710661 ATTTGAATATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
4710681 ATTTGACTATCGCAACGC-A
1 ATTTGAATATCGCAACGCGA
4710700 A----AA-ATCGCAACGCGA
1 ATTTGAATATCGCAACGCGA
*
4710715 ATTTGACTATCGCAACG
1 ATTTGAATATCGCAACG
4710732 AGAAAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
14 10 0.24
15 3 0.07
19 3 0.07
20 26 0.62
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:4710712 original size:34 final size:34
Alignment explanation
Indices: 4710669--4710763 Score: 147
Period size: 34 Copynumber: 2.8 Consensus size: 34
4710659 TCATTTGAAT
4710669 ATCGCAACGCGAATTTGACTATCGCAACGCA-AAA
1 ATCGCAACGCGAATTTGACTATCGCAACG-AGAAA
4710703 ATCGCAACGCGAATTTGACTATCGCAACGAGAAA
1 ATCGCAACGCGAATTTGACTATCGCAACGAGAAA
* * *
4710737 ATCGCAAAGCGTATTAGACTATCGCAA
1 ATCGCAACGCGAATTTGACTATCGCAA
4710764 TGCGAATTGA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 1 0.02
34 56 0.98
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (34 bp):
ATCGCAACGCGAATTTGACTATCGCAACGAGAAA
Found at i:4710780 original size:19 final size:20
Alignment explanation
Indices: 4710737--4710781 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
4710727 CAACGAGAAA
*
4710737 ATCGCAAAGCGTATTAGACT
1 ATCGCAAAGCGAATTAGACT
*
4710757 ATCGCAATGCGAATT-GACT
1 ATCGCAAAGCGAATTAGACT
*
4710776 TTCGCA
1 ATCGCA
4710782 TTACGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAAAGCGAATTAGACT
Found at i:4710852 original size:20 final size:20
Alignment explanation
Indices: 4710827--4710895 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
4710817 GCGGTTATCC
*
4710827 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAATTTCG
4710847 CGTTGCGATAGTC-ATTTCCG
1 CGTTGCGATAGTCAATTT-CG
*
4710867 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAATTTCG
4710887 CGTTGCGAT
1 CGTTGCGAT
4710896 TTTAAGTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 3 0.07
20 39 0.87
21 3 0.07
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTTCG
Found at i:4712853 original size:19 final size:19
Alignment explanation
Indices: 4712801--4712873 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
4712791 AATAGTTTCT
*
4712801 GAAACTTAAAATCGTAACAC
1 GAAAC-TAAAATCGCAACAC
* ** *
4712821 GAAAATGACTATCGCAACGC
1 GAAACT-AAAATCGCAACAC
*
4712841 GAAATTAAAATCGCAACAC
1 GAAACTAAAATCGCAACAC
4712860 GAAACTAAAATCGC
1 GAAACTAAAATCGC
4712874 GTTGCGATTT
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
19 24 0.57
20 18 0.43
ACGTcount: A:0.48, C:0.22, G:0.14, T:0.16
Consensus pattern (19 bp):
GAAACTAAAATCGCAACAC
Found at i:4713272 original size:20 final size:21
Alignment explanation
Indices: 4713247--4713295 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
4713237 TCTGAGAGAT
4713247 GGAGAT-AGACGAATTTCGTC
1 GGAGATGAGACGAATTTCGTC
* *
4713267 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGAATTTCGTC
4713289 GGAGATG
1 GGAGATG
4713296 GGGACGGATG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 18 0.72
ACGTcount: A:0.24, C:0.12, G:0.41, T:0.22
Consensus pattern (21 bp):
GGAGATGAGACGAATTTCGTC
Found at i:4713284 original size:22 final size:22
Alignment explanation
Indices: 4713254--4713304 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
4713244 GATGGAGATA
*
4713254 GACGAATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
4713276 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
4713298 GACGGAT
1 GACGGAT
4713305 GTTGCCGTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.43, T:0.22
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:4713496 original size:20 final size:20
Alignment explanation
Indices: 4713471--4713705 Score: 183
Period size: 20 Copynumber: 11.6 Consensus size: 20
4713461 ATTTTGTATT
4713471 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
4713491 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
4713512 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
4713532 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
4713553 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* **
4713573 ATCGCGTTGCGATTTTGT-ATT
1 ATCGCGTTGCGA--TAGTCAGA
4713594 ATCGCGTTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* * *
4713614 ATCGCGTTGCAAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * *
4713634 TTCACATTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* *
4713654 ATCGCGTTGCGAT-TTACATA
1 ATCGCGTTGCGATAGT-CAGA
* * *
4713674 TTCGCATTGCGATAGTCAAA
1 ATCGCGTTGCGATAGTCAGA
4713694 ATCGCGTTGCGA
1 ATCGCGTTGCGA
4713706 ATATGGAAAC
Statistics
Matches: 164, Mismatches: 38, Indels: 26
0.72 0.17 0.11
Matches are distributed among these distances:
19 11 0.07
20 103 0.63
21 41 0.25
22 9 0.05
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:4713506 original size:41 final size:41
Alignment explanation
Indices: 4713449--4713705 Score: 369
Period size: 41 Copynumber: 6.3 Consensus size: 41
4713439 GCGCTTTGAA
* *
4713449 AATCGCATTGTGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
4713490 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
4713531 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
4713572 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
* ** * *
4713613 AATCGCGTTGC-AATTTACA-TATTCACATTGCGATAGTCAG
1 AATCGCGTTGCGATTTTGTATTA-TCGCGTTGCGATAGTCAG
** * *
4713653 AATCGCGTTGCGA-TTTACA-TATTCGCATTGCGATAGTCAA
1 AATCGCGTTGCGATTTTGTATTA-TCGCGTTGCGATAGTCAG
4713693 AATCGCGTTGCGA
1 AATCGCGTTGCGA
4713706 ATATGGAAAC
Statistics
Matches: 205, Mismatches: 9, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
39 2 0.01
40 70 0.34
41 133 0.65
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAG
Found at i:4713517 original size:21 final size:21
Alignment explanation
Indices: 4713450--4713606 Score: 146
Period size: 21 Copynumber: 7.6 Consensus size: 21
4713440 CGCTTTGAAA
* *
4713450 ATCGCATTGTGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* **
4713471 ATCGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
4713491 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* **
4713512 ATCGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
4713532 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* **
4713553 ATCGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
4713573 ATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
4713594 ATCGCGTTGCGAT
1 ATCGCGTTGCGAT
4713607 AGTCAGAATC
Statistics
Matches: 107, Mismatches: 20, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
19 9 0.08
20 39 0.36
21 50 0.47
22 9 0.08
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:4713743 original size:20 final size:20
Alignment explanation
Indices: 4713470--4713757 Score: 136
Period size: 20 Copynumber: 14.3 Consensus size: 20
4713460 GATTTTGTAT
*
4713470 TATCGCGTTGCGATAGTCAGA
1 TATCGCGTTGCGATA-TTAGA
*
4713491 -ATCGCGTTGCGAT-TTTGTA
1 TATCGCGTTGCGATATTAG-A
*
4713510 TTATCGCGTTGCGATAGTCAGA
1 -TATCGCGTTGCGATA-TTAGA
*
4713532 -ATCGCGTTGCGAT-TTTGTA
1 TATCGCGTTGCGATATTAG-A
*
4713551 TTATCGCGTTGCGATAGTCAGA
1 -TATCGCGTTGCGATA-TTAGA
*
4713573 -ATCGCGTTGCGAT-TTTGTA
1 TATCGCGTTGCGATATTAG-A
*
4713592 TTATCGCGTTGCGATAGTCAGA
1 -TATCGCGTTGCGATA-TTAGA
* *
4713614 -ATCGCGTTGCAAT-TTACA
1 TATCGCGTTGCGATATTAGA
* * *
4713632 TATTCACATTGCGATAGTCAGA
1 TA-TCGCGTTGCGATA-TTAGA
*
4713654 -ATCGCGTTGCGAT-TTACA
1 TATCGCGTTGCGATATTAGA
* *
4713672 TATTCGCATTGCGATAGTCA-A
1 TA-TCGCGTTGCGATA-TTAGA
* *
4713693 AATCGCGTTGCGA-ATATGGA
1 TATCGCGTTGCGATAT-TAGA
* ** *
4713713 -AACTGATTTGCGATATTGGA
1 TATC-GCGTTGCGATATTAGA
4713733 TATCGCGTTGCGAT-TTAGA
1 TATCGCGTTGCGATATTAGA
*
4713752 GATCGC
1 TATCGC
4713758 ATTACGATTT
Statistics
Matches: 201, Mismatches: 38, Indels: 58
0.68 0.13 0.20
Matches are distributed among these distances:
18 13 0.06
19 17 0.08
20 111 0.55
21 46 0.23
22 8 0.04
23 6 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGATATTAGA
Found at i:4716746 original size:23 final size:23
Alignment explanation
Indices: 4716704--4716752 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
4716694 TAATCTACCA
* *
4716704 AAAGACATAGAAAAATGTGTCAT
1 AAAGACAAAGAAAAACGTGTCAT
*
4716727 AAAGACAAAGATAAACGTGTCAT
1 AAAGACAAAGAAAAACGTGTCAT
4716750 AAA
1 AAA
4716753 AGCAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.55, C:0.10, G:0.16, T:0.18
Consensus pattern (23 bp):
AAAGACAAAGAAAAACGTGTCAT
Found at i:4722231 original size:38 final size:38
Alignment explanation
Indices: 4722175--4722270 Score: 147
Period size: 38 Copynumber: 2.5 Consensus size: 38
4722165 TATAAGACAT
* * *
4722175 ATGATAGGTCCTACGGGACACAGATTACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
4722213 ATGACAGGTCTTTCGGGACACAGATGACATCCTTCGGG
1 ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
*
4722251 ATGATAGGTCCTTCGGGACA
1 ATGACAGGTCCTTCGGGACA
4722271 TAATTTATAC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 52 1.00
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (38 bp):
ATGACAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:4722250 original size:21 final size:21
Alignment explanation
Indices: 4722183--4722251 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
4722173 ATATGATAGG
* *
4722183 TCCTACGGGACACAGATTACA
1 TCCTTCGGGACACAGATGACA
*
4722204 TCCTTCGGGATGACAG--G---
1 TCCTTCGGGA-CACAGATGACA
*
4722221 TCTTTCGGGACACAGATGACA
1 TCCTTCGGGACACAGATGACA
4722242 TCCTTCGGGA
1 TCCTTCGGGA
4722252 TGATAGGTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
16 4 0.11
17 9 0.25
18 1 0.03
21 18 0.50
22 4 0.11
ACGTcount: A:0.25, C:0.26, G:0.26, T:0.23
Consensus pattern (21 bp):
TCCTTCGGGACACAGATGACA
Found at i:4723217 original size:21 final size:21
Alignment explanation
Indices: 4723175--4723217 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4723165 TTTCTGGGTT
* * *
4723175 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
4723196 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
4723217 A
1 A
4723218 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:4723277 original size:66 final size:68
Alignment explanation
Indices: 4723197--4723347 Score: 216
Period size: 67 Copynumber: 2.2 Consensus size: 68
4723187 ACCCATTCAA
*
4723197 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATACTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
4723261 -GG
66 TGG
* ** * * *
4723263 GGGGAACCGATACCCCCTCATCGTATTTGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
4723328 TGG
66 TGG
*
4723331 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
4723348 ATGAGAAAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
66 22 0.29
67 35 0.47
68 18 0.24
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATACTAGAGGGGAATCGATACCCCCA
TGG
Found at i:4723335 original size:21 final size:21
Alignment explanation
Indices: 4723310--4723350 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4723300 GAATGCTTGT
*
4723310 GGGGAATCGATACCCCCATGG
1 GGGGAACCGATACCCCCATGG
*
4723331 GGGGAACCGATTCCCCCATG
1 GGGGAACCGATACCCCCATG
4723351 AGAAAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.15
Consensus pattern (21 bp):
GGGGAACCGATACCCCCATGG
Found at i:4723693 original size:34 final size:29
Alignment explanation
Indices: 4723654--4723725 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
4723644 CATATTATGA
*
4723654 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
4723683 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
4723712 TACATGACATGAAT
1 TACATGACATGAAT
4723726 ATGCAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:4724093 original size:23 final size:23
Alignment explanation
Indices: 4724027--4724085 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
4724017 ATCATTATAT
*
4724027 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
4724049 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
4724072 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
4724086 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:4730178 original size:21 final size:21
Alignment explanation
Indices: 4730136--4730178 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
4730126 TTTCTGGGTT
* * *
4730136 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
4730157 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
4730178 A
1 A
4730179 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:4730236 original size:64 final size:67
Alignment explanation
Indices: 4730158--4730305 Score: 196
Period size: 64 Copynumber: 2.3 Consensus size: 67
4730148 ACCCATTCAA
*
4730158 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGATA-CCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
4730221 -G
66 GG
* ** * *
4730222 GGGGAACCGATA-CCCCTCATCGTATTTGAAATTCCAGAATGCTTGTGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
4730286 TGG
66 -GG
*
4730289 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
4730306 ATGAGAAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
63 9 0.12
64 42 0.58
65 5 0.07
67 12 0.17
68 4 0.06
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:4730293 original size:21 final size:21
Alignment explanation
Indices: 4730268--4730308 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4730258 GAATGCTTGT
*
4730268 GGGGAATCGATACCCCCATGG
1 GGGGAACCGATACCCCCATGG
*
4730289 GGGGAACCGATTCCCCCATG
1 GGGGAACCGATACCCCCATG
4730309 AGAAAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.32, G:0.32, T:0.15
Consensus pattern (21 bp):
GGGGAACCGATACCCCCATGG
Found at i:4730651 original size:34 final size:29
Alignment explanation
Indices: 4730612--4730683 Score: 126
Period size: 29 Copynumber: 2.5 Consensus size: 29
4730602 CATATTATGA
*
4730612 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
4730641 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
4730670 TACATGACATGAAT
1 TACATGACATGAAT
4730684 ATGCAGAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:4731051 original size:23 final size:23
Alignment explanation
Indices: 4730985--4731043 Score: 102
Period size: 22 Copynumber: 2.6 Consensus size: 23
4730975 ATCATTATAT
*
4730985 GGCACTACGGTGCAATTCTAC-G
1 GGCACTTCGGTGCAATTCTACGG
4731007 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTACGG
4731030 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
4731044 TTTATACGAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.19, C:0.27, G:0.31, T:0.24
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGG
Found at i:4738124 original size:2 final size:2
Alignment explanation
Indices: 4738117--4738149 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4738107 TTTTTCTTTA
4738117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4738150 AATTTATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4751677 original size:21 final size:22
Alignment explanation
Indices: 4751636--4751678 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4751626 TGAAATTTTC
4751636 GTTCAAGCCCAGAAAAATCATT
1 GTTCAAGCCCAGAAAAATCATT
* *
4751658 GTTCATGCCC-GAAAATTCATT
1 GTTCAAGCCCAGAAAAATCATT
4751679 ATCAACTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (22 bp):
GTTCAAGCCCAGAAAAATCATT
Found at i:4754372 original size:105 final size:107
Alignment explanation
Indices: 4754207--4754419 Score: 371
Period size: 105 Copynumber: 2.0 Consensus size: 107
4754197 AACACATAAC
*
4754207 GAAGAAGACATCATTAGTTTATTATTTTATATTTTATATTAATTTATTATATTTAAAATTATATT
1 GAAGAAGACATCATTAGTTTATTATTATATATTTTATATTAATTTATTATATTTAAAATTATATT
4754272 TGAATTAAACTTTTTATATATAAATTATATTCAAAAAAAATTAT
66 TGAATT-AACTTTTTATATATAAATTATATTC-AAAAAAATTAT
4754316 GAAGAAGACATCATTAGTTTA-TATTATATA-TTT-TA-TAATTTATTATATTTAAAATTATATT
1 GAAGAAGACATCATTAGTTTATTATTATATATTTTATATTAATTTATTATATTTAAAATTATATT
4754377 TGAATTAACTTTTTATATATAAATTATATTCAAAAAAATTAT
66 TGAATTAACTTTTTATATATAAATTATATTCAAAAAAATTAT
4754419 G
1 G
4754420 TTATATCAAT
Statistics
Matches: 103, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
103 12 0.12
104 25 0.24
105 32 0.31
106 2 0.02
107 3 0.03
108 8 0.08
109 21 0.20
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (107 bp):
GAAGAAGACATCATTAGTTTATTATTATATATTTTATATTAATTTATTATATTTAAAATTATATT
TGAATTAACTTTTTATATATAAATTATATTCAAAAAAATTAT
Found at i:4754889 original size:24 final size:24
Alignment explanation
Indices: 4754862--4754914 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
4754852 TATCGTATTC
4754862 GTGTTTATTTATTTATTTTTAAAA
1 GTGTTTATTTATTTATTTTTAAAA
*
4754886 GTGTTTGTTTATTTATTTTTAAAA
1 GTGTTTATTTATTTATTTTTAAAA
4754910 GTGTT
1 GTGTT
4754915 CGTGTTTGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.13, T:0.62
Consensus pattern (24 bp):
GTGTTTATTTATTTATTTTTAAAA
Done.