Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 18 of 208
Found at i:5325325 original size:18 final size:18
Alignment explanation
Indices: 5325267--5325325 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
5325257 TTAATTTAAT
*
5325267 TTTTAAAATATTTAAACA
1 TTTTAAAATATTTAAATA
* * *
5325285 TTTT-TAATATTCTTAGATT
1 TTTTAAAATA-T-TTAAATA
5325304 TTTTAAAATATTTAAATA
1 TTTTAAAATATTTAAATA
5325322 TTTT
1 TTTT
5325326 TATTTTTAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
17 4 0.13
18 14 0.45
19 9 0.29
20 4 0.13
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTAAAATATTTAAATA
Found at i:5325337 original size:25 final size:25
Alignment explanation
Indices: 5325303--5325352 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
5325293 ATTCTTAGAT
5325303 TTTTTAAAATATTTA-AATATTTTTA
1 TTTTTAAAATATTTACAAT-TTTTTA
*
5325328 TTTTTAAAATTTTTACAATTTTTTA
1 TTTTTAAAATATTTACAATTTTTTA
5325353 ATAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTTAAAATATTTACAATTTTTTA
Found at i:5325341 original size:9 final size:9
Alignment explanation
Indices: 5325264--5325383 Score: 75
Period size: 10 Copynumber: 13.0 Consensus size: 9
5325254 TATTTAATTT
5325264 AATTTTTAA
1 AATTTTTAA
*
5325273 AATATTTAA
1 AATTTTTAA
5325282 ACATTTTTAA
1 A-ATTTTTAA
* * *
5325292 TATTCTTAG
1 AATTTTTAA
*
5325301 ATTTTTTAA
1 AATTTTTAA
*
5325310 AATATTTAA
1 AATTTTTAA
5325319 ATATTTTT--
1 A-ATTTTTAA
5325327 -ATTTTTAA
1 AATTTTTAA
5325335 AATTTTTACA
1 AATTTTTA-A
*
5325345 ATTTTTTAA
1 AATTTTTAA
*
5325354 TAATTTATAA
1 -AATTTTTAA
* *
5325364 GTATGTTTAA
1 -AATTTTTAA
5325374 AAGTTTTTAA
1 AA-TTTTTAA
5325384 GCCACATGAA
Statistics
Matches: 82, Mismatches: 21, Indels: 15
0.69 0.18 0.13
Matches are distributed among these distances:
6 6 0.07
9 37 0.45
10 39 0.48
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (9 bp):
AATTTTTAA
Found at i:5326377 original size:18 final size:18
Alignment explanation
Indices: 5326327--5326378 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
5326317 TTACACTAAA
*
5326327 TAAAATTAAATTGATTCCT
1 TAAAATT-AATTTATTCCT
*
5326346 TAAAATAAATTTTATT-CT
1 TAAAATTAA-TTTATTCCT
5326364 TATAAATTAATTTAT
1 TA-AAATTAATTTAT
5326379 AAATTATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (18 bp):
TAAAATTAATTTATTCCT
Found at i:5333482 original size:2 final size:2
Alignment explanation
Indices: 5333440--5333468 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5333430 TTTTAGTATT
5333440 TA TA 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 TA TA T
5333469 TTCTTTTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5333544 original size:18 final size:20
Alignment explanation
Indices: 5333523--5333562 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
5333513 CTAAATAAAA
*
5333523 ATAAAAAT-TTATAAAT-TT
1 ATAAAAATATTAGAAATATT
5333541 ATAAAAATATTAGAAATATT
1 ATAAAAATATTAGAAATATT
5333561 AT
1 AT
5333563 TTGACACTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
ATAAAAATATTAGAAATATT
Found at i:5334422 original size:24 final size:24
Alignment explanation
Indices: 5334395--5334455 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
5334385 AGGGTTACAA
* *
5334395 GAAGATTAAAGGTGAAGAGTTAAG
1 GAAGATGAAAGGTGAAAAGTTAAG
*
5334419 GAAGATGAAAGGTGAAAAGTTGAG
1 GAAGATGAAAGGTGAAAAGTTAAG
*
5334443 GAATATGAAAGGT
1 GAAGATGAAAGGT
5334456 TGAACATCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.34, T:0.20
Consensus pattern (24 bp):
GAAGATGAAAGGTGAAAAGTTAAG
Found at i:5335092 original size:14 final size:14
Alignment explanation
Indices: 5335073--5335120 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
5335063 TCTCCTGCGG
*
5335073 TGGGTTTTGGGTTT
1 TGGGTTTAGGGTTT
5335087 TGGGTTTAGGG-TT
1 TGGGTTTAGGGTTT
*
5335100 AGGG-TTAGGGTTT
1 TGGGTTTAGGGTTT
5335113 TGGTGTTT
1 TGG-GTTT
5335121 TTAAGTTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 6 0.21
13 9 0.32
14 11 0.39
15 2 0.07
ACGTcount: A:0.06, C:0.00, G:0.44, T:0.50
Consensus pattern (14 bp):
TGGGTTTAGGGTTT
Found at i:5335289 original size:96 final size:94
Alignment explanation
Indices: 5335162--5335451 Score: 279
Period size: 96 Copynumber: 3.1 Consensus size: 94
5335152 CAAATAAGGG
** ** * * * * * * *
5335162 ATTAGGGTTTAGGGTTTGTCAATTAAATTAATTATAAATTTTTCAAAATTAGATTA-GTTTTCGT
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA-AAATTTTTAAAAATCAAATTAGGGTTTAGA
* ** *
5335226 GTTTATTGTTTTGTAAGAAAAAATTCAACTAA
65 GTTAAGGGTTTT-TAAGAAAAAA-TCAAATAA
* *
5335258 ATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAATTTTAAAAATCAAATTAGGGTTTAGA
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATT-AAAATTTTTAAAAATCAAATTAGGGTTTAGA
*
5335323 GTTAAGGGTTTTTAAGGAAAAATCAAATAA
65 GTTAAGGGTTTTTAAGAAAAAATCAAATAA
* *
5335353 ATTAGGGTTCAGGGTTACTTGAGTAAATTAATTAAAATTTTT--TAAT-AAATTA--GTTTA-AG
1 ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAATTTTTAAAAATCAAATTAGGGTTTAGA-
* *
5335412 GTTTAGGGTTTTTAAGTAAAAACTCAAATAA
65 GTTAAGGGTTTTTAAG-AAAAAATCAAATAA
5335443 ATTAGGGTT
1 ATTAGGGTT
5335452 CCGGGTTTAA
Statistics
Matches: 165, Mismatches: 25, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
88 1 0.01
89 20 0.12
90 21 0.13
91 6 0.04
92 3 0.02
94 8 0.05
95 38 0.23
96 53 0.32
97 15 0.09
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (94 bp):
ATTAGGGTTTAGGGTTACTTGAGTAAATTAATTAAAATTTTTAAAAATCAAATTAGGGTTTAGAG
TTAAGGGTTTTTAAGAAAAAATCAAATAA
Found at i:5335373 original size:95 final size:90
Alignment explanation
Indices: 5335233--5335458 Score: 276
Period size: 95 Copynumber: 2.4 Consensus size: 90
5335223 CGTGTTTATT
* * * *
5335233 GTTTTGTAAGAAAAAATTCAACTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAT
1 GTTTT-TAAGAAAAAACTCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATTAATT--AAAAT
5335298 TTTAAAAATCAAATTAGGGTTT-AGAGTTAAGG
63 TTT-AAAAT-AAATTA--GTTTAAG-GTTAAGG
*
5335330 GTTTTTAAGGAAAAA-TCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATTAATTAAAATTTT
1 GTTTTTAAGAAAAAACTCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATTAATTAAAATTTT
** *
5335394 TTAATAAATTAGTTTAAGGTTTAGG
66 AAAATAAATTAGTTTAAGGTTAAGG
* *
5335419 GTTTTTAAGTAAAAACTCAAATAAATTAGGGTTCCGGGTT
1 GTTTTTAAGAAAAAACTCAAATAAATTAGGGTTCAGGGTT
5335459 TAAGGTTACT
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
89 24 0.20
90 25 0.21
91 6 0.05
92 3 0.03
93 8 0.07
95 38 0.32
96 9 0.08
97 5 0.04
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (90 bp):
GTTTTTAAGAAAAAACTCAAATAAATTAGGGTTCAGGGTTACTTGAGTAAATTAATTAAAATTTT
AAAATAAATTAGTTTAAGGTTAAGG
Found at i:5335721 original size:126 final size:125
Alignment explanation
Indices: 5335495--5335906 Score: 639
Period size: 126 Copynumber: 3.3 Consensus size: 125
5335485 TAATTTAAAA
* *
5335495 AAGCTCCCACGTGGATGCGCTTTTGCTACAGTAGGTCCTGAAAAAATAATTTCGAGTAGACATTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC-TTT
* * *
5335560 CTGAGCAAACAGTGTCAAAGACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGGACTGAAAG
65 TTGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTGAAAG
*
5335621 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAGAATAATTTCGAGTAGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC-TTT
**
5335686 TTGAGCAAACAGTGTCAAAAACGCTTTAATTAGGATGCTTTGTCAGCAGAAGTACTGAAAG
65 TTGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTGAAAG
* * *
5335747 AAGCTCTCACGTGTACAG-GCTTTTGCTACAGTAGCCCCTGAAAAAATAATTTCGAGTAGACTTT
1 AAGCTCCCACGTGGAC-GCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACTTT
* * *
5335811 TTGAACAAACAGTGTCAAAAATGCTTTAAGCAA-GATGCTTTGTCAGCAGAAGTATTGAAAG
65 TTGAGCAAACAGTGTCAAAAACGCTTTAAG-AAGGATGCTTTGTCAGCAGAAGTACTGAAAG
*
5335872 AAGCTTCCACGTGGACGCGCTTTTGCTACAGTAGC
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
5335907 GCATGGTCTG
Statistics
Matches: 262, Mismatches: 21, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
124 1 0.00
125 87 0.33
126 173 0.66
127 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (125 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGACTTTT
TGAGCAAACAGTGTCAAAAACGCTTTAAGAAGGATGCTTTGTCAGCAGAAGTACTGAAAG
Found at i:5338218 original size:21 final size:21
Alignment explanation
Indices: 5338194--5338233 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5338184 TAACTTTGAT
*
5338194 AAATCATTATAAATTGTAAAA
1 AAATAATTATAAATTGTAAAA
* *
5338215 AAATAATTGTAATTTGTAA
1 AAATAATTATAAATTGTAA
5338234 TTTATATGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATAATTATAAATTGTAAAA
Found at i:5339778 original size:11 final size:11
Alignment explanation
Indices: 5339764--5339845 Score: 87
Period size: 11 Copynumber: 7.4 Consensus size: 11
5339754 TCTTTTAAAT
5339764 AGAAATTTGAG
1 AGAAATTTGAG
5339775 AGAAATTTGAG
1 AGAAATTTGAG
* *
5339786 AGGAAGTTGAG
1 AGAAATTTGAG
5339797 AGCAAA-TTGAG
1 AG-AAATTTGAG
5339808 AGGAAA-TTGAG
1 A-GAAATTTGAG
*
5339819 AGGAATTTGAG
1 AGAAATTTGAG
*
5339830 AGAATATTAGAG
1 AGAA-ATTTGAG
5339842 AGAA
1 AGAA
5339846 TATTAGAGAA
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
10 3 0.05
11 45 0.74
12 13 0.21
ACGTcount: A:0.45, C:0.01, G:0.32, T:0.22
Consensus pattern (11 bp):
AGAAATTTGAG
Found at i:5339809 original size:33 final size:33
Alignment explanation
Indices: 5339770--5339854 Score: 102
Period size: 33 Copynumber: 2.5 Consensus size: 33
5339760 AAATAGAAAT
5339770 TTGAGAGAAATTTGAGAGGAAGTTGAGAGCAA-A
1 TTGAGAGAAATTTGAGAGGAAGTTGAGAG-AATA
*
5339803 TTGAGAGGAAA-TTGAGAGGAATTTGAGAGAATA
1 TTGAGA-GAAATTTGAGAGGAAGTTGAGAGAATA
*
5339836 TTAGAGAGAATATTAGAGA
1 TT-GAGAGAA-ATTTGAGA
5339855 AAGGATTTAG
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
32 2 0.04
33 29 0.64
34 9 0.20
35 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.32, T:0.24
Consensus pattern (33 bp):
TTGAGAGAAATTTGAGAGGAAGTTGAGAGAATA
Found at i:5339844 original size:12 final size:12
Alignment explanation
Indices: 5339827--5339854 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5339817 AGAGGAATTT
5339827 GAGAGAATATTA
1 GAGAGAATATTA
5339839 GAGAGAATATTA
1 GAGAGAATATTA
5339851 GAGA
1 GAGA
5339855 AAGGATTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (12 bp):
GAGAGAATATTA
Found at i:5355063 original size:54 final size:54
Alignment explanation
Indices: 5354979--5355087 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 54
5354969 AATACTCAGG
*
5354979 CGGCAGGGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
1 CGGCAGAGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
*
5355033 CGGCAGAGTTGACCATATATTAAAGTCAACCCAAGTGCACTAAGTGCTTAGAAA
1 CGGCAGAGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
5355087 C
1 C
5355088 TTAAGGCTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (54 bp):
CGGCAGAGTTGACCATATATTAAAGCCAACCCAAGTGCACTAAGTGCTTAGAAA
Found at i:5361763 original size:151 final size:152
Alignment explanation
Indices: 5361475--5361782 Score: 476
Period size: 151 Copynumber: 2.0 Consensus size: 152
5361465 TCTCGAGCTA
* * * *
5361475 TTCACTTTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCGTTTCTATTCAGTGCTGCTCACAC
1 TTCACATTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCATTACTACTCAGTGCTGCTCACAC
*
5361540 AAGCTGTCAGGTATCTGCAACACATACTGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCAC
66 AAGCTGTCAGGTATCCGCAACACATACTGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCAC
5361605 CCAGATTCACTTTAGCCACACT
131 CCAGATTCACTTTAGCCACACT
* * *
5361627 TTCACATT-ACGGGTCTGCTCACACAAGCTGTCAGTCTTTTATTACTACTCAGTGTTGCTCACAC
1 TTCACATTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCATTACTACTCAGTGCTGCTCACAC
* * *
5361691 AAGCTGTCAGGTATCCGCAACACAT-GTCGGTATGCCCAGCCATTGGTAGAACTTAAGACCAGCA
66 AAGCTGTCAGGTATCCGCAACACATACT-GGTATACCCAGCCACTGGTAGAACTTAAGACCAGCA
* *
5361755 CCCGGATTCACTTTAGTCACACT
130 CCCAGATTCACTTTAGCCACACT
5361778 TTCAC
1 TTCAC
5361783 GTAGAACCTT
Statistics
Matches: 142, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
150 1 0.01
151 134 0.94
152 7 0.05
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (152 bp):
TTCACATTCACGGGTCTGCTCACACAAGCTGTCAGTCATTCATTACTACTCAGTGCTGCTCACAC
AAGCTGTCAGGTATCCGCAACACATACTGGTATACCCAGCCACTGGTAGAACTTAAGACCAGCAC
CCAGATTCACTTTAGCCACACT
Found at i:5366924 original size:13 final size:14
Alignment explanation
Indices: 5366887--5366918 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
5366877 ATGGCCTACA
5366887 ATTTCACGAAATCG
1 ATTTCACGAAATCG
5366901 ATTTCACGAAAT-G
1 ATTTCACGAAATCG
5366914 ATTTC
1 ATTTC
5366919 GTGAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (14 bp):
ATTTCACGAAATCG
Found at i:5378295 original size:18 final size:19
Alignment explanation
Indices: 5378262--5378297 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5378252 TCAAATGAAC
*
5378262 TAAAATCATAAATATGTAA
1 TAAAATAATAAATATGTAA
5378281 TAAAATAAT-AATATGTA
1 TAAAATAATAAATATGTA
5378298 TAGATACATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (19 bp):
TAAAATAATAAATATGTAA
Found at i:5380674 original size:111 final size:112
Alignment explanation
Indices: 5380483--5380702 Score: 343
Period size: 111 Copynumber: 2.0 Consensus size: 112
5380473 TGGATGTCAA
* ** *
5380483 AAAAAAAAAAAAAAGCCCACATCTAACTTGACTTAAATCTATCCAAAGATTTATTGTGTAGATTA
1 AAAAAAAAAAAAAAGCCCACATCTAACTTGACTTAAAGCTATCCAAAGATTTATTGTACAAATTA
* *
5380548 CTATTCCAAGATCTATCTAAATATTTGTTTGAAGAT-GGAGTGAGTC
66 CTATTCAAAGATCTATCTAAATATTTGTTTGAACATCGGAGTGAGTC
* * *
5380594 AAAATAAAAAAAAGGCCCACATCTAAGTTGACTTAAAGCTATCCAAAGATTTATTGTACAAATTA
1 AAAAAAAAAAAAAAGCCCACATCTAACTTGACTTAAAGCTATCCAAAGATTTATTGTACAAATTA
*
5380659 CTATTCAAATATCTATCTAAATATTTGTTTGAACATCGGAGTGA
66 CTATTCAAAGATCTATCTAAATATTTGTTTGAACATCGGAGTGA
5380703 ACAAGCAGTT
Statistics
Matches: 98, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
111 91 0.93
112 7 0.07
ACGTcount: A:0.41, C:0.15, G:0.13, T:0.31
Consensus pattern (112 bp):
AAAAAAAAAAAAAAGCCCACATCTAACTTGACTTAAAGCTATCCAAAGATTTATTGTACAAATTA
CTATTCAAAGATCTATCTAAATATTTGTTTGAACATCGGAGTGAGTC
Found at i:5382506 original size:15 final size:15
Alignment explanation
Indices: 5382486--5382534 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
5382476 TACTTTTCAA
5382486 TTTTTAAGAATTTAG
1 TTTTTAAGAATTTAG
* *
5382501 TTTTT-ATATTTGTA-
1 TTTTTAAGAATT-TAG
5382515 TTTTTAAGAATTTAG
1 TTTTTAAGAATTTAG
5382530 TTTTT
1 TTTTT
5382535 TTTAGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (15 bp):
TTTTTAAGAATTTAG
Found at i:5382902 original size:16 final size:16
Alignment explanation
Indices: 5382881--5382912 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5382871 TTTCAGATTT
5382881 ATTAACCACACACACG
1 ATTAACCACACACACG
*
5382897 ATTAACCACAGACACG
1 ATTAACCACACACACG
5382913 TGGCTCACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.44, C:0.34, G:0.09, T:0.12
Consensus pattern (16 bp):
ATTAACCACACACACG
Found at i:5384855 original size:15 final size:15
Alignment explanation
Indices: 5384835--5384864 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5384825 TTGACACAAC
*
5384835 TTACAAGTTGAAAAT
1 TTACAAGTTAAAAAT
5384850 TTACAAGTTAAAAAT
1 TTACAAGTTAAAAAT
5384865 ATTTTGCTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (15 bp):
TTACAAGTTAAAAAT
Found at i:5386829 original size:25 final size:26
Alignment explanation
Indices: 5386792--5386840 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5386782 TATGATCTAA
5386792 TTTTTTTTACTCTGTCTGTTGACAAG
1 TTTTTTTTACTCTGTCTGTTGACAAG
*
5386818 TTTTTTTT-CTCTGTCTTTTGACA
1 TTTTTTTTACTCTGTCTGTTGACA
5386841 CGCATTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.12, C:0.16, G:0.12, T:0.59
Consensus pattern (26 bp):
TTTTTTTTACTCTGTCTGTTGACAAG
Found at i:5386914 original size:44 final size:45
Alignment explanation
Indices: 5386864--5386958 Score: 167
Period size: 45 Copynumber: 2.1 Consensus size: 45
5386854 GGACTAGCTC
5386864 CTGTTTTTC-TTTTCTTAATTT-CTAGTTTTGGGTAACCTGCTTGT
1 CTGTTTTTCTTTTTCTTAATTTCCTA-TTTTGGGTAACCTGCTTGT
5386908 CTGTTTTTCTTTTTCTTAATTTCCTATTTTGGGTAACCTGCTTGT
1 CTGTTTTTCTTTTTCTTAATTTCCTATTTTGGGTAACCTGCTTGT
5386953 CTGTTT
1 CTGTTT
5386959 CCGTAGGAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
44 9 0.18
45 37 0.76
46 3 0.06
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.58
Consensus pattern (45 bp):
CTGTTTTTCTTTTTCTTAATTTCCTATTTTGGGTAACCTGCTTGT
Found at i:5389308 original size:15 final size:15
Alignment explanation
Indices: 5389288--5389317 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5389278 TTGACACAAC
*
5389288 TTACAAGTTGAAAAT
1 TTACAAGTTAAAAAT
5389303 TTACAAGTTAAAAAT
1 TTACAAGTTAAAAAT
5389318 ATTTTGCTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (15 bp):
TTACAAGTTAAAAAT
Found at i:5389680 original size:19 final size:19
Alignment explanation
Indices: 5389656--5389733 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
5389646 ATTTTTGAGA
5389656 ATATGCAATCTTAAATATG
1 ATATGCAATCTTAAATATG
*
5389675 ATATGCAATC-CAAGATATG
1 ATATGCAATCTTAA-ATATG
** *
5389694 ATATATATAATCTTAGATATG
1 --ATATGCAATCTTAAATATG
*
5389715 ATATGCAATATTAGAATAT
1 ATATGCAATCTTA-AATAT
5389734 ATGATTTTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 9
0.71 0.14 0.14
Matches are distributed among these distances:
18 2 0.04
19 25 0.56
20 4 0.09
21 13 0.29
22 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.36
Consensus pattern (19 bp):
ATATGCAATCTTAAATATG
Found at i:5390081 original size:21 final size:21
Alignment explanation
Indices: 5390041--5390081 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5390031 ATTAAGTTTT
*
5390041 TTTTATTTTTTTAATTTTCCC
1 TTTTATTTTTTTAATATTCCC
5390062 TTTTATTTATTTTAA-ATTCC
1 TTTTATTT-TTTTAATATTCC
5390082 AATTTGATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTTTTTTAATATTCCC
Found at i:5391190 original size:98 final size:98
Alignment explanation
Indices: 5391060--5391256 Score: 349
Period size: 98 Copynumber: 2.0 Consensus size: 98
5391050 TTAAAAATAA
* * * *
5391060 TAAAGGAAATATTCCGAGTTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5391125 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
*
5391158 TAAAAGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCTTAACGTATTGGGTGTGATTTC
1 TAAAAGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
5391223 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
5391256 T
1 T
5391257 TTTATTGTAC
Statistics
Matches: 94, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 94 1.00
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (98 bp):
TAAAAGAAATATTCCAAGTTTGGGATTCTAAAGGAATCGTGCCCTAACGTATTGGGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:5398237 original size:45 final size:44
Alignment explanation
Indices: 5398187--5398280 Score: 107
Period size: 44 Copynumber: 2.1 Consensus size: 44
5398177 TGCATCGAGC
* * *
5398187 GGAGCAGATCGAAGATGGAAAGTCTTATCTCCCTGAAATAGCAGT
1 GGAGCAAATCAAAG-TGGAAAGTCCTATCTCCCTGAAATAGCAGT
* * * * *
5398232 GGAGCAAATTAAAGTTGATAGTCCTATCTCCCTGAAGTTGCAGT
1 GGAGCAAATCAAAGTGGAAAGTCCTATCTCCCTGAAATAGCAGT
5398276 GGAGC
1 GGAGC
5398281 GGATTAAAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
44 30 0.73
45 11 0.27
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (44 bp):
GGAGCAAATCAAAGTGGAAAGTCCTATCTCCCTGAAATAGCAGT
Found at i:5398287 original size:44 final size:43
Alignment explanation
Indices: 5398206--5398932 Score: 468
Period size: 44 Copynumber: 16.6 Consensus size: 43
5398196 CGAAGATGGA
* * *
5398206 AAGTCTTATCTCCCTGAAATAGCAGTGGAGCAAATTAAAGTTG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTG
* * **
5398249 ATAGTCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCT-
1 A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGTTG
* * ** ***
5398293 CAGATCTTATCTCTCTGAAGTTGCAG-AAAGCAGATCGCA-TCT-
1 AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-TG
* *
5398335 -AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAAG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-TG
* *
5398377 CAAGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAA-TTAG
1 -AAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAGTT-G
* ***
5398422 CAAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGATTAAAGCCC
1 -AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTG
* * * * **
5398466 ATAATCCTATCTCCCTGAAGTTGCATTGGAGCGGATTAAAACCT-
1 A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGTTG
* * * ***
5398510 CAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCA-TT-
1 AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTG
* * * *
5398551 TAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACT-AAGTAAG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-TG
* * * *
5398594 CAAGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAGATGG
1 -AAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGATTAAAG-TTG
**
5398639 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG
1 -AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTG
* * * * **
5398683 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGACTAAAACCT-
1 A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGTTG
* * * *
5398727 CAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACT-AAGTAAG
1 AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-TG
* *
5398771 CAAGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAA-TTAG
1 -AAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TTAAAGTT-G
* *
5398816 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATTGG
1 -AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTT-G
* ** *
5398861 CAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGCCTAAA-TAAG
1 -AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-TG
5398905 CAAGTCTTATC-CTCCTGAAGTTGCAGTG
1 -AAGTCTTATCTC-CCTGAAGTTGCAGTG
5398933 AGGCAGACTG
Statistics
Matches: 545, Mismatches: 98, Indels: 81
0.75 0.14 0.11
Matches are distributed among these distances:
40 43 0.08
41 20 0.04
42 5 0.01
43 24 0.04
44 280 0.51
45 165 0.30
46 8 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (43 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTG
Found at i:5398448 original size:89 final size:87
Alignment explanation
Indices: 5398206--5398941 Score: 573
Period size: 89 Copynumber: 8.4 Consensus size: 87
5398196 CGAAGATGGA
* * * * * *
5398206 AAGTCTTATCTCCCTGAAATAGCAGTGGAGCAAATTAAAGT-TG-ATAGTCCTATCTCCCTGAAG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAA-TAAGCA-AGTCTTATCTCCCTGAAG
* * *
5398269 TTGCAGTGGAGCGGATTAA-AACC
64 TTGCAGTGGAGCAGACTAAGAAGC
* * ** ** *
5398292 TCAGATCTTATCTCTCTGAAGTTGCAG-AAAGCAGA-TCGCAT---CTAGTCTTATCTCCCTGAA
1 -AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAATAAGCAAGTCTTATCTCCCTGAA
5398352 GTTGCAGTGGAGCAGACTAAGTAAGC
63 GTTGCAGTGGAGCAGACTAAG-AAGC
* *
5398378 AAGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAATTAGCAAGTCTTATCTCCCTGAAG
1 AAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAATAAGCAAGTCTTATCTCCCTGAAG
* *
5398442 TTGCAGTGGGGCAGA-TTA-AAGCCC
64 TTGCAGTGGAGCAGACTAAGAAG--C
* * * * * * * *
5398466 ATAATCCTATCTCCCTGAAGTTGCATTGGAGCGGA-TTAA-AACCTCAGATCTTATCTCTCTGAA
1 A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGC-AAG-TCTTATCTCCCTGAA
* * * **
5398529 GTTGCAG-AGAGCAGA-T-CGCATT
63 GTTGCAGTGGAGCAGACTAAGAAGC
* * *
5398551 TAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGT
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCTTATCTC-CCTGAAGT
* *
5398615 TGCAGTGGGGCAGACTGAAGATGGC
65 TGCAGTGGAGCAGACT-AAGA-AGC
* *** * *
5398640 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCG-ATAATCCTATCTCCCTGAAGT
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCA-AGTCTTATCTCCCTGAAGT
* *
5398704 TGCAGTGGAGCGGACTAA-AACC
65 TGCAGTGGAGCAGACTAAGAAGC
* * *
5398726 TCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAA
1 -AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCTTATCTC-CCTGAA
*
5398790 GTTGCAGTGGGGCAGACTGAA-ATTAGC
63 GTTGCAGTGGAGCAGACT-AAGA--AGC
** *
5398817 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAATTGGCAAGTCTTATCTCCCTAAAGT
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAATAAGCAAGTCTTATCTCCCTGAAGT
* *
5398882 TGCAGTGGAGCAGCCTAAATAAGC
65 TGCAGTGGAGCAGACT-AAGAAGC
5398906 AAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACT
1 AAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT
5398942 GAAGATGACA
Statistics
Matches: 517, Mismatches: 92, Indels: 78
0.75 0.13 0.11
Matches are distributed among these distances:
83 2 0.00
84 101 0.20
85 17 0.03
86 18 0.03
87 24 0.05
88 115 0.22
89 194 0.38
90 42 0.08
91 4 0.01
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (87 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCAAGTCTTATCTCCCTGAAGTT
GCAGTGGAGCAGACTAAGAAGC
Found at i:5398582 original size:217 final size:217
Alignment explanation
Indices: 5398206--5398894 Score: 1060
Period size: 217 Copynumber: 3.2 Consensus size: 217
5398196 CGAAGATGGA
* * * ** *
5398206 AAGTCTTATCTCCCTGAAATAGCAGTGGAGCAAATTAAAGTTGATAGTCCTATCTCCCTGAAGTT
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTT
*
5398271 GCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAAAGCAGATCGCATCTA
66 GCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTA
5398336 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGC
131 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGC
*
5398401 AGTGGGGCAGACTGAAATTAGC
196 AGTGGGGCAGACTGAAATTGGC
* *
5398423 AAGTCTTATCTCCCTGAAGTTGCAGTGGGGCAGATTAAAGCCCATAATCCTATCTCCCTGAAGTT
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTT
* *
5398488 GCATTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATTTA
66 GCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTA
*
5398553 GTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGC
131 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGC
5398618 AGTGGGGCAGACTGAAGA-TGGC
196 AGTGGGGCAGACTGAA-ATTGGC
5398640 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTT
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTT
* * * *
5398705 GCAGTGGAGCGGACTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAGTAA
66 GCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CG-CA
* * * * *
5398770 GCAAGTCTTATC-CTCCTGAAGTTGCAGTGGGGCAGACTGAAATTAGCAAGTCTTAT-CTCCCTG
127 TCTAGTCTTATCTC-CCTGAAGTTGCAGTGGAGCAGACT-AAGTAAGCAAGTCTTATCCT-CCTG
* *
5398833 AAGTTGCAGTGGAGCAGACTAAAATTGGC
189 AAGTTGCAGTGGGGCAGACTGAAATTGGC
*
5398862 AAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAG
1 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAG
5398895 CCTAAATAAG
Statistics
Matches: 433, Mismatches: 30, Indels: 13
0.91 0.06 0.03
Matches are distributed among these distances:
217 311 0.72
218 8 0.02
219 1 0.00
220 2 0.00
221 35 0.08
222 76 0.18
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (217 bp):
AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTT
GCAGTGGAGCGGATTAAAACCTCAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTA
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGC
AGTGGGGCAGACTGAAATTGGC
Found at i:5399141 original size:19 final size:19
Alignment explanation
Indices: 5399117--5399191 Score: 105
Period size: 19 Copynumber: 3.8 Consensus size: 19
5399107 AATTTTTGAG
5399117 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
**
5399136 GATATACAATCCAAGATAT
1 GATATACAATCTTAGATAT
*
5399155 GATATATATAATCTTAGATAT
1 G--ATATACAATCTTAGATAT
5399176 GATATACAATCTTAGA
1 GATATACAATCTTAGA
5399192 ATATATGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 32 0.67
21 16 0.33
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:5399167 original size:21 final size:21
Alignment explanation
Indices: 5399118--5399181 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 21
5399108 ATTTTTGAGG
**
5399118 ATATACAATCTTAGATATG--
1 ATATACAATCCAAGATATGAT
5399137 ATATACAATCCAAGATATGAT
1 ATATACAATCCAAGATATGAT
* **
5399158 ATATATAATCTTAGATATGAT
1 ATATACAATCCAAGATATGAT
5399179 ATA
1 ATA
5399182 CAATCTTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 17 0.45
21 21 0.55
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (21 bp):
ATATACAATCCAAGATATGAT
Found at i:5399542 original size:21 final size:21
Alignment explanation
Indices: 5399502--5399542 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5399492 ATTAAATTTT
*
5399502 TTTTATTTTTTTAATTTTCCC
1 TTTTATTTTTTTAATATTCCC
5399523 TTTTATTTATTTTAA-ATTCC
1 TTTTATTT-TTTTAATATTCC
5399543 AATTTGATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.12, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTTTTTTAATATTCCC
Found at i:5401514 original size:14 final size:14
Alignment explanation
Indices: 5401495--5401534 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
5401485 TTGATTGGCA
5401495 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
5401509 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
5401523 GGAAAATGTTTT
1 GTAAAATGTTTT
5401535 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:5401547 original size:34 final size:35
Alignment explanation
Indices: 5401503--5401569 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
5401493 CAGTAAAATG
* *
5401503 TTTTCCGTAAAATGA-TTTCTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
*
5401537 TTTTCTGTAAAATGACTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGACTTACTGGAAAATATTTT
5401570 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.31, C:0.10, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGACTTACTGGAAAATATTTTAC
Found at i:5401556 original size:20 final size:20
Alignment explanation
Indices: 5401518--5401557 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5401508 CGTAAAATGA
**
5401518 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGACTTACT
*
5401538 TTTCTGTAAAATGACTTACT
1 TTTCTGGAAAATGACTTACT
5401558 GGAAAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTCTGGAAAATGACTTACT
Found at i:5404739 original size:40 final size:44
Alignment explanation
Indices: 5404644--5404839 Score: 220
Period size: 47 Copynumber: 4.4 Consensus size: 44
5404634 AATACTTTAA
5404644 TGTTTATTGCAAAAACATTATTTCTGTTTGATTATTTAAGTATTGT
1 TGTTTATTGCAAAAACATTATTTCTGTTTG--TATTTAAGTATTGT
*
5404690 TGTTTATTGCAAAAACATTATTTGTGTTTG-A-TT-A-TATTGT
1 TGTTTATTGCAAAAACATTATTTCTGTTTGTATTTAAGTATTGT
***
5404730 TGTTTATTGCAAAAACATTATTATAAATTTGATTATTTAAGTATTGT
1 TGTTTATTGCAAAAACATTATT-TCTGTTTG--TATTTAAGTATTGT
* ***
5404777 TGATTATTGCAAAAACATTATTATAAATTTGATTATTTAAGTATTGT
1 TGTTTATTGCAAAAACATTATT-TCTGTTTG--TATTTAAGTATTGT
5404824 TGTTTATTGCAAAAAC
1 TGTTTATTGCAAAAAC
5404840 TTGATTCAAG
Statistics
Matches: 137, Mismatches: 6, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
40 28 0.20
41 6 0.04
42 2 0.01
43 1 0.01
44 1 0.01
45 2 0.01
46 30 0.22
47 67 0.49
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.49
Consensus pattern (44 bp):
TGTTTATTGCAAAAACATTATTTCTGTTTGTATTTAAGTATTGT
Found at i:5404775 original size:47 final size:47
Alignment explanation
Indices: 5404724--5404839 Score: 223
Period size: 47 Copynumber: 2.5 Consensus size: 47
5404714 TGTTTGATTA
5404724 TATTGTTGTTTATTGCAAAAACATTATTATAAATTTGATTATTTAAG
1 TATTGTTGTTTATTGCAAAAACATTATTATAAATTTGATTATTTAAG
*
5404771 TATTGTTGATTATTGCAAAAACATTATTATAAATTTGATTATTTAAG
1 TATTGTTGTTTATTGCAAAAACATTATTATAAATTTGATTATTTAAG
5404818 TATTGTTGTTTATTGCAAAAAC
1 TATTGTTGTTTATTGCAAAAAC
5404840 TTGATTCAAG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.47
Consensus pattern (47 bp):
TATTGTTGTTTATTGCAAAAACATTATTATAAATTTGATTATTTAAG
Found at i:5405247 original size:16 final size:15
Alignment explanation
Indices: 5405226--5405257 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
5405216 ACGTAAACAA
5405226 ATTATACCAAATGCAT
1 ATTATACCAAAT-CAT
5405242 ATTATACCAAATCAT
1 ATTATACCAAATCAT
5405257 A
1 A
5405258 AATCAAGCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (15 bp):
ATTATACCAAATCAT
Found at i:5405424 original size:29 final size:29
Alignment explanation
Indices: 5405390--5405452 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
5405380 CAACAGGAGT
5405390 AAGAATGCTGAAGTAGAGGCTAGGACAGC
1 AAGAATGCTGAAGTAGAGGCTAGGACAGC
*
5405419 AAGAATGCTGAGGTAGAGGCTAGGACAGC
1 AAGAATGCTGAAGTAGAGGCTAGGACAGC
5405448 AAGAA
1 AAGAA
5405453 CTATACAGCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.40, C:0.13, G:0.35, T:0.13
Consensus pattern (29 bp):
AAGAATGCTGAAGTAGAGGCTAGGACAGC
Found at i:5408294 original size:3 final size:3
Alignment explanation
Indices: 5408286--5408401 Score: 146
Period size: 3 Copynumber: 38.7 Consensus size: 3
5408276 GTCCTTTAGC
5408286 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -TT CATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
* * *
5408331 -TT AAT GTG ATT ATCT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* **
5408376 ATA ATT ATT ATT ACC ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
5408402 AATTGCTCTT
Statistics
Matches: 97, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
2 4 0.04
3 88 0.91
4 5 0.05
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5408436 original size:17 final size:17
Alignment explanation
Indices: 5408411--5408449 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
5408401 TAATTGCTCT
*
5408411 TATATATATTATATATA
1 TATACATATTATATATA
* *
5408428 TATACATATTTTTTATA
1 TATACATATTATATATA
5408445 TATAC
1 TATAC
5408450 TTACGTACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (17 bp):
TATACATATTATATATA
Found at i:5409287 original size:109 final size:109
Alignment explanation
Indices: 5409153--5409674 Score: 863
Period size: 109 Copynumber: 4.8 Consensus size: 109
5409143 AAAGAAAATT
* *
5409153 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGTCCTAAGGTGCTGGGTGC
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
5409218 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
5409262 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
* *
5409327 CGTTTTTTCTCGTTCAACCAAATGGCTTAATATTCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
*
5409371 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGG-AAATTCGAGAAAACATGCCCTAAGGTGCTGGGTG
* * *
5409436 TCAATTTTTCTCATTCAACCAAATGGCTTAATATCTTTTTAAAAA
65 TCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
* *
5409481 TTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
*
5409546 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTGTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
* * * *
5409590 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGA-AGAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
5409654 CGA--TTTCTCG-TCTAACCAAAT
66 CGATTTTTCTCGTTC-AACCAAAT
5409675 TGCCAAATAT
Statistics
Matches: 392, Mismatches: 19, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
105 2 0.01
106 15 0.04
108 26 0.07
109 245 0.62
110 104 0.27
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.35
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGT
CGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAA
Found at i:5409535 original size:219 final size:218
Alignment explanation
Indices: 5409147--5409651 Score: 850
Period size: 219 Copynumber: 2.3 Consensus size: 218
5409137 TTCAAAAAAG
* *
5409147 AAAATTTTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGTCCTAAGGTGCT
1 AAAAATTTT-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCT
* *
5409212 GGGTGCCGATTTTTCTCGTTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATAAGGCA
65 GGGTGCCAATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATAAGGCA
*
5409277 ATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGTTTTTTCTCGTTC
130 ATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTC
* *
5409342 AACCAAATGGCTTAATATTCTTTT
195 AACCAAATGGCTTAATATCCTGTT
5409366 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAAATTCGAGAAAACATGCCCTAAGGTGCT
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGG-AAATTCGAGAAAACATGCCCTAAGGTGCT
* * *
5409431 GGGTGTCAATTTTTCTCATTCAACCAAATGGCTTAATATCTTTTTAAAAATTTTAAAATAAGGCA
65 GGGTGCCAATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATAAGGCA
*
5409496 ATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTC
130 ATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTC
5409561 AACCAAATGGCTTAATATCCTGTT
195 AACCAAATGGCTTAATATCCTGTT
* * * *
5409585 AAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGA-AGAACGTGCCCTAATGTGCTG
1 AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
5409649 GGT
66 GGT
5409652 TTCGATTTCT
Statistics
Matches: 270, Mismatches: 15, Indels: 4
0.93 0.05 0.01
Matches are distributed among these distances:
217 21 0.08
218 34 0.13
219 215 0.80
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.34
Consensus pattern (218 bp):
AAAAATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTG
GGTGCCAATTTTTCTCATTCAACCAAATGGCTTAATATCCTTTTAAAAATTTCAAAATAAGGCAA
TGTTTTGCGTTTGGAAATTCGAGAAAACATGCCCTAAGGTGCTGGGTGTCGATTTTTCTCGTTCA
ACCAAATGGCTTAATATCCTGTT
Found at i:5417618 original size:20 final size:21
Alignment explanation
Indices: 5417589--5417635 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
5417579 CATACTAATT
*
5417589 AATATAAATCTTA-TGTTCAA
1 AATATAAATCTAATTGTTCAA
* *
5417609 AATATTAATCTAATTTTTCAA
1 AATATAAATCTAATTGTTCAA
5417630 AATATA
1 AATATA
5417636 GTGAGGGCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.43
Consensus pattern (21 bp):
AATATAAATCTAATTGTTCAA
Found at i:5427273 original size:18 final size:18
Alignment explanation
Indices: 5427238--5427288 Score: 59
Period size: 20 Copynumber: 2.8 Consensus size: 18
5427228 TTAAAAAGAT
*
5427238 ATTTTAAAAAT-TAAAAA
1 ATTTAAAAAATATAAAAA
*
5427255 ATTTAAAAAATATATAAA
1 ATTTAAAAAATATAAAAA
5427273 ATTCATAAAAAATATA
1 ATT--TAAAAAATATA
5427289 GAGTACTTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 10 0.34
18 8 0.28
20 11 0.38
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTTAAAAAATATAAAAA
Found at i:5429526 original size:108 final size:109
Alignment explanation
Indices: 5429293--5429689 Score: 658
Period size: 109 Copynumber: 3.7 Consensus size: 109
5429283 GGTTAACTGT
* *
5429293 GAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
5429358 TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGA
66 TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGA
* * * *
5429402 GAAATCGAGACACAGTACCTTAGGGCACGTTCCTCAAATTTCCAAACGCAAAATATTGCCTTA-T
1 GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
5429466 TTTGAAAA-TTTTTGAAAAGGATATTAAG-TCATTTGGTCGAACGA
66 TTTGAAAAGTTTTT-AAAAGGATATTTAGCT-ATTTGGTCGAACGA
5429510 GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
5429575 TTTGAAAAGTTTTTAAAATGATATTTAGCTATTTGGTCGAACGA
66 TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGA
* *
5429619 GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGTAAAATATTGCCTTA-T
1 GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
5429683 TTTGAAA
66 TTTGAAA
5429690 TATTTCCCTT
Statistics
Matches: 268, Mismatches: 15, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
107 6 0.02
108 103 0.38
109 153 0.57
110 6 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (109 bp):
GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGA
Found at i:5429661 original size:217 final size:218
Alignment explanation
Indices: 5429293--5429694 Score: 734
Period size: 217 Copynumber: 1.8 Consensus size: 218
5429283 GGTTAACTGT
*
5429293 GAAATCGAAACCCAGCACCTTAGGGCACGTTTCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 GAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
*
5429358 TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCGAGACACAGTACCTT
66 TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACACAGTACCTT
5429423 AGGGCACGTTCCTCAAATTTCCAAACGCAAAATATTGCCTTATTTTGAAA-ATTTTTGAAAAGGA
131 AGGGCACGTTCCTCAAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATATTTTTGAAAAGGA
5429487 TATTAAGTCATTTGGTCGAACGA
196 TATTAAGTCATTTGGTCGAACGA
*
5429510 GAAATCGAAACCCAGTACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
1 GAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
* *
5429575 TTTGAAAAGTTTTTAAAATGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTT
66 TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACACAGTACCTT
* *
5429640 AGGGCACGTTCCTCGAATTTCCAAACGTAAAATATTGCCTTATTTTGAAATATTT
131 AGGGCACGTTCCTCAAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATATTT
5429695 CCCTTTTTTA
Statistics
Matches: 177, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
217 173 0.98
218 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (218 bp):
GAAATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAATTTCCAAACGCAAAACATTGCCTTATT
TTTGAAAAGTTTTTAAAAGGATATTTAGCTATTTGGTCGAACGAGAAATCGAAACACAGTACCTT
AGGGCACGTTCCTCAAATTTCCAAACGCAAAATATTGCCTTATTTTGAAATATTTTTGAAAAGGA
TATTAAGTCATTTGGTCGAACGA
Found at i:5430025 original size:2 final size:2
Alignment explanation
Indices: 5430018--5430050 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
5430008 AAGTGTTTAC
*
5430018 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5430051 GATTAATAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5430657 original size:3 final size:3
Alignment explanation
Indices: 5430649--5430696 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
5430639 NNNNNNNAGC
**
5430649 AAT AAT AAT AAT AAT AAT AAT AAT AA- AACT AATT AAT TTT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT
5430695 AA
1 AA
5430697 AGTAACCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
2 2 0.05
3 31 0.82
4 5 0.13
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:5437519 original size:26 final size:26
Alignment explanation
Indices: 5437490--5437552 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 26
5437480 TTTTCTTCTT
5437490 TTTCTTTCATTTTTGATTTTGA-TTGA
1 TTTCTTTC-TTTTTGATTTTGACTTGA
* *
5437516 TTTCTCT-TTTTTGTTTTTGACTTTGA
1 TTTCTTTCTTTTTGATTTTGAC-TTGA
5437542 TTT-TTTCTTTT
1 TTTCTTTCTTTT
5437553 ACTTTTTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 12 0.39
25 2 0.06
26 17 0.55
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (26 bp):
TTTCTTTCTTTTTGATTTTGACTTGA
Found at i:5437545 original size:20 final size:20
Alignment explanation
Indices: 5437522--5437594 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
5437512 TTGATTTCTC
5437522 TTTTTTGTTTTTGACTTTGA
1 TTTTTTGTTTTTGACTTTGA
*
5437542 TTTTTT-CTTTT-ACTTTTTTG-
1 TTTTTTGTTTTTGAC---TTTGA
* *
5437562 TTTTTTGATTTTGATTTTGA
1 TTTTTTGTTTTTGACTTTGA
5437582 TTTTTTGATTTTT
1 TTTTTTG-TTTTT
5437595 TTTTGGAATC
Statistics
Matches: 42, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
18 2 0.05
19 8 0.19
20 19 0.45
21 12 0.29
22 1 0.02
ACGTcount: A:0.10, C:0.04, G:0.11, T:0.75
Consensus pattern (20 bp):
TTTTTTGTTTTTGACTTTGA
Found at i:5437558 original size:26 final size:25
Alignment explanation
Indices: 5437488--5437559 Score: 63
Period size: 30 Copynumber: 2.6 Consensus size: 25
5437478 CTTTTTCTTC
* *
5437488 TTTTTCTTTCATTTTTGATTTTGAT
1 TTTTTCTTTTATTTTTGACTTTGAT
*
5437513 TGATTTCTCTTTTTTGTTTTTGACTTTGAT
1 T--TTT-TC--TTTTATTTTTGACTTTGAT
5437543 TTTTTCTTTTACTTTTT
1 TTTTTCTTTTA-TTTTT
5437560 TGTTTTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
25 5 0.14
26 5 0.14
27 5 0.14
28 5 0.14
30 17 0.46
ACGTcount: A:0.10, C:0.10, G:0.08, T:0.72
Consensus pattern (25 bp):
TTTTTCTTTTATTTTTGACTTTGAT
Found at i:5446695 original size:3 final size:3
Alignment explanation
Indices: 5446687--5446744 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
5446677 NNNNNNNNNN
5446687 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA CTAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA -TAA
**
5446733 TTT TAA TAA TAA
1 TAA TAA TAA TAA
5446745 AGTAACCAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
2 2 0.04
3 41 0.85
4 5 0.10
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5452016 original size:32 final size:32
Alignment explanation
Indices: 5451975--5452062 Score: 167
Period size: 32 Copynumber: 2.8 Consensus size: 32
5451965 ACATGACAGC
5451975 CTGGTGGAGGGCCTGCCACAGGCGATACCAAA
1 CTGGTGGAGGGCCTGCCACAGGCGATACCAAA
5452007 CTGGTGGAGGGCCTGCCACAGGCGATACCAAA
1 CTGGTGGAGGGCCTGCCACAGGCGATACCAAA
*
5452039 CTGGTGGAGGGCCTGTCACAGGCG
1 CTGGTGGAGGGCCTGCCACAGGCG
5452063 GCACAGGACT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 55 1.00
ACGTcount: A:0.22, C:0.27, G:0.38, T:0.14
Consensus pattern (32 bp):
CTGGTGGAGGGCCTGCCACAGGCGATACCAAA
Found at i:5454413 original size:23 final size:22
Alignment explanation
Indices: 5454386--5454503 Score: 73
Period size: 23 Copynumber: 5.2 Consensus size: 22
5454376 ATCTTACTCA
5454386 TTTTATCATGATGTCATAACATC
1 TTTTATCAT-ATGTCATAACATC
* * *
5454409 TTTTAGC-TATGGTCTTACTCAT-
1 TTTTATCATAT-GTCATA-ACATC
*
5454431 TTTTATCATGATGCCATAACATC
1 TTTTATCAT-ATGTCATAACATC
* * * *
5454454 TTTCAAC-TATGGTCTTACTCAT-
1 TTTTATCATAT-GTCATA-ACATC
5454476 TTTTATCATAATGTCATAACATC
1 TTTTATCAT-ATGTCATAACATC
5454499 TTTTA
1 TTTTA
5454504 GCTATGGACT
Statistics
Matches: 69, Mismatches: 16, Indels: 20
0.66 0.15 0.19
Matches are distributed among these distances:
21 4 0.06
22 28 0.41
23 33 0.48
24 4 0.06
ACGTcount: A:0.27, C:0.19, G:0.08, T:0.46
Consensus pattern (22 bp):
TTTTATCATATGTCATAACATC
Found at i:5454450 original size:45 final size:45
Alignment explanation
Indices: 5454349--5454519 Score: 245
Period size: 45 Copynumber: 3.8 Consensus size: 45
5454339 GTGCTTTCAT
* *** *
5454349 ATGATGTCATAGCATCTTCCGGCTATGATCTTACTCA-TTTTATC
1 ATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATTTTTATC
5454393 ATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATTTTTATC
1 ATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATTTTTATC
* * *
5454438 ATGATGCCATAACATCTTTCAACTATGGTCTTACTCATTTTTATC
1 ATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATTTTTATC
* *
5454483 ATAATGTCATAACATCTTTTAGCTATGGACTTACTCA
1 ATGATGTCATAACATCTTTTAGCTATGGTCTTACTCA
5454520 ATTTAGGCGT
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
44 32 0.28
45 81 0.72
ACGTcount: A:0.26, C:0.20, G:0.11, T:0.42
Consensus pattern (45 bp):
ATGATGTCATAACATCTTTTAGCTATGGTCTTACTCATTTTTATC
Found at i:5454962 original size:16 final size:17
Alignment explanation
Indices: 5454921--5454965 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
5454911 CATTTTTCTA
5454921 TATTTTTATAATAATATT
1 TATTTTT-TAATAATATT
* *
5454939 TATATTTTAA-AATTTT
1 TATTTTTTAATAATATT
5454955 TATTTTTTAAT
1 TATTTTTTAAT
5454966 TCATATAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 14 0.61
17 3 0.13
18 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTTTAATAATATT
Found at i:5455037 original size:9 final size:9
Alignment explanation
Indices: 5454978--5455071 Score: 55
Period size: 9 Copynumber: 9.9 Consensus size: 9
5454968 ATATAACTTT
*
5454978 TAATTTTTT
1 TAATTTTTA
*
5454987 TAA-TTTCA
1 TAATTTTTA
*
5454995 TAATTTATA
1 TAATTTTTA
5455004 TAATTATTTTA
1 TAA-T-TTTTA
* *
5455015 GTCAATTATAA
1 -T-AATTTTTA
5455026 TAATTTTTA
1 TAATTTTTA
5455035 TAATTTTTAAA
1 TAATTTTT--A
* *
5455046 TAATTATAA
1 TAATTTTTA
*
5455055 TATTTTTTA
1 TAATTTTTA
5455064 TAATTTTT
1 TAATTTTT
5455072 TGCACATTTA
Statistics
Matches: 63, Mismatches: 15, Indels: 14
0.68 0.16 0.15
Matches are distributed among these distances:
8 6 0.10
9 37 0.59
10 2 0.03
11 14 0.22
12 2 0.03
13 2 0.03
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
TAATTTTTA
Found at i:5455037 original size:31 final size:29
Alignment explanation
Indices: 5454978--5455072 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
5454968 ATATAACTTT
* *
5454978 TAATTTTTT--TAATT-TCATAATTTATA
1 TAATTTTTTAATAATTATAATAATTTTTA
*
5455004 TAATTATTTTAGTCAATTATAATAATTTTTA
1 TAATT-TTTTAAT-AATTATAATAATTTTTA
* *
5455035 TAATTTTTAAATAATTATAATATTTTTTA
1 TAATTTTTTAATAATTATAATAATTTTTA
5455064 TAATTTTTT
1 TAATTTTTT
5455073 GCACATTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
26 5 0.09
27 4 0.07
29 25 0.43
30 9 0.16
31 15 0.26
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (29 bp):
TAATTTTTTAATAATTATAATAATTTTTA
Found at i:5455050 original size:11 final size:10
Alignment explanation
Indices: 5455023--5455147 Score: 57
Period size: 10 Copynumber: 12.9 Consensus size: 10
5455013 TAGTCAATTA
5455023 TAATAATTTT
1 TAATAATTTT
5455033 T-ATAATTTT
1 TAATAATTTT
*
5455042 TAAATAA-TTA
1 T-AATAATTTT
5455052 TAAT-ATTTT
1 TAATAATTTT
*
5455061 TTATAATTTT
1 TAATAATTTT
* **
5455071 T--TGCACATT
1 TAAT-AATTTT
*
5455080 T-ATACTTTT
1 TAATAATTTT
** *
5455089 TTTTAATCTT
1 TAATAATTTT
5455099 TAAT-ATTTT
1 TAATAATTTT
*
5455108 TAATATTTTTT
1 TAATA-ATTTT
* *
5455119 TTATAAATTT
1 TAATAATTTT
*
5455129 TAATATTTTT
1 TAATAATTTT
5455139 TAATAATTT
1 TAATAATTT
5455148 GAAGTATAAA
Statistics
Matches: 82, Mismatches: 24, Indels: 18
0.66 0.19 0.15
Matches are distributed among these distances:
8 2 0.02
9 32 0.39
10 36 0.44
11 12 0.15
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.62
Consensus pattern (10 bp):
TAATAATTTT
Found at i:5455119 original size:30 final size:31
Alignment explanation
Indices: 5455085--5455143 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
5455075 ACATTTATAC
5455085 TTTTTTT-T-AATCTTTAATA-TTTTTAATAT
1 TTTTTTTATAAAT-TTTAATATTTTTTAATAT
5455114 TTTTTTTATAAATTTTAATATTTTTTAATA
1 TTTTTTTATAAATTTTAATATTTTTTAATA
5455144 ATTTGAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 7 0.26
30 8 0.30
31 12 0.44
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (31 bp):
TTTTTTTATAAATTTTAATATTTTTTAATAT
Found at i:5455539 original size:14 final size:15
Alignment explanation
Indices: 5455520--5455552 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
5455510 AATAATTATT
5455520 AAATATAATTTAA-A
1 AAATATAATTTAATA
5455534 AAATATAATTTAATA
1 AAATATAATTTAATA
5455549 AAAT
1 AAAT
5455553 TCTTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATAATTTAATA
Found at i:5455548 original size:24 final size:25
Alignment explanation
Indices: 5455485--5455553 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 25
5455475 TATAAATAAT
* *
5455485 ATATAATTTAATCATATTTTAACATA
1 ATATAATTTAAT-ATAATTTAACAAA
* *
5455511 ATAATTATTAAATATAATTTAA-AAA
1 AT-ATAATTTAATATAATTTAACAAA
*
5455536 ATATAATTTAATAAAATT
1 ATATAATTTAATATAATT
5455554 CTTAATATTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
24 13 0.37
25 4 0.11
26 10 0.29
27 8 0.23
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (25 bp):
ATATAATTTAATATAATTTAACAAA
Found at i:5455653 original size:29 final size:31
Alignment explanation
Indices: 5455620--5455694 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 31
5455610 AAATATAATT
*
5455620 TAAAATAATTATTATTAAATATAA-T-TTAA
1 TAAAATAATTATTATTAAATAAAATTCTTAA
* *
5455649 TAAAA-AATATATAATTTAATAAAATTCTTAA
1 TAAAATAAT-TATTATTAAATAAAATTCTTAA
* *
5455680 TAAAATTATTCTTAT
1 TAAAATAATTATTAT
5455695 ATGAATTTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
28 3 0.08
29 17 0.47
30 1 0.03
31 13 0.36
32 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
TAAAATAATTATTATTAAATAAAATTCTTAA
Found at i:5455707 original size:120 final size:114
Alignment explanation
Indices: 5455502--5455737 Score: 375
Period size: 120 Copynumber: 2.0 Consensus size: 114
5455492 TTAATCATAT
*
5455502 TTTAACATAATAATTATTAAATATAATTTAAAAAATATAATTTAATAAAATTCTTAATATTAAAT
1 TTTAAAATAATAATTATTAAATATAATTTAAAAAATATAATTTAATAAAATTCTTAATA-TAAAT
5455567 ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 ATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
*
5455618 TTTAAAATAATTATTATTAAATATAATTTAATAAAAAATATATAATTTAATAAAATTCTTAATA-
1 TTTAAAATAATAATTATTAAATATAA-TT--T-AAAAA-ATATAATTTAATAAAATTCTTAATAT
5455682 AAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
61 AAA-TATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
5455737 T
1 T
5455738 ATATAATCTA
Statistics
Matches: 112, Mismatches: 2, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
116 24 0.21
117 2 0.02
119 9 0.08
120 52 0.46
121 25 0.22
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.42
Consensus pattern (114 bp):
TTTAAAATAATAATTATTAAATATAATTTAAAAAATATAATTTAATAAAATTCTTAATATAAATA
TTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
Found at i:5455731 original size:60 final size:60
Alignment explanation
Indices: 5455546--5455732 Score: 201
Period size: 60 Copynumber: 3.1 Consensus size: 60
5455536 ATATAATTTA
5455546 ATAAAATTCTTAATATTAAA-TATTCTTATATGAATTTACTAAAATCATAATATATAATACT
1 ATAAAATTCTTAATA--AAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
* * * *
5455607 ATAAAATATAATTTAA-AATAATTATTATTAAATAT-AATTTAAT-AAA--A-AATATATAAT-T
1 ATAAAAT-T--CTTAATAA-AATTATTCTT--ATATGAATTTACTAAAATCATAATATATAATAC
5455665 T
60 T
5455666 AATAAAATTCTTAATAAAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
1 -ATAAAATTCTTAATAAAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
5455727 ATAAAA
1 ATAAAA
5455733 ATAATATATA
Statistics
Matches: 103, Mismatches: 8, Indels: 31
0.73 0.06 0.22
Matches are distributed among these distances:
55 4 0.04
56 7 0.07
57 16 0.16
58 2 0.02
59 3 0.03
60 33 0.32
61 10 0.10
62 3 0.03
63 10 0.10
64 11 0.11
65 4 0.04
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.41
Consensus pattern (60 bp):
ATAAAATTCTTAATAAAATTATTCTTATATGAATTTACTAAAATCATAATATATAATACT
Found at i:5458947 original size:25 final size:23
Alignment explanation
Indices: 5458914--5458965 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 23
5458904 TGCTTATATT
* *
5458914 AATATTTATATTTATATTAATTAAA
1 AATAATTATATTAATATTAA--AAA
5458939 AATAATTATATTAATATTAAAAA
1 AATAATTATATTAATATTAAAAA
5458962 AATA
1 AATA
5458966 TATTTTCCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 7 0.28
25 18 0.72
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATAATTATATTAATATTAAAAA
Found at i:5458959 original size:21 final size:18
Alignment explanation
Indices: 5458925--5458969 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
5458915 ATATTTATAT
5458925 TTATATTAATTAAAAATAA
1 TTATATTAATTAAAAA-AA
5458944 TTATATTAATATTAAAAAAA
1 TTATATT-A-ATTAAAAAAA
5458964 -TATATT
1 TTATATT
5458970 TTCCTCCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 13 0.54
20 3 0.12
21 8 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTATATTAATTAAAAAAA
Found at i:5460354 original size:43 final size:43
Alignment explanation
Indices: 5460026--5460337 Score: 471
Period size: 43 Copynumber: 7.3 Consensus size: 43
5460016 TTTTAGAAAT
* * * * * *
5460026 AAACGTCGCTAAAGGTCATGACCTTTAGCGGCACTTTTCCCTC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * *
5460069 AAGCGTCGCTATAAATCATGACTTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
*
5460112 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAT
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
*
5460155 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
*
5460198 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAA
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
* * *
5460241 AAACGCCACTATAGATCATGACTTTTAACGGCGCTTCTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
**
5460284 AAACGCCGCTATAGATCATGACTTTTAGCGGTACTTTTCCCAC
1 AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
5460327 AAACGCCGCTA
1 AAACGCCGCTA
5460338 AAGAACACGA
Statistics
Matches: 248, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 248 1.00
ACGTcount: A:0.25, C:0.29, G:0.18, T:0.28
Consensus pattern (43 bp):
AAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCAC
Found at i:5460688 original size:21 final size:21
Alignment explanation
Indices: 5460664--5460726 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
5460654 TTCTCCTCTG
* *
5460664 CTCTGTTGCTCTCGCTGTTGC
1 CTCTGCTGCTCTCGCTGCTGC
5460685 CTCTGCTGCTCTCGCTGCTGC
1 CTCTGCTGCTCTCGCTGCTGC
* *
5460706 CTCTGCTTCCCTCGCTGCTGC
1 CTCTGCTGCTCTCGCTGCTGC
5460727 ATCTACTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.00, C:0.41, G:0.22, T:0.37
Consensus pattern (21 bp):
CTCTGCTGCTCTCGCTGCTGC
Found at i:5463057 original size:9 final size:9
Alignment explanation
Indices: 5463039--5464234 Score: 189
Period size: 9 Copynumber: 139.8 Consensus size: 9
5463029 GTCTGATGTA
*
5463039 TTATGAAAG
1 TTATGTAAG
5463048 TTATGTAAG
1 TTATGTAAG
5463057 TTATGT-A-
1 TTATGTAAG
*
5463064 TTATGAAAG
1 TTATGTAAG
5463073 TTATGTAAG
1 TTATGTAAG
5463082 TTATGT-A-
1 TTATGTAAG
5463089 TTATGTAAG
1 TTATGTAAG
*
5463098 TTACGTAAG
1 TTATGTAAG
5463107 TTATGTAAG
1 TTATGTAAG
5463116 TTATGT-A-
1 TTATGTAAG
* *
5463123 TTATTTAAA
1 TTATGTAAG
* * *
5463132 TAATTTAAA
1 TTATGTAAG
5463141 TTATGTAAG
1 TTATGTAAG
5463150 TTATGT-A-
1 TTATGTAAG
*
5463157 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463166 TAATTTAAA
1 TTATGTAAG
5463175 TTATGTAAG
1 TTATGTAAG
5463184 TTATGT-A-
1 TTATGTAAG
*
5463191 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463200 TAATTTAAA
1 TTATGTAAG
5463209 TTATGTAAG
1 TTATGTAAG
5463218 TTATGT-A-
1 TTATGTAAG
* *
5463225 TTATTTAAA
1 TTATGTAAG
* * *
5463234 TAATATCATCAC
1 T--TAT-GTAAG
**
5463246 AAATGTAAG
1 TTATGTAAG
5463255 TTATGT-A-
1 TTATGTAAG
* *
5463262 TTATTTAAA
1 TTATGTAAG
* * *
5463271 TAATTTAAA
1 TTATGTAAG
5463280 TTATGTAAG
1 TTATGTAAG
5463289 TTATGT-A-
1 TTATGTAAG
* *
5463296 TTATGAAAA
1 TTATGTAAG
*
5463305 TAATGTAAG
1 TTATGTAAG
5463314 TTATGT-A-
1 TTATGTAAG
*
5463321 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463330 TAATTTAAA
1 TTATGTAAG
5463339 TTATGTAAG
1 TTATGTAAG
5463348 --A--TAAG
1 TTATGTAAG
5463353 TTATGT-A-
1 TTATGTAAG
*
5463360 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463369 TAATTTAAA
1 TTATGTAAG
5463378 TTATGTAAG
1 TTATGTAAG
5463387 TTATGT-A-
1 TTATGTAAG
*
5463394 TTATGAAAG
1 TTATGTAAG
5463403 TTATGT-A-
1 TTATGTAAG
* *
5463410 TTATTTAAA
1 TTATGTAAG
* * *
5463419 TAATATCATCAC
1 T--TAT-GTAAG
**
5463431 AAATGTAAG
1 TTATGTAAG
5463440 TTATGTAAG
1 TTATGTAAG
5463449 TTATGT-A-
1 TTATGTAAG
* *
5463456 TTATTTAAA
1 TTATGTAAG
* * *
5463465 TAATTTAAA
1 TTATGTAAG
5463474 TTATGTAAG
1 TTATGTAAG
5463483 TTATGT-A-
1 TTATGTAAG
*
5463490 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463499 TAATTTAAA
1 TTATGTAAG
5463508 TTATGTAAG
1 TTATGTAAG
5463517 TTATGT-A-
1 TTATGTAAG
5463524 TTATGTAAG
1 TTATGTAAG
5463533 TTATGT-A-
1 TTATGTAAG
*
5463540 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463549 TAATTTAAA
1 TTATGTAAG
5463558 TTATGTAAG
1 TTATGTAAG
*
5463567 TTACGT-A-
1 TTATGTAAG
*
5463574 TTATGAAAG
1 TTATGTAAG
5463583 TTATGT-A-
1 TTATGTAAG
* *
5463590 TTATTTAAA
1 TTATGTAAG
* * *
5463599 TAATATCATCAC
1 T--TAT-GTAAG
**
5463611 AAATGTAAG
1 TTATGTAAG
5463620 TTATGT-A-
1 TTATGTAAG
* *
5463627 TTATTTAAA
1 TTATGTAAG
* * *
5463636 TAATTTAAA
1 TTATGTAAG
5463645 TTATGTAAG
1 TTATGTAAG
5463654 TTATGT-A-
1 TTATGTAAG
* * *
5463661 CTATGAAAA
1 TTATGTAAG
*
5463670 TAATGTAAG
1 TTATGTAAG
5463679 TTATGT-A-
1 TTATGTAAG
*
5463686 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463695 TAATTTAAA
1 TTATGTAAG
5463704 TTATGTAAG
1 TTATGTAAG
5463713 TTATGT-A-
1 TTATGTAAG
* *
5463720 TTATTTAAA
1 TTATGTAAG
* * *
5463729 TAATTTAAA
1 TTATGTAAG
5463738 TTATGTAAG
1 TTATGTAAG
5463747 TTATGT-A-
1 TTATGTAAG
5463754 TTATGTAAG
1 TTATGTAAG
5463763 TTATGT-A-
1 TTATGTAAG
*
5463770 TTATGAAAG
1 TTATGTAAG
5463779 TTATGT-A-
1 TTATGTAAG
* *
5463786 TTATTTAAA
1 TTATGTAAG
* * *
5463795 TAATATCATCAC
1 T--TAT-GTAAG
** *
5463807 AAATATAAG
1 TTATGTAAG
5463816 TTATGT-A-
1 TTATGTAAG
* *
5463823 TTATTTAAA
1 TTATGTAAG
* * *
5463832 TAATTTAAA
1 TTATGTAAG
5463841 TTATGTAAG
1 TTATGTAAG
5463850 TTATGT-A-
1 TTATGTAAG
*
5463857 TTATGTAGG
1 TTATGTAAG
5463866 TTATGTAAG
1 TTATGTAAG
5463875 TTATGT-A-
1 TTATGTAAG
* *
5463882 TTATGAAAA
1 TTATGTAAG
*
5463891 TAATGTAAG
1 TTATGTAAG
*
5463900 TTAAGT-A-
1 TTATGTAAG
*
5463907 TTAT-TGAAA
1 TTATGT-AAG
* * *
5463916 TAATTTAAA
1 TTATGTAAG
*
5463925 TTAAGTTAAG
1 TTATG-TAAG
*
5463935 TATTAT-TGAAA
1 --TTATGT-AAG
* * *
5463946 TAATTTAAA
1 TTATGTAAG
5463955 TTATGTAAG
1 TTATGTAAG
5463964 TTATGT-A-
1 TTATGTAAG
* *
5463971 TTATTTAAA
1 TTATGTAAG
* * *
5463980 TAATTTAAA
1 TTATGTAAG
5463989 TTATGTAAG
1 TTATGTAAG
5463998 TTATGT-A-
1 TTATGTAAG
* *
5464005 TTATGAAAA
1 TTATGTAAG
*
5464014 TAATGTAAG
1 TTATGTAAG
5464023 TTATGT-A-
1 TTATGTAAG
* *
5464030 TTATTTACG
1 TTATGTAAG
*
5464039 TTACGTAAG
1 TTATGTAAG
5464048 TTATGTAAG
1 TTATGTAAG
*
5464057 TTGTGT-A-
1 TTATGTAAG
*
5464064 TTATGAAAG
1 TTATGTAAG
5464073 TTATGT-A-
1 TTATGTAAG
* *
5464080 TTATTTAAA
1 TTATGTAAG
* * *
5464089 TAATATCATCAC
1 T--TAT-GTAAG
**
5464101 AAATGTAAG
1 TTATGTAAG
5464110 TTATGT-A-
1 TTATGTAAG
*
5464117 TTAT-TGAAA
1 TTATGT-AAG
* * *
5464126 TAATTTAAA
1 TTATGTAAG
5464135 TTATGTAAG
1 TTATGTAAG
5464144 TTATGT-A-
1 TTATGTAAG
*
5464151 TTATGTAGG
1 TTATGTAAG
5464160 TTATGTAAG
1 TTATGTAAG
5464169 TTATGT-A-
1 TTATGTAAG
*
5464176 TTAT-TGAAA
1 TTATGT-AAG
* * *
5464185 TAATTTAAA
1 TTATGTAAG
5464194 TTATGTAAG
1 TTATGTAAG
5464203 TTATGT-A-
1 TTATGTAAG
5464210 TTATGTAAG
1 TTATGTAAG
*
5464219 TTACGTAAG
1 TTATGTAAG
5464228 TTATGTA
1 TTATGTA
5464235 TTATTTAAAT
Statistics
Matches: 877, Mismatches: 190, Indels: 240
0.67 0.15 0.18
Matches are distributed among these distances:
5 4 0.00
6 10 0.01
7 184 0.21
8 73 0.08
9 551 0.63
10 25 0.03
11 17 0.02
12 13 0.01
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (9 bp):
TTATGTAAG
Found at i:5463063 original size:25 final size:25
Alignment explanation
Indices: 5463034--5463113 Score: 142
Period size: 25 Copynumber: 3.2 Consensus size: 25
5463024 CATAAGTCTG
5463034 ATGTATTATGAAAGTTATGTAAGTT
1 ATGTATTATGAAAGTTATGTAAGTT
5463059 ATGTATTATGAAAGTTATGTAAGTT
1 ATGTATTATGAAAGTTATGTAAGTT
* *
5463084 ATGTATTATGTAAGTTACGTAAGTT
1 ATGTATTATGAAAGTTATGTAAGTT
5463109 ATGTA
1 ATGTA
5463114 AGTTATGTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.35, C:0.01, G:0.20, T:0.44
Consensus pattern (25 bp):
ATGTATTATGAAAGTTATGTAAGTT
Found at i:5463077 original size:34 final size:33
Alignment explanation
Indices: 5463066--5464029 Score: 540
Period size: 34 Copynumber: 29.4 Consensus size: 33
5463056 GTTATGTATT
* *
5463066 ATGAAAGTTATGTAAGTTATGTATTA-TGTAAGTT
1 ATGAAA-TTATGTAAGTTATGTATTATTG-AAATA
* * *
5463100 ACGTAAGTTATGTAAGTTATGTATTATTTAAATA
1 ATG-AAATTATGTAAGTTATGTATTATTGAAATA
*
5463134 ATTTAAATTATGTAAGTTATGTATTATTGAAATA
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
*
5463168 ATTTAAATTATGTAAGTTATGTATTATTGAAATA
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
* *
5463202 ATTTAAATTATGTAAGTTATGTATTATTTAAATA
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
** *
5463236 AT-ATCATCACAAATGTAAGTTATGTATTATTTAAATA
1 ATGA--A--A-TTATGTAAGTTATGTATTATTGAAATA
*
5463273 ATTTAAATTATGTAAGTTATGTATTA-TG-AA-A
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
5463304 AT---A--ATGTAAGTTATGTATTATTGAAATA
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
*
5463332 ATTTAAATTATGTAAGATAAGTTATGTATTATTGAAATA
1 A-TGAAATTA--T--G-TAAGTTATGTATTATTGAAATA
* *
5463371 ATTTAAATTATGTAAGTTATGTATTA-TGAAAGTT
1 A-TGAAATTATGTAAGTTATGTATTATTGAAA-TA
* * * * * * *
5463405 ATG-TATTATTTAA-ATA-ATATCA-TCACA-A
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
* *
5463433 ATGTAAGTTATGTAAGTTATGTATTATTTAAATA
1 ATG-AAATTATGTAAGTTATGTATTATTGAAATA
*
5463467 ATTTAAATTATGTAAGTTATGTATTATTGAAATA
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
* * *
5463501 ATTTAAATTATGTAAGTTATGTATTA-TGTAAGTT
1 A-TGAAATTATGTAAGTTATGTATTATTG-AAATA
* * * * * *
5463535 ATG-TATTAT-TGAAATAATTTAAATTA-TGTAAGTT
1 ATGAAATTATGT-AAGTTATGT--ATTATTG-AAATA
* * * *
5463569 ACG-TATTATGAAAGTTATGTATTATTTAAATA
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
** *
5463601 AT-ATCATCACAAATGTAAGTTATGTATTATTTAAATA
1 ATGA--A--A-TTATGTAAGTTATGTATTATTGAAATA
* *
5463638 ATTTAAATTATGTAAGTTATGTACTA-TG-AA-A
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
5463669 AT---A--ATGTAAGTTATGTATTATTGAAATA
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
* *
5463697 ATTTAAATTATGTAAGTTATGTATTATTTAAATA
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
* * *
5463731 ATTTAAATTATGTAAGTTATGTATTA-TGTAAGTT
1 A-TGAAATTATGTAAGTTATGTATTATTG-AAATA
* * *
5463765 ATG-TATTATGAAAGTTATGTATTATTTAAATA
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
** * *
5463797 AT-ATCATCACAAATATAAGTTATGTATTATTTAAATA
1 ATGA--A--A-TTATGTAAGTTATGTATTATTGAAATA
*
5463834 ATTTAAATTATGTAAGTTATGTATTA-TG---T-
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
*
5463863 A-G--GTTATGTAAGTTATGTATTA-TG-AA-A
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
*
5463890 AT---A--ATGTAAGTTAAGTATTATTGAAATA
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
** *
5463918 ATTTAA--AT-TAAGTTAAGTATTATTGAAATA
1 ATGAAATTATGTAAGTTATGTATTATTGAAATA
* *
5463948 ATTTAAATTATGTAAGTTATGTATTATTTAAATA
1 A-TGAAATTATGTAAGTTATGTATTATTGAAATA
*
5463982 ATTTAAATTATGTAAGTTATGTATTA-TGAAAATA
1 A-TGAAATTATGTAAGTTATGTATTATTG-AAATA
*
5464016 ATGTAAGTTATGTA
1 ATG-AAATTATGTA
5464030 TTATTTACGT
Statistics
Matches: 759, Mismatches: 90, Indels: 162
0.75 0.09 0.16
Matches are distributed among these distances:
25 70 0.09
26 6 0.01
27 9 0.01
28 10 0.01
29 3 0.00
30 40 0.05
31 16 0.02
32 62 0.08
33 24 0.03
34 389 0.51
35 8 0.01
36 4 0.01
37 79 0.10
38 4 0.01
39 35 0.05
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (33 bp):
ATGAAATTATGTAAGTTATGTATTATTGAAATA
Found at i:5463119 original size:68 final size:66
Alignment explanation
Indices: 5463038--5464216 Score: 500
Period size: 68 Copynumber: 18.4 Consensus size: 66
5463028 AGTCTGATGT
* * * * *
5463038 ATTATGAAAGTTATGTAAGTTATGTATTA-TGAAAGTTATGTAAGTTATGTATTA-TGTAAGTTA
1 ATTATGTAAGTTATGT-A-TTATGTATAATTTAAA-TTATGTAAGTTATGTATTATTG-AAATAA
5463101 CGTAA
62 CGTAA
* * **
5463106 GTTATGTAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTATTATTGAAATAATT
1 ATTATGTAAGTTATGTATTATGT--ATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACG
5463171 TAA
64 TAA
* *
5463174 ATTATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATTTAAATAATA
1 ATTATGTAAGTTATGTATTA-TG-TATAATTTAAATTATGTAAGTTATGTATTATTGAAAT-A-A
*
5463239 TCATCACA
62 -CGT-A-A
*
5463247 A--ATGTAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTATTA-TG-AA-AA--
1 ATTATGTAAGTTATGTATTATGT--ATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACG
5463305 T--
64 TAA
*
5463306 A--ATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGATAAGTTATGTATTATTGAAA
1 ATTATGTAAGTTATGTATTA-TG-TATAATTTAAATTA--T--G-TAAGTTATGTATTATTGAAA
**
5463369 TAATTTAA
59 TAACGTAA
** * * * * * * *
5463377 ATTATGTAAGTTATGTATTATG-A-AAGTTATGTATTATTTAA-ATA-ATATCA-TCACA-AATG
1 ATTATGTAAGTTATGTATTATGTATAA-TT-TAAATTATGTAAGTTATGTATTATTGAAATAACG
5463436 TAA
64 TAA
* * **
5463439 GTTATGTAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTATTATTGAAATAATT
1 ATTATGTAAGTTATGTATTATGT--ATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACG
5463504 TAA
64 TAA
* ** * * * * *
5463507 ATTATGTAAGTTATGTATTATGTA-AGTTATGTATTAT-TGAAATAATTTAAATTA-TGTAAGTT
1 ATTATGTAAGTTATGTATTATGTATAATT-TAAATTATGT-AAGTTATGT--ATTATTG-AAATA
5463569 ACGT--
61 ACGTAA
* * *
5463573 ATTATGAAAGTTATGTATTATTTAAATAATATCATCACAA--ATGTAAGTTATGTATTATTTAAA
1 ATTATGTAAGTTATGTATTATGT--ATAAT-T--T-A-AATTATGTAAGTTATGTATTATTGAAA
**
5463636 TAATTTAA
59 TAACGTAA
* * **
5463644 ATTATGTAAGTTATGTACTATG----A---AAATAATGTAAGTTATGTATTATTGAAATAATTTA
1 ATTATGTAAGTTATGTATTATGTATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACGTA
5463702 A
66 A
* * * *
5463703 ATTATGTAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTATTA-TGTAAGTTAT
1 ATTATGTAAGTTATGTATTATGT--ATAATTTAAATTATGTAAGTTATGTATTATTG-AAATAAC
5463767 GT--
63 GTAA
* * * *
5463769 ATTATGAAAGTTATGTATTATTTAAATAATATCATCACAA--ATATAAGTTATGTATTATTTAAA
1 ATTATGTAAGTTATGTATTATGT--ATAAT-T--T-A-AATTATGTAAGTTATGTATTATTGAAA
**
5463832 TAATTTAA
59 TAACGTAA
** *
5463840 ATTATGTAAGTTATGTATTATG-------TAGGTTATGTAAGTTATGTATTA-TGAAAATAATGT
1 ATTATGTAAGTTATGTATTATGTATAATTTAAATTATGTAAGTTATGTATTATTG-AAATAACGT
5463897 -A
65 AA
* * * **
5463898 A--GT-TAAG-TAT-TA-T-TGAAATAATTT-AA--AT-TAAGTTAAGTATTATTGAAATAATTT
1 ATTATGTAAGTTATGTATTATG-TATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACGT
5463952 AA
65 AA
* *
5463954 ATTATGTAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTATTA-TGAAAATAAT
1 ATTATGTAAGTTATGTATTATGT--ATAATTTAAATTATGTAAGTTATGTATTATTG-AAATAAC
5464018 GTAA
63 GTAA
* * ** * *
5464022 GTTATGT-A-TTA--T-TTACGT-T-ACGTAAGTTATGTAAGTTGTGTATTA-TG--A-AA-G--
1 ATTATGTAAGTTATGTATTATGTATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACGTA
5464073 -
66 A
* * * * * **
5464073 -TTATGT-A-TTATTTA-AATAATATCA-TCACAA--ATGTAAGTTATGTATTATTGAAATAATT
1 ATTATGTAAGTTATGTATTAT-GTATAATTTA-AATTATGTAAGTTATGTATTATTGAAATAACG
5464131 TAA
64 TAA
** **
5464134 ATTATGTAAGTTATGTATTATG-------TAGGTTATGTAAGTTATGTATTATTGAAATAATTTA
1 ATTATGTAAGTTATGTATTATGTATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACGTA
5464192 A
66 A
5464193 ATTATGTAAGTTATGTATTATGTA
1 ATTATGTAAGTTATGTATTATGTA
5464217 AGTTACGTAA
Statistics
Matches: 867, Mismatches: 119, Indels: 257
0.70 0.10 0.21
Matches are distributed among these distances:
50 10 0.01
51 2 0.00
52 3 0.00
53 19 0.02
54 8 0.01
55 29 0.03
56 9 0.01
57 4 0.00
58 7 0.01
59 188 0.22
60 5 0.01
61 3 0.00
62 33 0.04
63 11 0.01
64 41 0.05
65 19 0.02
66 83 0.10
67 17 0.02
68 190 0.22
69 48 0.06
70 10 0.01
71 104 0.12
72 4 0.00
73 20 0.02
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.45
Consensus pattern (66 bp):
ATTATGTAAGTTATGTATTATGTATAATTTAAATTATGTAAGTTATGTATTATTGAAATAACGTA
A
Found at i:5463305 original size:25 final size:25
Alignment explanation
Indices: 5463277--5463409 Score: 98
Period size: 25 Copynumber: 5.4 Consensus size: 25
5463267 TAAATAATTT
5463277 AAATTATGTAAGTTATGTATTATGA
1 AAATTATGTAAGTTATGTATTATGA
*
5463302 AAATAATGTAAGTTATGTATTATTG-
1 AAATTATGTAAGTTATGTATTA-TGA
* * *
5463327 AAATAATTTAAATTATGTA--A-GA
1 AAATTATGTAAGTTATGTATTATGA
* * * **
5463349 TAAGTTATGT-A-TTATTGAAATAATTT
1 -AAATTATGTAAGTTA-TG-TATTATGA
5463375 AAATTATGTAAGTTATGTATTATGA
1 AAATTATGTAAGTTATGTATTATGA
*
5463400 AAGTTATGTA
1 AAATTATGTA
5463410 TTATTTAAAT
Statistics
Matches: 83, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
21 4 0.05
22 3 0.04
23 8 0.10
25 60 0.72
26 5 0.06
27 3 0.04
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.44
Consensus pattern (25 bp):
AAATTATGTAAGTTATGTATTATGA
Found at i:5463354 original size:39 final size:39
Alignment explanation
Indices: 5463310--5463386 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
5463300 GAAAATAATG
5463310 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGA
1 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGA
5463349 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAG
1 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAG
5463387 TTATGTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.44
Consensus pattern (39 bp):
TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGA
Found at i:5463670 original size:25 final size:26
Alignment explanation
Indices: 5463642--5463710 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
5463632 TAAATAATTT
*
5463642 AAATTATGTAAGTTATGTACTA-TGA
1 AAATAATGTAAGTTATGTACTATTGA
*
5463667 AAATAATGTAAGTTATGTATTATTG-
1 AAATAATGTAAGTTATGTACTATTGA
* *
5463692 AAATAATTTAAATTATGTA
1 AAATAATGTAAGTTATGTA
5463711 AGTTATGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 37 0.95
26 2 0.05
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.42
Consensus pattern (26 bp):
AAATAATGTAAGTTATGTACTATTGA
Found at i:5463694 original size:196 final size:195
Alignment explanation
Indices: 5463471--5463974 Score: 687
Period size: 196 Copynumber: 2.5 Consensus size: 195
5463461 TAAATAATTT
5463471 AAATTATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGTAAGTTA
1 AAATTATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTAT-TAAGTTA
*
5463536 TGTATTATTGAAATAATTTAAATTATGTAAGTTACGTATTATGAAAGTTATGTATTATTTAAATA
65 TGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTATGTATTATTTAAATA
*
5463601 ATATCATCACAAATGTAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTACTATG
130 ATATCATCACAAATATAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTACTATG
5463666 A
195 A
* * *
5463667 AAATAATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATTTAAATAA
1 AAATTATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTA-TTAAGTTA
* * * *
5463732 TTTAAATTA-TGTAAGTTATGT--ATTATGTAAGTTATGTATTATGAAAGTTATGTATTATTTAA
65 TGT--ATTATTG-AAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTATGTATTATTTAA
*
5463794 ATAATATCATCACAAATATAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTATT
127 ATAATATCATCACAAATATAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTACT
*
5463859 ATGT
192 ATGA
** * * *
5463863 AGGTTATGTAAGTTATGTATTA-TGAAAATAATGTAAGTTAAGT-A-TTATTGAAATAATTTAAA
1 AAATTATGTAAGTTATGTATTATTG-AAATAATTTAAATTATGTAAGTTA-TG---T-A-TT--A
*
5463925 TTAAGTTAAGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTAT
57 TTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTAT
5463975 TTAAATAATT
Statistics
Matches: 268, Mismatches: 24, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
194 3 0.01
195 5 0.02
196 202 0.75
197 3 0.01
198 11 0.04
199 11 0.04
200 4 0.01
201 28 0.10
202 1 0.00
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (195 bp):
AAATTATGTAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATTAAGTTAT
GTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGAAAGTTATGTATTATTTAAATAA
TATCATCACAAATATAAGTTATGTATTATTTAAATAATTTAAATTATGTAAGTTATGTACTATGA
Found at i:5463869 original size:25 final size:25
Alignment explanation
Indices: 5463838--5463915 Score: 102
Period size: 25 Copynumber: 3.1 Consensus size: 25
5463828 TAAATAATTT
*
5463838 AAATTATGTAAGTTATGTATTATGT
1 AAATTATGTAAGTTATGTATTATGA
**
5463863 AGGTTATGTAAGTTATGTATTATGA
1 AAATTATGTAAGTTATGTATTATGA
* *
5463888 AAATAATGTAAGTTAAGTATTATTGA
1 AAATTATGTAAGTTATGTATTA-TGA
5463914 AA
1 AA
5463916 TAATTTAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
25 40 0.89
26 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (25 bp):
AAATTATGTAAGTTATGTATTATGA
Found at i:5463916 original size:25 final size:25
Alignment explanation
Indices: 5463868--5463949 Score: 85
Period size: 30 Copynumber: 3.1 Consensus size: 25
5463858 TATGTAGGTT
*
5463868 ATGTAAGTTATGTATTA-TGAAAATA
1 ATGTAAGTTAAGTATTATTG-AAATA
5463893 ATGTAAGTTAAGTATTATTGAAATA
1 ATGTAAGTTAAGTATTATTGAAATA
*
5463918 ATTTAAATTAAGTTAAGTATTATTGAAATA
1 A--T---GTAAGTTAAGTATTATTGAAATA
5463948 AT
1 AT
5463950 TTAAATTATG
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
25 22 0.45
26 2 0.04
27 1 0.02
28 1 0.02
30 23 0.47
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.41
Consensus pattern (25 bp):
ATGTAAGTTAAGTATTATTGAAATA
Found at i:5463953 original size:25 final size:25
Alignment explanation
Indices: 5463871--5463953 Score: 87
Period size: 25 Copynumber: 3.1 Consensus size: 25
5463861 GTAGGTTATG
* *
5463871 TAAGTTATGTATTA-TGAAAATAATG
1 TAAGTTAAGTATTATTG-AAATAATT
5463896 TAAGTTAAGTATTATTGAAATAATTTAAAT
1 TAAGTTAAGTATTATTGAAATAA--T---T
5463926 TAAGTTAAGTATTATTGAAATAATT
1 TAAGTTAAGTATTATTGAAATAATT
5463951 TAA
1 TAA
5463954 ATTATGTAAG
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
25 23 0.46
26 2 0.04
27 1 0.02
28 1 0.02
30 23 0.46
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (25 bp):
TAAGTTAAGTATTATTGAAATAATT
Found at i:5463976 original size:25 final size:25
Alignment explanation
Indices: 5463948--5463995 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5463938 TATTGAAATA
* *
5463948 ATTTAAATTATGTAAGTTATGTATT
1 ATTTAAATAATGTAAATTATGTATT
*
5463973 ATTTAAATAATTTAAATTATGTA
1 ATTTAAATAATGTAAATTATGTA
5463996 AGTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (25 bp):
ATTTAAATAATGTAAATTATGTATT
Found at i:5464014 original size:25 final size:25
Alignment explanation
Indices: 5463986--5464033 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
5463976 TAAATAATTT
*
5463986 AAATTATGTAAGTTATGTATTATGA
1 AAATAATGTAAGTTATGTATTATGA
5464011 AAATAATGTAAGTTATGTATTAT
1 AAATAATGTAAGTTATGTATTAT
5464034 TTACGTTACG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (25 bp):
AAATAATGTAAGTTATGTATTATGA
Found at i:5464146 original size:34 final size:34
Alignment explanation
Indices: 5464063--5464213 Score: 144
Period size: 34 Copynumber: 4.6 Consensus size: 34
5464053 TAAGTTGTGT
* *
5464063 ATTATGAAAGTTATGTATTATTTAAATAATATCATCACA
1 ATTATGTAAGTTATGTATTATTGAAATAAT-T--T-A-A
5464102 A--ATGTAAGTTATGTATTATTGAAATAATTTAA
1 ATTATGTAAGTTATGTATTATTGAAATAATTTAA
*
5464134 ATTATGTAAGTTATGTATTA-TG--------TAG
1 ATTATGTAAGTTATGTATTATTGAAATAATTTAA
*
5464159 GTTATGTAAGTTATGTATTATTGAAATAATTTAA
1 ATTATGTAAGTTATGTATTATTGAAATAATTTAA
5464193 ATTATGTAAGTTATGTATTAT
1 ATTATGTAAGTTATGTATTAT
5464214 GTAAGTTACG
Statistics
Matches: 95, Mismatches: 6, Indels: 27
0.74 0.05 0.21
Matches are distributed among these distances:
25 21 0.22
26 2 0.02
32 2 0.02
33 3 0.03
34 40 0.42
36 1 0.01
37 25 0.26
39 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (34 bp):
ATTATGTAAGTTATGTATTATTGAAATAATTTAA
Found at i:5464226 original size:25 final size:23
Alignment explanation
Indices: 5464134--5464238 Score: 93
Period size: 25 Copynumber: 4.2 Consensus size: 23
5464124 AATAATTTAA
5464134 ATTATGTAAGTTATGTATTATGT
1 ATTATGTAAGTTATGTATTATGT
*
5464157 AGGTTATGTAAGTTATGTATTATTGAA
1 A--TTATGTAAGTTATGTATTA-TG-T
* * *
5464184 ATAATTTAAATTATGTAAGTTATGT
1 ATTATGTAAGTTATGT-A-TTATGT
*
5464209 ATTATGTAAGTTACGTAAGTTATGT
1 ATTATGTAAGTTATGT-A-TTATGT
5464234 ATTAT
1 ATTAT
5464239 TTAAATAATA
Statistics
Matches: 67, Mismatches: 9, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
23 1 0.01
25 57 0.85
26 5 0.07
27 4 0.06
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.48
Consensus pattern (23 bp):
ATTATGTAAGTTATGTATTATGT
Found at i:5464232 original size:34 final size:34
Alignment explanation
Indices: 5464159--5464234 Score: 91
Period size: 34 Copynumber: 2.2 Consensus size: 34
5464149 TATTATGTAG
**
5464159 GTTATGTAAGTTATGTATTATTGAAATAATTTAA
1 GTTATGTAAGTTATGTATTATTGAAATAACGTAA
* * *
5464193 ATTATGTAAGTTATGTATTA-TGTAAGTTACGTAA
1 GTTATGTAAGTTATGTATTATTG-AAATAACGTAA
5464227 GTTATGTA
1 GTTATGTA
5464235 TTATTTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
33 2 0.06
34 33 0.94
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.46
Consensus pattern (34 bp):
GTTATGTAAGTTATGTATTATTGAAATAACGTAA
Found at i:5464235 original size:59 final size:59
Alignment explanation
Indices: 5463926--5464247 Score: 270
Period size: 59 Copynumber: 5.4 Consensus size: 59
5463916 TAATTTAAAT
* * *
5463926 TAAGTTAAGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATTTAAATAATTTAAATT
1 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATG---TA--T---T-ATGTAAGTT
5463991 ATG
57 ATG
* * * *
5463994 TAAGTTATGTATTA-TGAAAATAATGTAAGTTATGT-A-TTATTTACGTTACGTAAGTTATG
1 TAAGTTATGTATTATTG-AAATAATTTAAATTATGTAAGTTATGTA--TTATGTAAGTTATG
* * * * * * * * *
5464053 TAAGTTGTGTATTA-TGAAAGTTATGT--ATTATTTAA-ATA-ATATCAT-CACA--AATG
1 TAAGTTATGTATTATTGAAA-TAATTTAAATTATGTAAGTTATGTATTATGTA-AGTTATG
*
5464106 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGTAGGTTATG
1 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGTAAGTTATG
*
5464165 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGTAAGTTACG
1 TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGTAAGTTATG
*
5464224 TAAGTTATGTATTATTTAAATAAT
1 TAAGTTATGTATTATTGAAATAAT
5464248 ATCATCACAA
Statistics
Matches: 210, Mismatches: 32, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
53 20 0.10
54 6 0.03
55 11 0.05
56 2 0.01
57 12 0.06
58 7 0.03
59 112 0.53
60 1 0.00
63 3 0.01
66 4 0.02
67 3 0.01
68 29 0.14
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.46
Consensus pattern (59 bp):
TAAGTTATGTATTATTGAAATAATTTAAATTATGTAAGTTATGTATTATGTAAGTTATG
Found at i:5466577 original size:115 final size:113
Alignment explanation
Indices: 5466414--5466816 Score: 414
Period size: 115 Copynumber: 3.5 Consensus size: 113
5466404 AAGAAATAAA
* * * * * **
5466414 CTTTTGCGGCGTTTTTCTAAAAAAGCCACTAAAAAA-CCTACAAAAACGGTCACGTTTTGGTTAA
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAAATCCTA-TAGAACGG-CACGTTTTAATTAA
* * * * *
5466478 CAGAAAATAACATTTTGCGGCGTTTACAATATTGCGCCGTTAAATCCCGAC
64 -AAAAAATAACATTTTGCGGCGTTTACAACATAGCGCCGCTAAAGCCCGAC
* * *
5466529 CTTTTGTGGCTTTTTACCAAAAATGCCACTAAAAAATCCTATAGAACGGCACCGTTTTAATTGAA
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAAATCCTATAGAACGGCA-CGTTTTAATT-AA
* * * * *
5466594 ACAAAATAACATTTTGCAGCGTTTACTACCTAACGCCGCTAAAGCCCGAC
64 AAAAAATAACATTTTGCGGCGTTTACAACATAGCGCCGCTAAAGCCCGAC
* ** *
5466644 CTTTTGCGGCGTTTTACCAAAAACGCCACTAACAAATCCTATAGAACAACACTGTTTTTATTGAG
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAAATCCTATAGAACGGCAC-GTTTTAATT-A-
* * * * * *
5466709 AAAAAAA-AACATTGTGCGGTGTTTTCAACATAGCGCTGCTATAGCCCCAC
63 AAAAAAATAACATTTTGCGGCGTTTACAACATAGCGCCGCTAAAGCCCGAC
* * *
5466759 CTTTTGCGGCGTTTTACCAAAAACGCCACTAACATATCCTATAGAACGACACCGTTTT
1 CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAAATCCTATAGAACGGCA-CGTTTT
5466817 TGTTGAAACA
Statistics
Matches: 244, Mismatches: 38, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
114 3 0.01
115 228 0.93
116 13 0.05
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (113 bp):
CTTTTGCGGCGTTTTACCAAAAACGCCACTAAAAAATCCTATAGAACGGCACGTTTTAATTAAAA
AAAATAACATTTTGCGGCGTTTACAACATAGCGCCGCTAAAGCCCGAC
Found at i:5467474 original size:21 final size:21
Alignment explanation
Indices: 5467347--5467494 Score: 97
Period size: 21 Copynumber: 7.0 Consensus size: 21
5467337 ACTTAAATCG
* *
5467347 TAAACCTTAAACCCT-AACCTC
1 TAAACCTTAAACCATAAACC-A
* * *
5467368 TAAATCTTAAACCCT-AACCC
1 TAAACCTTAAACCATAAACCA
* * ** *
5467388 TATACCCTAAACTGTAAACCG
1 TAAACCTTAAACCATAAACCA
* * *
5467409 TAATCACTAAAACCATAATCCA
1 TAAAC-CTTAAACCATAAACCA
*
5467431 TAAACCTTAAA-TAGT-AACTCA
1 TAAACCTTAAACCA-TAAAC-CA
5467452 TAAACCTTAAACCATAAACCA
1 TAAACCTTAAACCATAAACCA
*
5467473 TAAACCATAAACCATAAACCA
1 TAAACCTTAAACCATAAACCA
5467494 T
1 T
5467495 GTATAATCCC
Statistics
Matches: 100, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
20 14 0.14
21 68 0.68
22 18 0.18
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (21 bp):
TAAACCTTAAACCATAAACCA
Found at i:5467512 original size:7 final size:7
Alignment explanation
Indices: 5467418--5467494 Score: 86
Period size: 7 Copynumber: 11.0 Consensus size: 7
5467408 GTAATCACTA
5467418 AAACCAT
1 AAACCAT
*
5467425 AATCCAT
1 AAACCAT
*
5467432 AAACCTT
1 AAACCAT
*
5467439 AAA-TAGT
1 AAACCA-T
5467446 -AACTCAT
1 AAAC-CAT
*
5467453 AAACCTT
1 AAACCAT
5467460 AAACCAT
1 AAACCAT
5467467 AAACCAT
1 AAACCAT
5467474 AAACCAT
1 AAACCAT
5467481 AAACCAT
1 AAACCAT
5467488 AAACCAT
1 AAACCAT
5467495 GTATAATCCC
Statistics
Matches: 58, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
6 2 0.03
7 52 0.90
8 4 0.07
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (7 bp):
AAACCAT
Found at i:5467967 original size:40 final size:40
Alignment explanation
Indices: 5467923--5468032 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 40
5467913 TTAATTTTTT
* * *
5467923 GCGACGTTTTCCAAAAAGCGCCACTAATGCTCGACCTATA
1 GCGACGTTTTCCAAAAACCGCCGCTAATGCTAGACCTATA
* * *
5467963 GCGACGTTTTTCAAAAACCGCCGCTAATGATAGACCTATG
1 GCGACGTTTTCCAAAAACCGCCGCTAATGCTAGACCTATA
* * *
5468003 GCGGCGTTTACCAGAAACCGCCGCTAATGC
1 GCGACGTTTTCCAAAAACCGCCGCTAATGC
5468033 CACTAAAGCT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (40 bp):
GCGACGTTTTCCAAAAACCGCCGCTAATGCTAGACCTATA
Found at i:5468121 original size:40 final size:40
Alignment explanation
Indices: 5468076--5468186 Score: 125
Period size: 41 Copynumber: 2.8 Consensus size: 40
5468066 CTTAATTTTT
* *
5468076 GCGGCGTTTTTCAAAAAGCGCTACTAATGCTCGACTTATA
1 GCGGCGTTTTTCAAAAAGCGCCACTAATGCTCGACCTATA
* * * *
5468116 GCGGCGATTTTT-AAGCAGGCGCCGCTAATGATCGACCTATA
1 GCGGCG-TTTTTCAA-AAAGCGCCACTAATGCTCGACCTATA
* *
5468157 GCGGCATTTTTCAAAAAGCGCCACAAATGC
1 GCGGCGTTTTTCAAAAAGCGCCACTAATGC
5468187 GCTAAAGCTC
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
40 24 0.43
41 32 0.57
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCACTAATGCTCGACCTATA
Found at i:5468218 original size:153 final size:148
Alignment explanation
Indices: 5467820--5468311 Score: 466
Period size: 154 Copynumber: 3.2 Consensus size: 148
5467810 ATTTATTTGC
* * * * *
5467820 TAAAAACGCCTCTAATGCTCGACATATAGCGGCATTTTTCCAAAAAACGCTGCTAATGCCAATAA
1 TAAAACCGCCGCTAATGATCGACCTATAGCGGCATTTTT-CAAAAAACGCCGCTAATGCC--TAA
* * * * * *
5467885 AGCTCAAGGAAAAACGACGGCGTTCTGCTTAATTTTTTGCGACGTTTTCCAAAAAGCGCCACTAA
63 AGCTCAA-AAAAAACGACGACGTTGTGCTTAA-TTTTTGCGGCGTTTTTCAAAAAGCGCTACTAA
*
5467950 TGCTCGACCTATAGCGACGTTTT
126 TGCTCGACCTATAGCGGCGTTTT
* * * ** * *
5467973 TCAAAAACCGCCGCTAATGATAGACCTATGGCGGCGTTTACCAGAAACCGCCGCTAATGCCACTA
1 T--AAAACCGCCGCTAATGATCGACCTATAGCGGCATTTTTCAAAAAACGCCGCTAATG-C-CTA
* *
5468038 AAGCTCAAAATAAAACAAC-AGCATTGTGCTTAATTTTTGCGGCGTTTTTCAAAAAGCGCTACTA
62 AAGCTCAAAA-AAAACGACGA-CGTTGTGCTTAATTTTTGCGGCGTTTTTCAAAAAGCGCTACTA
*
5468102 ATGCTCGACTTATAGCGGCGATTTT
125 ATGCTCGACCTATAGCGGCG-TTTT
** * * *
5468127 TAAGCAGGCGCCGCTAATGATCGACCTATAGCGGCATTTTTCAAAAAGCGCCACAAATGCGCTAA
1 TAA--AACCGCCGCTAATGATCGACCTATAGCGGCATTTTTCAAAAAACGCCGCTAATGC-CTAA
* * * * * *
5468192 AGCTCAACACAAAATGACGACGTTGTGCTTAAATTTTTGCGGCGTTTTT-AAACAATCACTGCTT
63 AGCTCAA-AAAAAACGACGACGTTGTGCTT-AATTTTTGCGGCGTTTTTCAAA-AAGCGCTACTA
5468256 ATGCTCGACCTATAGCGGCGCTTGTT
125 ATGCTCGACCTATAGCGGCG-TT-TT
* * *
5468282 TAAAATCACCGCTAATGCTCGACCTATAGC
1 TAAAACCGCCGCTAATGATCGACCTATAGC
5468312 AGTGTTTTTA
Statistics
Matches: 277, Mismatches: 48, Indels: 28
0.78 0.14 0.08
Matches are distributed among these distances:
152 2 0.01
153 101 0.36
154 138 0.50
155 35 0.13
156 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (148 bp):
TAAAACCGCCGCTAATGATCGACCTATAGCGGCATTTTTCAAAAAACGCCGCTAATGCCTAAAGC
TCAAAAAAAACGACGACGTTGTGCTTAATTTTTGCGGCGTTTTTCAAAAAGCGCTACTAATGCTC
GACCTATAGCGGCGTTTT
Found at i:5468334 original size:40 final size:40
Alignment explanation
Indices: 5468230--5468360 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 40
5468220 TTAAATTTTT
* * *
5468230 GCGGCGTTTTTAAACAATCACTGCTTATGCTCGACCTATA
1 GCGGCGTTTTTAAACAAGCACCGCTAATGCTCGACCTATA
*
5468270 GCGGCGCTTGTTT-AA-AATCACCGCTAATGCTCGACCTATA
1 GCGGCG-TT-TTTAAACAAGCACCGCTAATGCTCGACCTATA
* * * * *
5468310 GCAGTGTTTTTAAACAAGCGCCGCTAGTGCTTGACCTATA
1 GCGGCGTTTTTAAACAAGCACCGCTAATGCTCGACCTATA
5468350 GCGGCGTTTTT
1 GCGGCGTTTTT
5468361 TAAGAAGCGA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
38 3 0.04
39 4 0.05
40 63 0.82
41 4 0.05
42 3 0.04
ACGTcount: A:0.23, C:0.24, G:0.21, T:0.31
Consensus pattern (40 bp):
GCGGCGTTTTTAAACAAGCACCGCTAATGCTCGACCTATA
Found at i:5469539 original size:11 final size:10
Alignment explanation
Indices: 5469518--5469585 Score: 50
Period size: 11 Copynumber: 6.6 Consensus size: 10
5469508 AATATTTTAC
5469518 TTTTTTAAAA
1 TTTTTTAAAA
5469528 TTTTTTATAAA
1 TTTTTTA-AAA
**
5469539 TAATTTAAAA
1 TTTTTTAAAA
5469549 --TTTTAAAA
1 TTTTTTAAAA
*
5469557 TTATTTTAAATT
1 TT-TTTTAAA-A
*
5469569 TTATTTTATAA
1 TT-TTTTAAAA
5469580 TTTTTT
1 TTTTTT
5469586 TTGAGAGAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
8 7 0.15
10 14 0.30
11 17 0.36
12 9 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:5469562 original size:18 final size:19
Alignment explanation
Indices: 5469530--5469572 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5469520 TTTTAAAATT
5469530 TTTTATAAATAATTTAAAA
1 TTTTATAAATAATTTAAAA
* *
5469549 TTTTA-AAATTATTTTAAA
1 TTTTATAAATAATTTAAAA
5469567 TTTTAT
1 TTTTAT
5469573 TTTATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 16 0.76
19 5 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTATAAATAATTTAAAA
Found at i:5473229 original size:18 final size:18
Alignment explanation
Indices: 5473194--5473238 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
5473184 GCAATAAGTG
*
5473194 ACGTTTTGAAAATTAATA
1 ACGTTTTGAAAATGAATA
5473212 ACGTTTTGAAAGA-GAATA
1 ACGTTTTGAAA-ATGAATA
5473230 AC-TTTTGAA
1 ACGTTTTGAA
5473239 TACGAATCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 7 0.28
18 17 0.68
19 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.36
Consensus pattern (18 bp):
ACGTTTTGAAAATGAATA
Found at i:5475889 original size:25 final size:26
Alignment explanation
Indices: 5475855--5475915 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
5475845 TCTATTCAGT
* **
5475855 TCTGCTCTGTTTC-ATTTTGTTCTGC
1 TCTGTTCTGTTTCTATAATGTTCTGC
5475880 TCTGTTCTG-TTCTATAATGTTCTGC
1 TCTGTTCTGTTTCTATAATGTTCTGC
*
5475905 TCTGTCCTGTT
1 TCTGTTCTGTT
5475916 CTGGTTGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 3 0.10
25 26 0.87
26 1 0.03
ACGTcount: A:0.07, C:0.23, G:0.16, T:0.54
Consensus pattern (26 bp):
TCTGTTCTGTTTCTATAATGTTCTGC
Found at i:5478163 original size:26 final size:24
Alignment explanation
Indices: 5478134--5478203 Score: 74
Period size: 23 Copynumber: 2.9 Consensus size: 24
5478124 CAGCCATGAT
*
5478134 CGGTAAGCTCAT-TCTGAGTTGAAGAA
1 CGGTAAGCTCATATC-GAGCTG-A-AA
5478160 CGGTAAGCTC-TATCGAGCTGAAA
1 CGGTAAGCTCATATCGAGCTGAAA
*
5478183 CGGTAAGCTCATA-AGAGCTGA
1 CGGTAAGCTCATATCGAGCTGA
5478204 TATATCGGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 19 0.47
24 3 0.08
25 6 0.15
26 12 0.30
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (24 bp):
CGGTAAGCTCATATCGAGCTGAAA
Found at i:5491871 original size:10 final size:9
Alignment explanation
Indices: 5491848--5491939 Score: 71
Period size: 10 Copynumber: 9.6 Consensus size: 9
5491838 TTAAAATAAT
5491848 TAAAAATT-
1 TAAAAATTA
5491856 TAAAAATATTA
1 T-AAAA-ATTA
5491867 TAAAATATTA
1 TAAAA-ATTA
5491877 TAGAAAATCATA
1 TA-AAAAT--TA
*
5491889 AAAAAATT-
1 TAAAAATTA
5491897 TAAAAATTA
1 TAAAAATTA
5491906 TAAAAATTA
1 TAAAAATTA
* *
5491915 CAAAAAAATA
1 -TAAAAATTA
5491925 TAAAAATATA
1 TAAAAAT-TA
5491935 TAAAA
1 TAAAA
5491940 GTGAAAAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
8 8 0.12
9 19 0.28
10 30 0.43
11 9 0.13
12 3 0.04
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (9 bp):
TAAAAATTA
Found at i:5491947 original size:28 final size:28
Alignment explanation
Indices: 5491865--5491947 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
5491855 TTAAAAATAT
* *
5491865 TATAAAATATTATAGAAAATCATAAAAAAA
1 TATAAAA-ATTATA-AAAATGACAAAAAAA
* *
5491895 TTTAAAAATTATAAAAATTACAAAAAAA
1 TATAAAAATTATAAAAATGACAAAAAAA
*
5491923 TATAAAAATATATAAAAGTGA-AAAA
1 TATAAAAAT-TATAAAAATGACAAAA
5491948 TTTTGGGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 25 0.54
29 15 0.33
30 6 0.13
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (28 bp):
TATAAAAATTATAAAAATGACAAAAAAA
Found at i:5492005 original size:15 final size:14
Alignment explanation
Indices: 5491966--5492007 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
5491956 TTTTTTAATT
5491966 AAAAAA-GAA-TAC
1 AAAAAATGAATTAC
*
5491978 AAAAAATTAATTAC
1 AAAAAATGAATTAC
5491992 AAAAAATGATATTAC
1 AAAAAATGA-ATTAC
5492007 A
1 A
5492008 CCCAAATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 6 0.24
13 2 0.08
14 11 0.44
15 6 0.24
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (14 bp):
AAAAAATGAATTAC
Found at i:5495084 original size:22 final size:22
Alignment explanation
Indices: 5495035--5495076 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
5495025 TAGACAAGCC
*
5495035 ACCACATAATTGCCGATAAACG
1 ACCACATAATTGCAGATAAACG
5495057 ACCACATAATTGCAGATAAA
1 ACCACATAATTGCAGATAAA
5495077 TTGCCACAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (22 bp):
ACCACATAATTGCAGATAAACG
Found at i:5495342 original size:18 final size:19
Alignment explanation
Indices: 5495312--5495348 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
5495302 TTTGAACAAA
*
5495312 CATCACAATCACATAATAT
1 CATCACAATCACACAATAT
5495331 CATCAC-ATCACACAATAT
1 CATCACAATCACACAATAT
5495349 ACTTTTCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (19 bp):
CATCACAATCACACAATAT
Found at i:5502996 original size:96 final size:96
Alignment explanation
Indices: 5502832--5503025 Score: 370
Period size: 96 Copynumber: 2.0 Consensus size: 96
5502822 TTGAAACAAA
5502832 TAAATTCAGATTTTGGCTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
1 TAAATTCAGATTTTGGCTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
5502897 ACAAAATGCCACCAAAGTGACCTCTTTTGTG
66 ACAAAATGCCACCAAAGTGACCTCTTTTGTG
*
5502928 TAAATTTAGATTTTGGCTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
1 TAAATTCAGATTTTGGCTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
*
5502993 ACAAAATGCCGCCAAAGTGACCTCTTTTGTG
66 ACAAAATGCCACCAAAGTGACCTCTTTTGTG
5503024 TA
1 TA
5503026 GATTAGTTTA
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 96 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (96 bp):
TAAATTCAGATTTTGGCTTTTGGGTTTAATTAAGAATGTCTAATATTTTAAATAGATTAGTTGAA
ACAAAATGCCACCAAAGTGACCTCTTTTGTG
Found at i:5509337 original size:17 final size:17
Alignment explanation
Indices: 5509317--5509350 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5509307 TTTTGTTCTA
*
5509317 GTTTTGGTTTAAGTTTT
1 GTTTTGGTTTAAATTTT
*
5509334 GTTTTGTTTTAAATTTT
1 GTTTTGGTTTAAATTTT
5509351 TAAAATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.18, T:0.68
Consensus pattern (17 bp):
GTTTTGGTTTAAATTTT
Found at i:5510481 original size:23 final size:23
Alignment explanation
Indices: 5510454--5510497 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5510444 TTCACACCAA
5510454 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACATC
* *
5510477 AATTTGGGCAGCATATATACA
1 AATTTGGACAGCATAAATACA
5510498 ACAGTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACATC
Found at i:5510505 original size:23 final size:23
Alignment explanation
Indices: 5510454--5510505 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5510444 TTCACACCAA
*
5510454 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACAAC
* *
5510477 AATTTGGGCAGCATATATACAAC
1 AATTTGGACAGCATAAATACAAC
*
5510500 AGTTTG
1 AATTTG
5510506 AGCAACATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACAAC
Found at i:5510610 original size:47 final size:47
Alignment explanation
Indices: 5510541--5510728 Score: 286
Period size: 47 Copynumber: 4.0 Consensus size: 47
5510531 CAGCATATAT
*
5510541 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAATTTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* *
5510588 GCAACATTTAAGCATCAAAATTGGGCAGCATATATGTAGCAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* * *
5510635 GTAGCATTTAAGCATCAAAATTGGACAGCATATATGTAGCAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* * * *
5510682 GCAGCATTTAAGCATAAAAATTGGATAGCATACATGTAACAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
5510729 TTCAACTCAT
Statistics
Matches: 130, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 130 1.00
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (47 bp):
GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
Found at i:5510614 original size:24 final size:24
Alignment explanation
Indices: 5510545--5510705 Score: 139
Period size: 23 Copynumber: 6.8 Consensus size: 24
5510535 ATATATGCAA
*
5510545 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * * * *
5510569 CATATATGTAAC-AATTTGGGCAA
1 CATTTAAGCATCAAAATTGGGCAG
5510592 CATTTAAGCATCAAAATTGGGCAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * * *
5510616 CATATATGTAGC-AAATTGGGTAG
1 CATTTAAGCATCAAAATTGGGCAG
*
5510639 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATCAAAATTGGGCAG
* * * *
5510663 CATATATGTAGC-AAATTGGGCAG
1 CATTTAAGCATCAAAATTGGGCAG
*
5510686 CATTTAAGCATAAAAATTGG
1 CATTTAAGCATCAAAATTGG
5510706 ATAGCATACA
Statistics
Matches: 100, Mismatches: 34, Indels: 6
0.71 0.24 0.04
Matches are distributed among these distances:
23 51 0.51
24 49 0.49
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (24 bp):
CATTTAAGCATCAAAATTGGGCAG
Found at i:5510711 original size:24 final size:24
Alignment explanation
Indices: 5510545--5510712 Score: 96
Period size: 24 Copynumber: 7.1 Consensus size: 24
5510535 ATATATGCAA
*
5510545 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATAAAAATTGGACAG
* * * * *
5510569 CATATATG--TAACAATTTGGGCAA
1 CATTTAAGCATAA-AAATTGGACAG
* *
5510592 CATTTAAGCATCAAAATTGGGCAG
1 CATTTAAGCATAAAAATTGGACAG
* * * **
5510616 CATATATG--TAGCAAATTGGGTAG
1 CATTTAAGCATA-AAAATTGGACAG
*
5510639 CATTTAAGCATCAAAATTGGACAG
1 CATTTAAGCATAAAAATTGGACAG
* * * *
5510663 CATATATG--TAGCAAATTGGGCAG
1 CATTTAAGCATA-AAAATTGGACAG
*
5510686 CATTTAAGCATAAAAATTGGATAG
1 CATTTAAGCATAAAAATTGGACAG
5510710 CAT
1 CAT
5510713 ACATGTAACA
Statistics
Matches: 103, Mismatches: 32, Indels: 18
0.67 0.21 0.12
Matches are distributed among these distances:
22 4 0.04
23 46 0.45
24 48 0.47
25 5 0.05
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (24 bp):
CATTTAAGCATAAAAATTGGACAG
Found at i:5512869 original size:14 final size:15
Alignment explanation
Indices: 5512850--5512878 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5512840 TCACGAAACT
5512850 TTCACACAT-ATAAA
1 TTCACACATAATAAA
5512864 TTCACACATAATAAA
1 TTCACACATAATAAA
5512879 CACAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.28
Consensus pattern (15 bp):
TTCACACATAATAAA
Found at i:5517638 original size:23 final size:23
Alignment explanation
Indices: 5517604--5517647 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5517594 TTCACACCAA
5517604 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACATC
* *
5517627 AATTTGGGCAGCATATATACA
1 AATTTGGACAGCATAAATACA
5517648 ACAGTTTGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACATC
Found at i:5517655 original size:23 final size:23
Alignment explanation
Indices: 5517604--5517655 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
5517594 TTCACACCAA
*
5517604 AATTTGGACAGCATAAATACATC
1 AATTTGGACAGCATAAATACAAC
* *
5517627 AATTTGGGCAGCATATATACAAC
1 AATTTGGACAGCATAAATACAAC
*
5517650 AGTTTG
1 AATTTG
5517656 AGCAACATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (23 bp):
AATTTGGACAGCATAAATACAAC
Found at i:5517738 original size:23 final size:23
Alignment explanation
Indices: 5517709--5517832 Score: 97
Period size: 23 Copynumber: 5.3 Consensus size: 23
5517699 TTAAGCATCA
5517709 AAATTGGACAGCATATATGTAAC
1 AAATTGGACAGCATATATGTAAC
* * * * * *
5517732 AAATTGGGCAACATTTAAGCATC
1 AAATTGGACAGCATATATGTAAC
*
5517755 AAAATTGGACAGCATATATGTAGC
1 -AAATTGGACAGCATATATGTAAC
* ** * *
5517779 AAACTGGGTAGCATTTAAGCATAA-
1 AAATTGGACAGCATATATG--TAAC
*
5517803 AAATTGGACAGCATACATGTAAC
1 AAATTGGACAGCATATATGTAAC
5517826 AAATTGG
1 AAATTGG
5517833 TTCAACTCAT
Statistics
Matches: 73, Mismatches: 24, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
22 3 0.04
23 38 0.52
24 30 0.41
25 2 0.03
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (23 bp):
AAATTGGACAGCATATATGTAAC
Found at i:5517761 original size:47 final size:47
Alignment explanation
Indices: 5517692--5517832 Score: 228
Period size: 47 Copynumber: 3.0 Consensus size: 47
5517682 CAGCATATAT
5517692 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* *
5517739 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAGCAAACTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
* * * *
5517786 GTAGCATTTAAGCATAAAAATTGGACAGCATACATGTAACAAATTGG
1 GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
5517833 TTCAACTCAT
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 86 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.25
Consensus pattern (47 bp):
GCAACATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGG
Done.