Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009081.1 Hibiscus syriacus cultivar Beakdansim tig00112523_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1718667
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:223842 original size:40 final size:40
Alignment explanation
Indices: 223794--223877 Score: 168
Period size: 40 Copynumber: 2.1 Consensus size: 40
223784 TTGCGATTTT
223794 CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
223834 CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
1 CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
223874 CATT
1 CATT
223878 GCGATTTTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (40 bp):
CATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCG
Found at i:223873 original size:92 final size:90
Alignment explanation
Indices: 223676--223969 Score: 344
Period size: 92 Copynumber: 3.3 Consensus size: 90
223666 TCATTTCGCA
*
223676 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTCATTTCGCATTGCGATTT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG--TTGCGATTT
* * *
223736 TCATTTCGCATT-GCGATTTTC-ATTTCGTA
62 TCATTTCGCATTCGC-A-TTGCGATTTCATG
*
223765 TTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
223830 TTCGCATTTCGCATTGCGATTCTC-TCG
66 TTCGCA-TTCGCATTGCGATT-TCAT-G
223857 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
223922 TT--C---CGCATTGCGATTTTCATG
66 TTCGCATTCGCATTGCGA-TTTCATG
* *
223943 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
223970 GTATTTTCCG
Statistics
Matches: 186, Mismatches: 7, Indels: 27
0.85 0.03 0.12
Matches are distributed among these distances:
86 38 0.20
87 3 0.02
89 24 0.13
90 23 0.12
91 10 0.05
92 79 0.42
93 3 0.02
94 6 0.03
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (90 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTCGCATTGCGATTTCATG
Found at i:223893 original size:52 final size:54
Alignment explanation
Indices: 223657--223941 Score: 299
Period size: 52 Copynumber: 5.2 Consensus size: 54
223647 GCGATTCTCG
223657 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG-
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGA
223709 TTGCGA-TTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCG-A
* *
223765 TTGCGATTTTAATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG-
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCG-ATTGCGATTTTCATTTCGA
* *
223817 TTGCGATTTTCATTTCGCATTTCGCATTGCGATTCTCTCG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCG-ATTTC-A-T-T-TCGATTGCGATTTTCATTTCG-A
*
223876 TTGCGATTTTCATTTCGCATTGCGA-TTC-TCTCG-TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTT-CG-A
223929 TTGCGATTTTCAT
1 TTGCGATTTTCAT
223942 GTTGGGATTT
Statistics
Matches: 207, Mismatches: 9, Indels: 33
0.83 0.04 0.13
Matches are distributed among these distances:
51 37 0.18
52 49 0.24
53 22 0.11
54 17 0.08
55 4 0.02
56 12 0.06
57 42 0.20
58 1 0.00
59 23 0.11
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.47
Consensus pattern (54 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGATTGCGATTTTCATTTCGA
Found at i:223934 original size:34 final size:33
Alignment explanation
Indices: 223876--223969 Score: 136
Period size: 34 Copynumber: 2.8 Consensus size: 33
223866 TCATTTCGCA
223876 TTGCGATTTTCATTTCGCATTGCGATTCTC-TCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCAT-G
*
223909 TTGCGATTTTCATTTCCGCATTGCGATTTTCATG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCATG
* *
223943 TTGGGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
223970 GTATTTTCCG
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 26 0.46
34 29 0.52
35 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCATG
Found at i:227188 original size:20 final size:20
Alignment explanation
Indices: 227160--227524 Score: 431
Period size: 20 Copynumber: 18.4 Consensus size: 20
227150 AAATTTCAGT
* * * *
227160 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
227180 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
227200 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
227220 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
227240 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
227260 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
227280 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
227300 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
227320 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
227340 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
227360 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
227380 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
227400 GTTGCGA--TACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
227418 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
227438 GTTGCGA-TTACGGATACAC
1 GTTGCGATTTACGGATACGC
227457 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
227477 GTTGCGA-TTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
227496 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
227516 GTTGCGATT
1 GTTGCGATT
227525 ATGGAAAATC
Statistics
Matches: 303, Mismatches: 30, Indels: 24
0.85 0.08 0.07
Matches are distributed among these distances:
18 17 0.06
19 36 0.12
20 246 0.81
21 4 0.01
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:238983 original size:13 final size:13
Alignment explanation
Indices: 238965--238995 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
238955 GGTCATAACC
238965 TGACCCGACACGT
1 TGACCCGACACGT
*
238978 TGACCCGACCCGT
1 TGACCCGACACGT
238991 TGACC
1 TGACC
238996 TGTTAACCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.16
Consensus pattern (13 bp):
TGACCCGACACGT
Found at i:243451 original size:18 final size:18
Alignment explanation
Indices: 243428--243466 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
243418 ACCGGTCATA
243428 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
243446 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
243464 ACC
1 ACC
243467 GGTGTTGACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.18, C:0.51, G:0.21, T:0.10
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:247916 original size:18 final size:18
Alignment explanation
Indices: 247893--247931 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
247883 ACCGGTCATA
247893 ACCCGACCCAACCCGTTG
1 ACCCGACCCAACCCGTTG
**
247911 ACCCGACCTGACCCGTTG
1 ACCCGACCCAACCCGTTG
247929 ACC
1 ACC
247932 GGCGTTGACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.49, G:0.18, T:0.13
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTG
Found at i:250270 original size:24 final size:25
Alignment explanation
Indices: 250243--250350 Score: 86
Period size: 24 Copynumber: 4.5 Consensus size: 25
250233 AATTATTTTA
250243 TCTGATTTTC-GACTTGAATTCTGT
1 TCTGATTTTCTGACTTGAATTCTGT
* *
250267 TCTGA--TACATGACCTGAATTCTGT
1 TCTGATTTTC-TGACTTGAATTCTGT
*
250291 TCTGA-TTTCTGA-TCTGGATTCTGT
1 TCTGATTTTCTGACT-TGAATTCTGT
* **
250315 TCTGA-TATCTGTTTTGAATTCTGT
1 TCTGATTTTCTGACTTGAATTCTGT
*
250339 TTTGA-TTTCTGA
1 TCTGATTTTCTGA
250351 TATCTCCGTT
Statistics
Matches: 68, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
22 2 0.03
24 63 0.93
25 3 0.04
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.49
Consensus pattern (25 bp):
TCTGATTTTCTGACTTGAATTCTGT
Found at i:250295 original size:12 final size:12
Alignment explanation
Indices: 250257--250349 Score: 73
Period size: 12 Copynumber: 7.8 Consensus size: 12
250247 ATTTTCGACT
250257 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
250269 TG-ATACATGACC
1 TGAATTC-TGTTC
250281 TGAATTCTGTTC
1 TGAATTCTGTTC
* *
250293 TGATTTCTGATC
1 TGAATTCTGTTC
*
250305 TGGATTCTGTTC
1 TGAATTCTGTTC
*
250317 TG-ATATCTGTTT
1 TGAAT-TCTGTTC
*
250329 TGAATTCTGTTT
1 TGAATTCTGTTC
*
250341 TGATTTCTG
1 TGAATTCTG
250350 ATATCTCCGT
Statistics
Matches: 64, Mismatches: 13, Indels: 8
0.75 0.15 0.09
Matches are distributed among these distances:
11 5 0.08
12 54 0.84
13 5 0.08
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.49
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:250312 original size:48 final size:48
Alignment explanation
Indices: 250260--250351 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
250250 TTCGACTTGA
250260 ATTCTGTTCTGATA-CATGACCTGAATTCTGTTCTGATTTCTGATCTGG
1 ATTCTGTTCTGATATC-TGACCTGAATTCTGTTCTGATTTCTGATCTGG
*** *
250308 ATTCTGTTCTGATATCTGTTTTGAATTCTGTTTTGATTTCTGAT
1 ATTCTGTTCTGATATCTGACCTGAATTCTGTTCTGATTTCTGAT
250352 ATCTCCGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.50
Consensus pattern (48 bp):
ATTCTGTTCTGATATCTGACCTGAATTCTGTTCTGATTTCTGATCTGG
Found at i:250516 original size:2 final size:2
Alignment explanation
Indices: 250509--250535 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
250499 TAGGATGGGG
250509 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 T
250536 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:258424 original size:99 final size:99
Alignment explanation
Indices: 258253--258433 Score: 276
Period size: 99 Copynumber: 1.8 Consensus size: 99
258243 CAGGCCCAAA
*
258253 GAAGAGGATTACTTCTATTACAATCCAGAAGAATGCCTGCGACAACAATATGGTCAACTAAGTAG
1 GAAGAGGATTACTTCTATTACAATCCAGAAGAATGCCTGCGACAACAATACGGTCAACTAAGTAG
258318 CTCGTGATCCCTCTCTCGTGGGATTTGTAATACT
66 CTCGTGATCCCTCTCTCGTGGGATTTGTAATACT
* * * *
258352 GAAGAGGATTACTTGTA-TGCGAATTCAGAAGAATG-CTCGCGACAACAATACGGTCGACTAAGT
1 GAAGAGGATTACTTCTATTAC-AATCCAGAAGAATGCCT-GCGACAACAATACGGTCAACTAAGT
*
258415 AGCTCGTGATCTCTCTCTC
64 AGCTCGTGATCCCTCTCTC
258434 CAGGGATAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
98 4 0.05
99 70 0.95
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.27
Consensus pattern (99 bp):
GAAGAGGATTACTTCTATTACAATCCAGAAGAATGCCTGCGACAACAATACGGTCAACTAAGTAG
CTCGTGATCCCTCTCTCGTGGGATTTGTAATACT
Found at i:258860 original size:2 final size:2
Alignment explanation
Indices: 258855--258893 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
258845 TACACGTGTC
258855 TA TA TA TA TA 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 TA TA TA TA TA T
258894 GGTATAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:259943 original size:14 final size:14
Alignment explanation
Indices: 259924--259963 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
259914 CAAAGGATAA
259924 TAATTAATAAATCT
1 TAATTAATAAATCT
259938 TAATTAATAAATCT
1 TAATTAATAAATCT
*
259952 GAATTAATAAAT
1 TAATTAATAAAT
259964 AGTCAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (14 bp):
TAATTAATAAATCT
Found at i:265791 original size:3 final size:3
Alignment explanation
Indices: 265749--265778 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
265739 GAAGAGGACT
265749 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
265779 TAAAATAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:265805 original size:22 final size:22
Alignment explanation
Indices: 265763--265804 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
265753 GAGGAGGAGG
* *
265763 AGGAGGAGGAGGAGGATAAAAT
1 AGGAGGAAGAGGAGAATAAAAT
265785 AGGAGGAAGAGG-GAATAAAA
1 AGGAGGAAGAGGAGAATAAAA
265805 ACGGGATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.50, C:0.00, G:0.43, T:0.07
Consensus pattern (22 bp):
AGGAGGAAGAGGAGAATAAAAT
Found at i:267388 original size:12 final size:12
Alignment explanation
Indices: 267371--267395 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
267361 TTCGATAAAA
267371 AAATAATATTTT
1 AAATAATATTTT
267383 AAATAATATTTT
1 AAATAATATTTT
267395 A
1 A
267396 CCGAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATAATATTTT
Found at i:267388 original size:20 final size:20
Alignment explanation
Indices: 267338--267388 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
267328 TTTTACAGGT
* *
267338 TTTTAAATAGGAAAATTAATA
1 TTTTAAATA-AAAAAATAATA
**
267359 TTTTCGATAAAAAAATAATA
1 TTTTAAATAAAAAAATAATA
267379 TTTTAAATAA
1 TTTTAAATAA
267389 TATTTTACCG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (20 bp):
TTTTAAATAAAAAAATAATA
Found at i:267670 original size:22 final size:22
Alignment explanation
Indices: 267640--267681 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
267630 AAAATGCTTT
*
267640 TAAAAATTTAATTATTTTATTA
1 TAAAAATTTAAATATTTTATTA
*
267662 TAAACATTTAAATATTTTAT
1 TAAAAATTTAAATATTTTAT
267682 AACCTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAAATTTAAATATTTTATTA
Found at i:267740 original size:21 final size:22
Alignment explanation
Indices: 267710--267760 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
267700 ATTTCTAAAG
267710 ATAATAATTATTCTT-TTAATC-A
1 ATAA-AATTATT-TTGTTAATCTA
*
267732 ATAAAATTATTTTGTTACTCTA
1 ATAAAATTATTTTGTTAATCTA
267754 ATAAAAT
1 ATAAAAT
267761 ATTAAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 2 0.08
21 12 0.46
22 12 0.46
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAAAATTATTTTGTTAATCTA
Found at i:267804 original size:2 final size:2
Alignment explanation
Indices: 267797--267835 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
267787 TAATATTTAA
267797 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
267836 ATCACGAGTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:268350 original size:23 final size:22
Alignment explanation
Indices: 268324--268374 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
268314 AAATAAAGAT
*
268324 AATAATATATAAATT-TATGTAAA
1 AATAATACAT-AATTATATG-AAA
*
268347 AATATTACATAATTATATGAAA
1 AATAATACATAATTATATGAAA
268369 AATAAT
1 AATAAT
268375 TTTTTAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
AATAATACATAATTATATGAAA
Found at i:271100 original size:2 final size:2
Alignment explanation
Indices: 271093--271134 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
271083 TTTATCTAAC
271093 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271135 TATTGTAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:271214 original size:13 final size:13
Alignment explanation
Indices: 271196--271220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
271186 TCAATAAGAC
271196 CAATATAATTTAA
1 CAATATAATTTAA
271209 CAATATAATTTA
1 CAATATAATTTA
271221 TACATACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
CAATATAATTTAA
Found at i:271263 original size:2 final size:2
Alignment explanation
Indices: 271256--271311 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
271246 ATATTTAATA
271256 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271298 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
271312 TGGGACATGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:273097 original size:20 final size:20
Alignment explanation
Indices: 273064--273114 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
273054 TTAACGGATT
* *
273064 AAATAGTATCATATTTATAA
1 AAATAATATTATATTTATAA
273084 AAATAATATTATATTTATAA
1 AAATAATATTATATTTATAA
273104 AAATAATATTA
1 AAATAATATTA
273115 AATAAAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATAATATTATATTTATAA
Found at i:274339 original size:14 final size:14
Alignment explanation
Indices: 274320--274347 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
274310 CACTGGGCAT
274320 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
274334 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
274348 AAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:274374 original size:20 final size:22
Alignment explanation
Indices: 274315--274377 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 22
274305 CAACACACTG
274315 GGCATCCGAGGCCATCCGACCGA
1 GGCATCCGAGGCCATCCGA-CGA
*
274338 GGCCATCCGAAAG-CATCCGA-GA
1 GG-CATCCG-AGGCCATCCGACGA
274360 -GCATCCGAGGCCATCCGA
1 GGCATCCGAGGCCATCCGA
274378 ATGAGCTATG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
21 1 0.03
22 2 0.06
23 2 0.06
24 13 0.37
25 2 0.06
ACGTcount: A:0.25, C:0.37, G:0.29, T:0.10
Consensus pattern (22 bp):
GGCATCCGAGGCCATCCGACGA
Found at i:274503 original size:14 final size:14
Alignment explanation
Indices: 274481--274520 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
274471 CCTCGCATAG
*
274481 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
274495 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
274509 CTCGGTCGGATG
1 CTCGGTCGGATG
274521 AAGACATGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.07, C:0.28, G:0.40, T:0.25
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:290232 original size:4 final size:4
Alignment explanation
Indices: 290187--290213 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
290177 TCACAAATAC
290187 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
290214 GCTTGAGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:290921 original size:29 final size:29
Alignment explanation
Indices: 290836--290921 Score: 100
Period size: 29 Copynumber: 3.0 Consensus size: 29
290826 CCCAACCCAT
* ****
290836 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
**
290865 AGGTCGCCATGCACTCTGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
290894 AGGTCGCCATGCACGCCCGGCGACCAAG
1 AGGTCGCCATGCACTCCCGGCGACCAAG
290922 CTTTTAACCC
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 47 1.00
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAAGG
Found at i:294545 original size:35 final size:35
Alignment explanation
Indices: 294494--294605 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
294484 AAAATAGTCC
* * *
294494 TCAATTTCATTCTAAACCCCAATTTCTAAAGTAAT
1 TCAATTTCATTATAAACCCCAAATTCTAAAATAAT
* *
294529 TCAATTTCATTATAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTATAAACCCCAAATTCTAAAATAAT
** * *
294564 TCAATTAAATTTTAAACCCCAAATTCTAAAATACT
1 TCAATTTCATTATAAACCCCAAATTCTAAAATAAT
294599 TCAATTT
1 TCAATTT
294606 AAGGTTTAGA
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.42, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTATAAACCCCAAATTCTAAAATAAT
Found at i:294669 original size:35 final size:35
Alignment explanation
Indices: 294601--294675 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
294591 AAAATACTTC
* * *
294601 AATTTAAGGTTTAGAATGTAATTGAATTATTTTGG
1 AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
* *
294636 AATTTAGGGTTTAGAATGAAATT-AAGGTGTTTTGA
1 AATTTAAGGTTTAGAATGAAATTGAA-GTATTTTGA
294671 AATTT
1 AATTT
294676 TGAACATGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 2 0.06
35 32 0.94
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (35 bp):
AATTTAAGGTTTAGAATGAAATTGAAGTATTTTGA
Found at i:297473 original size:15 final size:16
Alignment explanation
Indices: 297446--297475 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
297436 CTTATTTTAT
297446 TAATATATAATTAAAA
1 TAATATATAATTAAAA
297462 TAATAT-TAATTAAA
1 TAATATATAATTAAA
297476 TATTTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAATATATAATTAAAA
Found at i:297534 original size:29 final size:30
Alignment explanation
Indices: 297485--297541 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
297475 ATATTTTTAA
297485 AAAATTATATTGAAACAAAAA-ATATTCCC
1 AAAATTATATTGAAACAAAAAGATATTCCC
**
297514 AAAATTATAATT-AAATTAAAAGATATTC
1 AAAATTAT-ATTGAAACAAAAAGATATTC
297542 TCTATGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 15 0.62
30 9 0.38
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAATTATATTGAAACAAAAAGATATTCCC
Found at i:297774 original size:18 final size:18
Alignment explanation
Indices: 297751--297790 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
297741 GAAAAGAAAA
*
297751 AAATGTTGCATCATACAT
1 AAATGTTACATCATACAT
297769 AAATGTTACATCATACAT
1 AAATGTTACATCATACAT
297787 AAAT
1 AAAT
297791 ATTAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (18 bp):
AAATGTTACATCATACAT
Found at i:297932 original size:31 final size:31
Alignment explanation
Indices: 297897--297974 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
297887 GAAACAAATA
297897 GGAGGGCCAAATTGAGTTATTTTCTTGAGTT
1 GGAGGGCCAAATTGAGTTATTTTCTTGAGTT
*
297928 GGAGGGCAAAATTGAGTTATTTTCTTGAGTT
1 GGAGGGCCAAATTGAGTTATTTTCTTGAGTT
*
297959 GGAGGGCCAGATTGAG
1 GGAGGGCCAAATTGAG
297975 AGAGAAATAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (31 bp):
GGAGGGCCAAATTGAGTTATTTTCTTGAGTT
Found at i:298853 original size:17 final size:17
Alignment explanation
Indices: 298831--298864 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
298821 TAATTAGCCT
298831 CTAAATAATGAAAATAA
1 CTAAATAATGAAAATAA
298848 CTAAATAATGAAAATAA
1 CTAAATAATGAAAATAA
298865 GACGGTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (17 bp):
CTAAATAATGAAAATAA
Found at i:302381 original size:29 final size:29
Alignment explanation
Indices: 302349--302405 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
302339 TGTCTGTATG
*
302349 ATAAAATAGTTCAT-CGACTATTAAAAGTT
1 ATAAAAT-GATCATCCGACTATTAAAAGTT
*
302378 ATAAAATGATCATCCGACTATTGAAAGT
1 ATAAAATGATCATCCGACTATTAAAAGT
302406 CTACAAGATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (29 bp):
ATAAAATGATCATCCGACTATTAAAAGTT
Found at i:302523 original size:129 final size:131
Alignment explanation
Indices: 302265--302527 Score: 431
Period size: 129 Copynumber: 2.0 Consensus size: 131
302255 CTGCGTTGAA
*
302265 TGAAAGTCTACATGATCGAAGAGTATAAGAAAGATTTATCATAATAAACAATCACCTTTGGGGTT
1 TGAAAGTCTACAAGATCGAAGAGTATAAGAAAGATTTATCATAATAAACAATCACCTTTGGGGTT
* *
302330 TCATTTTACTGTCTGTATGATAAAATAGTTCATCGACTATTAAAAGTTATAAAATGATCATCCGA
66 CCATTTTA---TCTGTATGATAAAATAGTTCATCAACTATTAAAAGTTATAAAATGATCATCCGA
302395 CTAT
128 CTAT
*
302399 TGAAAGTCTACAAGATCGAAGAGTATAAG-AAGATTTATCATAATAAACAATCGCCTTTGGGGTT
1 TGAAAGTCTACAAGATCGAAGAGTATAAGAAAGATTTATCATAATAAACAATCACCTTTGGGGTT
* *
302463 CCATTTTA-CTGTATGATAAAATAGTTCCTCAACTATTAAAAGTTATAAAATGATCGTCCGACTA
66 CCATTTTATCTGTATGATAAAATAGTTCATCAACTATTAAAAGTTATAAAATGATCATCCGACTA
302527 T
131 T
302528 AGAATGTTGA
Statistics
Matches: 123, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
129 54 0.44
133 41 0.33
134 28 0.23
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (131 bp):
TGAAAGTCTACAAGATCGAAGAGTATAAGAAAGATTTATCATAATAAACAATCACCTTTGGGGTT
CCATTTTATCTGTATGATAAAATAGTTCATCAACTATTAAAAGTTATAAAATGATCATCCGACTA
T
Found at i:302526 original size:29 final size:29
Alignment explanation
Indices: 302494--302588 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
302484 TAGTTCCTCA
*
302494 ACTATTAAAAGTTATAAAATGATCGTCCG
1 ACTATTAAAAGTTATAAAATGATCATCCG
* ** * * *
302523 ACTA-TAGAATGTTGATTTATTGAGTCCTTCG
1 ACTATTA-AAAGTT-ATAAAATGA-TCATCCG
* *
302554 ACTATTAAAAGTTACAAAATGATCACCCG
1 ACTATTAAAAGTTATAAAATGATCATCCG
302583 ACTATT
1 ACTATT
302589 CATTATGTTC
Statistics
Matches: 48, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
28 2 0.04
29 19 0.40
30 11 0.23
31 14 0.29
32 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (29 bp):
ACTATTAAAAGTTATAAAATGATCATCCG
Found at i:303772 original size:10 final size:10
Alignment explanation
Indices: 303757--303786 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
303747 ATTTAAATGA
303757 TAAACGAACG
1 TAAACGAACG
303767 TAAACGAACG
1 TAAACGAACG
*
303777 CAAACGAACG
1 TAAACGAACG
303787 AACATAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.50, C:0.23, G:0.20, T:0.07
Consensus pattern (10 bp):
TAAACGAACG
Found at i:304911 original size:18 final size:18
Alignment explanation
Indices: 304888--304927 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
304878 GGCATAACTC
*
304888 TCCCGATCCGACTCCGAA
1 TCCCGACCCGACTCCGAA
*
304906 TCCCGACCCGACTCTGAA
1 TCCCGACCCGACTCCGAA
304924 TCCC
1 TCCC
304928 AACGAGGCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.20, C:0.47, G:0.15, T:0.17
Consensus pattern (18 bp):
TCCCGACCCGACTCCGAA
Found at i:321289 original size:17 final size:17
Alignment explanation
Indices: 321267--321307 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
321257 AAATAACGTT
*
321267 ATAGCGGTATCACACCA
1 ATAGCGGTATCACACAA
321284 ATAGCGGTATCACACAA
1 ATAGCGGTATCACACAA
321301 ATAGCGG
1 ATAGCGG
321308 CCGCAACTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (17 bp):
ATAGCGGTATCACACAA
Found at i:327319 original size:3 final size:3
Alignment explanation
Indices: 327311--327341 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
327301 CACTCTTGGG
327311 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
327342 GGTTTCATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:333706 original size:58 final size:58
Alignment explanation
Indices: 333611--333722 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
333601 AACGATTCTC
* * * * *
333611 CGACTATATGATATTACTTTATTGAGCCTTTTGACTATTAAAAGTTACCAAATGGTTT
1 CGACTATAGGATATTACTTTATTAAGCCTCTTAACTATTAAAAGTTACAAAATGGTTT
* * *
333669 CGACTATAGGATTTTACTTTTTTAAGTCTCTTAACTATTAAAAGTTACAAAATG
1 CGACTATAGGATATTACTTTATTAAGCCTCTTAACTATTAAAAGTTACAAAATG
333723 ATCACTCGAC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (58 bp):
CGACTATAGGATATTACTTTATTAAGCCTCTTAACTATTAAAAGTTACAAAATGGTTT
Found at i:337189 original size:21 final size:23
Alignment explanation
Indices: 337149--337190 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
337139 GATAATTGGA
337149 AAGATAACATATAGTAAAATAAG
1 AAGATAACATATAGTAAAATAAG
*
337172 AAGATAA-A-ATATTAAAATA
1 AAGATAACATATAGTAAAATA
337191 TTTAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.64, C:0.02, G:0.10, T:0.24
Consensus pattern (23 bp):
AAGATAACATATAGTAAAATAAG
Found at i:337969 original size:29 final size:30
Alignment explanation
Indices: 337873--337981 Score: 116
Period size: 29 Copynumber: 3.7 Consensus size: 30
337863 TGAAAAATAA
* * *
337873 TTTACGTAAAATAAATCACATG-AAATTGT
1 TTTACGTAAAATGAATTACATGAAAACTGT
337902 TTTACGTAAAATGAATTACATGAAAACTGT
1 TTTACGTAAAATGAATTACATGAAAACTGT
* * *
337932 TTGAAGTAAAGTGAATTATC-T-AAAACTGT
1 TTTACGTAAAATGAATTA-CATGAAAACTGT
**
337961 TTTACGTAAAATTCATTACAT
1 TTTACGTAAAATGAATTACAT
337982 TTTTCTGGAA
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
28 1 0.02
29 42 0.64
30 22 0.33
31 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (30 bp):
TTTACGTAAAATGAATTACATGAAAACTGT
Found at i:338397 original size:22 final size:21
Alignment explanation
Indices: 338371--338431 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
338361 TTTATTTAAA
338371 AATATAATATCATAAATATTAT
1 AATATAATATCATAAATATT-T
* *
338393 AATAT-ATATGAGTATATA-TT
1 AATATAATATCA-TAAATATTT
* *
338413 AATATAATATTAAAAATAT
1 AATATAATATCATAAATAT
338432 AATATTATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 10 0.32
21 11 0.35
22 10 0.32
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (21 bp):
AATATAATATCATAAATATTT
Found at i:338436 original size:19 final size:18
Alignment explanation
Indices: 338357--338455 Score: 62
Period size: 17 Copynumber: 5.5 Consensus size: 18
338347 ATAAATATTA
*
338357 ATAATTTAT-TTAAAAAT
1 ATAATATATATTAAAAAT
* *
338374 ATAATATCATA--AATATT
1 ATAATAT-ATATTAAAAAT
* * *
338391 ATAATATATATGAGTATAT
1 ATAATATATATTA-AAAAT
338410 ATTAATATAATATTAAAAAT
1 A-TAATAT-ATATTAAAAAT
*
338430 ATAATAT-TATTAAAATT
1 ATAATATATATTAAAAAT
*
338447 ATATTATAT
1 ATAATATAT
338456 GTATACTAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.05
17 32 0.52
18 4 0.06
19 8 0.13
20 10 0.16
21 5 0.08
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAATATATATTAAAAAT
Found at i:340559 original size:31 final size:31
Alignment explanation
Indices: 340521--340644 Score: 133
Period size: 31 Copynumber: 4.0 Consensus size: 31
340511 CCCCGACAAC
* *
340521 TGTCCATATGATCCAAAGAACCTAGGTAAAT
1 TGTCCATATGTTCCAAAGAACATAGGTAAAT
** * *
340552 TGTCCATATGTTCCTCAGAACATAGGTATAC
1 TGTCCATATGTTCCAAAGAACATAGGTAAAT
* *
340583 TGTCCATATGTCTCAAAAG-ACATAGGTAATT
1 TGTCCATATGT-TCCAAAGAACATAGGTAAAT
**
340614 ATGTCCATATGTTCCGTAGAACATAGGTAAA
1 -TGTCCATATGTTCCAAAGAACATAGGTAAA
340645 CCCTCGACTC
Statistics
Matches: 74, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
31 49 0.66
32 25 0.34
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.30
Consensus pattern (31 bp):
TGTCCATATGTTCCAAAGAACATAGGTAAAT
Found at i:340628 original size:63 final size:62
Alignment explanation
Indices: 340519--340642 Score: 173
Period size: 62 Copynumber: 2.0 Consensus size: 62
340509 AACCCCGACA
*
340519 ACTGTCCATATGATCCAAAGAACCTAGGTAAATTGTCCATATGTTCC-TCAGAACATAGGTAT
1 ACTGTCCATATGATCCAAAGAACATAGGTAAATTGTCCATATGTTCCGT-AGAACATAGGTAT
*
340581 ACTGTCCATATG-TCTCAAA-AGACATAGGTAATTATGTCCATATGTTCCGTAGAACATAGGTA
1 ACTGTCCATATGATC-CAAAGA-ACATAGGTAAAT-TGTCCATATGTTCCGTAGAACATAGGTA
340643 AACCCTCGAC
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
61 3 0.05
62 26 0.46
63 26 0.46
64 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (62 bp):
ACTGTCCATATGATCCAAAGAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAGGTAT
Found at i:342950 original size:16 final size:17
Alignment explanation
Indices: 342927--342960 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
342917 GACTTTTTTA
342927 TATATATATAAAATAGTT
1 TATATA-ATAAAATAGTT
*
342945 TATATAATAAATTAGT
1 TATATAATAAAATAGT
342961 ACCTAAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TATATAATAAAATAGTT
Found at i:343447 original size:13 final size:13
Alignment explanation
Indices: 343429--343453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343419 ACTCAACTCG
343429 AATTATTGATGAA
1 AATTATTGATGAA
343442 AATTATTGATGA
1 AATTATTGATGA
343454 GTTGAAACAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (13 bp):
AATTATTGATGAA
Found at i:344357 original size:15 final size:15
Alignment explanation
Indices: 344337--344366 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
344327 AATATATTGA
*
344337 AATAATATACTAAAT
1 AATAATAAACTAAAT
344352 AATAATAAACTAAAT
1 AATAATAAACTAAAT
344367 CTCAACCATT
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:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (15 bp):
AATAATAAACTAAAT
Found at i:357995 original size:195 final size:195
Alignment explanation
Indices: 357663--358054 Score: 784
Period size: 195 Copynumber: 2.0 Consensus size: 195
357653 ATGGATGATA
357663 CAACTTTGATGATCTTATTAGTAAAATTAGTGTTGTTTGCACTTTTCAAATAAGCATACGCATAT
1 CAACTTTGATGATCTTATTAGTAAAATTAGTGTTGTTTGCACTTTTCAAATAAGCATACGCATAT
357728 GTATCTGTTTTACCTGGGCAATCAGTTCTGGGAGAGGTTAATTCCCTGACAACGTTCTCGAAAGT
66 GTATCTGTTTTACCTGGGCAATCAGTTCTGGGAGAGGTTAATTCCCTGACAACGTTCTCGAAAGT
357793 TCCGGCCCAAGCATCTCTGTGAGTCAAGAAATTGGACGAGAGATTGAACATTTTCTTTATTGTTG
131 TCCGGCCCAAGCATCTCTGTGAGTCAAGAAATTGGACGAGAGATTGAACATTTTCTTTATTGTTG
357858 CAACTTTGATGATCTTATTAGTAAAATTAGTGTTGTTTGCACTTTTCAAATAAGCATACGCATAT
1 CAACTTTGATGATCTTATTAGTAAAATTAGTGTTGTTTGCACTTTTCAAATAAGCATACGCATAT
357923 GTATCTGTTTTACCTGGGCAATCAGTTCTGGGAGAGGTTAATTCCCTGACAACGTTCTCGAAAGT
66 GTATCTGTTTTACCTGGGCAATCAGTTCTGGGAGAGGTTAATTCCCTGACAACGTTCTCGAAAGT
357988 TCCGGCCCAAGCATCTCTGTGAGTCAAGAAATTGGACGAGAGATTGAACATTTTCTTTATTGTTG
131 TCCGGCCCAAGCATCTCTGTGAGTCAAGAAATTGGACGAGAGATTGAACATTTTCTTTATTGTTG
358053 CA
1 CA
358055 GGGATTGATG
Statistics
Matches: 197, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
195 197 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (195 bp):
CAACTTTGATGATCTTATTAGTAAAATTAGTGTTGTTTGCACTTTTCAAATAAGCATACGCATAT
GTATCTGTTTTACCTGGGCAATCAGTTCTGGGAGAGGTTAATTCCCTGACAACGTTCTCGAAAGT
TCCGGCCCAAGCATCTCTGTGAGTCAAGAAATTGGACGAGAGATTGAACATTTTCTTTATTGTTG
Found at i:359822 original size:27 final size:28
Alignment explanation
Indices: 359779--359831 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
359769 GTCTGTCATT
359779 TATAATTAATTAATT-AAAATAAAATAA
1 TATAATTAATTAATTAAAAATAAAATAA
*
359806 TATAATATAA-TAGTTAAAAATAAAAT
1 TATAAT-TAATTAATTAAAAATAAAAT
359832 TTATTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
TATAATTAATTAATTAAAAATAAAATAA
Found at i:362223 original size:76 final size:77
Alignment explanation
Indices: 362097--362251 Score: 303
Period size: 76 Copynumber: 2.0 Consensus size: 77
362087 ATTAAAGTTA
362097 CAAAATGATCATCTAAATATAGAATCTTTATTGAGTTCTTCGACTATTAAAAGTTATAAAATGGT
1 CAAAATGATCATCTAAATATAGAATCTTTATTGAGTTCTTCGACTATTAAAAGTTATAAAATGGT
362162 CATCC-ACTATT
66 CATCCAACTATT
362173 CAAAATGATCATCTAAATATAGAATCTTTATTGAGTTCTTCGACTATTAAAAGTTATAAAATGGT
1 CAAAATGATCATCTAAATATAGAATCTTTATTGAGTTCTTCGACTATTAAAAGTTATAAAATGGT
362238 CATCCAACTATT
66 CATCCAACTATT
362250 CA
1 CA
362252 TGAGTTCCAA
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 70 0.90
77 8 0.10
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (77 bp):
CAAAATGATCATCTAAATATAGAATCTTTATTGAGTTCTTCGACTATTAAAAGTTATAAAATGGT
CATCCAACTATT
Found at i:366255 original size:43 final size:43
Alignment explanation
Indices: 366207--366294 Score: 176
Period size: 43 Copynumber: 2.0 Consensus size: 43
366197 AGTGTACCTT
366207 GCCCGGATTATTAATGTACCTGCTAACAGCTCCCACTGCATGA
1 GCCCGGATTATTAATGTACCTGCTAACAGCTCCCACTGCATGA
366250 GCCCGGATTATTAATGTACCTGCTAACAGCTCCCACTGCATGA
1 GCCCGGATTATTAATGTACCTGCTAACAGCTCCCACTGCATGA
366293 GC
1 GC
366295 AATATCTGGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (43 bp):
GCCCGGATTATTAATGTACCTGCTAACAGCTCCCACTGCATGA
Found at i:369606 original size:16 final size:17
Alignment explanation
Indices: 369578--369610 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
369568 ATCGCCGATA
369578 AAATTTCACTATTCACG
1 AAATTTCACTATTCACG
369595 AAATTT-ACTATTCACG
1 AAATTTCACTATTCACG
369611 TGAATAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (17 bp):
AAATTTCACTATTCACG
Found at i:371684 original size:21 final size:22
Alignment explanation
Indices: 371659--371704 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
371649 AAATTACACA
*
371659 TTTAGTACTTAAACTATC-ATT
1 TTTAGTACCTAAACTATCAATT
*
371680 TTTAGTACCTAAACTTTCAATT
1 TTTAGTACCTAAACTATCAATT
371702 TTT
1 TTT
371705 TCAAAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.50
Consensus pattern (22 bp):
TTTAGTACCTAAACTATCAATT
Found at i:372157 original size:2 final size:2
Alignment explanation
Indices: 372150--372179 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
372140 TCTATACTCT
372150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
372180 AAAGTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:374310 original size:20 final size:20
Alignment explanation
Indices: 374216--374584 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
374206 GATTTTCCAT
* ** *
374216 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
374236 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
374256 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
374276 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
374296 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
374316 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
374336 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
374356 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
374376 AA-CTGCAACGTGTATCCGTA
1 AATC-GCAACGCGTATCCGTA
374396 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
374416 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
374436 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
374456 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
*
374476 AATCGCAACGCTTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
374496 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
374516 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
374536 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
374556 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
374576 AATCACAAC
1 AATCGCAAC
374585 ACTTAAATTT
Statistics
Matches: 305, Mismatches: 34, Indels: 20
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.01
20 297 0.97
21 4 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:375306 original size:24 final size:24
Alignment explanation
Indices: 375267--375313 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
375257 AAATTTGGTC
375267 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
375291 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
375314 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:375504 original size:12 final size:12
Alignment explanation
Indices: 375487--375511 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
375477 ATATAATCCT
375487 GAAGAAGAAAAA
1 GAAGAAGAAAAA
375499 GAAGAAGAAAAA
1 GAAGAAGAAAAA
375511 G
1 G
375512 TCCCGAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:377809 original size:19 final size:19
Alignment explanation
Indices: 377787--378040 Score: 316
Period size: 19 Copynumber: 14.4 Consensus size: 19
377777 CGGAAAATAC
*
377787 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
377806 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
377820 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
377840 AATCGCAA--CG--A-G-A
1 AATCGCAATGCGAAATGAA
377853 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
377872 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
377891 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
377905 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
377924 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
377943 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
377962 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
377981 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
378000 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
378014 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
378033 AATCGCAA
1 AATCGCAA
378041 CGAGATAATC
Statistics
Matches: 207, Mismatches: 6, Indels: 44
0.81 0.02 0.17
Matches are distributed among these distances:
13 9 0.04
14 29 0.14
15 3 0.01
16 12 0.06
17 13 0.06
18 2 0.01
19 126 0.61
20 13 0.06
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:377909 original size:52 final size:52
Alignment explanation
Indices: 377815--378040 Score: 364
Period size: 52 Copynumber: 4.2 Consensus size: 52
377805 AAATCCCAAC
*
377815 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-AATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
377867 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
377919 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAA
377976 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
378028 ATGAAAATCGCAA
1 ATGAAAATCGCAA
378041 CGAGATAATC
Statistics
Matches: 164, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
51 20 0.12
52 88 0.54
54 5 0.03
55 6 0.04
57 45 0.27
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:378018 original size:33 final size:33
Alignment explanation
Indices: 377872--378062 Score: 256
Period size: 33 Copynumber: 5.5 Consensus size: 33
377862 GCGAAATGAA
*
377872 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
*
377905 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
377941 AAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 --AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
377979 AAAATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 --AATCGCAATGCGAAATGAAAATCGCAACGAAAG
* *
378014 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
378047 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
378063 TATAAACGCA
Statistics
Matches: 148, Mismatches: 5, Indels: 10
0.91 0.03 0.06
Matches are distributed among these distances:
33 73 0.49
35 5 0.03
36 6 0.04
38 64 0.43
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:378078 original size:52 final size:53
Alignment explanation
Indices: 377815--378078 Score: 230
Period size: 52 Copynumber: 5.0 Consensus size: 53
377805 AAATCCCAAC
* *
377815 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA--CG--AGAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GC-G-AATGAAAATCGCAATGCGAAATAAAACGCAATGCGAA
* * *
377867 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGACA-GAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATAAAACGCAATGCGAA
*
377919 ATTAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAAT-AAAA-CGCAATGCGAA
* *
377976 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAAA-GAATCGCAATGCGAA
1 ATGAAAATCGCAA-GCG-AATGAAAATCGCAATGCGAAATAAAACGCAATGCGAA
* *
378028 ATGAAAATCGCAA-CG-A-GATAATCGCAATGCGAAATTATAAACGCATTGCGA
1 ATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAA-TA-AAACGCAATGCGA
378079 TTTTCATTTC
Statistics
Matches: 188, Mismatches: 12, Indels: 24
0.84 0.05 0.11
Matches are distributed among these distances:
47 10 0.05
48 1 0.01
49 5 0.03
50 2 0.01
51 18 0.10
52 96 0.51
53 3 0.02
54 4 0.02
55 5 0.03
56 2 0.01
57 42 0.22
ACGTcount: A:0.46, C:0.17, G:0.21, T:0.16
Consensus pattern (53 bp):
ATGAAAATCGCAAGCGAATGAAAATCGCAATGCGAAATAAAACGCAATGCGAA
Found at i:378113 original size:19 final size:19
Alignment explanation
Indices: 378069--378170 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
378059 AAATTATAAA
378069 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
378088 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
* *
378108 CGCATTGC-A-ATTC-TCT
1 CGCATTGCGATTTTCATTT
378124 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
378141 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
378160 CGCATTGCGAT
1 CGCATTGCGAT
378171 AGTCTTTTTG
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
14 4 0.05
15 1 0.01
16 7 0.10
17 7 0.10
18 1 0.01
19 34 0.47
20 19 0.26
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:378294 original size:14 final size:14
Alignment explanation
Indices: 378275--378311 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
378265 CATCAATTAC
378275 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
378289 ACAAATCATCTTTT
1 ACAAATCAACTTTT
378303 ACAAATCAA
1 ACAAATCAA
378312 TTAACAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:378393 original size:12 final size:12
Alignment explanation
Indices: 378376--378411 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
378366 AACTTTTACA
378376 AATCAATTAAAC
1 AATCAATTAAAC
**
378388 AATCAAAAAAAC
1 AATCAATTAAAC
378400 AATCAATTAAAC
1 AATCAATTAAAC
378412 TATTGAATCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (12 bp):
AATCAATTAAAC
Found at i:380284 original size:14 final size:14
Alignment explanation
Indices: 380265--380321 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
380255 GCGAAATGAA
*
380265 AATCGCAACGACAG
1 AATCGCAACGAAAG
380279 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
380296 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
380312 AATCGCAACG
1 AATCGCAACG
380322 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:380292 original size:33 final size:33
Alignment explanation
Indices: 380246--380338 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
380236 GCGAAACCAA
*
380246 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
380279 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
380312 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
380339 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:380303 original size:19 final size:19
Alignment explanation
Indices: 380209--380343 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
380199 TAGTTTACTT
* *
380209 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
380229 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
380248 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
380267 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
380281 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
380300 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
380314 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
380333 TCGCAATGCGA
1 TCGCAACGCGA
380344 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:380361 original size:19 final size:18
Alignment explanation
Indices: 380339--380467 Score: 112
Period size: 19 Copynumber: 7.3 Consensus size: 18
380329 AAAATCGCAA
380339 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
380358 TGCGATCTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
380372 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
380391 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
380405 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
380424 TGCGATTTTTGTTTCGCGT
1 TGCGA-TTTTGTTTCGCGT
*
380443 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT--GTTTCGCGT
380463 TGCGA
1 TGCGA
380468 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 7, Indels: 25
0.74 0.06 0.20
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 6 0.07
19 40 0.44
20 17 0.19
ACGTcount: A:0.09, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:380381 original size:33 final size:33
Alignment explanation
Indices: 380339--380430 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
380329 AAAATCGCAA
380339 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
380372 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
380405 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
380431 TTTGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:380704 original size:92 final size:93
Alignment explanation
Indices: 380598--380969 Score: 712
Period size: 93 Copynumber: 4.0 Consensus size: 93
380588 TGGCAGCAAC
380598 CTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTAG
1 CTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
380662 CAGAATTGGCAGCAACCGAACAAATTTA
66 CAGAATTGGCAGCAACCGAACAAATTTA
380690 CTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
1 CTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
380755 CAGAATTGGCAGCAACCGAACAAATTTA
66 CAGAATTGGCAGCAACCGAACAAATTTA
*
380783 CTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATATACAGTTTAG
1 CTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
380847 CAGAATTGGCAGCAACCGAACAAATTTA
66 CAGAATTGGCAGCAACCGAACAAATTTA
380875 CTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
1 CTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
*
380940 CAGAATTGGCAGCAACCGAATAAATTTA
66 CAGAATTGGCAGCAACCGAACAAATTTA
380968 CT
1 CT
380970 AAGCAATCTA
Statistics
Matches: 275, Mismatches: 3, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 123 0.45
93 152 0.55
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
CTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAG
CAGAATTGGCAGCAACCGAACAAATTTA
Found at i:380910 original size:185 final size:185
Alignment explanation
Indices: 380598--380969 Score: 726
Period size: 185 Copynumber: 2.0 Consensus size: 185
380588 TGGCAGCAAC
380598 CTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGC
1 CTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGC
380663 AGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT
66 AGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT
380728 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTA
131 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTA
*
380783 CTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATATACAGTTTAGC
1 CTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGC
380848 AGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT
66 AGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT
*
380913 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAATTTA
131 CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTA
380968 CT
1 CT
380970 AAGCAATCTA
Statistics
Matches: 185, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 185 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
CTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACACAGTTTAGC
AGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTT
CACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTA
Found at i:382693 original size:14 final size:14
Alignment explanation
Indices: 382674--382763 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
382664 GTTGAAATGA
382674 AATCGCAACGAGAG
1 AATCGCAACGAGAG
382688 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
382705 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
382721 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
382740 AATCGCAACAAGAG
1 AATCGCAACGAGAG
382754 AATCGCAACG
1 AATCGCAACG
382764 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:382711 original size:33 final size:33
Alignment explanation
Indices: 382667--382780 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
382657 TCTTTTGGTT
382667 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
382699 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
382732 GAAATGAAAATCGCAACAAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
382765 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
382781 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
32 5 0.07
33 71 0.93
ACGTcount: A:0.46, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:382712 original size:19 final size:19
Alignment explanation
Indices: 382688--382785 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
382678 GCAACGAGAG
* *
382688 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
*
382707 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
382721 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
382740 AATCGCAA--C--AA-GAG
1 AATCGCAACGCGAAATGAA
382754 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
382773 AATCGCAATGCGA
1 AATCGCAACGCGA
382786 TTTTGGTTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
14 20 0.31
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 32 0.50
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:382816 original size:14 final size:14
Alignment explanation
Indices: 382797--382851 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
382787 TTTGGTTTCG
382797 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
382811 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
382830 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
382844 CGTTGCGA
1 CGTTGCGA
382852 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:382829 original size:33 final size:33
Alignment explanation
Indices: 382781--382851 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
382771 AAAATCGCAA
**
382781 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
382814 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
382847 TGCGA
1 TGCGA
382852 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:382859 original size:33 final size:33
Alignment explanation
Indices: 382792--382873 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
382782 GCGATTTTGG
***
382792 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
382825 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
382858 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
382874 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:382878 original size:20 final size:20
Alignment explanation
Indices: 382804--382892 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
382794 TCGCGTTGCG
382804 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
382824 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
382837 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
382857 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
382877 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
382893 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:383014 original size:32 final size:32
Alignment explanation
Indices: 382975--383043 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
382965 ACTAACTTGA
*
382975 AAATCGCAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
383007 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
383039 AAATC
1 AAATC
383044 TAAGTGAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:383017 original size:18 final size:18
Alignment explanation
Indices: 382994--383043 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
382984 CGAGAGAATA
382994 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
383012 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
383026 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
383044 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:383272 original size:22 final size:22
Alignment explanation
Indices: 383220--383274 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
383210 TGGTTGTGAG
**
383220 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
383242 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
383264 GGATTTCTTCG
1 GGATTTCTTCG
383275 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:383445 original size:20 final size:20
Alignment explanation
Indices: 383420--383612 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
383410 CTTTAAATAT
383420 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
383440 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
383462 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
383481 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
383501 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
383521 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
383541 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
383561 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
383581 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
383601 CGCGTTGCGATT
1 CGCGTTGCGATT
383613 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:383607 original size:60 final size:60
Alignment explanation
Indices: 383420--383612 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
383410 CTTTAAATAT
**
383420 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
383481 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
383541 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
383601 CGCGTTGCGATT
1 CGCGTTGCGATT
383613 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:383693 original size:20 final size:20
Alignment explanation
Indices: 383668--383719 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
383658 AAGAATCGCG
*
383668 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
383688 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
383708 TTGCGATTCTGG
1 TTGCGATTCTGG
383720 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:385577 original size:60 final size:60
Alignment explanation
Indices: 385497--385630 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
385487 GTCGAGTGAT
* * * *
385497 CATTTTGTAACTTTTAATAGTCGAGAGACTCAATAAAGCAATACTCTATAGTTGGA-GGAC
1 CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAATACCCTATAGTT-GATGGAC
* * * *
385557 CATTTTATAATTTTTAATAGTCGAGTGACTTAACAAAATAATACCCTATAGTTGATGGAC
1 CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAATACCCTATAGTTGATGGAC
385617 CATTTT-TATACTTT
1 CATTTTATA-ACTTT
385631 AACCTAAGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 4 0.06
60 59 0.94
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Consensus pattern (60 bp):
CATTTTATAACTTTTAATAGTCGAGAGACTCAACAAAACAATACCCTATAGTTGATGGAC
Found at i:389277 original size:2 final size:2
Alignment explanation
Indices: 389229--389258 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
389219 ATTTTTTTAT
389229 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
389259 AAATCTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:395262 original size:19 final size:19
Alignment explanation
Indices: 395238--395277 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
395228 TCTCGACGAT
395238 TAATAAATGATAACTATGA
1 TAATAAATGATAACTATGA
395257 TAATAAATGATAACTATGA
1 TAATAAATGATAACTATGA
395276 TA
1 TA
395278 GTATATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
TAATAAATGATAACTATGA
Found at i:395706 original size:31 final size:31
Alignment explanation
Indices: 395671--395740 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
395661 TTGTCCATCC
* **
395671 AGGTGTCTAATATTACAAATGTTACTATTTT
1 AGGTGTCTAACATTACAAACATTACTATTTT
*
395702 AGGTGTCTAACATTACAAACATTATTATTTT
1 AGGTGTCTAACATTACAAACATTACTATTTT
*
395733 AAGTGTCT
1 AGGTGTCT
395741 CGGAGTTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (31 bp):
AGGTGTCTAACATTACAAACATTACTATTTT
Found at i:398335 original size:16 final size:16
Alignment explanation
Indices: 398304--398335 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
398294 ATTGAAACTC
*
398304 GACTCGAACTCGAAAA
1 GACTCGAACTCAAAAA
398320 GACTCGAACTCAAAAA
1 GACTCGAACTCAAAAA
398336 AAAATTCAAG
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:0.47, C:0.25, G:0.16, T:0.12
Consensus pattern (16 bp):
GACTCGAACTCAAAAA
Found at i:400997 original size:34 final size:34
Alignment explanation
Indices: 400957--401025 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
400947 AGTATACATT
400957 CGATATAAGTGTTTGAAACTTTATTAGTTTCTTA
1 CGATATAAGTGTTTGAAACTTTATTAGTTTCTTA
400991 CGATATAAGTGTTTGAAACTTTATTAGTTTCTTA
1 CGATATAAGTGTTTGAAACTTTATTAGTTTCTTA
401025 C
1 C
401026 ATTTTGAGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.46
Consensus pattern (34 bp):
CGATATAAGTGTTTGAAACTTTATTAGTTTCTTA
Found at i:408023 original size:4 final size:4
Alignment explanation
Indices: 408014--408048 Score: 52
Period size: 4 Copynumber: 8.2 Consensus size: 4
408004 TCAATCATTA
408014 TATT TATT TATT TCATT ATATT TATT TATT TATT T
1 TATT TATT TATT T-ATT -TATT TATT TATT TATT T
408049 TACTTAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 22 0.76
5 6 0.21
6 1 0.03
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:408031 original size:18 final size:18
Alignment explanation
Indices: 408008--408044 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
407998 AAATAGTCAA
408008 TCATTATATTTATTTATT
1 TCATTATATTTATTTATT
408026 TCATTATATTTATTTATT
1 TCATTATATTTATTTATT
408044 T
1 T
408045 ATTTTACTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (18 bp):
TCATTATATTTATTTATT
Found at i:408037 original size:14 final size:12
Alignment explanation
Indices: 408014--408048 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 12
408004 TCAATCATTA
408014 TATTTATTTATT
1 TATTTATTTATT
408026 TCATTATATTTATT
1 T-ATT-TATTTATT
408040 TATTTATTT
1 TATTTATTT
408049 TACTTAAACA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 6 0.29
14 9 0.43
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TATTTATTTATT
Found at i:409086 original size:24 final size:26
Alignment explanation
Indices: 409042--409090 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
409032 AAATATATAA
*
409042 TTAAAGTATATTATTTTTTAAAATAT
1 TTAAAGTATATTATTTGTTAAAATAT
409068 TTAAAGTAT-TT-TTTGTTAAAATA
1 TTAAAGTATATTATTTGTTAAAATA
409091 AATATTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 2 0.09
26 9 0.41
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (26 bp):
TTAAAGTATATTATTTGTTAAAATAT
Found at i:409284 original size:28 final size:27
Alignment explanation
Indices: 409243--409304 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 27
409233 AGATGAAAAT
* *
409243 ATTAAAATAGTTTAGGTATCTATTTTG
1 ATTAAAATACTTTAAGTATCTATTTTG
*
409270 ATATAAAATACTTTAAGTATTTATTTTG
1 AT-TAAAATACTTTAAGTATCTATTTTG
409298 ATTAAAA
1 ATTAAAA
409305 AGATAACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 7 0.23
28 24 0.77
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (27 bp):
ATTAAAATACTTTAAGTATCTATTTTG
Found at i:409305 original size:28 final size:28
Alignment explanation
Indices: 409263--409352 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 28
409253 TTTAGGTATC
*
409263 TATTTTGA-TATAAAATACTTTAAGTATT
1 TATTTTGATTA-AAAATACTTTAAATATT
409291 TATTTTGATTAAAAAGATAACTTTAAATATT
1 TATTTTGATT-AAAA-AT-ACTTTAAATATT
*
409322 TAATTTT-ATAAAAAAATACTTTAAATATT
1 T-ATTTTGAT-TAAAAATACTTTAAATATT
409351 TA
1 TA
409353 AATAAAATAT
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
28 9 0.17
29 17 0.31
30 5 0.09
31 18 0.33
32 5 0.09
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (28 bp):
TATTTTGATTAAAAATACTTTAAATATT
Found at i:409344 original size:29 final size:31
Alignment explanation
Indices: 409274--409353 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 31
409264 ATTTTGATAT
*
409274 AAAATACTTTAAGTATTT-ATTTTGATTAAA
1 AAAATACTTTAAATATTTAATTTTGATTAAA
*
409304 AAGATAACTTTAAATATTTAATTTT-A-TAAA
1 AAAAT-ACTTTAAATATTTAATTTTGATTAAA
409334 AAAATACTTTAAATATTTAA
1 AAAATACTTTAAATATTTAA
409354 ATAAAATATA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
29 15 0.33
30 12 0.27
31 13 0.29
32 5 0.11
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (31 bp):
AAAATACTTTAAATATTTAATTTTGATTAAA
Found at i:425151 original size:23 final size:24
Alignment explanation
Indices: 425116--425161 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
425106 ATATTTTTTT
*
425116 AATGTATAGATGAATATATTTACG
1 AATGTATAAATGAATATATTTACG
*
425140 AATG-ATAAATGAATATGTTTAC
1 AATGTATAAATGAATATATTTAC
425162 AAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.37
Consensus pattern (24 bp):
AATGTATAAATGAATATATTTACG
Found at i:425394 original size:2 final size:2
Alignment explanation
Indices: 425387--425424 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
425377 CTGTCCCCAG
425387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
425425 TATCAATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:426979 original size:28 final size:28
Alignment explanation
Indices: 426943--427006 Score: 119
Period size: 28 Copynumber: 2.3 Consensus size: 28
426933 GTGCCTTGGT
*
426943 ATTTTTCCATTACAATGGCATTTTCTTA
1 ATTTATCCATTACAATGGCATTTTCTTA
426971 ATTTATCCATTACAATGGCATTTTCTTA
1 ATTTATCCATTACAATGGCATTTTCTTA
426999 ATTTATCC
1 ATTTATCC
427007 CATGTTGTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.19, G:0.06, T:0.48
Consensus pattern (28 bp):
ATTTATCCATTACAATGGCATTTTCTTA
Found at i:427613 original size:15 final size:15
Alignment explanation
Indices: 427579--427630 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
427569 AAGTCAACGG
* *
427579 GTTGAATCAGA-CGG
1 GTTGACTCAGACCGA
**
427593 GTTGACTCAGATTGA
1 GTTGACTCAGACCGA
427608 GTTGACTCAGACCGA
1 GTTGACTCAGACCGA
427623 GTTGACTC
1 GTTGACTC
427631 GATGATTGGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
14 10 0.31
15 22 0.69
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (15 bp):
GTTGACTCAGACCGA
Found at i:429850 original size:21 final size:21
Alignment explanation
Indices: 429826--429874 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
429816 GACTTTATCG
429826 TTTCCGATGCCGGAAACAGCC
1 TTTCCGATGCCGGAAACAGCC
429847 TTTCCGATGCCGGAAACAGCC
1 TTTCCGATGCCGGAAACAGCC
429868 TTTCCGA
1 TTTCCGA
429875 GCACGTTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.33, G:0.22, T:0.22
Consensus pattern (21 bp):
TTTCCGATGCCGGAAACAGCC
Found at i:435699 original size:2 final size:2
Alignment explanation
Indices: 435692--435726 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
435682 CTTTTTCATT
435692 TA TA TA 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 TA TA TA T
435727 TTCATTCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:435940 original size:17 final size:17
Alignment explanation
Indices: 435913--435945 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
435903 TATTTTTTCC
435913 TTTTGATTTTTTGATTTA
1 TTTTGATTTTTT-ATTTA
435931 TTTT-ATTTTTTATTT
1 TTTTGATTTTTTATTT
435946 TTATTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (17 bp):
TTTTGATTTTTTATTTA
Found at i:438870 original size:19 final size:19
Alignment explanation
Indices: 438842--438886 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
438832 AAAAAAATGA
438842 TATAATTTAAATAATTATTT
1 TATAA-TTAAATAATTATTT
* *
438862 TATAATTAATTCATTATTT
1 TATAATTAAATAATTATTT
*
438881 AATAAT
1 TATAAT
438887 AATTTAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TATAATTAAATAATTATTT
Found at i:448630 original size:19 final size:20
Alignment explanation
Indices: 448599--448658 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
448589 CAAGACCGTG
*
448599 TCCCAAAAGTTTCGATACTT
1 TCCCTAAAGTTTCGATACTT
* *
448619 T-TC-AAGAGTTTCGAAACTT
1 TCCCTAA-AGTTTCGATACTT
448638 TCCCTAAAGTTTCGATACTT
1 TCCCTAAAGTTTCGATACTT
448658 T
1 T
448659 GGCTCAAACG
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.42
20 15 0.45
21 2 0.06
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (20 bp):
TCCCTAAAGTTTCGATACTT
Found at i:449584 original size:30 final size:30
Alignment explanation
Indices: 449548--449608 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
449538 TCAAAATAAT
449548 TTTTAGAGCTATTTTGACCGGTTTGACCGG
1 TTTTAGAGCTATTTTGACCGGTTTGACCGG
449578 TTTTAGAGCTATTTTGACCGGTTTGACCGG
1 TTTTAGAGCTATTTTGACCGGTTTGACCGG
449608 T
1 T
449609 CACAACCCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.41
Consensus pattern (30 bp):
TTTTAGAGCTATTTTGACCGGTTTGACCGG
Found at i:449636 original size:18 final size:18
Alignment explanation
Indices: 449613--449655 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
449603 ACCGGTCACA
*
449613 ACCCGATCCGACCCGATG
1 ACCCGACCCGACCCGATG
*
449631 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGATG
449649 ACCCGAC
1 ACCCGAC
449656 TCGAACCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.49, G:0.21, T:0.09
Consensus pattern (18 bp):
ACCCGACCCGACCCGATG
Found at i:452185 original size:24 final size:24
Alignment explanation
Indices: 452158--452269 Score: 138
Period size: 24 Copynumber: 4.7 Consensus size: 24
452148 ATTTGAATTA
*
452158 TGATCTGATACTTGACAAGGATTC
1 TGATCTGATACTTGACATGGATTC
*
452182 TGATATGATA-TCTGACATGGATTC
1 TGATCTGATACT-TGACATGGATTC
*
452206 TGATCTGATACTTGACTTGGATTC
1 TGATCTGATACTTGACATGGATTC
*
452230 TGATCTGATACTTGACCT-GATTTC
1 TGATCTGATACTTGACATGGA-TTC
* *
452254 TGATATGATGCTTGAC
1 TGATCTGATACTTGAC
452270 CTGATTTATG
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
23 3 0.04
24 74 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATCTGATACTTGACATGGATTC
Found at i:452292 original size:24 final size:24
Alignment explanation
Indices: 452230--452279 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
452220 ACTTGGATTC
* * *
452230 TGATCTGATACTTGACCTGATTTC
1 TGATATGATGCTTGACCTGATTTA
452254 TGATATGATGCTTGACCTGATTTA
1 TGATATGATGCTTGACCTGATTTA
452278 TG
1 TG
452280 TTTTGATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (24 bp):
TGATATGATGCTTGACCTGATTTA
Found at i:452453 original size:43 final size:43
Alignment explanation
Indices: 452387--452481 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
452377 GGGCCTTACT
452387 TGGTGTGTTGGTGGGTGTATGGTTCTGGGG-AACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTC-GGGGAAACCTACACATTA
*
452430 TGGTATGTTGGTGGGTGTATGGTTCGGGGAAACCTACACATTA
1 TGGTGTGTTGGTGGGTGTATGGTTCGGGGAAACCTACACATTA
452473 TGGTGTGTT
1 TGGTGTGTT
452482 CGGTTGGAGG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
42 4 0.08
43 45 0.92
ACGTcount: A:0.17, C:0.11, G:0.37, T:0.36
Consensus pattern (43 bp):
TGGTGTGTTGGTGGGTGTATGGTTCGGGGAAACCTACACATTA
Done.