Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002177.1 Hibiscus syriacus cultivar Beakdansim tig00004436_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: 192623
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:6564 original size:16 final size:17
Alignment explanation
Indices: 6539--6572 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
6529 TTTTGAGTTT
*
6539 TTTTTAGTTTTTCAAAA
1 TTTTTAGTTTTTAAAAA
6556 TTTTT-GTTTTTAAAAA
1 TTTTTAGTTTTTAAAAA
6572 T
1 T
6573 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTTAGTTTTTAAAAA
Found at i:16869 original size:2 final size:2
Alignment explanation
Indices: 16862--16891 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
16852 ATTATTAATA
16862 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
16892 TTACTCTCGA
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):
AT
Found at i:20215 original size:74 final size:72
Alignment explanation
Indices: 19900--20292 Score: 326
Period size: 74 Copynumber: 5.4 Consensus size: 72
19890 CCTATATAAA
*
19900 TATAATTTATAAT-TTTTTATATATTTTTTATTTTTGTTAATGAGAA-AAATAATTCTTA-ATTT
1 TATAATTTATAATATTTTTATATA-TTTTTA-TTTT-TTAATG-GAAGAAACAATTCTTAGA-TT
19962 TTATTTATTAA-
61 TTATTTATTAAC
* * * * * *
19973 AATTAATTTACAACTTTTTTTATATATTTTAAAATTTTGTTAATAGAAGAAATAA-T-TT-G---
1 TA-TAATTTATAA-TATTTTTATATATTTT--TATTTT-TTAATGGAAGAAACAATTCTTAGATT
20032 -TATTTATTAAC
61 TTATTTATTAAC
* * * * * ** **
20043 TATATTTTATAATATTTATATATATTTTTAATTTTTAATGGAATAAAGAATAATTATTTTTTATT
1 TATAATTTATAATATTTTTATATATTTTTATTTTTTAATGGAAGAAACAATTCTTAGATTTTATT
*
20108 TACTAAC
66 TATTAAC
*
20115 TATAATTTAT-ATATTTTTATACATTTTTAGTTTTCATTAATGGAAGAAACAATTCTTA-ATTTT
1 TATAATTTATAATATTTTTATATATTTTTA-TTTT--TTAATGGAAGAAACAATTCTTAGATTTT
20178 ATTTATTAAC
63 ATTTATTAAC
* * * *
20188 TATAATTTATAATATTTTTATATATTTTTAATTTTTGTTAAAGAAAGAAATAATTCTTAGTTTTT
1 TATAATTTATAATATTTTTATATATTTTT-A-TTTT-TTAATGGAAGAAACAATTCTTAGATTTT
20253 ATTTATTAAC
63 ATTTATTAAC
* * *
20263 TATTATTTACAACATTTTTATATATTTTTA
1 TATAATTTATAATATTTTTATATATTTTTA
20293 ATATAATAAA
Statistics
Matches: 262, Mismatches: 37, Indels: 41
0.77 0.11 0.12
Matches are distributed among these distances:
65 13 0.05
66 4 0.02
67 2 0.01
68 14 0.05
69 18 0.07
70 1 0.00
71 17 0.06
72 22 0.08
73 24 0.09
74 66 0.25
75 54 0.21
76 26 0.10
77 1 0.00
ACGTcount: A:0.37, C:0.04, G:0.05, T:0.54
Consensus pattern (72 bp):
TATAATTTATAATATTTTTATATATTTTTATTTTTTAATGGAAGAAACAATTCTTAGATTTTATT
TATTAAC
Found at i:20219 original size:64 final size:64
Alignment explanation
Indices: 20151--20335 Score: 172
Period size: 75 Copynumber: 2.7 Consensus size: 64
20141 TTAGTTTTCA
* * *
20151 TTAATGGAAGAAACAATTCTTAATTTTATTTATTAACTATAATTTATAATATTTTTATATATTT
1 TTAATGGAAGAAATAATTCTTAATTTTATTTATTAACTATAATTTACAACATTTTTATATATTT
* *
20215 TTAATTTTTGTTAAAGAAAGAAATAATTCTTAGTTTTTATTTATTAACTATTATTTACAACATTT
1 TTAA----TG-----G-AAGAAATAATTCTTA-ATTTTATTTATTAACTATAATTTACAACATTT
20280 TTATATATTT
55 TTATATATTT
** * * * *
20290 TTAATATAATAAATATTTCTTAAATTTATTTATTAATTATAATTTA
1 TTAATGGAAGAAATAATTCTTAATTTTATTTATTAACTATAATTTA
20336 ATAGTTATAC
Statistics
Matches: 97, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
64 24 0.25
65 13 0.13
68 2 0.02
71 1 0.01
73 1 0.01
74 14 0.14
75 42 0.43
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (64 bp):
TTAATGGAAGAAATAATTCTTAATTTTATTTATTAACTATAATTTACAACATTTTTATATATTT
Found at i:20240 original size:145 final size:148
Alignment explanation
Indices: 20025--20292 Score: 373
Period size: 145 Copynumber: 1.8 Consensus size: 148
20015 ATAGAAGAAA
* * *
20025 TAATTTGTATTTATTAACTATATTTTATAATATTTATATATATTTTTAATTTTTAATGGAATAAA
1 TAATTTGTATTTATTAACTATAATTTATAATATTTATATATATTTTTAATTTTTAATGAAAGAAA
* * *
20090 GAATAA-TTATTTTTTATTTACTAACTATAATTTA-TATATTTTTATACATTTTTAGTTTTCATT
66 GAATAATTTAGTTTTTATTTACTAACTATAATTTACAACATTTTTATACATTTTTAGTTTTCATT
20153 AATGGAAGAAACAATTCT
131 AATGGAAGAAACAATTCT
* * *
20171 TAATTT-TATTTATTAACTATAATTTATAATATTTTTATATATTTTTAATTTTT-GTTAAAGAAA
1 TAATTTGTATTTATTAACTATAATTTATAATATTTATATATATTTTTAATTTTTAATGAAAGAAA
* * *
20234 GAAATAATTCTTAGTTTTTATTTATTAACTATTATTTACAACATTTTTATATATTTTTA
66 G-AATAA-T-TTAGTTTTTATTTACTAACTATAATTTACAACATTTTTATACATTTTTA
20293 ATATAATAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
144 7 0.07
145 50 0.48
146 6 0.06
148 25 0.24
149 17 0.16
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (148 bp):
TAATTTGTATTTATTAACTATAATTTATAATATTTATATATATTTTTAATTTTTAATGAAAGAAA
GAATAATTTAGTTTTTATTTACTAACTATAATTTACAACATTTTTATACATTTTTAGTTTTCATT
AATGGAAGAAACAATTCT
Found at i:20412 original size:19 final size:20
Alignment explanation
Indices: 20388--20426 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
20378 TTTTTCCTTG
20388 AAAAAAATT-TAAAATATAT
1 AAAAAAATTATAAAATATAT
*
20407 AAAAAAATTATAAATTATAT
1 AAAAAAATTATAAAATATAT
20427 TCAAATGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATTATAAAATATAT
Found at i:21343 original size:22 final size:21
Alignment explanation
Indices: 21314--21355 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
21304 TGATCAAATG
21314 ATATTATTTTAGT-ATTTTTAT
1 ATATTATTTT-GTGATTTTTAT
21335 ATATATATTTTGTGATTTTTA
1 ATAT-TATTTTGTGATTTTTA
21356 GGTAGAATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
ATATTATTTTGTGATTTTTAT
Found at i:30272 original size:12 final size:12
Alignment explanation
Indices: 30244--30280 Score: 65
Period size: 12 Copynumber: 3.0 Consensus size: 12
30234 TTTGGTAATC
30244 CCCGCCCCGATTA
1 CCCGCCCCGA-TA
30257 CCCGCCCCGATA
1 CCCGCCCCGATA
30269 CCCGCCCCGATA
1 CCCGCCCCGATA
30281 AATATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 14 0.58
13 10 0.42
ACGTcount: A:0.16, C:0.57, G:0.16, T:0.11
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:30354 original size:23 final size:23
Alignment explanation
Indices: 30324--30371 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
30314 ATATTAATAA
30324 ATTTAATTTAAATAAAAATATAT
1 ATTTAATTTAAATAAAAATATAT
* *
30347 ATTTAATTTAAATATATATATAT
1 ATTTAATTTAAATAAAAATATAT
30370 AT
1 AT
30372 ACCCGGCCCG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTAATTTAAATAAAAATATAT
Found at i:30414 original size:12 final size:12
Alignment explanation
Indices: 30370--30423 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
30360 ATATATATAT
* *
30370 ATACCCGGCCCG
1 ATACCCGACCCA
* *
30382 ATTCCCGGCCCA
1 ATACCCGACCCA
30394 ATA-CCGACCCA
1 ATACCCGACCCA
*
30405 ATACCCGACCTA
1 ATACCCGACCCA
30417 ATACCCG
1 ATACCCG
30424 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
11 10 0.28
12 26 0.72
ACGTcount: A:0.26, C:0.46, G:0.15, T:0.13
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:31660 original size:60 final size:61
Alignment explanation
Indices: 31545--31723 Score: 152
Period size: 60 Copynumber: 3.0 Consensus size: 61
31535 TATAATCTGA
* * *
31545 GATGAAATTGAAATGTTCAAAAATTTTGGGGACCAATTTAGAATGAAGGTCATAGTTTGAT
1 GATGAAATTAAAATATTCAAAAATTTTGAGGACCAATTTAGAATGAAGGTCATAGTTTGAT
* * * * *
31606 GATGAAATTAAAATATTCTAAAGTTTT-AGGACTAATTTAGAATGATA-GTTATAGTTT-AGG
1 GATGAAATTAAAATATTCAAAAATTTTGAGGACCAATTTAGAATGA-AGGTCATAGTTTGA-T
* * * * * * * * *
31666 GATGAAAGTGATATATT-AAAAGTTTAG-GGAACAATTTAAAATGAAGATCATACTTTGA
1 GATGAAATTAAAATATTCAAAAATTTTGAGGACCAATTTAGAATGAAGGTCATAGTTTGA
31724 GGACATGTGT
Statistics
Matches: 94, Mismatches: 19, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
58 1 0.01
59 29 0.31
60 40 0.43
61 24 0.26
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (61 bp):
GATGAAATTAAAATATTCAAAAATTTTGAGGACCAATTTAGAATGAAGGTCATAGTTTGAT
Found at i:34063 original size:21 final size:22
Alignment explanation
Indices: 34037--34086 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 22
34027 AATGAAAGTG
34037 TTTTTCTAAGTTAAAGATTATT
1 TTTTTCTAAGTTAAAGATTATT
*
34059 TTTTCTCATAAGTTAGAGATTATT
1 TTTT-TC-TAAGTTAAAGATTATT
34083 TTTT
1 TTTT
34087 CTCATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 4 0.16
23 2 0.08
24 19 0.76
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTTTCTAAGTTAAAGATTATT
Found at i:34073 original size:24 final size:24
Alignment explanation
Indices: 34043--34093 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
34033 AGTGTTTTTC
34043 TAAGTTAAAGATTATTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTCTCA
*
34067 TAAGTTAGAGATTATTTTTTCTCA
1 TAAGTTAAAGATTATTTTTTCTCA
34091 TAA
1 TAA
34094 TAAATTAAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (24 bp):
TAAGTTAAAGATTATTTTTTCTCA
Found at i:35105 original size:40 final size:40
Alignment explanation
Indices: 35052--35166 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 40
35042 TGGTTCAAAA
* * *
35052 TTAATATTTTATTAAAATATATACTCAAATATCAAGATTT
1 TTAATACTATATTAAAATATATACTCAAATATCAAAATTT
* *
35092 TTAATGCTATATTAAAATATATACTCAAATATTAAAATTT
1 TTAATACTATATTAAAATATATACTCAAATATCAAAATTT
* * * *
35132 TTAATACTATATCAAAATCTGTTCTCAAATATCAA
1 TTAATACTATATTAAAATATATACTCAAATATCAA
35167 TGTATATCAT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (40 bp):
TTAATACTATATTAAAATATATACTCAAATATCAAAATTT
Found at i:35125 original size:20 final size:20
Alignment explanation
Indices: 35061--35129 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
35051 ATTAATATTT
35061 TATTAAAATATATACTCAAA
1 TATTAAAATATATACTCAAA
* * * * * *
35081 TATCAAGATTTTTAATGC-TA
1 TATTAAAATATATACT-CAAA
35101 TATTAAAATATATACTCAAA
1 TATTAAAATATATACTCAAA
35121 TATTAAAAT
1 TATTAAAAT
35130 TTTTAATACT
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (20 bp):
TATTAAAATATATACTCAAA
Found at i:35143 original size:20 final size:19
Alignment explanation
Indices: 35088--35149 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
35078 AAATATCAAG
35088 ATTTTTAATGCTATATTAAA
1 ATTTTTAAT-CTATATTAAA
* * * *
35108 ATATATACTCAAATATTAAA
1 ATTTTTAATC-TATATTAAA
*
35128 ATTTTTAATACTATATCAAA
1 ATTTTTAAT-CTATATTAAA
35148 AT
1 AT
35150 CTGTTCTCAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTTTTAATCTATATTAAA
Found at i:40413 original size:2 final size:2
Alignment explanation
Indices: 40406--40434 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
40396 ATTTTTAAGC
40406 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 A
40435 ATAACATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43392 original size:2 final size:2
Alignment explanation
Indices: 43385--43433 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
43375 GAATCTCTTT
43385 TA TA TA TA TA TA 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 TA TA TA TA TA TA
43427 TA TA TA T
1 TA TA TA T
43434 TAAAAAAATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52223 original size:3 final size:3
Alignment explanation
Indices: 52217--52243 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
52207 ACAGCAGCAG
52217 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
52244 GGTTTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:55185 original size:42 final size:42
Alignment explanation
Indices: 55126--55210 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
55116 ATAGATGGTG
55126 ATCCATGTTGAAATATCTTTTTTCACTAATATTTCAAAATTA
1 ATCCATGTTGAAATATCTTTTTTCACTAATATTTCAAAATTA
55168 ATCCATGTTGAAATATCTTTTTTCACTAATATTTCAAAATTA
1 ATCCATGTTGAAATATCTTTTTTCACTAATATTTCAAAATTA
55210 A
1 A
55211 CATTTTAATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (42 bp):
ATCCATGTTGAAATATCTTTTTTCACTAATATTTCAAAATTA
Found at i:61834 original size:15 final size:15
Alignment explanation
Indices: 61814--61843 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
61804 TATCACAATC
61814 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
61829 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
61844 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:72930 original size:60 final size:60
Alignment explanation
Indices: 72864--73030 Score: 167
Period size: 60 Copynumber: 2.8 Consensus size: 60
72854 AATTGGAATA
* * * * *
72864 TTAAAAAGTTTGAGTACTAATTTGGAAAGAGTGTAATATTTTAGGGATGAAATTAAAATT
1 TTAAAAAGTTTAAATACTAATTTAGAAAGAGAGTAATAGTTTAGGGATGAAATTAAAATT
* * * * **
72924 TTAAAAAGTTTAAATACTAATTTAGAATGAGAGTCATAGTTTGGGGATGAAATTAGAACA
1 TTAAAAAGTTTAAATACTAATTTAGAAAGAGAGTAATAGTTTAGGGATGAAATTAAAATT
* * * *
72984 TTCAAAAGTTT-AATGACCAATTTA-AAATGAGGGTTATAGTTTAGGGA
1 TTAAAAAGTTTAAAT-ACTAATTTAGAAA-GAGAGTAATAGTTTAGGGA
73031 CATATGATGC
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
59 5 0.06
60 83 0.94
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.34
Consensus pattern (60 bp):
TTAAAAAGTTTAAATACTAATTTAGAAAGAGAGTAATAGTTTAGGGATGAAATTAAAATT
Found at i:81612 original size:29 final size:29
Alignment explanation
Indices: 81570--81628 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
81560 ATTTTCACCT
*
81570 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
81599 AACTAAATTGATGTAAACAATGACATCAA
1 AACTAAATTGATGTAAACAATGACATCAA
81628 A
1 A
81629 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAACAATGACATCAA
Found at i:90979 original size:17 final size:17
Alignment explanation
Indices: 90957--90990 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
90947 AGTTATTAAT
*
90957 ATTTATACTTTTTATTA
1 ATTTATACTTTATATTA
*
90974 ATTTATTCTTTATATTA
1 ATTTATACTTTATATTA
90991 TTAGTTAAAT
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:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTATACTTTATATTA
Found at i:90998 original size:24 final size:24
Alignment explanation
Indices: 90951--91007 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
90941 AAATCTAGTT
* *
90951 ATTAATATTTATACTTTTTATTAA
1 ATTAATCTTTATACTTATTATTAA
* *
90975 TTTATTCTTTATA-TTATTAGTTAA
1 ATTAATCTTTATACTTATTA-TTAA
90999 ATTAATCTT
1 ATTAATCTT
91008 AAACCTTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTAATCTTTATACTTATTATTAA
Found at i:92410 original size:37 final size:38
Alignment explanation
Indices: 92333--92410 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
92323 ACAAGTTGAA
* *
92333 AAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
* *
92371 AAAT-TTTATATAATTTTTTTTACAAAATTGAAAAT-AT
1 AAATATTTATAT-ATTTTCTTTAAAAAATTGAAAATCAT
92408 AAA
1 AAA
92411 AAGGTTTAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 12 0.34
38 23 0.66
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.47
Consensus pattern (38 bp):
AAATATTTATATATTTTCTTTAAAAAATTGAAAATCAT
Found at i:107000 original size:17 final size:18
Alignment explanation
Indices: 106978--107011 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
106968 GATATAATTT
106978 TCATATTA-ATTTTAATA
1 TCATATTATATTTTAATA
106995 TCATATTATATTTTAAT
1 TCATATTATATTTTAAT
107012 TATTTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TCATATTATATTTTAATA
Found at i:109018 original size:2 final size:2
Alignment explanation
Indices: 109011--109072 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
109001 CTCTTTTTAA
109011 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
109053 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
109073 CGGTATTCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:116320 original size:18 final size:18
Alignment explanation
Indices: 116299--116394 Score: 58
Period size: 18 Copynumber: 5.3 Consensus size: 18
116289 TCTTCGATCA
116299 GGATGATGAGCTTGTATC
1 GGATGATGAGCTTGTATC
** *
116317 GGATGA--ATTTTATGATC
1 GGATGATGAGCTTGT-ATC
*
116334 AGGATGATGTGCTTGTATC
1 -GGATGATGAGCTTGTATC
*
116353 GGATGA--A-TTTGATAATC
1 GGATGATGAGCTTG-T-ATC
*
116370 AGGATGATGTGCTTGTATC
1 -GGATGATGAGCTTGTATC
116389 GGATGA
1 GGATGA
116395 ATTTGATGAT
Statistics
Matches: 57, Mismatches: 11, Indels: 20
0.65 0.12 0.23
Matches are distributed among these distances:
15 3 0.05
16 5 0.09
17 6 0.11
18 30 0.53
19 6 0.11
20 4 0.07
21 3 0.05
ACGTcount: A:0.26, C:0.08, G:0.30, T:0.35
Consensus pattern (18 bp):
GGATGATGAGCTTGTATC
Found at i:116322 original size:36 final size:35
Alignment explanation
Indices: 116294--116493 Score: 276
Period size: 36 Copynumber: 5.6 Consensus size: 35
116284 TGAAGTCTTC
116294 GATCAGGATGATGAGCTTGTATCGGATGAATTTTAT
1 GATCAGGATGATGAGCTTGTATCGGATGAA-TTTAT
*
116330 GATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
1 GATCAGGATGATGAGCTTGTATCGGATGAATTT-AT
* *
116366 AATCAGGATGATGTGCTTGTATCGGATGAATTTGAT
1 GATCAGGATGATGAGCTTGTATCGGATGAATTT-AT
*
116402 GATCAGGATGATGCA-CTTGTATCGGAAGAATTTGAT
1 GATCAGGATGATG-AGCTTGTATCGGATGAATTT-AT
* *
116438 GATCAGGATGATGTGCTTGTATTGGATGAATTTGAT
1 GATCAGGATGATGAGCTTGTATCGGATGAATTT-AT
*
116474 GATCAGGATGATGAGTTTGT
1 GATCAGGATGATGAGCTTGT
116494 TGAAGTAGAA
Statistics
Matches: 151, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
35 3 0.02
36 148 0.98
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.35
Consensus pattern (35 bp):
GATCAGGATGATGAGCTTGTATCGGATGAATTTAT
Found at i:116404 original size:72 final size:72
Alignment explanation
Indices: 116295--116486 Score: 321
Period size: 72 Copynumber: 2.7 Consensus size: 72
116285 GAAGTCTTCG
* * ** *
116295 ATCAGGATGATGAGCTTGTATCGGATGAATTTTATGATCAGGATGATGTGCTTGTATCGGATGAA
1 ATCAGGATGATGTGCTTGTATCGGATGAATTTGATGATCAGGATGATGCACTTGTATCGGAAGAA
116360 TTTGATA
66 TTTGATA
116367 ATCAGGATGATGTGCTTGTATCGGATGAATTTGATGATCAGGATGATGCACTTGTATCGGAAGAA
1 ATCAGGATGATGTGCTTGTATCGGATGAATTTGATGATCAGGATGATGCACTTGTATCGGAAGAA
*
116432 TTTGATG
66 TTTGATA
*
116439 ATCAGGATGATGTGCTTGTATTGGATGAATTTGATGATCAGGATGATG
1 ATCAGGATGATGTGCTTGTATCGGATGAATTTGATGATCAGGATGATG
116487 AGTTTGTTGA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 113 1.00
ACGTcount: A:0.28, C:0.08, G:0.29, T:0.35
Consensus pattern (72 bp):
ATCAGGATGATGTGCTTGTATCGGATGAATTTGATGATCAGGATGATGCACTTGTATCGGAAGAA
TTTGATA
Found at i:119632 original size:31 final size:31
Alignment explanation
Indices: 119594--119749 Score: 260
Period size: 31 Copynumber: 5.0 Consensus size: 31
119584 CCCGAAGGAC
* * *
119594 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
119625 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
119656 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
119687 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
119718 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
119749 C
1 C
119750 CCTCGACCCT
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 118 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:120706 original size:21 final size:21
Alignment explanation
Indices: 120682--120726 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
120672 TCTTGTTCGT
* *
120682 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
120703 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
120724 TTG
1 TTG
120727 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:123927 original size:31 final size:31
Alignment explanation
Indices: 123887--124013 Score: 211
Period size: 31 Copynumber: 4.1 Consensus size: 31
123877 GTCCCGAAGG
* *
123887 AACAGTCCATA-GATTCCGAAGAACCTAGGTA
1 AACAGTCCATATG-TCCCGAAGAACATAGGTA
*
123918 ATCAGTCCATATGTCCCGAAGAACATAGGTA
1 AACAGTCCATATGTCCCGAAGAACATAGGTA
123949 AACAGTCCATATGTCCCGAAGAACATAGGTA
1 AACAGTCCATATGTCCCGAAGAACATAGGTA
123980 AACAGTCCATATGTCCCGAAGAACATAGGTA
1 AACAGTCCATATGTCCCGAAGAACATAGGTA
124011 AAC
1 AAC
124014 CCTCGACCCT
Statistics
Matches: 91, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 90 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
AACAGTCCATATGTCCCGAAGAACATAGGTA
Found at i:124970 original size:21 final size:21
Alignment explanation
Indices: 124946--124990 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
124936 TCTTGTTCGT
* *
124946 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
124967 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
124988 TTG
1 TTG
124991 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:129091 original size:20 final size:19
Alignment explanation
Indices: 129066--129104 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
129056 CTATATATAT
129066 ATATATATATATATGATCTC
1 ATATATATATATA-GATCTC
*
129086 ATATATCTATATAGATCTC
1 ATATATATATATAGATCTC
129105 GTCCATAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.44
Consensus pattern (19 bp):
ATATATATATATAGATCTC
Found at i:133851 original size:30 final size:29
Alignment explanation
Indices: 133817--133892 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
133807 AAATTTGATA
*
133817 TTAAATTTTATATAAAATGTCATTTT-ACCT
1 TTAAATTTTATATAAAATAT-ATTTTCA-CT
* *
133847 TTAAATTTTAGATAAGAATATATTTTCATT
1 TTAAATTTTATATAA-AATATATTTTCACT
133877 TTAAATTTTATATAAA
1 TTAAATTTTATATAAA
133893 TCTTCAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 34 0.85
31 5 0.12
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (29 bp):
TTAAATTTTATATAAAATATATTTTCACT
Found at i:136376 original size:17 final size:17
Alignment explanation
Indices: 136336--136390 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
136326 TTATGTGATT
*
136336 AAAAATAATTATATAGATA
1 AAAAATAA-TATA-ATATA
136355 TAAAAATAATATAATATA
1 -AAAAATAATATAATATA
136373 AAAAATCAATA-AATATA
1 AAAAAT-AATATAATATA
136390 A
1 A
136391 TTAGACAGGA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 13 0.39
18 8 0.24
19 4 0.12
20 8 0.24
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAAATAATATAATATA
Found at i:137595 original size:27 final size:27
Alignment explanation
Indices: 137557--137610 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
137547 AACCATTATA
137557 TTATATAATAATATTT-TTTATACTTTT
1 TTATATAATAATATTTGTTTA-ACTTTT
137584 TTATATAATAATATTTGTTTAACTTTT
1 TTATATAATAATATTTGTTTAACTTTT
137611 CGGTATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (27 bp):
TTATATAATAATATTTGTTTAACTTTT
Found at i:137617 original size:27 final size:27
Alignment explanation
Indices: 137559--137618 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 27
137549 CCATTATATT
**
137559 ATATAATAATATTTTTTATACTTTTTT
1 ATATAATAATATTTTTTATACTTTTCG
137586 ATATAATAATATTTGTTTA-ACTTTTCG
1 ATATAATAATATTT-TTTATACTTTTCG
*
137613 GTATAA
1 ATATAA
137619 AAAAAATTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (27 bp):
ATATAATAATATTTTTTATACTTTTCG
Found at i:138230 original size:23 final size:23
Alignment explanation
Indices: 138197--138247 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
138187 CGTACGACCG
*
138197 GTTTTTTTATGAT-TTTATAGA-AT
1 GTTTTTATATG-TCTTTAT-GACAT
138220 GTTTTTATATGTCTTTATGACAT
1 GTTTTTATATGTCTTTATGACAT
138243 GTTTT
1 GTTTT
138248 ACTTTGTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.22, C:0.04, G:0.14, T:0.61
Consensus pattern (23 bp):
GTTTTTATATGTCTTTATGACAT
Found at i:141795 original size:16 final size:16
Alignment explanation
Indices: 141774--141812 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
141764 AGGACTCCAA
*
141774 CGTTTATGTTTGTGTT
1 CGTTTATGTTCGTGTT
141790 CGTTTATGTTCGTGTT
1 CGTTTATGTTCGTGTT
141806 CGTTTAT
1 CGTTTAT
141813 TTATTAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.08, C:0.10, G:0.23, T:0.59
Consensus pattern (16 bp):
CGTTTATGTTCGTGTT
Found at i:143231 original size:2 final size:2
Alignment explanation
Indices: 143226--143255 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
143216 AAAAGTAGCA
143226 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
143256 TAAAAAAACA
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):
AT
Found at i:146816 original size:14 final size:14
Alignment explanation
Indices: 146797--146826 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
146787 TTTAGATTTT
*
146797 TTAAAATTACATTA
1 TTAAAAATACATTA
146811 TTAAAAATACATTA
1 TTAAAAATACATTA
146825 TT
1 TT
146827 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:148859 original size:46 final size:44
Alignment explanation
Indices: 148775--148874 Score: 116
Period size: 47 Copynumber: 2.2 Consensus size: 44
148765 AGCTTGAATC
148775 GAGTTTGAGTTTTGAGCTTCAGTCGAGTTTTTAAA-TTTTTTTT
1 GAGTTTGAGTTTTGAGCTTCAGTCGAGTTTTTAAATTTTTTTTT
*
148818 GAGTTTGAGCTTTTTCGAG-TTCGAGTCTAG-TTTTAACATTTTTTTTT
1 GAGTTTGAG--TTTT-GAGCTTC-AGTCGAGTTTTTAA-ATTTTTTTTT
*
148865 GAATTTGAGT
1 GAGTTTGAGT
148875 CGAGCTTAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
43 9 0.18
45 14 0.29
46 10 0.20
47 16 0.33
ACGTcount: A:0.19, C:0.08, G:0.21, T:0.52
Consensus pattern (44 bp):
GAGTTTGAGTTTTGAGCTTCAGTCGAGTTTTTAAATTTTTTTTT
Found at i:152003 original size:14 final size:14
Alignment explanation
Indices: 151984--152025 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
151974 GTGGCACCCA
151984 TTTTATTTTCTCTT
1 TTTTATTTTCTCTT
*
151998 TTTTA-TTTCTTTT
1 TTTTATTTTCTCTT
*
152011 TTTTCATTTTATCTT
1 TTTT-ATTTTCTCTT
152026 AATCCTCCAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.48
14 6 0.26
15 6 0.26
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTATTTTCTCTT
Found at i:165086 original size:2 final size:2
Alignment explanation
Indices: 165079--165105 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
165069 TTCAGCATTG
165079 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
165106 CAATTAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:170771 original size:75 final size:75
Alignment explanation
Indices: 170678--170828 Score: 284
Period size: 75 Copynumber: 2.0 Consensus size: 75
170668 CAGGTGCAGA
*
170678 TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCGAGAAGATGTGGCGT
1 TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
170743 GAGGATTGAG
66 GAGGATTGAG
*
170753 TCCGGTCAGCTGATGAGCCAGCAATGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
1 TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
170818 GAGGATTGAG
66 GAGGATTGAG
170828 T
1 T
170829 ACATGTTATC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 74 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (75 bp):
TCCGGTCAGCTGATGAGCCAGCAACGACATTCTATCAGTGCTTGAAATGCCAGAAGATGTGGCGT
GAGGATTGAG
Found at i:171420 original size:26 final size:26
Alignment explanation
Indices: 171391--171446 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
171381 CAAATACGTT
*
171391 GAGCAGGATAATGACTACCAAAAGAA
1 GAGCAGGATAATGACTACCAAAAAAA
* *
171417 GAGCCGGGTAATGACTACCAAAAAAA
1 GAGCAGGATAATGACTACCAAAAAAA
171443 GAGC
1 GAGC
171447 CGCTCCCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (26 bp):
GAGCAGGATAATGACTACCAAAAAAA
Found at i:171447 original size:26 final size:26
Alignment explanation
Indices: 171399--171448 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
171389 TTGAGCAGGA
*
171399 TAATGACTACCAAAAGAAGAGCCGGG
1 TAATGACTACCAAAAAAAGAGCCGGG
171425 TAATGACTACCAAAAAAAGAGCCG
1 TAATGACTACCAAAAAAAGAGCCG
171449 CTCCCGATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (26 bp):
TAATGACTACCAAAAAAAGAGCCGGG
Found at i:177544 original size:15 final size:15
Alignment explanation
Indices: 177504--177545 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
177494 TTAGGCACCA
* *
177504 AAACTTTCAATGTTT
1 AAACTTTCAATCTAT
*
177519 ACACTTT-AATCTAT
1 AAACTTTCAATCTAT
177533 AAACTTTCAATCT
1 AAACTTTCAATCT
177546 TTAGAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (15 bp):
AAACTTTCAATCTAT
Found at i:182853 original size:2 final size:2
Alignment explanation
Indices: 182844--182929 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
182834 ATAGCATTAA
182844 AT AT -T 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
182885 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
182927 AT A
1 AT A
182930 CTATCAATTT
Statistics
Matches: 83, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 82 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185765 original size:29 final size:29
Alignment explanation
Indices: 185722--185876 Score: 154
Period size: 29 Copynumber: 5.1 Consensus size: 29
185712 TTTCTAGATC
*
185722 ACCAAAGTTTGAAATTTGTAACATCAAGA
1 ACCAAAGTTTGAAATTTGTAACAACAAGA
* **
185751 ACCAAAGTTTTAAATTTGTAACAACACCA
1 ACCAAAGTTTGAAATTTGTAACAACAAGA
185780 ACCAAAAGTTTGAAATTTGT---AACAAGA
1 ACC-AAAGTTTGAAATTTGTAACAACAAGA
*
185807 ACCAAAAGTTTGAGATTTGAAATTTGCAACAACAAGA
1 ACC--AA-----AG-TTTGAAATTTGTAACAACAAGA
*
185844 ACCAAAGTCTGAAATTTGTAACAACAAGA
1 ACCAAAGTTTGAAATTTGTAACAACAAGA
185873 ACCA
1 ACCA
185877 TAGATTCTAT
Statistics
Matches: 105, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
27 8 0.08
28 3 0.03
29 52 0.50
30 17 0.16
33 2 0.02
34 11 0.10
35 2 0.02
37 10 0.10
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (29 bp):
ACCAAAGTTTGAAATTTGTAACAACAAGA
Found at i:188973 original size:18 final size:19
Alignment explanation
Indices: 188948--188993 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
188938 TAATATTATT
188948 TTTATAATA-ATTTTAT-A
1 TTTATAATACATTTTATGA
188965 TTGTATAATATCATTTTATGA
1 TT-TATAATA-CATTTTATGA
188986 TTTATAAT
1 TTTATAAT
188994 CATAATGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.08
18 7 0.28
20 13 0.52
21 3 0.12
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (19 bp):
TTTATAATACATTTTATGA
Found at i:188988 original size:64 final size:64
Alignment explanation
Indices: 188869--188990 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
188859 CATTGATTAT
* ** * *
188869 TATGTTAATATTATTTTTATAAATATTTGTAGTTGTATTTTACCTTTTCTAGATTTATTATTGA
1 TATGTTAATATTATTTTTATAAATATTTGTAATTGTATAATACATTTTATAGATTTATTATTGA
188933 TATGTTAATATTATTTTTAT-AATAATTT-TATATTGTATAATATCATTTTAT-GATTTAT
1 TATGTTAATATTATTTTTATAAAT-ATTTGTA-ATTGTATAATA-CATTTTATAGATTTAT
188991 AATCATAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
63 5 0.10
64 39 0.78
65 6 0.12
ACGTcount: A:0.31, C:0.03, G:0.07, T:0.58
Consensus pattern (64 bp):
TATGTTAATATTATTTTTATAAATATTTGTAATTGTATAATACATTTTATAGATTTATTATTGA
Found at i:189511 original size:34 final size:35
Alignment explanation
Indices: 189469--189543 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 35
189459 TTTTTATAGT
189469 TAAG-ATAAAATAAAACATA-TTTTAAAAT-TAAAA
1 TAAGAATAAAAT-AAACATATTTTTAAAATATAAAA
* *
189502 TAAGAATAAAATATATATATTTTTAAAATATAAAA
1 TAAGAATAAAATAAACATATTTTTAAAATATAAAA
189537 TAA-AATA
1 TAAGAATA
189544 TCTATATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
33 9 0.24
34 20 0.54
35 8 0.22
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (35 bp):
TAAGAATAAAATAAACATATTTTTAAAATATAAAA
Found at i:189570 original size:33 final size:32
Alignment explanation
Indices: 189460--189573 Score: 98
Period size: 29 Copynumber: 3.7 Consensus size: 32
189450 ATAAATATTT
*
189460 TTTTATAGTTAAGATAAAAT-AAA-A-C-ATA
1 TTTTAAAGTTAAGATAAAATAAAATATCTATA
* * *
189488 TTTTAAAATTAAAATAAGAATAAAATATATATA
1 TTTTAAAGTTAAGATAA-AATAAAATATCTATA
* *
189521 TTTTTAA---AATATAAAATAAAATATCTATA
1 TTTTAAAGTTAAGATAAAATAAAATATCTATA
*
189550 TTTTCAAGTTAAGATAAAAATAAA
1 TTTTAAAGTTAAGAT-AAAATAAA
189574 TAATATTAAA
Statistics
Matches: 68, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
28 14 0.21
29 23 0.34
30 9 0.13
31 1 0.01
32 4 0.06
33 17 0.25
ACGTcount: A:0.56, C:0.03, G:0.04, T:0.37
Consensus pattern (32 bp):
TTTTAAAGTTAAGATAAAATAAAATATCTATA
Found at i:190829 original size:4 final size:4
Alignment explanation
Indices: 190809--190846 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
190799 TATAAATTAT
190809 ATAA ATATA AT-A ATAA ATAA ATAA ATAA AT-A ATAA ATA
1 ATAA ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
190847 GTATATTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 6 0.19
4 22 0.71
5 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
ATAA
Done.