Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000144.1 Hibiscus syriacus cultivar Beakdansim tig00000259_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: 63400
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:2543 original size:18 final size:17
Alignment explanation
Indices: 2497--2544 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
2487 TCTATTAAAA
*
2497 TATTATTATATTATTAT
1 TATTATTATAATATTAT
* *
2514 TAATATAAATAATATTAT
1 TATTAT-TATAATATTAT
2532 TCATTATTATAAT
1 T-ATTATTATAAT
2545 TTAATAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
17 5 0.21
18 15 0.62
19 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TATTATTATAATATTAT
Found at i:2550 original size:26 final size:29
Alignment explanation
Indices: 2489--2552 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
2479 TAAATATCTC
*
2489 TATTAA-AATATTATTATATTATTATTAA
1 TATTAATAATATTATTACATTATTATTAA
*
2517 TATAAATAATATTATT-CATTATTA-TAA
1 TATTAATAATATTATTACATTATTATTAA
2544 T-TTAATAAT
1 TATTAATAAT
2553 TTTTTCTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 7 0.22
27 4 0.12
28 12 0.38
29 9 0.28
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (29 bp):
TATTAATAATATTATTACATTATTATTAA
Found at i:2662 original size:94 final size:95
Alignment explanation
Indices: 2491--2672 Score: 207
Period size: 93 Copynumber: 1.9 Consensus size: 95
2481 AATATCTCTA
* *
2491 TTAAAATATTATTATATTATTATTAATATAAATAATATTATTCATTATTATAATTTAATAATTTT
1 TTAAAATATTATTATATTATTATTAAAATAAATAATATAATTCATTATTATAATTTAATAATTTT
* *
2556 TTCTATGAATTAATA-ATAATATAAATTTT
66 TTCTATAAATTAAAATATAATATAAATTTT
*
2585 TTAATAAT-TTATTATA-TATTATTAAAATAAA-AATATAATATC-TTA-TATTA-TTAATAATT
1 TTAA-AATATTATTATATTATTATTAAAATAAATAATATAAT-TCATTATTATAATTTAATAA-T
*
2644 GATTTTTTTATAATATTAAAATATAATAT
63 --TTTTTCTATAA-ATTAAAATATAATAT
2673 TCTATTAGAA
Statistics
Matches: 75, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
90 7 0.09
91 5 0.07
92 10 0.13
93 25 0.33
94 18 0.24
95 10 0.13
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (95 bp):
TTAAAATATTATTATATTATTATTAAAATAAATAATATAATTCATTATTATAATTTAATAATTTT
TTCTATAAATTAAAATATAATATAAATTTT
Found at i:4300 original size:16 final size:17
Alignment explanation
Indices: 4261--4293 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
4251 CACGGAATGT
4261 AAGA-TACCAGGGAATA
1 AAGATTACCAGGGAATA
4277 AAGATTACCAGGGAATA
1 AAGATTACCAGGGAATA
4294 GGATTACTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.48, C:0.12, G:0.24, T:0.15
Consensus pattern (17 bp):
AAGATTACCAGGGAATA
Found at i:15470 original size:16 final size:16
Alignment explanation
Indices: 15449--15487 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
15439 GGTATTACCC
*
15449 GACCTGTTTTCAACCT
1 GACCTGTTATCAACCT
*
15465 GACCTGTTATGAACCT
1 GACCTGTTATCAACCT
15481 GACCTGT
1 GACCTGT
15488 AATTGACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.33
Consensus pattern (16 bp):
GACCTGTTATCAACCT
Found at i:16891 original size:22 final size:23
Alignment explanation
Indices: 16852--16905 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
16842 AAACATACAC
*
16852 AATATTAATACTAATAATAATTAT
1 AATATT-ATAATAATAATAATTAT
*
16876 AAT-TTATAATAATAATTATTAT
1 AATATTATAATAATAATAATTAT
16898 AATATTAT
1 AATATTAT
16906 TTTTTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 18 0.67
23 6 0.22
24 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AATATTATAATAATAATAATTAT
Found at i:16972 original size:31 final size:30
Alignment explanation
Indices: 16937--17140 Score: 86
Period size: 33 Copynumber: 6.6 Consensus size: 30
16927 GGGTGTCAAC
16937 ATATAGTATATAAATATAAACTATAGTATAT
1 ATATAGTATATAAATATAAACTATA-TATAT
** * *
16968 ATATA-TAGGTCATATGTAAACTATATA-AT
1 ATATAGTATAT-AAATATAAACTATATATAT
* * *
16997 ATATA-AATATCAACTATAGTA-TATATATAT
1 ATATAGTATAT-AAATATA-AACTATATATAT
* * *
17027 ATATAGGT-CAT--ATGTAAACTATATAGTTT
1 ATATA-GTATATAAATATAAACTATATA-TAT
*
17056 ATATATGTAGT-T-CATACGTAAACTATAGTTCATAT
1 ATATA-GTA-TATAAATA--TAAACTATA--T-ATAT
17091 ATATAGTATATAAATATAAACTATAGTTTATAT
1 ATATAGTATATAAATATAAACTATA---TATAT
*
17124 AAATAGTATA-AAATATA
1 ATATAGTATATAAATATA
17141 GTATATAAAT
Statistics
Matches: 131, Mismatches: 24, Indels: 35
0.69 0.13 0.18
Matches are distributed among these distances:
27 1 0.01
28 9 0.07
29 29 0.22
30 14 0.11
31 21 0.16
32 7 0.05
33 32 0.24
34 6 0.05
35 11 0.08
36 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (30 bp):
ATATAGTATATAAATATAAACTATATATAT
Found at i:17000 original size:33 final size:33
Alignment explanation
Indices: 16958--17100 Score: 108
Period size: 33 Copynumber: 4.5 Consensus size: 33
16948 AAATATAAAC
*
16958 TATAGTATATATATATAGGTCATATGTAAACTA
1 TATAATATATATATATAGGTCATATGTAAACTA
*
16991 TATAATATATA-A-ATA--TCA-A-CT--A-TA
1 TATAATATATATATATAGGTCATATGTAAACTA
17015 GTAT-ATATATATATATAGGTCATATGTAAACTA
1 -TATAATATATATATATAGGTCATATGTAAACTA
* * * * *
17048 TATAGTTTATATATGTAGTTCATACGTAAACTA
1 TATAATATATATATATAGGTCATATGTAAACTA
*
17081 TAGTTCATATATATAGTATA
1 TA--TAATATATATA-TATA
17101 TAAATATAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 25
0.69 0.10 0.21
Matches are distributed among these distances:
24 9 0.11
25 5 0.06
26 3 0.04
27 1 0.01
28 4 0.05
29 4 0.05
30 1 0.01
31 3 0.04
32 5 0.06
33 38 0.45
35 8 0.10
36 3 0.04
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.41
Consensus pattern (33 bp):
TATAATATATATATATAGGTCATATGTAAACTA
Found at i:17000 original size:53 final size:54
Alignment explanation
Indices: 16937--17051 Score: 178
Period size: 57 Copynumber: 2.1 Consensus size: 54
16927 GGGTGTCAAC
*
16937 ATATAGTATATAAATATAAACTATAG-TATATATATATAGGTCATATGTAAACT
1 ATATAATATATAAATATAAACTATAGATATATATATATAGGTCATATGTAAACT
*
16990 ATATAATATATAAATATCAACTATAGTATATATATATATATAGGTCATATGTAAACT
1 ATATAATATATAAATATAAACTATAG---ATATATATATATAGGTCATATGTAAACT
17047 ATATA
1 ATATA
17052 GTTTATATAT
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
53 24 0.43
57 32 0.57
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (54 bp):
ATATAATATATAAATATAAACTATAGATATATATATATAGGTCATATGTAAACT
Found at i:17011 original size:22 final size:24
Alignment explanation
Indices: 16986--17030 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
16976 GTCATATGTA
16986 AACTATA-TA-ATATATAAATATC
1 AACTATAGTATATATATAAATATC
*
17008 AACTATAGTATATATATATATAT
1 AACTATAGTATATATATAAATAT
17031 AGGTCATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (24 bp):
AACTATAGTATATATATAAATATC
Found at i:17111 original size:33 final size:33
Alignment explanation
Indices: 16989--17140 Score: 125
Period size: 33 Copynumber: 4.6 Consensus size: 33
16979 ATATGTAAAC
* * *
16989 TATATAATATATAAATATCAACTATAGTATATA
1 TATATAGTATATAAATATAAACTATAGTTTATA
* *
17022 TATATA-TATAGGTCATATGTAAACTATATAGTTTATA
1 TATATAGTATA--T-AAATATAAAC--TATAGTTTATA
* ** *
17059 TATGTAGT-TCAT--ACGTAAACTATAGTTCATA
1 TATATAGTAT-ATAAATATAAACTATAGTTTATA
17090 TATATAGTATATAAATATAAACTATAGTTTATA
1 TATATAGTATATAAATATAAACTATAGTTTATA
*
17123 TAAATAGTATA-AAATATA
1 TATATAGTATATAAATATA
17141 GTATATAAAT
Statistics
Matches: 97, Mismatches: 12, Indels: 21
0.75 0.09 0.16
Matches are distributed among these distances:
31 19 0.20
32 12 0.12
33 39 0.40
34 1 0.01
35 7 0.07
36 1 0.01
37 16 0.16
38 2 0.02
ACGTcount: A:0.46, C:0.06, G:0.08, T:0.40
Consensus pattern (33 bp):
TATATAGTATATAAATATAAACTATAGTTTATA
Found at i:17115 original size:20 final size:20
Alignment explanation
Indices: 17091--17164 Score: 85
Period size: 20 Copynumber: 3.5 Consensus size: 20
17081 TAGTTCATAT
17091 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
17111 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATAT-AA-A-TATAAA
17136 ATATAGTATATAAATATAAA
1 ATATAGTATATAAATATAAA
*
17156 TTATAGTAT
1 ATATAGTAT
17165 GTAGTTTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
20 19 0.41
21 1 0.02
22 7 0.15
23 7 0.15
24 1 0.02
25 11 0.24
ACGTcount: A:0.53, C:0.01, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATAGTATATAAATATAAA
Found at i:17140 original size:25 final size:23
Alignment explanation
Indices: 17091--17151 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
17081 TAGTTCATAT
17091 ATATAGTATAT-AA-A-TATAAA
1 ATATAGTATATAAATAGTATAAA
*
17111 CTATAGTTTATATAAATAGTATAAA
1 ATATAG--TATATAAATAGTATAAA
17136 ATATAGTATATAAATA
1 ATATAGTATATAAATA
17152 TAAATTATAG
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 5 0.15
22 5 0.15
23 12 0.35
24 1 0.03
25 11 0.32
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.38
Consensus pattern (23 bp):
ATATAGTATATAAATAGTATAAA
Found at i:17143 original size:12 final size:13
Alignment explanation
Indices: 17104--17153 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
17094 TAGTATATAA
17104 ATATAAACTATAGT
1 ATATAAA-TATAGT
*
17118 TTATATAA-ATAGT
1 ATATA-AATATAGT
17131 ATA-AAATATAGT
1 ATATAAATATAGT
17143 ATATAAATATA
1 ATATAAATATA
17154 AATTATAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 2 0.06
12 9 0.29
13 14 0.45
14 4 0.13
15 2 0.06
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (13 bp):
ATATAAATATAGT
Found at i:17155 original size:29 final size:29
Alignment explanation
Indices: 17120--17188 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
17110 ACTATAGTTT
17120 ATATAAATAGTATAAAATATAG-TATATAA
1 ATATAAATA-TATAAAATATAGTTATATAA
** *
17149 ATATAAAT-TATAGTATGTAGTTTATATAA
1 ATATAAATATATAAAATATAG-TTATATAA
17178 ATATAAATATA
1 ATATAAATATA
17189 AACCCTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (29 bp):
ATATAAATATATAAAATATAGTTATATAA
Found at i:17204 original size:7 final size:7
Alignment explanation
Indices: 17174--17232 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
17164 TGTAGTTTAT
17174 ATAAAT-
1 ATAAATC
17180 ATAAAT-
1 ATAAATC
*
17186 ATAAACC
1 ATAAATC
*
17193 CTAAATC
1 ATAAATC
*
17200 TTAAATC
1 ATAAATC
*
17207 ATAAACC
1 ATAAATC
*
17214 CTAAATC
1 ATAAATC
*
17221 ATAAACC
1 ATAAATC
17228 ATAAA
1 ATAAA
17233 ACTTTGATCC
Statistics
Matches: 42, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
6 11 0.26
7 31 0.74
ACGTcount: A:0.56, C:0.19, G:0.00, T:0.25
Consensus pattern (7 bp):
ATAAATC
Found at i:17211 original size:21 final size:21
Alignment explanation
Indices: 17175--17232 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
17165 GTAGTTTATA
17175 TAAAT-ATAAAT-ATAAACCC
1 TAAATCATAAATCATAAACCC
*
17194 TAAATCTTAAATCATAAACCC
1 TAAATCATAAATCATAAACCC
*
17215 TAAATCATAAACCATAAA
1 TAAATCATAAATCATAAA
17233 ACTTTGATCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 5 0.15
20 5 0.15
21 24 0.71
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAATCATAAATCATAAACCC
Found at i:17317 original size:22 final size:24
Alignment explanation
Indices: 17283--17415 Score: 87
Period size: 26 Copynumber: 5.3 Consensus size: 24
17273 ATATACTATA
*
17283 TATATATATATAAACTATATAGTT
1 TATATATATATAAACTATATAATT
17307 TATAT-TA-ATAAACTATATAATT
1 TATATATATATAAACTATATAATT
* * *
17329 TATACGATATATATTA-TTTATAATT
1 TATA-TATATATA-AACTATATAATT
*
17354 ATACATAATATATAAA-TATA-AATT
1 -TATAT-ATATATAAACTATATAATT
*
17378 GTATAGTTTATATATAATTCATATATAATT
1 -TATA---TATATATAA-AC-TATATAATT
17408 TATATATA
1 TATATATA
17416 AACTATGTAG
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
22 18 0.21
23 2 0.02
24 14 0.16
25 15 0.18
26 23 0.27
27 1 0.01
29 8 0.09
30 4 0.05
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (24 bp):
TATATATATATAAACTATATAATT
Found at i:17411 original size:9 final size:10
Alignment explanation
Indices: 17335--17416 Score: 53
Period size: 11 Copynumber: 7.8 Consensus size: 10
17325 AATTTATACG
17335 ATATAT-ATT
1 ATATATAATT
*
17344 ATTTATAATT
1 ATATATAATT
*
17354 ATACATAATAT
1 ATATATAAT-T
17365 ATAAATATAAATT
1 AT--ATAT-AATT
*
17378 GTATAGT--TT
1 ATATA-TAATT
17387 ATATATAATT
1 ATATATAATT
17397 CATATATAATTT
1 -ATATATAA-TT
17409 ATATATAA
1 ATATATAA
17417 ACTATGTAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
8 1 0.02
9 11 0.19
10 12 0.21
11 22 0.39
12 3 0.05
13 5 0.09
14 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (10 bp):
ATATATAATT
Found at i:17456 original size:17 final size:17
Alignment explanation
Indices: 17434--17468 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
17424 AGCATATATA
17434 ATTTATATAAAAATTAT
1 ATTTATATAAAAATTAT
17451 ATTTATATAAAAATTAT
1 ATTTATATAAAAATTAT
17468 A
1 A
17469 GTATGTAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTATATAAAAATTAT
Found at i:17519 original size:27 final size:26
Alignment explanation
Indices: 17483--17539 Score: 80
Period size: 27 Copynumber: 2.2 Consensus size: 26
17473 GTAGTTTATA
17483 TAAATATAAAT-ATAAACTCTAAACCC
1 TAAATATAAATCATAAAC-CTAAACCC
*
17509 TAAATCATAAATCATAAACCTAAATCC
1 TAAAT-ATAAATCATAAACCTAAACCC
17536 TAAA
1 TAAA
17540 CCATGAACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 5 0.18
27 17 0.61
28 6 0.21
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.26
Consensus pattern (26 bp):
TAAATATAAATCATAAACCTAAACCC
Found at i:17530 original size:20 final size:20
Alignment explanation
Indices: 17489--17560 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
17479 TATATAAATA
17489 TAAAT-ATAAACTC-TAAACCC
1 TAAATCATAAA-TCATAAA-CC
17509 TAAATCATAAATCATAAACC
1 TAAATCATAAATCATAAACC
* * *
17529 TAAATCCTAAACCATGAACCC
1 TAAATCATAAATCAT-AAACC
*
17550 TAAACCATAAA
1 TAAATCATAAA
17561 CATTTATCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
20 22 0.50
21 22 0.50
ACGTcount: A:0.51, C:0.25, G:0.01, T:0.22
Consensus pattern (20 bp):
TAAATCATAAATCATAAACC
Found at i:17937 original size:215 final size:215
Alignment explanation
Indices: 17562--18064 Score: 891
Period size: 215 Copynumber: 2.3 Consensus size: 215
17552 AACCATAAAC
17562 ATTT-ATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
1 ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
* *
17626 TTCAATTTAGTTCTCCAAATTTTATTTGCATATGAAATTGACCCATACTTATTACTTATTTATAT
66 TTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTATAT
* *
17691 TTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTTAATATTTTTTGTATTAATTTCAACAT
131 TTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTCAATACTTTTTGTATTAATTTCAACAT
17756 CACAATTTAAAATTATTTCG
196 CACAATTTAAAATTATTTCG
17776 ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
1 ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
* * * *
17841 TTCAATTTAGTCCTCCAAATTTTATTTGTATCTGAAATTGATCCATACTTATTACTTAATTCTAT
66 TTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTATAT
* * *
17906 TTTTTAATTGTCCCATAACTTTTTAAATGGGTATAATTCAATACTTTTTGTATTAATTTCAACCT
131 TTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTCAATACTTTTTGTATTAATTTCAACAT
*
17971 CACAATTTAAAATTATTTTG
196 CACAATTTAAAATTATTTCG
17991 ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
1 ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
18056 TTCAATTTA
66 TTCAATTTA
18065 ATTCTTAAAT
Statistics
Matches: 276, Mismatches: 12, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
214 4 0.01
215 272 0.99
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (215 bp):
ATTTGATCCCTCATCAATGTGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTG
TTCAATTTAGTCCTCCAAATTTTATTTGCATATGAAATTGACCCATACTTATTACTTAATTATAT
TTTTAAATTGACCCATAACTTTTTAAATGGGTATAATTCAATACTTTTTGTATTAATTTCAACAT
CACAATTTAAAATTATTTCG
Found at i:25875 original size:22 final size:21
Alignment explanation
Indices: 25833--25872 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25823 GAGTTTGTTT
*
25833 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
25854 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
25873 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:37598 original size:136 final size:136
Alignment explanation
Indices: 37354--37627 Score: 512
Period size: 136 Copynumber: 2.0 Consensus size: 136
37344 CTATGGATTG
*
37354 GAGAAAACTATTTGGGTATTCAACGGGCTACGACCTCGAATTTTCCCCCCTAGGGTTTGCGACGG
1 GAGAAAACTATTTGGGTATTCAACGGGCTACGACCTCGAATTTTCCCCCCTAGGGTTTACGACGG
37419 AGTCAAAACTGTTCAACCCCCACAAGAAGTGCTCGAAGCAGGGATTCAGGAATGGAACCTGTCGC
66 AGTCAAAACTGTTCAACCCCCACAAGAAGTGCTCGAAGCAGGGATTCAGGAATGGAACCTGTCGC
37484 TTGTGA
131 TTGTGA
* * *
37490 GAGAAAACTATTTGGGTGTTCAGCGGGGTACGACCTCGAATTTTCCCCCCTAGGGTTTACGACGG
1 GAGAAAACTATTTGGGTATTCAACGGGCTACGACCTCGAATTTTCCCCCCTAGGGTTTACGACGG
37555 AGTCAAAACTGTTCAACCCCCACAAGAAGTGCTCGAAGCAGGGATTCAGGAATGGAACCTGTCGC
66 AGTCAAAACTGTTCAACCCCCACAAGAAGTGCTCGAAGCAGGGATTCAGGAATGGAACCTGTCGC
37620 TTGTGA
131 TTGTGA
37626 GA
1 GA
37628 CAAATTCTTG
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
136 134 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.23
Consensus pattern (136 bp):
GAGAAAACTATTTGGGTATTCAACGGGCTACGACCTCGAATTTTCCCCCCTAGGGTTTACGACGG
AGTCAAAACTGTTCAACCCCCACAAGAAGTGCTCGAAGCAGGGATTCAGGAATGGAACCTGTCGC
TTGTGA
Found at i:38348 original size:17 final size:17
Alignment explanation
Indices: 38326--38360 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
38316 ACTATTGTTA
38326 AATATGACTCTAGTACT
1 AATATGACTCTAGTACT
38343 AATATGACTCTAGTACT
1 AATATGACTCTAGTACT
38360 A
1 A
38361 TAGTAGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (17 bp):
AATATGACTCTAGTACT
Found at i:44354 original size:17 final size:17
Alignment explanation
Indices: 44332--44376 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
44322 TTGAAGTTAT
44332 GCTTTTCTTTCATCTCC
1 GCTTTTCTTTCATCTCC
44349 GCTTTTCTTTCATCTCC
1 GCTTTTCTTTCATCTCC
*
44366 ACTTTTCTTTC
1 GCTTTTCTTTC
44377 TTTATTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.07, C:0.33, G:0.04, T:0.56
Consensus pattern (17 bp):
GCTTTTCTTTCATCTCC
Found at i:44384 original size:13 final size:13
Alignment explanation
Indices: 44368--44401 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
44358 TCATCTCCAC
*
44368 TTTTCTTTCTTTA
1 TTTTCTTTCATTA
44381 TTTTCTTTCATTA
1 TTTTCTTTCATTA
44394 TTTTCTTT
1 TTTTCTTT
44402 TTACAATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.09, C:0.15, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCTTTCATTA
Found at i:45009 original size:13 final size:13
Alignment explanation
Indices: 44985--45057 Score: 51
Period size: 13 Copynumber: 5.3 Consensus size: 13
44975 CTATTAAATT
44985 CTTTACTTTATTTA
1 CTTTA-TTTATTTA
*
44999 CTTTATTTATTTT
1 CTTTATTTATTTA
45012 CTCCTTATTT-TTTA
1 CT--TTATTTATTTA
*
45026 TTCATTATTTATTT-
1 --CTTTATTTATTTA
*
45040 TTATTATTTATTTA
1 CT-TTATTTATTTA
45054 CTTT
1 CTTT
45058 CATTAATTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
13 21 0.46
14 15 0.33
15 9 0.20
16 1 0.02
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (13 bp):
CTTTATTTATTTA
Found at i:45042 original size:17 final size:17
Alignment explanation
Indices: 45020--45053 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
45010 TTCTCCTTAT
45020 TTTTTATTCA-TTATTTA
1 TTTTTATT-ATTTATTTA
45037 TTTTTATTATTTATTTA
1 TTTTTATTATTTATTTA
45054 CTTTCATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.06
17 15 0.94
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTATTATTTATTTA
Found at i:49109 original size:31 final size:30
Alignment explanation
Indices: 49070--49135 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
49060 GTCGAGGGTT
**
49070 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
49100 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
49131 TTACC
1 TTACC
49136 GAGGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:49249 original size:29 final size:30
Alignment explanation
Indices: 49124--49246 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
49114 AAGGAACATA
49124 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
49154 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
49184 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
49214 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
49243 TGGA
1 TGGA
49247 TAGGTCTTCG
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:53487 original size:31 final size:30
Alignment explanation
Indices: 53448--53513 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
53438 GTCGAGGGTT
**
53448 TTACCTATG-TCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAACGA-ACATATGGACAG
*
53478 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAACGAACATATGGACAG
53509 TTACC
1 TTACC
53514 GAGGATCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
30 5 0.16
31 21 0.68
32 5 0.16
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (30 bp):
TTACCTATGTTCTAACGAACATATGGACAG
Found at i:53627 original size:29 final size:30
Alignment explanation
Indices: 53502--53624 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
53492 AAGGAACATA
53502 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
53532 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
53562 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
53592 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
53621 TGGA
1 TGGA
53625 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:57833 original size:13 final size:13
Alignment explanation
Indices: 57817--57864 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
57807 TTCATCTCCA
57817 ATTTTCTTTCTTT
1 ATTTTCTTTCTTT
*
57830 ATTTTCTATCTTT
1 ATTTTCTTTCTTT
57843 ATTTTCTTT-TATT
1 ATTTTCTTTCT-TT
*
57856 GTTTTCTTT
1 ATTTTCTTT
57865 TCACAATGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
12 1 0.03
13 30 0.97
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (13 bp):
ATTTTCTTTCTTT
Found at i:61603 original size:10 final size:9
Alignment explanation
Indices: 61572--61617 Score: 60
Period size: 9 Copynumber: 5.3 Consensus size: 9
61562 AAATTTAAAA
61572 AAAATATTT
1 AAAATATTT
61581 AAAATATTT
1 AAAATATTT
*
61590 AAAATATAT
1 AAAATATTT
*
61599 GAAA-ATTT
1 AAAATATTT
61607 AAAAT-TTT
1 AAAATATTT
61615 AAA
1 AAA
61618 CCTCATTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 12 0.38
9 20 0.62
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (9 bp):
AAAATATTT
Done.