Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001657.1 Hibiscus syriacus cultivar Beakdansim tig00003313_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: 106433
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Found at i:2962 original size:31 final size:31
Alignment explanation
Indices: 2927--3016 Score: 112
Period size: 32 Copynumber: 2.9 Consensus size: 31
2917 GTAGGCTCTG
2927 CGGCCCTGAGATCATTCTTGGGTAGGCCCCA
1 CGGCCCTGAGATCATTCTTGGGTAGGCCCCA
* *
2958 CGGCCCTAAGAT-ATGTTCTTAGGTAGGCCCCA
1 CGGCCCTGAGATCA--TTCTTGGGTAGGCCCCA
*
2990 CGGCCCTGAAATC-TATCTTGGGTAGGC
1 CGGCCCTGAGATCAT-TCTTGGGTAGGC
3017 TCTCAGGCCA
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
30 2 0.04
31 22 0.44
32 26 0.52
ACGTcount: A:0.19, C:0.29, G:0.28, T:0.24
Consensus pattern (31 bp):
CGGCCCTGAGATCATTCTTGGGTAGGCCCCA
Found at i:2983 original size:32 final size:31
Alignment explanation
Indices: 2911--2996 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 31
2901 CTAATGTGAC
* ** *
2911 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCCACGGCCCTAAGATCAT
*
2942 TCTTGGGTAGGCCCCACGGCCCTAAGAT-ATGT
1 TCTTAGGTAGGCCCCACGGCCCTAAGATCA--T
2974 TCTTAGGTAGGCCCCACGGCCCT
1 TCTTAGGTAGGCCCCACGGCCCT
2997 GAAATCTATC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 1 0.02
31 23 0.49
32 23 0.49
ACGTcount: A:0.16, C:0.30, G:0.28, T:0.26
Consensus pattern (31 bp):
TCTTAGGTAGGCCCCACGGCCCTAAGATCAT
Found at i:3041 original size:63 final size:64
Alignment explanation
Indices: 2910--3044 Score: 161
Period size: 63 Copynumber: 2.1 Consensus size: 64
2900 CCTAATGTGA
* ** * *
2910 CTCTTAGGTAGGCTCTGCGGCCCTGAGATCATTCTTGGGTAGGCCCCACGGCCCTAAGATATGT
1 CTCTTAGGTAGGCCCCACGGCCCTGAAATCATTCTTGGGTAGGCCCCACGGCCATAAGATATGT
* *
2974 -TCTTAGGTAGGCCCCACGGCCCTGAAATC-TATCTTGGGTAGGCTCTCA-GGCCATAAGATGT-
1 CTCTTAGGTAGGCCCCACGGCCCTGAAATCAT-TCTTGGGTAGGC-CCCACGGCCATAAGATATG
3035 T
64 T
3036 CTCTTAGGT
1 CTCTTAGGT
3045 TAACTCTTTG
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
62 2 0.03
63 56 0.92
64 3 0.05
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.28
Consensus pattern (64 bp):
CTCTTAGGTAGGCCCCACGGCCCTGAAATCATTCTTGGGTAGGCCCCACGGCCATAAGATATGT
Found at i:3899 original size:17 final size:17
Alignment explanation
Indices: 3877--3910 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3867 TGATGCTATA
3877 ATTTTTGTAATTATTTT
1 ATTTTTGTAATTATTTT
* *
3894 ATTTTTTTGATTATTTT
1 ATTTTTGTAATTATTTT
3911 CAAAAATTTT
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:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (17 bp):
ATTTTTGTAATTATTTT
Found at i:6036 original size:2 final size:2
Alignment explanation
Indices: 6029--6061 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6019 TTTAAAATAC
6029 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 T
6062 TTTTCTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11905 original size:26 final size:26
Alignment explanation
Indices: 11874--11924 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
11864 GTTAAATTAT
11874 TTTA-TTATAAAATATAATTTATTTTA
1 TTTATTTATAAAA-ATAATTTATTTTA
* *
11900 TTTATTTTTCAAAATAATTTATTTT
1 TTTATTTATAAAAATAATTTATTTT
11925 CTTGAAGAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTATTTATAAAAATAATTTATTTTA
Found at i:12875 original size:18 final size:18
Alignment explanation
Indices: 12852--12891 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
12842 TTGTAATTTT
*
12852 TTTTATTATTTT-TGAATA
1 TTTTATCATTTTAT-AATA
12870 TTTTATCATTTTATAATA
1 TTTTATCATTTTATAATA
12888 TTTT
1 TTTT
12892 TAATAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTTATCATTTTATAATA
Found at i:16289 original size:2 final size:2
Alignment explanation
Indices: 16282--16326 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16272 TTTGAAATAC
16282 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
16324 TA T
1 TA T
16327 TCTTAAATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17360 original size:66 final size:67
Alignment explanation
Indices: 17180--17391 Score: 265
Period size: 66 Copynumber: 3.2 Consensus size: 67
17170 TGTGCATTAA
* *
17180 CATAAAAGGTGCCACTAATAAAAATT-ATCGATCGATTTTGATTAATGCATAACGGTGCATTATC
1 CATAAAAGATGCCACTAATAAAAATTAATCGATCGATTTTGATTAATGCATAACAGTGCATTATC
17244 AG
66 AG
* * *
17246 CATAAAA-ATGTCACTATTAAAAA--AATCAATCGATTTTGATTAATGCATAACAGTGCATTATC
1 CATAAAAGATGCCACTAATAAAAATTAATCGATCGATTTTGATTAATGCATAACAGTGCATTATC
*
17308 GG
66 AG
* * * * *
17310 CTTAAAAGTTGCCACTAATGAAAATTAAT-GATCGATTTTGTTTAATGCATAATAGTGCATTATC
1 CATAAAAGATGCCACTAATAAAAATTAATCGATCGATTTTGATTAATGCATAACAGTGCATTATC
17374 AG
66 AG
*
17376 TATAAAATG-TGCCACT
1 CATAAAA-GATGCCACT
17392 CATGGTATTC
Statistics
Matches: 124, Mismatches: 17, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
64 43 0.35
65 25 0.20
66 52 0.42
67 4 0.03
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (67 bp):
CATAAAAGATGCCACTAATAAAAATTAATCGATCGATTTTGATTAATGCATAACAGTGCATTATC
AG
Found at i:20814 original size:18 final size:18
Alignment explanation
Indices: 20791--20825 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20781 TTCCATCCGG
*
20791 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
20809 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
20826 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:27473 original size:21 final size:21
Alignment explanation
Indices: 27443--27492 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
27433 GTTAATCGTT
*
27443 AACT-TTGATTGTTGACTTTTG
1 AACTGTTGATTGTTAAC-TTTG
27464 -ACTGTTGATTGTTAACTTTG
1 AACTGTTGATTGTTAACTTTG
27484 AACTGTTGA
1 AACTGTTGA
27493 CGTTTTCTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (21 bp):
AACTGTTGATTGTTAACTTTG
Found at i:27478 original size:34 final size:35
Alignment explanation
Indices: 27421--27498 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 35
27411 CCAATGATCA
*
27421 TTGAC-TTTGACCGTTAATCGTTAACTTTG-ATTG
1 TTGACTTTTGACCGTTAATCGTTAACTTTGAACTG
* * *
27454 TTGACTTTTGACTGTTGATTGTTAACTTTGAACTG
1 TTGACTTTTGACCGTTAATCGTTAACTTTGAACTG
27489 TTGACGTTTT
1 TTGAC-TTTT
27499 CTAAAGACCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
33 5 0.13
34 21 0.55
35 8 0.21
36 4 0.11
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.49
Consensus pattern (35 bp):
TTGACTTTTGACCGTTAATCGTTAACTTTGAACTG
Found at i:30362 original size:27 final size:26
Alignment explanation
Indices: 30332--30401 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 26
30322 AATTTCAAAT
30332 TATTAAAAATATTATAAAATGATAAAA
1 TATTAAAAATATTATAAAAT-ATAAAA
* * *
30359 TATTCAAAAT-TAATCAAAATATAAAT
1 TATTAAAAATATTAT-AAAATATAAAA
30385 TAATTACAAAA-ATTATA
1 T-ATTA-AAAATATTATA
30402 GCATCATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
26 9 0.26
27 18 0.53
28 7 0.21
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.34
Consensus pattern (26 bp):
TATTAAAAATATTATAAAATATAAAA
Found at i:30485 original size:2 final size:2
Alignment explanation
Indices: 30474--30553 Score: 146
Period size: 2 Copynumber: 41.0 Consensus size: 2
30464 GAATTTAAGA
30474 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
30515 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
30554 TTCAAAAATT
Statistics
Matches: 76, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 74 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35218 original size:14 final size:14
Alignment explanation
Indices: 35199--35226 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
35189 CAAAAGTTTT
35199 TTAAAAAATTTAAA
1 TTAAAAAATTTAAA
35213 TTAAAAAATTTAAA
1 TTAAAAAATTTAAA
35227 AATATTAGAA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TTAAAAAATTTAAA
Found at i:41878 original size:2 final size:2
Alignment explanation
Indices: 41871--41927 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
41861 TGATTTAAGA
41871 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
41913 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
41928 GTATTTCAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:46913 original size:2 final size:2
Alignment explanation
Indices: 46906--46932 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
46896 GAATTTAAGA
46906 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
46933 CAATATTTCA
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:53879 original size:18 final size:19
Alignment explanation
Indices: 53840--53886 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
53830 GAAAAATTTC
* *
53840 AAATTATTAAAATATTATA
1 AAATTATTAAAATAATAAA
53859 AAATTA-TAAAATAATAAA
1 AAATTATTAAAATAATAAA
*
53877 AAATAATTAA
1 AAATTATTAA
53887 TTATTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTATTAAAATAATAAA
Found at i:53935 original size:14 final size:14
Alignment explanation
Indices: 53916--53943 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
53906 CAAGAGTTTT
53916 TTAAAAATTTTAAA
1 TTAAAAATTTTAAA
53930 TTAAAAATTTTAAA
1 TTAAAAATTTTAAA
53944 AATATTAGAA
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATTTTAAA
Found at i:56107 original size:21 final size:21
Alignment explanation
Indices: 56082--56130 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
56072 ACTTGTAATA
*
56082 TATTTTAATTTTTATTAATCT
1 TATTTTAATTTTTAGTAATCT
* * *
56103 TATTTCATTTTTTAGTAATTT
1 TATTTTAATTTTTAGTAATCT
56124 TAGTTTT
1 TA-TTTT
56131 TTTAAGATGA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (21 bp):
TATTTTAATTTTTAGTAATCT
Found at i:56225 original size:20 final size:21
Alignment explanation
Indices: 56200--56238 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
56190 TGATCATTCA
56200 CACATG-ACAACCATGTAAAT
1 CACATGAACAACCATGTAAAT
*
56220 CACATGAACTACCATGTAA
1 CACATGAACAACCATGTAA
56239 CAATTGTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.21
Consensus pattern (21 bp):
CACATGAACAACCATGTAAAT
Found at i:60442 original size:27 final size:25
Alignment explanation
Indices: 60412--60480 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 25
60402 AATTTCAAAT
*
60412 TATTAAAAATATTATAAAATGATAAAA
1 TATTAAAAA-ATTATAAAA-AATAAAA
* *
60439 TATTAAAAAATAATCAAAAAATAAAT
1 TATTAAAAAATTAT-AAAAAATAAAA
60465 TAATTAAAAAATTATA
1 T-ATTAAAAAATTATA
60481 GCATTAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 11 0.31
27 25 0.69
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (25 bp):
TATTAAAAAATTATAAAAAATAAAA
Found at i:60559 original size:2 final size:2
Alignment explanation
Indices: 60552--60586 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60542 ATAAGAAAAT
60552 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
60587 GTCATAAAGG
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:62790 original size:2 final size:2
Alignment explanation
Indices: 62779--62810 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
62769 GAATTTAAGA
62779 AT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
62811 TTCAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73200 original size:76 final size:70
Alignment explanation
Indices: 73095--73295 Score: 232
Period size: 67 Copynumber: 2.8 Consensus size: 70
73085 TATTTTAAAC
*
73095 ATTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATAT
1 ATTAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTA-G--AT
*
73160 TATTTTTATATT
62 TA---TTAGATT
*
73172 -TTATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGATTAT
1 ATTAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGATTAT
73235 TAGATT
65 TAGATT
* * * *
73241 ATTATTTT-T-TTGGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 ATTATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTA
73296 AGATGTTTTA
Statistics
Matches: 115, Mismatches: 7, Indels: 14
0.85 0.05 0.10
Matches are distributed among these distances:
66 1 0.01
67 41 0.36
68 1 0.01
69 9 0.08
70 4 0.03
72 4 0.03
74 1 0.01
75 22 0.19
76 32 0.28
ACGTcount: A:0.28, C:0.01, G:0.12, T:0.58
Consensus pattern (70 bp):
ATTATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGATTATT
AGATT
Found at i:81644 original size:16 final size:16
Alignment explanation
Indices: 81620--81650 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
81610 AAAACAATGC
*
81620 AGTGTAGAAAAAAAAT
1 AGTGCAGAAAAAAAAT
81636 AGTGCAGAAAAAAAA
1 AGTGCAGAAAAAAAA
81651 ATAGATTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.03, G:0.19, T:0.13
Consensus pattern (16 bp):
AGTGCAGAAAAAAAAT
Found at i:83134 original size:75 final size:74
Alignment explanation
Indices: 83044--83207 Score: 238
Period size: 75 Copynumber: 2.2 Consensus size: 74
83034 TTAAACTCAA
*
83044 ATTTAGGATAATATTTTAAACATTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTAT
1 ATTTAGGATATTATTTTAAACATTATATTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTAT
83109 TTTAATTAAG
65 TTTAATTAAG
* * ** *
83119 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 ATTTAGGATATTA-TTTTAAACATTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
83184 TTTAATTAGG
65 TTTAATTAAG
*
83194 ATTTAGAATATTAT
1 ATTTAGGATATTAT
83208 ATTTTTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
74 1 0.01
75 40 0.51
76 38 0.48
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.56
Consensus pattern (74 bp):
ATTTAGGATATTATTTTAAACATTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAG
Found at i:83170 original size:76 final size:68
Alignment explanation
Indices: 83066--83262 Score: 233
Period size: 64 Copynumber: 2.8 Consensus size: 68
83056 ATTTTAAACA
*
83066 TTATATTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGTTTTAGGATATT
1 TTAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTA-GA-A-T
83131 ATTTTTATATT
62 A---TTATA-T
*
83142 TTATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTATTTTAATTAGGATTTAGAATATT
1 TTAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATT
83206 ATAT
65 ATAT
* * *
83210 TT-TTTT-T-TTTGTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 TTATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTA
83263 AGATGTTTTA
Statistics
Matches: 115, Mismatches: 5, Indels: 14
0.86 0.04 0.10
Matches are distributed among these distances:
63 1 0.01
64 42 0.37
65 1 0.01
66 3 0.03
67 1 0.01
68 3 0.03
69 5 0.04
72 2 0.02
73 1 0.01
74 2 0.02
75 22 0.19
76 32 0.28
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (68 bp):
TTATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTAAGATTTAGAATATTA
TAT
Found at i:83290 original size:64 final size:64
Alignment explanation
Indices: 83158--83290 Score: 153
Period size: 64 Copynumber: 2.1 Consensus size: 64
83148 TTATCTTTGT
** ** * *
83158 ATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTTTTTTTTTTGT
1 ATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATAGCTTGCTTTTAGG
* * *
83222 ATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA-AGATGTTTTAGCTTGCTTTTAG
1 ATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAGA-ATATTATAGCTTGCTTTTAG
83285 G
64 G
83286 ATTTT
1 ATTTT
83291 GAAGGCTATA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
63 6 0.10
64 52 0.90
ACGTcount: A:0.27, C:0.02, G:0.15, T:0.56
Consensus pattern (64 bp):
ATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATAGCTTGCTTTTAGG
Found at i:83880 original size:22 final size:22
Alignment explanation
Indices: 83855--83904 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 22
83845 CTTTAATTTG
83855 TTTATTTAA-TTATTTTTTTACT
1 TTTATTTAATTTATTTTTTTA-T
83877 TTTATTTAATTCTTATTTTTTTAT
1 TTTATTTAA-T-TTATTTTTTTAT
83901 TTTA
1 TTTA
83905 ACCACAACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 9 0.36
24 5 0.20
25 11 0.44
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTAATTTATTTTTTTAT
Found at i:83973 original size:18 final size:19
Alignment explanation
Indices: 83939--83980 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
83929 CCTTTTATAT
83939 TTATTACTATTAATATTTA
1 TTATTACTATTAATATTTA
* *
83958 TTATTA-TATTATTATTTT
1 TTATTACTATTAATATTTA
83976 TTATT
1 TTATT
83981 TTAATATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTACTATTAATATTTA
Found at i:86652 original size:10 final size:10
Alignment explanation
Indices: 86619--86662 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
86609 ACTTGAAGTG
86619 AAAA-ATTAT
1 AAAATATTAT
*
86628 AAATTATTA-
1 AAAATATTAT
86637 AAAATATTAT
1 AAAATATTAT
86647 AAAATA--AT
1 AAAATATTAT
86655 AAAATATT
1 AAAATATT
86663 CGAAAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
8 8 0.28
9 11 0.38
10 10 0.34
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAATATTAT
Found at i:86658 original size:18 final size:19
Alignment explanation
Indices: 86619--86678 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 19
86609 ACTTGAAGTG
* *
86619 AAAA-ATTATAAATTATTA
1 AAAATATTATAAAATAATA
86637 AAAATATTATAAAATAAT-
1 AAAATATTATAAAATAATA
**
86655 AAAATATTCGAAAATAATCA
1 AAAATATTATAAAATAAT-A
86675 AAAA
1 AAAA
86679 AAAATAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 20 0.57
19 11 0.31
20 4 0.11
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATATTATAAAATAATA
Found at i:87702 original size:15 final size:16
Alignment explanation
Indices: 87648--87706 Score: 50
Period size: 15 Copynumber: 3.7 Consensus size: 16
87638 ACTCTTCAAG
** *
87648 AAAATAATTTATTTTG
1 AAAATAATTTATAATA
*
87664 AAAATAA-TTAAAATA
1 AAAATAATTTATAATA
87679 AAATTATAATTTATAAT-
1 AAA--ATAATTTATAATA
87696 AAAATAATTTA
1 AAAATAATTTA
87707 ACCACCAAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 15 0.43
16 7 0.20
17 7 0.20
18 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AAAATAATTTATAATA
Found at i:88901 original size:28 final size:30
Alignment explanation
Indices: 88870--88932 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 30
88860 TCTTGAAGTG
* * *
88870 AAAAATTACAAATTATTA-AAAAT-ATTAT
1 AAAAATGACAAAATATTAGAAAATAATAAT
*
88898 -AAAATGATAAAATATTAGAAAATAATAAT
1 AAAAATGACAAAATATTAGAAAATAATAAT
88927 AAAAAT
1 AAAAAT
88933 AAATTAATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 14 0.50
28 5 0.18
29 4 0.14
30 5 0.18
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (30 bp):
AAAAATGACAAAATATTAGAAAATAATAAT
Found at i:88909 original size:18 final size:18
Alignment explanation
Indices: 88888--88925 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
88878 CAAATTATTA
* *
88888 AAAATATTATAAAATGAT
1 AAAATATTAGAAAATAAT
88906 AAAATATTAGAAAATAAT
1 AAAATATTAGAAAATAAT
88924 AA
1 AA
88926 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (18 bp):
AAAATATTAGAAAATAAT
Found at i:88942 original size:28 final size:26
Alignment explanation
Indices: 88879--88947 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
88869 GAAAAATTAC
*
88879 AAATTATTAAAAATATTATAAAATGAT
1 AAATTATTAAAAATATAATAAAA-GAT
*
88906 AAAATATTAGAAAATAATAATAAAA-AT
1 AAATTATTA-AAAAT-ATAATAAAAGAT
88933 AAATTAATTACAAAA
1 AAATT-ATTA-AAAA
88948 ATTATAGCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 14 0.40
28 13 0.37
29 8 0.23
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
AAATTATTAAAAATATAATAAAAGAT
Found at i:94377 original size:28 final size:26
Alignment explanation
Indices: 94325--94380 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
94315 ACTCTTCAAG
*
94325 AAAATAAATTATTTTTAAAAATAAAT
1 AAAATAAATTATATTTAAAAATAAAT
* *
94351 AAAATAAAATTATAATTTATAATTAAAT
1 AAAAT-AAATTAT-ATTTAAAAATAAAT
94379 AA
1 AA
94381 TTTAACCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 7 0.28
28 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAAATTATATTTAAAAATAAAT
Found at i:96610 original size:28 final size:26
Alignment explanation
Indices: 96558--96613 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
96548 ACTCTTCAAG
*
96558 AAAATAAATTATTTTTAAAAATAAAT
1 AAAATAAATTATATTTAAAAATAAAT
* *
96584 AAAATAAAATTATAATTTATAATTAAAT
1 AAAAT-AAATTAT-ATTTAAAAATAAAT
96612 AA
1 AA
96614 TTTAACCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 7 0.28
28 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAAATTATATTTAAAAATAAAT
Found at i:98844 original size:28 final size:26
Alignment explanation
Indices: 98792--98847 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
98782 ACTCTTCAAG
*
98792 AAAATAAATTATTTTTAAAAATAAAT
1 AAAATAAATTATATTTAAAAATAAAT
* *
98818 AAAATAAAATTATAATTTATAATTAAAT
1 AAAAT-AAATTAT-ATTTAAAAATAAAT
98846 AA
1 AA
98848 TTTAACCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 7 0.28
28 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAAATTATATTTAAAAATAAAT
Found at i:103319 original size:28 final size:26
Alignment explanation
Indices: 103267--103322 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 26
103257 ACTCTTCAAG
*
103267 AAAATAAATTATTTTTAAAAATAAAT
1 AAAATAAATTATATTTAAAAATAAAT
* *
103293 AAAATAAAATTATAATTTATAATTAAAT
1 AAAAT-AAATTAT-ATTTAAAAATAAAT
103321 AA
1 AA
103323 TTTAACCACC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.20
27 7 0.28
28 13 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (26 bp):
AAAATAAATTATATTTAAAAATAAAT
Done.