Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000007.1 Hibiscus syriacus cultivar Beakdansim tig00000013_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: 109239
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:17816 original size:3 final size:3
Alignment explanation
Indices: 17810--17835 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
17800 CTTAATAATA
17810 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
17836 CATCATCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:17874 original size:13 final size:13
Alignment explanation
Indices: 17856--17880 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17846 TAAATAAATA
17856 AAAATAAAATAAT
1 AAAATAAAATAAT
17869 AAAATAAAATAA
1 AAAATAAAATAA
17881 GTACACTACC
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:25601 original size:18 final size:18
Alignment explanation
Indices: 25570--25604 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25560 ACTGAATATT
*
25570 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
25588 TGTCCTGAAGGACCACT
1 TGTCCCGAAGGACCACT
25605 GATAATCCCT
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:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:26251 original size:64 final size:65
Alignment explanation
Indices: 26176--26336 Score: 188
Period size: 64 Copynumber: 2.5 Consensus size: 65
26166 CCCTTGACGG
* *
26176 GTGCATCGATGCACTATC-TATGCATCGGTACA-TAAATCCCATTCGATGTTTATATTTT-AAGC
1 GTGCATCGATGCACTATCATGTGCATCGATACACT-AATCCCATTCGATGTTTATATTTTAAAG-
26238 GA
64 GA
* * * ** *
26240 GTGCATTGATGCACTA-CTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAGGA
1 GTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTATATTTTAAAGGA
*
26304 GTGCATCGATACACT-TCATGTGCATCGATACAC
1 GTGCATCGATGCACTATCATGTGCATCGATACAC
26337 CTTGAACAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 78 0.94
65 4 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (65 bp):
GTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTATATTTTAAAGGA
Found at i:26666 original size:19 final size:18
Alignment explanation
Indices: 26642--26683 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
26632 CGATGACAAG
26642 TCAAAT-TCAACCTCTGATT
1 TCAAATATCAA-CTCT-ATT
*
26661 TCAAATATGAACTCTATT
1 TCAAATATCAACTCTATT
26679 TCAAA
1 TCAAA
26684 ATTCCATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 10 0.48
20 3 0.14
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (18 bp):
TCAAATATCAACTCTATT
Found at i:28808 original size:24 final size:24
Alignment explanation
Indices: 28781--28837 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
28771 GTAAACGGAG
*
28781 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATCC
* *
28805 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAAAACAGAATCC
*
28829 AGATCAGAA
1 ATATCAGAA
28838 TTCAGGTAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATCC
Found at i:28812 original size:12 final size:12
Alignment explanation
Indices: 28783--28842 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
28773 AAACGGAGAT
* *
28783 ATCAGAAATCAA
1 ATCAGAATTCAG
* *
28795 AACAGAATTCAT
1 ATCAGAATTCAG
28807 ATCAG-ATATCAG
1 ATCAGAAT-TCAG
* *
28819 AACAGAATCCAG
1 ATCAGAATTCAG
28831 ATCAGAATTCAG
1 ATCAGAATTCAG
28843 GTAACGTATC
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.48, C:0.18, G:0.13, T:0.20
Consensus pattern (12 bp):
ATCAGAATTCAG
Found at i:29976 original size:18 final size:18
Alignment explanation
Indices: 29953--29987 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
29943 TGCCATCCGG
*
29953 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
29971 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
29988 GTCCTTTTGA
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:31326 original size:13 final size:13
Alignment explanation
Indices: 31308--31351 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
31298 CAATGGTCAA
31308 CGGGTCAACGGGT
1 CGGGTCAACGGGT
31321 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
31334 C-GGTCAACAGGT
1 CGGGTCAACGGGT
31346 CGGGTC
1 CGGGTC
31352 GGGTTGTGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.16, C:0.25, G:0.43, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:31340 original size:12 final size:12
Alignment explanation
Indices: 31310--31348 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
31300 ATGGTCAACG
31310 GGTCAACGGGTC
1 GGTCAACGGGTC
31322 GGGTCAACGGGTC
1 -GGTCAACGGGTC
*
31335 GGTCAACAGGTC
1 GGTCAACGGGTC
31347 GG
1 GG
31349 GTCGGGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
12 13 0.52
13 12 0.48
ACGTcount: A:0.18, C:0.23, G:0.44, T:0.15
Consensus pattern (12 bp):
GGTCAACGGGTC
Found at i:36005 original size:31 final size:31
Alignment explanation
Indices: 35967--36044 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
35957 ATTTCAAAAG
* * * *
35967 TAACAAAATGGTTAGTAACATTATTGATTTT
1 TAACAAAATGGTCACTAACATTATCGATTTA
* *
35998 TAACAAAATTGTCACTAACGTTATCGATTTA
1 TAACAAAATGGTCACTAACATTATCGATTTA
*
36029 TAAGAAAATGGTCACT
1 TAACAAAATGGTCACT
36045 CCGCCGTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (31 bp):
TAACAAAATGGTCACTAACATTATCGATTTA
Found at i:36671 original size:31 final size:31
Alignment explanation
Indices: 36636--36714 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
36626 ATAATGGTGG
* * * *
36636 AGTGATCAGTTTGTTACAAATTGATAACGTT
1 AGTGACCAGTTTGTTACAAACTAATAACATT
*
36667 AGTGACCATTTTGTTACAAACTAATAACATT
1 AGTGACCAGTTTGTTACAAACTAATAACATT
* *
36698 AGTGACTATTTTGTTAC
1 AGTGACCAGTTTGTTAC
36715 TTTTGAAACT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (31 bp):
AGTGACCAGTTTGTTACAAACTAATAACATT
Found at i:39287 original size:24 final size:24
Alignment explanation
Indices: 39260--39332 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
39250 CACGTACGTA
39260 AATTTTCTTAAGGATTAGATTAAT
1 AATTTTCTTAAGGATTAGATTAAT
39284 AATTTTCTTAAGGATTAGATTAAT
1 AATTTTCTTAAGGATTAGATTAAT
* *
39308 AATTTTCTTAAAGATATAGAATAAT
1 AATTTTCTTAAGGAT-TAGATTAAT
39333 TAAGGAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 38 0.83
25 8 0.17
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (24 bp):
AATTTTCTTAAGGATTAGATTAAT
Found at i:45992 original size:22 final size:24
Alignment explanation
Indices: 45965--46008 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
45955 AAAGATGGTG
45965 CTTCTTT-TAGTTT-ATCTATTCT
1 CTTCTTTCTAGTTTCATCTATTCT
*
45987 CTTCTTTCTCGTTTCATCTATT
1 CTTCTTTCTAGTTTCATCTATT
46009 ATTCTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 5 0.26
24 7 0.37
ACGTcount: A:0.11, C:0.23, G:0.05, T:0.61
Consensus pattern (24 bp):
CTTCTTTCTAGTTTCATCTATTCT
Found at i:57068 original size:2 final size:2
Alignment explanation
Indices: 57061--57088 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
57051 GGTTAATTGC
57061 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
57089 GTAACAACCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57835 original size:10 final size:10
Alignment explanation
Indices: 57806--57874 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
57796 GCTGCTGGAA
57806 AACCGGTTTG
1 AACCGGTTTG
*
57816 -ACCAGTTTTG
1 AACC-GGTTTG
57826 AACCGGTTTG
1 AACCGGTTTG
*
57836 -ACCGGTTCG
1 AACCGGTTTG
57845 AACCGGTTTG
1 AACCGGTTTG
*
57855 -ACCGGTCTG
1 AACCGGTTTG
*
57864 AACCGGGTTG
1 AACCGGTTTG
57874 A
1 A
57875 CCCGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:57849 original size:19 final size:19
Alignment explanation
Indices: 57806--57876 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
57796 GCTGCTGGAA
* *
57806 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
57826 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
57845 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
*
57864 AACCGGGTTGACC
1 AACCGGTTTGACC
57877 CGACCCGACT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
18 2 0.04
19 32 0.68
20 13 0.28
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:57892 original size:17 final size:17
Alignment explanation
Indices: 57870--57910 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
57860 TCTGAACCGG
*
57870 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
57887 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
57904 GTTGACC
1 GTTGACC
57911 GTTGACCGTG
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:0.17, C:0.41, G:0.24, T:0.17
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:57912 original size:7 final size:7
Alignment explanation
Indices: 57900--57936 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
57890 GACCCGACCC
57900 GACCGTT
1 GACCGTT
57907 GACCGTT
1 GACCGTT
57914 GACCG-T
1 GACCGTT
57920 GACCGTT
1 GACCGTT
57927 GACCGTT
1 GACCGTT
57934 GAC
1 GAC
57937 TTTCTTTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:57924 original size:13 final size:13
Alignment explanation
Indices: 57900--57932 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
57890 GACCCGACCC
57900 GACCGTTGACCGTT
1 GACCG-TGACCGTT
57914 GACCGTGACCGTT
1 GACCGTGACCGTT
57927 GACCGT
1 GACCGT
57933 TGACTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (13 bp):
GACCGTGACCGTT
Found at i:65121 original size:10 final size:10
Alignment explanation
Indices: 65092--65160 Score: 81
Period size: 10 Copynumber: 7.1 Consensus size: 10
65082 GCTGCTGGAA
65092 AACCGGTTTG
1 AACCGGTTTG
*
65102 -ACCAGTTTTG
1 AACC-GGTTTG
65112 AACCGGTTTG
1 AACCGGTTTG
*
65122 -ACCGGTTCG
1 AACCGGTTTG
65131 AACCGGTTTG
1 AACCGGTTTG
*
65141 -ACCGGTCTG
1 AACCGGTTTG
65150 AACCGGTTTG
1 AACCGGTTTG
65160 A
1 A
65161 CCCGACCCGA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
9 19 0.39
10 27 0.55
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:65135 original size:19 final size:19
Alignment explanation
Indices: 65092--65162 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
65082 GCTGCTGGAA
* *
65092 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTTCG
65112 AACCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTCG
65131 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTC-G
65150 AACCGGTTTGACC
1 AACCGGTTTGACC
65163 CGACCCGACT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
18 2 0.04
19 33 0.69
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.28
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTCG
Found at i:65179 original size:17 final size:17
Alignment explanation
Indices: 65157--65212 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
65147 CTGAACCGGT
65157 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACTG
65174 TTGACCCGACCCGACTG
1 TTGACCCGACCCGACTG
*
65191 TTGACCCGACCCGACCG
1 TTGACCCGACCCGACTG
65208 TTGAC
1 TTGAC
65213 TGTTGACCGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 38 1.00
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (17 bp):
TTGACCCGACCCGACTG
Found at i:68425 original size:15 final size:15
Alignment explanation
Indices: 68402--68444 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
68392 AATTAAGAAG
*
68402 AAGGATGTTGTGGAT
1 AAGGCTGTTGTGGAT
68417 AAGGCTGTTGTGGAT
1 AAGGCTGTTGTGGAT
68432 AAGGCTGTTGTGG
1 AAGGCTGTTGTGG
68445 GAGTTGTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.21, C:0.05, G:0.42, T:0.33
Consensus pattern (15 bp):
AAGGCTGTTGTGGAT
Found at i:72777 original size:24 final size:23
Alignment explanation
Indices: 72750--72809 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 23
72740 ATTTAAAAAA
*
72750 ATTAAAAAAACTAAAATTAATTTT
1 ATTAAAAAAAATAAAATT-ATTTT
*
72774 ATTAAAAAATAAATATAATTATTTT
1 ATT-AAAAA-AAATAAAATTATTTT
72799 -TTAAAAAAAAT
1 ATTAAAAAAAAT
72810 CCCCCCCGTC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 4 0.12
23 5 0.16
24 5 0.16
25 10 0.31
26 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTAAAAAAAATAAAATTATTTT
Found at i:76233 original size:21 final size:19
Alignment explanation
Indices: 76192--76246 Score: 74
Period size: 21 Copynumber: 2.8 Consensus size: 19
76182 TATTGTTCAT
76192 AGTTTGGAAACTTTGTAAG
1 AGTTTGGAAACTTTGTAAG
*
76211 AGTTTGGAAACTCTTATTAAG
1 AGTTTGGAAACT-TT-GTAAG
*
76232 AGTTTCGAAACTTTG
1 AGTTTGGAAACTTTG
76247 CACCTAGAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 12 0.39
20 4 0.13
21 15 0.48
ACGTcount: A:0.31, C:0.09, G:0.22, T:0.38
Consensus pattern (19 bp):
AGTTTGGAAACTTTGTAAG
Found at i:76319 original size:9 final size:9
Alignment explanation
Indices: 76305--76386 Score: 83
Period size: 9 Copynumber: 8.4 Consensus size: 9
76295 TAAGTAAGAG
76305 TTTCGAAAC
1 TTTCGAAAC
76314 TTTCGAAAC
1 TTTCGAAAC
*
76323 TTTCGTCAAAG
1 TTTCG--AAAC
76334 TTTCGAAAC
1 TTTCGAAAC
*
76343 TTTCGTCAAAG
1 TTTCG--AAAC
76354 TTTCGAAAC
1 TTTCGAAAC
*
76363 TTTCGTCAAAG
1 TTTCG--AAAC
76374 TTTCGAAAC
1 TTTCGAAAC
76383 TTTC
1 TTTC
76387 AAGAACAGTG
Statistics
Matches: 61, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
9 37 0.61
11 24 0.39
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (9 bp):
TTTCGAAAC
Found at i:76339 original size:20 final size:20
Alignment explanation
Indices: 76314--76386 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
76304 GTTTCGAAAC
76314 TTTCGAAACTTTCGTCAAAG
1 TTTCGAAACTTTCGTCAAAG
76334 TTTCGAAACTTTCGTCAAAG
1 TTTCGAAACTTTCGTCAAAG
76354 TTTCGAAACTTTCGTCAAAG
1 TTTCGAAACTTTCGTCAAAG
76374 TTTCGAAACTTTC
1 TTTCGAAACTTTC
76387 AAGAACAGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.37
Consensus pattern (20 bp):
TTTCGAAACTTTCGTCAAAG
Found at i:76357 original size:11 final size:11
Alignment explanation
Indices: 76323--76378 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
76313 CTTTCGAAAC
76323 TTTCGTCAAAG
1 TTTCGTCAAAG
*
76334 TTTCG--AAAC
1 TTTCGTCAAAG
76343 TTTCGTCAAAG
1 TTTCGTCAAAG
*
76354 TTTCG--AAAC
1 TTTCGTCAAAG
76363 TTTCGTCAAAG
1 TTTCGTCAAAG
76374 TTTCG
1 TTTCG
76379 AAACTTTCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.38
Consensus pattern (11 bp):
TTTCGTCAAAG
Found at i:76455 original size:20 final size:20
Alignment explanation
Indices: 76402--76455 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
76392 CAGTGTGTTT
*
76402 AAAAGTTTTGATACTTTCAC
1 AAAAGTTTTGAAACTTTCAC
*
76422 AAAA-TTTTGAAACTTTCTC
1 AAAAGTTTTGAAACTTTCAC
*
76441 AAAAGTTTCGAAACT
1 AAAAGTTTTGAAACT
76456 ACATGTGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (20 bp):
AAAAGTTTTGAAACTTTCAC
Found at i:77613 original size:17 final size:18
Alignment explanation
Indices: 77591--77630 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
77581 TTAAATTATA
77591 TATTTAATTATT-TATTT
1 TATTTAATTATTATATTT
* *
77608 TATTTAATTCTTATCTTT
1 TATTTAATTATTATATTT
77626 TATTT
1 TATTT
77631 TAAAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTTAATTATTATATTT
Found at i:82914 original size:14 final size:14
Alignment explanation
Indices: 82895--82981 Score: 83
Period size: 13 Copynumber: 6.1 Consensus size: 14
82885 AGACACTAGT
82895 TTTTTTTCATT-TTA
1 TTTTTTT-ATTATTA
82909 TTTTTTTATT-TT-
1 TTTTTTTATTATTA
82921 TTTATTTTATTATTA
1 TTT-TTTTATTATTA
82936 TTATTATTATATTATTA
1 TT-TT-TT-TATTATTA
82953 TTTTTTTA-TATTA
1 TTTTTTTATTATTA
**
82966 TTAATTTATTATTA
1 TTTTTTTATTATTA
82980 TT
1 TT
82982 ACATATTACA
Statistics
Matches: 64, Mismatches: 2, Indels: 14
0.80 0.03 0.17
Matches are distributed among these distances:
12 3 0.05
13 23 0.36
14 18 0.28
15 5 0.08
16 5 0.08
17 10 0.16
ACGTcount: A:0.24, C:0.01, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTTTTATTATTA
Found at i:82915 original size:8 final size:8
Alignment explanation
Indices: 82904--82961 Score: 62
Period size: 8 Copynumber: 6.8 Consensus size: 8
82894 TTTTTTTTCA
82904 TTTTATTT
1 TTTTATTT
82912 TTTTATTT
1 TTTTATTT
82920 TTTTATTT
1 TTTTATTT
*
82928 TATTATTAT
1 TTTTATT-T
*
82937 TATTATTAT
1 TTTTATT-T
82946 ATTATTATTT
1 -TT-TTATTT
82956 TTTTAT
1 TTTTAT
82962 ATTATTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
8 26 0.58
9 12 0.27
10 2 0.04
11 5 0.11
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTATTT
Found at i:82915 original size:16 final size:16
Alignment explanation
Indices: 82894--82975 Score: 69
Period size: 16 Copynumber: 5.1 Consensus size: 16
82884 AAGACACTAG
*
82894 TTTTTTT-TCATTTTA
1 TTTTTTTATTATTTTA
*
82909 TTTTTTTATTTTTTTA
1 TTTTTTTATTATTTTA
*
82925 TTTTATTATTATTATTA
1 TTTTTTTATTATT-TTA
* *
82942 TTATATTATTATTTT-
1 TTTTTTTATTATTTTA
* *
82957 TTTATATTATTAATTTA
1 TTT-TTTTATTATTTTA
82974 TT
1 TT
82976 ATTATTACAT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
15 9 0.16
16 30 0.54
17 17 0.30
ACGTcount: A:0.23, C:0.01, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTTATTATTTTA
Found at i:82933 original size:3 final size:3
Alignment explanation
Indices: 82922--82982 Score: 69
Period size: 3 Copynumber: 22.0 Consensus size: 3
82912 TTTTATTTTT
*
82922 TTA TT- TTA TTA TTA TTA TTA TTA -TA TTA TTA TT- TTT TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
82966 TTA AT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
82983 CATATTACAG
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
2 9 0.18
3 41 0.82
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:82982 original size:14 final size:14
Alignment explanation
Indices: 82930--82982 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
82920 TTTTATTTTA
82930 TTATTATTATT-AT
1 TTATTATTATTAAT
**
82943 TATATTATTATTTTT
1 T-TATTATTATTAAT
82958 TTA-TATTATTAAT
1 TTATTATTATTAAT
82971 TTATTATTATTA
1 TTATTATTATTA
82983 CATATTACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 12 0.35
14 20 0.59
15 2 0.06
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TTATTATTATTAAT
Found at i:82987 original size:24 final size:23
Alignment explanation
Indices: 82923--82989 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
82913 TTTATTTTTT
*
82923 TATT-TTATTATTATTATTATTA
1 TATTATTATTATTAATATTATTA
* *
82945 TATTATTATTTTTTTATATTATTA
1 TATTATTA-TTATTAATATTATTA
82969 -ATTTATTATTATTACATATTA
1 TA-TTATTATTATTA-ATATTA
82990 CAGGCCCATT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
22 4 0.11
23 8 0.22
24 24 0.67
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (23 bp):
TATTATTATTATTAATATTATTA
Found at i:83998 original size:15 final size:14
Alignment explanation
Indices: 83960--84001 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
83950 TTCCTATACC
83960 TTATAATTTAGTCT
1 TTATAATTTAGTCT
*
83974 TT-TAATTTTATTTCT
1 TTATAA-TTTA-GTCT
83989 TTATAATTTAGTC
1 TTATAATTTAGTC
84002 ATTGACCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
13 3 0.13
14 8 0.35
15 9 0.39
16 3 0.13
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (14 bp):
TTATAATTTAGTCT
Found at i:84350 original size:21 final size:20
Alignment explanation
Indices: 84326--84365 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
84316 ATTTTAGTCA
*
84326 TTATTTATTTATTATTTAATT
1 TTATTGATTTATT-TTTAATT
*
84347 TTATTGGTTTATTTTTAAT
1 TTATTGATTTATTTTTAAT
84366 ATATTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTATTGATTTATTTTTAATT
Found at i:84379 original size:3 final size:3
Alignment explanation
Indices: 84371--84395 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
84361 TTAATATATT
84371 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
84396 TATTATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:84796 original size:2 final size:2
Alignment explanation
Indices: 84789--84822 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
84779 ATAAAATTAA
84789 AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84823 TTTCTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85365 original size:26 final size:27
Alignment explanation
Indices: 85313--85370 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
85303 TAATTCTTTC
*
85313 TTTTCAAAATTTTTATATATACTTATTA
1 TTTTCAAAATATTTATATATAC-TATTA
* *
85341 TTTTCATAATATTTATATGTA-TATTA
1 TTTTCAAAATATTTATATATACTATTA
85367 TTTT
1 TTTT
85371 TTTATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTCAAAATATTTATATATACTATTA
Found at i:85379 original size:29 final size:30
Alignment explanation
Indices: 85313--85382 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
85303 TAATTCTTTC
*
85313 TTTTCA-AA-ATTTTTATATATACTTATTA
1 TTTTCATAATATTTATATATATACTTATTA
*
85341 TTTTCATAATATTTATATGTATA-TTATT-
1 TTTTCATAATATTTATATATATACTTATTA
*
85369 TTTTTATTAATATT
1 TTTTCA-TAATATT
85383 ATTTTATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 11 0.31
29 14 0.39
30 11 0.31
ACGTcount: A:0.33, C:0.04, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTCATAATATTTATATATATACTTATTA
Found at i:85392 original size:22 final size:23
Alignment explanation
Indices: 85350--85392 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
85340 ATTTTCATAA
*
85350 TATTTATATGTATATTATTTTTT
1 TATTAATATGTATATTATTTTTT
*
85373 TATTAATAT-TATTTTATTTT
1 TATTAATATGTATATTATTTT
85393 CAAGTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TATTAATATGTATATTATTTTTT
Found at i:86291 original size:35 final size:36
Alignment explanation
Indices: 86244--86311 Score: 102
Period size: 35 Copynumber: 1.9 Consensus size: 36
86234 CTATGCACAC
* *
86244 AAAGATTCTGTTATATTAATACCAAAAGTATTCCAA
1 AAAGATTCTGTTAGATTAATACCAAAAGCATTCCAA
*
86280 AAAGA-TCTGTTAGATTGATACCAAAAGCATTC
1 AAAGATTCTGTTAGATTAATACCAAAAGCATTC
86312 TATGGTAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 24 0.83
36 5 0.17
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (36 bp):
AAAGATTCTGTTAGATTAATACCAAAAGCATTCCAA
Found at i:89912 original size:8 final size:8
Alignment explanation
Indices: 89899--89928 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
89889 ATCCTTGCAA
89899 ATATATGT
1 ATATATGT
*
89907 ATATATAT
1 ATATATGT
89915 ATATATGT
1 ATATATGT
89923 ATATAT
1 ATATAT
89929 ATCCCTTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (8 bp):
ATATATGT
Found at i:93767 original size:75 final size:75
Alignment explanation
Indices: 93635--93803 Score: 239
Period size: 75 Copynumber: 2.3 Consensus size: 75
93625 ACAAGAAGCA
* * * * *
93635 AATGATGGAGCATGCTGAAAGCCCATTTCAATCATAATCAGGAATATTGACACATTTTGAACGTT
1 AATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATATTGACACATTTTGAACGTT
93700 TGTATTAGCC
66 TGTATTAGCC
* * *** *
93710 AATGTTGGGGCATGCTGAAAACCCCTTTCAATCAGAATCAAGAATGTTGATTTATTTTGAATGTT
1 AATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATATTGACACATTTTGAACGTT
93775 TGTATTAGCC
66 TGTATTAGCC
93785 AATGTTGGGGCATGCTGAA
1 AATGTTGGGGCATGCTGAA
93804 GATCCATATC
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (75 bp):
AATGTTGGGGCATGCTGAAAACCCATTTCAATCAGAATCAAGAATATTGACACATTTTGAACGTT
TGTATTAGCC
Found at i:95101 original size:22 final size:22
Alignment explanation
Indices: 95076--95127 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
95066 TACATTCTTA
95076 AAAGATGATAAATTCTCTTTTC
1 AAAGATGATAAATTCTCTTTTC
* *
95098 AAAGATGATAGATTCTCTTTTT
1 AAAGATGATAAATTCTCTTTTC
*
95120 ATAGATGA
1 AAAGATGA
95128 AAGCCTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (22 bp):
AAAGATGATAAATTCTCTTTTC
Found at i:95681 original size:112 final size:113
Alignment explanation
Indices: 95484--96034 Score: 774
Period size: 112 Copynumber: 4.9 Consensus size: 113
95474 GATTCAAATC
** * * * *
95484 CATCACTTAATGGATCAACATTTCCA-G-AGAAGTTCATAATGAGAAGAACTTATTTGAAGAAGG
1 CATCACTCGATGGATCAGCATTGCCAGGTAG-AGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
95547 AAGAAGAAGATCATAATGAGAAGAACTTCTTCAACCTTTTGCTCGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* * *
95596 CATCACTCGATGGATCAGCATAGCCAGTTAGAGTTCATAATGAGTAGAACTCATCTGAAGAAGG-
1 CATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
95660 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
*
95708 CATCACTTGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
95773 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCAAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* * *
95821 AATCACTCGATGGATCA-AATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAATAAGG-
1 CATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * *
95884 AGAATAAGTTCATAATGAGAAGAGCTTGTTCAACTTTTTACTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* ** * * *
95932 CATCACTAGATAAATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTTATCTGAAG-AGG
1 CATCACTCGATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
95995 AAGAAGAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
96035 TCTTGACGCT
Statistics
Matches: 395, Mismatches: 38, Indels: 12
0.89 0.09 0.03
Matches are distributed among these distances:
111 58 0.15
112 243 0.62
113 92 0.23
114 2 0.01
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
CATCACTCGATGGATCAGCATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
Found at i:96049 original size:112 final size:113
Alignment explanation
Indices: 95484--96278 Score: 772
Period size: 112 Copynumber: 6.9 Consensus size: 113
95474 GATTCAAATC
* * *
95484 CATCACTTA-ATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTTATTTGAAGAAGG
1 CATCAC-TAGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
95547 AAGAAGAAGATCATAATGAGAAGAACTTCTTCAACCTTTTGCTCGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* * * ** * *
95596 CATCACTCGATGGATCAGCATAGCCAGTTAGAGTTCATAATGAGTAGAACTCATCTGAAGAAGG-
1 CATCACTAGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
95660 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* * *
95708 CATCACTTGATGGATCAGCATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCACTAGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* *
95772 AAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTCAAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
* * * *
95821 AATCACTCGATGGATCAA-ATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAATAAGG
1 CATCACTAGATGGATCAACATTGCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * * *
95884 -AGAATAAGTTCATAATGAGAAGAGCTTGTTCAACTTTTTACTCGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
** *
95932 CATCACTAGATAAATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGA
1 CATCACTAGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* * * * *
95996 AGAAGAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTTTCTTGACGCTAT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGA--AT-T
** * * * *
96047 CA-CAGAAAGAGATAGATCAACATACACTTTTCCAGAGAAAGTTCATATTGAGAAGAACTTATCT
1 CATC---ACTAGATGGAT---CA-ACA--TTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
* * * * * *
96111 GAA-CAGGAAGATGAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTAG-T-GTAACT
57 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCG-AATT
* * * * *
96166 CTATCACAGAAGGAGATAGGTTAGCATCAACATTTCCACA-AGGAGTTCATAATTAGAAGAACTC
1 C-ATCAC-----TAGAT--G---G-ATCAACATTGCCAGAGA-AAGTTCATAATGAGAAGAACTC
*
96230 ATCTGAAGAAGG-AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
53 ATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
96279 GCCTTAATTC
Statistics
Matches: 584, Mismatches: 63, Indels: 61
0.82 0.09 0.09
Matches are distributed among these distances:
111 60 0.10
112 246 0.42
113 92 0.16
114 2 0.00
115 3 0.01
117 8 0.01
118 1 0.00
119 2 0.00
120 3 0.01
121 5 0.01
122 3 0.01
123 148 0.25
124 3 0.01
125 3 0.01
126 2 0.00
128 1 0.00
129 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (113 bp):
CATCACTAGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTCGAATT
Found at i:96105 original size:123 final size:123
Alignment explanation
Indices: 95938--96278 Score: 417
Period size: 123 Copynumber: 2.8 Consensus size: 123
95928 AATTCATCAC
* *
95938 TAGAT-AA-ATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 TAGATCAACATCAACATTTCCAGAGAAAGTTCATATTGAGAAGAACTTATCTGAAGAGGAAGAAG
* * *
96001 AAGTTCATAATAAGAAGAGCTTGTTCAACCTTT-TTCTTGACGCTATCACAGAAAGAGA
66 AAGTTCATAATAAGAAGAGCTTGTTCAACCTTTAGT-GTAACGCTATCACAGAAAGAGA
* * *
96059 TAGATCAACAT-ACACTTTTCCAGAGAAAGTTCATATTGAGAAGAACTTATCTGAACAGGAAGAT
1 TAGATCAACATCA-ACATTTCCAGAGAAAGTTCATATTGAGAAGAACTTATCTGAAGAGGAAGAA
* *
96123 GAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTAGTGTAACTCTATCACAGAAGGAGA
65 GAAGTTCATAATAAGAAGAGCTTGTTCAACCTTTAGTGTAACGCTATCACAGAAAGAGA
* * * * * *
96182 TAGGTTAGCATCAACATTTCCACA-AGGAGTTCATAATT-AGAAGAACTCATCTGAAGAAGG-AG
1 TAGATCAACATCAACATTTCCAGAGA-AAGTTCAT-ATTGAGAAGAACTTATCTGAAG-AGGAAG
* **
96244 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
63 AAGAAGTTCATAATAAGAAGAGCTTGTTCAACCTT
96279 GCCTTAATTC
Statistics
Matches: 190, Mismatches: 22, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
121 5 0.03
122 4 0.02
123 173 0.91
124 8 0.04
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.26
Consensus pattern (123 bp):
TAGATCAACATCAACATTTCCAGAGAAAGTTCATATTGAGAAGAACTTATCTGAAGAGGAAGAAG
AAGTTCATAATAAGAAGAGCTTGTTCAACCTTTAGTGTAACGCTATCACAGAAAGAGA
Found at i:96639 original size:6 final size:6
Alignment explanation
Indices: 96628--96667 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
96618 CACTAGTTTT
96628 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
96668 GTTTTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCA
Found at i:96679 original size:6 final size:6
Alignment explanation
Indices: 96627--96734 Score: 58
Period size: 6 Copynumber: 17.3 Consensus size: 6
96617 ACACTAGTTT
* * * * *
96627 TTTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTGT- TTTTTA
1 TTTTT-A TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT-TA TTTTTA
* * * * *
96676 TTTTTA TTTTTA TTATTTTA TTTGTTTA TTATTA TTATTA -TATTA TTATTG
1 TTTTTA TTTTTA -T-TTTTA -TT-TTTA TTTTTA TTTTTA TTTTTA TTTTTA
96727 TTTTTA TT
1 TTTTTA TT
96735 ATTAATTTAT
Statistics
Matches: 89, Mismatches: 6, Indels: 13
0.82 0.06 0.12
Matches are distributed among these distances:
5 6 0.07
6 64 0.72
7 8 0.09
8 11 0.12
ACGTcount: A:0.19, C:0.06, G:0.03, T:0.73
Consensus pattern (6 bp):
TTTTTA
Found at i:96694 original size:8 final size:8
Alignment explanation
Indices: 96683--96747 Score: 55
Period size: 8 Copynumber: 8.1 Consensus size: 8
96673 TTATTTTTAT
96683 TTTTATTA
1 TTTTATTA
96691 TTTTATT-
1 TTTTATTA
96698 TGTTTATTA
1 T-TTTATTA
96707 TTATTATTA
1 TT-TTATTA
*
96716 TATTATTA
1 TTTTATTA
96724 TTGTT-TT-
1 TT-TTATTA
*
96731 TATTATTA
1 TTTTATTA
*
96739 ATTTATTA
1 TTTTATTA
96747 T
1 T
96748 CATTACATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
6 2 0.04
7 4 0.09
8 29 0.64
9 10 0.22
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (8 bp):
TTTTATTA
Found at i:96694 original size:14 final size:15
Alignment explanation
Indices: 96669--96738 Score: 74
Period size: 14 Copynumber: 4.7 Consensus size: 15
96659 TTTCATTTTG
*
96669 TTTT-TTATTTTTAT
1 TTTTATTATTATTAT
96683 TTTTATTATT-TTATT
1 TTTTATTATTATTA-T
96698 TGTTTATTATTATTA-
1 T-TTTATTATTATTAT
* *
96713 TTATATTATTATTGT
1 TTTTATTATTATTAT
96728 TTTTATTATTA
1 TTTTATTATTA
96739 ATTTATTATC
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
14 18 0.38
15 18 0.38
16 9 0.19
17 3 0.06
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTTATTATTATTAT
Found at i:96707 original size:3 final size:3
Alignment explanation
Indices: 96673--96752 Score: 62
Period size: 3 Copynumber: 28.0 Consensus size: 3
96663 ATTTTGTTTT
* *
96673 TTA TTT TTA TTT TTA TTA TT- TTA TT- TGT- TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
* * * *
96716 -TA TTA TTA TTG TTT TTA TTA TTA AT- TTA TTA TCA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
96753 CATATTACAG
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
2 7 0.11
3 54 0.89
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:98193 original size:15 final size:14
Alignment explanation
Indices: 98155--98205 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
98145 CATTGTTTAG
98155 TTAT-TATTTAATT
1 TTATATATTTAATT
* *
98168 TTATATGTTTATTT
1 TTATATATTTAATT
98182 TTAATATATTTAATT
1 TT-ATATATTTAATT
98197 ATTAT-TATT
1 -TTATATATT
98206 ATTATGTAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 13 0.42
15 12 0.39
16 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (14 bp):
TTATATATTTAATT
Found at i:99377 original size:5 final size:5
Alignment explanation
Indices: 99367--99447 Score: 67
Period size: 5 Copynumber: 15.8 Consensus size: 5
99357 TCCGATCTAT
*
99367 TTTTA TTTTA TTTTA TTTTA TTTTA TTACTT- TTTTA TTTTTA TTTTG
1 TTTTA TTTTA TTTTA TTTTA TTTTA TT--TTA TTTTA -TTTTA TTTTA
* * * *
99414 TGTTTT TTTTA -TTTA ATTAA TTTTA TTATA TTTT
1 T-TTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
99448 TCTCTGAACA
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
4 6 0.10
5 43 0.69
6 11 0.18
7 2 0.03
ACGTcount: A:0.20, C:0.01, G:0.02, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:100479 original size:68 final size:68
Alignment explanation
Indices: 100370--100506 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
100360 GCCTATACGT
100370 TTATATTTCCACTAGTGAACCAAATTTGAGTCTATTTGTCTTTCTTTGTTTTACACCTCATAATT
1 TTATATTTCCACTAGTGAACCAAATTTGAGTCTATTTGTCTTTCTTTGTTTTACACCTCATAATT
100435 AAA
66 AAA
*
100438 TTATATTTCCACTAGTGAACTAAATTTGAGTCTATTTGTCTTTCTTTGTTTTACACCTCATAATT
1 TTATATTTCCACTAGTGAACCAAATTTGAGTCTATTTGTCTTTCTTTGTTTTACACCTCATAATT
100503 AAA
66 AAA
100506 T
1 T
100507 CCGAAACCTT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.47
Consensus pattern (68 bp):
TTATATTTCCACTAGTGAACCAAATTTGAGTCTATTTGTCTTTCTTTGTTTTACACCTCATAATT
AAA
Found at i:102710 original size:26 final size:28
Alignment explanation
Indices: 102669--102809 Score: 78
Period size: 29 Copynumber: 5.0 Consensus size: 28
102659 TAGTCCACAG
*
102669 TAAA-AATTACAGAAATGTCA-T-TTTT
1 TAAACAATTACAGAAATATCACTGTTTT
102694 TAAACAATTACCA-AAATATCACTGTTTT
1 TAAACAATTA-CAGAAATATCACTGTTTT
* * **
102722 TAACAATAATTACCGAAATATCACCATTTT
1 T-A-AACAATTACAGAAATATCACTGTTTT
* * **
102752 AACAATAATTACCA-AAATATCACCATTTT
1 TA-AACAATTA-CAGAAATATCACTGTTTT
* *
102781 AACAATAATTACCA-AAATATCACTGTTTT
1 TA-AACAATTA-CAGAAATATCACTGTTTT
102810 AACAATAATT
Statistics
Matches: 99, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
25 4 0.04
26 12 0.12
27 3 0.03
28 5 0.05
29 54 0.55
30 21 0.21
ACGTcount: A:0.45, C:0.17, G:0.04, T:0.35
Consensus pattern (28 bp):
TAAACAATTACAGAAATATCACTGTTTT
Found at i:102761 original size:29 final size:29
Alignment explanation
Indices: 102699--102953 Score: 244
Period size: 29 Copynumber: 8.7 Consensus size: 29
102689 TTTTTTAAAC
**
102699 AATTACCAAAATATCACTGTTTTTAACAAT
1 AATTACCAAAATATCAC-CATTTTAACAAT
*
102729 AATTACCGAAATATCACCATTTTAACAAT
1 AATTACCAAAATATCACCATTTTAACAAT
102758 AATTACCAAAATATCACCATTTTAACAAT
1 AATTACCAAAATATCACCATTTTAACAAT
**
102787 AATTACCAAAATATCACTGTTTTAACAAT
1 AATTACCAAAATATCACCATTTTAACAAT
* *** *
102816 AATTGCCAAAATATCATTGTTTTAACTAT
1 AATTACCAAAATATCACCATTTTAACAAT
* **
102845 AATTGCCAAAATATCACTGTTTTAA-AATT
1 AATTACCAAAATATCACCATTTTAACAA-T
* * * *
102874 AATTACGAAAATAACACCTTTTTTTAAAAAT
1 AATTACCAAAATATCACC--ATTTTAACAAT
* * * *
102905 AAATACGAAAATAACA-CACTTTTAAAAAT
1 AATTACCAAAATATCACCA-TTTTAACAAT
* *
102934 AATTACGAAAATAACACCAT
1 AATTACCAAAATATCACCAT
102954 AACCGAAATT
Statistics
Matches: 200, Mismatches: 19, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
28 1 0.00
29 156 0.78
30 19 0.09
31 22 0.11
32 2 0.01
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (29 bp):
AATTACCAAAATATCACCATTTTAACAAT
Found at i:102841 original size:87 final size:88
Alignment explanation
Indices: 102699--102953 Score: 291
Period size: 87 Copynumber: 2.9 Consensus size: 88
102689 TTTTTTAAAC
*
102699 AATTACCAAAATATCACTGTTTTTAACAATAATTACCGAAATATCACCATTTTAACAATAATTAC
1 AATTACCAAAATATCACTGTTTTTAACAATAATTACCAAAATATCACCATTTTAACAATAATTAC
102764 CAAAATATCACCATTTTAACAA-T
66 CAAAATATCACCATTTTAA-AATT
* *** * *
102787 AATTACCAAAATATCACTG-TTTTAACAATAATTGCCAAAATATCATTGTTTTAACTATAATTGC
1 AATTACCAAAATATCACTGTTTTTAACAATAATTACCAAAATATCACCATTTTAACAATAATTAC
**
102851 CAAAATATCACTGTTTTAAAATT
66 CAAAATATCACCATTTTAAAATT
* * * * * * * *
102874 AATTACGAAAATAACACCTTTTTTTAAAAATAAATACGAAAATAACA-CACTTTTAAAAATAATT
1 AATTACCAAAATATCA-CTGTTTTTAACAATAATTACCAAAATATCACCA-TTTTAACAATAATT
* *
102938 ACGAAAATAACACCAT
64 ACCAAAATATCACCAT
102954 AACCGAAATT
Statistics
Matches: 137, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
86 2 0.01
87 70 0.51
88 21 0.15
89 44 0.32
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (88 bp):
AATTACCAAAATATCACTGTTTTTAACAATAATTACCAAAATATCACCATTTTAACAATAATTAC
CAAAATATCACCATTTTAAAATT
Found at i:104840 original size:17 final size:18
Alignment explanation
Indices: 104818--104859 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
104808 CTTTAAATTA
*
104818 TTTATTTAATTATT-TCT
1 TTTATTTAATTATTATAT
104835 TTTATTTAATTATTATAT
1 TTTATTTAATTATTATAT
104853 TTTATTT
1 TTTATTT
104860 TAAAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTATTTAATTATTATAT
Found at i:104917 original size:15 final size:15
Alignment explanation
Indices: 104897--104934 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
104887 ATTTTACTAC
104897 TATTATTTAT-TATTT
1 TATTA-TTATCTATTT
104912 TATTATTATCTATTT
1 TATTATTATCTATTT
104927 TATT-TTAT
1 TATTATTAT
104935 TAAATCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTATTATCTATTT
Found at i:105429 original size:24 final size:24
Alignment explanation
Indices: 105377--105466 Score: 141
Period size: 23 Copynumber: 3.9 Consensus size: 24
105367 GAGTGCCATA
105377 TTTGTCC-GAAGGACCACATA-GT
1 TTTGTCCTGAAGGACCACATAGGT
105399 TTTGTCCTGAAGGACCACATAGGT
1 TTTGTCCTGAAGGACCACATAGGT
105423 TTTGTCCTGAAGGACCACATAGG-
1 TTTGTCCTGAAGGACCACATAGGT
* *
105446 TTTGTCCCGAAGGACAACATA
1 TTTGTCCTGAAGGACCACATA
105467 TAACCCTCGA
Statistics
Matches: 64, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
22 7 0.11
23 32 0.50
24 25 0.39
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
TTTGTCCTGAAGGACCACATAGGT
Found at i:105450 original size:47 final size:46
Alignment explanation
Indices: 105377--105466 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 46
105367 GAGTGCCATA
* * *
105377 TTTGTCCGAAGGACCACATAGTTTTGTCCTGAAGGACCACATAGGT
1 TTTGTCCGAAGGACCACATAGGTTTGTCCCGAAGGACAACATAGGT
105423 TTTGTCCTGAAGGACCACATAGGTTTGTCCCGAAGGACAACATA
1 TTTGTCC-GAAGGACCACATAGGTTTGTCCCGAAGGACAACATA
105467 TAACCCTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
46 7 0.17
47 33 0.82
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (46 bp):
TTTGTCCGAAGGACCACATAGGTTTGTCCCGAAGGACAACATAGGT
Done.