Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007055.1 Hibiscus syriacus cultivar Beakdansim tig00018307_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: 113378
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3784 original size:14 final size:15
Alignment explanation
Indices: 3742--3792 Score: 52
Period size: 14 Copynumber: 3.4 Consensus size: 15
3732 AAAAAAAGGT
*
3742 AATAAAAACTA-ACAA
1 AATAAAAAC-AGATAA
*
3757 AATAGAAAACAGATGA
1 AATA-AAAACAGATAA
3773 AATAAAAA-AGATAA
1 AATAAAAACAGATAA
3787 AATAAA
1 AATAAA
3793 CGAATAAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 11 0.35
15 9 0.29
16 11 0.35
ACGTcount: A:0.73, C:0.06, G:0.08, T:0.14
Consensus pattern (15 bp):
AATAAAAACAGATAA
Found at i:3833 original size:5 final size:5
Alignment explanation
Indices: 3817--3956 Score: 56
Period size: 5 Copynumber: 28.8 Consensus size: 5
3807 CAAAGAAAAT
*
3817 AATAA TAATAA AATAA AGATAA CAAGT-A AATAA AAT-A AACAA AATAAA
1 AATAA -AATAA AATAA A-ATAA -AA-TAA AATAA AATAA AATAA AAT-AA
3865 AATAA AGA-AA CAA-AA AGA-AA AAT-A AAT-A AATAA AATAA AA-AA
1 AATAA A-ATAA -AATAA A-ATAA AATAA AATAA AATAA AATAA AATAA
* * *
3907 ACAT-A AA-AA AAT-A AATAG AGTCAA GA-AA AAT-A AATAA AAT-A AATAA
1 A-ATAA AATAA AATAA AATAA AAT-AA AATAA AATAA AATAA AATAA AATAA
3953 AATA
1 AATA
3957 CATGAAAATA
Statistics
Matches: 106, Mismatches: 8, Indels: 41
0.68 0.05 0.26
Matches are distributed among these distances:
4 36 0.34
5 49 0.46
6 19 0.18
7 2 0.02
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (5 bp):
AATAA
Found at i:3860 original size:9 final size:9
Alignment explanation
Indices: 3843--3956 Score: 77
Period size: 9 Copynumber: 12.2 Consensus size: 9
3833 AGATAACAAG
*
3843 TAAATAAAA
1 TAAAAAAAA
*
3852 TAAACAAAA
1 TAAAAAAAA
3861 TAAAAATAAA
1 TAAAAA-AAA
*
3871 GAAACAAAAA
1 TAAA-AAAAA
*
3881 GAAAAATAAA
1 TAAAAA-AAA
*
3891 TAAATAAAA
1 TAAAAAAAA
3900 TAAAAAAACA
1 TAAAAAAA-A
3910 T-AAAAAAA
1 TAAAAAAAA
* * *
3918 TAAATAGAG
1 TAAAAAAAA
*
3927 TCAAGAAAAA
1 T-AAAAAAAA
*
3937 TAAATAAAA
1 TAAAAAAAA
*
3946 TAAATAAAA
1 TAAAAAAAA
3955 TA
1 TA
3957 CATGAAAATA
Statistics
Matches: 84, Mismatches: 15, Indels: 12
0.76 0.14 0.11
Matches are distributed among these distances:
8 2 0.02
9 53 0.63
10 27 0.32
11 2 0.02
ACGTcount: A:0.76, C:0.04, G:0.04, T:0.16
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:3863 original size:14 final size:14
Alignment explanation
Indices: 3772--3921 Score: 66
Period size: 14 Copynumber: 10.5 Consensus size: 14
3762 AAAACAGATG
3772 AAATAAA-AAAGATA
1 AAATAAACAAA-ATA
3786 AAATAAACGAATAAATA
1 AAATAAAC--A-AAATA
* *
3803 AAGACAAAGAAAATA
1 AA-ATAAACAAAATA
*
3818 ATAAT-AATAAAATA
1 A-AATAAACAAAATA
3832 AAGAT-AACAAGTAAATA
1 AA-ATAAAC-A--AAATA
3849 AAATAAACAAAATAA
1 AAATAAACAAAAT-A
* *
3864 AAATAAA-GAAACA
1 AAATAAACAAAATA
*
3877 AAA-AGA-AAAAT-
1 AAATAAACAAAATA
*
3888 AAATAAATAAAATA
1 AAATAAACAAAATA
3902 AAA-AAACATAAA-A
1 AAATAAACA-AAATA
3915 AAATAAA
1 AAATAAA
3922 TAGAGTCAAG
Statistics
Matches: 107, Mismatches: 12, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
11 3 0.03
12 7 0.07
13 18 0.17
14 36 0.34
15 16 0.15
16 5 0.05
17 16 0.15
18 6 0.06
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (14 bp):
AAATAAACAAAATA
Found at i:3920 original size:31 final size:32
Alignment explanation
Indices: 3773--3923 Score: 105
Period size: 33 Copynumber: 4.5 Consensus size: 32
3763 AAACAGATGA
**
3773 AATAAAAAAGATAAAATAAA-CGAATAAATAAAGAC
1 AATAAAAAA-AT-AAATAAATAAAATAAA-AAA-AC
*
3808 AA-AGAAAATAAT-AAT-AATAAAATAAAGATAAC
1 AATA-AAAA-AATAAATAAATAAAATAAA-AAAAC
* *
3840 AAGTAAATAAAATAAACAAAATAAAAATAAAGAAAC
1 AA-TAAA-AAAATAAA-TAAAT-AAAATAAAAAAAC
*
3876 AAAAAGAAAAATAAATAAATAAAATAAAAAAAC
1 AATAA-AAAAATAAATAAATAAAATAAAAAAAC
3909 -ATAAAAAAATAAATA
1 AATAAAAAAATAAATA
3924 GAGTCAAGAA
Statistics
Matches: 94, Mismatches: 11, Indels: 26
0.72 0.08 0.20
Matches are distributed among these distances:
31 11 0.12
32 9 0.10
33 28 0.30
34 10 0.11
35 18 0.19
36 10 0.11
37 8 0.09
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.15
Consensus pattern (32 bp):
AATAAAAAAATAAATAAATAAAATAAAAAAAC
Found at i:3969 original size:18 final size:18
Alignment explanation
Indices: 3772--4004 Score: 97
Period size: 19 Copynumber: 12.4 Consensus size: 18
3762 AAAACAGATG
3772 AAATAAAA-AAGATAAAAT
1 AAATAAAATAA-ATAAAAT
** *
3790 AAA-CGAATAAATAAAGAC
1 AAATAAAATAAATAAA-AT
*
3808 AAAGAAAAT-AAT--AAT
1 AAATAAAATAAATAAAAT
3823 -AATAAAATAAAGATAACAAGT
1 AAATAAAAT-AA-ATAA-AA-T
*
3844 AAATAAAATAAACAAAAT
1 AAATAAAATAAATAAAAT
* * * *
3862 AAAAATAAAGAAACAAAAAG
1 AAATA-AAATAAA-TAAAAT
*
3882 AAAAATAAATAAATAAAAT
1 AAATA-AAATAAATAAAAT
*
3901 AAAAAAACATAAA-AAAAT
1 AAATAAA-ATAAATAAAAT
* *
3919 AAATAGAGTCAAGA-AAAAT
1 AAATAAAAT-AA-ATAAAAT
3938 AAATAAAATAAATAAAAT
1 AAATAAAATAAATAAAAT
*
3956 ACATGAAAATAATAGTGAAAAT
1 AAAT-AAAATAA-A-T-AAAAT
*
3978 AATATACATAGTAAAT-AAAT
1 AA-ATA-A-AATAAATAAAAT
3998 AAATAAA
1 AAATAAA
4005 TGCAAGAGAA
Statistics
Matches: 168, Mismatches: 23, Indels: 49
0.70 0.10 0.20
Matches are distributed among these distances:
14 7 0.04
15 1 0.01
16 2 0.01
17 12 0.07
18 42 0.25
19 48 0.29
20 28 0.17
21 4 0.02
22 16 0.10
23 4 0.02
24 4 0.02
ACGTcount: A:0.72, C:0.04, G:0.06, T:0.18
Consensus pattern (18 bp):
AAATAAAATAAATAAAAT
Found at i:4072 original size:23 final size:22
Alignment explanation
Indices: 4031--4078 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
4021 TAGATATAAG
*
4031 ATAAGTATACAAAAAAATAGAT
1 ATAAGTAAACAAAAAAATAGAT
* *
4053 ATAAGATAAACAAAATAATATAT
1 ATAAG-TAAACAAAAAAATAGAT
4076 ATA
1 ATA
4079 TATACTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (22 bp):
ATAAGTAAACAAAAAAATAGAT
Found at i:16122 original size:2 final size:2
Alignment explanation
Indices: 16115--16141 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16105 TGCATCTCTT
16115 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16142 GCAAGAACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16689 original size:6 final size:6
Alignment explanation
Indices: 16678--16703 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16668 ATAAATGGGG
16678 CCTTTT CCTTTT CCTTTT CCTTTT CC
1 CCTTTT CCTTTT CCTTTT CCTTTT CC
16704 ATCATTCTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (6 bp):
CCTTTT
Found at i:19374 original size:35 final size:35
Alignment explanation
Indices: 19335--19409 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
19325 AAAATATTTC
*
19335 AATTTAGGGTTTAGAATGTAATTGAAGTATTTTGG
1 AATTTAGGGTTTAGAATATAATTGAAGTATTTTGG
* *
19370 AATTTGGGGTTTAGAATATAATTGAAGTGTTTTGG
1 AATTTAGGGTTTAGAATATAATTGAAGTATTTTGG
19405 AATTT
1 AATTT
19410 TGAACATGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (35 bp):
AATTTAGGGTTTAGAATATAATTGAAGTATTTTGG
Found at i:24082 original size:20 final size:21
Alignment explanation
Indices: 24039--24082 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
24029 ATAAAAAAAA
* *
24039 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATCAATATTT
24060 TTACCTAAAACATCAAT-TTT
1 TTACCTAAAACATCAATATTT
24080 TTA
1 TTA
24083 ACATTTTCGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (21 bp):
TTACCTAAAACATCAATATTT
Found at i:26570 original size:21 final size:21
Alignment explanation
Indices: 26540--26583 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
26530 TAATTTTCAA
26540 ACATTATTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
*
26561 ACATTGTTGCACCTAATTTTG
1 ACATTATTGCACCTAATTTTG
26582 AC
1 AC
26584 GTTGCAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (21 bp):
ACATTATTGCACCTAATTTTG
Found at i:26589 original size:18 final size:19
Alignment explanation
Indices: 26546--26589 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
26536 TCAAACATTA
26546 TTGCACCTAATTTTGACATTG
1 TTGCACCTAATTTTGAC--TG
26567 TTGCACCTAATTTTGAC-G
1 TTGCACCTAATTTTGACTG
26585 TTGCA
1 TTGCA
26590 ATATTAGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.26
21 17 0.74
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (19 bp):
TTGCACCTAATTTTGACTG
Found at i:31228 original size:21 final size:21
Alignment explanation
Indices: 31198--31245 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
31188 TAATTTTCAA
*
31198 ACATTATTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
31219 ACATTGTTGCACCTAATTTTG
1 ACATTGTTGCACCTAATTTTG
31240 ACATTG
1 ACATTG
31246 CAATATTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (21 bp):
ACATTGTTGCACCTAATTTTG
Found at i:47078 original size:2 final size:2
Alignment explanation
Indices: 47071--47099 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
47061 AAATAAAACC
47071 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47100 AAATAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:51237 original size:23 final size:23
Alignment explanation
Indices: 51207--51284 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 23
51197 AGATATTTCG
* *
51207 TTTATTTAGCGTTTGTG-ATCATA
1 TTTATTTAACATTTGTGAAT-ATA
*
51230 TTTATTTAATATTTGTGAATATA
1 TTTATTTAACATTTGTGAATATA
* *
51253 TTTATTTAATATTTGTGGATATA
1 TTTATTTAACATTTGTGAATATA
51276 -TTA-TTAACA
1 TTTATTTAACA
51285 ACCAGTTGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 5 0.10
22 3 0.06
23 39 0.80
24 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.54
Consensus pattern (23 bp):
TTTATTTAACATTTGTGAATATA
Found at i:51282 original size:21 final size:23
Alignment explanation
Indices: 51218--51277 Score: 95
Period size: 23 Copynumber: 2.6 Consensus size: 23
51208 TTATTTAGCG
51218 TTTGT-GATCATATTTATTTAATA
1 TTTGTGGAT-ATATTTATTTAATA
*
51241 TTTGTGAATATATTTATTTAATA
1 TTTGTGGATATATTTATTTAATA
51264 TTTGTGGATATATT
1 TTTGTGGATATATT
51278 ATTAACAACC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 32 0.94
24 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTGTGGATATATTTATTTAATA
Found at i:55772 original size:2 final size:2
Alignment explanation
Indices: 55765--55831 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
55755 AATTGGAGTT
55765 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
55807 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
55832 CATGTATGAA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:59993 original size:16 final size:17
Alignment explanation
Indices: 59969--60001 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
59959 TTATGATATT
59969 GAATATAA-TTTAAATA
1 GAATATAATTTTAAATA
*
59985 GAATTTAATTTTAAATA
1 GAATATAATTTTAAATA
60002 TTAGACATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
GAATATAATTTTAAATA
Found at i:60138 original size:158 final size:152
Alignment explanation
Indices: 59856--60159 Score: 538
Period size: 158 Copynumber: 2.0 Consensus size: 152
59846 CTAAATGTTG
59856 ATGGTTTGATAAAATTGAAAGTTTAGTATTAAAACGGACCAAACTGATAGTTTAGTACTAAATAC
1 ATGGTTTGATAAAATTGAAAGTTTAGTATTAAAACGGACCAAACTGATAGTTTAGTACTAAATAC
59921 AGTGTGCCTACTATTAGTACAAATGAAATATGTTTATTTTATGATATTGAATATAATTTAAATAG
66 AGTGTGCCTACTATTAGTACAAATGAAATATGTTTATTTTATGATATTGAATATAATTTAAATAG
59986 AATTTAATTTTAAATATTAGAC
131 AATTTAATTTTAAATATTAGAC
60008 ATGGTTTGATAAAATTGAAAGTTTAGGTATTAAAACGGACCAAAACTGATAGTTTAGATACTAAA
1 ATGGTTTGATAAAATTGAAAGTTTA-GTATTAAAACGGACC-AAACTGATAGTTTAG-TACTAAA
60073 TACATGTGTGCCCTACTATTAAGTACAAATGAAATATG-TTATTTTTATGATATTGAATATAATT
63 TACA-GTGTG-CCTACTATT-AGTACAAATGAAATATGTTTA-TTTTATGATATTGAATATAATT
60137 TAAATAGAATTTAATTTTAAATA
124 TAAATAGAATTTAATTTTAAATA
60160 CATTACTATG
Statistics
Matches: 145, Mismatches: 0, Indels: 8
0.95 0.00 0.05
Matches are distributed among these distances:
152 25 0.17
153 15 0.10
154 15 0.10
155 11 0.08
156 5 0.03
157 12 0.08
158 62 0.43
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (152 bp):
ATGGTTTGATAAAATTGAAAGTTTAGTATTAAAACGGACCAAACTGATAGTTTAGTACTAAATAC
AGTGTGCCTACTATTAGTACAAATGAAATATGTTTATTTTATGATATTGAATATAATTTAAATAG
AATTTAATTTTAAATATTAGAC
Found at i:60151 original size:16 final size:17
Alignment explanation
Indices: 60127--60159 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
60117 TTATGATATT
60127 GAATATAA-TTTAAATA
1 GAATATAATTTTAAATA
*
60143 GAATTTAATTTTAAATA
1 GAATATAATTTTAAATA
60160 CATTACTATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
GAATATAATTTTAAATA
Found at i:61876 original size:51 final size:52
Alignment explanation
Indices: 61800--61904 Score: 194
Period size: 51 Copynumber: 2.0 Consensus size: 52
61790 ATTCGCTGGA
61800 TCAAAACTTTCATTGATGATCTGGGGGTA-TCCCTGGGGTAACTGCAGAAAG
1 TCAAAACTTTCATTGATGATCTGGGGGTACTCCCTGGGGTAACTGCAGAAAG
61851 TCAAAACTTTCATTGATGATCTGGGGGTATCTCCCTGGGGTAACTGCAGAAAG
1 TCAAAACTTTCATTGATGATCTGGGGGTA-CTCCCTGGGGTAACTGCAGAAAG
61904 T
1 T
61905 TTTGCCAATG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
51 29 0.56
53 23 0.44
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (52 bp):
TCAAAACTTTCATTGATGATCTGGGGGTACTCCCTGGGGTAACTGCAGAAAG
Found at i:65335 original size:14 final size:14
Alignment explanation
Indices: 65316--65372 Score: 53
Period size: 13 Copynumber: 3.9 Consensus size: 14
65306 AATATTTTAA
65316 TAATATTATATTTT
1 TAATATTATATTTT
*
65330 TAATATTACA-TTT
1 TAATATTATATTTT
*
65343 TAATAATATAATTTT
1 TAATATTAT-ATTTT
*
65358 ACTTATATTATATTT
1 --TAATATTATATTT
65373 GATTAGTAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
13 10 0.29
14 10 0.29
15 3 0.09
16 4 0.12
17 7 0.21
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.58
Consensus pattern (14 bp):
TAATATTATATTTT
Found at i:67423 original size:28 final size:28
Alignment explanation
Indices: 67364--67623 Score: 337
Period size: 28 Copynumber: 9.3 Consensus size: 28
67354 AACATTTTTT
* *
67364 ATAATTACGAAAATATCACCTTTTTCAAA
1 ATAATTACCAAAATATCA-CTTTTTCGAA
* *
67393 ATAATTACGAAAATAGCACTTTTTCGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
67421 ATAATTACCAAAATATCACTTTTTCAAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
67449 ATAATTACCAAATTATCACTTTTTCGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
67477 ATAATTACCAAATTATCAC-TTTT-GAA
1 ATAATTACCAAAATATCACTTTTTCGAA
* *
67503 ATAATTACCAAAATATCATTTTTTTTGAA
1 ATAATTACCAAAATATCA-CTTTTTCGAA
*
67532 ATAATTACCAAAATATTACTTTTTCGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
* *
67560 ATAATTATCAAAATATCATTTTTTTCGAA
1 ATAATTACCAAAATATCA-CTTTTTCGAA
* *
67589 ATAATTACAAAAATATCA-TTTTTTGAA
1 ATAATTACCAAAATATCACTTTTTCGAA
*
67616 ATATTTAC
1 ATAATTAC
67624 GAAACTAACA
Statistics
Matches: 208, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
26 20 0.10
27 19 0.09
28 107 0.51
29 62 0.30
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (28 bp):
ATAATTACCAAAATATCACTTTTTCGAA
Found at i:67707 original size:28 final size:28
Alignment explanation
Indices: 67605--67709 Score: 140
Period size: 29 Copynumber: 3.7 Consensus size: 28
67595 ACAAAAATAT
*
67605 CATTTTTTGA-AATATTTACGAAACTAA
1 CATTTTTTAACAATATTTACGAAACTAA
* * *
67632 CACCTTCTTAACAGTATTTACGAAACTAA
1 CA-TTTTTTAACAATATTTACGAAACTAA
*
67661 CATTTGTTTAATAATATTTACGAAACTAA
1 CATTT-TTTAACAATATTTACGAAACTAA
67690 CATTTTTTAACAATATTTAC
1 CATTTTTTAACAATATTTAC
67710 AAAAATACCA
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
27 2 0.03
28 21 0.32
29 43 0.65
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (28 bp):
CATTTTTTAACAATATTTACGAAACTAA
Found at i:68288 original size:20 final size:20
Alignment explanation
Indices: 68263--68315 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
68253 CACTTCATTT
68263 TATTTTATTCT-TAGTGCTAA
1 TATTTTATT-TATAGTGCTAA
*
68283 TATTTTATTTATAGTGCTAT
1 TATTTTATTTATAGTGCTAA
68303 TAATTTT-TTTATA
1 T-ATTTTATTTATA
68316 TTATATTGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 1 0.03
20 24 0.80
21 5 0.17
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (20 bp):
TATTTTATTTATAGTGCTAA
Found at i:68547 original size:35 final size:36
Alignment explanation
Indices: 68508--68633 Score: 102
Period size: 35 Copynumber: 3.6 Consensus size: 36
68498 TAGTTTACAC
68508 TAAAATATTTAATATATATATATATA-TATAATAAA
1 TAAAATATTTAATATATATATATATATTATAATAAA
* * * * ** *
68543 TAAAA-ATATTAGTTTA-ATTAAAAATATTATTTTAAC
1 TAAAATAT-TTAATATATA-TATATATATTATAATAAA
*
68579 TAAAATATTT-ATGTATATATATATAATTATAAT-AA
1 TAAAATATTTAATATATATATATAT-ATTATAATAAA
*
68614 TATAATATTTAATAT-TATAT
1 TAAAATATTTAATATATATAT
68634 TGATATATAC
Statistics
Matches: 68, Mismatches: 16, Indels: 14
0.69 0.16 0.14
Matches are distributed among these distances:
34 3 0.04
35 40 0.59
36 23 0.34
37 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (36 bp):
TAAAATATTTAATATATATATATATATTATAATAAA
Found at i:68566 original size:18 final size:18
Alignment explanation
Indices: 68543--68587 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
68533 ATATAATAAA
*
68543 TAAAAATATTAGTTTAAT
1 TAAAAATATTAGTTTAAC
*
68561 TAAAAATATTATTTTAAC
1 TAAAAATATTAGTTTAAC
68579 T-AAAATATT
1 TAAAAATATT
68588 TATGTATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAAAATATTAGTTTAAC
Found at i:69456 original size:21 final size:21
Alignment explanation
Indices: 69414--69457 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
69404 TTGTATTGAA
*
69414 TTTTATTCACTTTTAATTCTT
1 TTTTATTCACTTTTAATACTT
*
69435 TTTTATTACATTTTTAA-ACTT
1 TTTTATT-CACTTTTAATACTT
69456 TT
1 TT
69458 AAAATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.23, C:0.11, G:0.00, T:0.66
Consensus pattern (21 bp):
TTTTATTCACTTTTAATACTT
Found at i:69492 original size:21 final size:22
Alignment explanation
Indices: 69458--69502 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
69448 TTAAACTTTT
69458 AAAATAAATAAAAA-TGTAATAA
1 AAAATAAATAAAAAGTG-AATAA
*
69480 AAAAT-AATTAAAAGTGAATAA
1 AAAATAAATAAAAAGTGAATAA
69501 AA
1 AA
69503 TTCAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (22 bp):
AAAATAAATAAAAAGTGAATAA
Found at i:69699 original size:31 final size:31
Alignment explanation
Indices: 69664--69737 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
69654 ATTAATTTTT
69664 TTAAAATCAATAAAAATACAATA-AAAAAGAA
1 TTAAAATCAAT-AAAATACAATACAAAAAGAA
* * *
69695 TTAAAAGTAAATGAAATTCAATACAAAAAGAA
1 TTAAAA-TCAATAAAATACAATACAAAAAGAA
*
69727 TATAAAGTCAA
1 T-TAAAATCAA
69738 ATTTTTTTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
31 15 0.43
32 16 0.46
33 4 0.11
ACGTcount: A:0.65, C:0.07, G:0.07, T:0.22
Consensus pattern (31 bp):
TTAAAATCAATAAAATACAATACAAAAAGAA
Found at i:69734 original size:32 final size:32
Alignment explanation
Indices: 69677--69739 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
69667 AAATCAATAA
69677 AAATACAATAAAAAAGAATTAAAAGT-AAATG
1 AAATACAATAAAAAAGAATTAAAAGTCAAATG
*
69708 AAATTCAATACAAAAAGAA-TATAAAGTCAAAT
1 AAATACAATA-AAAAAGAATTA-AAAGTCAAAT
69740 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 11 0.39
32 13 0.46
33 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.21
Consensus pattern (32 bp):
AAATACAATAAAAAAGAATTAAAAGTCAAATG
Found at i:69781 original size:26 final size:27
Alignment explanation
Indices: 69741--69791 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
69731 AAGTCAAATT
69741 TTTTTTAAAAATATATAAA-ATTTATAA
1 TTTTTTAAAAATATA-AAATATTTATAA
*
69768 TTTTTT-AAATTATAAAATATTTAT
1 TTTTTTAAAAATATAAAATATTTAT
69792 TATTATCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 3 0.14
26 13 0.59
27 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTTTTTAAAAATATAAAATATTTATAA
Found at i:71850 original size:148 final size:146
Alignment explanation
Indices: 71552--71852 Score: 462
Period size: 148 Copynumber: 2.0 Consensus size: 146
71542 TCCTCAAGGA
*
71552 TCATATTAAGAACCTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAATTTAAATGGC
1 TCATATTAAGAACCTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAAGTTAAATGGC
* ** *
71617 ATCTCTCAAGGCAAGCTACTGCTATAATTTTTGGGATGTTGCATATAATGATTGGAACATGAAGT
66 AACTCTCAAGGCAAGCTACTAATATAATTTTTGGGATGTTGCACATAATGATTGGAACATGAAGT
* *
71682 AACATTCATGTTAATG
131 AACATTCAAGTCAATG
*
71698 TCATATTAAGAACATACTACAACTGGGAAGA-C-AACCATTCAACGATTCCGATACAAGTTAAAT
1 TCATATTAAGAAC---CTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAAGTTAAAT
* *
71761 GGCAACTCTCAAGGCAAGCTACTAATATTAATTTTTGGGATGTTGCACATAATTATTGGAGCATG
63 GGCAACTCTCAAGGCAAGCTACTAATA-TAATTTTTGGGATGTTGCACATAATGATTGGAACATG
71826 AAGTAACATTCAAGTCAATG
127 AAGTAACATTCAAGTCAATG
71846 TCATATT
1 TCATATT
71853 TGTGTCCAAG
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
146 13 0.09
147 54 0.38
148 60 0.43
149 14 0.10
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (146 bp):
TCATATTAAGAACCTACAAATGGGAAGACCAAACCATTCAACGATTCCGATACAAGTTAAATGGC
AACTCTCAAGGCAAGCTACTAATATAATTTTTGGGATGTTGCACATAATGATTGGAACATGAAGT
AACATTCAAGTCAATG
Found at i:80626 original size:121 final size:122
Alignment explanation
Indices: 80472--80727 Score: 371
Period size: 121 Copynumber: 2.1 Consensus size: 122
80462 TAAGACTTAA
80472 AAAAT-AAAATGAATTTAATATTTTTTATTTAAATTATTTTTTACAAA-TATTTTAAAA-ATATA
1 AAAATAAAAAT-AATTTAATATTTTTTATTTAAATTATTTTTTA-AAATTATTTTAAAATA-ATA
* *
80534 ATATACAAATTATATTAA-AAATAAAATTATGTTAAAATTAGTTAGAGAATCCAAATCAC-
63 ATATACAAATTATAGTAACAAATAAAATTATATTAAAATTAGTTAGAGAATCCAAATC-CT
*
80593 AAAATAAAAATAAGTTTAATA-TTTTTATTTAAATTATTTTTTAAAATTATTTTTAAATAATAAT
1 AAAATAAAAATAA-TTTAATATTTTTTATTTAAATTATTTTTTAAAATTATTTTAAAATAATAAT
* *
80657 ATATAAATTATAGTAAGCAAATAAAATTATATTAAAATTATTTAGAGAATCCAAATCCT
65 ATACAAATTATAGTAA-CAAATAAAATTATATTAAAATTAGTTAGAGAATCCAAATCCT
80716 AAAATAAAAATA
1 AAAATAAAAATA
80728 TTAAACTCAT
Statistics
Matches: 123, Mismatches: 5, Indels: 12
0.88 0.04 0.09
Matches are distributed among these distances:
120 3 0.02
121 57 0.46
122 14 0.11
123 49 0.40
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (122 bp):
AAAATAAAAATAATTTAATATTTTTTATTTAAATTATTTTTTAAAATTATTTTAAAATAATAATA
TACAAATTATAGTAACAAATAAAATTATATTAAAATTAGTTAGAGAATCCAAATCCT
Found at i:86121 original size:20 final size:20
Alignment explanation
Indices: 86074--86121 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
86064 TTGTTCATTG
*
86074 TTTTCTTCAGCCTGTTTCTT
1 TTTTCTTTAGCCTGTTTCTT
86094 TTTTCTTTAGCCTGTTTCTT
1 TTTTCTTTAGCCTGTTTCTT
86114 TTTTCTTT
1 TTTTCTTT
86122 TATCATCTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.04, C:0.21, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTTCTTTAGCCTGTTTCTT
Found at i:103152 original size:31 final size:31
Alignment explanation
Indices: 103089--103153 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
103079 TTCTAAACTA
* ** *
103089 TTTTTTATCAAAATAAGTATTTAATTTTATT
1 TTTTTTATCAAAATAAGTACTTAAAGTAATT
103120 TTTTTTATCAAAAT-AGATACTTAAAGTAATT
1 TTTTTTATCAAAATAAG-TACTTAAAGTAATT
103151 TTT
1 TTT
103154 AGTCAAAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 27 0.93
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (31 bp):
TTTTTTATCAAAATAAGTACTTAAAGTAATT
Found at i:103457 original size:21 final size:21
Alignment explanation
Indices: 103340--103477 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
103330 ACGCGAAATA
**
103340 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
103360 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
103380 AAAATCACAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
103401 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
103422 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * *
103443 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
103463 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
103478 ACACATAAAT
Statistics
Matches: 87, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 46 0.53
22 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:103506 original size:20 final size:20
Alignment explanation
Indices: 103444--103637 Score: 203
Period size: 20 Copynumber: 9.7 Consensus size: 20
103434 CGATTTTCCA
* ** *
103444 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
103464 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
103484 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
103504 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
103524 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
103544 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
103564 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* ***
103584 AAATCGCAACG-ATAATAAAT
1 AAATCGCAACGCGT-ATCCGT
*
103604 AAAATCACAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
103625 AAATCGCAACGCG
1 AAATCGCAACGCG
103638 ATATTTAAAG
Statistics
Matches: 142, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.87
21 15 0.11
22 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:103528 original size:60 final size:60
Alignment explanation
Indices: 103444--103637 Score: 235
Period size: 60 Copynumber: 3.2 Consensus size: 60
103434 CGATTTTCCA
* ** * * *
103444 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* * *** *
103504 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* ** *
103564 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATAAATAAAATCACAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAAT-AAATCGCAACGCGTATCCGT
103625 AAATCGCAACGCG
1 AAATCGCAACGCG
103638 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 22, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 81 0.73
61 30 0.27
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
Found at i:104059 original size:33 final size:33
Alignment explanation
Indices: 104020--104090 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
104010 TTCACTTAGA
*
104020 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
104053 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
104086 TTTCA
1 TTTCA
104091 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:104214 original size:20 final size:20
Alignment explanation
Indices: 104170--104279 Score: 108
Period size: 21 Copynumber: 5.8 Consensus size: 20
104160 TGTAGAAGAG
*
104170 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATGAAAA
***
104191 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGAAAA
104211 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAG-AATGAAAA
104232 TCGCAAC--GAG-A-G--AA
1 TCGCAACGAGAGAATGAAAA
*
104246 TCGCAACGCGA-AATGAAAA
1 TCGCAACGAGAGAATGAAAA
104265 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
104280 CGCAACGCGA
Statistics
Matches: 73, Mismatches: 8, Indels: 17
0.74 0.08 0.17
Matches are distributed among these distances:
14 9 0.12
16 4 0.05
17 2 0.03
19 15 0.21
20 20 0.27
21 23 0.32
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (20 bp):
TCGCAACGAGAGAATGAAAA
Found at i:104227 original size:41 final size:38
Alignment explanation
Indices: 104163--104279 Score: 145
Period size: 41 Copynumber: 3.1 Consensus size: 38
104153 TTCAATTTGT
* *
104163 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
104201 AGAATGACTGTCGCAACGAGAGAAATGAAAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
104242 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
104275 AGAAT
1 AGAAT
104280 CGCAACGCGA
Statistics
Matches: 71, Mismatches: 3, Indels: 13
0.82 0.03 0.15
Matches are distributed among these distances:
33 23 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 33 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:104249 original size:14 final size:14
Alignment explanation
Indices: 104230--104286 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
104220 GAGAAATGAA
104230 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
104244 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
104263 AATCGCAACGAGAG
1 AATCGCAACGAGAG
104277 AATCGCAACG
1 AATCGCAACG
104287 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:104262 original size:33 final size:33
Alignment explanation
Indices: 104222--104302 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
104212 CGCAACGAGA
104222 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
104255 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
104288 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
104303 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:104320 original size:19 final size:19
Alignment explanation
Indices: 104298--104395 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
104288 GAAACCAAAA
*
104298 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
104317 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
104331 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
104350 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
104364 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
104383 TCGCGTTGCGATT
1 TCGCGTTGCGATT
104396 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:104339 original size:14 final size:14
Alignment explanation
Indices: 104320--104409 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
104310 TTTCATTTCG
104320 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
104334 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
104353 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
104367 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
104386 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
104400 CGTTGCGATT
1 CGTTGCGATT
104410 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:104345 original size:33 final size:33
Alignment explanation
Indices: 104303--104417 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
104293 CAAAATCGCA
104303 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
104336 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
104369 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
104402 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
104418 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:106275 original size:93 final size:93
Alignment explanation
Indices: 106116--106582 Score: 904
Period size: 93 Copynumber: 5.1 Consensus size: 93
106106 TAGATTGCTT
*
106116 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
106181 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
106209 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
106274 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
106302 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
106367 TTTGTCTTTGTTTTGTCTTTTGGTT-AA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
106394 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTA-TCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
106458 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
106486 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
106551 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
106578 AGTAA
1 AGTAA
106583 TGCAATCCAT
Statistics
Matches: 371, Mismatches: 1, Indels: 5
0.98 0.00 0.01
Matches are distributed among these distances:
91 47 0.13
92 94 0.25
93 230 0.62
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:106515 original size:184 final size:185
Alignment explanation
Indices: 106116--106582 Score: 900
Period size: 184 Copynumber: 2.5 Consensus size: 185
106106 TAGATTGCTT
*
106116 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
106181 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTT-AAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
106246 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
130 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
106302 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
106367 TTTGTCTTTGTTTTGTCTTTTGGTTAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
66 TTTGTCTTTGTTTTGTCTTTTGGTTAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
106432 TGTA-TCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
106486 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
106551 TTTGTCTTTGTTTTGTCTTTTGGTTGAAGTAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTAAAGTAA
106583 TGCAATCCAT
Statistics
Matches: 279, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
184 146 0.52
185 44 0.16
186 89 0.32
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTG
TGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:106670 original size:19 final size:19
Alignment explanation
Indices: 106630--106764 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
106620 TAGTTTACTT
* *
106630 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
106650 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
106669 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
106688 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
106702 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
106721 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
106735 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
106754 TCGCAATGCGA
1 TCGCAACGCGA
106765 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:106705 original size:14 final size:14
Alignment explanation
Indices: 106686--106742 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
106676 GCGAAATGAA
*
106686 AATCGCAACGACAG
1 AATCGCAACGAAAG
106700 AATCGCAACGCGAAATG
1 AATCGCAA--CGAAA-G
106717 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
106733 AATCGCAACG
1 AATCGCAACG
106743 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.25, G:0.21, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:106709 original size:33 final size:33
Alignment explanation
Indices: 106667--106759 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
106657 GCGAAACCAA
*
106667 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
106700 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
106733 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
106760 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.47, C:0.23, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:106756 original size:52 final size:54
Alignment explanation
Indices: 106630--106764 Score: 131
Period size: 52 Copynumber: 2.5 Consensus size: 54
106620 TAGTTTACTT
*
106630 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAACGCGAAACCAAAATCGCAAC-CGAAATG-AAA
* **
106688 TCGCAA-CGACA-G--AATCGCAACGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
*
106735 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAACGCGA
106765 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
47 8 0.12
49 5 0.08
50 6 0.09
52 37 0.56
56 4 0.06
58 6 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.10
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAACGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:106782 original size:19 final size:19
Alignment explanation
Indices: 106760--106888 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
106750 AAAATCGCAA
106760 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
106779 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
106793 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
106812 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
106826 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
106845 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
106864 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
106884 TGCGA
1 TGCGA
106889 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:106802 original size:33 final size:33
Alignment explanation
Indices: 106760--106851 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
106750 AAAATCGCAA
106760 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
106793 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
106826 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
106852 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:109662 original size:24 final size:24
Alignment explanation
Indices: 109628--109674 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
109618 CTGAAACATC
109628 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
109652 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
109675 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:110384 original size:20 final size:20
Alignment explanation
Indices: 110356--110565 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
110346 AAATTTCAGT
* * * *
110356 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
110376 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
110396 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
110416 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
110436 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
110456 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
110476 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
110496 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
110516 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
110536 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
110556 GTTGCGATTT
1 GTTGCGATTT
110566 TGGAAAATCG
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:110582 original size:21 final size:21
Alignment explanation
Indices: 110552--110634 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
110542 ATTTATGTGT
*
110552 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
110573 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
110594 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
110615 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
110635 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:110864 original size:32 final size:30
Alignment explanation
Indices: 110800--110912 Score: 88
Period size: 29 Copynumber: 3.7 Consensus size: 30
110790 ATTTTGACAT
* * *
110800 AAAATACCTTAGGTA-TCTATTTTGAAGTAAA
1 AAAATACTTTAAGTACT-TATTTTGAA-AAAA
*
110831 AAGATAACTTTATA-TACTTATTTTGAAAAAA
1 AAAAT-ACTTTA-AGTACTTATTTTGAAAAAA
** *
110862 AAAATACTTTAAGTACTTA-AATGAAAAAG
1 AAAATACTTTAAGTACTTATTTTGAAAAAA
**
110891 AGTATACTTTAAGTACTTATTT
1 AAAATACTTTAAGTACTTATTT
110913 GTTAATATAA
Statistics
Matches: 65, Mismatches: 12, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
29 25 0.38
30 12 0.18
31 11 0.17
32 16 0.25
33 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (30 bp):
AAAATACTTTAAGTACTTATTTTGAAAAAA
Found at i:110871 original size:30 final size:32
Alignment explanation
Indices: 110817--110880 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 32
110807 CTTAGGTATC
* *
110817 TATTTTGAAGTAAAAAGATAACTTTATA-TACT
1 TATTTTGAAGAAAAAAAATAACTTTA-AGTACT
110849 TATTTTGAA-AAAAAAAAT-ACTTTAAGTACT
1 TATTTTGAAGAAAAAAAATAACTTTAAGTACT
110879 TA
1 TA
110881 AATGAAAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 1 0.03
30 12 0.41
31 7 0.24
32 9 0.31
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (32 bp):
TATTTTGAAGAAAAAAAATAACTTTAAGTACT
Done.