Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168300.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_526, 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: 23913
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.36
Found at i:837 original size:17 final size:17
Alignment explanation
Indices: 815--848 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
805 TTAGATTTAC
815 TTATAATAGATAATAGA
1 TTATAATAGATAATAGA
832 TTATAATAGATAATAGA
1 TTATAATAGATAATAGA
849 ATAAGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
TTATAATAGATAATAGA
Found at i:891 original size:21 final size:20
Alignment explanation
Indices: 835--964 Score: 97
Period size: 19 Copynumber: 6.2 Consensus size: 20
825 TAATAGATTA
*
835 TAAT-AGATAATAGAATAAG
1 TAATAAGATAATATAATAAG
**
854 TAATAAG-TAATCGAATAAG
1 TAATAAGATAATATAATAAG
873 TAATAAGGATAATATAATAAG
1 TAATAA-GATAATATAATAAG
*
894 T-ATAAAATAAGTATAAATAAG
1 TAATAAGATAA-TAT-AATAAG
915 TATAAAATAAGTATAAGTATAAATAAG
1 --T--AATAAG-ATAA-TAT-AATAAG
*
942 T-ATAATATAATATAATAAG
1 TAATAAGATAATATAATAAG
961 TAAT
1 TAAT
965 GGACAACCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
19 32 0.34
20 15 0.16
21 21 0.23
22 4 0.04
23 1 0.01
25 1 0.01
26 4 0.04
27 15 0.16
ACGTcount: A:0.58, C:0.01, G:0.12, T:0.30
Consensus pattern (20 bp):
TAATAAGATAATATAATAAG
Found at i:902 original size:11 final size:11
Alignment explanation
Indices: 888--930 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
878 AGGATAATAT
888 AATAAGTATAA
1 AATAAGTATAA
899 AATAAGTAT-A
1 AATAAGTATAA
909 AATAAGTATAA
1 AATAAGTATAA
920 AATAAGTATAA
1 AATAAGTATAA
931 GTATAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (11 bp):
AATAAGTATAA
Found at i:919 original size:27 final size:26
Alignment explanation
Indices: 889--956 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
879 GGATAATATA
*
889 ATAAGTATAAAATAAGTATAAATAAGT
1 ATAA-TATAATATAAGTATAAATAAGT
*
916 ATAAAATAAGTATAAGTATAAATAAGT
1 ATAATATAA-TATAAGTATAAATAAGT
943 ATAATATAATATAA
1 ATAATATAATATAA
957 TAAGTAATGG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.24
27 28 0.76
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (26 bp):
ATAATATAATATAAGTATAAATAAGT
Found at i:1153 original size:13 final size:13
Alignment explanation
Indices: 1137--1205 Score: 76
Period size: 13 Copynumber: 5.5 Consensus size: 13
1127 AAAAAAAAAG
1137 AAATATTAAAATT
1 AAATATTAAAATT
1150 AAATATTAAAATATT
1 AAATATT-AAA-ATT
1165 AAA-ATTAAATATT
1 AAATATTAAA-ATT
1178 AAA-A--AAAATT
1 AAATATTAAAATT
1188 AAATATTAAAA-T
1 AAATATTAAAATT
1200 AAATAT
1 AAATAT
1206 ATATTGTGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 11
0.82 0.00 0.18
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
12 7 0.14
13 22 0.43
14 6 0.12
15 6 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAATATTAAAATT
Found at i:1163 original size:21 final size:21
Alignment explanation
Indices: 1137--1200 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
1127 AAAAAAAAAG
1137 AAATATTAAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
1158 AAATATTAAAATTAAATATT-
1 AAATATTAAAATTAAATATTA
1178 AAA-A--AAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
1196 AAATA
1 AAATA
1201 AATATATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.32
18 3 0.07
19 2 0.05
20 3 0.07
21 20 0.49
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATATTAAAATTAAATATTA
Found at i:1210 original size:16 final size:17
Alignment explanation
Indices: 1144--1203 Score: 75
Period size: 17 Copynumber: 3.3 Consensus size: 17
1134 AAGAAATATT
1144 AAAATTAAATATTAAAATA
1 AAAATTAAATATT-AAA-A
1163 TTAAAATTAAATATTAAAA
1 --AAAATTAAATATTAAAA
1182 AAAATTAAATATTAAAA
1 AAAATTAAATATTAAAA
*
1199 TAAAT
1 AAAAT
1204 ATATATTGTG
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
17 21 0.55
19 1 0.03
20 3 0.08
21 13 0.34
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAAATATTAAAA
Found at i:3640 original size:1 final size:1
Alignment explanation
Indices: 3634--3658 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
3624 TGCTGTTCAA
3634 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
3659 CAGTTCGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:4658 original size:22 final size:22
Alignment explanation
Indices: 4627--4677 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
4617 GTTGTTTTTA
*
4627 GAATTATAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
4649 GAATTCTAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
4671 -AATTCTA
1 GAATTCTA
4678 TTTAGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
GAATTCTAATTATATAAGAAAT
Found at i:5745 original size:25 final size:25
Alignment explanation
Indices: 5712--5763 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
5702 ATTATTTATT
*
5712 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
5737 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
5762 TT
1 TT
5764 AGGAGTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTTTAGTTTACAGTCTTCGAATGA
Found at i:5770 original size:25 final size:25
Alignment explanation
Indices: 5717--5770 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
5707 TTATTTTTTT
* ***
5717 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
5742 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
5767 AGTT
1 AGTT
5771 GGATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (25 bp):
AGTTTACAGTCTTCGAATGATTAGG
Found at i:5870 original size:15 final size:15
Alignment explanation
Indices: 5850--5899 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
5840 CATAATGATT
5850 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
5865 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
5883 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
5898 AT
1 AT
5900 ATTGTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 17 0.53
18 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
ATTTTAATATTGTTA
Found at i:5882 original size:18 final size:18
Alignment explanation
Indices: 5859--5896 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5849 TATTTTAATA
5859 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
5877 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
5895 TT
1 TT
5897 AATATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TTGTTAATTTTAATATTG
Found at i:5918 original size:17 final size:17
Alignment explanation
Indices: 5898--5931 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5888 AATATTGTTA
*
5898 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
5915 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
5932 CATTACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
ATATTGTATGATTTATT
Found at i:5955 original size:19 final size:19
Alignment explanation
Indices: 5933--5982 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
5923 TGATTTATTC
*
5933 ATTACTATATTTTTTAGTT
1 ATTACTATATTTTGTAGTT
*
5952 ATTACTATATTTTGTATTT
1 ATTACTATATTTTGTAGTT
5971 ATTACTATATTT
1 ATTACTATATTT
5983 CATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTACTATATTTTGTAGTT
Found at i:6000 original size:19 final size:19
Alignment explanation
Indices: 5966--6020 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
5956 CTATATTTTG
*
5966 TATTTATTACTATATTTCAT
1 TATTTATTTCT-TATTTCAT
*
5986 TATTTATTTCTTATTTTAT
1 TATTTATTTCTTATTTCAT
* *
6005 TAATTATTTATTATTT
1 TATTTATTTCTTATTT
6021 TCGTGTCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTATTTCTTATTTCAT
Found at i:6001 original size:38 final size:38
Alignment explanation
Indices: 5928--6002 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
5918 TTGTATGATT
*
5928 TATTCATTACTATATTTTTTAGTTATTACTATATTTTG
1 TATTCATTACTATATTTATTAGTTATTACTATATTTTG
* * *
5966 TATTTATTACTATATTTCATTATTTATTTCT-TATTTT
1 TATTCATTACTATATTT-ATTAGTTATTACTATATTTT
6003 ATTAATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 22 0.69
39 10 0.31
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (38 bp):
TATTCATTACTATATTTATTAGTTATTACTATATTTTG
Found at i:6059 original size:17 final size:18
Alignment explanation
Indices: 6033--6221 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
6023 GTGTCGGTTC
*
6033 TATATATATTTA-TAAAT
1 TATATTTATTTATTAAAT
6050 TATATTTATTTATT--AT
1 TATATTTATTTATTAAAT
* * *
6066 T-TATGTA-TTATCACAGT
1 TATATTTATTTATTA-AAT
**
6083 TATAGATATTTATTTAAAT
1 TATATTTATTTA-TTAAAT
*
6102 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* **
6119 TATATTAAAATATTAAAT
1 TATATTTATTTATTAAAT
6137 TATATTTATATT-TTATATAT
1 TATATTTAT-TTATTA-A-AT
** *
6157 TAAATATATTAAAATATGAAAT
1 T--ATAT-TT-ATTTATTAAAT
*
6179 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* ** *
6196 TATATTAAAATATGAAAT
1 TATATTTATTTATTAAAT
6214 TATATTTA
1 TATATTTA
6222 AATAAATATC
Statistics
Matches: 130, Mismatches: 25, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
14 4 0.03
15 5 0.04
16 3 0.02
17 42 0.32
18 35 0.27
19 18 0.14
20 9 0.07
22 7 0.05
23 4 0.03
24 3 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATTTATTTATTAAAT
Found at i:6115 original size:8 final size:8
Alignment explanation
Indices: 6102--6208 Score: 72
Period size: 8 Copynumber: 12.6 Consensus size: 8
6092 TTATTTAAAT
*
6102 TATATTTA
1 TATATTAA
6110 TATATTAAA
1 TATATT-AA
6119 TATATTAA
1 TATATTAA
*
6127 AATATTAAA
1 TATATT-AA
*
6136 TTATATTTA
1 -TATATTAA
*
6145 TAT-TTTA
1 TATATTAA
6152 TATATTAAA
1 TATATT-AA
6161 TATATTAA
1 TATATTAA
* *
6169 AATATGAAA
1 TATAT-TAA
*
6178 TTATATTTA
1 -TATATTAA
6187 TATATTAAA
1 TATATT-AA
6196 TATATTAA
1 TATATTAA
*
6204 AATAT
1 TATAT
6209 GAAATTATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.09
8 36 0.46
9 27 0.34
10 9 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (8 bp):
TATATTAA
Found at i:6132 original size:77 final size:76
Alignment explanation
Indices: 6063--6221 Score: 205
Period size: 77 Copynumber: 2.1 Consensus size: 76
6053 ATTTATTTAT
* * * *
6063 TATTTATGTATTATCACAGTTATAGATATT-TAT-TTAAATTATATTTATATATTAAATATATTA
1 TATTTATATATTAT-ACA-TTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTA
6126 AAATATTAAATTA
64 AAATATTAAATTA
* * *
6139 TATTTATATTTTATATATTAAATATATTAAAATATGAAATTATATTTATATATTAAATATATTAA
1 TATTTATATATTATACATTAAAGATATT-AAATATGAAATTATATTTATATATTAAATATATTAA
*
6204 AATATGAAATTA
65 AATATTAAATTA
6216 TATTTA
1 TATTTA
6222 AATAAATATC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 9 0.12
75 2 0.03
76 14 0.19
77 47 0.65
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (76 bp):
TATTTATATATTATACATTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTAAA
ATATTAAATTA
Found at i:6135 original size:35 final size:35
Alignment explanation
Indices: 6098--6221 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
6088 ATATTTATTT
*
6098 AAATTATATTTATATATTAAATATATTAAAATATTAA
1 AAATTATATTTATATATTAAATATATTAAAATA-T-G
6135 ATTATATTTATATTTTATATATTAAATATATTAAAATATG
1 A--A-A-TTATA-TTTATATATTAAATATATTAAAATATG
6175 AAATTATATTTATATATTAAATATATTAAAATATG
1 AAATTATATTTATATATTAAATATATTAAAATATG
6210 AAATTATATTTA
1 AAATTATATTTA
6222 AATAAATATC
Statistics
Matches: 81, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
35 39 0.48
36 5 0.06
37 2 0.02
38 1 0.01
39 1 0.01
40 2 0.02
41 6 0.07
42 25 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (35 bp):
AAATTATATTTATATATTAAATATATTAAAATATG
Found at i:6240 original size:4 final size:4
Alignment explanation
Indices: 6233--6360 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
6223 ATAAATATCT
*
6233 ATAA AT-A ATATA AT-A ATAAA ATAA ACT-A ATAAA ATAA ACAA ATAA
1 ATAA ATAA ATA-A ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA
* *
6278 AT-A ATAA ATAA ATAA TTAAA ATAA ACT-A ATAAA ATAA ACAA ATAA AT-A
1 ATAA ATAA ATAA ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA ATAA
*
6326 AGAA ATAA AT-A ATAA ATAA AT-A ATACA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA A
6361 AAAAACAAAG
Statistics
Matches: 99, Mismatches: 8, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
3 22 0.22
4 57 0.58
5 20 0.20
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:6255 original size:13 final size:13
Alignment explanation
Indices: 6246--6323 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
6236 AATAATATAA
6246 TAATAAAATAAAC
1 TAATAAAATAAAC
6259 TAATAAAATAAAC
1 TAATAAAATAAAC
6272 -----AAATAAA-
1 TAATAAAATAAAC
6279 TAAT-AAATAAA-
1 TAATAAAATAAAC
6290 TAATTAAAATAAAC
1 TAA-TAAAATAAAC
6304 TAATAAAATAAAC
1 TAATAAAATAAAC
*
6317 AAATAAA
1 TAATAAA
6324 TAAGAAATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
8 7 0.12
11 10 0.18
12 1 0.02
13 36 0.63
14 3 0.05
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (13 bp):
TAATAAAATAAAC
Found at i:6360 original size:45 final size:44
Alignment explanation
Indices: 6239--6356 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 44
6229 ATCTATAAAT
*
6239 AATATAATAATAAAATAAACTAATAAAATAAACAAATAAATAATA
1 AATA-AATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
6284 AATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATAAGA
1 AATAAATAA-TAAAATAAACTAATAAAATAAACAAATAAATAAGA
*
6329 AATAAATAAT-AAATAAA-TAATACAATAA
1 AATAAATAATAAAATAAACTAATAAAATAA
6357 TAAAAAAAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
42 10 0.14
43 7 0.10
44 6 0.09
45 47 0.67
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (44 bp):
AATAAATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
Found at i:8479 original size:30 final size:30
Alignment explanation
Indices: 8445--8784 Score: 680
Period size: 30 Copynumber: 11.3 Consensus size: 30
8435 AAATGGTGTT
8445 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8475 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8505 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8535 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8565 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8595 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8625 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8655 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8685 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8715 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8745 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
8775 CCATTGTCGT
1 CCATTGTCGT
8785 TAACTAGTCT
Statistics
Matches: 310, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 310 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (30 bp):
CCATTGTCGTCAAATGGTGGTCTTCCATTG
Found at i:8825 original size:18 final size:18
Alignment explanation
Indices: 8798--9032 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
8788 CTAGTCTCCA
*
8798 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
8816 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8834 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8852 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8870 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8888 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8906 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8924 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8942 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
8960 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8978 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
8996 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9014 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
9032 T
1 T
9033 CTCGATTCTG
Statistics
Matches: 213, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.02
18 205 0.96
19 4 0.02
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (18 bp):
TTTTTCATTCACTATAGG
Found at i:9373 original size:18 final size:18
Alignment explanation
Indices: 9350--9387 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9340 TTTTTTGCGC
9350 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
9368 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
9386 AT
1 AT
9388 GGAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
ATTGCATACGGCTTTACA
Found at i:11323 original size:78 final size:78
Alignment explanation
Indices: 11194--11362 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
11184 AGTAAAAAGA
* *
11194 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
11259 TTATCTTAATAAT
66 TTATCTTAATAAT
11272 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
11337 TTATCTTAATAAT
66 TTATCTTAATAAT
11350 ATGTAATATTATA
1 ATGTAATATTATA
11363 ATATGTAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (78 bp):
ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
TTATCTTAATAAT
Found at i:11365 original size:15 final size:15
Alignment explanation
Indices: 11345--11377 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11335 TCTTATCTTA
11345 ATAATATGTAATATT
1 ATAATATGTAATATT
11360 ATAATATGTAATATT
1 ATAATATGTAATATT
11375 ATA
1 ATA
11378 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:11458 original size:15 final size:15
Alignment explanation
Indices: 11438--11470 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11428 TCTTATCTTA
11438 ATAATATGTAATATT
1 ATAATATGTAATATT
11453 ATAATATGTAATATT
1 ATAATATGTAATATT
11468 ATA
1 ATA
11471 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:11559 original size:93 final size:93
Alignment explanation
Indices: 11267--11543 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
11257 TCTTATCTTA
11267 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
11332 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
11360 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
11425 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
11453 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
11518 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
11544 ATGGTCTTAA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 184 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (93 bp):
ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
TGGTCTTATCTTAATAATATGTAATATT
Found at i:13950 original size:21 final size:20
Alignment explanation
Indices: 13925--13992 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
13915 TTCCATTATT
*
13925 ATATAATTATATAAATAATAT
1 ATATAATTATATAAAT-ATAA
13946 ATATAA--ATATAAATATAA
1 ATATAATTATATAAATATAA
*
13964 ATATAAATAATATAAATATAA
1 ATAT-AATTATATAAATATAA
13985 ATATAATT
1 ATATAATT
13993 TCAAGATCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.17
19 10 0.24
20 3 0.07
21 22 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAATTATATAAATATAA
Found at i:13957 original size:6 final size:6
Alignment explanation
Indices: 13933--13990 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
13923 TTATATAATT
*
13933 ATATAA ATAATAT ATATAA ATATAA ATATAA ATAT-A A-AT-A ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
13979 ATATAA ATATAA
1 ATATAA ATATAA
13991 TTTCAAGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 34 0.72
7 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:13969 original size:27 final size:26
Alignment explanation
Indices: 13925--13990 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
13915 TTCCATTATT
*
13925 ATATAATTATATAAAT-AATATATATAA
1 ATATAAATATA-AAATAAATA-ATATAA
13952 ATATAAATATAAATATAAATAATATAA
1 ATATAAATATAAA-ATAAATAATATAA
13979 ATATAAATATAA
1 ATATAAATATAA
13991 TTTCAAGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.06
27 30 0.83
28 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAATATAAAATAAATAATATAA
Found at i:15959 original size:23 final size:23
Alignment explanation
Indices: 15933--15978 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
15923 TATATTGTAA
15933 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
15956 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
15979 GGGGAGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (23 bp):
CCAATCATTTATCTTATTACTTG
Found at i:21489 original size:21 final size:21
Alignment explanation
Indices: 21465--21508 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
21455 GATTCTTTGC
21465 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
21486 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
21507 TT
1 TT
21509 ATAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTGAGATTTTATCTGATCTA
Found at i:21516 original size:21 final size:21
Alignment explanation
Indices: 21465--21516 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
21455 GATTCTTTGC
*
21465 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
21486 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
21507 TTAT-AAATTT
1 TT-TGAAATTT
21517 GTATATCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTGAAATTTTATCTGATCTA
Found at i:21712 original size:20 final size:20
Alignment explanation
Indices: 21687--21765 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
21677 AACAATCAAA
21687 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
***
21707 TAAAATGAAAATAAAA-AAA
1 TAAAATGAAAATAAAATTTT
*
21726 AAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
21746 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
21766 CGCGGGCGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.30
20 35 0.70
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAATGAAAATAAAATTTT
Found at i:22040 original size:24 final size:25
Alignment explanation
Indices: 21997--22060 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
21987 TGGAGCCTTA
**
21997 ATTTAATATTTAATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
22022 ATTTAATAAA-AATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
22046 ATTTAATAAATAATA
1 ATTTAATAAATAATA
22061 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAATAAATAATAAAAATTTAAT
Found at i:22055 original size:18 final size:18
Alignment explanation
Indices: 21996--22034 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
21986 ATGGAGCCTT
21996 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
22014 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
22032 AAT
1 AAT
22035 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATATTTAATAAA
Found at i:22061 original size:14 final size:14
Alignment explanation
Indices: 22042--22069 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
22032 AATAAAAATT
22042 TAATATTTAATAAA
1 TAATATTTAATAAA
22056 TAATATTTAATAAA
1 TAATATTTAATAAA
22070 AAAATTTGTT
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):
TAATATTTAATAAA
Found at i:22074 original size:18 final size:18
Alignment explanation
Indices: 22000--22074 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
21990 AGCCTTAATT
**
22000 TAATATTTAATAAAAATT
1 TAATATTTAATAAAAAAA
22018 TAATATTTAATAAAAATAA
1 TAATATTTAATAAAAA-AA
*
22037 -AA-ATTTAATATTTAATAAA
1 TAATATTTAATA---AAAAAA
22056 TAATATTTAATAAAAAAA
1 TAATATTTAATAAAAAAA
22074 T
1 T
22075 TTGTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 8 0.17
18 24 0.51
19 2 0.04
20 5 0.11
21 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATTTAATAAAAAAA
Done.