Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168121.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_365, 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: 30763
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Found at i:440 original size:21 final size:22
Alignment explanation
Indices: 394--448 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
384 CTATATTATT
* *
394 AATGATTTGCTATTATGCTATA
1 AATGATTTACTATTAAGCTATA
*
416 AATGATTTACTA-TAAGCTATC
1 AATGATTTACTATTAAGCTATA
*
437 AATGTTTTACTA
1 AATGATTTACTA
449 CCAAATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (22 bp):
AATGATTTACTATTAAGCTATA
Found at i:473 original size:11 final size:11
Alignment explanation
Indices: 454--531 Score: 63
Period size: 11 Copynumber: 7.4 Consensus size: 11
444 TACTACCAAA
*
454 TTATTAATAAT
1 TTATGAATAAT
465 TTATGAATAAT
1 TTATGAATAAT
* * *
476 TTATTACTAAA
1 TTATGAATAAT
*
487 TTATGAATGAT
1 TTATGAATAAT
498 TTAT---TAAT
1 TTATGAATAAT
*
506 TTATGATTAAT
1 TTATGAATAAT
* *
517 TTATCAGTAAT
1 TTATGAATAAT
528 TTAT
1 TTAT
532 TACAAAGTTA
Statistics
Matches: 53, Mismatches: 11, Indels: 6
0.76 0.16 0.09
Matches are distributed among these distances:
8 7 0.13
11 46 0.87
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (11 bp):
TTATGAATAAT
Found at i:511 original size:19 final size:21
Alignment explanation
Indices: 454--531 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
444 TACTACCAAA
454 TTATTAATAATTTATGAATAAT
1 TTATT-ATAATTTATGAATAAT
* *
476 TTATTACTAAATTATGAATGAT
1 TTATTA-TAATTTATGAATAAT
*
498 TTA-T-TAATTTATGATTAAT
1 TTATTATAATTTATGAATAAT
*
517 TTATCAGTAATTTAT
1 TTATTA-TAATTTAT
532 TACAAAGTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 15 0.33
21 2 0.04
22 29 0.63
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (21 bp):
TTATTATAATTTATGAATAAT
Found at i:835 original size:16 final size:15
Alignment explanation
Indices: 810--853 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
800 TATCTAATAT
*
810 TAAAAAATAAAAAAG
1 TAAAAAATAAAAAAC
*
825 TAAAAATATAATAAAC
1 TAAAAA-ATAAAAAAC
*
841 TAAAAAACAAAAA
1 TAAAAAATAAAAA
854 GCAAAAAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (15 bp):
TAAAAAATAAAAAAC
Found at i:2949 original size:15 final size:16
Alignment explanation
Indices: 2929--2965 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2919 TTATACCTAA
2929 AAAAATC-CAAAAAAT
1 AAAAATCACAAAAAAT
*
2944 AAAAATCATAAAAAAT
1 AAAAATCACAAAAAAT
2960 AAAAAT
1 AAAAAT
2966 GATTTTTCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATCACAAAAAAT
Found at i:3213 original size:20 final size:20
Alignment explanation
Indices: 3179--3230 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3169 TTGCCAAACT
3179 AGAAAA-GAAAAGAAAAAGA
1 AGAAAAGGAAAAGAAAAAGA
* *
3198 AGAAAAGGAAATGAAAGAGA
1 AGAAAAGGAAAAGAAAAAGA
*
3218 AAAAAAGAGAAAA
1 AGAAAAG-GAAAA
3231 TAGTGATAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.22
20 17 0.63
21 4 0.15
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (20 bp):
AGAAAAGGAAAAGAAAAAGA
Found at i:3308 original size:29 final size:29
Alignment explanation
Indices: 3273--3331 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
3263 AATGTCAGAC
*
3273 ATTCGGTAATGGTGACAACCTTGGAGCGT
1 ATTCGGTAATGGTGACAACCCTGGAGCGT
3302 ATTCGGTAATGGTGACAACCCTGGAGCGT
1 ATTCGGTAATGGTGACAACCCTGGAGCGT
3331 A
1 A
3332 AGAATCTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (29 bp):
ATTCGGTAATGGTGACAACCCTGGAGCGT
Found at i:6294 original size:38 final size:38
Alignment explanation
Indices: 6245--6338 Score: 134
Period size: 38 Copynumber: 2.5 Consensus size: 38
6235 AAATGATGGA
*
6245 AATAATAAGATAATATATGTACCCCATCTTATGCACAT
1 AATAATAAGATAATATATGTACCCAATCTTATGCACAT
* * * *
6283 AATAATAAGATAATACATGTACCCAATTTTCTGCATAT
1 AATAATAAGATAATATATGTACCCAATCTTATGCACAT
*
6321 CATAATAAGATAATATAT
1 AATAATAAGATAATATAT
6339 ACATTTCATC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (38 bp):
AATAATAAGATAATATATGTACCCAATCTTATGCACAT
Found at i:12932 original size:77 final size:78
Alignment explanation
Indices: 12815--12961 Score: 199
Period size: 77 Copynumber: 1.9 Consensus size: 78
12805 TAAATAATCA
* * *
12815 CATTTGCATCAATGACATGAGCATCATCAGGAAAACATTTGATCTATATGTTGTTAAAAAAA-AA
1 CATTTGCATCAATGACATGAGCATCATCAGGAAAACATTTGATCTACATGCTGTAAAAAAAACAA
12879 AAAAAGACATTTG
66 AAAAAGACATTTG
* * * * *
12892 CATTTGCATCAATGACATGTGCATCATGA-TAAGGATATTTGATCTACATGCTGTAAAAAAAACA
1 CATTTGCATCAATGACATGAGCATCATCAGGAA-AACATTTGATCTACATGCTGTAAAAAAAACA
12956 AAAAAA
65 AAAAAA
12962 ATAAAAAACA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
76 2 0.03
77 51 0.85
78 7 0.12
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (78 bp):
CATTTGCATCAATGACATGAGCATCATCAGGAAAACATTTGATCTACATGCTGTAAAAAAAACAA
AAAAAGACATTTG
Found at i:12969 original size:17 final size:17
Alignment explanation
Indices: 12948--12980 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12938 CATGCTGTAA
12948 AAAAAACAAAA-AAAAT
1 AAAAAACAAAAGAAAAT
12964 AAAAAACAAAAGAAAAT
1 AAAAAACAAAAGAAAAT
12981 CGCATTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.85, C:0.06, G:0.03, T:0.06
Consensus pattern (17 bp):
AAAAAACAAAAGAAAAT
Found at i:12987 original size:91 final size:87
Alignment explanation
Indices: 12870--13047 Score: 221
Period size: 91 Copynumber: 2.0 Consensus size: 87
12860 ATATGTTGTT
* * * * * * * *
12870 AAAAAAAAAAAAAAGACATTTGCATTTGCATCAATGACATGTGCATCATGATAAGGATATTTGAT
1 AAAAAAAAAAAAAAGAAAATCGCATTTACATCAATGACATGTGCATCATGAGAAAGACAATTGAT
12935 CTACATGCTGTAAAAAAAACAAAA
66 CTACATGCTG-AAAAAAAA-AAAA
* *
12959 AAAATAAAAAACAAAAGAAAATCGCATTTATATCAATTACATGTGCATCATGAGAAAGACAATTG
1 AAAA-AAAAAA-AAAAGAAAATCGCATTTACATCAATGACATGTGCATCATGAGAAAGACAATTG
*
13024 ATCTACATGTTGAAAAAAAAAAAA
64 ATCTACATGCTGAAAAAAAAAAAA
13048 GACATTCACA
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 8 0.11
90 14 0.18
91 54 0.71
ACGTcount: A:0.52, C:0.12, G:0.12, T:0.24
Consensus pattern (87 bp):
AAAAAAAAAAAAAAGAAAATCGCATTTACATCAATGACATGTGCATCATGAGAAAGACAATTGAT
CTACATGCTGAAAAAAAAAAAA
Found at i:13930 original size:104 final size:104
Alignment explanation
Indices: 13736--14267 Score: 494
Period size: 104 Copynumber: 5.1 Consensus size: 104
13726 GGCATCCAAG
* * *
13736 ATAATCTTTAAGA-CTTCTAGGCAAAACATTTTTAAATTTTTAAAGTTTTAATGCC-TCTAATAC
1 ATAATCTCTAAGACCTT-TAAGCAAAACA-TTTTAAATTTTTAAAGTTTTAATGCCTTC-GATAC
** *
13799 GATAAG--CATTCAAAGATGTCGAG-TTTGTAAGACCTTCAAGC
63 -A-AAGAACATTCAAAGATGTTAAGATTTGTAAGACCTTCAGGC
* * *
13840 ATAATCTTTAAGGCCTTTAAACAAAACATTTTAAAATTTTT-AAGTTTTAATGCCTTCGATACAA
1 ATAATCTCTAAGACCTTTAAGCAAAACATTTT-AAATTTTTAAAGTTTTAATGCCTTCGATACAA
* *
13904 AGAACATTCAAAGATGTTAAAATTTGTAAGACC-TCTAGGT
65 AGAACATTCAAAGATGTTAAGATTTGTAAGACCTTC-AGGC
* * * * *
13944 ATAATCTCTAA-AACTTTCGAGCAAAATATTTTAAATTTTTAAAGTTTCAATGCC-TC--TAAAA
1 ATAATCTCTAAGACCTTT-AAGCAAAACATTTTAAATTTTTAAAGTTTTAATGCCTTCGATACAA
*
14005 CGAGAAGCATTCAAAGATGTTGAGATTTGTAAGACCTTCAGGC
65 --AGAA-CATTCAAAGATGTTAAGATTTGTAAGACCTTCAGGC
* * * * * * * **
14048 ATAATCTGTAAGACCTCTAAGTAAAATATTTTAAAATTTTAAAGTTTTAATGCCTTTGGTATGAA
1 ATAATCTCTAAGACCTTTAAGCAAAACATTTTAAATTTTTAAAGTTTTAATGCCTTCGATACAAA
* * * * * *
14113 GAGCATTCAAAGATATCAAGAGTTG-AGAGATCTTCAGGT
66 GAACATTCAAAGATGTTAAGATTTGTA-AGACCTTCAGGC
* * * *
14152 ATAATCTCTAAAACCTCTAAGCAAAACATTTTAAATTTTTAAAGTTTCAATGCCTTTGATACAAA
1 ATAATCTCTAAGACCTTTAAGCAAAACATTTTAAATTTTTAAAGTTTTAATGCCTTCGATACAAA
* * * * * *
14217 GAGCATTCACATATGTTGAGATTTGTAAGACCTCCATGC
66 GAACATTCAAAGATGTTAAGATTTGTAAGACCTTCAGGC
14256 ATAATCTCTAAG
1 ATAATCTCTAAG
14268 CCTCTGATTG
Statistics
Matches: 352, Mismatches: 57, Indels: 38
0.79 0.13 0.09
Matches are distributed among these distances:
101 7 0.02
102 1 0.00
103 56 0.16
104 271 0.77
105 14 0.04
107 3 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (104 bp):
ATAATCTCTAAGACCTTTAAGCAAAACATTTTAAATTTTTAAAGTTTTAATGCCTTCGATACAAA
GAACATTCAAAGATGTTAAGATTTGTAAGACCTTCAGGC
Found at i:14095 original size:208 final size:207
Alignment explanation
Indices: 13736--14272 Score: 652
Period size: 208 Copynumber: 2.6 Consensus size: 207
13726 GGCATCCAAG
* * * * *
13736 ATAATCTTTAAGACTTCTAGGCAAAACATTTTTAAATTTTTAAAGTTTTAATGCCTCTAATACGA
1 ATAATCTCTAAAACCTCTAAGCAAAACA-TTTTAAATTTTTAAAGTTTCAATGCCTCTAATACGA
* * * *
13801 TAAGCATTCAAAGATGTCGAG-TTTGTAAGACCTTCAAGCATAATCTTTAAGGCCTTTAAACAAA
65 AAAGCATTCAAAGATGTTGAGATTTGTAAGACCTTCAAGCATAATCTCTAA-GCCTCTAAACAAA
* * * *
13865 ACATTTTAAAATTTTTAAGTTTTAATGCCTTCGATACAAAGAACATTCAAAGATGTTAAAATTTG
129 ACATTTTAAAATTTTAAAGTTTTAATGCCTTCGATACAAAGAACATTCAAAGATATCAAAAGTTG
13930 TA-AGACC-TCTAGGT
194 -AGAGACCTTC-AGGT
* * * *
13944 ATAATCTCTAAAA-CTTTCGAGCAAAATATTTTAAATTTTTAAAGTTTCAATGCCTCTAAAACGA
1 ATAATCTCTAAAACCTCT-AAGCAAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTAATACGA
* * * **
14008 GAAGCATTCAAAGATGTTGAGATTTGTAAGACCTTCAGGCATAATCTGTAAGACCTCTAAGTAAA
65 AAAGCATTCAAAGATGTTGAGATTTGTAAGACCTTCAAGCATAATCTCTAAG-CCTCTAAACAAA
* * * ** * *
14073 ATATTTTAAAATTTTAAAGTTTTAATGCCTTTGGTATGAAGAGCATTCAAAGATATCAAGAGTTG
129 ACATTTTAAAATTTTAAAGTTTTAATGCCTTCGATACAAAGAACATTCAAAGATATCAAAAGTTG
*
14138 AGAGATCTTCAGGT
194 AGAGACCTTCAGGT
* *
14152 ATAATCTCTAAAACCTCTAAGCAAAACATTTTAAATTTTTAAAGTTTCAATGCCTTTGATAC-AA
1 ATAATCTCTAAAACCTCTAAGCAAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTAATACGAA
* * * *
14216 AGAGCATTCACATATGTTGAGATTTGTAAGACCTCCATGCATAATCTCTAAGCCTCT
66 A-AGCATTCAAAGATGTTGAGATTTGTAAGACCTTCAAGCATAATCTCTAAGCCTCT
14273 GATTGTGAGG
Statistics
Matches: 282, Mismatches: 40, Indels: 15
0.84 0.12 0.04
Matches are distributed among these distances:
207 64 0.23
208 213 0.76
209 5 0.02
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (207 bp):
ATAATCTCTAAAACCTCTAAGCAAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTAATACGAA
AAGCATTCAAAGATGTTGAGATTTGTAAGACCTTCAAGCATAATCTCTAAGCCTCTAAACAAAAC
ATTTTAAAATTTTAAAGTTTTAATGCCTTCGATACAAAGAACATTCAAAGATATCAAAAGTTGAG
AGACCTTCAGGT
Found at i:16623 original size:6 final size:6
Alignment explanation
Indices: 16612--16664 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
16602 AAAATTTTAA
*
16612 TATTTT TATTTT TA-TTT TATTTT TATAATTT TA--TT TA-TTT TGTTTT
1 TATTTT TATTTT TATTTT TATTTT TAT--TTT TATTTT TATTTT TATTTT
16658 TATTTT T
1 TATTTT T
16665 CTAAACCTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
4 4 0.10
5 8 0.20
6 23 0.57
8 5 0.12
ACGTcount: A:0.19, C:0.00, G:0.02, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:16631 original size:11 final size:11
Alignment explanation
Indices: 16615--16663 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
16605 ATTTTAATAT
16615 TTTTATTTTTA
1 TTTTATTTTTA
16626 TTTTATTTTTA
1 TTTTATTTTTA
*
16637 TAATTT-TATTTA
1 T--TTTATTTTTA
*
16649 TTTTGTTTTTA
1 TTTTATTTTTA
16660 TTTT
1 TTTT
16664 TCTAAACCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 3 0.09
11 21 0.64
12 6 0.18
13 3 0.09
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:16645 original size:19 final size:16
Alignment explanation
Indices: 16612--16662 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
16602 AAAATTTTAA
16612 TATTTTTATTTTTATTT
1 TATTTTTATTTTTA-TT
16629 TATTTTTATAATTTTATT
1 TATTTTTAT--TTTTATT
*
16647 TA-TTTTGTTTTTATT
1 TATTTTTATTTTTATT
16662 T
1 T
16663 TTCTAAACCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
15 8 0.26
17 14 0.45
18 4 0.13
19 5 0.16
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (16 bp):
TATTTTTATTTTTATT
Found at i:16742 original size:21 final size:21
Alignment explanation
Indices: 16717--16767 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
16707 ACAAATAATA
*
16717 AAAATAAAAA-TTTCAATCTT
1 AAAATAAAAATTTTCAACCTT
16737 ACAAATAAATAATTTTCAACCTT
1 A-AAATAAA-AATTTTCAACCTT
16760 AAAA-AAAA
1 AAAATAAAA
16768 TAAAAGACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 2 0.07
21 10 0.37
22 5 0.19
23 10 0.37
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAATAAAAATTTTCAACCTT
Found at i:16760 original size:23 final size:21
Alignment explanation
Indices: 16717--16770 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
16707 ACAAATAATA
*
16717 AAAATAAA-AATTTCAATCTT
1 AAAATAAATAATTTCAACCTT
16737 ACAAATAAATAATTTTCAACCTT
1 A-AAATAAATAA-TTTCAACCTT
*
16760 AAAAAAAATAA
1 AAAATAAATAA
16771 AAGACAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 1 0.03
21 7 0.24
22 11 0.38
23 10 0.34
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAATAAATAATTTCAACCTT
Found at i:18368 original size:16 final size:16
Alignment explanation
Indices: 18330--18364 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
18320 AATTTTTATT
18330 AAATAAATAAAGAAAA
1 AAATAAATAAAGAAAA
*
18346 AAATAAATAGA-AAAA
1 AAATAAATAAAGAAAA
18361 AAAT
1 AAAT
18365 TAAAAAGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.80, C:0.00, G:0.06, T:0.14
Consensus pattern (16 bp):
AAATAAATAAAGAAAA
Found at i:18556 original size:20 final size:20
Alignment explanation
Indices: 18533--18573 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
18523 ATAGAAAAAG
18533 TATTAAAAAAATTTATCTAA
1 TATTAAAAAAATTTATCTAA
18553 TATTAAAAAAATTTATCTAA
1 TATTAAAAAAATTTATCTAA
18573 T
1 T
18574 CTTGTAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTAAAAAAATTTATCTAA
Found at i:19104 original size:16 final size:17
Alignment explanation
Indices: 19080--19122 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
19070 ATAATATTTG
19080 TAATA-AATAAAAATAT
1 TAATATAATAAAAATAT
**
19096 TAA-ATAATAAATTTAT
1 TAATATAATAAAAATAT
19112 TAATATAATAA
1 TAATATAATAA
19123 TATAAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 1 0.04
16 15 0.65
17 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAATATAATAAAAATAT
Found at i:20084 original size:3 final size:3
Alignment explanation
Indices: 20076--20108 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20066 GCTTAAACAA
20076 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20109 TTTAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20333 original size:61 final size:61
Alignment explanation
Indices: 20238--20354 Score: 189
Period size: 61 Copynumber: 1.9 Consensus size: 61
20228 ATAAAAATCA
20238 ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTGCATAT
1 ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTGCATAT
* * * * *
20299 ACAAAGACCAATTCTATCTACTGTTATAGGTTTTTGTCAATAAAAGCAGGTGTGTG
1 ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTG
20355 TATACATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (61 bp):
ACAAAGACCAATTCTACCTACTATAAAAGGTTTTTGTCAATAAAAGCAGCTGTGTGCATAT
Found at i:22692 original size:2 final size:2
Alignment explanation
Indices: 22685--22718 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
22675 CGATAAATAC
22685 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
22719 GTGATAAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:26259 original size:39 final size:36
Alignment explanation
Indices: 26190--26263 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 36
26180 ATAAAGATTG
*
26190 AAAATAAAAAAATTATTAATTTAATAATTAAATTAT
1 AAAATAAAAAAATTATAAATTTAATAATTAAATTAT
*
26226 AAAATAAAAAACAATTATAAATTTTAATCATTAAATTA
1 AAAAT-AAAAA-AATTATAAA-TTTAATAATTAAATTA
26264 ATAATTTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 5 0.15
37 5 0.15
38 8 0.24
39 15 0.45
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (36 bp):
AAAATAAAAAAATTATAAATTTAATAATTAAATTAT
Found at i:26948 original size:40 final size:41
Alignment explanation
Indices: 26872--26951 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
26862 AATACTATAT
* * **
26872 TATTTATTTTTATCTTTATATTTAATAAAATTTTAAAATTA
1 TATTCATTGTTATCTTTATATTTAATAAAAAATTAAAATTA
26913 TATTCATTGTTAT-TTT-TATTTAAATAAAAAATTAAAATT
1 TATTCATTGTTATCTTTATATTT-AATAAAAAATTAAAATT
26952 TTAATTAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.15
40 18 0.53
41 11 0.32
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (41 bp):
TATTCATTGTTATCTTTATATTTAATAAAAAATTAAAATTA
Found at i:27357 original size:12 final size:12
Alignment explanation
Indices: 27342--27371 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
27332 ATATCAATAA
27342 TATTTAAAAAAT
1 TATTTAAAAAAT
*
27354 TATTTAAAATAT
1 TATTTAAAAAAT
27366 TATTTA
1 TATTTA
27372 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTTAAAAAAT
Found at i:27438 original size:26 final size:27
Alignment explanation
Indices: 27396--27448 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
27386 TAAATAGTTA
*
27396 TTTAACAATAAACATTT-TATTAAAAT
1 TTTAACAATAAACATTTATATAAAAAT
*
27422 TTTAACTAA-AAATATTTATATAAAAAT
1 TTTAAC-AATAAACATTTATATAAAAAT
27449 ATATCAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (27 bp):
TTTAACAATAAACATTTATATAAAAAT
Found at i:30562 original size:7 final size:8
Alignment explanation
Indices: 30548--30572 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
30538 TCTTTTGACA
30548 CTTTTTTT
1 CTTTTTTT
30556 CTTTTTTT
1 CTTTTTTT
30564 CTTTTTTT
1 CTTTTTTT
30572 C
1 C
30573 ATCTTTTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
CTTTTTTT
Done.