Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167879.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_147, 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: 65193
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1077 original size:6 final size:6
Alignment explanation
Indices: 1047--1076 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1037 TTGAACTTTA
*
1047 GCTATG GCTATG GCTATG GCTATG ACTATG
1 GCTATG GCTATG GCTATG GCTATG GCTATG
1077 AAAGAAGCAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.33
Consensus pattern (6 bp):
GCTATG
Found at i:5944 original size:154 final size:155
Alignment explanation
Indices: 5781--6191 Score: 425
Period size: 154 Copynumber: 2.8 Consensus size: 155
5771 TCTTCATCCA
* * * * * **
5781 TTGGAGTCTGTAATTTTACAGAAGACCCCAT-CTTAAATTTCT-AGTCTTGTGTTATGTATTCCA
1 TTGGAGTCTGAAATTTTACACAAAACCAC-TCCATAAATTTCTAAG-CTTGTGTTACATATTCCA
** *
5844 TCCCTCTA-ACCACTACCCATCAAAGCAAGTTATTCAGGCAGGTTT-AATTGTTCATACTTTTGA
64 T-CCTCTAGACCAAAACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATACTTTTGA
5907 AAAAAAAAAAAAAAAAACGCTTCACCGT
128 AAAAAAAAAAAAAAAAACGCTTCACCGT
*
5935 TTGGAGTCTGAAATTTTACACAAAACCACTCCATAAATTTCTAAGCTTTTGTTACATATTCCATC
1 TTGGAGTCTGAAATTTTACACAAAACCACTCCATAAATTTCTAAGCTTGTGTTACATATTCCATC
*
6000 CTCTAGACCAAAACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATATTTTTG----
66 CTCTAGACCAAAACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATACTTTTGAAAA
* *
6061 ---AAAAAAAAAATCTCTTCACC--
131 AAAAAAAAAAAAAACGCTTCACCGT
* ** * * *
6081 -------CT--AATTTTACACAAAACCCCAACTTAAATTTCTAATCTTTTGTTACATATTCCATC
1 TTGGAGTCTGAAATTTTACACAAAACCACTCCATAAATTTCTAAGCTTGTGTTACATATTCCATC
* * *
6137 ACTCTTGCCCAAAACCCATCAAATCAAGTTATTCAGGAAGGTTTAAATTGTTCAT
66 -CTCTAGACCAAAACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCAT
6192 TTTTTTTTCT
Statistics
Matches: 230, Mismatches: 22, Indels: 26
0.83 0.08 0.09
Matches are distributed among these distances:
137 49 0.21
138 51 0.22
139 2 0.01
148 18 0.08
153 7 0.03
154 85 0.37
155 18 0.08
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.33
Consensus pattern (155 bp):
TTGGAGTCTGAAATTTTACACAAAACCACTCCATAAATTTCTAAGCTTGTGTTACATATTCCATC
CTCTAGACCAAAACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATACTTTTGAAAA
AAAAAAAAAAAAAACGCTTCACCGT
Found at i:6196 original size:137 final size:137
Alignment explanation
Indices: 5946--6197 Score: 414
Period size: 138 Copynumber: 1.8 Consensus size: 137
5936 TGGAGTCTGA
**
5946 AATTTTACACAAAACCACTCCATAAATTTCTAAGCTTTTGTTACATATTCCATCCTCTAGACCAA
1 AATTTTACACAAAACCACAACATAAATTTCTAAGCTTTTGTTACATATTCCATCCTCTAGACCAA
6011 AACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATATTTTTGAAAAAAAAAATCTCT
66 AACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATATTTTTGAAAAAAAAAATCTCT
6076 TCACCCT
131 TCACCCT
* * * * *
6083 AATTTTACACAAAACCCCAACTTAAATTTCTAATCTTTTGTTACATATTCCATCACTCTTGCCCA
1 AATTTTACACAAAACCACAACATAAATTTCTAAGCTTTTGTTACATATTCCATC-CTCTAGACCA
* *
6148 AAACCCATCAAATCAAGTTATTCAGGAAGGTTTAAATTGTTCATTTTTTT
65 AAACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATATTTTT
6198 TTCTTTTTTG
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
137 49 0.47
138 56 0.53
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (137 bp):
AATTTTACACAAAACCACAACATAAATTTCTAAGCTTTTGTTACATATTCCATCCTCTAGACCAA
AACCCATCAAAGCAAGTTATTCAGGAAGGTTTAAATTGTTCATATTTTTGAAAAAAAAAATCTCT
TCACCCT
Found at i:11843 original size:3 final size:3
Alignment explanation
Indices: 11835--11864 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
11825 TCTCGCTAGA
11835 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
11865 TTTGCTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:14496 original size:24 final size:24
Alignment explanation
Indices: 14465--14514 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
14455 GGGGGTCGCA
14465 ATCAACTAGATAGGGATAATCTTC
1 ATCAACTAGATAGGGATAATCTTC
14489 ATCAACTAGATAGGGATAATCTTC
1 ATCAACTAGATAGGGATAATCTTC
14513 AT
1 AT
14515 TCTCTTTCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (24 bp):
ATCAACTAGATAGGGATAATCTTC
Found at i:17920 original size:19 final size:18
Alignment explanation
Indices: 17883--17921 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
17873 TATAAAATAT
17883 AATTTTTTAATTTTATTA
1 AATTTTTTAATTTTATTA
17901 AATTTATTTATATTTT-TTA
1 AATTT-TTTA-ATTTTATTA
17920 AA
1 AA
17922 AATTTAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
AATTTTTTAATTTTATTA
Found at i:19193 original size:15 final size:15
Alignment explanation
Indices: 19141--19343 Score: 127
Period size: 15 Copynumber: 13.5 Consensus size: 15
19131 ACTTATAAAT
*
19141 AATATTATATTAATA
1 AATAATATATTAATA
19156 AATAAATCATATT-ATA
1 AAT-AAT-ATATTAATA
* *
19172 TTACAATATATTAATAA
1 -AATAATATATTAAT-A
*
19189 GCAATATTATATGT-ATA
1 --AATAATATAT-TAATA
* *
19206 AATAATATACTATTA
1 AATAATATATTAATA
*
19221 ATGTAATATATTAATA
1 A-ATAATATATTAATA
19237 AATAATATATTAAT-
1 AATAATATATTAATA
*
19251 -AT-AT-TAATAA-A
1 AATAATATATTAATA
*
19262 AATATTATATTAATA
1 AATAATATATTAATA
19277 AATAATATATTAATA
1 AATAATATATTAATA
* *
19292 AATATTATTATAAATA
1 AATAATA-TATTAATA
*
19308 AAT-ATATACTAATA
1 AATAATATATTAATA
* * *
19322 TATTA-ATAGTAATA
1 AATAATATATTAATA
19336 AATAATAT
1 AATAATAT
19344 TATATTATAT
Statistics
Matches: 144, Mismatches: 27, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
11 5 0.03
12 4 0.03
13 3 0.02
14 25 0.17
15 57 0.40
16 32 0.22
17 8 0.06
18 9 0.06
19 1 0.01
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (15 bp):
AATAATATATTAATA
Found at i:19232 original size:13 final size:14
Alignment explanation
Indices: 19206--19377 Score: 91
Period size: 13 Copynumber: 12.7 Consensus size: 14
19196 TATATGTATA
19206 AATAAT-ATACTATT
1 AATAATAATA-TATT
*
19220 AAT-GTAATATATT
1 AATAATAATATATT
19233 AATAAATAATATATT
1 AAT-AATAATATATT
*
19248 AAT-AT-AT-TAAT
1 AATAATAATATATT
* *
19259 AAAAATATTATATT
1 AATAATAATATATT
19273 AATAAATAATATATT
1 AAT-AATAATATATT
19288 AAT-A-AATATTATT
1 AATAATAATA-TATT
19301 -ATAAATAA-ATA-T
1 AAT-AATAATATATT
*
19313 -ATACTAATATATT
1 AATAATAATATATT
* *
19326 AATAGTAATA-AAT
1 AATAATAATATATT
*
19339 AATATTATATTATATT
1 AATA--ATAATATATT
* *
19355 AATAA-AAAATATA
1 AATAATAATATATT
*
19368 AAGAATAATA
1 AATAATAATA
19378 AATAGTTTTA
Statistics
Matches: 121, Mismatches: 19, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
11 9 0.07
12 16 0.13
13 34 0.28
14 25 0.21
15 31 0.26
16 6 0.05
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (14 bp):
AATAATAATATATT
Found at i:19243 original size:99 final size:94
Alignment explanation
Indices: 19135--19360 Score: 217
Period size: 104 Copynumber: 2.3 Consensus size: 94
19125 AAATTTACTT
*
19135 ATAAATAATATTATATTAATAAATAAATCATATT-ATATTACAATATATTAATAAGCAATATTAT
1 ATAAATAATATTATATTAATAAATAAATCATATTAATA-AACAATATATTAAT-A--AATA-T-T
* * *
19199 ATGTATAAAT-AATATACTATTAATGTAAT-ATATTA
60 AT-TATAAATAAATATA-TACTAATATAATAATAGTA
* *
19234 ATAAATAATATATTAATATATTAATAAA-AATATTATATTAATAAATAATATATTAATAAATATT
1 ATAAAT-A-ATA-T--TATATTAATAAATAA-ATCATATTAATAAACAATATATTAATAAATATT
*
19298 ATTATAAATAAATATATACTAATATATTAATAGTA
60 ATTATAAATAAATATATACTAATATAATAATAGTA
*
19333 ATAAATAATATTATATTATATTAATAAA
1 ATAAATAATATTATATTA-ATAAATAAA
19361 AAATATAAAG
Statistics
Matches: 108, Mismatches: 8, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
94 7 0.06
95 5 0.05
96 3 0.03
97 3 0.03
98 17 0.16
99 26 0.24
100 2 0.02
101 7 0.06
102 1 0.01
103 3 0.03
104 31 0.29
105 3 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (94 bp):
ATAAATAATATTATATTAATAAATAAATCATATTAATAAACAATATATTAATAAATATTATTATA
AATAAATATATACTAATATAATAATAGTA
Found at i:19305 original size:44 final size:45
Alignment explanation
Indices: 19226--19347 Score: 141
Period size: 40 Copynumber: 2.8 Consensus size: 45
19216 TATTAATGTA
19226 ATATATTAATAAATAATATATTAAT--ATATTA--AT-AA-AAAT
1 ATATATTAATAAATAATATATTAATAAATATTATTATAAATAAAT
19265 ATTATATTAATAAATAATATATTAATAAATATTATTATAAATAAAT
1 A-TATATTAATAAATAATATATTAATAAATATTATTATAAATAAAT
* * * * *
19311 ATATACTAATATATTA-ATAGTAATAAATAATATTATA
1 ATATATTAATAAATAATATATTAATAAATATTATTATA
19348 TTATATTAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
39 1 0.01
40 24 0.34
42 6 0.08
44 21 0.30
45 14 0.20
46 5 0.07
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (45 bp):
ATATATTAATAAATAATATATTAATAAATATTATTATAAATAAAT
Found at i:19361 original size:99 final size:99
Alignment explanation
Indices: 19135--19362 Score: 245
Period size: 99 Copynumber: 2.3 Consensus size: 99
19125 AAATTTACTT
* * * *
19135 ATAAATAATATTATATTA-ATAAATAAATCATATTATATTACAATATATTAATAAGCAATATTAT
1 ATAAATAATATTATATTATATTAATAAA-AATATTATATTAAAATATATTAATAAGAAATATTAT
** * *
19199 ATGTATAAATAATATACTATTAATGTAATATATTA
65 ATAAATAAATAATATACTAATAATGTAATATAGTA
* * *
19234 ATAAATAATA-TATTAATATATTAATAAAAATATTATATTAATAA-ATAATATATTAATAAATAT
1 ATAAATAATATTA-TATTATATTAATAAAAATATTATATTAA-AATAT-AT-TAATAAGAAATAT
19297 TATTATAAATAAAT-ATATACTAATATAT-T-A-ATAGTA
62 TA-TATAAATAAATAATATACTAATA-ATGTAATATAGTA
19333 ATAAATAATATTATATTATATTAATAAAAA
1 ATAAATAATATTATATTATATTAATAAAAA
19363 ATATAAAGAA
Statistics
Matches: 109, Mismatches: 12, Indels: 16
0.80 0.09 0.12
Matches are distributed among these distances:
98 2 0.02
99 58 0.53
100 15 0.14
101 23 0.21
102 11 0.10
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (99 bp):
ATAAATAATATTATATTATATTAATAAAAATATTATATTAAAATATATTAATAAGAAATATTATA
TAAATAAATAATATACTAATAATGTAATATAGTA
Found at i:19369 original size:32 final size:31
Alignment explanation
Indices: 19274--19374 Score: 61
Period size: 29 Copynumber: 3.3 Consensus size: 31
19264 TATTATATTA
* * *
19274 ATAAATAATATATTAATAAATATT-ATTATAA-
1 ATAAATAATATACTAAT--ATATTAATAAAAAT
**
19305 ATAAAT-ATATACTAATATATTAAT-AGTA-
1 ATAAATAATATACTAATATATTAATAAAAAT
*
19333 ATAAATAATATTA-TATTATATTAATAAAAAAT
1 ATAAATAATA-TACTAATATATTAAT-AAAAAT
*
19365 ATAAAGAATA
1 ATAAATAATA
19375 ATAAATAGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
28 13 0.23
29 16 0.28
30 11 0.19
31 8 0.14
32 9 0.16
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.39
Consensus pattern (31 bp):
ATAAATAATATACTAATATATTAATAAAAAT
Found at i:19440 original size:19 final size:19
Alignment explanation
Indices: 19395--19440 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
19385 TTATTTTAAG
*
19395 TATTTTTATATTAACATAA
1 TATTTTAATATTAACATAA
*
19414 TATTTTAATATTAA-ATAT
1 TATTTTAATATTAACATAA
19432 TATTATTAA
1 TATT-TTAA
19441 AAATATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTTTAATATTAACATAA
Found at i:19467 original size:16 final size:15
Alignment explanation
Indices: 19442--19494 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
19432 TATTATTAAA
19442 AATATAATTATTTTTT
1 AATATAATTA-TTTTT
* *
19458 AATATTATTAATTTT
1 AATATAATTATTTTT
*
19473 AATAATAAATAATTTTT
1 AAT-AT-AATTATTTTT
19490 AATAT
1 AATAT
19495 TTTAAAGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 7 0.23
16 13 0.43
17 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATAATTATTTTT
Found at i:19472 original size:15 final size:16
Alignment explanation
Indices: 19411--19499 Score: 60
Period size: 15 Copynumber: 5.8 Consensus size: 16
19401 TATATTAACA
*
19411 TAATATT-TTAATATT
1 TAATATTATTAATTTT
* **
19426 AAATATTATT-ATTAA
1 TAATATTATTAATTTT
* * *
19441 AAATATAATTATTTTT
1 TAATATTATTAATTTT
19457 TAATATTATTAA-TTT
1 TAATATTATTAATTTT
* *
19472 TAATAATAAATAATTTT
1 TAAT-ATTATTAATTTT
19489 TAATATT-TTAA
1 TAATATTATTAA
19500 AGTTATATTA
Statistics
Matches: 55, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
15 27 0.49
16 21 0.38
17 7 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TAATATTATTAATTTT
Found at i:19890 original size:19 final size:19
Alignment explanation
Indices: 19863--19899 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
19853 TTTATTATCC
*
19863 TTATATTTTTAATATTTTA
1 TTATATTTTAAATATTTTA
*
19882 TTATTTTTTAAATATTTT
1 TTATATTTTAAATATTTT
19900 TTAAAATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATATTTTAAATATTTTA
Found at i:22663 original size:9 final size:9
Alignment explanation
Indices: 22651--22680 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
22641 TGTATTTTTT
22651 TAATTAAAA
1 TAATTAAAA
22660 TAATTAAAA
1 TAATTAAAA
22669 TATATTAAAA
1 TA-ATTAAAA
22679 TA
1 TA
22681 TATAAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:22687 original size:8 final size:10
Alignment explanation
Indices: 22653--22683 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
22643 TATTTTTTTA
22653 ATTAAAATA-
1 ATTAAAATAT
22662 ATTAAAATAT
1 ATTAAAATAT
22672 ATTAAAATAT
1 ATTAAAATAT
22682 AT
1 AT
22684 AAATTAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:22694 original size:19 final size:19
Alignment explanation
Indices: 22653--22694 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
22643 TATTTTTTTA
*
22653 ATTAAAATAATTAAAATAT
1 ATTAAAATAATTAAAATAG
*
22672 ATTAAAAT-ATATAAATTAG
1 ATTAAAATAAT-TAAAATAG
22691 ATTA
1 ATTA
22695 GACTCATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATTAAAATAATTAAAATAG
Found at i:30220 original size:31 final size:31
Alignment explanation
Indices: 30185--30250 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
30175 TAGTACACAA
30185 AATCTAAACACAGACTGAGATGATTGCAGGC
1 AATCTAAACACAGACTGAGATGATTGCAGGC
*
30216 AATCTAAACACAGACTGGGATGATTGCAGGC
1 AATCTAAACACAGACTGAGATGATTGCAGGC
30247 AATC
1 AATC
30251 ACAAGAGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (31 bp):
AATCTAAACACAGACTGAGATGATTGCAGGC
Found at i:38987 original size:25 final size:25
Alignment explanation
Indices: 38955--39011 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
38945 AAACAGTAAT
* * *
38955 AAAAATTATTATAATTGTGATTGAA
1 AAAAATTATTATAATTATAATTAAA
38980 AAAAATTATTATAATTATAATTAAA
1 AAAAATTATTATAATTATAATTAAA
39005 AAAAATT
1 AAAAATT
39012 TAATAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (25 bp):
AAAAATTATTATAATTATAATTAAA
Found at i:39644 original size:32 final size:32
Alignment explanation
Indices: 39608--39671 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
39598 ACATGGGCAG
39608 CCATTTCAATTAAGGATTAAATTAGGTAACAT
1 CCATTTCAATTAAGGATTAAATTAGGTAACAT
39640 CCATTTCAATTAAGGATTAAATTAGGTAACAT
1 CCATTTCAATTAAGGATTAAATTAGGTAACAT
39672 GTGTCTATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (32 bp):
CCATTTCAATTAAGGATTAAATTAGGTAACAT
Found at i:42346 original size:17 final size:18
Alignment explanation
Indices: 42309--42348 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
42299 AAATTCATGA
**
42309 AATATAAAATAAAATTGG
1 AATATAAAATAAAATAAG
42327 AATATAAAA-AAAATAAG
1 AATATAAAATAAAATAAG
42344 AATAT
1 AATAT
42349 GACTTTAAAA
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:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
AATATAAAATAAAATAAG
Found at i:42387 original size:18 final size:18
Alignment explanation
Indices: 42351--42388 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
42341 AAGAATATGA
*
42351 CTTTAAAAAAATATTTTT
1 CTTTAAAAAAATATATTT
42369 CTTTAAACAAAAT-TATTT
1 CTTTAAA-AAAATATATTT
42387 CT
1 CT
42389 AGTTTTGTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (18 bp):
CTTTAAAAAAATATATTT
Found at i:42846 original size:3 final size:3
Alignment explanation
Indices: 42838--42863 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42828 AATTTCTTAT
42838 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
42864 TACTTTGTAG
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:51950 original size:28 final size:28
Alignment explanation
Indices: 51918--51984 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 28
51908 ATATAAAAAT
**
51918 TTTATTT-ATAATTTAAATTTAATTAATA
1 TTTATTTAATAATAAAAATTT-ATTAATA
*
51946 TTTATTTAATAATAAAAATTTGTTAATA
1 TTTATTTAATAATAAAAATTTATTAATA
51974 TTGTTATTTAA
1 -T-TTATTTAA
51985 AAAATATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 13 0.39
29 12 0.36
30 8 0.24
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
TTTATTTAATAATAAAAATTTATTAATA
Found at i:52090 original size:24 final size:23
Alignment explanation
Indices: 52063--52122 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
52053 GAATTTATTC
*
52063 ATTTTAATTTAATTATT-TTTAATA
1 ATTTT-ATTTAATT-TTATTAAATA
*
52087 ATTTTTTTTTAATTTTACTTAAATA
1 A-TTTTATTTAATTTTA-TTAAATA
52112 ATTTTATTTAA
1 ATTTTATTTAA
52123 ATCTTTTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 2 0.07
24 17 0.57
25 11 0.37
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (23 bp):
ATTTTATTTAATTTTATTAAATA
Found at i:52304 original size:29 final size:30
Alignment explanation
Indices: 52263--52319 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
52253 AATAAAATAT
* *
52263 TAAAATAAAAATATTTATATT-TATATTTA
1 TAAAATAAAAATAATTAAATTATATATTTA
* *
52292 TAAAATTATAATAATTAAATTATATATT
1 TAAAATAAAAATAATTAAATTATATATT
52320 ATTATTCGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 17 0.74
30 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAAAATAAAAATAATTAAATTATATATTTA
Found at i:60725 original size:31 final size:31
Alignment explanation
Indices: 60684--60748 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
60674 CGATGCAAGA
*
60684 ATTT-ATATA-TATATATATATATATGAATTTAT
1 ATTTGATATATTAT-TA-ATATATA-AAATTTAT
60716 ATTTGATATATTATTAATATATAAAATTTAT
1 ATTTGATATATTATTAATATATAAAATTTAT
60747 AT
1 AT
60749 ATTATTAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
31 9 0.30
32 11 0.37
33 7 0.23
34 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTTGATATATTATTAATATATAAAATTTAT
Found at i:60766 original size:24 final size:24
Alignment explanation
Indices: 60691--60766 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
60681 AGAATTTATA
*
60691 TATATATATATATATATGAATTTATATT
1 TATATAT-TAT-TA-ATGAA-TTAAATT
*
60719 TGATATATTATTAAT-ATATAAAATT
1 T-ATATATTATTAATGA-ATTAAATT
60744 TATATATTATTAATGAATTAAAT
1 TATATATTATTAATGAATTAAAT
60767 AATGATAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
24 19 0.45
25 8 0.19
26 3 0.07
27 2 0.05
28 4 0.10
29 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
TATATATTATTAATGAATTAAATT
Found at i:60791 original size:26 final size:28
Alignment explanation
Indices: 60745--60825 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 28
60735 TATAAAATTT
* *
60745 ATATATTATTAATGAATTAAATAATGAT-
1 ATATTTTATTAAT-AAATAAATAATGATA
60773 A-A-TTTATTAATAAAATAAATTTAATGATA
1 ATATTTTATTAAT-AAATAAA--TAATGATA
60802 ATATTTTATTAATAAATAAATAAT
1 ATATTTTATTAATAAATAAATAAT
60826 TTTATTTTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
26 14 0.31
27 1 0.02
28 12 0.27
29 1 0.02
30 8 0.18
31 9 0.20
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (28 bp):
ATATTTTATTAATAAATAAATAATGATA
Found at i:62517 original size:22 final size:22
Alignment explanation
Indices: 62487--62533 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
62477 ATTATTCTTT
**
62487 TTTTAATGCTGTTTCACTATGA
1 TTTTAATGCAATTTCACTATGA
* *
62509 TTTTCATGCAATTTCACTCTGA
1 TTTTAATGCAATTTCACTATGA
62531 TTT
1 TTT
62534 GATCTCACTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (22 bp):
TTTTAATGCAATTTCACTATGA
Done.