Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168316.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_540, 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: 23611
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Found at i:1181 original size:25 final size:25
Alignment explanation
Indices: 1152--1210 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 25
1142 ACCCAATTTA
1152 ATTTGGATTAATTCAAAACTTTATT
1 ATTTGGATTAATTCAAAACTTTATT
1177 ATTTGG---AATTCAAAACTTTATT
1 ATTTGGATTAATTCAAAACTTTATT
1199 ATTTGGACTTAA
1 ATTTGGA-TTAA
1211 ATAGCTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 22 0.73
25 6 0.20
26 2 0.07
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (25 bp):
ATTTGGATTAATTCAAAACTTTATT
Found at i:1189 original size:22 final size:22
Alignment explanation
Indices: 1161--1205 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1151 AATTTGGATT
1161 AATTCAAAACTTTATTATTTGG
1 AATTCAAAACTTTATTATTTGG
1183 AATTCAAAACTTTATTATTTGG
1 AATTCAAAACTTTATTATTTGG
1205 A
1 A
1206 CTTAAATAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (22 bp):
AATTCAAAACTTTATTATTTGG
Found at i:2805 original size:3 final size:3
Alignment explanation
Indices: 2797--2856 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
2787 CTTTAAATTT
2797 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2845 ATA ATA ATA ATA
1 ATA ATA ATA ATA
2857 TAAAAATTTT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:6168 original size:12 final size:12
Alignment explanation
Indices: 6151--6175 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6141 TCCTTATTCC
6151 CCTTTTTCTTTT
1 CCTTTTTCTTTT
6163 CCTTTTTCTTTT
1 CCTTTTTCTTTT
6175 C
1 C
6176 TCTCACTCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CCTTTTTCTTTT
Found at i:6460 original size:24 final size:24
Alignment explanation
Indices: 6412--6457 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
6402 GAAAGTTTCC
*
6412 AAAAAATTTCCAGAAAAAAATTTA
1 AAAAAATTTCCAAAAAAAAATTTA
6436 AAAAAATTT-CAAAAAAAAATTT
1 AAAAAATTTCCAAAAAAAAATTT
6458 TAAGCTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAAAATTTCCAAAAAAAAATTTA
Found at i:6688 original size:15 final size:14
Alignment explanation
Indices: 6668--6698 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
6658 TAACACCTAC
6668 TTTTTATTTTTTCTA
1 TTTTTATTTTTT-TA
6683 TTTTTATTTTTTTA
1 TTTTTATTTTTTTA
6697 TT
1 TT
6699 AACAAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTATTTTTTTA
Found at i:6970 original size:42 final size:42
Alignment explanation
Indices: 6913--7018 Score: 133
Period size: 44 Copynumber: 2.5 Consensus size: 42
6903 CAAAGGCTGG
*
6913 AATGACTTTTGAAAAATAAAAGGCTCCTCTAAATAGAGGCTC
1 AATGACTTTTGAAAAATAAAAGGCTCCTCTAAATAGAGACTC
* * *
6955 AATGAC-TTTGAAAAAAATAAAAAGGTTTCTTTAAATAGAGACTC
1 AATGACTTTTG--AAAAAT-AAAAGGCTCCTCTAAATAGAGACTC
*
6999 AATAACTTTTGAAAAATAAA
1 AATGACTTTTGAAAAATAAA
7019 CAAAGCTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
41 4 0.07
42 9 0.16
43 12 0.22
44 26 0.47
45 4 0.07
ACGTcount: A:0.47, C:0.11, G:0.13, T:0.28
Consensus pattern (42 bp):
AATGACTTTTGAAAAATAAAAGGCTCCTCTAAATAGAGACTC
Found at i:7328 original size:20 final size:21
Alignment explanation
Indices: 7280--7328 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
7270 ATTTTGGAGA
*
7280 TTCACATACAAAGTTCAAAGC
1 TTCACATTCAAAGTTCAAAGC
* *
7301 TTCTCATTC-AAGTTCAAAGG
1 TTCACATTCAAAGTTCAAAGC
7321 TTCACATT
1 TTCACATT
7329 TGACAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 17 0.71
21 7 0.29
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (21 bp):
TTCACATTCAAAGTTCAAAGC
Found at i:7601 original size:24 final size:23
Alignment explanation
Indices: 7530--7610 Score: 85
Period size: 25 Copynumber: 3.5 Consensus size: 23
7520 GATTCTCAAC
*
7530 GATTATCATTT-AAAA-CTCAAA
1 GATTATCATTTGAAAATCTTAAA
* *
7551 GGTTCTCATTTGAAAATGTCTTAAA
1 GATTATCATTTGAAAA--TCTTAAA
7576 GATTATCATTTGAAACATCTTAAA
1 GATTATCATTTGAAA-ATCTTAAA
*
7600 GATTCTCATTT
1 GATTATCATTT
7611 AAGATTCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
21 9 0.18
22 4 0.08
24 17 0.35
25 18 0.37
26 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (23 bp):
GATTATCATTTGAAAATCTTAAA
Found at i:8821 original size:23 final size:22
Alignment explanation
Indices: 8795--8840 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
8785 TCAATTTAAG
8795 TCTTTTTTTTCTCTCATT-TTTCA
1 TCTTTTTTTT-TC-CATTCTTTCA
8818 TCTTTTTTTTTCCATTCTTTCA
1 TCTTTTTTTTTCCATTCTTTCA
8840 T
1 T
8841 TTACTCATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 4 0.18
22 8 0.36
23 10 0.45
ACGTcount: A:0.09, C:0.22, G:0.00, T:0.70
Consensus pattern (22 bp):
TCTTTTTTTTTCCATTCTTTCA
Found at i:8823 original size:22 final size:22
Alignment explanation
Indices: 8798--8840 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8788 ATTTAAGTCT
8798 TTTTTTTCTCTCATT-TTTCATC
1 TTTTTTTCTC-CATTCTTTCATC
*
8820 TTTTTTTTTCCATTCTTTCAT
1 TTTTTTTCTCCATTCTTTCAT
8841 TTACTCATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTTTCTCCATTCTTTCATC
Found at i:8894 original size:16 final size:15
Alignment explanation
Indices: 8848--8893 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
8838 CATTTACTCA
* *
8848 TTTTCTCTCATTTTCC
1 TTTTTTCTC-TTTTTC
8864 TTTTTTCATCTTTTTC
1 TTTTTTC-TCTTTTTC
8880 TTTTTTCTCTTTTT
1 TTTTTTCTCTTTTT
8894 TATTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 7 0.26
16 18 0.67
17 2 0.07
ACGTcount: A:0.04, C:0.22, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTTCTCTTTTTC
Found at i:8899 original size:15 final size:16
Alignment explanation
Indices: 8858--8907 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
8848 TTTTCTCTCA
*
8858 TTTTCCTTTTTTCATC
1 TTTTTCTTTTTTCATC
8874 TTTTTCTTTTTTC-TC
1 TTTTTCTTTTTTCATC
*
8889 TTTTTTATTTTTTTCATC
1 -TTTTT-CTTTTTTCATC
8907 T
1 T
8908 ATTAGTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 2 0.07
16 17 0.59
17 8 0.28
18 2 0.07
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCTTTTTTCATC
Found at i:9299 original size:16 final size:17
Alignment explanation
Indices: 9280--9311 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
9270 TTTCTCTCTC
9280 TTTTTTTCTT-TTTTTT
1 TTTTTTTCTTCTTTTTT
9296 TTTTTTTCTTCTTTTT
1 TTTTTTTCTTCTTTTT
9312 CTTTGAGACC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTTT
Found at i:11238 original size:18 final size:18
Alignment explanation
Indices: 11215--11249 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
11205 TCCAAGATCG
11215 TATACCCTACAAGATATA
1 TATACCCTACAAGATATA
* *
11233 TATACCTTACAGGATAT
1 TATACCCTACAAGATAT
11250 GTAAACTGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (18 bp):
TATACCCTACAAGATATA
Found at i:11484 original size:14 final size:15
Alignment explanation
Indices: 11465--11494 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
11455 TTTGAGATAG
11465 TTGAAATT-TTTTGT
1 TTGAAATTATTTTGT
11479 TTGAAATTATTTTGT
1 TTGAAATTATTTTGT
11494 T
1 T
11495 CTATCTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.63
Consensus pattern (15 bp):
TTGAAATTATTTTGT
Found at i:13384 original size:198 final size:196
Alignment explanation
Indices: 13030--13397 Score: 419
Period size: 198 Copynumber: 1.9 Consensus size: 196
13020 ACACTTACTT
* * *
13030 TTATTGAAATTTCATCTAAATTATTCCATCATTTAGGGATAAATCTAGAGAAATTTCTCACCTAA
1 TTATTGAAATTTCATCTAAATTATTCCACCATTTAGGGACAAATCTAGAAAAATTTCTCACCTAA
* * * * ** *
13095 AGATTTTTTAATAAATTTACCATTTGAAATTTCTAAGAATCTCATCCTTAGTTATTCTTATTTTA
66 AGATTTTATAAGAAATTTACCATTTGAAATTTCTAAGAATCTCATCATTAGTAATTAATATCTTA
* *
13160 TTCCAAAATTTTTATTAATATTTTTATTTTTTTGCTTTTTTTTGTTTGAAAATAAATATTAATTA
131 TTCCAAAAATATTATTAATATTTTTA-TTTTTTG-TTTTTTTTGTTTGAAAATAAATATTAATTA
13225 TTG
194 TTG
* * * *
13228 TTATTGAAATTTTATCTAAATTATTCTACCATTT-GGGACAATTTTAGGAAAAATTTCTCACCT-
1 TTATTGAAATTTCATCTAAATTATTCCACCATTTAGGGACAAATCTA-GAAAAATTTCTCACCTA
* *
13291 AAGAATTTTAT-AGAAATTTACTATTTGAAATTTCTCAA-AAT-TCCATCATTGGATAATTAATA
65 AAG-ATTTTATAAGAAATTTACCATTTGAAATTTCT-AAGAATCT-CATCATTAG-TAATTAATA
*
13353 -CTTATTCTCAAAAAAATATT-TT-ATTTTTTTATTTTTTGTTTTTTT
126 TCTTATTC-C--AAAAATATTATTAATATTTTTATTTTTTGTTTTTTT
13398 CCAAATTTAA
Statistics
Matches: 143, Mismatches: 19, Indels: 18
0.79 0.11 0.10
Matches are distributed among these distances:
196 8 0.06
197 57 0.40
198 69 0.48
199 2 0.01
200 7 0.05
ACGTcount: A:0.33, C:0.11, G:0.07, T:0.49
Consensus pattern (196 bp):
TTATTGAAATTTCATCTAAATTATTCCACCATTTAGGGACAAATCTAGAAAAATTTCTCACCTAA
AGATTTTATAAGAAATTTACCATTTGAAATTTCTAAGAATCTCATCATTAGTAATTAATATCTTA
TTCCAAAAATATTATTAATATTTTTATTTTTTGTTTTTTTTGTTTGAAAATAAATATTAATTATT
G
Found at i:14034 original size:11 final size:10
Alignment explanation
Indices: 14009--14033 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
13999 TTAGAATCTG
14009 AAAAATTTTC
1 AAAAATTTTC
14019 AAAAATTTTC
1 AAAAATTTTC
14029 AAAAA
1 AAAAA
14034 AAAATTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (10 bp):
AAAAATTTTC
Found at i:14666 original size:268 final size:264
Alignment explanation
Indices: 14140--14669 Score: 970
Period size: 268 Copynumber: 2.0 Consensus size: 264
14130 TCTGTGTGAG
*
14140 TATCTATTTATAAGGTTCTGATCCGAGATCCCAAACCAGAAAAAATTTCAATTCCTTCTTAATTT
1 TATCTATTTATAAGGTTCTGATACGAGATCCCAAACCAGAAAAAATTTCAATTCCTTCTTAATTT
*
14205 TAACTCTCAATTTTAATTCAACTTAAATTCTTCATACAATTTCACACAAACTTAATACCTATTTT
66 TAACTCTCAATTTTAATTCAACTTAAACTCTTCATACAATTTCACACAAACTTAATACCTATTTT
14270 TTTTTTTTATTATTTTTTATTAACAAAACCAAAGTCCAATAGACCCAGACAGATTAGGGTATCTA
131 TTTTTTTTATTATTTTTTATTAACAAAACCAAAGTCCAATAGACCCAGACAGATTAGGGTATCTA
14335 CCGTGCCAAGCTTTTAACATATGATCTTTCTACAGCCCATTTGATCAACTGCCACGGCTTCAATG
196 CCGTGCCAAGCTTTTAACATATGATCTTTCTACAGCCCATTTGATCAACTGCCACGGCTTCAATG
14400 ACAA
261 ACAA
* * *
14404 TATCTATTTATAGGGTTCTGATATGAGATCCCAAACCAGAAAAAATTTCAATTTCTTCTTAATTT
1 TATCTATTTATAAGGTTCTGATACGAGATCCCAAACCAGAAAAAATTTCAATTCCTTCTTAATTT
*
14469 TAACTCTCAATTTTAATTCAACTTAAACTCTTCATATAATTTCACACAAACTTAATACCTATTTT
66 TAACTCTCAATTTTAATTCAACTTAAACTCTTCATACAATTTCACACAAACTTAATACCTA---T
14534 TTTTATTTTTTTATTATTTTTTATTAACAAAACCAAAGTCCAATAGACCCAGACAGATTAGGGTA
128 TTTT-TTTTTTTATTATTTTTTATTAACAAAACCAAAGTCCAATAGACCCAGACAGATTAGGGTA
14599 TCTACCGTGCCAAGCTTTTAACATATGATCTTTCTACAGCCCATTTGATCAACTGCCACGGCTTC
192 TCTACCGTGCCAAGCTTTTAACATATGATCTTTCTACAGCCCATTTGATCAACTGCCACGGCTTC
14664 AATGAC
257 AATGAC
14670 GCGAGCTTCG
Statistics
Matches: 256, Mismatches: 6, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
264 120 0.47
267 5 0.02
268 131 0.51
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (264 bp):
TATCTATTTATAAGGTTCTGATACGAGATCCCAAACCAGAAAAAATTTCAATTCCTTCTTAATTT
TAACTCTCAATTTTAATTCAACTTAAACTCTTCATACAATTTCACACAAACTTAATACCTATTTT
TTTTTTTTATTATTTTTTATTAACAAAACCAAAGTCCAATAGACCCAGACAGATTAGGGTATCTA
CCGTGCCAAGCTTTTAACATATGATCTTTCTACAGCCCATTTGATCAACTGCCACGGCTTCAATG
ACAA
Found at i:16454 original size:19 final size:17
Alignment explanation
Indices: 16416--16448 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16406 ACACTACTTT
*
16416 AAAATTATACTTTCTCA
1 AAAATTACACTTTCTCA
16433 AAAATTACACTTTCTC
1 AAAATTACACTTTCTC
16449 TCAAAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTACACTTTCTCA
Found at i:16994 original size:2 final size:2
Alignment explanation
Indices: 16987--17019 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
16977 GTTCACACTT
16987 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17020 AGGGAGGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18635 original size:26 final size:27
Alignment explanation
Indices: 18565--18641 Score: 77
Period size: 26 Copynumber: 2.9 Consensus size: 27
18555 TCATAAACTC
18565 TTACTTTGCCTCCTTTCTCTATTATAA
1 TTACTTTGCCTCCTTTCTCTATTATAA
* **** *
18592 TTATTGTTTTGACC-TTCTC-ATTATTA
1 TTACT-TTGCCTCCTTTCTCTATTATAA
18618 TTACTTTGCCTCCTTTCTCTATTA
1 TTACTTTGCCTCCTTTCTCTATTA
18642 AGATTATATT
Statistics
Matches: 36, Mismatches: 11, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
25 4 0.11
26 15 0.42
27 13 0.36
28 4 0.11
ACGTcount: A:0.17, C:0.23, G:0.05, T:0.55
Consensus pattern (27 bp):
TTACTTTGCCTCCTTTCTCTATTATAA
Found at i:18739 original size:36 final size:36
Alignment explanation
Indices: 18697--18769 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
18687 AAATATAATT
*
18697 TATAAGTTTAAATTTGATGCACTATCAATGTACAAA
1 TATAAGTTTAAATTCGATGCACTATCAATGTACAAA
*
18733 TATAAGTTTAAATTCGATGCACTATCAATGTATAAA
1 TATAAGTTTAAATTCGATGCACTATCAATGTACAAA
18769 T
1 T
18770 CTTATATACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (36 bp):
TATAAGTTTAAATTCGATGCACTATCAATGTACAAA
Done.