Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167846.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_117, 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: 80462
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:9774 original size:76 final size:76
Alignment explanation
Indices: 9687--9845 Score: 273
Period size: 76 Copynumber: 2.1 Consensus size: 76
9677 TAATTATGGA
* * *
9687 ATGAATGAAGAGCGTTTTATTTTATTTATAAAACAATGAATGAATTTTGATTATAATTCATACGT
1 ATGAATTAAGAGAGTTTTATTTTATTTATAAAACAATGAATGAATTTTAATTATAATTCATACGT
*
9752 TGATGGAATGT
66 TGATGGAACGT
*
9763 ATGAATTAAGAGAGTTTTATTTTATTTATAAAACAATGAATGAATTTTAATTATAATTCATATGT
1 ATGAATTAAGAGAGTTTTATTTTATTTATAAAACAATGAATGAATTTTAATTATAATTCATACGT
9828 TGATGGAACGT
66 TGATGGAACGT
9839 ATGAATT
1 ATGAATT
9846 CAATGCCATG
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 78 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (76 bp):
ATGAATTAAGAGAGTTTTATTTTATTTATAAAACAATGAATGAATTTTAATTATAATTCATACGT
TGATGGAACGT
Found at i:11641 original size:34 final size:34
Alignment explanation
Indices: 11603--11673 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
11593 GTATAAATTG
11603 GGGGGAGTGATTGACACGCTAACAAATTAGAAAT
1 GGGGGAGTGATTGACACGCTAACAAATTAGAAAT
11637 GGGGGAGTGATTGACACGCTAACAAATTAGAAAT
1 GGGGGAGTGATTGACACGCTAACAAATTAGAAAT
11671 GGG
1 GGG
11674 CATTTGCTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.32, T:0.20
Consensus pattern (34 bp):
GGGGGAGTGATTGACACGCTAACAAATTAGAAAT
Found at i:11718 original size:69 final size:67
Alignment explanation
Indices: 11637--11773 Score: 238
Period size: 69 Copynumber: 2.0 Consensus size: 67
11627 AATTAGAAAT
*
11637 GGGGGAGTGATTGACACGCTAACAAATTAGAAATGGGCATTTGCTTGATTTTCTTTTTCGTATAA
1 GGGGGAGTGATTGACACGCTAACAAATTAGAAATAGGCATTTGCTTGA--TTCTTTTTCGTATAA
11702 ATTG
64 ATTG
*
11706 GGGGGAGTGATTGACACGCTAACGAATTAGAAATAGGCATTTGCTTGATTCTTTTTCGTATAAAT
1 GGGGGAGTGATTGACACGCTAACAAATTAGAAATAGGCATTTGCTTGATTCTTTTTCGTATAAAT
11771 TG
66 TG
11773 G
1 G
11774 TGTGGAGTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 20 0.30
69 46 0.70
ACGTcount: A:0.28, C:0.12, G:0.26, T:0.35
Consensus pattern (67 bp):
GGGGGAGTGATTGACACGCTAACAAATTAGAAATAGGCATTTGCTTGATTCTTTTTCGTATAAAT
TG
Found at i:14947 original size:12 final size:12
Alignment explanation
Indices: 14930--14965 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
14920 TTATATTTCA
*
14930 AATATCTATTTT
1 AATATCTATCTT
14942 AATATCTATCTT
1 AATATCTATCTT
*
14954 AATATCTTTCTT
1 AATATCTATCTT
14966 TTAAATTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.56
Consensus pattern (12 bp):
AATATCTATCTT
Found at i:19732 original size:2 final size:2
Alignment explanation
Indices: 19725--19759 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19715 TTTCCAATAG
*
19725 TA TA TA TA TA TA TA TA TA GA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19760 GTATGTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:22114 original size:18 final size:17
Alignment explanation
Indices: 22091--22133 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
22081 TCTTTTCATT
**
22091 TTTATTACTTATTTTTAA
1 TTTATTACCAATTTTT-A
22109 TTTATTAACCAATTTTTA
1 TTTATT-ACCAATTTTTA
22127 TTTATTA
1 TTTATTA
22134 TTTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 13 0.59
19 8 0.36
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (17 bp):
TTTATTACCAATTTTTA
Found at i:22332 original size:206 final size:209
Alignment explanation
Indices: 21952--22339 Score: 459
Period size: 206 Copynumber: 1.9 Consensus size: 209
21942 ATTTAATTAT
* * *
21952 ATTGAAGATTTTCTATAAATATTCCAATACGCTGGTAATATTTTATAAAAAATCTTCTCACCTAG
1 ATTGAAAATTTTCTATAAATACTCCAATACACTGGTAATATTTTATAAAAAATCTTCTCACCTAG
* ** * ** *
22017 AGATTTCTTAAAGCATCTCTACTCAGAATACTTTTAGAATCCCATCATTGGATTAAATTTCTTTT
66 AGATTTCATAAAGCATCAATACTCAGAATACCTTTAGAATCCCATCATCAGATAAAATTTCTTTT
* * * *
22082 CTTTTCATTTTTATTACTTATTTTTAATTTATTAACCAATTTTTAT-TTATTATTTAAAAAAAAG
131 CTCTACATTTTTATTACTTAGTATTAATTTATTAACCAATTTTTATATTATTATTTAAAAAAAAG
22146 AAAATCTTTACTGC
196 AAAATCTTTACTGC
* * *
22160 ATTGAAAATTTTTTATAAATACTCCAATACACTGGTAGTA-TTT-TAAAAAATCTTTTCACCTAG
1 ATTGAAAATTTTCTATAAATACTCCAATACACTGGTAATATTTTATAAAAAATCTTCTCACCTAG
* * * *
22223 AGATTTCAT-AGGCATCAATACTCGGAATACCTTT-GAATCTCATCGTCAGATAAAAATTTCCTT
66 AGATTTCATAAAGCATCAATACTCAGAATACCTTTAGAATCCCATCATCAGAT-AAAATTT-CTT
***
22286 TTC-CTACATTTTTTATTACTTTAGTATT-A-TTATTAAGTTTATTTTTATATTATT
129 TTCTCTACA-TTTTTATTAC-TTAGTATTAATTTATTAA-CCAATTTTTATATTATT
22340 GTTTTTAAAG
Statistics
Matches: 150, Mismatches: 24, Indels: 13
0.80 0.13 0.07
Matches are distributed among these distances:
204 13 0.09
205 36 0.24
206 52 0.35
207 14 0.09
208 35 0.23
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (209 bp):
ATTGAAAATTTTCTATAAATACTCCAATACACTGGTAATATTTTATAAAAAATCTTCTCACCTAG
AGATTTCATAAAGCATCAATACTCAGAATACCTTTAGAATCCCATCATCAGATAAAATTTCTTTT
CTCTACATTTTTATTACTTAGTATTAATTTATTAACCAATTTTTATATTATTATTTAAAAAAAAG
AAAATCTTTACTGC
Found at i:22551 original size:13 final size:13
Alignment explanation
Indices: 22531--22565 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
22521 GGTCAATGTA
22531 CGGTTCGGTTCGG
1 CGGTTCGGTTCGG
* *
22544 CTGTTCGGTTTGG
1 CGGTTCGGTTCGG
22557 CGGTTCGGT
1 CGGTTCGGT
22566 CTGGCGATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.43, T:0.37
Consensus pattern (13 bp):
CGGTTCGGTTCGG
Found at i:23536 original size:16 final size:16
Alignment explanation
Indices: 23517--23569 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
23507 TTTTGTTCTA
23517 TTTTTTTTCATATTTT
1 TTTTTTTTCATATTTT
**
23533 TTTTGTATTTTGTATTTT
1 TTTT-T-TTTCATATTTT
*
23551 TTTTATTTCATATTTT
1 TTTTTTTTCATATTTT
23567 TTT
1 TTT
23570 ATTGTATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 16 0.53
17 1 0.03
18 13 0.43
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (16 bp):
TTTTTTTTCATATTTT
Found at i:23543 original size:20 final size:18
Alignment explanation
Indices: 23522--23586 Score: 80
Period size: 18 Copynumber: 3.6 Consensus size: 18
23512 TTCTATTTTT
23522 TTTCATATTTTTTTTGTA
1 TTTCATATTTTTTTTGTA
**
23540 TTTTGTA-TTTTTTT-TA
1 TTTCATATTTTTTTTGTA
23556 TTTCATATTTTTTTATTGTA
1 TTTCATA-TTTTTT-TTGTA
23576 TTTCATATTTT
1 TTTCATATTTT
23587 ATACGTACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
16 7 0.18
17 7 0.18
18 10 0.26
19 6 0.15
20 9 0.23
ACGTcount: A:0.17, C:0.05, G:0.05, T:0.74
Consensus pattern (18 bp):
TTTCATATTTTTTTTGTA
Found at i:23560 original size:34 final size:33
Alignment explanation
Indices: 23497--23578 Score: 98
Period size: 33 Copynumber: 2.5 Consensus size: 33
23487 GCCATCCTTG
23497 ATTTTTTTTG--TTTTGTTCTATTTTTTTTCAT
1 ATTTTTTTTGTATTTTGTTCTATTTTTTTTCAT
*
23528 ATTTTTTTTGTATTTTGTAT-TTTTTTTATTTCAT
1 ATTTTTTTTGTATTTTGT-TCTATTTTT-TTTCAT
23562 ATTTTTTTATTGTATTT
1 A-TTTTTT-TTGTATTT
23579 CATATTTTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 10 0.23
33 12 0.27
34 8 0.18
35 6 0.14
36 8 0.18
ACGTcount: A:0.13, C:0.04, G:0.06, T:0.77
Consensus pattern (33 bp):
ATTTTTTTTGTATTTTGTTCTATTTTTTTTCAT
Found at i:23585 original size:36 final size:33
Alignment explanation
Indices: 23517--23586 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 33
23507 TTTTGTTCTA
**
23517 TTTTTTTTCATATTTTTTTTGTATTTTGTATTT
1 TTTTTTTTCATATTTTTTTTGTATTTCATATTT
23550 TTTTTATTTCATATTTTTTTATTGTATTTCATATTT
1 TTTTT-TTTCATA-TTTTTT-TTGTATTTCATATTT
23586 T
1 T
23587 ATACGTACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
33 5 0.16
34 7 0.22
35 6 0.19
36 14 0.44
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.76
Consensus pattern (33 bp):
TTTTTTTTCATATTTTTTTTGTATTTCATATTT
Found at i:24000 original size:92 final size:90
Alignment explanation
Indices: 23853--24235 Score: 457
Period size: 92 Copynumber: 4.2 Consensus size: 90
23843 AACAACTTTA
* *
23853 AACAA-TTTAAAATC-TGAAAAAGCTTCTCTTAGCAGAGGCTCAACAACTTTAAAATCTCATTTG
1 AACAACTTTAAAATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTG
*
23916 AAAAGGGCTCCTCTCAACAAAGGCTC
66 AAAA-GGCTCCTCTCAACAGAGGCTC
* * *
23942 AGCAACTTTAAAATCTTGAAAAAAGCTCCTCTCAGCAGAGGCTCAACGACTTTAAAATCTTATTT
1 AACAACTTTAAAATCTTG-AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTT
24007 GAAAAGGGCTCCTCTCAACAGAGGCTC
65 GAAAA-GGCTCCTCTCAACAGAGGCTC
* * * **
24034 AACAACTTTAAAATCTTTAAAAAGGCTCCTCTCAACAAAGGCTCAATGACTTTAAAATCTCATTT
1 AACAACTTTAAAATCTTGAAAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTT
* **
24099 GAAAAAGCTCCTCTCAGTAGAGGCTC
65 GAAAAGGCTCCTCTCAACAGAGGCTC
* *
24125 AACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTT
1 AACAACTTT--AAA----ATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCT
** *
24190 CATCTTGGAAAA-GCTCCTCTCAGTAGAGGCTT
60 CAT-TT-GAAAAGGCTCCTCTCAACAGAGGCTC
*
24222 AATAACTTTAAAAT
1 AACAACTTTAAAAT
24236 TTCATCTTCT
Statistics
Matches: 258, Mismatches: 24, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
89 4 0.02
90 9 0.03
91 36 0.14
92 126 0.49
93 3 0.01
95 3 0.01
96 34 0.13
97 38 0.15
98 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (90 bp):
AACAACTTTAAAATCTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATTTG
AAAAGGCTCCTCTCAACAGAGGCTC
Found at i:24042 original size:140 final size:140
Alignment explanation
Indices: 23771--24234 Score: 482
Period size: 140 Copynumber: 3.3 Consensus size: 140
23761 TTAAAATCTA
* ** * * **
23771 AAAAAGCTCCTCTCTGCAGAGGCTTAACAACTTTAAAATCTCATTTGGAAATGGCTCCTCTCA-C
1 AAAAGGCTCCTCTCAACAAAGGCTCAACAACTTTAAAA-CTCA-TT-GAAAAAGCTCCTCTCAGC
* * * * *
23835 AGAGGCTCAACAACTTTAAACAATTTAAAATC-TGAAAAAGCTTCTCTTAGCAGAGGCTCAACAA
63 AGAGGCTCAACAACTTTAAA-AATTT--CATCTTGGAAAAGCTCCTCTCAACAGAGGCTCAACAA
23899 CTTTAAAATCTCATTTG
125 CTTTAAAAT-TCATTTG
*
23916 AAAAGGGCTCCTCTCAACAAAGGCTCAGCAACTTTAAAA-TC-TTGAAAAAAGCTCCTCTCAGCA
1 AAAA-GGCTCCTCTCAACAAAGGCTCAACAACTTTAAAACTCATTG-AAAAAGCTCCTCTCAGCA
*
23979 GAGGCTCAACGACTTT-AAAATCTT-AT-TT-GAAAAGGGCTCCTCTCAACAGAGGCTCAACAAC
64 GAGGCTCAACAACTTTAAAAAT-TTCATCTTGGAAAA--GCTCCTCTCAACAGAGGCTCAACAAC
*
24040 TTTAAAA-TC-TTTA
126 TTTAAAATTCATTTG
** *
24053 AAAAGGCTCCTCTCAACAAAGGCTCAATGACTTTAAAATCTCATTTGAAAAAGCTCCTCTCAGTA
1 AAAAGGCTCCTCTCAACAAAGGCTCAACAACTTTAAAA-CTCA-TTGAAAAAGCTCCTCTCAGCA
*
24118 GAGGCTCAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT
64 GAGGCTCAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTCTCAACAGAGGCTCAACAACTTT
24183 AAAATTTCATCTTGG
129 AAAA-TTCAT-TT-G
** * * *
24198 AAAA-GCTCCTCTCAGTAGAGGCTTAATAACTTTAAAA
1 AAAAGGCTCCTCTCAACAAAGGCTCAACAACTTTAAAA
24235 TTTCATCTTC
Statistics
Matches: 273, Mismatches: 26, Indels: 41
0.80 0.08 0.12
Matches are distributed among these distances:
136 31 0.11
137 7 0.03
138 8 0.03
139 37 0.14
140 72 0.26
141 6 0.02
142 26 0.10
143 18 0.07
144 32 0.12
145 8 0.03
146 28 0.10
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (140 bp):
AAAAGGCTCCTCTCAACAAAGGCTCAACAACTTTAAAACTCATTGAAAAAGCTCCTCTCAGCAGA
GGCTCAACAACTTTAAAAATTTCATCTTGGAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAA
AATTCATTTG
Found at i:24243 original size:48 final size:47
Alignment explanation
Indices: 23870--24240 Score: 395
Period size: 48 Copynumber: 7.9 Consensus size: 47
23860 TAAAATCTGA
* * *
23870 AAAAGCTTCTCTTAGCAGAGGCTCAACAACTTTAAAATCTCATTT-G
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATTTGG
* * * *
23916 AAAAGGGCTCCTCTCAACAAAGGCTCAGCAACTTTAAAA--TC--TTGAA
1 AAAA--GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATTTG-G
*
23962 AAAAGCTCCTCTCAGCAGAGGCTCAACGACTTTAAAATCTT-ATTT-G
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT-TTCATTTGG
* *
24008 AAAAGGGCTCCTCTCAACAGAGGCTCAACAACTTTAAAA--TC-TTT-A
1 AAAA--GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATTTGG
* * ** * *
24053 AAAAGGCTCCTCTCAACAAAGGCTCAATGACTTTAAAATCTCATTTGA
1 AAAA-GCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATTTGG
*
24101 AAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATTTCATCTTGG
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTTCAT-TTGG
24150 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTGG
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCAT-TTGG
* * *
24198 AAAAGCTCCTCTCAGTAGAGGCTTAATAACTTTAAAATTTCAT
1 AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCAT
24241 CTTCTCTCAA
Statistics
Matches: 279, Mismatches: 28, Indels: 34
0.82 0.08 0.10
Matches are distributed among these distances:
44 62 0.22
45 8 0.03
46 16 0.06
47 28 0.10
48 130 0.47
49 35 0.13
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (47 bp):
AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATTTGG
Found at i:32595 original size:2 final size:2
Alignment explanation
Indices: 32588--32612 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
32578 GTCTAATGTA
32588 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 A
32613 ATGAGGGATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35596 original size:27 final size:27
Alignment explanation
Indices: 35558--35641 Score: 150
Period size: 27 Copynumber: 3.0 Consensus size: 27
35548 TAAAACATGT
35558 TTGGAAGGATTCAAAGGTGTGTGACTA
1 TTGGAAGGATTCAAAGGTGTGTGACTA
35585 TTGGAAGGATTCAAAGGTGTGTGTGACTA
1 TTGGAAGGATTCAAA-G-GTGTGTGACTA
35614 TTGGAAGGATTCAAAGGTGTGTGACTA
1 TTGGAAGGATTCAAAGGTGTGTGACTA
35641 T
1 T
35642 CATTTTTCTT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
27 27 0.49
28 2 0.04
29 26 0.47
ACGTcount: A:0.29, C:0.07, G:0.33, T:0.31
Consensus pattern (27 bp):
TTGGAAGGATTCAAAGGTGTGTGACTA
Found at i:35616 original size:29 final size:29
Alignment explanation
Indices: 35558--35636 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
35548 TAAAACATGT
35558 TTGGAAGGATTCAAA-G-GTGTGTGACTA
1 TTGGAAGGATTCAAAGGTGTGTGTGACTA
35585 TTGGAAGGATTCAAAGGTGTGTGTGACTA
1 TTGGAAGGATTCAAAGGTGTGTGTGACTA
35614 TTGGAAGGATTCAAAGGTGTGTG
1 TTGGAAGGATTCAAAGGTGTGTG
35637 ACTATCATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 15 0.30
28 1 0.02
29 34 0.68
ACGTcount: A:0.28, C:0.06, G:0.35, T:0.30
Consensus pattern (29 bp):
TTGGAAGGATTCAAAGGTGTGTGTGACTA
Found at i:38482 original size:12 final size:12
Alignment explanation
Indices: 38465--38498 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38455 ATCGCACTAC
*
38465 ATATCTTTTTTA
1 ATATCTTTCTTA
*
38477 ATATCTATCTTA
1 ATATCTTTCTTA
38489 ATATCTTTCT
1 ATATCTTTCT
38499 CCTAAAATTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATCTTTCTTA
Found at i:40805 original size:14 final size:14
Alignment explanation
Indices: 40768--40805 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
40758 ACAACAAAAC
*
40768 AAAACAAAAA-AAT
1 AAAACAAAAAGAAG
*
40781 AAAAAAAAAAGAAG
1 AAAACAAAAAGAAG
40795 AAAACAAAAAG
1 AAAACAAAAAG
40806 CAGGGGGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.84, C:0.05, G:0.08, T:0.03
Consensus pattern (14 bp):
AAAACAAAAAGAAG
Found at i:42355 original size:7 final size:7
Alignment explanation
Indices: 42345--42465 Score: 66
Period size: 7 Copynumber: 16.7 Consensus size: 7
42335 ATTCAAAATT
42345 CTAAACC
1 CTAAACC
*
42352 CTAAAAC
1 CTAAACC
42359 CTCAAACC
1 CT-AAACC
*
42367 TTAAACC
1 CTAAACC
**
42374 CTAAAAA
1 CTAAACC
*
42381 CTAAATC
1 CTAAACC
42388 CTAAACC
1 CTAAACC
*
42395 CTCCAAACA
1 CT--AAACC
**
42404 CTAAAAT
1 CTAAACC
*
42411 CAAAACC
1 CTAAACC
42418 CTAAACTC
1 CTAAAC-C
42426 TCTAAACC
1 -CTAAACC
**
42434 CTAAAAT
1 CTAAACC
*
42441 CAAAACC
1 CTAAACC
42448 C-AAA-C
1 CTAAACC
42453 CTCAAACC
1 CT-AAACC
42461 CTAAA
1 CTAAA
42466 ACCTTTAAAC
Statistics
Matches: 85, Mismatches: 21, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
5 2 0.02
6 3 0.04
7 58 0.68
8 10 0.12
9 12 0.14
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.17
Consensus pattern (7 bp):
CTAAACC
Found at i:42408 original size:30 final size:30
Alignment explanation
Indices: 42369--42466 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 30
42359 CTCAAACCTT
* *
42369 AAACCCTAAAAACTAAATCCTAAACCCTCC
1 AAACCCTAAAAACAAAACCCTAAACCCTCC
* * * *
42399 AAACACTAAAATCAAAACCCTAAACTCTCT
1 AAACCCTAAAAACAAAACCCTAAACCCTCC
*
42429 AAACCCTAAAATCAAAACCC-AAA-CCT-C
1 AAACCCTAAAAACAAAACCCTAAACCCTCC
42456 AAACCCTAAAA
1 AAACCCTAAAA
42467 CCTTTAAACC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 11 0.19
28 2 0.03
29 3 0.05
30 43 0.73
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (30 bp):
AAACCCTAAAAACAAAACCCTAAACCCTCC
Found at i:42458 original size:44 final size:44
Alignment explanation
Indices: 42413--42604 Score: 130
Period size: 44 Copynumber: 4.4 Consensus size: 44
42403 ACTAAAATCA
42413 AAACCCT-AAACTCTCTAAACCCTAAAATC-AAAACCCAAACCTC
1 AAACCCTAAAAC-CTCTAAACCCTAAAATCGAAAACCCAAACCTC
* * * *
42456 AAACCCTAAAACCTTTAAACCTTAAAATCGAAACCCCAAACCTT
1 AAACCCTAAAACCTCTAAACCCTAAAATCGAAAACCCAAACCTC
** * * * * * *
42500 AAATTCTAAAA--TCGAAACCCCAAACCTC-AAATCCTAAA-ATC
1 AAACCCTAAAACCTCTAAACCCTAAA-ATCGAAAACCCAAACCTC
* * * *
42541 GAAACCCTAAACCCTCTAAACCTTAAAA-CTAAAACCCTAAACCCC
1 -AAACCCTAAAACCTCTAAACCCTAAAATCGAAAACCC-AAACCTC
*
42586 AAACTCTCAAAACCT-TAAA
1 AAACCCT-AAAACCTCTAAA
42605 ACTCAAGCCC
Statistics
Matches: 111, Mismatches: 28, Indels: 19
0.70 0.18 0.12
Matches are distributed among these distances:
41 1 0.01
42 26 0.23
43 29 0.26
44 48 0.43
45 7 0.06
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (44 bp):
AAACCCTAAAACCTCTAAACCCTAAAATCGAAAACCCAAACCTC
Found at i:42475 original size:43 final size:44
Alignment explanation
Indices: 42413--42498 Score: 122
Period size: 43 Copynumber: 2.0 Consensus size: 44
42403 ACTAAAATCA
42413 AAACCCTAAACTCTCTAAACCCTAAAATC-AAAACCCAAACCTC
1 AAACCCTAAACTCTCTAAACCCTAAAATCGAAAACCCAAACCTC
* * *
42456 AAACCCTAAAAC-CTTTAAACCTTAAAATCGAAACCCCAAACCT
1 AAACCCT-AAACTCTCTAAACCCTAAAATCGAAAACCCAAACCT
42499 TAAATTCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 22 0.58
44 16 0.42
ACGTcount: A:0.47, C:0.35, G:0.01, T:0.17
Consensus pattern (44 bp):
AAACCCTAAACTCTCTAAACCCTAAAATCGAAAACCCAAACCTC
Found at i:42509 original size:28 final size:28
Alignment explanation
Indices: 42478--42553 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
42468 CTTTAAACCT
* *
42478 TAAAATCGAAACCCCAAACCTTAAATTC
1 TAAAATCGAAACCCCAAACCTCAAATCC
42506 TAAAATCGAAACCCCAAACCTCAAATCC
1 TAAAATCGAAACCCCAAACCTCAAATCC
*
42534 TAAAATCGAAACCCTAAACC
1 TAAAATCGAAACCCCAAACC
42554 CTCTAAACCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.47, C:0.32, G:0.04, T:0.17
Consensus pattern (28 bp):
TAAAATCGAAACCCCAAACCTCAAATCC
Found at i:42551 original size:14 final size:14
Alignment explanation
Indices: 42399--42551 Score: 62
Period size: 14 Copynumber: 10.7 Consensus size: 14
42389 TAAACCCTCC
* *
42399 AAACACTAAAATCA
1 AAACCCTAAAATCG
* *
42413 AAACCCTAAACTCTCT
1 AAACCCTAAA--ATCG
*
42429 AAACCCTAAAATCA
1 AAACCCTAAAATCG
*
42443 AAACCC-AAACCTC-
1 AAACCCTAAA-ATCG
**
42456 AAACCCTAAAACCTTT
1 AAACCCTAAAA--TCG
*
42472 AAACCTTAAAATCG
1 AAACCCTAAAATCG
* * *
42486 AAACCC-CAAACCTT
1 AAACCCTAAAATC-G
**
42500 AAATTCTAAAATCG
1 AAACCCTAAAATCG
* *
42514 AAACCCCAAACCTC-
1 AAACCCTAAA-ATCG
*
42528 AAATCCTAAAATCG
1 AAACCCTAAAATCG
42542 AAACCCTAAA
1 AAACCCTAAA
42552 CCCTCTAAAC
Statistics
Matches: 100, Mismatches: 28, Indels: 22
0.67 0.19 0.15
Matches are distributed among these distances:
13 15 0.15
14 56 0.56
15 7 0.07
16 22 0.22
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (14 bp):
AAACCCTAAAATCG
Found at i:42583 original size:37 final size:38
Alignment explanation
Indices: 42542--42631 Score: 119
Period size: 37 Copynumber: 2.4 Consensus size: 38
42532 CCTAAAATCG
*
42542 AAACCCTAAACCCTCTAAACCTTAAAACTAAAACCCT-
1 AAACCCTAAACCCTCAAAACCTTAAAACTAAAACCCTA
* * * *
42579 AAACCCCAAACTCTCAAAACCTTAAAACTCAAGCCCTA
1 AAACCCTAAACCCTCAAAACCTTAAAACTAAAACCCTA
42617 AAACCTCTAAACCCT
1 AAACC-CTAAACCCT
42632 AATATTGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
37 32 0.73
38 5 0.11
39 7 0.16
ACGTcount: A:0.44, C:0.37, G:0.01, T:0.18
Consensus pattern (38 bp):
AAACCCTAAACCCTCAAAACCTTAAAACTAAAACCCTA
Found at i:42597 original size:23 final size:22
Alignment explanation
Indices: 42514--42630 Score: 67
Period size: 23 Copynumber: 5.3 Consensus size: 22
42504 TCTAAAATCG
* *
42514 AAACCCCAAA-CCTCAAATCCT
1 AAACCCCAAACCCTAAAACCCT
** * *
42535 AAAATCGAAACCCTAAACCCTCT
1 AAACCCCAAACCCTAAAACC-CT
** *
42558 AAACCTTAAA-ACTAAAACCCT
1 AAACCCCAAACCCTAAAACCCT
* *
42579 AAACCCCAAACTCTCAAAACCTT
1 AAACCCCAAACCCT-AAAACCCT
* * *
42602 AAAACTCAAGCCCTAAAACCTCT
1 AAACCCCAAACCCTAAAACC-CT
42625 AAACCC
1 AAACCC
42631 TAATATTGAA
Statistics
Matches: 68, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
21 17 0.25
22 21 0.31
23 30 0.44
ACGTcount: A:0.45, C:0.37, G:0.02, T:0.16
Consensus pattern (22 bp):
AAACCCCAAACCCTAAAACCCT
Found at i:45198 original size:17 final size:18
Alignment explanation
Indices: 45176--45213 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
45166 ATTAGCCAAA
45176 AAATGA-TTAAAAAATTC
1 AAATGACTTAAAAAATTC
45193 AAATGATCGTTAAAAAATTC
1 AAATGA-C-TTAAAAAATTC
45213 A
1 A
45214 TCAAAAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
20 12 0.67
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (18 bp):
AAATGACTTAAAAAATTC
Found at i:45743 original size:20 final size:19
Alignment explanation
Indices: 45727--45800 Score: 98
Period size: 20 Copynumber: 3.9 Consensus size: 19
45717 AGTATAAATA
45727 AATAAAATA-AATAATAAT
1 AATAAAATATAATAATAAT
45745 AATAAAATAGTAATAATAAT
1 AATAAAATA-TAATAATAAT
45765 AATAATAATATAATAATAAT
1 AATAA-AATATAATAATAAT
* *
45785 AATGATAT-TAATAATA
1 AATAAAATATAATAATA
45801 GTATACCATA
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
18 17 0.33
19 2 0.04
20 28 0.55
21 4 0.08
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
AATAAAATATAATAATAAT
Found at i:45744 original size:3 final size:3
Alignment explanation
Indices: 45727--45857 Score: 92
Period size: 3 Copynumber: 43.7 Consensus size: 3
45717 AGTATAAATA
*
45727 AAT AA- AAT AAAT AAT AAT AAT AA- AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
45771 AAT -AT AAT AAT AAT AAT GAT ATT AAT AAT AGT -AT ACCAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT
* * * * *
45816 ATAT TAT AAT -AT ATAT TAT AAT AAT AAC AAA AAT ACT AAT AA
1 A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
45858 CAAAAACAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
2 9 0.09
3 81 0.82
4 6 0.06
5 3 0.03
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:45765 original size:26 final size:26
Alignment explanation
Indices: 45722--45800 Score: 97
Period size: 26 Copynumber: 3.0 Consensus size: 26
45712 AATATAGTAT
45722 AAATAAATAA-AATAAATAATAATAATA
1 AAAT-AATAATAAT-AATAATAATAATA
*
45749 AAATAGTAATAATAATAATAATAATA
1 AAATAATAATAATAATAATAATAATA
* * *
45775 TAATAATAATAATGATATTAATAATA
1 AAATAATAATAATAATAATAATAATA
45801 GTATACCATA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
26 39 0.85
27 7 0.15
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (26 bp):
AAATAATAATAATAATAATAATAATA
Found at i:45796 original size:23 final size:23
Alignment explanation
Indices: 45723--45857 Score: 96
Period size: 23 Copynumber: 5.6 Consensus size: 23
45713 ATATAGTATA
45723 AATAA-ATAA-AATAAATAATAAT
1 AATAATATAATAAT-AATAATAAT
* *
45745 AATAAAATAGTAATAATAATAAT
1 AATAATATAATAATAATAATAAT
45768 AATAATATAATAATAATAATGATATT
1 AATAATATAATAATAATAAT-A-A-T
*
45794 AATAATAGT-ATACCATAATATTATAT
1 AATAATA-TAATA--ATAATAATA-AT
* * *
45820 TATAATATATATTATAATAATAAC
1 AATAATATA-ATAATAATAATAAT
*
45844 AAAAATACTAATAA
1 AATAATA-TAATAA
45858 CAAAAACAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
22 5 0.05
23 30 0.33
24 13 0.14
25 12 0.13
26 18 0.20
27 6 0.07
28 7 0.08
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (23 bp):
AATAATATAATAATAATAATAAT
Found at i:54084 original size:16 final size:16
Alignment explanation
Indices: 54063--54095 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
54053 AAAATCATCG
54063 TAAATCATCATTATCA
1 TAAATCATCATTATCA
54079 TAAATCATCATTATCA
1 TAAATCATCATTATCA
54095 T
1 T
54096 TCAAATCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATCATCATTATCA
Found at i:54109 original size:15 final size:15
Alignment explanation
Indices: 54089--54136 Score: 96
Period size: 15 Copynumber: 3.2 Consensus size: 15
54079 TAAATCATCA
54089 TTATCATTCAAATCG
1 TTATCATTCAAATCG
54104 TTATCATTCAAATCG
1 TTATCATTCAAATCG
54119 TTATCATTCAAATCG
1 TTATCATTCAAATCG
54134 TTA
1 TTA
54137 GCTACGGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (15 bp):
TTATCATTCAAATCG
Found at i:72563 original size:115 final size:115
Alignment explanation
Indices: 72358--72571 Score: 268
Period size: 115 Copynumber: 1.9 Consensus size: 115
72348 CCGATCGATC
* ** * * * * ** *
72358 CTTCCATTAAAAGGATTAATCTTTTTTTTATACAGAATGTAATATGGGTTTGAAAATGCATAAAA
1 CTTCCATTAAAAGGATCAATCCATTTTTTACACAGAAAGCAAAATGGGTTTGAAAATAAACAAAA
*
72423 GGGATCGATCTCCCCACATAAGGGATCAATCACCAAGCATGGGATTGATT
66 AGGATCGATCTCCCCACATAAGGGATCAATCACCAAGCATGGGATTGATT
* * *
72473 CTTCCCTTAAAAGGATCGATCCATTTTTTACACAGAAAGCAAAATTGGTTTGAAAATAAACAAAA
1 CTTCCATTAAAAGGATCAATCCATTTTTTACACAGAAAGCAAAATGGGTTTGAAAATAAACAAAA
* *
72538 AGGATCGATC-CCCTCACATAGGGGATCGATCACC
66 AGGATCGATCTCCC-CACATAAGGGATCAATCACC
72572 CAAGGAATGG
Statistics
Matches: 82, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
114 3 0.04
115 79 0.96
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (115 bp):
CTTCCATTAAAAGGATCAATCCATTTTTTACACAGAAAGCAAAATGGGTTTGAAAATAAACAAAA
AGGATCGATCTCCCCACATAAGGGATCAATCACCAAGCATGGGATTGATT
Found at i:80224 original size:9 final size:9
Alignment explanation
Indices: 80211--80266 Score: 94
Period size: 9 Copynumber: 6.2 Consensus size: 9
80201 GTAACATTTC
80211 CCTCATTCT
1 CCTCATTCT
*
80220 TCTCATTCT
1 CCTCATTCT
80229 CCTCATTCT
1 CCTCATTCT
*
80238 TCTCATTCT
1 CCTCATTCT
80247 CCTCATTCT
1 CCTCATTCT
80256 CCTCATTCT
1 CCTCATTCT
80265 CC
1 CC
80267 ACCTCTTCCT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 43 1.00
ACGTcount: A:0.11, C:0.43, G:0.00, T:0.46
Consensus pattern (9 bp):
CCTCATTCT
Done.