Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168392.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_609, 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: 21625
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:670 original size:57 final size:57
Alignment explanation
Indices: 550--880 Score: 496
Period size: 56 Copynumber: 5.8 Consensus size: 57
540 TTTTTTTTGT
*
550 AGGAAAATTGATACTTTCAACTTTTCTC-AAAA-A--TTTTTTGAAAATTTATTTCTA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTG-AAATTTATTTCTA
604 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATTT-TA
1 AGGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTTTGAAATTTATTTCTA
661 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGGAAATTTATTTTTCTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTT-GAAATTTA--TTTC-TA
* *
722 AGGAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTT-AAATTTATTTCTG
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGAAATTTATTTCTA
778 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTTTGAAATTTATTTCT-
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATA--TTTTTTTTGAAATTTATTTCTA
836 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTT
1 AGGAAAATTGATACTTTCAACTTTTCCC-AAAAATAT-TTTTTTT
881 TGGAATTTTT
Statistics
Matches: 258, Mismatches: 4, Indels: 26
0.90 0.01 0.09
Matches are distributed among these distances:
54 25 0.10
55 2 0.01
56 57 0.22
57 41 0.16
58 53 0.21
59 36 0.14
61 44 0.17
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (57 bp):
AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGAAATTTATTTCTA
Found at i:798 original size:117 final size:115
Alignment explanation
Indices: 550--880 Score: 514
Period size: 117 Copynumber: 2.9 Consensus size: 115
540 TTTTTTTTGT
* *
550 AGGAAAATTGATACTTTCAACTTTTCTC-AAAA-A--TTTTTTGAAAATTTATTTCTAAGGAAAA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGGAAATTTATTTCTAAGGAAAA
*
611 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTATTTTA
66 TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTA
661 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGGAAATTTATTTTTCTTAAGGA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGGAAATTTA--TTTC-TAAGGA
*
726 AAATTGATACTTTCAACTTTT-CCTAAAAATATTTTTTTT-AAATTTATTTCTG
63 AAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTT-TA
*
778 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTTTGAAATTTATTTCT-AGGAAA
1 AGGAAAATTGATACTTTCAACTTTTCCCAAAAATA-TTTTTTTTGGAAATTTATTTCTAAGGAAA
842 ATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTT
65 ATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTT
881 TGGAATTTTT
Statistics
Matches: 204, Mismatches: 5, Indels: 17
0.90 0.02 0.08
Matches are distributed among these distances:
111 27 0.13
112 4 0.02
113 1 0.00
114 25 0.12
115 26 0.13
116 21 0.10
117 57 0.28
118 43 0.21
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (115 bp):
AGGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTTGGAAATTTATTTCTAAGGAAAA
TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTTA
Found at i:1342 original size:20 final size:20
Alignment explanation
Indices: 1317--1354 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1307 GAACACCGGT
*
1317 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
1337 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
1355 CACCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:1360 original size:19 final size:20
Alignment explanation
Indices: 1318--1362 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1308 AACACCGGTG
* *
1318 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCA
1338 CCGGAATCTGGAAA-TTTCA
1 CCGGAATCTGGAAATTTTCA
1357 CCGGAA
1 CCGGAA
1363 GTTGGCCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCA
Found at i:1460 original size:31 final size:31
Alignment explanation
Indices: 1417--1484 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
1407 GGGCAGGTCG
* ** *
1417 CCGGAAACTTCAATGTTGGCCGGAATTTTCA
1 CCGGAAAATTCAAACTTCGCCGGAATTTTCA
*
1448 CCGGAAAATTCAAACTTCGCCGGAATTTTCG
1 CCGGAAAATTCAAACTTCGCCGGAATTTTCA
1479 CCGGAA
1 CCGGAA
1485 TCTGGAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (31 bp):
CCGGAAAATTCAAACTTCGCCGGAATTTTCA
Found at i:1875 original size:13 final size:13
Alignment explanation
Indices: 1859--1918 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
1849 AAATAATATC
1859 AGATAATAAAAAA
1 AGATAATAAAAAA
** *
1872 AGATAA-ATTAAC
1 AGATAATAAAAAA
*
1884 AGATATTAAAAAA
1 AGATAATAAAAAA
1897 A-ATAATAAAATAA
1 AGATAATAAAA-AA
1910 A-ATAATAAA
1 AGATAATAAA
1919 CCAAAAATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
12 16 0.43
13 21 0.57
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (13 bp):
AGATAATAAAAAA
Found at i:2003 original size:90 final size:90
Alignment explanation
Indices: 1899--2066 Score: 198
Period size: 90 Copynumber: 1.9 Consensus size: 90
1889 TTAAAAAAAA
* *
1899 TAATAAAATAAAAT-AATAAACCAAAAATATATACAAAAAAAAAAATAATAATAATATATAACT-
1 TAATAAAATAAAATAAATAAA-CAAAAATATACACAAAAAAAAAAATAATAATAATAAATAA-TA
1962 ATAAATAAAATACATATAAATCTAATC
64 ATAAATAAAATACATATAAATCTAATC
* * * * * *
1989 TAATAAAA-ATAAATAAATAAATAAAGATATACATAATAATAATAATAATAATAATAAATAATAA
1 TAATAAAATA-AAATAAATAAACAAAAATATACACAAAAAAAAAAATAATAATAATAAATAAT-A
*
2053 ATACATAAAATACA
64 ATAAATAAAATACA
2067 AAAGAAGAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
89 2 0.03
90 44 0.68
91 19 0.29
ACGTcount: A:0.67, C:0.06, G:0.01, T:0.26
Consensus pattern (90 bp):
TAATAAAATAAAATAAATAAACAAAAATATACACAAAAAAAAAAATAATAATAATAAATAATAAT
AAATAAAATACATATAAATCTAATC
Found at i:2012 original size:12 final size:11
Alignment explanation
Indices: 1990--2060 Score: 55
Period size: 10 Copynumber: 6.8 Consensus size: 11
1980 AATCTAATCT
1990 AATAAA-AATA
1 AATAAATAATA
2000 AATAAATAAATA
1 AATAAAT-AATA
* *
2012 AAGATATACAT-
1 AATAAATA-ATA
2023 AAT-AATAAT-
1 AATAAATAATA
2032 AAT-AATAAT-
1 AATAAATAATA
2041 AATAAATAATA
1 AATAAATAATA
*
2052 AATACATAA
1 AATAAATAA
2061 AATACAAAAG
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
9 14 0.27
10 15 0.29
11 11 0.22
12 11 0.22
ACGTcount: A:0.69, C:0.03, G:0.01, T:0.27
Consensus pattern (11 bp):
AATAAATAATA
Found at i:2029 original size:3 final size:3
Alignment explanation
Indices: 2021--2052 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
2011 AAAGATATAC
2021 ATA ATA ATA ATA ATA ATA ATA ATAA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA A
2053 ATACATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:2250 original size:1 final size:1
Alignment explanation
Indices: 2239--2328 Score: 99
Period size: 1 Copynumber: 90.0 Consensus size: 1
2229 CAACTCAACA
* * * * * * *
2239 TTTTTTGTTTTTTTTTTTTTGTTTTTTTTTTTGTTTTTGTTTTTTTGTTTTTTTGTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
2304 TTTTTGTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
2329 CCAAAGCTCC
Statistics
Matches: 71, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (1 bp):
T
Found at i:2252 original size:8 final size:8
Alignment explanation
Indices: 2239--2328 Score: 109
Period size: 8 Copynumber: 11.5 Consensus size: 8
2229 CAACTCAACA
2239 TTTTTTG-
1 TTTTTTGT
2246 TTTTTT-T
1 TTTTTTGT
2253 TTTTTTGTT
1 TTTTTTG-T
*
2262 TTTTTTTT
1 TTTTTTGT
2270 TGTTTTTGT
1 T-TTTTTGT
2279 TTTTTTGT
1 TTTTTTGT
2287 TTTTTTG-
1 TTTTTTGT
2294 TTTTTTGT
1 TTTTTTGT
2302 TTTTTT-T
1 TTTTTTGT
2309 GTTTTTTGT
1 -TTTTTTGT
2318 TTTTTT-T
1 TTTTTTGT
2325 TTTT
1 TTTT
2329 CCAAAGCTCC
Statistics
Matches: 74, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
7 25 0.34
8 34 0.46
9 15 0.20
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (8 bp):
TTTTTTGT
Found at i:2265 original size:16 final size:16
Alignment explanation
Indices: 2239--2325 Score: 122
Period size: 16 Copynumber: 5.4 Consensus size: 16
2229 CAACTCAACA
2239 TTTTTTGTTTTTTTTT
1 TTTTTTGTTTTTTTTT
2255 TTTTGTT-TTTTTTTTT
1 TTTT-TTGTTTTTTTTT
* *
2271 GTTTTTGTTTTTTTGT
1 TTTTTTGTTTTTTTTT
*
2287 TTTTTTGTTTTTTGTT
1 TTTTTTGTTTTTTTTT
2303 TTTTTTGTTTTTTGTTT
1 TTTTTTGTTTTTT-TTT
2320 TTTTTT
1 TTTTTT
2326 TTTCCAAAGC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
15 2 0.03
16 50 0.81
17 10 0.16
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (16 bp):
TTTTTTGTTTTTTTTT
Found at i:2713 original size:116 final size:119
Alignment explanation
Indices: 2334--2887 Score: 955
Period size: 116 Copynumber: 4.6 Consensus size: 119
2324 TTTTTCCAAA
2334 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGGG
1 GCTCCTCTAAACAGAGG--CAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAAC--G
2399 ACTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
62 ACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
2456 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
2521 ACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
62 ACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
2580 GCTCCTCTAAACAGAGGC-ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGC-ACGACTT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
2643 TGAAAAGTAAATTGCTCCTCTAAACAGAGG-ACCACGACTTTGAAAAGTAAATT
66 TGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
2696 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
2761 TGAAAA-TAAATTGCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATT
66 TGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
2812 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAAC-
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACG-ACT
2876 TTG-AAAGTAAAT
65 TTGAAAAGTAAAT
2888 ACTCCTAGAC
Statistics
Matches: 421, Mismatches: 0, Indels: 28
0.94 0.00 0.06
Matches are distributed among these distances:
115 3 0.01
116 130 0.31
117 92 0.22
118 22 0.05
120 2 0.00
121 38 0.09
122 62 0.15
123 1 0.00
124 71 0.17
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (119 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTT
TGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:2730 original size:39 final size:39
Alignment explanation
Indices: 2334--2887 Score: 922
Period size: 41 Copynumber: 14.0 Consensus size: 39
2324 TTTTTCCAAA
2334 GCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGG--CAACGACTTTGAAAAGTAAATT
2375 GCTCCTCTAAACAGAGGCAACGGGACTTTG-AAAGTAAATT
1 GCTCCTCTAAACAGAGGCAAC--GACTTTGAAAAGTAAATT
2415 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATT
2456 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATT
2497 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTT-GAAAAGTAAATT
2539 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATT
2580 GCTCCTCTAAACAGAGGC-ACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
2618 GCTCCTCTAAACAGAGGC-ACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
*
2656 GCTCCTCTAAACAGAGGACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGG-CAACGACTTTGAAAAGTAAATT
2696 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
2735 GCTCCTCTAAACAGAGGCAACGACTTTGAAAA-TAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
2773 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
2812 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
2851 GCTCCTCTAAACAGAGGCAACGAAC-TTG-AAAGTAAAT
1 GCTCCTCTAAACAGAGGCAACG-ACTTTGAAAAGTAAAT
2888 ACTCCTAGAC
Statistics
Matches: 502, Mismatches: 1, Indels: 23
0.95 0.00 0.04
Matches are distributed among these distances:
38 122 0.24
39 128 0.25
40 75 0.15
41 134 0.27
42 43 0.09
ACGTcount: A:0.37, C:0.22, G:0.18, T:0.23
Consensus pattern (39 bp):
GCTCCTCTAAACAGAGGCAACGACTTTGAAAAGTAAATT
Found at i:4072 original size:9 final size:9
Alignment explanation
Indices: 4052--4107 Score: 64
Period size: 8 Copynumber: 6.4 Consensus size: 9
4042 TTTGAATCTC
4052 TTTTTTCA-
1 TTTTTTCAT
4060 TTTTTTCAT
1 TTTTTTCAT
4069 TTTTTTCA-
1 TTTTTTCAT
*
4077 TTTTCTC-T
1 TTTTTTCAT
*
4085 TTTTTTCTT
1 TTTTTTCAT
4094 TTTTTCTCAT
1 TTTTT-TCAT
4104 TTTT
1 TTTT
4108 CATCCATTGT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
8 20 0.49
9 14 0.34
10 7 0.17
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTTCAT
Found at i:4072 original size:17 final size:16
Alignment explanation
Indices: 4052--4110 Score: 73
Period size: 17 Copynumber: 3.6 Consensus size: 16
4042 TTTGAATCTC
4052 TTTTTTCATTTTTTCAT
1 TTTTTTCATTTTTTC-T
*
4069 TTTTTTCATTTTCTCT
1 TTTTTTCATTTTTTCT
*
4085 TTTTTTCTTTTTTTCT
1 TTTTTTCATTTTTTCT
*
4101 CATTTTTCAT
1 -TTTTTTCAT
4111 CCATTGTTGA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
16 15 0.42
17 21 0.58
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTTCATTTTTTCT
Found at i:8177 original size:60 final size:60
Alignment explanation
Indices: 7920--8268 Score: 444
Period size: 60 Copynumber: 5.7 Consensus size: 60
7910 TTTTTTGTAG
7920 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA---TTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTT--ATTTCT-AA
*** *
7979 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAA-CCCTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTTTGGAAATTTATTTCTAA
8038 GGAAAATTGATACTTTCAACTTTTCCCT-AAAATATATTTTTTTTGGAAATTTATTTTTCTTTTA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTTGGAAATTTA--TTTC---TA
8102 A
60 A
* *
8103 GGAAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTCGAAATTTATTTCTGA
1 GG-AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
* * *
8164 GGAAAATTGATACTTTCAACTTTTCCC-CAAAATATTTTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTTGGAAATTTATTTCTAA
8224 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTTT
8269 TTGGAATTTT
Statistics
Matches: 261, Mismatches: 11, Indels: 34
0.85 0.04 0.11
Matches are distributed among these distances:
58 7 0.03
59 65 0.25
60 96 0.37
61 31 0.12
62 4 0.02
64 4 0.02
65 5 0.02
66 42 0.16
67 7 0.03
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.46
Consensus pattern (60 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTATTTCTAA
Found at i:8746 original size:20 final size:20
Alignment explanation
Indices: 8721--8758 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
8711 AACCACCGGT
*
8721 GCCGGATTCTGGAAATTTTC
1 GCCGGAATCTGGAAATTTTC
8741 GCCGGAATCTGGAAATTT
1 GCCGGAATCTGGAAATTT
8759 CACCCGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
GCCGGAATCTGGAAATTTTC
Found at i:8765 original size:20 final size:20
Alignment explanation
Indices: 8722--8767 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
8712 ACCACCGGTG
* *
8722 CCGGATTCTGGAAATTTTCG
1 CCGGAATCTGGAAATTTTCC
8742 CCGGAATCTGGAAA-TTTCAC
1 CCGGAATCTGGAAATTTTC-C
8762 CCGGAA
1 CCGGAA
8768 GTTGGCCCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (20 bp):
CCGGAATCTGGAAATTTTCC
Found at i:9292 original size:28 final size:26
Alignment explanation
Indices: 9239--9310 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 26
9229 AGAAAATCAA
*
9239 AATTAAAAAATAAAA-ATAATATCAGAT
1 AATTAAAAAA-AAAATA-AATAACAGAT
9266 AATTCAAAAAAAAAATAAATTAACAGAT
1 AATT-AAAAAAAAAATAAA-TAACAGAT
9294 -A-TAAAAAAAATAATAAA
1 AATTAAAAAAAA-AATAAA
9311 AATAAAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 8 0.20
26 7 0.17
27 11 0.28
28 14 0.35
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.22
Consensus pattern (26 bp):
AATTAAAAAAAAAATAAATAACAGAT
Found at i:9336 original size:28 final size:28
Alignment explanation
Indices: 9244--9336 Score: 64
Period size: 30 Copynumber: 3.2 Consensus size: 28
9234 ATCAAAATTA
* * **
9244 AAAAATAAAAATAATATCAGAT-AATTC
1 AAAAATAAAAATAAAATAAGATAAAAAC
* *
9271 AAAAA-AAAAATAAATTAACAGATATAAAAA
1 AAAAATAAAAATAAAAT-A-AGATA-AAAAC
**
9301 AAATAATAAAAATAAAATAAGATAAACCC
1 AAA-AATAAAAATAAAATAAGATAAAAAC
9330 AAAAATA
1 AAAAATA
9337 TATTACAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
26 9 0.18
27 5 0.10
28 8 0.16
29 5 0.10
30 10 0.20
31 3 0.06
32 10 0.20
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.19
Consensus pattern (28 bp):
AAAAATAAAAATAAAATAAGATAAAAAC
Found at i:9413 original size:31 final size:28
Alignment explanation
Indices: 9352--9457 Score: 94
Period size: 28 Copynumber: 3.7 Consensus size: 28
9342 CAAAAAAAAA
* *
9352 AAATAATAATAATAATATATAACTATAT
1 AAATAATAATAATAAAATATAACTAAAT
*
9380 AAATAATAATACATATAAATCTAATCTAAAT
1 AAATAATAATA-ATA-AAATATAA-CTAAAT
9411 AAA-AATAAATAA-ATAAATATATAC-ATAAT
1 AAATAAT-AATAATA-AAATATA-ACTA-AAT
9440 -AATAATAATAATAAAATA
1 AAATAATAATAATAAAATA
9458 CATAAAATAC
Statistics
Matches: 66, Mismatches: 4, Indels: 16
0.77 0.05 0.19
Matches are distributed among these distances:
28 24 0.36
29 19 0.29
30 11 0.17
31 12 0.18
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATAATAATAATAAAATATAACTAAAT
Found at i:13091 original size:10 final size:10
Alignment explanation
Indices: 13076--13102 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
13066 AAAAAAATAT
13076 TTTTAATAAG
1 TTTTAATAAG
13086 TTTTAATAAG
1 TTTTAATAAG
13096 TTTTAAT
1 TTTTAAT
13103 TAAATTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (10 bp):
TTTTAATAAG
Found at i:14410 original size:38 final size:38
Alignment explanation
Indices: 14359--14432 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
14349 AGAAATTTAA
*
14359 ACTTGACATCTTATCCGAAGGTGAAGCGTGGGCTTTTT
1 ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTTTT
14397 ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTT
1 ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTT
14433 GTTCAAAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (38 bp):
ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTTTT
Found at i:16702 original size:43 final size:43
Alignment explanation
Indices: 16641--16728 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
16631 TTAAATTATA
16641 TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
1 TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
* * *
16684 TTAGTAACTAAACTAAATTTGTACTTATTACGTGGCTTGCAAG
1 TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
16727 TT
1 TT
16729 GAGAAAGCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (43 bp):
TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
Found at i:17637 original size:10 final size:10
Alignment explanation
Indices: 17622--17654 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
17612 TTGCAAATAA
17622 AAAAGAAAAT
1 AAAAGAAAAT
17632 AAAAG-AAAT
1 AAAAGAAAAT
17641 AAAAGAATAAT
1 AAAAGAA-AAT
17652 AAA
1 AAA
17655 GGCAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 6 0.29
11 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:18372 original size:2 final size:2
Alignment explanation
Indices: 18365--18394 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18355 TGATAATCTA
18365 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18395 ACAACATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19774 original size:14 final size:13
Alignment explanation
Indices: 19754--19792 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
19744 TTTAGTGAAC
19754 AATATTATTTATA
1 AATATTATTTATA
*
19767 ATATATTATATATA
1 A-ATATTATTTATA
19781 AATTATTATTTA
1 AA-TATTATTTA
19793 ATTATAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTATTTATA
Found at i:19933 original size:2 final size:2
Alignment explanation
Indices: 19926--19957 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
19916 ATAGATTGTA
*
19926 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19958 GATTTGGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Done.