Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168110.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_355, 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: 31963
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Found at i:1609 original size:18 final size:19
Alignment explanation
Indices: 1588--1637 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
1578 ATTTATGTAA
1588 ATATAAAATATTATA-TTT
1 ATATAAAATATTATATTTT
**
1606 ATATATTATATTATATTTT
1 ATATAAAATATTATATTTT
1625 ATATAAAA-ATTAT
1 ATATAAAATATTAT
1638 GTATTATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATAAAATATTATATTTT
Found at i:1636 original size:23 final size:24
Alignment explanation
Indices: 1610--1659 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
1600 ATATTTATAT
*
1610 ATTA-TATTATATTTTATATAAAA
1 ATTAGTATTATAATTTATATAAAA
*
1633 ATTATGTATTATAATTTATATCAAA
1 ATTA-GTATTATAATTTATATAAAA
1658 AT
1 AT
1660 AAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
25 19 0.83
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTAGTATTATAATTTATATAAAA
Found at i:2193 original size:45 final size:45
Alignment explanation
Indices: 2129--2218 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
2119 TGGCAGCTGC
2129 ACATTTCTTTTTCAAAATGACAGCAATTAATACATTTGCATTTGG
1 ACATTTCTTTTTCAAAATGACAGCAATTAATACATTTGCATTTGG
**
2174 ACATTTCTTTTTCAAAATGACTTCAATTAATACATTTGCATTTGG
1 ACATTTCTTTTTCAAAATGACAGCAATTAATACATTTGCATTTGG
2219 TACTTGCTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (45 bp):
ACATTTCTTTTTCAAAATGACAGCAATTAATACATTTGCATTTGG
Found at i:2405 original size:27 final size:27
Alignment explanation
Indices: 2374--2426 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
2364 ACAATACGAT
* *
2374 AATATTATATGAAAATTATATAAAAAC
1 AATATGATATAAAAATTATATAAAAAC
2401 AATATGATATAAAAATTATATAAAAA
1 AATATGATATAAAAATTATATAAAAA
2427 GACATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (27 bp):
AATATGATATAAAAATTATATAAAAAC
Found at i:2439 original size:27 final size:27
Alignment explanation
Indices: 2385--2439 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
2375 ATATTATATG
* *
2385 AAAATTATATAAAAACAATATGATATA
1 AAAATTATATAAAAACAATATAAAATA
*
2412 AAAATTATATAAAAAGACATA-AAAATA
1 AAAATTATATAAAAACA-ATATAAAATA
2439 A
1 A
2440 TATTCTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 21 0.88
28 3 0.12
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (27 bp):
AAAATTATATAAAAACAATATAAAATA
Found at i:4898 original size:2 final size:2
Alignment explanation
Indices: 4891--4921 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4881 CCTCTTCCTA
4891 AT AT AT 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 AT AT AT A
4922 GACACATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5310 original size:55 final size:55
Alignment explanation
Indices: 5250--5360 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
5240 AAAATGAGAA
5250 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
1 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
5305 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
1 AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
5360 A
1 A
5361 TCATACATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.25
Consensus pattern (55 bp):
AGTCAAATCTCAATACCGTATACCAAACAAATTAAAATGTTACAATGCCCTTACG
Found at i:10731 original size:34 final size:34
Alignment explanation
Indices: 10693--10787 Score: 93
Period size: 34 Copynumber: 2.8 Consensus size: 34
10683 TTAAATATAT
* * *
10693 AAACGTCGTTAAAATAGCAACGTTTTCTAGATAC
1 AAACGTCGTTAATATAGCAACATTTTCTAAATAC
*** *
10727 AAACGT-GATTAATATAGTTGCATTTTCTAAATTC
1 AAACGTCG-TTAATATAGCAACATTTTCTAAATAC
* *
10761 AAACATCGTTAATATAGCAACCTTTTC
1 AAACGTCGTTAATATAGCAACATTTTC
10788 CACCTACAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
33 1 0.02
34 45 0.96
35 1 0.02
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (34 bp):
AAACGTCGTTAATATAGCAACATTTTCTAAATAC
Found at i:11422 original size:17 final size:19
Alignment explanation
Indices: 11402--11441 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11392 AAAAACATTG
11402 AAAAAATA-A-ATAAAACA
1 AAAAAATATATATAAAACA
*
11419 AAAAAATATATATAATACA
1 AAAAAATATATATAAAACA
11438 AAAA
1 AAAA
11442 GTTAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 11 0.55
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAAAATATATATAAAACA
Found at i:11978 original size:26 final size:26
Alignment explanation
Indices: 11948--11997 Score: 84
Period size: 26 Copynumber: 1.9 Consensus size: 26
11938 AGCTTTTGAT
11948 TTCAATTTAAATAA-TTATGTAAAATA
1 TTCAATTTAAATAATTTAT-TAAAATA
11974 TTCAATTTAAATAATTTATTAAAA
1 TTCAATTTAAATAATTTATTAAAA
11998 AAATTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TTCAATTTAAATAATTTATTAAAATA
Found at i:12521 original size:18 final size:16
Alignment explanation
Indices: 12487--12521 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
12477 AATTGATAAA
12487 TATATATATATTTATT
1 TATATATATATTTATT
12503 TATATATACTATTTGATT
1 TATATATA-TATTT-ATT
12521 T
1 T
12522 GATTCATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 5 0.29
18 4 0.24
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (16 bp):
TATATATATATTTATT
Found at i:14896 original size:17 final size:17
Alignment explanation
Indices: 14874--14908 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
14864 ATTAGCGCCT
14874 AAACTTATTACCTTTCC
1 AAACTTATTACCTTTCC
14891 AAACTTATTACCTTTCC
1 AAACTTATTACCTTTCC
14908 A
1 A
14909 TTTGACTTCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.29, G:0.00, T:0.40
Consensus pattern (17 bp):
AAACTTATTACCTTTCC
Found at i:15160 original size:3 final size:3
Alignment explanation
Indices: 15154--15205 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
15144 TATTTTAAAT
15154 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
15202 TTA T
1 TTA T
15206 CCATCAATTG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:15781 original size:18 final size:18
Alignment explanation
Indices: 15743--15787 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
15733 AATATAATTT
15743 TAATTTTTTT-TGTCTGA
1 TAATTTTTTTATGTCTGA
15760 -AATTTTTTTATGT-TCGA
1 TAATTTTTTTATGTCT-GA
*
15777 TAATTATTTTA
1 TAATTTTTTTA
15788 AATTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 10 0.42
17 5 0.21
18 9 0.38
ACGTcount: A:0.24, C:0.04, G:0.09, T:0.62
Consensus pattern (18 bp):
TAATTTTTTTATGTCTGA
Found at i:18148 original size:25 final size:25
Alignment explanation
Indices: 18120--18195 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
18110 CCGACGGATT
18120 GACCTCAGGCAGTGGTGGGCGACTG
1 GACCTCAGGCAGTGGTGGGCGACTG
18145 GACCTCAGGCAGTGGTGGGCGACTG
1 GACCTCAGGCAGTGGTGGGCGACTG
18170 GACCTCAGGCAGTGGTGGGCGACTG
1 GACCTCAGGCAGTGGTGGGCGACTG
18195 G
1 G
18196 TTGGAACAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (25 bp):
GACCTCAGGCAGTGGTGGGCGACTG
Found at i:18385 original size:79 final size:79
Alignment explanation
Indices: 18170--18379 Score: 366
Period size: 79 Copynumber: 2.6 Consensus size: 79
18160 TGGGCGACTG
* * *
18170 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCTCTTCCAGTTCTAGGCGTAGTC
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
18235 CCTTCCGACGGATC
66 CCTTCCGACGGATC
*
18249 GACCTCAGGCAGTGGTGGGCGATTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
18314 CCTTCCGACGGATC
66 CCTTCCGACGGATC
*
18328 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAG
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAA-CAGATTTGGGCGCATCCAG
18380 ACTGGGGGTC
Statistics
Matches: 124, Mismatches: 6, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
79 106 0.85
80 18 0.15
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (79 bp):
GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
CCTTCCGACGGATC
Found at i:18482 original size:118 final size:118
Alignment explanation
Indices: 18274--18496 Score: 412
Period size: 118 Copynumber: 1.9 Consensus size: 118
18264 TGGGCGATTG
18274 GTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
18339 GTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
66 GTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
*
18392 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCGACTTCAGGC
1 GTTGGAA-CAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGC
*
18456 AGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCA
65 AGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCA
18497 ATTCTGGGCG
Statistics
Matches: 102, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
118 79 0.77
119 23 0.23
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (118 bp):
GTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
GTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTCTT
Found at i:18524 original size:198 final size:197
Alignment explanation
Indices: 18195--18577 Score: 660
Period size: 198 Copynumber: 1.9 Consensus size: 197
18185 TGGGCGACTG
* *
18195 GTTGGAACAGATTTGGGCTCTTCCAGTTCTAGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
1 GTTGGAACAGATTTGGGCGCATCCAGTTCTAGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
* *
18260 GTGGTGGGCGATTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGG
66 GTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAATTCTGGGCGTAGTCCCTTCCGACGG
* *
18325 ATCGACCTCAGGCAGTGGTGGGCGACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTC
131 ATCGACCTCAAGCAGTGGTGGGCAACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTC
18390 TT
196 TT
*
18392 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCGACTTCAGGC
1 GTTGGAA-CAGATTTGGGCGCATCCAGTTCTAGGCGTAGTCCCTTCCGACGGATCGACCTCAGGC
*
18456 AGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAATTCTGGGCGTAGTCCCTTCTGAC
65 AGTGGTGGGCGACTGGTTGGAA-CAGATTTGGGCGCATCCAATTCTGGGCGTAGTCCCTTCCGAC
*
18521 GGATCGACCTCAAGCAGTGGTGGGCAACTGGTTGGAACCAGATTTGGGCGCATCCAG
129 GGATCGACCTCAAGCAGTGGTGGGCAACTGGTTGGAACCAGATTCGGGCGCATCCAG
18578 TTCTGGGCAT
Statistics
Matches: 175, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
197 60 0.34
198 115 0.66
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.24
Consensus pattern (197 bp):
GTTGGAACAGATTTGGGCGCATCCAGTTCTAGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCA
GTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAATTCTGGGCGTAGTCCCTTCCGACGG
ATCGACCTCAAGCAGTGGTGGGCAACTGGTTGGAACCAGATTCGGGCGCATCCAGACTGGGGGTC
TT
Found at i:18540 original size:80 final size:80
Alignment explanation
Indices: 18392--18657 Score: 462
Period size: 80 Copynumber: 3.3 Consensus size: 80
18382 TGGGGGTCTT
* * *
18392 GTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTAGTCCCTTCCGACGGATCGACTTCAGGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACCTCAAGC
18456 AGTGGTGGGCGACTG
66 AGTGGTGGGCGACTG
*
18471 GTTGGAACCAGATTTGGGCGCATCCAATTCTGGGCGTAGTCCCTTCTGACGGATCGACCTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACCTCAAGC
*
18536 AGTGGTGGGCAACTG
66 AGTGGTGGGCGACTG
*
18551 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCATAGTCCCTTCTGACGGATCGACCTCAAGC
1 GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACCTCAAGC
18616 AGTGGTGGGCGACTG
66 AGTGGTGGGCGACTG
*
18631 GTTGGAACCAGATTCGGGCGCATCCAG
1 GTTGGAACCAGATTTGGGCGCATCCAG
18658 ACTGGGGGTC
Statistics
Matches: 177, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
79 30 0.17
80 147 0.83
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.23
Consensus pattern (80 bp):
GTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCTGACGGATCGACCTCAAGC
AGTGGTGGGCGACTG
Found at i:18698 original size:278 final size:277
Alignment explanation
Indices: 18170--18814 Score: 1082
Period size: 277 Copynumber: 2.3 Consensus size: 277
18160 TGGGCGACTG
* * *
18170 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCTCTTCCAGTTCTAGGCGTAGTC
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
* *
18235 CCTTCCGACGGATCGACCTCAGGCAGTGGTGGGCGATTGGTTGGAACAGATTTGGGCGCATCCAG
66 CCTTCCGACGGATCGACCTCAGGCAGTGGTGGGCAACTGGTTGGAACAGATTTGGGCGCATCCAG
* *
18300 TTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAGGCAGTGGTGGGCGACTGGTTGGAACCAGA
131 TTCTGGGCATAGTCCCTTCCGACGGATCGACCTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGA
18365 TTCGGGCGCATCCAGACTGGGGGTCTTGTTGGAACCAGATTTGGGCGCATCCAGTTCT-GGCGTA
196 TTCGGGCGCATCCAGACTGGGGGTCTTGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTA
18429 GTCCCTTCCGACGGATC
261 GTCCCTTCCGACGGATC
* *
18446 GACTTCAGGCAGTGGTGGGCGACTGGTTGGAACCAGATTTGGGCGCATCCAATTCTGGGCGTAGT
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAA-CAGATTTGGGCGCATCCAGTTCTGGGCGTAGT
* *
18511 CCCTTCTGACGGATCGACCTCAAGCAGTGGTGGGCAACTGGTTGGAACCAGATTTGGGCGCATCC
65 CCCTTCCGACGGATCGACCTCAGGCAGTGGTGGGCAACTGGTTGGAA-CAGATTTGGGCGCATCC
*
18576 AGTTCTGGGCATAGTCCCTTCTGACGGATCGACCTCAAGCAGTGGTGGGCGACTGGTTGGAACCA
129 AGTTCTGGGCATAGTCCCTTCCGACGGATCGACCTCAAGCAGTGGTGGGCGACTGGTTGGAACCA
*
18641 GATTCGGGCGCATCCAGACTGGGGGTCTTGTTGGAACCAGATTTGGGCGCATCCAGTTTTGGGCG
194 GATTCGGGCGCATCCAGACTGGGGGTCTTGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCG
18706 TAGTCCCTTCCGACGGATC
259 TAGTCCCTTCCGACGGATC
* *
18725 GACCTCAAGCA--GGTGGGCGACTGGTTGGAATCAGATTCGGGCGCATCCAGTTCTGAGG-GTAG
1 GACCTCAGGCAGTGGTGGGCGACTGGTTGGAA-CAGATTTGGGCGCATCCAGTTCTG-GGCGTAG
*
18787 TCCCTTCCGACTGATCGACCTCAGGCAG
64 TCCCTTCCGACGGATCGACCTCAGGCAG
18815 GTGGGCGACT
Statistics
Matches: 344, Mismatches: 21, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
276 31 0.09
277 141 0.41
278 140 0.41
279 32 0.09
ACGTcount: A:0.18, C:0.25, G:0.34, T:0.24
Consensus pattern (277 bp):
GACCTCAGGCAGTGGTGGGCGACTGGTTGGAACAGATTTGGGCGCATCCAGTTCTGGGCGTAGTC
CCTTCCGACGGATCGACCTCAGGCAGTGGTGGGCAACTGGTTGGAACAGATTTGGGCGCATCCAG
TTCTGGGCATAGTCCCTTCCGACGGATCGACCTCAAGCAGTGGTGGGCGACTGGTTGGAACCAGA
TTCGGGCGCATCCAGACTGGGGGTCTTGTTGGAACCAGATTTGGGCGCATCCAGTTCTGGGCGTA
GTCCCTTCCGACGGATC
Found at i:18803 original size:78 final size:78
Alignment explanation
Indices: 18670--18824 Score: 249
Period size: 78 Copynumber: 2.0 Consensus size: 78
18660 TGGGGGTCTT
* *
18670 GTTGGAACCAGATTTGGGCGCATCCAGTTTTGGGCGTAGTCCCTTCCGACGGATCGACCTCAAGC
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAAGC
18735 AGGTGGGCGACTG
66 AGGTGGGCGACTG
* * *
18748 GTTGGAATCAGATTCGGGCGCATCCAGTTCTGAGG-GTAGTCCCTTCCGACTGATCGACCTCAGG
1 GTTGGAACCAGATTCGGGCGCATCCAGTTCTG-GGCGTAGTCCCTTCCGACGGATCGACCTCAAG
18812 CAGGTGGGCGACT
65 CAGGTGGGCGACT
18825 ATGTGTTTGT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
78 69 0.97
79 2 0.03
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (78 bp):
GTTGGAACCAGATTCGGGCGCATCCAGTTCTGGGCGTAGTCCCTTCCGACGGATCGACCTCAAGC
AGGTGGGCGACTG
Found at i:21785 original size:16 final size:13
Alignment explanation
Indices: 21754--21807 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 13
21744 GGTAAATAAT
21754 ATTATT-TTTTTA
1 ATTATTATTTTTA
21766 ATTAATTCATTTTTA
1 ATT-ATT-ATTTTTA
21781 TATTATTATTTTTAA
1 -ATTATTATTTTT-A
21796 ATATATTATTTT
1 AT-TATTATTTT
21808 ATGAGATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.08
13 3 0.08
14 8 0.22
15 19 0.53
16 3 0.08
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
ATTATTATTTTTA
Found at i:21809 original size:28 final size:28
Alignment explanation
Indices: 21752--21807 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
21742 TTGGTAAATA
*
21752 ATATTATTTTTTTAATTAATTCATTTTT
1 ATATTATTTTTTTAAATAATTCATTTTT
21780 ATATTATTATTTTTAAATATATT-ATTTT
1 ATATTATT-TTTTTAAATA-ATTCATTTT
21808 ATGAGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 8 0.32
29 14 0.56
30 3 0.12
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (28 bp):
ATATTATTTTTTTAAATAATTCATTTTT
Found at i:22170 original size:61 final size:61
Alignment explanation
Indices: 22062--22177 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
22052 TGAATTTTAG
*
22062 TTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGGTAAGAATTTATGAGTTTGAA
1 TTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGATAAGAATTTATGAGTTTGAA
* * * * * *
22123 TTTACTATA-TTTTATGTATTTTATAATTCTATTATTTATGATGAGAATTTATGAG
1 TTTACTA-AGTTTTATATATTTCATAATTCCATCATCTATGATAAGAATTTATGAG
22178 ATTTTTATTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
61 46 0.98
62 1 0.02
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.50
Consensus pattern (61 bp):
TTTACTAAGTTTTATATATTTCATAATTCCATCATCTATGATAAGAATTTATGAGTTTGAA
Found at i:24574 original size:2 final size:2
Alignment explanation
Indices: 24567--24596 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
24557 ACCCCTCTGA
24567 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24597 CAAGAGCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29816 original size:15 final size:17
Alignment explanation
Indices: 29796--29834 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
29786 TGAAATATTG
*
29796 TTAAAAA-TTAT-AAGA
1 TTAAAAATTTATGAAAA
29811 TTAAAAATTTATGAAAA
1 TTAAAAATTTATGAAAA
29828 TTAAAAA
1 TTAAAAA
29835 ATTCGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TTAAAAATTTATGAAAA
Found at i:30019 original size:36 final size:35
Alignment explanation
Indices: 29952--30020 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 35
29942 TTATAATAAA
* * * *
29952 AAAATCTAAAATTTTTTGAAAATTTTCCAAATTAG
1 AAAATCTAAAATTTTTTAAAAAATCTACAAATTAG
*
29987 AAAATCTAAATTTTTTTTAAAAAATCTACAAATT
1 AAAATCTAAA-ATTTTTTAAAAAATCTACAAATT
30021 TTTAAATAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
35 10 0.36
36 18 0.64
ACGTcount: A:0.48, C:0.09, G:0.03, T:0.41
Consensus pattern (35 bp):
AAAATCTAAAATTTTTTAAAAAATCTACAAATTAG
Done.