Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014319.1 Corchorus olitorius cultivar O-4 contig14352, 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: 68186
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Found at i:10011 original size:20 final size:20
Alignment explanation
Indices: 9986--10027 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
9976 CGATAAAGTT
9986 TGATGGTTTAATTTATTGTA
1 TGATGGTTTAATTTATTGTA
10006 TGATGGTTTAATTTATTGTA
1 TGATGGTTTAATTTATTGTA
10026 TG
1 TG
10028 TGTTATATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (20 bp):
TGATGGTTTAATTTATTGTA
Found at i:12205 original size:16 final size:16
Alignment explanation
Indices: 12184--12215 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
12174 TTCACGTATT
12184 ATGTATATGCTAGTCC
1 ATGTATATGCTAGTCC
12200 ATGTATATGCTAGTCC
1 ATGTATATGCTAGTCC
12216 GGTTAGCTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (16 bp):
ATGTATATGCTAGTCC
Found at i:15322 original size:16 final size:16
Alignment explanation
Indices: 15301--15333 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
15291 TAACTTTCAC
*
15301 TGTAACATGATGACCA
1 TGTAACATGATAACCA
15317 TGTAACATGATAACCA
1 TGTAACATGATAACCA
15333 T
1 T
15334 ATGTAGAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.27
Consensus pattern (16 bp):
TGTAACATGATAACCA
Found at i:18911 original size:21 final size:21
Alignment explanation
Indices: 18887--18928 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
18877 TTATTTACTC
* *
18887 ATTATCTTGTAAAGTTTCATA
1 ATTATCCTGCAAAGTTTCATA
18908 ATTATCCTGCAAAGTTTCATA
1 ATTATCCTGCAAAGTTTCATA
18929 GTTTCTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (21 bp):
ATTATCCTGCAAAGTTTCATA
Found at i:27727 original size:33 final size:34
Alignment explanation
Indices: 27690--27755 Score: 98
Period size: 36 Copynumber: 1.9 Consensus size: 34
27680 GGTAATAAAG
*
27690 AGTAATTAAATTC-AAAGAGTAAAATGGTAAATC
1 AGTAATTAAATTCTAAAAAGTAAAATGGTAAATC
27723 AGTAATTAAATTCTGTAAAAAGTAAAATGGTAA
1 AGTAATTAAATTC--TAAAAAGTAAAATGGTAA
27756 TCAATAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 13 0.45
36 16 0.55
ACGTcount: A:0.52, C:0.05, G:0.15, T:0.29
Consensus pattern (34 bp):
AGTAATTAAATTCTAAAAAGTAAAATGGTAAATC
Found at i:27765 original size:57 final size:54
Alignment explanation
Indices: 27704--27809 Score: 176
Period size: 57 Copynumber: 1.9 Consensus size: 54
27694 ATTAAATTCA
27704 AAGAGTAAAATGGTAAATCAGTAATTAAATTCTGTAAAAAGTAAAATGGTAATCAAT
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTC---AAAAAGTAAAATGGTAATCAAT
*
27761 AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATGGTAA
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAAAGTAAAATGGTAA
27810 ATCAGTGGTA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
54 16 0.33
57 32 0.67
ACGTcount: A:0.52, C:0.05, G:0.17, T:0.26
Consensus pattern (54 bp):
AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAAAGTAAAATGGTAATCAAT
Found at i:27803 original size:33 final size:33
Alignment explanation
Indices: 27761--27971 Score: 180
Period size: 33 Copynumber: 6.6 Consensus size: 33
27751 GGTAATCAAT
27761 AAGAGTAAAATGGTAAATCAGTAATTAAATTCA
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTCA
**
27794 AAGAGTAAAATGGTAAATCAGT-GGT-AA-TCA
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTCA
* * *
27824 GAA-A--AAAA-AGTAAAATGA-TAATT--AGT-A
1 -AAGAGTAAAATGGT-AAATCAGTAATTAAATTCA
27851 A-GAGTAAAATGGTAAATCAGTAATTAAATTCA
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTCA
*
27883 AAGAGTACAATGGTAAATCAGTAATTAAATTCA
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTCA
* * *
27916 AAGAGTAAAATGATAAGTCAAG-AATTTAATTCGGTA
1 AAGAGTAAAATGGTAAATC-AGTAATTAAATTC---A
*
27952 AAAAGTAAAATGGT-AATCAG
1 AAGAGTAAAATGGTAAATCAG
27972 GAAGTGTAAA
Statistics
Matches: 144, Mismatches: 17, Indels: 33
0.74 0.09 0.17
Matches are distributed among these distances:
26 2 0.01
27 5 0.03
28 20 0.14
29 7 0.05
30 4 0.03
31 6 0.04
32 3 0.02
33 77 0.53
34 4 0.03
35 3 0.02
36 13 0.09
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.26
Consensus pattern (33 bp):
AAGAGTAAAATGGTAAATCAGTAATTAAATTCA
Found at i:27871 original size:89 final size:90
Alignment explanation
Indices: 27690--27936 Score: 335
Period size: 89 Copynumber: 2.8 Consensus size: 90
27680 GGTAATAAAG
* * * *
27690 AGTAATTAAATTCAAAGAGTAAAATGGTAAATCAGTAATTAAATTCTGTAAAAAGTAAAATGGTA
1 AGTAATTAAATTCAAAGAGTAAAATGGTAAATCAGTAAGTAAATTCAGAAAAAAGTAAAATGATA
27755 ATCAATAAGAGTAAAATGGTAAATC
66 ATCAATAAGAGTAAAATGGTAAATC
*
27780 AGTAATTAAATTCAAAGAGTAAAATGGTAAATCAGT-GGT-AA-TCAGAAAAAAAAGTAAAATGA
1 AGTAATTAAATTCAAAGAGTAAAATGGTAAATCAGTAAGTAAATTCAG--AAAAAAGTAAAATGA
* *
27842 TAATTAGTAAGAGTAAAATGGTAAATC
64 TAATCAATAAGAGTAAAATGGTAAATC
* * *
27869 AGTAATTAAATTCAAAGAGTACAATGGTAAATCAGTAATTAAATTC---AAAGAGTAAAATGATA
1 AGTAATTAAATTCAAAGAGTAAAATGGTAAATCAGTAAGTAAATTCAGAAAAAAGTAAAATGATA
27931 AGTCAA
66 A-TCAA
27937 GAATTTAATT
Statistics
Matches: 138, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
87 19 0.14
88 4 0.03
89 74 0.54
90 37 0.27
91 2 0.01
92 2 0.01
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.26
Consensus pattern (90 bp):
AGTAATTAAATTCAAAGAGTAAAATGGTAAATCAGTAAGTAAATTCAGAAAAAAGTAAAATGATA
ATCAATAAGAGTAAAATGGTAAATC
Found at i:28007 original size:123 final size:122
Alignment explanation
Indices: 27761--28013 Score: 359
Period size: 123 Copynumber: 2.1 Consensus size: 122
27751 GGTAATCAAT
*
27761 AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATGGTAAATCAGTGGTAATCAGA
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATGATAAATCAGTGGTAATCAGA
* *
27826 AAAAAAAGTAAAATGATAATTAGTAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
66 AAAAAAAGTAAAATGATAATCAGGAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
* * *
27883 AAGAGTACAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATGATAAGTCAAGAAT-TTAATT
1 AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATGATAAATC-AG--TGGTAA-T
** * *
27947 C-G-GTAAAAAGTAAAATGGTAATCAGGAAGTGTAAAATGGTAAATCAGTAATTAAATTCA
62 CAGAAAAAAAAGTAAAATGATAATCAGGAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
28006 AAGAGTAA
1 AAGAGTAA
28014 GAAAAAGGTA
Statistics
Matches: 116, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
122 49 0.42
123 60 0.52
124 4 0.03
125 3 0.03
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.26
Consensus pattern (122 bp):
AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATGATAAATCAGTGGTAATCAGA
AAAAAAAGTAAAATGATAATCAGGAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
Found at i:28078 original size:35 final size:35
Alignment explanation
Indices: 28035--28104 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
28025 TCGGTAATTT
*
28035 AGTTAAAAAGAGTAAAAATGGAATTTAGTAATTAA
1 AGTTAAAAAGAATAAAAATGGAATTTAGTAATTAA
* *
28070 AGTTAAAAATAATAAAAATGGTATTTAGTAATTAA
1 AGTTAAAAAGAATAAAAATGGAATTTAGTAATTAA
28105 GTTCCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (35 bp):
AGTTAAAAAGAATAAAAATGGAATTTAGTAATTAA
Found at i:28078 original size:123 final size:122
Alignment explanation
Indices: 27761--28051 Score: 304
Period size: 123 Copynumber: 2.4 Consensus size: 122
27751 GGTAATCAAT
* * * *
27761 AAGAGTAAAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATG-GTAAATC-AG--TGGTAAT
1 AAGAGTAAAAAGGTAAATCAGTAATTAAATTAAAAGAGTAAAATGAG-AAGTCAAGAAT-TTAAT
** * *
27822 CAGAAAAAAAAGTAAAATGATAATTAGTAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
64 -AG-GTAAAAAGTAAAATGATAATCAGGAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
* * * * *
27883 AAGAGTACAATGGTAAATCAGTAATTAAATTCAAAGAGTAAAATGATAAGTCAAGAATTTAATTC
1 AAGAGTAAAAAGGTAAATCAGTAATTAAATTAAAAGAGTAAAATGAGAAGTCAAGAATTTAA-TA
* *
27948 GGTAAAAAGTAAAATGGTAATCAGGAAGTGTAAAATGGTAAATCAGTAATTAAATTCA
65 GGTAAAAAGTAAAATGATAATCAGGAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
* * *
28006 AAGAGTAAGAAAAAGGT-AATCGGTAATTTAGTTAAAAAGAGTAAAA
1 AAGAGT---AAAAAGGTAAATCAGTAATTAAATT-AAAAGAGTAAAA
28052 ATGGAATTTA
Statistics
Matches: 143, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
122 48 0.34
123 59 0.41
124 4 0.03
125 15 0.10
126 17 0.12
ACGTcount: A:0.51, C:0.05, G:0.18, T:0.25
Consensus pattern (122 bp):
AAGAGTAAAAAGGTAAATCAGTAATTAAATTAAAAGAGTAAAATGAGAAGTCAAGAATTTAATAG
GTAAAAAGTAAAATGATAATCAGGAAGAGTAAAATGGTAAATCAGTAATTAAATTCA
Found at i:28214 original size:33 final size:34
Alignment explanation
Indices: 28177--28469 Score: 248
Period size: 35 Copynumber: 8.6 Consensus size: 34
28167 TAAAAAGGTG
* *
28177 AATGGTAATTAGTAAGTTAAATTCAAAGA-GT-AA
1 AATGGTAATTAGTAA-TTAAATTAAAAAAGGTAAA
* *
28210 AATGGAAAATAGTAATTAAATTAAAAAAGGTAAA
1 AATGGTAATTAGTAATTAAATTAAAAAAGGTAAA
28244 AATGGT-ATTCAGTAATTAAATTTAAAAAAGGTAAA
1 AATGGTAATT-AGTAATTAAA-TTAAAAAAGGTAAA
**
28279 AATGGT-ATTCAGTTTTTAAATTGAAAAAAAGGTAAA
1 AATGGTAATT-AGTAATTAAATT--AAAAAAGGTAAA
*
28315 AATGGT-ATTCAGTAA-TAAGTT-AAAAAGAGTAAA
1 AATGGTAATT-AGTAATTAAATTAAAAAAG-GTAAA
*
28348 AATGGTATTTAGTAATTAAATTAAAAAAAGGTAAA
1 AATGGTAATTAGTAATTAAATT-AAAAAAGGTAAA
* * *
28383 AACGGT-ATTCAGTAA-TAAGTT-AAAAAGAATAAA
1 AATGGTAATT-AGTAATTAAATTAAAAAAG-GTAAA
* * * *
28416 AATGGTATTTAGTAGTTAAAGCT-AAAAAGAGAAAA
1 AATGGTAATTAGTAATTAAA-TTAAAAAAG-GTAAA
*
28451 AATGGTATTTAGTAATTAA
1 AATGGTAATTAGTAATTAA
28470 GGTCAAACAA
Statistics
Matches: 219, Mismatches: 25, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
32 23 0.11
33 46 0.21
34 38 0.17
35 81 0.37
36 31 0.14
ACGTcount: A:0.52, C:0.02, G:0.16, T:0.29
Consensus pattern (34 bp):
AATGGTAATTAGTAATTAAATTAAAAAAGGTAAA
Found at i:28276 original size:35 final size:35
Alignment explanation
Indices: 28220--28501 Score: 284
Period size: 35 Copynumber: 8.3 Consensus size: 35
28210 AATGGAAAAT
28220 AGTAATTAAA-TTAAAAAAGGTAAAAATGGTATTC
1 AGTAATTAAAGTTAAAAAAGGTAAAAATGGTATTC
*
28254 AGTAATTAAATTTAAAAAAGGTAAAAATGGTATTC
1 AGTAATTAAAGTTAAAAAAGGTAAAAATGGTATTC
**
28289 AGTTTTTAAA-TTGAAAAAAAGGTAAAAATGGTATTC
1 AGTAATTAAAGTT--AAAAAAGGTAAAAATGGTATTC
*
28325 AGTAA-T-AAGTT-AAAAAGAGTAAAAATGGTATTT
1 AGTAATTAAAGTTAAAAAAG-GTAAAAATGGTATTC
*
28358 AGTAATTAAA-TTAAAAAAAGGTAAAAACGGTATTC
1 AGTAATTAAAGTT-AAAAAAGGTAAAAATGGTATTC
* *
28393 AGTAA-T-AAGTT-AAAAAGAATAAAAATGGTATTT
1 AGTAATTAAAGTTAAAAAAG-GTAAAAATGGTATTC
* * * *
28426 AGTAGTTAAAGCT-AAAAAGAGAAAAAATGGTATTT
1 AGTAATTAAAGTTAAAAAAG-GTAAAAATGGTATTC
* * * *
28461 AGTAATTAAGGTCAAACAA--TAAAAA-GGTAATC
1 AGTAATTAAAGTTAAAAAAGGTAAAAATGGTATTC
28493 AGTAATTAA
1 AGTAATTAA
28502 GTTTGAAAAG
Statistics
Matches: 212, Mismatches: 22, Indels: 30
0.80 0.08 0.11
Matches are distributed among these distances:
32 26 0.12
33 42 0.20
34 21 0.10
35 88 0.42
36 35 0.17
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (35 bp):
AGTAATTAAAGTTAAAAAAGGTAAAAATGGTATTC
Found at i:28347 original size:104 final size:103
Alignment explanation
Indices: 28233--28469 Score: 320
Period size: 104 Copynumber: 2.3 Consensus size: 103
28223 AATTAAATTA
* * * **
28233 AAAAAG-GTAAAAATGGTATTCAGTAATTAAATTTAAAAAAGGTAAAAATGGTATTCAGTTTTTA
1 AAAAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAACGGTATTCAG-TAATA
*
28297 AATTGAAAAA-AAGGTAAAAATGGTATTCAGTA-AT-AAGTT
65 AATT-AAAAAGAA--TAAAAATGGTATTCAGTAGATAAAGCT
28336 AAAAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAACGGTATTCAGTAATAA
1 AAAAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAACGGTATTCAGTAATAA
* * *
28401 GTTAAAAAGAATAAAAATGGTATTTAGTAGTTAAAGCT
66 ATTAAAAAGAATAAAAATGGTATTCAGTAGATAAAGCT
*
28439 AAAAAGAGAAAAAATGGTATTTAGTAATTAA
1 AAAAAGAGTAAAAATGGTATTTAGTAATTAA
28470 GGTCAAACAA
Statistics
Matches: 120, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
101 17 0.14
102 6 0.05
103 48 0.40
104 49 0.41
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (103 bp):
AAAAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAACGGTATTCAGTAATAA
ATTAAAAAGAATAAAAATGGTATTCAGTAGATAAAGCT
Found at i:28390 original size:68 final size:68
Alignment explanation
Indices: 28201--28466 Score: 333
Period size: 68 Copynumber: 3.9 Consensus size: 68
28191 AGTTAAATTC
* **
28201 AAAGAGT-AAAATGGAAAATAGTAATTAAATT-AAAAAAGGTAAAAATGGTATTCAGTAATTAAA
1 AAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAATGGTATTCAGTAA-T-AA
*
28264 TTTAA
64 GTTAA
* **
28269 AAA-AGGTAAAAATGGTATTCAGTTTTTAAATTGAAAAAAAGGTAAAAATGGTATTCAGTAATAA
1 AAAGA-GTAAAAATGGTATTTAGTAATTAAATT-AAAAAAAGGTAAAAATGGTATTCAGTAATAA
28333 GTTAA
64 GTTAA
*
28338 AAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAACGGTATTCAGTAATAAGT
1 AAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAATGGTATTCAGTAATAAGT
28403 TAA
66 TAA
* * * * * *
28406 AAAGAATAAAAATGGTATTTAGTAGTTAAAGCTAAAAAGA-GAAAAAATGGTATTTAGTAAT
1 AAAGAGTAAAAATGGTATTTAGTAATTAAA-TTAAAAAAAGGTAAAAATGGTATTCAGTAAT
28467 TAAGGTCAAA
Statistics
Matches: 174, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
67 1 0.01
68 86 0.49
69 58 0.33
70 2 0.01
71 27 0.16
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.29
Consensus pattern (68 bp):
AAAGAGTAAAAATGGTATTTAGTAATTAAATTAAAAAAAGGTAAAAATGGTATTCAGTAATAAGT
TAA
Found at i:28482 original size:68 final size:68
Alignment explanation
Indices: 28219--28501 Score: 317
Period size: 68 Copynumber: 4.1 Consensus size: 68
28209 AAATGGAAAA
**
28219 TAGTAATTAAATT-AAAAAAGGTAAAAATGGTATTCAGTAATTAAATTTAAAAAAGGTAAAAATG
1 TAGTAATTAAATTAAAAAAAGGTAAAAATGGTATTCAGTAA-TAAGGTTAAAAAA-GTAAAAATG
28283 GTATT
64 GTATT
* **
28288 CAGTTTTTAAATTGAAAAAAAGGTAAAAATGGTATTCAGTAATAA-GTTAAAAAGAGTAAAAATG
1 TAGTAATTAAATT-AAAAAAAGGTAAAAATGGTATTCAGTAATAAGGTTAAAAA-AGTAAAAATG
28352 GTATT
64 GTATT
* *
28357 TAGTAATTAAATTAAAAAAAGGTAAAAACGGTATTCAGTAATAA-GTTAAAAAGAATAAAAATGG
1 TAGTAATTAAATTAAAAAAAGGTAAAAATGGTATTCAGTAATAAGGTTAAAAA-AGTAAAAATGG
28421 TATT
65 TATT
* * * * * * *
28425 TAGTAGTTAAAGCTAAAAAGA-GAAAAAATGGTATTTAGTAATTAAGGTCAAACAA-TAAAAA-G
1 TAGTAATTAAA-TTAAAAAAAGGTAAAAATGGTATTCAGTAA-TAAGGTTAAAAAAGTAAAAATG
*
28487 GTAAT
64 GTATT
*
28492 CAGTAATTAA
1 TAGTAATTAA
28502 GTTTGAAAAG
Statistics
Matches: 188, Mismatches: 20, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
67 13 0.07
68 86 0.46
69 52 0.28
70 10 0.05
71 27 0.14
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (68 bp):
TAGTAATTAAATTAAAAAAAGGTAAAAATGGTATTCAGTAATAAGGTTAAAAAAGTAAAAATGGT
ATT
Found at i:28499 original size:32 final size:31
Alignment explanation
Indices: 28461--28530 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
28451 AATGGTATTT
*
28461 AGTAATTAAGGTCAAACAATAAAAAGGTAATC
1 AGTAATTAAGGTCAAA-AAGAAAAAGGTAATC
* **
28493 AGTAATTAAGTTTGAAAAGAAAAAGGTAATC
1 AGTAATTAAGGTCAAAAAGAAAAAGGTAATC
*
28524 AATAATT
1 AGTAATT
28531 TAGAGTAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
31 20 0.61
32 13 0.39
ACGTcount: A:0.53, C:0.06, G:0.16, T:0.26
Consensus pattern (31 bp):
AGTAATTAAGGTCAAAAAGAAAAAGGTAATC
Found at i:30853 original size:60 final size:60
Alignment explanation
Indices: 30785--30897 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
30775 CCCCCTTGGT
*
30785 GGTGGTGGTGGTTCA-TCTGATGGAGCTATGAAGGCCTTTGATGAA-GATGGAGCTTTAGGA
1 GGTGGTGGTGATTCAGT-TGATGGAGCTATGAAGGCCTTTGAT-AAGGATGGAGCTTTAGGA
* * *
30845 GGTGGTGGTGATTCAGTTGTTGGAGCTGTGAAGGCGTTTGATAAGGATGGAGC
1 GGTGGTGGTGATTCAGTTGATGGAGCTATGAAGGCCTTTGATAAGGATGGAGC
30898 ACTAGGAGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
59 2 0.04
60 44 0.94
61 1 0.02
ACGTcount: A:0.20, C:0.09, G:0.41, T:0.30
Consensus pattern (60 bp):
GGTGGTGGTGATTCAGTTGATGGAGCTATGAAGGCCTTTGATAAGGATGGAGCTTTAGGA
Found at i:31477 original size:2 final size:2
Alignment explanation
Indices: 31470--31500 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31460 ATTGTCTCCA
31470 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
31501 CTTTATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:38976 original size:13 final size:13
Alignment explanation
Indices: 38958--38983 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38948 ACTAGTTTGC
38958 AAAATTCTGAAAT
1 AAAATTCTGAAAT
38971 AAAATTCTGAAAT
1 AAAATTCTGAAAT
38984 TTATTTGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (13 bp):
AAAATTCTGAAAT
Found at i:43472 original size:13 final size:13
Alignment explanation
Indices: 43454--43487 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
43444 AGTTGCCAAA
43454 TGGTGCGAAATCT
1 TGGTGCGAAATCT
43467 TGGTGCGAAATCT
1 TGGTGCGAAATCT
43480 TGGTGCGA
1 TGGTGCGA
43488 TGCATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.35, T:0.29
Consensus pattern (13 bp):
TGGTGCGAAATCT
Found at i:49961 original size:17 final size:17
Alignment explanation
Indices: 49939--49972 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
49929 AAGTAATCAA
49939 AACCTAATTTTCTTTCT
1 AACCTAATTTTCTTTCT
49956 AACCTAATTTTCTTTCT
1 AACCTAATTTTCTTTCT
49973 CTCTTCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (17 bp):
AACCTAATTTTCTTTCT
Found at i:50831 original size:2 final size:2
Alignment explanation
Indices: 50824--50854 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
50814 AGAAAACTGA
50824 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
50855 AGGAAAAGAG
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:53029 original size:5 final size:5
Alignment explanation
Indices: 53019--53063 Score: 54
Period size: 5 Copynumber: 8.6 Consensus size: 5
53009 TATTATTATT
* *
53019 ATAAA ATAAA ATATAA TTATAT ATAAA ATAAA ATAAA ATAAA ATA
1 ATAAA ATAAA ATA-AA ATA-AA ATAAA ATAAA ATAAA ATAAA ATA
53064 TAAGACTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 27 0.77
6 8 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (5 bp):
ATAAA
Found at i:53044 original size:22 final size:21
Alignment explanation
Indices: 53013--53053 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
53003 TATTATTATT
53013 ATTATTATAAAATAAAATATA
1 ATTATTATAAAATAAAATATA
53034 ATTATATATAAAATAAAATA
1 ATTAT-TATAAAATAAAATA
53054 AAATAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
ATTATTATAAAATAAAATATA
Found at i:53064 original size:22 final size:22
Alignment explanation
Indices: 53018--53066 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
53008 TTATTATTAT
* * *
53018 TATAAAATAAAATATAATTATA
1 TATAAAATAAAATAAAATAAAA
53040 TATAAAATAAAATAAAATAAAA
1 TATAAAATAAAATAAAATAAAA
53062 TATAA
1 TATAA
53067 GACTTTGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
TATAAAATAAAATAAAATAAAA
Found at i:67050 original size:35 final size:38
Alignment explanation
Indices: 67002--67078 Score: 106
Period size: 35 Copynumber: 2.1 Consensus size: 38
66992 AGCTTTTCAT
67002 ATTGTTTTAGTTTTTACTATAAT-GT-T-ATTATTTTG
1 ATTGTTTTAGTTTTTACTATAATAGTATCATTATTTTG
* * *
67037 ATTGTTTTGGTTTTTACTTTAATATTATCATTATTTTG
1 ATTGTTTTAGTTTTTACTATAATAGTATCATTATTTTG
67075 ATTG
1 ATTG
67079 CTTAAAGATA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
35 21 0.58
36 1 0.03
37 1 0.03
38 13 0.36
ACGTcount: A:0.22, C:0.04, G:0.12, T:0.62
Consensus pattern (38 bp):
ATTGTTTTAGTTTTTACTATAATAGTATCATTATTTTG
Done.