Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022732.1 Corchorus olitorius cultivar O-4 contig22765, 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: 57364
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:5196 original size:47 final size:46
Alignment explanation
Indices: 5144--6608 Score: 644
Period size: 47 Copynumber: 30.5 Consensus size: 46
5134 AATTAGAAGA
*
5144 GTAATTAAACTGAATAGTAAAAGGAGAAGAGATTAGTTTAATTCAGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* * *
5191 GTAATTAAACTAGACAGTAAAAGGAGAAGAAATTAGTTTAATTCAGG
1 GTAATTAAACTA-ATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
*
5238 GTAATTAAACTAAATAGTAAAAGAAGAAGATG-TTAGTTTAATTCTGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGA-GATTAGTTTAATTCAGG
5285 GTAATTAAACTAAATAGTAAAA-AAGAAGAGATTAGTTTAATT-ATGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCA-GG
* ** * *
5331 GTAGTTAAACTAAGTAGTAACCGAAGAACAGATTAGTTTAATTCAAG
1 GTAATTAAACTAA-TAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* ** * * *
5378 ATAATTAAACTAAGTAGTAAAAGAAGAAGGTAAAAGGAGAAGAGATTAGTTTAATCCTGG
1 GTAATTAAACTAA-TAGT--AA-AAGAA-G---AA-GAGATTAG--T--TTAATT-CAGG
* ** * * **
5438 GTAATTAAAATAAGTAGTAAAAGAAGAAGTTAAAAGGAGAAGATATTAGTTTAATT
1 GTAATTAAACTAA-TAGTAAAAGAAGAAG-----A-GATTAG-T-TTA-ATTCAGG
* * ** * * * **
5494 CTAGGTAATTAAACTAAGTAGTAAAAGAAGAAAGTAAAAGGAGAAGAGATTAGTTTTATT
1 GTA---ATT-AAACTAA-TAGT--AA-AAG-AAG---AA-GAGATTAGTTTA-ATTCAGG
* * *
5554 CTAGGTAATTAAACTAAGTAGTTAAAGAAGAAGAGATTAGTTTAATTCTA-G
1 GTA---ATT-AAACTAA-TAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
* *
5605 GTAATTAAACTAAGTAGCAAAAGAAGAAGAGGTTAGTTTAATTCTA-G
1 GTAATTAAACTAA-TAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
* *
5652 GTAATTAAACTAAGTAGTAAATGAAGCAG-GATTAGTTTAATTCCA-G
1 GTAATTAAACTAA-TAGTAAAAGAAGAAGAGATTAGTTTAATT-CAGG
* *
5698 GTAATTAAAC-CA-AGTAAAAGGAGAAGAGATTAGTTTAATTCTA-G
1 GTAATTAAACTAATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
5742 GTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTA-G
1 GTAATTAAACTAA-TAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
* * **
5789 GTAATTAAACTAAGTAGCAAAAGGAGAAGATG-TTAGTTTAATTCTTG
1 GTAATTAAACTAA-TAGTAAAAGAAGAAGA-GATTAGTTTAATTCAGG
* *
5836 GTAATTAAACTAAATAGTAAAAGAGGAAAAGATTAGTTTAATTCTA-G
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
**
5883 GTAATTAAACTAAGTAGTAACCGAAGAAGAGATTAGTTTAATTCTA-G
1 GTAATTAAACTAA-TAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
* *
5930 GTAATTAAACTAAGAATTAAAAGAAGAAGAGATTAGTTTAATTCCA-G
1 GTAATTAAACTAA-TAGTAAAAGAAGAAGAGATTAGTTTAATT-CAGG
5977 GTAATTAAAC------T-AAAGAAG-AG-G-TTAGTTTAATTCTA-G
1 GTAATTAAACTAATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
* * * *
6013 GAAATTAAACTAAGTAGCAAATGAAGAACAAGCAATTAGTTTAA-TCATGG
1 GTAATTAAACTAA-TAGTAAAAGAAGAA-GAG--ATTAGTTTAATTCA-GG
* * * ** * *
6063 GTAATTAAATTAAAGAGGAAAAGAAGAAGTA-AACAG---AA-ACTGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAG-AGATTAGTTTAATTCAGG
* * * * **
6106 GTTAATTAAACTAAAAATTAAGAGAAGAAGAAAAGAGTTTAATTCCA-G
1 G-TAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATT-CAGG
* * * * ** * *
6154 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACATTTTAATTCTGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* * * * * * ** *
6201 GTAACTAAACTAAAAATTAAGAGAAGATGAAAAGAGTTTAATTCCGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* **
6248 GTAATTAAACTAAATAGTAAAAGAAGAAGAAAAGAGTTTAATTCTA-G
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGG
* * * * ** *
6295 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACATTTTAATT-ATGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCA-GG
* * * * **
6342 GTAACTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCAGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* * * * ** **
6389 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* * *
6436 GTAATCAAACTAA-AGACTAAAAGAAGAAGTACATAGAGGCTAGTTTAATTCTGG
1 GTAATTAAACTAATAG--TAAAAGAAGAAG-----AGA--TTAGTTTAATTCAGG
* * * ** *
6490 GTAATTAAACTAAAAAGTAAAAGAGGAAGAAAAGAGTTTAATTAAGG
1 GTAATTAAACT-AATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* * * * * ** * *
6537 GTAATTAAACAAAAGAGCAAGAGAAGAAGAAAACAGTTTGATTCTGG
1 GTAATTAAAC-TAATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
* *
6584 GTAATCAAGCTAAGTAGTAAAAGAA
1 GTAATTAAACTAA-TAGTAAAAGAA
6609 AGAGTAATCA
Statistics
Matches: 1152, Mismatches: 168, Indels: 196
0.76 0.11 0.13
Matches are distributed among these distances:
35 1 0.00
36 22 0.02
37 1 0.00
38 2 0.00
39 7 0.01
40 1 0.00
43 16 0.01
44 61 0.05
45 9 0.01
46 69 0.06
47 732 0.64
48 12 0.01
49 7 0.01
50 34 0.03
51 7 0.01
52 13 0.01
53 4 0.00
54 35 0.03
55 7 0.01
56 10 0.01
57 12 0.01
58 7 0.01
59 6 0.01
60 61 0.05
62 6 0.01
63 4 0.00
64 3 0.00
67 2 0.00
68 1 0.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (46 bp):
GTAATTAAACTAATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGG
Found at i:5225 original size:87 final size:87
Alignment explanation
Indices: 5088--5406 Score: 243
Period size: 93 Copynumber: 3.5 Consensus size: 87
5078 GTCACCAATA
* * * *
5088 GTTAGTTTAATTCAGAGCAATTAAGCTAGGAAGTAGAAGA-AAGAGTAATTAG-A-AGAGTAATT
1 GTTAGTTTAATTCAGGGTAATTAAACTA-GAAGTAAAAGAGAAGA--AATTAGTATAGAGTAATT
* *
5150 AAACTGAATAGTAAAAGGAGAAGA-
63 AAACTAAATAGTAAAAGAAGAAGAT
*
5174 GATTAGTTTAATTCAGGGTAATTAAACTAGACAGTAAAAGGAGAAGAAATTAGTTTAATTCAGGG
1 G-TTAGTTTAATTCAGGGTAATTAAACTAGA-AGTAAAA-GAGAAGAAATTAG--T-A-T-AGAG
5239 TAATTAAACTAAATAGTAAAAGAAGAAGAT
58 TAATTAAACTAAATAGTAAAAGAAGAAGAT
* * * * *
5269 GTTAGTTTAATTCTGGGTAATTAAACTAAATAGTAAAAAAGAAGAGATTAGTTTAATTATGGGTA
1 GTTAGTTTAATTCAGGGTAATTAAACTAGA-AGTAAAAGAGAAGAAATTAG--T-A-TA-GAGTA
* * ** *
5334 GTTAAACTAAGTAGTAACCGAAGAACA-
60 ATTAAACTAAATAGTAAAAGAAGAAGAT
* * *
5361 GATTAGTTTAATTCAAGATAATTAAACTAAGTAGTAAAAGAAGAAG
1 G-TTAGTTTAATTCAGGGTAATTAAACT-AGAAGTAAAAG-AGAAG
5407 GTAAAAGGAG
Statistics
Matches: 194, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
86 3 0.02
87 36 0.19
88 2 0.01
89 4 0.02
91 1 0.01
92 2 0.01
93 75 0.39
94 70 0.36
95 1 0.01
ACGTcount: A:0.47, C:0.05, G:0.21, T:0.27
Consensus pattern (87 bp):
GTTAGTTTAATTCAGGGTAATTAAACTAGAAGTAAAAGAGAAGAAATTAGTATAGAGTAATTAAA
CTAAATAGTAAAAGAAGAAGAT
Found at i:5266 original size:94 final size:93
Alignment explanation
Indices: 5144--6608 Score: 906
Period size: 94 Copynumber: 15.3 Consensus size: 93
5134 AATTAGAAGA
* * * *
5144 GTAATTAAACTGAATAGTAAAAGGAGAAGAGATTAGTTTAATTCAGGGTAATTAAACTAGACAGT
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTCA-GGTAATTAAACTAAATAGT
*
5209 AAAAGGAGAAGAAATTAGTTTAATTCAGG
65 AAAAGAAGAAGAAATTAGTTTAATTCAGG
*
5238 GTAATTAAACTAAATAGTAAAAGAAGAAGATG-TTAGTTTAATTCTGGGTAATTAAACTAAATAG
1 GTAATTAAACTAAATAGTAAAAGAAGAAGA-GATTAGTTTAATTC-AGGTAATTAAACTAAATAG
*
5302 TAAAA-AAGAAGAGATTAGTTTAATT-ATGG
64 TAAAAGAAGAAGAAATTAGTTTAATTCA-GG
* * ** * * *
5331 GTAGTTAAACTAAGTAGTAACCGAAGAACAGATTAGTTTAATTCAAGATAATTAAACTAAGTAGT
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGGTAATTAAACTAAATAGT
* *
5396 AAAAGAAGAAGGTAAAAGGAGAAGAGATTAGTTTAATCCTGG
65 --AA-AAGAA-G----A--AG-A-A-ATTAGTTTAATTCAGG
* *
5438 GTAATTAAAATAAGTAGTAAAAGAAGAAGTTAAAAGGAGAAGATATTAGTTTAATTCTAGGTAAT
1 GTAATTAAACTAAATAGT--AA-AAGAAG-----A--AG-AG--ATTAGTTTAATTC-AGGTAAT
* *
5503 TAAACTAAGTAGTAAAAGAAGAAAGTAAAAGGAGAAGAGATTAGTTTTATTCTA-G
52 TAAACTAAATAGT--AA-AAG-AAG----A--AG-A-A-ATTAGTTTAATTC-AGG
* * * *
5558 GTAATTAAACTAAGTAGTTAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGC
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGGTAATTAAACTAAATAGT
**
5623 AAAAGAAGAAGAGGTTAGTTTAATTCTA-G
65 AAAAGAAGAAGAAATTAGTTTAATTC-AGG
* * * *
5652 GTAATTAAACTAAGTAGTAAATGAAGCAG-GATTAGTTTAATTCCAGGTAATTAAAC--CA-AGT
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATT-CAGGTAATTAAACTAAATAGT
* *
5713 AAAAGGAGAAGAGATTAGTTTAATTCTA-G
65 AAAAGAAGAAGAAATTAGTTTAATTC-AGG
* * *
5742 GTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGC
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGGTAATTAAACTAAATAGT
* ** **
5807 AAAAGGAGAAGATGTTAGTTTAATTCTTG
65 AAAAGAAGAAGAAATTAGTTTAATTCAGG
* * *
5836 GTAATTAAACTAAATAGTAAAAGAGGAAAAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGT
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGGTAATTAAACTAAATAGT
** *
5901 AACCGAAGAAGAGATTAGTTTAATTCTA-G
65 AAAAGAAGAAGAAATTAGTTTAATTC-AGG
*
5930 GTAATTAAACTAAGA-ATTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACT-AA-AG
1 GTAATTAAACTAA-ATAGTAAAAGAAGAAGAGATTAGTTTAATT-CAGGTAATTAAACTAAATAG
5992 ---AAG-AG--G---TTAGTTTAATTCTA-G
64 TAAAAGAAGAAGAAATTAGTTTAATTC-AGG
* * * * * *
6013 GAAATTAAACTAAGTAGCAAATGAAGAACAAGCAATTAGTTTAA-TCATGGGTAATTAAATTAAA
1 GTAATTAAACTAAATAGTAAAAGAAGAA-GAG--ATTAGTTTAATTCA--GGTAATTAAACTAAA
* * * * *
6077 GAGGAAAAGAAGAAGTAAA-CAG---AA-ACTGG
61 TAGTAAAAGAAGAAG-AAATTAGTTTAATTCAGG
* * * * ** *
6106 GTTAATTAAACTAAAAATTAAGAGAAGAAGAAAAGAGTTTAATTCCAGGTAATTAAACTAAAGAG
1 G-TAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATT-CAGGTAATTAAACTAAATAG
* * ** * *
6171 CAAGAGAAGAAGAAAACATTTTAATTCTGG
64 TAAAAGAAGAAGAAATTAGTTTAATTCAGG
* * * * * * ** *
6201 GTAACTAAACTAAAAATTAAGAGAAGATGAAAAGAGTTTAATTCCGGGTAATTAAACTAAATAGT
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATT-CAGGTAATTAAACTAAATAGT
**
6266 AAAAGAAGAAGAAAAGAGTTTAATTCTA-G
65 AAAAGAAGAAGAAATTAGTTTAATTC-AGG
* * * * ** * * *
6295 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACATTTTAATT-ATGGGTAACTAAACTAAAAAG
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTCA--GGTAATTAAACTAAATAG
* **
6359 TAAGAGAAGAAGAAAAGAGTTTAATTCAGG
64 TAAAAGAAGAAGAAATTAGTTTAATTCAGG
* * * * ** * * * *
6389 GTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATCAAACTAAAGACT
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTC-AGGTAATTAAACTAAATAGT
* *
6454 AAAAGAAGAAGTACATAGAGGCTAGTTTAATTCTGG
65 AAAAGAAGAAG---A-A-A--TTAGTTTAATTCAGG
* * * ** * * * *
6490 GTAATTAAACTAAAAAGTAAAAGAGGAAGAAAAGAGTTTAATTAAGGGTAATTAAACAAAAGAGC
1 GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTCA-GGTAATTAAACTAAATAGT
* ** * *
6555 AAGAGAAGAAGAAAACAGTTTGATTCTGG
65 AAAAGAAGAAGAAATTAGTTTAATTCAGG
* * *
6584 GTAATCAAGCTAAGTAGTAAAAGAA
1 GTAATTAAACTAAATAGTAAAAGAA
6609 AGAGTAATCA
Statistics
Matches: 1143, Mismatches: 143, Indels: 170
0.79 0.10 0.12
Matches are distributed among these distances:
83 37 0.03
84 4 0.00
85 1 0.00
86 22 0.02
87 2 0.00
88 4 0.00
89 1 0.00
90 60 0.05
91 65 0.06
92 7 0.01
93 107 0.09
94 549 0.48
95 10 0.01
96 4 0.00
97 8 0.01
98 3 0.00
99 2 0.00
101 75 0.07
102 1 0.00
103 3 0.00
104 5 0.00
105 3 0.00
107 62 0.05
109 4 0.00
110 6 0.01
112 1 0.00
115 1 0.00
117 7 0.01
118 3 0.00
120 84 0.07
121 2 0.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (93 bp):
GTAATTAAACTAAATAGTAAAAGAAGAAGAGATTAGTTTAATTCAGGTAATTAAACTAAATAGTA
AAAGAAGAAGAAATTAGTTTAATTCAGG
Found at i:5427 original size:60 final size:60
Alignment explanation
Indices: 5355--5586 Score: 365
Period size: 60 Copynumber: 3.9 Consensus size: 60
5345 TAGTAACCGA
* * *
5355 AGAACAGATTAGTTTAATTCAAGATAATTAAACTAAGTAGTAAAAGAAGAAGGTAAAAGG
1 AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGGTAAAAGG
* * * *
5415 AGAAGAGATTAGTTTAATCCTGGGTAATTAAAATAAGTAGTAAAAGAAGAAGTTAAAAGG
1 AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGGTAAAAGG
* *
5475 AGAAGATATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAAGTAAAAGG
1 AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGGTAAAAGG
* *
5535 AGAAGAGATTAGTTTTATTCTAGGTAATTAAACTAAGTAGTTAAAGAAGAAG
1 AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAG
5587 AGATTAGTTT
Statistics
Matches: 155, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 155 1.00
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (60 bp):
AGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGGTAAAAGG
Found at i:5741 original size:184 final size:185
Alignment explanation
Indices: 5525--6057 Score: 750
Period size: 184 Copynumber: 2.9 Consensus size: 185
5515 TAAAAGAAGA
*
5525 AAGTAAAAGGAGAAGAGATTAGTTTTATTCTAGGTAATTAAACTAAGTAGTTAAAGAAGAAGAGA
1 AAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTTAAAGAAGAAGAGA
5590 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTA
66 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTA
* *
5655 ATTAAACTAAGTAGTAAATGAAG-CAGGATTAGTTTAATTCCAGGTAATTAAACC
131 ATTAAACTAAGTAGTAAATGAAGAAAAGATTAGTTTAATTCCAGGTAATTAAACC
*
5709 AAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGA
1 AAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTTAAAGAAGAAGAGA
* * *
5774 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGGAGAAGATGTTAGTTTAATTCTTGGTA
66 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTA
* * * * *
5839 ATTAAACTAAATAGTAAAAGAGGAAAAGATTAGTTTAATTCTAGGTAATTAAACT
131 ATTAAACTAAGTAGTAAATGAAGAAAAGATTAGTTTAATTCCAGGTAATTAAACC
* * *
5894 AAGTAGTAACCGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAG-AATTAAAAGAAGAA
1 AAGTA--AA-AGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTT-AAAGAAGAA
*
5958 GAGATTAGTTTAATTCCAGGTAATTAAAC----T------A-AAGAAGAGGTTAGTTTAATTCTA
62 GAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGGTTAGTTTAATTCTA
* *
6012 GGAAATTAAACTAAGTAGCAAATGAAGAACAAGCAATTAGTTTAAT
127 GGTAATTAAACTAAGTAGTAAATGAAGAA-AAG--ATTAGTTTAAT
6058 CATGGGTAAT
Statistics
Matches: 316, Mismatches: 25, Indels: 20
0.88 0.07 0.06
Matches are distributed among these distances:
177 44 0.14
178 4 0.01
180 11 0.03
184 146 0.46
185 32 0.10
187 4 0.01
188 75 0.24
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (185 bp):
AAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTTAAAGAAGAAGAGA
TTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTA
ATTAAACTAAGTAGTAAATGAAGAAAAGATTAGTTTAATTCCAGGTAATTAAACC
Found at i:5901 original size:141 final size:140
Alignment explanation
Indices: 5526--6608 Score: 808
Period size: 141 Copynumber: 7.7 Consensus size: 140
5516 AAAAGAAGAA
* * * * * *
5526 AGTAAAAGGAGAAGAGATTAGTTTTATTCTAGGTAATTAAACTAAGTAGTTAAAGAAGAAGAGAT
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAAAGAT
*
5591 TAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGGTTAGTTTAATTCTAGGTAA
66 TAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAA
5656 TTAAACTAAG
131 TTAAACTAAG
* * * * *
5666 TAGTAAATGAAGCAG-GATTAGTTTAATTCCAGGTAATTAAAC--CA-AGTAAAAGGAGAAGAGA
1 -AGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAAAGA
*
5727 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTA
65 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGATTAGTTTAATTCTAGGTA
5792 ATTAAACTAAG
130 ATTAAACTAAG
* * ** *
5803 TAGCAAAAGGAGAAGATG-TTAGTTTAATTCTTGGTAATTAAACTAAATAGTAAAAGAGGAAAAG
1 -AGTAAAAGAAGAAGA-GATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAAAG
* **
5867 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGTAACCGAAGAAGAGATTAGTTTAATTCTAGGT
64 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGATTAGTTTAATTCTAGGT
5932 AATTAAACTAAG
129 AATTAAACTAAG
*
5944 AATTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACT-AA-AG---AAG-AG----G-
1 -AGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAAAGA
* * * *
5998 TTAGTTTAATTCTAGGAAATTAAACTAAGTAGCAAATGAAGAACAAGCAATTAGTTTAA-TCATG
65 TTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAA-GAG--ATTAGTTTAATTC-TA
*
6062 GGTAATTAAATTAAAG
126 GGTAATTAAACT-AAG
* ** * ** * * *
6078 AGGAAAAGAAGAAGTA-AACAG---AA-ACTGGGTTAATTAAACTAAAAATTAAGAGAAGAAGAA
1 AGTAAAAGAAGAAG-AGATTAGTTTAATTCCAGG-TAATTAAACTAAATAGTAAAAGAAGAA-AA
** * * * ** * *
6138 -AAGAGTTTAATTCCAGGTAATTAAACTAAAG-AGCAAGAGAAGAAGAAAACATTTTAATTCTGG
63 GATTAGTTTAATTCTAGGTAATTAAACT-AAGTAGCAAAAGAAGAAGAGATTAGTTTAATTCTAG
* *
6201 GTAACTAAACTAAAA
127 GTAATTAAACT-AAG
* * * * ** *
6216 ATTAAGAGAAGATGAAAAGAGTTTAATTCCGGGTAATTAAACTAAATAGTAAAAGAAGAAGAA-A
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAA-AAGA
** * * ** * * *
6280 AGAGTTTAATTCTAGGTAATTAAACTAAAG-AGCAAGAGAAGAAGAAAACATTTTAATTATGGGT
65 TTAGTTTAATTCTAGGTAATTAAACT-AAGTAGCAAAAGAAGAAGAGATTAGTTTAATTCTAGGT
* *
6344 AACTAAACTAAAA
129 AATTAAACT-AAG
* * ** * * *
6357 AGTAAGAGAAGAAGAAAAGAGTTTAATT-CAGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAA-
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCCA-GGTAATTAAACTAAATAGTAAAAGAAGAA-AAG
** * * *
6420 AACAGTTTAATTCTTGGTAATCAAACTAA--AGACTAAAAGAAGAAGTACATAGAGGCTAGTTTA
64 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAG-C-AAAAGAAGAAG-----AGA--TTAGTTTA
* *
6483 ATTCTGGGTAATTAAACTAAAA
120 ATTCTAGGTAATTAAACT-AAG
* * ** * * * * *
6505 AGTAAAAGAGGAAGAAAAGAGTTTAATT-AAGGGTAATTAAACAAAAGAGCAAGAGAAGAAGAA-
1 AGTAAAAGAAGAAGAGATTAGTTTAATTCCA-GGTAATTAAACTAAATAGTAAAAGAAGAA-AAG
** * * * * *
6568 AACAGTTTGATTCTGGGTAATCAAGCTAAGTAGTAAAAGAA
64 ATTAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAA
6609 AGAGTAATCA
Statistics
Matches: 802, Mismatches: 96, Indels: 81
0.82 0.10 0.08
Matches are distributed among these distances:
129 3 0.00
130 51 0.06
131 5 0.01
132 3 0.00
133 37 0.05
134 4 0.00
135 3 0.00
136 5 0.01
137 101 0.13
138 59 0.07
139 7 0.01
140 34 0.04
141 362 0.45
142 7 0.01
146 2 0.00
148 117 0.15
150 2 0.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.26
Consensus pattern (140 bp):
AGTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAAATAGTAAAAGAAGAAAAGAT
TAGTTTAATTCTAGGTAATTAAACTAAGTAGCAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAA
TTAAACTAAG
Found at i:5995 original size:36 final size:36
Alignment explanation
Indices: 5953--6025 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
5943 GAATTAAAAG
*
5953 AAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTA
1 AAGAAGAGATTAGTTTAATTCCAGGAAATTAAACTA
* *
5989 AAGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTA
1 AAGAAGAGATTAGTTTAATTCCAGGAAATTAAACTA
6025 A
1 A
6026 GTAGCAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.45, C:0.07, G:0.18, T:0.30
Consensus pattern (36 bp):
AAGAAGAGATTAGTTTAATTCCAGGAAATTAAACTA
Found at i:6080 original size:83 final size:83
Alignment explanation
Indices: 5906--6078 Score: 215
Period size: 83 Copynumber: 2.0 Consensus size: 83
5896 GTAGTAACCG
* * ** *
5906 AAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGAATTAAAAGAAGAAGAGATTAGTTTAA
1 AAGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAGAAGCAAAAGAAGAAAAGATTAGTTTAA
5971 TTCCAGGTAATTAAACTA
66 TTCCAGGTAATTAAACTA
* *
5989 AAGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAGTAGCAAATGAAGAACAAGCAATTAGTT
1 AAGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAGAAGCAAAAGAAGAA-AAG--ATTAGTT
*
6054 TAA-T-CATGGGTAATTAAATTA
63 TAATTCCA--GGTAATTAAACTA
6075 AAGA
1 AAGA
6079 GGAAAAGAAG
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
83 46 0.60
84 4 0.05
85 1 0.01
86 26 0.34
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (83 bp):
AAGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAGAAGCAAAAGAAGAAAAGATTAGTTTAA
TTCCAGGTAATTAAACTA
Found at i:6089 original size:177 final size:175
Alignment explanation
Indices: 5813--6169 Score: 402
Period size: 177 Copynumber: 2.0 Consensus size: 175
5803 TAGCAAAAGG
* * * * *
5813 AGAAGATGTTAGTTTAATTCTTGGTAATTAAACTAAATAGTAAAAGAGGAAAAGATTAGTTTAAT
1 AGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAATAGCAAAAGAAGAAAAGATTAGTTTAAT
* * ** *
5878 TCTAGGTAATTAAACTAAGTAGTAAC-CGAAGAAG-AGATTAGTTTAATTCTAGG-TAATTAAAC
66 TCTAGGTAATTAAACTAAGTAGGAACAAGAAGAAGTA-AACAG---AA-ACTAGGTTAATTAAAC
* * **
5940 TAAGAATTAAAAGAAGAAGAGATTAGTTTAATTCCAGGTAATTAAACTAA
126 TAAAAATTAAAAGAAGAAGAAAAGAGTTTAATTCCAGGTAATTAAACTAA
* *
5990 AGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAGTAGCAAATGAAGAACAAGCAATTAGTTT
1 AGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAATAGCAAAAGAAGAA-AAG--ATTAGTTT
* * *
6055 AA-TCATGGGTAATTAAATTAAAG-AGGAA-AAGAAGAAGTAAACAGAAACTGGGTTAATTAAAC
63 AATTC-TAGGTAATTAAACT-AAGTAGGAACAAGAAGAAGTAAACAGAAACTAGGTTAATTAAAC
*
6117 TAAAAATTAAGAGAAGAAGAAAAGAGTTTAATTCCAGGTAATTAAACTAA
126 TAAAAATTAAAAGAAGAAGAAAAGAGTTTAATTCCAGGTAATTAAACTAA
6167 AGA
1 AGA
6170 GCAAGAGAAG
Statistics
Matches: 152, Mismatches: 20, Indels: 16
0.81 0.11 0.09
Matches are distributed among these distances:
176 4 0.03
177 103 0.68
178 3 0.02
179 2 0.01
180 36 0.24
181 4 0.03
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (175 bp):
AGAAGAGGTTAGTTTAATTCTAGGAAATTAAACTAAATAGCAAAAGAAGAAAAGATTAGTTTAAT
TCTAGGTAATTAAACTAAGTAGGAACAAGAAGAAGTAAACAGAAACTAGGTTAATTAAACTAAAA
ATTAAAAGAAGAAGAAAAGAGTTTAATTCCAGGTAATTAAACTAA
Found at i:6630 original size:22 final size:22
Alignment explanation
Indices: 6599--6728 Score: 151
Period size: 22 Copynumber: 6.1 Consensus size: 22
6589 CAAGCTAAGT
6599 AGTAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
6621 AGTAATAGAAAGAGTAATCA-A
1 AGTAAAAGAAAGAGTAATCAGA
* * *
6642 AGTAAAAGGAAGAATAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
** * *
6664 AGCCAAAGAAATAGTAATTAGA
1 AGTAAAAGAAAGAGTAATCAGA
6686 AG---AAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
*
6705 AGTAAAAGAAAGATTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
6727 AG
1 AG
6729 ATTAGAGTAA
Statistics
Matches: 90, Mismatches: 14, Indels: 8
0.80 0.12 0.07
Matches are distributed among these distances:
19 17 0.19
21 18 0.20
22 55 0.61
ACGTcount: A:0.58, C:0.05, G:0.21, T:0.15
Consensus pattern (22 bp):
AGTAAAAGAAAGAGTAATCAGA
Found at i:6647 original size:43 final size:42
Alignment explanation
Indices: 6599--6724 Score: 132
Period size: 43 Copynumber: 3.0 Consensus size: 42
6589 CAAGCTAAGT
6599 AGTAAAAGAAAGAGTAATCAGAAGTAATAGAAAGAGTAATCAA
1 AGTAAAAGAAAGAGTAATCAGAAGTAA-AGAAAGAGTAATCAA
* * * * * *
6642 AGTAAAAGGAAGAATAATCAAAAGCCAAAGAAATAGTAAT--T
1 AGTAAAAGAAAGAGTAATCAGAAG-TAAAGAAAGAGTAATCAA
*
6683 AG-AAGAAGAAAGAGTAATCAGAAGTAAAAGAAAGATTAATCA
1 AGTAA-AAGAAAGAGTAATCAGAAGT-AAAGAAAGAGTAATCA
6725 GAAGATTAGA
Statistics
Matches: 66, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
40 2 0.03
41 30 0.45
43 32 0.48
44 2 0.03
ACGTcount: A:0.59, C:0.06, G:0.20, T:0.16
Consensus pattern (42 bp):
AGTAAAAGAAAGAGTAATCAGAAGTAAAGAAAGAGTAATCAA
Found at i:6691 original size:19 final size:19
Alignment explanation
Indices: 6669--6729 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
6659 TCAAAAGCCA
* *
6669 AAGAAATAGTAATTAGAAG
1 AAGAAAGAGTAATCAGAAG
6688 AAGAAAGAGTAATCAGAAG
1 AAGAAAGAGTAATCAGAAG
*
6707 TAAAAGAAAGATTAATCAGAAG
1 ---AAGAAAGAGTAATCAGAAG
6729 A
1 A
6730 TTAGAGTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
19 18 0.50
22 18 0.50
ACGTcount: A:0.59, C:0.03, G:0.21, T:0.16
Consensus pattern (19 bp):
AAGAAAGAGTAATCAGAAG
Found at i:6713 original size:41 final size:41
Alignment explanation
Indices: 6604--6729 Score: 137
Period size: 41 Copynumber: 3.0 Consensus size: 41
6594 TAAGTAGTAA
*
6604 AAGAAAGAGTAATCAGAAGTAATAGAAAGAGTAATCA-AAG
1 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGAAG
* * * ** * *
6644 TAAAAGGAAGAATAATCAAAAGCCAAAGAAATAGTAATTAGAAG
1 ---AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGAAG
*
6688 AAGAAAGAGTAATCAGAAGTAAAAGAAAGATTAATCAGAAG
1 AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGAAG
6729 A
1 A
6730 TTAGAGTAAT
Statistics
Matches: 66, Mismatches: 16, Indels: 4
0.77 0.19 0.05
Matches are distributed among these distances:
41 34 0.52
43 29 0.44
44 3 0.05
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.15
Consensus pattern (41 bp):
AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCAGAAG
Found at i:6753 original size:47 final size:46
Alignment explanation
Indices: 6702--6795 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 46
6692 AAGAGTAATC
* *
6702 AGAAGTAAAAGAAAGATTAATCAGAAGATTAGAG-TAATTAAGCTAAA
1 AGAAGTAAAAGAAAGAGTAATCAGAAG--TAAAGTTAATTAAGCTAAA
* *
6749 AGAAGTAAAAGCAAGAGTAATCAGTAGTAAAGTTAATTAAGCTAAA
1 AGAAGTAAAAGAAAGAGTAATCAGAAGTAAAGTTAATTAAGCTAAA
6795 A
1 A
6796 ACTAAAAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
45 4 0.10
46 14 0.33
47 24 0.57
ACGTcount: A:0.54, C:0.05, G:0.19, T:0.21
Consensus pattern (46 bp):
AGAAGTAAAAGAAAGAGTAATCAGAAGTAAAGTTAATTAAGCTAAA
Found at i:7385 original size:18 final size:19
Alignment explanation
Indices: 7357--7393 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
7347 ATAGACATGA
7357 TTTTCTCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
7376 TTTT-TCTTCTAGTTTTAG
1 TTTTCTCTTCTAGTTTTAG
7394 GGTTGGGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.11, C:0.14, G:0.11, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTCTAGTTTTAG
Found at i:16425 original size:21 final size:20
Alignment explanation
Indices: 16399--16445 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
16389 AATCTATTAA
*
16399 ATATATAATTAATTATGTTTT
1 ATATATAATGAA-TATGTTTT
* *
16420 ATATATAATGCATATTTTTT
1 ATATATAATGAATATGTTTT
16440 ATATAT
1 ATATAT
16446 TAATATTCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
ATATATAATGAATATGTTTT
Found at i:16474 original size:10 final size:10
Alignment explanation
Indices: 16461--16498 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
16451 TTCTATATTA
16461 TTATATTAAT
1 TTATATTAAT
16471 TTATA-TAA-
1 TTATATTAAT
*
16479 ATATATTAAT
1 TTATATTAAT
16489 TTATATTAAT
1 TTATATTAAT
16499 AATACTCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
8 4 0.17
9 6 0.25
10 14 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTATATTAAT
Found at i:16483 original size:18 final size:18
Alignment explanation
Indices: 16462--16499 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
16452 TCTATATTAT
16462 TATATTAATTTATATAAA
1 TATATTAATTTATATAAA
*
16480 TATATTAATTTATATTAA
1 TATATTAATTTATATAAA
16498 TA
1 TA
16500 ATACTCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATATTAATTTATATAAA
Found at i:16533 original size:9 final size:10
Alignment explanation
Indices: 16509--16602 Score: 67
Period size: 9 Copynumber: 9.7 Consensus size: 10
16499 AATACTCTAT
16509 TATTATTA-A
1 TATTATTACA
*
16518 TACTATTACA
1 TATTATTACA
16528 -ATTATTACA
1 TATTATTACA
16537 TATTATTA-A
1 TATTATTACA
*
16546 TTACTATTACA
1 -TATTATTACA
16557 -ATTATTACA
1 TATTATTACA
16566 TA-TATTTA-A
1 TATTA-TTACA
*
16575 TTACTATTACA
1 -TATTATTACA
*
16586 -ATCATTACA
1 TATTATTACA
16595 TATATATT
1 TAT-TATT
16603 TAAATTTATT
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
9 34 0.51
10 26 0.39
11 7 0.10
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (10 bp):
TATTATTACA
Found at i:16550 original size:29 final size:29
Alignment explanation
Indices: 16509--16602 Score: 147
Period size: 29 Copynumber: 3.2 Consensus size: 29
16499 AATACTCTAT
16509 TATTATTAA-TACTATTACAATTATTACA
1 TATTATTAATTACTATTACAATTATTACA
16537 TATTATTAATTACTATTACAATTATTACA
1 TATTATTAATTACTATTACAATTATTACA
*
16566 TA-TATTTAATTACTATTACAATCATTACA
1 TATTA-TTAATTACTATTACAATTATTACA
16595 TATATATT
1 TAT-TATT
16603 TAAATTTATT
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
28 11 0.18
29 46 0.75
30 2 0.03
31 2 0.03
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (29 bp):
TATTATTAATTACTATTACAATTATTACA
Found at i:16630 original size:21 final size:22
Alignment explanation
Indices: 16606--16653 Score: 80
Period size: 21 Copynumber: 2.2 Consensus size: 22
16596 ATATATTTAA
16606 ATTTATTATTCCGTTTATAT-T
1 ATTTATTATTCCGTTTATATAT
*
16627 ATTTATTATTCTGTTTATATAT
1 ATTTATTATTCCGTTTATATAT
16649 ATTTA
1 ATTTA
16654 AATAATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTATTATTCCGTTTATATAT
Found at i:16905 original size:50 final size:50
Alignment explanation
Indices: 16845--16969 Score: 198
Period size: 50 Copynumber: 2.5 Consensus size: 50
16835 GACGACTTCA
* * *
16845 TATAACATAGAATTTGAAGACAGTTCGAAGGATAAGTGGAAGACGGTCCT
1 TATAAGATAGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCT
16895 TATAAGATAGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCT
1 TATAAGATAGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCT
* *
16945 T-TATGATTGAATTGGAAGACAGTTC
1 TATAAGATAGAATTGGAAGACAGTTC
16970 AATTCAGAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
49 22 0.31
50 48 0.69
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (50 bp):
TATAAGATAGAATTGGAAGACAGTTCGAAGGATAAGCGGAAGACGGTCCT
Found at i:20250 original size:6 final size:6
Alignment explanation
Indices: 20208--20242 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
20198 CAGATTATAC
* *
20208 AAAAAC AAAAAG AAAATG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
20243 AAAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.83, C:0.03, G:0.11, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:34754 original size:2 final size:2
Alignment explanation
Indices: 34749--34775 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
34739 CCGGTGTGTG
34749 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
34776 GTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35997 original size:32 final size:32
Alignment explanation
Indices: 35931--36012 Score: 105
Period size: 32 Copynumber: 2.6 Consensus size: 32
35921 ATTTTACTAA
** *
35931 TTTCCAAAATCTCCTTTT--GAATTTCCTTAT
1 TTTCCAAAATCTCCTTTTGGGAATAACCTTAC
*
35961 TTTCCAAAATCTCCTTTTGGGGATAACCTTAC
1 TTTCCAAAATCTCCTTTTGGGAATAACCTTAC
*
35993 TTTCCAAAATCTTCTTTTGG
1 TTTCCAAAATCTCCTTTTGG
36013 AAATGCTTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
30 18 0.40
32 27 0.60
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.45
Consensus pattern (32 bp):
TTTCCAAAATCTCCTTTTGGGAATAACCTTAC
Found at i:36500 original size:10 final size:10
Alignment explanation
Indices: 36485--36510 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
36475 TACAAACCAA
36485 GGCCAAACCG
1 GGCCAAACCG
36495 GGCCAAACCG
1 GGCCAAACCG
36505 GGCCAA
1 GGCCAA
36511 TTAACAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.38, G:0.31, T:0.00
Consensus pattern (10 bp):
GGCCAAACCG
Found at i:40431 original size:27 final size:28
Alignment explanation
Indices: 40377--40498 Score: 183
Period size: 28 Copynumber: 4.4 Consensus size: 28
40367 AGTAGACTTT
* * *
40377 AAATGACCAAAACGCCCCTGAACATGCA
1 AAATGACCAAAATGCCCCTGGACTTGCA
*
40405 AAATGACCAAAATG-GCCTGGACTTGCA
1 AAATGACCAAAATGCCCCTGGACTTGCA
*
40432 AAATGACCAAAATGCCCCTGGGCTTGCA
1 AAATGACCAAAATGCCCCTGGACTTGCA
*
40460 AAATGACCAAAATGCCCCTGGGCTTGCA
1 AAATGACCAAAATGCCCCTGGACTTGCA
40488 AAATGACCAAA
1 AAATGACCAAA
40499 GTAAGGAGTA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
27 24 0.28
28 63 0.72
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.16
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACTTGCA
Found at i:40438 original size:55 final size:56
Alignment explanation
Indices: 40377--40498 Score: 183
Period size: 55 Copynumber: 2.2 Consensus size: 56
40367 AGTAGACTTT
*
40377 AAATGACCAAAACGCCCCTGAACATGCAAAATGACCAAAATG-GCCTGGACTTGCA
1 AAATGACCAAAACGCCCCTGAACATGCAAAATGACCAAAATGCCCCTGGACTTGCA
* ** * *
40432 AAATGACCAAAATGCCCCTGGGCTTGCAAAATGACCAAAATGCCCCTGGGCTTGCA
1 AAATGACCAAAACGCCCCTGAACATGCAAAATGACCAAAATGCCCCTGGACTTGCA
40488 AAATGACCAAA
1 AAATGACCAAA
40499 GTAAGGAGTA
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
55 38 0.63
56 22 0.37
ACGTcount: A:0.39, C:0.27, G:0.19, T:0.16
Consensus pattern (56 bp):
AAATGACCAAAACGCCCCTGAACATGCAAAATGACCAAAATGCCCCTGGACTTGCA
Found at i:49310 original size:51 final size:51
Alignment explanation
Indices: 49206--49478 Score: 451
Period size: 51 Copynumber: 5.4 Consensus size: 51
49196 AATCAACTTA
* * *
49206 TTTGAACTGTCTTTCAATTCAATCTT-AAAAGGACCGTCTTCCGTTTATCC
1 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCC
* *
49256 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTCTAC
1 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCC
*
49307 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCACTTATCC
1 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCC
49358 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCC
*
49409 TTTGAACTGTCTTCCAATTCAATCTT-AAAAGGACCGTCTTCCGCTTATCC
1 TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCC
* *
49459 TCTGAACTGTCTTCCAATTC
1 TTTGAACTATCTTCCAATTC
49479 TTAAAAATCA
Statistics
Matches: 211, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 67 0.32
51 144 0.68
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (51 bp):
TTTGAACTATCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATCC
Found at i:49779 original size:65 final size:64
Alignment explanation
Indices: 49706--50012 Score: 294
Period size: 65 Copynumber: 4.6 Consensus size: 64
49696 CCGATGCATC
* * * *
49706 TCTTAACAAGATCGTCTTCCAATCAACTTCTGAAACCTTTTTGAGAAACTATCTTCTGGTGTACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTGTTGAGAAACCATCTTCTGGTGTACT
* * *
49771 TTTTAACAAGATCGTCTTCCGATCAACTTTTGAAAACTCCTGAAAAACTCTTGAGAAACCATTTT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAA-T--TG--------TTGAGAAACCATCTT
*
49836 CTCGTGTACT
55 CTGGTGTACT
* * * * *
49846 TCTTGACAAGATTGTCTTCTGATCATCTTCTGAAAATTGTTGAGAAACCATCTTTTGGTGTACT
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
* * *
49910 TCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTGTTGAGAAAACCATCTTCTGGAGTAAC
1 TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAG-AAACCATCTTCTGGTGT-AC
49975 T
64 T
* * *
49976 T-TTAACAAAATTGTCTTCCAATCAACATT-TGAAAATT
1 TCTTAACAAGATCGTCTTCCGATCAAC-TTCTGAAAATT
50013 CTTTCTAACA
Statistics
Matches: 202, Mismatches: 26, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
64 64 0.32
65 76 0.38
66 6 0.03
67 1 0.00
72 2 0.01
74 1 0.00
75 52 0.26
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (64 bp):
TCTTAACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACT
Found at i:49912 original size:64 final size:64
Alignment explanation
Indices: 49821--50012 Score: 246
Period size: 64 Copynumber: 3.0 Consensus size: 64
49811 TGAAAAACTC
* *
49821 TTGAGAAACCAT-TTTCTCGTGTACTTCTTGACAAGATTGTCTTCTGATCATCTTCTGAAAATTG
1 TTGAGAAACCATCTTT-TGGTGTACTTCTTGACAAGATTGTCTTCCGATCATCTTCTGAAAATTG
*
49885 TTGAGAAACCATCTTTTGGTGTACTTCTTGACAAGATCGTCTTCCGATCATCTTCTGAAAATTG
1 TTGAGAAACCATCTTTTGGTGTACTTCTTGACAAGATTGTCTTCCGATCATCTTCTGAAAATTG
* * * * * *
49949 TTGAGAAAACCATCTTCTGGAGTAACTT-TTAACAAAATTGTCTTCCAATCAACATT-TGAAAAT
1 TTGAG-AAACCATCTTTTGGTGT-ACTTCTTGACAAGATTGTCTTCCGATCATC-TTCTGAAAAT
50012 T
63 T
50013 CTTTCTAACA
Statistics
Matches: 114, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
64 62 0.54
65 46 0.40
66 6 0.05
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (64 bp):
TTGAGAAACCATCTTTTGGTGTACTTCTTGACAAGATTGTCTTCCGATCATCTTCTGAAAATTG
Found at i:51857 original size:12 final size:12
Alignment explanation
Indices: 51840--51864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51830 TTTGATTCAC
51840 TTTTGATTTGAA
1 TTTTGATTTGAA
51852 TTTTGATTTGAA
1 TTTTGATTTGAA
51864 T
1 T
51865 CACTTGATGA
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:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (12 bp):
TTTTGATTTGAA
Found at i:52177 original size:14 final size:13
Alignment explanation
Indices: 52151--52211 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 13
52141 TAAAAGACTC
52151 AAAACCTTTTTTG
1 AAAACCTTTTTTG
52164 AAAACCTATTTTTG
1 AAAACCT-TTTTTG
52178 AAAACCTTTTTCTTG
1 AAAACC-TTTT-TTG
*
52193 AAAACAATTTTCTTG
1 AAAAC-CTTTT-TTG
52208 AAAA
1 AAAA
52212 ACATGTCTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
13 7 0.16
14 15 0.35
15 21 0.49
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.41
Consensus pattern (13 bp):
AAAACCTTTTTTG
Found at i:52193 original size:15 final size:14
Alignment explanation
Indices: 52151--52211 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
52141 TAAAAGACTC
52151 AAAACC-TTTTTTG
1 AAAACCTTTTTTTG
*
52164 AAAACCTATTTTTG
1 AAAACCTTTTTTTG
52178 AAAACCTTTTTCTTG
1 AAAACCTTTTT-TTG
* *
52193 AAAACAATTTTCTTG
1 AAAAC-CTTTTTTTG
52208 AAAA
1 AAAA
52212 ACATGTCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.15
14 16 0.39
15 15 0.37
16 4 0.10
ACGTcount: A:0.38, C:0.15, G:0.07, T:0.41
Consensus pattern (14 bp):
AAAACCTTTTTTTG
Found at i:53424 original size:42 final size:42
Alignment explanation
Indices: 53341--53428 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
53331 CGACCTATGC
* * * * **
53341 ATGAACATATATACGAAGGAATGGATACTGCCTGATGGATGT
1 ATGAACATATATACGAAAGAATGGACAATGCATGAAAGATGT
53383 ATGAACATATATAC-AAAGACATGGACAATGCATGAAAGATGT
1 ATGAACATATATACGAAAGA-ATGGACAATGCATGAAAGATGT
53425 ATGA
1 ATGA
53429 CCTATATCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 4 0.10
42 35 0.90
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (42 bp):
ATGAACATATATACGAAAGAATGGACAATGCATGAAAGATGT
Done.