Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009584.1 Corchorus olitorius cultivar O-4 contig09616, 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: 8766
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Found at i:941 original size:22 final size:22
Alignment explanation
Indices: 913--982 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
903 ATTAAGCTAG
* *
913 GAAGTAGAAGAAAGGGTAATCA
1 GAAGTAGAAGAAAGAGTAATTA
* * *
935 GAAGTAGAAGGAAGAATAATTG
1 GAAGTAGAAGAAAGAGTAATTA
*
957 GAAGTAAAAGAAAGAGTAATTA
1 GAAGTAGAAGAAAGAGTAATTA
979 GAAG
1 GAAG
983 AGTAATTAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.53, C:0.01, G:0.30, T:0.16
Consensus pattern (22 bp):
GAAGTAGAAGAAAGAGTAATTA
Found at i:1185 original size:75 final size:76
Alignment explanation
Indices: 1060--1201 Score: 189
Period size: 75 Copynumber: 1.9 Consensus size: 76
1050 GAGTAGAAGA
* *** * *
1060 AGAAGTAAAGCAGAAGTTAGTTTAATTTTGGGCAATTAAACTAAAGAGTAAAAGAGGAAGAGTTT
1 AGAAGTAAAGCAGAAGGTAGTTTAATTCCAGGCAATTAAACTAAAGAGTAAAAGAAGAAGAGATT
1125 AGAGAAAAGTG
66 AGAGAAAAGTG
* *
1136 AGAAGTAAA-CAGAGGGTAGTTTAATTCCAGGTAATTAAACT-AAGTAGTAAAAGAAGAAGAGAT
1 AGAAGTAAAGCAGAAGGTAGTTTAATTCCAGGCAATTAAACTAAAG-AGTAAAAGAAGAAGAGAT
1199 TAG
65 TAG
1202 TTTAATTCCA
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
74 3 0.05
75 45 0.79
76 9 0.16
ACGTcount: A:0.46, C:0.05, G:0.25, T:0.23
Consensus pattern (76 bp):
AGAAGTAAAGCAGAAGGTAGTTTAATTCCAGGCAATTAAACTAAAGAGTAAAAGAAGAAGAGATT
AGAGAAAAGTG
Found at i:1209 original size:47 final size:46
Alignment explanation
Indices: 1152--2313 Score: 821
Period size: 47 Copynumber: 24.8 Consensus size: 46
1142 AAACAGAGGG
** * *
1152 TAGTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAAAA
*** * * *
1199 TAGTTTAATTCCAAGTAATTGAACT-A-AGTAAAAGAAGAAGAGAT
1 TAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAGAAGAAGAAAA
* *
1243 TAGTTTAATTCTAGGTAATTAAAC------T--AAGAA-AAG--AT
1 TAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAGAAGAAGAAAA
* * * * * *
1278 TCGTTTAATTCTAGGTGATTAAACT-A-AGTAAAAGGAGAAGAGAT
1 TAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAGAAGAAGAAAA
* * * * * *
1322 TAGTTTAATTCTAGGTGATTAAACT--TAGTAAAAGGAGAAGAGAT
1 TAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAGAAGAAGAAAA
* * * * * *
1366 TAGTTTAATTCTAGGTGATTAAACTAAGTAGTAGAAGAAGAGGAGAT
1 TAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAAGAAGAAAA
* * * * ***
1413 TAGTTTAACTCTAGGTAATTAAATCAAATAGTAAAAGAAGAAGAGGT
1 TAGTTTAATTCTGGGTAATTAAA-CTAAGAGTAAAAGAAGAAGAAAA
* *
1460 TAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * *
1507 CAGTTTAATTCTTGGTAATTAAACCAAAGAGTAAAGGAAGAAGTAAACAGA
1 TAGTTTAATTCTGGGTAATTAAA-CTAAGAGTAAAAGAAGAAG--AA-A-A
1558 GGCTAGTTTAATTCTGGGTAATTAAACT---A--AAAAGTAAGAAGAAAA
1 ---TAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAG-AAGAAGAAAA
* * * * *
1603 GAGTTTAATTCTGGGCAATTAAACTAAAAAGTAAGAGAAGAAGGAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * *
1650 GAGTTTAATTCTGGGTAATTAAACTAAAAATTAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * *
1697 TAGTTAAATTCGGGGTAATTAAACTAAAAATTAAAAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * *
1744 TAGTTTAATTCGGGGTAATTAAACTAAAAATTAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * * *
1791 TAGTTTAATTCAGAGTAATTAAATTAAAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * *
1838 CAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * *
1885 CAGTTTAATTCTGGGTAATTAAACTATAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACTA-AGAGTAAAAGAAGAAGAAAA
* * *
1932 CAGTTTTAAACAATTATGGGTAATTAAACTAAAGAGTAAAGGAAGAAGTAAACAGAGA
1 TAG-TTT----AATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAG---A-A-A-A
*
1990 CTAGTTTAATTCCGGGTAATTAAACT---A--AAAAGTAAGAAGAAAA
1 -TAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAG-AAGAAGAAAA
* * * * *
2033 GAGTTTAATTCTAGGTAATTAAACTAAAGGGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * *
2080 CAATTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * *
2127 CAATTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTACACAGTGGC
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAG-A-A-A----A
* * * *
2181 TAGCTTAATTCTGGGTAATTAAACTAAAAAGTGAAAGAAGAAGAATA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * *
2228 GAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACT-AAGAGTAAAAGAAGAAGAAAA
* * * *
2275 CAGTTTGATTCTGGGTAATCAAGCTAAGAAGTAAAAGAA
1 TAGTTTAATTCTGGGTAATTAAACTAAG-AGTAAAAGAA
2314 AGAGTAATCA
Statistics
Matches: 952, Mismatches: 104, Indels: 118
0.81 0.09 0.10
Matches are distributed among these distances:
35 24 0.03
37 3 0.00
38 5 0.01
39 1 0.00
40 1 0.00
41 4 0.00
42 48 0.05
43 1 0.00
44 109 0.11
45 2 0.00
46 9 0.01
47 582 0.61
48 24 0.03
49 15 0.02
50 4 0.00
51 1 0.00
52 32 0.03
53 3 0.00
54 75 0.08
55 1 0.00
56 1 0.00
57 1 0.00
58 4 0.00
59 2 0.00
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (46 bp):
TAGTTTAATTCTGGGTAATTAAACTAAGAGTAAAAGAAGAAGAAAA
Found at i:1272 original size:35 final size:35
Alignment explanation
Indices: 1233--1311 Score: 122
Period size: 35 Copynumber: 2.2 Consensus size: 35
1223 TAAGTAAAAG
*
1233 AAGAAGAGATTAGTTTAATTCTAGGTAATTAAACT
1 AAGAAAAGATTAGTTTAATTCTAGGTAATTAAACT
* *
1268 AAGAAAAGATTCGTTTAATTCTAGGTGATTAAACT
1 AAGAAAAGATTAGTTTAATTCTAGGTAATTAAACT
1303 AAGTAAAAG
1 AAG-AAAAG
1312 GAGAAGAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
35 35 0.88
36 5 0.12
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (35 bp):
AAGAAAAGATTAGTTTAATTCTAGGTAATTAAACT
Found at i:1284 original size:79 final size:81
Alignment explanation
Indices: 1189--1530 Score: 303
Period size: 79 Copynumber: 4.0 Consensus size: 81
1179 GTAGTAAAAG
* * * * *
1189 AAGAAGAGATTAGTTTAATTCCAAGTAATTGAACTAAGTAAAAGAAGAAGAGATTAGTTTAATTC
1 AAGAAAAGATTAGTTTAATTCTAGGTGATTAAACTAAGTAAAAGAAGAAGAGATTAGTTTAATTC
1254 TAGGTAATTAAAC-T-
66 TAGGTAATTAAACTTA
* *
1268 AAGAAAAGATTCGTTTAATTCTAGGTGATTAAACTAAGTAAAAGGAGAAGAGATTAGTTTAATTC
1 AAGAAAAGATTAGTTTAATTCTAGGTGATTAAACTAAGTAAAAGAAGAAGAGATTAGTTTAATTC
*
1333 TAGGTGATTAAACTTAGTAA
66 TAGGTAATTAAAC-T--T-A
*
1353 AAGGAGAAGAGATTAGTTTAATTCTAGGTGATTAAACTAAGTAGTAGAAGAAGAGGAGATTAGTT
1 AA-GA-AA-AGATTAGTTTAATTCTAGGTGATTAAACTAAGTA--A-AAGAAGAAGAGATTAGTT
*
1418 TAACTCTAGGTAATTAAATCAAATAGTAA
60 TAATTCTAGGTAATTAAA-C---T--T-A
* * * **
1447 AAGAAGAAGAGGTTAGTTTAATTCTGGGTAATTAAACTAAAG-AGCAAGAGAAGAAGAAAACAGT
1 AAGAA-AAGA--TTAGTTTAATTCTAGGTGATTAAACT-AAGTA--AA-AGAAGAAGAGATTAGT
*
1511 TTAATTCTTGGTAATTAAAC
59 TTAATTCTAGGTAATTAAAC
1531 CAAAGAGTAA
Statistics
Matches: 220, Mismatches: 23, Indels: 26
0.82 0.09 0.10
Matches are distributed among these distances:
79 70 0.32
83 1 0.00
85 2 0.01
86 2 0.01
87 2 0.01
88 33 0.15
90 1 0.00
91 32 0.15
92 5 0.02
93 5 0.02
94 64 0.29
95 3 0.01
ACGTcount: A:0.44, C:0.06, G:0.20, T:0.29
Consensus pattern (81 bp):
AAGAAAAGATTAGTTTAATTCTAGGTGATTAAACTAAGTAAAAGAAGAAGAGATTAGTTTAATTC
TAGGTAATTAAACTTA
Found at i:1332 original size:123 final size:125
Alignment explanation
Indices: 1154--1393 Score: 367
Period size: 123 Copynumber: 1.9 Consensus size: 125
1144 ACAGAGGGTA
1154 GTTTAATTCCAGGTAATTAAACTAAGTAGTAAAAGAAGAAGAGATTAGTTTAATTCCAAGTAATT
1 GTTTAATTCCAGGTAATTAAACTAAG-AGTAAAAGAAGAAGAGATTAGTTTAATTCCAAGTAATT
*
1219 GAACTAAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGAAAAGATTC
65 AAACTAAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGAAAAGATTC
* * * * * *
1280 GTTTAATTCTAGGTGATTAAACT-A-AGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTGATTA
1 GTTTAATTCCAGGTAATTAAACTAAGAGTAAAAGAAGAAGAGATTAGTTTAATTCCAAGTAATTA
* * *
1343 AACTTAGTAAAAGGAGAAGAGATTAGTTTAATTCTAGGTGATTAAACTAAG
66 AACTAAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAG
1394 TAGTAGAAGA
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
123 82 0.79
125 1 0.01
126 21 0.20
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (125 bp):
GTTTAATTCCAGGTAATTAAACTAAGAGTAAAAGAAGAAGAGATTAGTTTAATTCCAAGTAATTA
AACTAAGTAAAAGAAGAAGAGATTAGTTTAATTCTAGGTAATTAAACTAAGAAAAGATTC
Found at i:2058 original size:195 final size:192
Alignment explanation
Indices: 1408--2293 Score: 983
Period size: 190 Copynumber: 4.6 Consensus size: 192
1398 AGAAGAAGAG
* * * * *
1408 GAGATTAGTTTAACTCTAGGTAATTAAA-TCAAATAGTAAAAGAAGAAG-AGGTTAGTTTAATTC
1 GAGACTAGTTTAATTCTGGGTAATTAAACT-AAAAAGT-AAAGAAGAAGAAAG--AGTTTAATTC
* *
1471 TGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACCAAAG
62 TGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAG
* *
1536 AGTAA-AGGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGT----AAG
127 AGCAAGA-GAAGAAG--AA-A-A--C-AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAGAAG
1596 AAG--AA-A
184 AAGTAAACA
*
1602 -AG---AGTTTAATTCTGGGCAATTAAACTAAAAAGTAAGAGAAGAAGGAAAGAGTTTAATTCTG
1 GAGACTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAA-AGAAGAA-GAAAGAGTTTAATTCTG
* ** * * * * *
1663 GGTAATTAAACTAAAAATTAAGAGAAGAAGAAAATAGTTAAATTCGGGGTAATTAAACTAAAAAT
64 GGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAG
* * * * * *
1728 TAAAAGAAGAAGAAAATAGTTTAATTCGGGGTAATTAAACTAAA-AATTAAG-AGAAG-AAGA-A
129 CAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAGAAGAAGTAA-ACA
* * * * * *
1789 -A-A-TAGTTTAATTCAGAGTAATTAAATTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTG
1 GAGACTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAA-AGAAGAAG-AAAGAGTTTAATTCTG
*
1851 GGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTATAGAG
64 GGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAG
*
1916 CAAGAGAAGAAGAAAACAGTTTTAAACAATTATGGGTAATTAAACTAAAGAGTAAAGGAAGAAGT
129 CAAGAGAAGAAGAAAACAG-TTT----AATTCTGGGTAATTAAACTAAAGAGTAAA-GAAGAAGT
1981 AAACA
188 AAACA
* *
1986 GAGACTAGTTTAATTCCGGGTAATTAAACTAAAAAGT-AAGAAG-A-AAAGAGTTTAATTCTAGG
1 GAGACTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAGAAGAAGAAAGAGTTTAATTCTGGG
* *
2048 TAATTAAACTAAAGGGCAAGAGAAGAAGAAAACAATTTAATTCTGGGTAATTAAACTAAAGAGCA
66 TAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCA
* * *
2113 AGAGAAGAAGAAAACAATTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTACACA
131 AGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGT-AAAGAAGAAGTAAACA
* * *
2176 GTGGCTAGCTTAATTCTGGGTAATTAAACTAAAAAGTGAAAGAAGAAGAATAGAGTTTAATTCTG
1 GAGACTAGTTTAATTCTGGGTAATTAAACTAAAAAGT-AAAGAAGAAGAA-AGAGTTTAATTCTG
*
2241 GGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTGATTCTGGGTAAT
64 GGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAAT
2294 CAAGCTAAGA
Statistics
Matches: 596, Mismatches: 63, Indels: 65
0.82 0.09 0.09
Matches are distributed among these distances:
182 2 0.00
183 26 0.04
185 5 0.01
186 2 0.00
187 5 0.01
188 124 0.21
189 5 0.01
190 178 0.30
191 6 0.01
192 8 0.01
193 23 0.04
194 9 0.02
195 158 0.27
196 6 0.01
197 4 0.01
198 6 0.01
199 2 0.00
200 27 0.05
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (192 bp):
GAGACTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAGAAGAAGAAAGAGTTTAATTCTGGG
TAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCA
AGAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAGAAGAAGTAAACA
Found at i:2060 original size:430 final size:429
Alignment explanation
Indices: 1461--2293 Score: 1244
Period size: 430 Copynumber: 1.9 Consensus size: 429
1451 AGAAGAGGTT
* *
1461 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTATGGGTAAT
* *
1526 TAAACCAAAGAGTAAAGGAAGAAGTAAACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAA
66 TAAACCAAAGAGTAAAGGAAGAAGTAAACAGAGACTAGTTTAATTCCGGGTAATTAAACTAAAAA
* * * * *
1591 GTAAGAAGAAAAGAGTTTAATTCTGGGCAATTAAACTAAAAAGTAAGAGAAGAAGGAAAGAGTTT
131 GTAAGAAGAAAAGAGTTTAATTCTAGGCAATTAAACTAAAAAGCAAGAGAAGAAGAAAACAATTT
** * *
1656 AATTCTGGGTAATTAAACTAAAAATTAAGAGAAGAAGAAAATAGTTAAATTCGGGGTAATTAAAC
196 AATTCTGGGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAACAATTAAATTCGGGGTAATTAAAC
* * *
1721 TAAAAATTAAAAGAAGAAG-A-A-A-ATAGTTTAATTCGGGGTAATTAAACTAAAAA-TTAAGAG
261 TAAAAAGTAAAAGAAGAAGTACACAGATAGCTTAATTCGGGGTAATTAAACTAAAAAGTGAA-AG
* *
1781 AAGAAGAAAATAGTTTAATTCAGAGTAATTAAATTAAAGAGCAAGAGAAGAAGAAAACAGTTTAA
325 AAGAAGAAAAGAGTTTAATTCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAA
1846 TTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
390 TTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
*
1886 AGTTTAATTCTGGGTAATTAAACTATAGAGCAAGAGAAGAAGAAAACAGTTTTAAACAATTATGG
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAG-TTT----AATTATGG
*
1951 GTAATTAAACTAAAGAGTAAAGGAAGAAGTAAACAGAGACTAGTTTAATTCCGGGTAATTAAACT
61 GTAATTAAACCAAAGAGTAAAGGAAGAAGTAAACAGAGACTAGTTTAATTCCGGGTAATTAAACT
* **
2016 AAAAAGTAAGAAGAAAAGAGTTTAATTCTAGGTAATTAAACTAAAGGGCAAGAGAAGAAGAAAAC
126 AAAAAGTAAGAAGAAAAGAGTTTAATTCTAGGCAATTAAACTAAAAAGCAAGAGAAGAAGAAAAC
* * **
2081 AATTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTTGGTAAT
191 AATTTAATTCTGGGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAACAATTAAATTCGGGGTAAT
* * *
2146 TAAACTAAAGAGTAAAAGAAGAAGTACACAGTGGCTAGCTTAATTCTGGGTAATTAAACTAAAAA
256 TAAACTAAAAAGTAAAAGAAGAAGTACACA---GATAGCTTAATTCGGGGTAATTAAACTAAAAA
* * *
2211 GTGAAAGAAGAAGAATAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
318 GTGAAAGAAGAAGAAAAGAGTTTAATTCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
*
2276 AGTTTGATTCTGGGTAAT
383 AGTTTAATTCTGGGTAAT
2294 CAAGCTAAGA
Statistics
Matches: 361, Mismatches: 34, Indels: 14
0.88 0.08 0.03
Matches are distributed among these distances:
425 48 0.13
426 3 0.01
430 204 0.57
431 1 0.00
432 1 0.00
433 1 0.00
437 100 0.28
438 3 0.01
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (429 bp):
AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTATGGGTAAT
TAAACCAAAGAGTAAAGGAAGAAGTAAACAGAGACTAGTTTAATTCCGGGTAATTAAACTAAAAA
GTAAGAAGAAAAGAGTTTAATTCTAGGCAATTAAACTAAAAAGCAAGAGAAGAAGAAAACAATTT
AATTCTGGGTAATTAAACTAAAAAGCAAGAGAAGAAGAAAACAATTAAATTCGGGGTAATTAAAC
TAAAAAGTAAAAGAAGAAGTACACAGATAGCTTAATTCGGGGTAATTAAACTAAAAAGTGAAAGA
AGAAGAAAAGAGTTTAATTCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAAT
TCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
Found at i:2332 original size:22 final size:22
Alignment explanation
Indices: 2301--2458 Score: 192
Period size: 22 Copynumber: 7.2 Consensus size: 22
2291 AATCAAGCTA
2301 AGAAGTAAAAGAAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* *
2323 AGGAGTAAAAGGAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* ** *
2345 AAAAACAGAAGAAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* *
2367 AG-AGTAAGAGGAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* *
2388 AAAAGCAAAAGAAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
* * *
2410 AGAAGCATAAGAAAGAGTGATC
1 AGAAGTAAAAGAAAGAGTAATC
2432 AGAAGTAAAAGAAAGAGTAATC
1 AGAAGTAAAAGAAAGAGTAATC
2454 AGAAG
1 AGAAG
2459 ATTAGAGTGA
Statistics
Matches: 111, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
21 15 0.14
22 96 0.86
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.12
Consensus pattern (22 bp):
AGAAGTAAAAGAAAGAGTAATC
Found at i:2384 original size:65 final size:66
Alignment explanation
Indices: 2301--2458 Score: 219
Period size: 65 Copynumber: 2.4 Consensus size: 66
2291 AATCAAGCTA
* * *
2301 AGAAGTAAAAGAAAGAGTAATCAGGAGTAAAAGGAAGAGTAATCAAAAACAGAAGAAAGAGTAAT
1 AGAAGTAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAAAAACAGAAGAAAGAGTAAT
2366 C
66 C
* * * * * * *
2367 AG-AGTAAGAGGAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAGAAGCATAAGAAAGAGTGAT
1 AGAAGTAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAAAAACAGAAGAAAGAGTAAT
2431 C
66 C
2432 AGAAGTAAAAGAAAGAGTAATCAGAAG
1 AGAAGTAAAAGAAAGAGTAATCAGAAG
2459 ATTAGAGTGA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
65 55 0.71
66 23 0.29
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.12
Consensus pattern (66 bp):
AGAAGTAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAAAAACAGAAGAAAGAGTAAT
C
Found at i:6199 original size:13 final size:14
Alignment explanation
Indices: 6173--6203 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
6163 AACCAATCCA
6173 AAAAAGAAATAAAG
1 AAAAAGAAATAAAG
6187 AAAAAGAAA-AAAG
1 AAAAAGAAATAAAG
6200 AAAA
1 AAAA
6204 GATAGAGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAGAAATAAAG
Found at i:7421 original size:41 final size:41
Alignment explanation
Indices: 7365--7609 Score: 248
Period size: 41 Copynumber: 6.0 Consensus size: 41
7355 TCCGGGTAAC
* * * *
7365 ATTT-CAGCAGCCCCGAACAGGCTTTTCAGTAGTCGAGTAG
1 ATTTCCAGTAGCCCCGAGCAGGCTTTTCAGTATTCAAGTAG
* * *
7405 ATTTCCAGTAACCCCGAGCAGACTTTTCAGTACTCAAGTAG
1 ATTTCCAGTAGCCCCGAGCAGGCTTTTCAGTATTCAAGTAG
*
7446 ATTTCCAGTAGCCCCGAGCGGGCTTTTCAGTATTCAAGTAG
1 ATTTCCAGTAGCCCCGAGCAGGCTTTTCAGTATTCAAGTAG
* *
7487 ATTTCCAGTAGCCCCGAGCAGGCCTTTCCGTATTCAAGTAG
1 ATTTCCAGTAGCCCCGAGCAGGCTTTTCAGTATTCAAGTAG
* * * * *
7528 AGTTCCAG-CGCCCCAAGCAGGCATCTTTTA-TATTTAAGTAG
1 ATTTCCAGTAGCCCCGAGCAGGC-T-TTTCAGTATTCAAGTAG
* ** * *
7569 ATTT-CAGCAGCCTTGAGCAGGCCTTTT-AGCATTTAAGTAG
1 ATTTCCAGTAGCCCCGAGCAGG-CTTTTCAGTATTCAAGTAG
7609 A
1 A
7610 GCTTCGGCGC
Statistics
Matches: 173, Mismatches: 26, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 33 0.19
41 135 0.78
42 4 0.02
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.28
Consensus pattern (41 bp):
ATTTCCAGTAGCCCCGAGCAGGCTTTTCAGTATTCAAGTAG
Done.