Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024261.1 Corchorus olitorius cultivar O-4 contig24294, 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: 26830
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:611 original size:15 final size:15
Alignment explanation
Indices: 591--620 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
581 ATCAGGCTGC
*
591 CACGATACACGATAT
1 CACGATACACAATAT
606 CACGATACACAATAT
1 CACGATACACAATAT
621 TTCAACCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:3479 original size:148 final size:141
Alignment explanation
Indices: 3210--4175 Score: 998
Period size: 148 Copynumber: 6.6 Consensus size: 141
3200 TACAATCAAA
* ** * *
3210 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGAAGAAGATTAGAGTTTAATTCGGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAAAGTTTAATTCTGGGTAAT
* * * ** * *
3275 TAAACTAAAAAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAATTTAAAGAGTAAAAG
66 TAAACTAAAAAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAG
3340 AAGAAGTACACAGAGAC
131 AAGAAG---A-A-A-AC
* * * * * *
3357 TAGTTTAATTCTGGGTACTTAAACTAAAAAGTAAAAGAAGAAGAAAAAAGTTTAAATCAGAGTAA
1 -AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAAAGTTTAATTCTGGGTAA
* * * * *
3422 TTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTGGGTAATTAAACTAAAGGGCAAGA
65 TTAAACTAAAAAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGA
3487 GAAGAAGAAAAC
130 GAAGAAGAAAAC
* * *
3499 AATTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGGCTAGTTTAATTAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAG--AA-AAA----AGTTTAATTCT
* * *
3564 GGGTAATTAAACTAAAAAGTAAGTA-AAGAAGAAAAGAGTTTAATTCGGGGTAATTAAACTAAAG
59 GGGTAATTAAACTAAAAAGTAA-AAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAG
3628 AGCAAGAGAAGAAGAAAAC
123 AGCAAGAGAAGAAGAAAAC
* * * *
3647 AATTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTACACAGAGGCTAGTTTAATTCT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAG-A-A-A-A---AAGTTTAATTCT
* * * * *
3712 GGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAAAGTTTAAATCAGAGTTATTAAACTAAAGA
59 GGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGA
3777 GCAAGAGAAGAAGAAAAC
124 GCAAGAGAAGAAGAAAAC
* * * *
3795 AGTTTAATTCTGGGTAATTAAACTAAAGTGCAAGAGAAGAAGAAAACAGTTTAACTCTGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAAAGTTTAATTCTGGGTAAT
* * *
3860 TAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGGCTAGTTTAATTATGGGTAATTAAACTAAAAA
66 TAAACTAAAAAGTAAAAGAAGAAG---A-AAA--C-AGTTTAATTCTGGGTAATTAAACTAAAGA
* *
3925 GTAAGAGAAGAAGAAAAG
124 GCAAGAGAAGAAGAAAAC
* * * * *
3943 AATTTAATTCGGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAAAGTTTAATTCTGGGTAAT
* * * *
4008 TAAACTAAAGAGTAAAAGAAGAAGTACATAGAGGCTAGTTTAATTCAGGGTAATAAAACTAAAAA
66 TAAACTAAAAAGTAAAAGAAGAAG-A-A-A-A--C-AGTTTAATTCTGGGTAATTAAACTAAAGA
* * *
4073 GTAAAAGAAGAAGAAAAG
124 GCAAGAGAAGAAGAAAAC
* * * *
4091 GGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTGATTCTGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAAAGTTTAATTCTGGGTAAT
* * **
4156 CAAGCTAAGCAGTAAAAGAA
66 TAAACTAAAAAGTAAAAGAA
4176 AGAGTAATCA
Statistics
Matches: 718, Mismatches: 77, Indels: 46
0.85 0.09 0.05
Matches are distributed among these distances:
141 79 0.11
142 2 0.00
143 3 0.00
144 6 0.01
145 5 0.01
146 4 0.01
147 4 0.01
148 613 0.85
149 2 0.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (141 bp):
AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAAAGTTTAATTCTGGGTAAT
TAAACTAAAAAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAG
AAGAAGAAAAC
Found at i:3539 original size:195 final size:189
Alignment explanation
Indices: 3207--4155 Score: 1051
Period size: 195 Copynumber: 4.9 Consensus size: 189
3197 GAATACAATC
* * ** * *
3207 AAAAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGAAGAAGATTAGAGTTTAATTCGGGGT
1 AAAAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGT
* * * * **
3272 AATTAAACTAAAAAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAATTTAAAGAGTAA
66 AATTAAACTAAAGAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAA
* * *
3337 AAGAAGAAGTACACAGAGACTAGTTTAATTCTGGGTACTTAAACTAAAAAGTAAAAGAAGAAGAA
131 AAGAAGAAG-A-A-A-AGA--AGTTTAATTCTGGGTAATTAAACTAAAAAGCAAGAGAAGAAGAA
* * * *
3402 AAAAGTTTAAATCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTGGGT
1 AAAAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGT
* * * *
3467 AATTAAACTAAAGGGCAAGAGAAGAAGAAAACAATTTAATTCTGGGTAATTAAACTAAAGAGTAA
66 AATTAAACTAAAGAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAA
* * *
3532 AAGAAGAAGTAAACAAAGGCTAGTTTAATTATGGGTAATTAAACTAAAAAGTAAGTA-AAGAAGA
131 AAGAAGAAG---A-AAA-G-AAGTTTAATTCTGGGTAATTAAACTAAAAAGCAAG-AGAAGAAGA
3596 A
189 A
* * * *
3597 AAGAGTTTAATTCGGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTTGGT
1 AAAAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGT
3662 AATTAAACTAAAGAGTAAAAGAAGAAGTACACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAA
66 AATTAAACTAAAGAGTAAAAGAAGAAG-A-A-A-A--C-AGTTTAATTCTGGGTAATTAAACTAA
* * * * * *
3727 AAAGTAAAAGAAGAAGAAAA-AAGTTTAAATCAGAGTTATTAAACTAAAGAGCAAGAGAAGAAGA
124 AGAGTAAAAGAAGAAGAAAAGAAGTTTAATTCTGGGTAATTAAACTAAAAAGCAAGAGAAGAAGA
3791 A
189 A
* * *
3792 AACAGTTTAATTCTGGGTAATTAAACTAAAGTGCAAGAGAAGAAGAAAACAGTTTAACTCTGGGT
1 AAAAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGT
*
3857 AATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGGCTAGTTTAATTATGGGTAATTAAACTAA
66 AATTAAACTAAAGAGTAAAAGAAGAAG---A-AAA--C-AGTTTAATTCTGGGTAATTAAACTAA
* * * *
3922 AAAGTAAGAGAAGAAGAAAAGAA-TTTAATTCGGGGTAATTAAACTAAAGAGCAAGAGAAGAAGA
124 AGAGTAAAAGAAGAAGAAAAGAAGTTTAATTCTGGGTAATTAAACTAAAAAGCAAGAGAAGAAGA
3986 A
189 A
* * * *
3987 AACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTACATAGAGGCTAGTTTAAT
1 AAAAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAG-A-A-A-A--C-AGTTTAAT
* * * **
4052 TCAGGGTAATAAAACTAAAAAGTAAAAGAAGAAGAAAAGGGTTTAATTCTGGGTAATTAAACTAA
59 TCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAA
* * * *
4117 AGAGCAAGAGAAGAAGAAAA-TAGTTTGATTCTGGGTAAT
124 AGAGTAAAAGAAGAAGAAAAGAAGTTTAATTCTGGGTAAT
4156 CAAGCTAAGC
Statistics
Matches: 662, Mismatches: 68, Indels: 48
0.85 0.09 0.06
Matches are distributed among these distances:
194 2 0.00
195 552 0.83
196 8 0.01
197 8 0.01
198 8 0.01
199 4 0.01
201 2 0.00
202 78 0.12
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (189 bp):
AAAAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGT
AATTAAACTAAAGAGTAAAAGAAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAA
AAGAAGAAGAAAAGAAGTTTAATTCTGGGTAATTAAACTAAAAAGCAAGAGAAGAAGAA
Found at i:3836 original size:343 final size:343
Alignment explanation
Indices: 3210--4155 Score: 1651
Period size: 343 Copynumber: 2.8 Consensus size: 343
3200 TACAATCAAA
* **
3210 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGAAGAAGATTAGAGTTTAATTCGGGGTAAT
1 AGTTTAATTATGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCGGGGTAAT
* **
3275 TAAACTAAAAAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAATTTAAAGAGTAAAAG
66 TAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAG
* *
3340 AAGAAGTACACAGAGACTAGTTTAATTCTGGGTACTTAAACTAAAAAGTAAAAGAAGAAGAAAAA
131 AAGAAGTACACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAA
*
3405 AGTTTAAATCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTGGGTAAT
196 AGTTTAAATCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAAT
*
3470 TAAACTAAAGGGCAAGAGAAGAAGAAAACAATTTAATTCTGGGTAATTAAACTAAAGAGTAAAAG
261 TAAACTAAAGGGCAAGAGAAGAAGAAAACAATTTAACTCTGGGTAATTAAACTAAAGAGTAAAAG
3535 AAGAAGTAAACAAAGGCT
326 AAGAAGTAAACAAAGGCT
3553 AGTTTAATTATGGGTAATTAAACTAAAAAGTAAGTA-AAGAAGAAAAGAGTTTAATTCGGGGTAA
1 AGTTTAATTATGGGTAATTAAACTAAAAAGTAAG-AGAAGAAGAAAAGAGTTTAATTCGGGGTAA
*
3617 TTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTTGGTAATTAAACTAAAGAGTAAAA
65 TTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAA
3682 GAAGAAGTACACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAA
130 GAAGAAGTACACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAA
*
3747 AAGTTTAAATCAGAGTTATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAA
195 AAGTTTAAATCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAA
* *
3812 TTAAACTAAAGTGCAAGAGAAGAAGAAAACAGTTTAACTCTGGGTAATTAAACTAAAGAGTAAAA
260 TTAAACTAAAGGGCAAGAGAAGAAGAAAACAATTTAACTCTGGGTAATTAAACTAAAGAGTAAAA
3877 GAAGAAGTAAACAAAGGCT
325 GAAGAAGTAAACAAAGGCT
*
3896 AGTTTAATTATGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAATTTAATTCGGGGTAAT
1 AGTTTAATTATGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCGGGGTAAT
3961 TAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAG
66 TAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAG
* * * *
4026 AAGAAGTACATAGAGGCTAGTTTAATTCAGGGTAATAAAACTAAAAAGTAAAAGAAGAAGAAAAG
131 AAGAAGTACACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAA
* * * * * *
4091 GGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTGATTCTGGGTAAT
196 AGTTTAAATCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAAT
4156 CAAGCTAAGC
Statistics
Matches: 574, Mismatches: 27, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
342 1 0.00
343 572 1.00
344 1 0.00
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (343 bp):
AGTTTAATTATGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCGGGGTAAT
TAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAG
AAGAAGTACACAGAGGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAA
AGTTTAAATCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTAATTCTGGGTAAT
TAAACTAAAGGGCAAGAGAAGAAGAAAACAATTTAACTCTGGGTAATTAAACTAAAGAGTAAAAG
AAGAAGTAAACAAAGGCT
Found at i:4172 original size:101 final size:95
Alignment explanation
Indices: 3210--4155 Score: 715
Period size: 101 Copynumber: 9.7 Consensus size: 95
3200 TACAATCAAA
* * ** * *
3210 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGAAGAAGATTAGAGTTTAATTCGGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAAT
* *
3275 --TAAACTAAAAAGCAAGAGAAGAAGAAAAC
66 AATAAAGTAAAAAG-AAAAGAAGAAGAAAAC
* ** * *
3304 AGTTTAATTCTTGGTAATTAATTTAAAGAGTAAAAGAAGAAGTACACAGAGACTAGTTTAATTCT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAG---A-A-A-A-TAGTTTAATTCT
* * *
3369 GGGTACT--TAAACTAAAAAGTAAAAGAAGAAGAAAAA
59 GGGTAATAATAAAGTAAAAAG-AAAAGAAGAAGAAAAC
* * * * *
3405 AGTTTAAATCAGAGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAAT
* ** *
3470 --TAAACTAAAGGGCAAGAGAAGAAGAAAAC
66 AATAAAGTAAAAAG-AAAAGAAGAAGAAAAC
* * * *
3499 AATTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGGCTAGTTTAATTAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAG---A-AAA---TAGTTTAATTCT
* * *
3564 GGGTAAT--TAAACTAAAAAG-TAAGTAAAGAAGAAAAG
59 GGGTAATAATAAAGTAAAAAGAAAAG--AAGAAGAAAAC
* * * *
3600 AGTTTAATTCGGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAATTTAATTCTTGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAAT
* *
3665 --TAAACTAAAGAGTAAAAGAAGAAGTACACAGAGGC
66 AATAAAGTAAAAAG-AAAAGAAGAAG-A-A-A-A--C
* * * * * * *
3700 TAGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAGAAGAAGAAAAAAGTTTAAATCAGAGT--
1 -AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAA
* * * *
3763 TATTAAACTAAAGAGCAAGAGAAGAAGAAAAC
65 TAATAAAGTAAAAAG-AAAAGAAGAAGAAAAC
* * *
3795 AGTTTAATTCTGGGTAATTAAACTAAAGTGCAAGAGAAGAAGAAAACAGTTTAACTCTGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAAT
* *
3860 --TAAACTAAAGAGTAAAAGAAGAAGTAAACAAAGGC
66 AATAAAGTAAAAAG-AAAAGAAGAAG---A-AAA--C
* * * * * *
3895 TAGTTTAATTATGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAATTTAATTCGGGGTAA
1 -AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAA
* * *
3960 T--TAAACTAAAGAGCAAGAGAAGAAGAAAAC
65 TAATAAAGTAAAAAG-AAAAGAAGAAGAAAAC
* * * *
3990 AGTTTAATTCTTGGTAATTAAACTAAAGAGTAAAAGAAGAAGTACATAGAGGCTAGTTTAATTCA
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAG-A-A-A-A---TAGTTTAATTCT
* *
4055 GGGTAAT-A-AAACTAAAAAGTAAAAGAAGAAGAAAAG
59 GGGTAATAATAAAGTAAAAAG-AAAAGAAGAAGAAAAC
* *
4091 GGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTGATTCTGGGTAAT
1 AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAAT
4156 CAAGCTAAGC
Statistics
Matches: 705, Mismatches: 103, Indels: 88
0.79 0.11 0.10
Matches are distributed among these distances:
94 276 0.39
95 5 0.01
96 7 0.01
97 14 0.02
98 13 0.02
99 5 0.01
100 4 0.01
101 381 0.54
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.23
Consensus pattern (95 bp):
AGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAATAGTTTAATTCTGGGTAAT
AATAAAGTAAAAAGAAAAGAAGAAGAAAAC
Found at i:4194 original size:22 final size:22
Alignment explanation
Indices: 4166--4342 Score: 239
Period size: 22 Copynumber: 8.1 Consensus size: 22
4156 CAAGCTAAGC
*
4166 AGTAAAAGAAAGAGTAATCAGG
1 AGTAAAAGAAAGAGTAATCAGA
*
4188 AGTAAAAGAAAGAGTAATCAGG
1 AGTAAAAGAAAGAGTAATCAGA
* *
4210 AGTAAAAGGAAGAGTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
* *
4232 AGCAGAAGAAAGAGTAATCAG-
1 AGTAAAAGAAAGAGTAATCAGA
* * *
4253 AGTAAAAGGAAGATTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
*
4275 AGCAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
* *
4297 AGCAGAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
4319 AGTAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
4341 AG
1 AG
4343 ATTAGAGTAA
Statistics
Matches: 135, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
21 16 0.12
22 119 0.88
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.12
Consensus pattern (22 bp):
AGTAAAAGAAAGAGTAATCAGA
Found at i:4356 original size:87 final size:87
Alignment explanation
Indices: 4166--4340 Score: 242
Period size: 87 Copynumber: 2.0 Consensus size: 87
4156 CAAGCTAAGC
* * ** * * * *
4166 AGTAAAAGAAAGAGTAATCAGGAGTAAAAGAAAGAGTAATCAGGAGTAAAAGGAAGAGTAATCAA
1 AGTAAAAGGAAGATTAATCAAAAGCAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAA
*
4231 AAGCAGAAGAAAGAGTAATCAG
66 AAGCAAAAGAAAGAGTAATCAG
* *
4253 AGTAAAAGGAAGATTAATCAAAAGCAAAAGAAAGAGTAATCAGAAGCAGAAGAAAGAGTAATCAG
1 AGTAAAAGGAAGATTAATCAAAAGCAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAA
*
4318 AAGTAAAAGAAAGAGTAATCAG
66 AAGCAAAAGAAAGAGTAATCAG
4340 A
1 A
4341 AGATTAGAGT
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.57, C:0.06, G:0.25, T:0.13
Consensus pattern (87 bp):
AGTAAAAGGAAGATTAATCAAAAGCAAAAGAAAGAGTAATCAGAAGCAAAAGAAAGAGTAATCAA
AAGCAAAAGAAAGAGTAATCAG
Found at i:4411 original size:47 final size:47
Alignment explanation
Indices: 4316--4416 Score: 122
Period size: 47 Copynumber: 2.2 Consensus size: 47
4306 AAGAGTAATC
*
4316 AGAAGTAAAAGAAAGAGTAATCAGAAGATTAGAGTAATTAAGCTAAA
1 AGAAGTAAAAGAAAGAGTAATCAGAAGATAAGAGTAATTAAGCTAAA
* *
4363 AGAAGTAAAAGCAAA-AGTAATTAGTAG-TAAG-GTTAATTAAGCT-AA
1 AGAAGTAAAAG-AAAGAGTAATCAGAAGATAAGAG-TAATTAAGCTAAA
4408 A-AAGTAAAA
1 AGAAGTAAAA
4417 AGTAATAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
44 8 0.16
45 4 0.08
46 13 0.27
47 21 0.43
48 3 0.06
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (47 bp):
AGAAGTAAAAGAAAGAGTAATCAGAAGATAAGAGTAATTAAGCTAAA
Found at i:9993 original size:19 final size:18
Alignment explanation
Indices: 9960--9995 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9950 TTGAAATAAT
*
9960 TCTTCAATGATCTTCAAA
1 TCTTCAATCATCTTCAAA
9978 TCTTCAAATCATCTTCAA
1 TCTTC-AATCATCTTCAA
9996 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAATCATCTTCAAA
Found at i:10003 original size:11 final size:10
Alignment explanation
Indices: 9960--10006 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
9950 TTGAAATAAT
9960 TCTTCAATGA
1 TCTTCAATGA
9970 TCTTCAA--A
1 TCTTCAATGA
*
9978 TCTTCAAATCA
1 TCTTC-AATGA
9989 TCTTCAATGA
1 TCTTCAATGA
9999 GTCTTCAA
1 -TCTTCAA
10007 ACACGAGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.38
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:12655 original size:21 final size:22
Alignment explanation
Indices: 12629--12680 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
12619 TTCTTATCGA
12629 CTTGCTTTAGTCGACTTCTTC-
1 CTTGCTTTAGTCGACTTCTTCT
**
12650 CTTGCTCAAGTCGACTTCTTCT
1 CTTGCTTTAGTCGACTTCTTCT
12672 CTTGCTTTA
1 CTTGCTTTA
12681 ACCGAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.12, C:0.29, G:0.13, T:0.46
Consensus pattern (22 bp):
CTTGCTTTAGTCGACTTCTTCT
Found at i:18643 original size:22 final size:22
Alignment explanation
Indices: 18613--18661 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
18603 ACTAAGGAAG
*
18613 CAATCAAGAAAATTAAAGAAAA
1 CAATTAAGAAAATTAAAGAAAA
18635 CAATTAAGAAAATTAAAGAAAA
1 CAATTAAGAAAATTAAAGAAAA
18657 CAATT
1 CAATT
18662 GATAAGAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.65, C:0.08, G:0.08, T:0.18
Consensus pattern (22 bp):
CAATTAAGAAAATTAAAGAAAA
Found at i:18645 original size:12 final size:13
Alignment explanation
Indices: 18623--18661 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
18613 CAATCAAGAA
18623 AATTAAAGAAAAC
1 AATTAAAGAAAAC
18636 AATT-AAG--AA-
1 AATTAAAGAAAAC
18645 AATTAAAGAAAAC
1 AATTAAAGAAAAC
18658 AATT
1 AATT
18662 GATAAGAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 8
0.73 0.00 0.27
Matches are distributed among these distances:
9 4 0.18
10 5 0.23
12 5 0.23
13 8 0.36
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (13 bp):
AATTAAAGAAAAC
Found at i:19282 original size:29 final size:30
Alignment explanation
Indices: 19235--19294 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
19225 GAAGTTCGTG
* *
19235 TTTGAAGACTCATTGAAGACTTATTTGAAGA
1 TTTGAAGAC-CATTGAAGAATTATTTCAAGA
19266 TTTGAAGA-CATTGAAGAATTATTTCAAGA
1 TTTGAAGACCATTGAAGAATTATTTCAAGA
19295 GGAAAGAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 19 0.70
31 8 0.30
ACGTcount: A:0.38, C:0.08, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTGAAGACCATTGAAGAATTATTTCAAGA
Found at i:20838 original size:19 final size:18
Alignment explanation
Indices: 20805--20840 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20795 TTGAAATAAT
*
20805 TCTTCAATGATCTTCAAA
1 TCTTCAATCATCTTCAAA
20823 TCTTCAAATCATCTTCAA
1 TCTTC-AATCATCTTCAA
20841 TGAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAATCATCTTCAAA
Found at i:20848 original size:11 final size:10
Alignment explanation
Indices: 20805--20851 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
20795 TTGAAATAAT
20805 TCTTCAATGA
1 TCTTCAATGA
20815 TCTTCAA--A
1 TCTTCAATGA
*
20823 TCTTCAAATCA
1 TCTTC-AATGA
20834 TCTTCAATGA
1 TCTTCAATGA
20844 GTCTTCAA
1 -TCTTCAA
20852 ACACGAGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
8 6 0.19
9 2 0.06
10 11 0.34
11 13 0.41
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.38
Consensus pattern (10 bp):
TCTTCAATGA
Found at i:23014 original size:21 final size:21
Alignment explanation
Indices: 22988--23029 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
22978 GCATAAAGAA
*
22988 GTTTCAAGCTCATTGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
23009 GTTTCAAGCTCATCGGAGTTG
1 GTTTCAAGCTCATCGGAGTTG
23030 CCTAAGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.36
Consensus pattern (21 bp):
GTTTCAAGCTCATCGGAGTTG
Found at i:23323 original size:65 final size:65
Alignment explanation
Indices: 23219--23348 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 65
23209 GCTTGCTATT
* *
23219 GATTCCAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAAGGTACCCCATGCATGGGTTGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAAGGTACCCCATGCATGGGTAGGAC
* *
23284 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTCGGCCAAGGGTACCCCATGCATGGGTAGGAC
1 GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAAGGTACCCCATGCATGGGTAGGAC
23349 CAGTTTTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 61 1.00
ACGTcount: A:0.22, C:0.28, G:0.30, T:0.21
Consensus pattern (65 bp):
GATTCAAACTTTCTGCACTAGCCCAGGCGTGGGTAGGCCAAAGGTACCCCATGCATGGGTAGGAC
Found at i:24412 original size:26 final size:23
Alignment explanation
Indices: 24366--24412 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
24356 TCCTTCTACT
24366 CATCTATCATCAAGTTTTTCATC
1 CATCTATCATCAAGTTTTTCATC
24389 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATC-AAGTTTTTCA
24413 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (23 bp):
CATCTATCATCAAGTTTTTCATC
Done.