Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016475.1 Corchorus olitorius cultivar O-4 contig16508, 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: 70336
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:381 original size:45 final size:45
Alignment explanation
Indices: 330--419 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
320 TGATACGCAG
*
330 CAATTTCTATTCTCAAGAGAAAGATTAGATCAAAGAGATTAACAA
1 CAATTTCTATTCTCAAGAGAAAGATTAGAACAAAGAGATTAACAA
375 CAATTTCTATTCTCAAGAGAAAGATTAGAACAAAGAGATTAACAA
1 CAATTTCTATTCTCAAGAGAAAGATTAGAACAAAGAGATTAACAA
420 AAAAACAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (45 bp):
CAATTTCTATTCTCAAGAGAAAGATTAGAACAAAGAGATTAACAA
Found at i:6329 original size:333 final size:331
Alignment explanation
Indices: 5678--10693 Score: 5451
Period size: 332 Copynumber: 15.1 Consensus size: 331
5668 TTGGTCATTT
* * * *
5678 TTTTTGTAAAATTTTAGCCGAAATCGTGTACGTTAA--ATCACAGA-TTTTGGCTAAAAAGGTGT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAACCATCA-TGATTTTTGGCTAAAAACGCGT
* * **
5740 TTAGTGG-CCACAACTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTC
63 TTCG-GGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTC
* ** * *
5804 ATCTAATCAAATATCACCCACATTGAATTTAAGGATTTGTTTTTATGAGAATCTAAATCTTGTTT
127 ATCTAAT-AAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
* * *
5869 CGATTTGATTATAAATTAATTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC
191 TGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCC
* ** * * *
5933 AAT-ATTTTTGGTGTTAAATTATATGTATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAAT
255 AATCTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAAT
5997 TTTTCGGGTCAC
320 TTTTCGGGTCAC
* *
6009 TTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCATTGTTTTTTTGGCTAAAAACGCGTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-TG-ATTTTTGGCTAAAAACGCGTT
* * ** *
6074 TCGGGACCCCCGCTTAGTTTTGCATGAATTTTGGGGCCGAGACTCCAAGAAATATCTATATTCAT
64 TCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCAT
* * * * *
6139 CTAATAAATTTCGGCCACAATGAATTTAAGTATTTTTTTTTATGAGCATCTAAATCTTGTTTTGA
129 CTAATAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
* * * *
6204 TTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATCTTAAAAGCGTAAAAAGTATTCAATC
194 TTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCTCCAATC
* * * *
6269 TTTTTTGACATTTAATTATATATATTTTATGAATATTTTAGCCAAAAATTGGCCGAAAAATTTTT
259 TTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATTTTT
** *
6334 TTGGTCAT
324 CGGGTCAC
* * * ** * * *
6342 TTTTTGTAAAACTTTAGCCGAAATCGTGTACAAATTATCA-CATATTTTAGCTAAAAAGGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGAT-TTTTGGCTAAAAACGCGTTT
* * * * *
6406 CGGGGCCCCGGCTTGGTTTTGCATGATTTTTGGTACTGAGACTCCATGAAATATCTTTATTCATC
65 CGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATC
* ** * *
6471 TAATCAAATATCAACCACATTGAATTTAAGGATTTGTTTTTACGAGCATCCAAATCTTGTTTCGA
130 TAAT-AAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
* * *
6536 TTTGATTATAAATTAATTCA-AAAAACTATGAAAAACGATATTGAAAGCGTGAAAAGTCCTCCAA
194 TTTAATTAGAAATTAATTCAGAAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCAA
* * * * * *
6600 T-ATTTTTGGCGTTAAATTATATGTATTTTATGAGTATTTTGGCCAAAAATTGACGGAAAAATTT
257 TCTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATTT
6664 TTCGGGTCAC
322 TTCGGGTCAC
* *
6674 TTTTTGCAAAATTTTAACCGAAACCGTGTACTAACCATCATGGATTTTTGGCTAAAAACGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAT-GATTTTTGGCTAAAAACGCGTTT
* * *
6739 CGGGACTCCGGCTTAGTTTTGCATGATTTTTGGCTCCGACACTCCATGAAATATCTATATTCATC
65 CGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATC
* * *
6804 TAATCAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTTCGAGCATCTAAATCTTGTTTTGAT
130 TAATAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGAT
** *
6869 TTAATTACTAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTATTCCAATC
195 TTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCAATC
* * * * *
6934 TTTTTTTGACATTTAATTATATATTTTTTATGAGTATTTTATCCAAAAATTGACAAAAAAAATTT
259 -TTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATTTT
*
6999 T--GGTCAT
323 TCGGGTCAC
* * *
7006 TTTTTGTAAAATTTTAGCCGAAATCGTGTACGTTAA--ATCACAGA-TTTTGGCTAAAAAGGCGT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAACCATCA-TGATTTTTGGCTAAAAACGCGT
* **
7068 TTCGGGGA-CACAACTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATG-AA-A--TATATTC
63 TTC-GGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTC
* **
7128 ATCTAATCAAATATCACCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
127 ATCTAAT-AAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
* * * *
7193 CT-ATTTGATTATAAATTAATTCAAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTC
191 -TGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTC
* * * * * *
7257 CAAT-ATTTGTGGCGTTAAATTATATGTATTTTATGAGTATTTTAGCCAAAAATTGAC-GGAAAA
254 CAATCTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAA
7320 TGTTTTCGGGTCAC
319 T-TTTTCGGGTCAC
* * *
7334 TTTTTGCAAAATTTTAGACGAAA-C-CGTA-T---CAT--GGATTTTTGGCTAAAAACGCGTTTC
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAACGCGTTTC
* * * * *
7391 GGGACCTCGGCTTAGTTTTGCATGATTTTTGGCGCCGACACTCCATGAAATATTTATATTTATCT
66 GGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATCT
* * * * *
7456 AATCAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTTCGAGCATCTGAATCTTATTTTGATT
131 AATAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGATT
* *
7521 TAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTACTCCAATCT
196 TAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCAATC-
** * * * *
7586 TTTTTTGATATTTAATTATATATATTTTATGAATATTTTAGCTAAATATTGGCAGAAAAATTTTT
259 TTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATTTTT
7651 CGGGTCAC
324 CGGGTCAC
* *
7659 TTTTTACAAAATTTTCGCCGAAATCGTGTACTAACCATCATGCATTTTTGGCTAAAAACGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATG-ATTTTTGGCTAAAAACGCGTTT
* * * *
7724 CGGGACCCCGGCTTAGTTTTGCATGATTTTTGACGCCGACACTCCATGAAATATTTATATTCATC
65 CGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATC
* * * *
7789 TAATTAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGGGCATCTAAATGTTGTTTTGAT
130 TAATAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGAT
* *
7854 TTAATTAGAAATTAATTCA-AAAAATATGAAAAACTATATTAAAAGTGTGAAAAGTACTCCAATC
195 TTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCAATC
* *
7918 TTTTTTTGGCATTTAATTATATATATTTTATGTGTATTTTATCCAAAAATTGACAGAAAAATATT
259 -TTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAAT-TT
** *
7983 TTTTGGTCAT
322 TTCGGGTCAC
* * * *
7993 TTTTTGTAAAATTTTAGCCGAAATCGTGTACGTTAA--ATCACAGA-TTTTGACTAAAAAGGCGT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAACCATCA-TGATTTTTGGCTAAAAACGCGT
* * **
8055 TTTGGGGCCCTAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCA
63 TTCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCA
* * *
8120 TCTAATCAAATATC-ACCACATTGAATTTAAGGATTTG-TTTTACGAGCATCTAAATCTTGTTTC
128 TCTAAT-AAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTT
* * * *
8183 GATTTGATTATAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAGAGTCCTCCA
192 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCA
* * * * * * *
8248 AT-ATTTTTGGCGTTAAATTATATGTATTTTATAAGTATTTTAGCCAAAAGTTGACGGAAAAATT
256 ATCTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATT
8312 TTTCGGGTCAC
321 TTTCGGGTCAC
*
8323 TTTTTGCAAAATTTTAGCCGAAAATCGTGTACTAACCATCATGGATTTTTAGCTAAAAACGCGTT
1 TTTTTGCAAAATTTTAGCCG-AAATCGTGTACTAACCATCAT-GATTTTTGGCTAAAAACGCGTT
* * ** *
8388 TCGGGACCTCAGCTTAGTTTTGCATGATTTTTGGCGGCGAGACTCCATGTAATATCTATATTCAT
64 TCGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCAT
* * * * * * *
8453 ATAATCAATTTCTGGCACATTGAATTTAAGTATTTGTTTTGATGAGCATCTGAATCTTGTTTTGA
129 CTAATAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
* *
8518 TTTAATTAGAAATTAATTCAGAAAAATATGAAAATCTATATTAAAAGCGTGAAAAGTACTCCAAT
194 TTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCAAT
** *
8583 CTTTTTTTAACATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACTGAAAAATAT
258 C-TTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAAT-T
* *
8648 TTT-TGGTCAT
321 TTTCGGGTCAC
* * *
8658 TTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGA-TTTTGGCTAAAAA-GACGTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-TGATTTTTGGCTAAAAACG-CGTT
* * * * * * *
8721 TCGTTG-CGCCGACTTAGTTTTGCATGATTTTTGGCACCGATAGTCCAAGAAATATCTATGTTCA
64 TCG-GGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCA
* * * * *
8785 TCTAATCAAATATCTGCCACTTTGAATTTAAGGATTTGCTTTTACGAGCATCCAAATCTTGTTTC
128 TCTAAT-AAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTT
* * *
8850 GATTTGATTATAAATTAATTCA-AAAAATGTGAAAAAC-AGTATTAAAAGCGTGAAAAGTCCTCC
192 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGA-TATTAAAAGCGTGAAAAGT-CTCC
* * * * *
8913 AAT-ATTTTTGGC-TTTAAATTATATTTATTTTATGAGTATTTTAGTCAAAACTTGACGGAAAAA
255 AATCTTTTTTGGCATTT-AATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAA
8976 TTTTTCGGGTCAC
319 TTTTTCGGGTCAC
*
8989 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAATCATAGATTTTTGGCTAAAAACGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAT-GATTTTTGGCTAAAAACGCGTTT
* * * * ** *
9054 CGGGACCCTGGCTTAATTTTGCATGATTTCTGGCGCCGACTCTCCATGAAATATTTATATTCATC
65 CGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATC
* * * *
9119 TAATCAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTTCGAGCATCTGAATCTTGTTTTGAT
130 TAATAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGAT
* * **
9184 TTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTACTAAAATC
195 TTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCAATC
*
9249 TTTTTTTGACATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATATA
259 -TTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAAT-T-
* *
9314 TTT-TGGTCATT
321 TTTCGGGTCA-C
* * * * *
9325 TTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGA-TTTTGGCAAAAAAGGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA-TGATTTTTGGCTAAAAACGCGTTT
* * *
9389 CGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATAAAATATCTATATTCATC
65 CGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATC
* * ** * *
9454 TAATCAAATATCTGCCACTTTGAATTTAAGGATTTACTTTTACGAGCATCTGAATTTTGTTTTGA
130 TAAT-AAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
* * * *
9519 TTTAATTAGAAATTAATTTAAAAAAATATGAAAAATGTTATTAAAAGCGTGAAAAGTCCTCCAAT
194 TTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CTCCAAT
** * * * *
9584 -AGTTTTGGCATTAAACTATATCT-TTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAATTTT
258 CTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATTTT
*
9647 TCGTGTCAC
323 TCGGGTCAC
* *
9656 TTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACCATCATGGTTTTTTGGCTAAAAACGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAT-GATTTTTGGCTAAAAACGCGTTT
* * * ** *
9721 TGGGACCTCGGCTTAGTTTTGCATGATTTTTTGCGGCGAGACTCCATGAAATATCTATATTCATA
65 CGGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATC
* * * * *
9786 TAATCAAATTTCTGGCACATTGAATTTAAGTATTTGTTTTGACGAGCATCTAAATCTTGCTTCGA
130 TAAT-AAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
* * * * *
9851 TTTTACTAGAAATTAATTCAGAAAAATATGAAAAAGGGTATTAAAAGCATGAAAAGTCTTCCAAT
194 TTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC-TCCAAT
* * * * * * * *
9916 C---TTTGACATTTAGTTATATATATTTAATTAGTATTGTGGCTAAAAATTGA-AGAAATAATAT
258 CTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAA-AATTT
* * *
9977 TTCGGATTAG
322 TTCGGGTCAC
* ** * **
9987 TTTTTGCAAAATTTTAGCCGAAATCGTGTAC-CATTA-CTTTTTTTTTGGCTTAAAAACGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGC-TAAAAACGCGTTT
* * * * * ***
10050 GGGGGCCCC--ATCAGTTTTGCATGATTTTTGTGGCA---AAACTATTTGAAATATCTATATTCA
65 CGGGACCCCGGCTTAGTTTTGCATGA-TTTT-TGGCACCGAGACTCCATGAAATATCTATATTCA
* * * * * * * *
10110 TCTAAACAAATCTT-AGCCACATTGGATTTAAGGATTTGTTTTTATGAGCATTTGAATCATATTT
128 TCT-AATAAAT-TTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
* * * * * * * *
10174 CGATTTAATTATAAATTAATT-TGAAAAAAAAGAAGAAGAACGATATTAGAAGCGTGAGAAGCGC
191 TGATTTAATTAGAAATTAATTCAGAAAAATATG-A-AA-AACGATATTAAAAGCGTGAAAAG-TC
* * * * * * **
10238 TTCAATC-TTTTCGGCATTGAATTATATATTTTTTATGAGTATTATGGATAAAAATTG--AGAAA
252 TCCAATCTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAA
* *
10300 AATATTTT-TGGTCAA
317 AAT-TTTTCGGGTCAC
** **** ** ** *
10315 TTTTTGCAAAATTTTAGATGAAATCGTGTACCATTATGGTTTTTTTTTTTTTGCTAAAAACGCG-
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTA-C--TAACCATCATGATTTTTGGCTAAAAACGCGT
** ** * * * * * * *
10379 TTCTGGGGTCGTGGATCAATTTTGCATGATTTTTGACACCAAGACTCCTTAAAATATATCTATAT
63 TTC-GGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCAT-GAA-ATATCTATAT
* * * * * **
10444 TCATTTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGTTTCTAAATCTTGT
125 TCATCTAA-TAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * * *
10509 TTCGATTTAATCAGAAATTAATTTC-GAAATAAAATAGGAAAACGATTTTAGAAGTGTGAAAAAG
189 TTTGATTTAATTAGAAATTAA-TTCAGAAA-AATAT-GAAAAACGATATTAAAAGCGTG-AAAAG
* * * * * * * *
10573 GCTTTCAAT-TTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCA-CTAGAAATCG--A
250 TC-TCCAATCTTTTTTGGCATTTAATTATATATATTTTATGAGTATTTT-AGCCAAAAATTGACA
* *
10634 GTAAAAATCTTTCGGGTCAA
313 G-AAAAATTTTTCGGGTCAC
10654 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
10694 CGGTTTTCAC
Statistics
Matches: 3970, Mismatches: 589, Indels: 247
0.83 0.12 0.05
Matches are distributed among these distances:
319 6 0.00
320 57 0.01
321 2 0.00
322 4 0.00
323 111 0.03
324 13 0.00
325 86 0.02
326 144 0.04
327 37 0.01
328 208 0.05
329 42 0.01
330 98 0.02
331 523 0.13
332 876 0.22
333 779 0.20
334 439 0.11
335 169 0.04
336 168 0.04
337 97 0.02
338 66 0.02
339 44 0.01
340 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (331 bp):
TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGATTTTTGGCTAAAAACGCGTTTC
GGGACCCCGGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTCATCT
AATAAATTTCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTTGATT
TAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCTCCAATCTT
TTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATTTTTCG
GGTCAC
Found at i:8450 original size:665 final size:666
Alignment explanation
Indices: 5678--10693 Score: 5584
Period size: 665 Copynumber: 7.6 Consensus size: 666
5668 TTGGTCATTT
* * * *
5678 TTTTTGTAAAATTTTAGCCGAAATCGTGTACGTTAA--ATCACAGA-TTTTGGCTAAAAAGGTGT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAACCATCATAGATTTTTGGCTAAAAACGCGT
* ** *
5740 TTAGTGG-CCACAACTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTATATTC
64 TTCG-GGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTC
* ** * * *
5804 ATCTAATCAAATATCACCCACATTGAATTTAAGGATTTGTTTTTATGAGAATCTAAATCTTGTTT
128 ATCTAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTT
* * * *
5869 CGATTTGATTATAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
193 TGATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTACTCCA
** * * *
5934 A--TATTTTTGGTGTTAAATTATATGTATTTTATGAGTATTTTAGCCAAAAATTGACGGAAAAAT
258 ATCTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAAT
* * * *
5997 -TTTTCGGGTCACTTTTTGGAAAATTTTAGCCGAAATCGTGTACTAACCATCATTGTTTTTTTGG
323 ATTTTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCATAG--ATTTTGG
* * * ** *
6061 CTAAAAACGCGTTTCGGGACCCCCGCTTAGTTTTGCATGAATTTTGGGGCCGAGACTCCAAGAAA
385 CTAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAA
* * * * * *
6126 TATCTATATTCATCTAAT-AAATTTCGGCCACAATGAATTTAAGTATTTTTTTTTATGAGCATCT
450 TATCTATATTCATCTAATCAAATATCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCT
* * * *
6190 AAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATCTTAAAAGCGTA
515 AAATCTTGTTTTGATTTAATTATAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTG
* * * * * *
6255 AAAAGT-ATTCAATCTTTTTTGACATTTAATTATATATATTTTATGAATATTTTAGCCAAAAATT
580 AAAAGTCCTCCAAT-ATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATT
* * ** *
6319 GGCCGAAAAATTTTTTTGGTCAT
644 GACGGAAAAATTTTTCGGGTCAC
* * * ** * * * *
6342 TTTTTGTAAAACTTTAGCCGAAATCGTGTACAAATTATCACATA-TTTTAGCTAAAAAGGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGATTTTTGGCTAAAAACGCGTTT
* * * ** * *
6406 CGGGGCCCCGGCTTGGTTTTGCATGATTTTTGGTACTGAGACTCCATGAAATATCTTTATTCATC
66 CGGGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCATC
* ** * * *
6471 TAATCAAATATCAACCACATTGAATTTAAGGATTTGTTTTTACGAGCATCCAAATCTTGTTTCGA
131 TAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
* * * *
6536 TTTGATTATAAATTAATTCAAAAAACTATGAAAAACGATATTGAAAGCGTGAAAAGTCCTCCAA-
196 TTTAATTAGAAATTAATTCAAAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGTACTCCAAT
* * * * *
6600 -TATTTTTGGCGTTAAATTATATGTATTTTATGAGTATTTTGGCCAAAAATTGACGGAAAAAT-T
260 CTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATAT
* * * *
6663 TTTCGGGTCACTTTTTGCAAAATTTTAACCGAAACCGTGTACTAACCATCATGGATTTTTGGCTA
325 TTTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCATAGA-TTTTGGCTA
* * * * *
6728 AAAACGCGTTTCGGGACTCCGGCTTAGTTTTGCATGATTTTTGGCTCCGACACTCCATGAAATAT
388 AAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATAT
* * *
6793 CTATATTCATCTAATC-AATTTCTGCCACATTGAATTTAAGTATTTGTTTTTTCGAGCATCTAAA
453 CTATATTCATCTAATCAAATATCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAA
*
6857 TCTTGTTTTGATTTAATTACT-AATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTGAA
518 TCTTGTTTTGATTTAATTA-TAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAA
** * * * * *
6921 AAGTATTCCAATCTTTTTTTGACATTTAATTATATATTTTTTATGAGTATTTTATCCAAAAATTG
582 AAGTCCTCCAA--TATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
** * *
6986 ACAAAAAAAATTTT--GGTCAT
645 ACGGAAAAATTTTTCGGGTCAC
* * *
7006 TTTTTGTAAAATTTTAGCCGAAATCGTGTACGTTAA--ATCACAGA-TTTTGGCTAAAAAGGCGT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAACCATCATAGATTTTTGGCTAAAAACGCGT
** *
7068 TTCGGGGA-CACAACTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATG-AA-A--TATATTC
64 TTC-GGGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTC
* ** *
7128 ATCTAATCAAATATCACCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTT
128 ATCTAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTT
* * * *
7193 CT-ATTTGATTATAAATTAATTCAAAAAAATATGAAAAACAATATTAAAAGCGTGAAAAGTCCTC
193 -TGATTTAATTAGAAATTAATTC-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTACTC
* * * * *
7257 CAA--TATTTGTGGCGTTAAATTATATGTATTTTATGAGTATTTTAGCCAAAAATTGAC-GGAAA
256 CAATCTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAA
* * * * *
7319 ATGTTTTCGGGTCACTTTTTGCAAAATTTTAGACGAAA-C-CG---T---ATCATGGATTTTTGG
321 ATATTTTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCATAGA-TTTTGG
* * * * *
7376 CTAAAAACGCGTTTCGGGACCTCGGCTTAGTTTTGCATGATTTTTGGCGCCGACACTCCATGAAA
385 CTAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAA
* * * * *
7441 TATTTATATTTATCTAATC-AATTTCTGCCACATTGAATTTAAGTATTTGTTTTTTCGAGCATCT
450 TATCTATATTCATCTAATCAAATATCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCT
* * * *
7505 GAATCTTATTTTGATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGTGTG
515 AAATCTTGTTTTGATTTAATTATAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTG
* * ** * * * *
7570 AAAAGTACTCCAATCTTTTTTTGATATTTAATTATATATATTTTATGAATATTTTAGCTAAATAT
580 AAAAGTCCTCCAA--TATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAAT
* *
7635 TGGCAGAAAAATTTTTCGGGTCAC
643 TGACGGAAAAATTTTTCGGGTCAC
* *
7659 TTTTTACAAAATTTTCGCCGAAATCGTGTACTAACCATCAT-GCATTTTTGGCTAAAAACGCGTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAG-ATTTTTGGCTAAAAACGCGTT
* * * *
7723 TCGGGACCCCGGCTTAGTTTTGCATGATTTTTGACGCCGACACTCCATGAAATATTTATATTCAT
65 TCGGGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCAT
* * *
7788 CTAAT-TAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGGGCATCTAAATGTTGTTTTG
130 CTAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTTTG
* *
7852 ATTTAATTAGAAATTAATTCAAAAAATATGAAAAACTATATTAAAAGTGTGAAAAGTACTCCAAT
195 ATTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTACTCCAAT
* * *
7917 CTTTTTTTGGCATTTAATTATATATATTTTATGTGTATTTTATCCAAAAATTGACAGAAAAATAT
260 CTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATAT
* * * * *
7982 TTTTTGGTCATTTTTTGTAAAATTTTAGCCGAAATCGTGTACGTTAA-ATCACAGATTTTGACTA
325 TTTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTAC--TAACATCATAGATTTTGGCTA
* * *
8046 AAAAGGCGTTTTGGGGCCCTAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATAT
388 AAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATAT
*
8111 CTATATTCATCTAATCAAATATC-ACCACATTGAATTTAAGGATTTG-TTTTACGAGCATCTAAA
453 CTATATTCATCTAATCAAATATCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAA
* * *
8174 TCTTGTTTCGATTTGATTATAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAG
518 TCTTGTTTTGATTTAATTATAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAA
* * * *
8239 AGTCCTCCAATATTTTTGGCGTTAAATTATATGTATTTTATAAGTATTTTAGCCAAAAGTTGACG
583 AGTCCTCCAATATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACG
8304 GAAAAATTTTTCGGGTCAC
648 GAAAAATTTTTCGGGTCAC
* *
8323 TTTTTGCAAAATTTTAGCCGAAAATCGTGTACTAACCATCATGGATTTTTAGCTAAAAACGCGTT
1 TTTTTGCAAAATTTTAGCCG-AAATCGTGTACTAACCATCATAGATTTTTGGCTAAAAACGCGTT
* * * *
8388 TCGGGACCTCAGCTTAGTTTTGCATGATTTTTGGCGGCGAGACTCCATGTAATATCTATATTCAT
65 TCGGGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCAT
* * * * *
8453 ATAATC-AATTTCTGGCACATTGAATTTAAGTATTTGTTTTGATGAGCATCTGAATCTTGTTTTG
130 CTAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTTTG
* *
8517 ATTTAATTAGAAATTAATTCAGAAAAATATGAAAATCTATATTAAAAGCGTGAAAAGTACTCCAA
195 ATTTAATTAGAAATTAATTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTACTCCAA
* ** *
8582 TCTTTTTTTAACATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACTGAAAAATA
259 TCTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATA
* * *
8647 TTTTT-GGTCATTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGATTTTGGCTA
324 TTTTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC-ATCATAGATTTTGGCTA
** * * * *
8711 AAAA-GACGTTTCGTTGCGCC-GACTTAGTTTTGCATGATTTTTGGCACCGATAGTCCAAGAAAT
388 AAAACG-CGTTTCGGGGCCCCAG-CTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAAT
* * * *
8774 ATCTATGTTCATCTAATCAAATATCTGCCACTTTGAATTTAAGGATTTGCTTTTACGAGCATCCA
451 ATCTATATTCATCTAATCAAATATCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTA
* * *
8839 AATCTTGTTTCGATTTGATTATAAATTAATTC-AAAAAATGTGAAAAAC-AGTATTAAAAGCGTG
516 AATCTTGTTTTGATTTAATTATAAATTAATTCAAAAAAATATGAAAAACGA-TATTAAAAGCGTG
* * * *
8902 AAAAGTCCTCCAATATTTTTGGCTTTAAATTATATTTATTTTATGAGTATTTTAGTCAAAACTTG
580 AAAAGTCCTCCAATATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
8967 ACGGAAAAATTTTTCGGGTCAC
645 ACGGAAAAATTTTTCGGGTCAC
*
8989 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACAATCATAGATTTTTGGCTAAAAACGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGATTTTTGGCTAAAAACGCGTTT
* * ** *
9054 CGGGACC-CTGGCTTAATTTTGCATGATTTCTGGCGCCGACTCTCCATGAAATATTTATATTCAT
66 CGGGACCAC-GGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCAT
* *
9118 CTAATC-AATTTCTGCCACATTGAATTTAAGTATTTGTTTTTTCGAGCATCTGAATCTTGTTTTG
130 CTAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTTTG
* **
9182 ATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTACTAAAA
195 ATTTAATTAGAAATTAATTC-AAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTACTCCAA
* *
9247 TCTTTTTTTGACATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATA
259 TCTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATA
* * *
9312 TATTTT-GGTCATTTTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGATTTTGGC
324 T-TTTTGGGTCA-CTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC-ATCATAGATTTTGGC
* * *
9376 AAAAAAGGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATAAAAT
386 TAAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAAT
* ** *
9441 ATCTATATTCATCTAATCAAATATCTGCCACTTTGAATTTAAGGATTTACTTTTACGAGCATCTG
451 ATCTATATTCATCTAATCAAATATCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTA
* * * * *
9506 AATTTTGTTTTGATTTAATTAGAAATTAATTTAAAAAAATATGAAAAATGTTATTAAAAGCGTGA
516 AATCTTGTTTTGATTTAATTATAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGA
* * *
9571 AAAGTCCTCCAATAGTTTTGGCATTAAACTATATCT-TTTTATGAGTATTTTAGCCAAAAATTGA
581 AAAGTCCTCCAATATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA
*
9635 CGGAAAAATTTTTCGTGTCAC
646 CGGAAAAATTTTTCGGGTCAC
* * *
9656 TTTTTGCAAAATTTTAGCCGAAATTGTGTACTAACCATCATGGTTTTTTGGCTAAAAACGCGTTT
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGATTTTTGGCTAAAAACGCGTTT
* * * * *
9721 TGGGACCTCGGCTTAGTTTTGCATGATTTTTTGCGGCGAGACTCCATGAAATATCTATATTCATA
66 CGGGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCATC
* * * *
9786 TAATCAAATTTCTGGCACATTGAATTTAAGTATTTGTTTTGACGAGCATCTAAATCTTGCTTCGA
131 TAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
* * * * *
9851 TTTTACTAGAAATTAATTCAGAAAAATATGAAAAAGGGTATTAAAAGCATGAAAAGT-CTTCCAA
196 TTTAATTAGAAATTAATTCA-AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTAC-TCCAA
* * * * * * *
9915 TC----TTTGACATTTAGTTATATATATTTAATTAGTATTGTGGCTAAAAATTGA-AGAAATAAT
259 TCTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAA-AAT
* * * * * ** * ***
9975 A-TTTCGGATTAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACCATTA-CTTTTTTTTTGGCTT
323 ATTTTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCATAGATTTTGGC-T
* * * ***
10038 AAAAACGCGTTTGGGGGCCCCA--TCAGTTTTGCATGATTTTTGTGGCA---AAACTATTTGAAA
387 AAAAACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGA-TTTT-TGGCACCGAGACTCCATGAAA
* * * * *
10098 TATCTATATTCATCTAAACAAATCT-TAGCCACATTGGATTTAAGGATTTGTTTTTATGAGCATT
450 TATCTATATTCATCTAATCAAATATCT-GCCACATTGAATTTAAGGATTTGTTTTTACGAGCATC
* * * * * * * * *
10162 TGAATCATATTTCGATTTAATTATAAATTAATTTGAAAAAAAAGAAGAAGAACGATATTAGAAGC
514 TAAATCTTGTTTTGATTTAATTATAAATTAA-TT-CAAAAAAATATGAAAAACGATATTAAAAGC
* * * * * * * * **
10227 GTGAGAAG-CGCTTCAATCTTTTCGGCATTGAATTATATATTTTTTATGAGTATTATGGATAAAA
577 GTGAAAAGTC-CTCCAATATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAA
* *
10291 ATTGA--GAAAAATATTTT-TGGTCAA
641 ATTGACGGAAAAAT-TTTTCGGGTCAC
** * *** ** *** *
10315 TTTTTGCAAAATTTTAGATGAAATCGTGTACCATTATGGTTTTTTTTTTTTTGCTAAAAACGCG-
1 TTTTTGCAAAATTTTAGCCGAAATCGTGTA-C-TAACCATCATAGATTTTTGGCTAAAAACGCGT
** ** * * * * * * * *
10379 TTCTGGGGTCGTGGATCAATTTTGCATGATTTTTGACACCAAGACTCCTTAAAATATATCTATAT
64 TTC-GGGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCAT-GAA-ATATCTATAT
* * * * * * **
10444 TCATTTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGTTTCTAAATCTTGT
126 TCATCTAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * *
10509 TTCGATTTAATCAGAAATTAATTTCGAAATAAA-ATAGGAAAACGATTTTAGAAGTGTGAAAAAG
191 TTTGATTTAATTAGAAATTAA-TTC-AAA-AAATAT-GAAAAACGATATTAAAAGCGTG-AAAAG
* * * * * * * *
10573 -GCTTTCAAT-T-TTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTCA-CTAGAAATCG-
251 TAC-TCCAATCTATTTTTGGCATTTAATTATATATATTTTATGAGTATTTT-AGCCAAAAATTGA
* * *
10633 -AGTAAAAAT-CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCA
314 CAG-AAAAATATTTTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAA-CATCA
10694 CGGTTTTCAC
Statistics
Matches: 3837, Mismatches: 420, Indels: 185
0.86 0.09 0.04
Matches are distributed among these distances:
651 272 0.07
652 1 0.00
653 42 0.01
654 56 0.01
655 3 0.00
656 43 0.01
657 69 0.02
658 150 0.04
659 97 0.03
660 283 0.07
661 112 0.03
662 39 0.01
663 97 0.03
664 619 0.16
665 756 0.20
666 423 0.11
667 553 0.14
668 221 0.06
669 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (666 bp):
TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATAGATTTTTGGCTAAAAACGCGTTT
CGGGACCACGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCATGAAATATCTATATTCATC
TAATCAAATTTCTGCCACATTGAATTTAAGTATTTGTTTTTACGAGCATCTAAATCTTGTTTTGA
TTTAATTAGAAATTAATTCAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTACTCCAATC
TATTTTTGGCATTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACAGAAAAATATT
TTTGGGTCACTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACATCATAGATTTTGGCTAAAA
ACGCGTTTCGGGGCCCCAGCTTAGTTTTGCATGATTTTTGGCACCGAGACTCCATGAAATATCTA
TATTCATCTAATCAAATATCTGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTAAATCT
TGTTTTGATTTAATTATAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT
CCTCCAATATTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGGAA
AAATTTTTCGGGTCAC
Found at i:11857 original size:30 final size:30
Alignment explanation
Indices: 11823--11884 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
11813 ATTTTTATCT
11823 TGACTTTCCTCTTATA-CCATCAAATTTTAA
1 TGACTTTCCTCTTATATCC-TCAAATTTTAA
*
11853 TGACTTTTCTCTTATATCCTCAAATTTTAA
1 TGACTTTCCTCTTATATCCTCAAATTTTAA
11883 TG
1 TG
11885 GCTTATTAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.93
31 2 0.07
ACGTcount: A:0.27, C:0.21, G:0.05, T:0.47
Consensus pattern (30 bp):
TGACTTTCCTCTTATATCCTCAAATTTTAA
Found at i:12168 original size:14 final size:15
Alignment explanation
Indices: 12125--12166 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
12115 TGATGCAAAC
* *
12125 AAAAACAAAACAAAAT
1 AAAAACAAAA-AATAG
12141 AAAAACAAAAAATAG
1 AAAAACAAAAAATAG
12156 AAAAACAAAAA
1 AAAAACAAAAA
12167 TAATGCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.83, C:0.10, G:0.02, T:0.05
Consensus pattern (15 bp):
AAAAACAAAAAATAG
Found at i:12215 original size:41 final size:41
Alignment explanation
Indices: 12170--12251 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
12160 ACAAAAATAA
12170 TGCCAAACGACCCCTTAGTAAATCAAAATGCCTCCATCCTT
1 TGCCAAACGACCCCTTAGTAAATCAAAATGCCTCCATCCTT
*
12211 TGCCAAACGACCCCTTAGTAAATCAAAATGCTTCCATCCTT
1 TGCCAAACGACCCCTTAGTAAATCAAAATGCCTCCATCCTT
12252 AGCGTAAGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.32, C:0.33, G:0.10, T:0.26
Consensus pattern (41 bp):
TGCCAAACGACCCCTTAGTAAATCAAAATGCCTCCATCCTT
Found at i:12370 original size:20 final size:20
Alignment explanation
Indices: 12333--12371 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12323 TAGTTGTGTC
*
12333 TTTCTTTTATTATTACTTTT
1 TTTCTTTTATTATGACTTTT
* *
12353 TTTCTTTTTTTCTGACTTT
1 TTTCTTTTATTATGACTTT
12372 GATGTTTTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTCTTTTATTATGACTTTT
Found at i:12852 original size:51 final size:50
Alignment explanation
Indices: 12776--13028 Score: 398
Period size: 51 Copynumber: 5.0 Consensus size: 50
12766 TAAAAAATAT
12776 GACAACTCATCATAGTCAATTGCCAGATGAAATTTGCGAGGAAATCTTAGA
1 GACAACTCATCATAGTCAATTGCCAGATGAAATTTGC-AGGAAATCTTAGA
12827 GACAACTCATCATAGTCAATTGCCAGATGAAATTTGCAAGGAAATCTTAGA
1 GACAACTCATCATAGTCAATTGCCAGATGAAATTTGC-AGGAAATCTTAGA
* *
12878 AACAACTCATCATAGTCAATTACCAGATGAAATTTGCAAGGAAATCTTAGA
1 GACAACTCATCATAGTCAATTGCCAGATGAAATTTGC-AGGAAATCTTAGA
** * *
12929 GACAACTCATCATAGTCAATTTTCAGAGGAAATTTGCATGGAAATTTTAGA
1 GACAACTCATCATAGTCAATTGCCAGATGAAATTTGCA-GGAAATCTTAGA
*
12980 GACAACTCATCATAGTCAATTGCCAGAGGAAATTTGCATGGAAATCTTA
1 GACAACTCATCATAGTCAATTGCCAGATGAAATTTGCA-GGAAATCTTA
13029 AAAAAAATTA
Statistics
Matches: 190, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 1 0.01
51 189 0.99
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (50 bp):
GACAACTCATCATAGTCAATTGCCAGATGAAATTTGCAGGAAATCTTAGA
Found at i:19113 original size:51 final size:52
Alignment explanation
Indices: 19029--19133 Score: 158
Period size: 51 Copynumber: 2.0 Consensus size: 52
19019 TAAAAAATAT
19029 GACAACTAATCATAGTAAATTGCCAGAGAAAATTTGCACGGAAATCTT-AGA
1 GACAACTAATCATAGTAAATTGCCAGAGAAAATTTGCACGGAAATCTTAAGA
* * * * *
19080 GACAACTCATCATAGTCAATTGCTAGAGGAAATTTGCATGGAAATCTTAAGA
1 GACAACTAATCATAGTAAATTGCCAGAGAAAATTTGCACGGAAATCTTAAGA
19132 GA
1 GA
19134 GATTACATGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 43 0.90
52 5 0.10
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (52 bp):
GACAACTAATCATAGTAAATTGCCAGAGAAAATTTGCACGGAAATCTTAAGA
Found at i:19160 original size:60 final size:59
Alignment explanation
Indices: 19087--19198 Score: 170
Period size: 60 Copynumber: 1.9 Consensus size: 59
19077 AGAGACAACT
* * *
19087 CATCATAGTCAATTGCTAGAGGAAATTTGCATGGAAATCTTAAGAGAGATTACATGATTA
1 CATCATAGTCAATTGCCAAAGGAAATGTGCATGGAAAT-TTAAGAGAGATTACATGATTA
* *
19147 CATCATAGTCAATTGCCAAAGGAAATGTGCATGGAGATTTTAGAGAGATTAC
1 CATCATAGTCAATTGCCAAAGGAAATGTGCATGGAAATTTAAGAGAGATTAC
19199 CCGTTAAGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 13 0.28
60 34 0.72
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (59 bp):
CATCATAGTCAATTGCCAAAGGAAATGTGCATGGAAATTTAAGAGAGATTACATGATTA
Found at i:19739 original size:9 final size:9
Alignment explanation
Indices: 19725--19763 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
19715 GGACAAGGGT
*
19725 TGAAGATGG
1 TGAAGATGA
19734 TGAAGATGA
1 TGAAGATGA
19743 TGAAGATGA
1 TGAAGATGA
*
19752 TGAAGAAGA
1 TGAAGATGA
19761 TGA
1 TGA
19764 TGCTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.21
Consensus pattern (9 bp):
TGAAGATGA
Found at i:31363 original size:13 final size:13
Alignment explanation
Indices: 31345--31371 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31335 AAGGCATACT
31345 ATTCTAAATTCAA
1 ATTCTAAATTCAA
31358 ATTCTAAATTCAA
1 ATTCTAAATTCAA
31371 A
1 A
31372 GGAAACCCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTCTAAATTCAA
Found at i:46041 original size:22 final size:21
Alignment explanation
Indices: 46007--46050 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 21
45997 AGTAAATTAT
*
46007 TGAATGTCATGAAGAATATTTTC
1 TGAACGTCATG-A-AATATTTTC
46030 TGAACGTC-TGAAATATTTTC
1 TGAACGTCATGAAATATTTTC
46050 T
1 T
46051 TCCAAGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 10 0.50
21 1 0.05
22 2 0.10
23 7 0.35
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (21 bp):
TGAACGTCATGAAATATTTTC
Found at i:54814 original size:30 final size:30
Alignment explanation
Indices: 54778--54836 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
54768 AATTACATTC
54778 TACTAGTTTTAACTTAAGAACTATACGCTT
1 TACTAGTTTTAACTTAAGAACTATACGCTT
54808 TACTAGTTTTAACTTAAGAACTATACGCT
1 TACTAGTTTTAACTTAAGAACTATACGCT
54837 CATACCCGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (30 bp):
TACTAGTTTTAACTTAAGAACTATACGCTT
Found at i:60908 original size:62 final size:64
Alignment explanation
Indices: 60807--60934 Score: 215
Period size: 62 Copynumber: 2.0 Consensus size: 64
60797 TTTTATTATC
60807 ATTCTGTATATATGTAGTATTATAAAATACTGTACATATGAAATGTTTTTCTTAATTTGGTAAT
1 ATTCTGTATATATGTAGTATTATAAAATACTGTACATATGAAATGTTTTTCTTAATTTGGTAAT
* **
60871 ATTCTGTATATATGTAGTA-T-TAAAATACTGTATATATGATCTGTTTTTCTTAATTTGGTAAT
1 ATTCTGTATATATGTAGTATTATAAAATACTGTACATATGAAATGTTTTTCTTAATTTGGTAAT
60933 AT
1 AT
60935 ATGAAAGAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 41 0.67
63 1 0.02
64 19 0.31
ACGTcount: A:0.33, C:0.06, G:0.12, T:0.48
Consensus pattern (64 bp):
ATTCTGTATATATGTAGTATTATAAAATACTGTACATATGAAATGTTTTTCTTAATTTGGTAAT
Found at i:65135 original size:14 final size:15
Alignment explanation
Indices: 65118--65155 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
65108 TCAAAACATA
65118 ATTTTTA-AAAATTT
1 ATTTTTATAAAATTT
*
65132 ATTTTTATATAATTT
1 ATTTTTATAAAATTT
65147 -TTTTTATAA
1 ATTTTTATAA
65156 TTAATGATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTATAAAATTT
Found at i:67229 original size:36 final size:36
Alignment explanation
Indices: 67180--67258 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
67170 TGAGTGGGGA
67180 ATTAT-ATGATGATCATCATCATCTTAATATAATAT
1 ATTATGATGATGATCATCATCATCTTAATATAATAT
67215 ATTATGATGATGATCATCATCATCTTAATATAATAT
1 ATTATGATGATGATCATCATCATCTTAATATAATAT
67251 ATTATGAT
1 ATTATGAT
67259 ATATATGGAT
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 5 0.12
36 38 0.88
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (36 bp):
ATTATGATGATGATCATCATCATCTTAATATAATAT
Found at i:69098 original size:18 final size:18
Alignment explanation
Indices: 69075--69128 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
69065 GAGTTAATGT
69075 CGATGGGGATTCAAAAAC
1 CGATGGGGATTCAAAAAC
*
69093 CGATGGGAATTCAAAAAC
1 CGATGGGGATTCAAAAAC
69111 CGATGGGGATTCAAAAAC
1 CGATGGGGATTCAAAAAC
69129 ATACAAGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.41, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
CGATGGGGATTCAAAAAC
Done.