Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022495.1 Corchorus olitorius cultivar O-4 contig22528, 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: 69667
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:9534 original size:331 final size:330
Alignment explanation
Indices: 8657--9982 Score: 1367
Period size: 329 Copynumber: 4.0 Consensus size: 330
8647 CTCAAAATTA
*
8657 ATTTAAGAATTTGTTTTTACG-TCTATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAGA
1 ATTTAAG-ATTTGTTTTTACGAGC-ATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAG-
* * * * * **
8721 AAAAATAAGAAATACGATATTAAAATCATAAAAAGCCCTCCAATCTTTTTGGAATTGAATTATAT
63 AAAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATAT
* * * *
8786 ATTTTTATAAGTATTTTAGCCAAAAATTGAGGAGAAATCTTTCGTGTCAGTTTTTGCAAAATTTT
128 ATTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTT
* * * * * *
8851 AGCCGAGATTGTGTACTAACACTTAAACCATCACGGTTTTTGGCTAAAAACA-CATTC-CGGGGA
193 AGCCGAAATCGTG---T-A-A--T-AACCATCACGATTTTTGCCTAAAAA-AGCGTTCTCGGGGC
* * * * * * *
8914 CCCAACTCAATTTTGCATGATTTTTTTGGCTCCGAGATTACTTGAAATATCTACATTCATCTAAT
249 CCCAGCTCAATTTTGCATGA--TTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAAT
* *
8979 CAATTCTCAGTCACATTGG
312 CAAATCTCAGCCACATTGG
* * * * *
8998 ATTTAAAGATTTTTTTTTTACGAGCATATGAATCTTATTTTGATTTGATTAGAAATTAATTTGGA
1 ATTT-AAGA-TTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAGA
* * ** * *
9063 ATAAA-AGGAAAAACAATATTAAAAATGTCAAAAGCCCGT-CAAT-TTTTTGGTGTTGAATTATA
64 A-AAATATGAAAAACGATATTAAAAGCGTGAAAAGCCC-TCCAATCTTTTTGGCGTTGAATTATA
* * *
9125 TATTTTTCATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGAGTCAATTTTTACAAAATT
127 TATTTTT-ATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATT
*
9190 TTAGCCGAAATCGTGTAATAATCATCAC-ATTTTTGCCTAAAAAAGCGTTCT-GGGGCCCCAGCT
191 TTAGCCGAAATCGTGTAATAACCATCACGATTTTTGCCTAAAAAAGCGTTCTCGGGGCCCCAGCT
* *
9253 CAGTTTTGCATGATTTTTGACACCAAGACTCCTT-AAGATATCCATATTCATCTAATCAAATCTC
256 CAATTTTGCATGATTTTTGACACCAAGACTCCTTGAA-ATATCTATATTCATCTAATCAAATCTC
*
9317 AGGCACATTGG
320 AGCCACATTGG
* *
9328 ATTTAAGTATTTGTTTTTACAAGCATCTGAATCTTATTTCGATTTAATTAGAATTTAATTTA-AA
1 ATTTAAG-ATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAGAA
* *
9392 AAATTATGAAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTAAATTATAT
65 AAA-TATG-AAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATAT
* * * * * * *
9457 AGATTTTATGAGTGTTTTAGCGAAAAATTGAGGAAAAATTTTTTGGGTCATTTTTTGCAAATTTT
128 A-TTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTT
* * * * *
9522 TAGTCAAAATCGTGTATTAACCATCACGGTTTTT-CGCTAAAAACGCGTT-TCGGGGCCCC-GCC
192 TAGCCGAAATCGTGTAATAACCATCACGATTTTTGC-CTAAAAAAGCGTTCTCGGGGCCCCAG-C
* *** * * *
9584 TCAGTTTTGCATGATTTTTGGTGGCGAA-ACTCCTTAAAATATCTATATTCATCAAAT-AAATCT
255 TCAATTTTGCATGATTTTT-GACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT
* *
9647 TAGCCACATTGC
319 CAGCCACATTGG
* *
9659 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAGA-TCAGA
1 ATTTAA-GATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTA-ATTTAGA
* * *
9723 AAAATATGAAAAACGATATTAAAAGTGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATCATATA
64 AAAATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATA
** * * * *
9788 TTTTTATGAGTATCAT-GCCTGAAAATTGAGGAAATATCTTTGGGGTCAATTTTTGGAAAATTTT
129 TTTTTATGAGTATTTTAGCC-AAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTT
* * * * * * * * * * *
9852 AGACGAAATCTTGTAATAATCAGCACAATTTATTG-ATAAAAATGTGTTTTCGGGG-CCCGGTTC
193 AGCCGAAATCGTGTAATAACCATCACGATTT-TTGCCTAAAAAAGCGTTCTCGGGGCCCCAGCTC
* * * * *
9915 AATTTTGAATGATTTTTGACACCGAGACTCCTTGAAATATTTATATTCATCTAACCAAATCCCAG
257 AATTTTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAG
9980 CCA
322 CCA
9983 TTGTTTTTAC
Statistics
Matches: 828, Mismatches: 125, Indels: 75
0.81 0.12 0.07
Matches are distributed among these distances:
327 3 0.00
328 7 0.01
329 181 0.22
330 154 0.19
331 168 0.20
332 119 0.14
333 14 0.02
334 1 0.00
336 1 0.00
337 1 0.00
338 1 0.00
340 24 0.03
341 100 0.12
342 53 0.06
343 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (330 bp):
ATTTAAGATTTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTTAGAAA
AATATGAAAAACGATATTAAAAGCGTGAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATATT
TTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
CGAAATCGTGTAATAACCATCACGATTTTTGCCTAAAAAAGCGTTCTCGGGGCCCCAGCTCAATT
TTGCATGATTTTTGACACCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAC
ATTGG
Found at i:10997 original size:2 final size:2
Alignment explanation
Indices: 10990--11019 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
10980 TTAGATTTGA
*
10990 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11020 GTTATGAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13183 original size:2 final size:2
Alignment explanation
Indices: 13176--13205 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13166 AAATTTCTAA
13176 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13206 TTGTTTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13631 original size:113 final size:107
Alignment explanation
Indices: 13506--13800 Score: 310
Period size: 113 Copynumber: 2.7 Consensus size: 107
13496 ATTTTTTTTA
* * * * **
13506 TTATAGACTTTTAGAAATAAAATATTAAATTAATTTCACTAAGTTTAGTTCCAAATTAAAATTTT
1 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACCAAGTTTAGCCCCAAATTAAAATTTT
**
13571 ATTTTTATTTGTATTTTGAAGGTAAATTTTA-AATTTAATAATTTATTG
66 ATTTTTATTT-TA-----AAGGTAAATTCCATAA-TTAATAATTTATTG
*
13619 TTATAGAGTTTTAGAAATAAAATACAAAACTAATTTCACCAAGTTTAGCCCCAAATTAAAATTTT
1 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACCAAGTTTAGCCCCAAATTAAAATTTT
* *
13684 ATTTTTATTTTAAGGGTAAATTCCATGATTAATAATTTATTG
66 ATTTTTATTTTAAAGGTAAATTCCATAATTAATAATTTATTG
* * * * ** * **
13726 TTATAG-GGTTTAGAAATAAAATATATAACTAA-CTAATTAAGTTTAG-CCCAAAATAAAATTAA
1 TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACCAAGTTTAGCCCCAAATTAAAATTTT
*
13788 AATTTTATTTTAA
66 ATTTTTATTTTAA
13801 GGGTTAGAAA
Statistics
Matches: 159, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
104 25 0.16
105 10 0.06
106 23 0.14
107 30 0.19
108 1 0.01
112 2 0.01
113 68 0.43
ACGTcount: A:0.42, C:0.07, G:0.08, T:0.43
Consensus pattern (107 bp):
TTATAGAGTTTTAGAAATAAAATATAAAACTAATTTCACCAAGTTTAGCCCCAAATTAAAATTTT
ATTTTTATTTTAAAGGTAAATTCCATAATTAATAATTTATTG
Found at i:13815 original size:110 final size:107
Alignment explanation
Indices: 13605--13804 Score: 280
Period size: 104 Copynumber: 1.9 Consensus size: 107
13595 AATTTTAAAT
* * *
13605 TTAATAATTTATTGTTATAGAGTTTTAGAAATAAAATACAAAACTAATTTCACCAAGTTTAGCCC
1 TTAATAATTTATTGTTATAGAGGTTTAGAAATAAAATACAAAACTAATCTAACCAAGTTTAGCCC
* ** *
13670 CAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATGA
66 CAAAATAAAATTAAAATTTTATTTTAAGGGTAAATTCCATGA
* * **
13712 TTAATAATTTATTGTTATAG-GGTTTAGAAATAAAATATATAACTAA-CTAATTAAGTTTAG-CC
1 TTAATAATTTATTGTTATAGAGGTTTAGAAATAAAATACAAAACTAATCTAACCAAGTTTAGCCC
13774 CAAAATAAAATTAAAATTTTATTTTAAGGGT
66 CAAAATAAAATTAAAATTTTATTTTAAGGGT
13805 TAGAAAAAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
104 29 0.35
105 10 0.12
106 23 0.28
107 20 0.24
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (107 bp):
TTAATAATTTATTGTTATAGAGGTTTAGAAATAAAATACAAAACTAATCTAACCAAGTTTAGCCC
CAAAATAAAATTAAAATTTTATTTTAAGGGTAAATTCCATGA
Found at i:22277 original size:19 final size:20
Alignment explanation
Indices: 22253--22310 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
22243 CTGTTTGGCA
22253 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTAGC
* *
22272 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTA-GC
22293 ACTGTACAGATGAGATTA
1 ACTGTACAGATGAGATTA
22311 TTAGAGCAGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (20 bp):
ACTGTACAGATGAGATTAGC
Found at i:22298 original size:21 final size:20
Alignment explanation
Indices: 22253--22311 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
22243 CTGTTTGGCA
22253 ACTGTACAGATGAGATTA-C
1 ACTGTACAGATGAGATTATC
* *
22272 ACTGTACAGATTAGATTATGT
1 ACTGTACAGATGAGATTAT-C
22293 ACTGTACAGATGAGATTAT
1 ACTGTACAGATGAGATTAT
22312 TAGAGCAGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
19 17 0.49
21 18 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ACTGTACAGATGAGATTATC
Found at i:23186 original size:11 final size:12
Alignment explanation
Indices: 23170--23198 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
23160 ACTCATACCC
23170 TTTTTC-TTTTT
1 TTTTTCGTTTTT
23181 TTTTTCGTTTTT
1 TTTTTCGTTTTT
23193 TTTTTC
1 TTTTTC
23199 ATTACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.86
Consensus pattern (12 bp):
TTTTTCGTTTTT
Found at i:27181 original size:655 final size:650
Alignment explanation
Indices: 25626--27415 Score: 1884
Period size: 655 Copynumber: 2.7 Consensus size: 650
25616 AAGATGCCAA
* *
25626 AAAAAGATTGGAGGACTTTTCACGATTTTAATATCGTTTTTCATAATTTTTCTAAATTAATTTCT
1 AAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCAT-ATTTTTCTAAATTAATTTCT
* * * * * *
25691 AATTAAATTGAAACAAGATTCAGATGCACATAAAAGCAAATCCTTAAATCCAATGTGGCTAAGAT
65 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACAATGTGGCTGAGA-
* *
25756 TTTGTTAGATAAATAAAGATATTTCAAGGAGTCTCGCCGCCAAAAATCATGCAAAAC-AGAGCCG
129 TTTGTTAGAT-AATATAGATATTTCAAGGAGTCTCGGCG-CAAAAATCATGCAAAACTA-A-CCG
** * * *
25820 TGA-CCCTCTAACGCGTTTTTAGCCAAAAATCGTGAT-G--AATACACGATTTTGGCT-AAAATT
190 -GAGCCCTGAAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATT
*
25880 TTGCAAAAATTGACCCGAAAAATATTTTCTCAATTTTTGACTAAAATACTCATAAAAAATATATA
254 TTAC-AAAATTGACCCG-AAAAT-TTTTCTCAATTTTTGAC-AAAATACTCATAAAAAATATATA
* * *
25945 ATTCGATAT-CAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTTTTTTTTTCC
315 ATTC-A-ATCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTT-C
* * *
26009 TAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAA
377 AAATTAATTTCTAATTAAATCGAAAC-AAATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAA
* * *
26074 TGTGGCTGAGATTTGGTTAGAAGAATATAAAGATTTCAAGGAGTCTTGCCACCAAAAATCATGCA
441 TGTGGCTGAGATTTTGTTAGATGAATATAAAGATTTCAAGGAATCTTGCCACCAAAAATCATGCA
* * * * * ** *
26139 AAACTGAGCTGGGCCCTGAACGCATTTTTAGTCGAAAACCATGATGGTTAATACACGATTTCGGT
506 AAACTGACCTGGGCCCAGAACACATTTTTAGCCAAAAAAAATGATGGATAATACACGATTTCGGT
* * * * * * *
26204 TAAATTTTGTAAAAATTGACCCAATTATTTTTCCTCGTTATCTAGCGAAAATACTCATAAAAAAT
571 AAAATTTTGCAAAAATTGACCCAAATATTTTTCCTCATTATCTAGCCAAAAGAATCATAAAAAAT
26269 ATATAATTCAACGCC
636 ATATAATTCAACGCC
* * * * * * * *
26284 AAAAAAATTGAAAGCCTTTTCAAGCTTCTAATATCGTTTTCTTATTTTATTTCAAAATTAATTTC
1 AAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTT-TCATATT-TTTCTAAATTAATTTC
* * ** * **
26349 TAATTAAATCGAAACAAGATTAAAAAACTCGTACAAACAAATCCTTAAATACAATGTGAATGAGA
64 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACAATGTGGCTGAGA
* * * *
26414 TTTGGTT--AT-ATAT--ATA--TAAAGGAGTCTTGGCGCTAAAAATCATGCAAAACTGACCTAG
129 TTT-GTTAGATAATATAGATATTTCAAGGAGTCTCGGCGC-AAAAATCATGCAAAACTAACC-GG
* * * **** * *
26472 AGCCCTGGAATGCATTTTTAGCCAAAAAAAAAACCATGATT-GTACACAATTTCGGCTAAAAATT
191 AGCCCTGAAACGCGTTTTTAGCC--AAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATT
* * *
26536 TTACAGAAATTGACCCGAAATATTTTTCTTAATTTTTAGTCACAATACTCATAAAAAATATATAA
254 TTACA-AAATTGACCCGAAA-ATTTTTCTCAATTTTT-GACAAAATACTCATAAAAAATATATAA
* *
26601 TTCAATGCCAAAAAGATTGAAGGGCTTCTCACACTTCTAATATCGTTTTTCCTATTTGTTTTCAA
316 TTCAAT-CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTT-TTTTCAA
* * * * *
26666 ATTAATTTCTAATTAAATTGAAATATGATTCAAATGCTCGTAAAAATAAATCCTTAAATCCATTG
379 ATTAATTTCTAATTAAATCGAAACA-AATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATG
* * * *
26731 TGGCTAAGATTTTGTTAGATGAATATAGATG-TTTCAAGGAATGTTGCCACTAAAAATCATGCAA
443 TGGCTGAGATTTTGTTAGATGAATATA-AAGATTTCAAGGAATCTTGCCACCAAAAATCATGCAA
*
26795 AACTGACCTGGGGCCCCAGAACACGTTTTTAGCCAAAAAAAACTG-T-GATAATACACGATTTCG
507 AACTGACCT-GGG-CCCAGAACACATTTTTAGCCAAAAAAAA-TGATGGATAATACACGATTTCG
* *
26858 GCTAAAATTTTGCAAAAATTGACCCGAAATA-TTTTCCTCCATT-TTTAGCCACAGGAGAAT-AT
569 G-TAAAATTTTGCAAAAATTGACCC-AAATATTTTTCCT-CATTATCTAGCCA-A-AAGAATCAT
*
26920 -ATAAA-AT-T-A-T-AA-GCC
629 AAAAAATATATAATTCAACGCC
** * *
26935 AAAAAGATTGAAGGACTCGTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATCAAATTCTA
1 AAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTA
* * *
27000 ATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAGTTCAATGTGGCTGAGATT
66 ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACAATGTGGCTGAGATT
27065 TGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCAGCAAAAATCATGCAAAACTAACCGGAG
131 TG-TTAGAT-AATATAGATATTTCAAGGAGTCTCGGC-GCAAAAATCATGCAAAACTAACCGGAG
* * *
27130 TCCC-GAAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGT
193 -CCCTGAAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTT-T
* *
27194 A-AAAAATGACCCGAAAACTTTTTCCGTCAATTTTTGGCATAAATACTCATAATATATATATATA
256 ACAAAATTGACCCGAAAA-TTTTT-C-TCAATTTTTGACA-AAATACTCAT-A-A-A-A-A-ATA
* * * *
27258 TATAATTTAACTCCAAAAGGATTG--GGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTT
311 TATAATTCAA-TCCAAAAAGATTGAAGGG-CTTTTCACGCTTCTAATATCGTTTTTCCTATTTTT
* * *
27321 CT-GAATTAATTTCTAATTAAATCGAAACAAAGTTCAGATGCTCGTAAAAATAAATTCTTAAATC
374 TTCAAATTAATTTCTAATTAAATCGAAACAAA-TTCAGATGCTCGTAAAAATAAATCCTTAAATC
*
27385 CAATGTAGCTGAGA-TTTGATTAGATGAATAT
438 CAATGTGGCTGAGATTTTG-TTAGATGAATAT
27416 GGATATCTCA
Statistics
Matches: 933, Mismatches: 143, Indels: 111
0.79 0.12 0.09
Matches are distributed among these distances:
648 1 0.00
649 73 0.08
650 10 0.01
651 85 0.09
652 2 0.00
653 18 0.02
654 31 0.03
655 254 0.27
656 87 0.09
657 99 0.11
658 58 0.06
659 154 0.17
660 7 0.01
661 30 0.03
662 23 0.02
663 1 0.00
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (650 bp):
AAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTAAATTAATTTCTA
ATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATACAATGTGGCTGAGATT
TGTTAGATAATATAGATATTTCAAGGAGTCTCGGCGCAAAAATCATGCAAAACTAACCGGAGCCC
TGAAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAAATTTTACAAA
ATTGACCCGAAAATTTTTCTCAATTTTTGACAAAATACTCATAAAAAATATATAATTCAATCCAA
AAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCAAATTAATTTCTAA
TTAAATCGAAACAAATTCAGATGCTCGTAAAAATAAATCCTTAAATCCAATGTGGCTGAGATTTT
GTTAGATGAATATAAAGATTTCAAGGAATCTTGCCACCAAAAATCATGCAAAACTGACCTGGGCC
CAGAACACATTTTTAGCCAAAAAAAATGATGGATAATACACGATTTCGGTAAAATTTTGCAAAAA
TTGACCCAAATATTTTTCCTCATTATCTAGCCAAAAGAATCATAAAAAATATATAATTCAACGCC
Found at i:29094 original size:51 final size:50
Alignment explanation
Indices: 28993--29094 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
28983 GTTCTTCATA
* **
28993 TTTTCCTTATTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTATTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
29043 TTTTCTCTTATTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTTC-CTTATTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
29094 T
1 T
29095 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 7 0.16
51 37 0.82
52 1 0.02
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (50 bp):
TTTTCCTTATTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:32638 original size:15 final size:16
Alignment explanation
Indices: 32620--32649 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32610 ATAAATAATA
32620 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
32635 ATATTATAATCTAAA
1 ATATTATAATCTAAA
32650 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:32909 original size:2 final size:2
Alignment explanation
Indices: 32897--32939 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
32887 TTCGTGATTT
*
32897 TA TA TA GTA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
32940 CTAGTTAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 36 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:38729 original size:25 final size:24
Alignment explanation
Indices: 38695--38741 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
38685 ACGTTTGCAC
38695 AAATACCTAAGAATTTGAATTAAAA
1 AAATACCTAAGAATTT-AATTAAAA
*
38720 AAATATCTAAGAATTTAATTAA
1 AAATACCTAAGAATTTAATTAA
38742 TGTAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (24 bp):
AAATACCTAAGAATTTAATTAAAA
Found at i:38786 original size:39 final size:40
Alignment explanation
Indices: 38732--38812 Score: 137
Period size: 39 Copynumber: 2.0 Consensus size: 40
38722 ATATCTAAGA
*
38732 ATTTAATTAATGTAAGTATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
*
38771 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
38811 AT
1 AT
38813 AGGAATTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.37, C:0.04, G:0.09, T:0.51
Consensus pattern (40 bp):
ATTTAATTAATGTAAGTATTTCAGTTATTATATATATTAC
Found at i:39090 original size:5 final size:5
Alignment explanation
Indices: 39080--39123 Score: 51
Period size: 5 Copynumber: 9.6 Consensus size: 5
39070 AAGATAGTAG
*
39080 GATAA GATAA GATAA GAT-A G-TAA GAT-A G-TAA AATAA GATAA GAT
1 GATAA GATAA GATAA GATAA GATAA GATAA GATAA GATAA GATAA GAT
39124 TATTATCAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
3 2 0.06
4 7 0.21
5 24 0.73
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (5 bp):
GATAA
Found at i:39092 original size:18 final size:17
Alignment explanation
Indices: 39069--39123 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
39059 ATATATATAG
39069 TAAGATAGTAGGATAAGA
1 TAAGATAGTA-GATAAGA
39087 TAAGATA--AGAT-AG-
1 TAAGATAGTAGATAAGA
*
39100 TAAGATAGTAAAATAAGA
1 TAAGATAGT-AGATAAGA
39118 TAAGAT
1 TAAGAT
39124 TATTATCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
13 7 0.23
14 2 0.06
15 3 0.10
16 4 0.13
17 2 0.06
18 13 0.42
ACGTcount: A:0.55, C:0.00, G:0.22, T:0.24
Consensus pattern (17 bp):
TAAGATAGTAGATAAGA
Found at i:39100 original size:31 final size:31
Alignment explanation
Indices: 39065--39123 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
39055 ATAAATATAT
**
39065 ATAGTAAGATAGTAGGATAAGATAAGATAAG
1 ATAGTAAGATAGTAAAATAAGATAAGATAAG
39096 ATAGTAAGATAGTAAAATAAGATAAGAT
1 ATAGTAAGATAGTAAAATAAGATAAGAT
39124 TATTATCAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (31 bp):
ATAGTAAGATAGTAAAATAAGATAAGATAAG
Found at i:40501 original size:18 final size:19
Alignment explanation
Indices: 40478--40518 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
40468 CAACCTGAAC
* *
40478 TTGTATGATTTT-GATGTT
1 TTGTATAATTTTGGACGTT
40496 TTGTATAATTTTGGACGTT
1 TTGTATAATTTTGGACGTT
40515 TTGT
1 TTGT
40519 CCACTGAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.17, C:0.02, G:0.22, T:0.59
Consensus pattern (19 bp):
TTGTATAATTTTGGACGTT
Found at i:45632 original size:28 final size:28
Alignment explanation
Indices: 45592--45647 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
45582 AGTCCTTATT
45592 GGTTTCTAAAGCCCAACCAATCTTTGCA
1 GGTTTCTAAAGCCCAACCAATCTTTGCA
45620 GGTTTCTAAAGCCCAACCAATCTTTGCA
1 GGTTTCTAAAGCCCAACCAATCTTTGCA
45648 ACAGTGCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (28 bp):
GGTTTCTAAAGCCCAACCAATCTTTGCA
Found at i:51764 original size:12 final size:12
Alignment explanation
Indices: 51747--51771 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
51737 GGAGGCTAAG
51747 TTTGTGTTAGTA
1 TTTGTGTTAGTA
51759 TTTGTGTTAGTA
1 TTTGTGTTAGTA
51771 T
1 T
51772 AAATAGAGAT
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:0.16, C:0.00, G:0.24, T:0.60
Consensus pattern (12 bp):
TTTGTGTTAGTA
Found at i:56276 original size:23 final size:22
Alignment explanation
Indices: 56246--56288 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
56236 TTTTTCTGCG
56246 TTTTTTTTAAAATCTTTTTAGA
1 TTTTTTTTAAAATCTTTTTAGA
**
56268 TTTTCTTTTAATTTCTTTTTA
1 TTTT-TTTTAAAATCTTTTTA
56289 TCTTTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTTTTTTAAAATCTTTTTAGA
Found at i:58625 original size:131 final size:132
Alignment explanation
Indices: 58389--58649 Score: 425
Period size: 131 Copynumber: 2.0 Consensus size: 132
58379 TGTTGGTTCC
* * *
58389 TTTGCTCAGTGTTTGGTTTGTTTCTTTTTCTCCTAATTAGTAATCTTCTTTTATTCAAGAGCGTG
1 TTTGCTCAGTGTTTGGTTTGTTTCTTTTTCTCCTAATTAATAATCCTCTTTTATTCAAGAGCCTG
* *
58454 CAGGGTTCTTCCCATCTTTGCAAACCCAATTTCCAAAAGCAAATTTTTAGAGGAAAAAGCAGAGG
66 CAGGGTTCTTCCCATCTTTGCAAAACCAATTTCCAAAAGCAAATTATTAGAGGAAAAAGCAGAGG
58519 TA
131 TA
*
58521 TTTGCTTAGTGTTTGGTTTGTTTCTTTTTCTCCTAATTAATAA-CCTCTTTTATTCAAGAGCCTG
1 TTTGCTCAGTGTTTGGTTTGTTTCTTTTTCTCCTAATTAATAATCCTCTTTTATTCAAGAGCCTG
* ** *
58585 CAGTGTTCTTCCCATCTTTGCAAAACCAATTTCCCGAAGCAAATTATTAGCGGAAAAAGCAGAGG
66 CAGGGTTCTTCCCATCTTTGCAAAACCAATTTCCAAAAGCAAATTATTAGAGGAAAAAGCAGAGG
58650 CAATTATAAA
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
131 78 0.66
132 41 0.34
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (132 bp):
TTTGCTCAGTGTTTGGTTTGTTTCTTTTTCTCCTAATTAATAATCCTCTTTTATTCAAGAGCCTG
CAGGGTTCTTCCCATCTTTGCAAAACCAATTTCCAAAAGCAAATTATTAGAGGAAAAAGCAGAGG
TA
Found at i:64574 original size:336 final size:331
Alignment explanation
Indices: 63421--64629 Score: 1064
Period size: 336 Copynumber: 3.6 Consensus size: 331
63411 AATTTGACGT
* * * * ** * **
63421 CAAAAAAATTGAAGGCCTTTTAACACTTCTAATATTATTTTTC-CTTTTTTTCCGAATTAATTTC
1 CAAAAAGATTGAA-GACTTTTCACGCTTCTAATATCGTTTTTCTATTTTTTTCTAAATTAATTTC
63485 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
65 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* *
63550 TTTGGTTAGATGAATATAGATATTTGATATTTCAAGGAGTCTTTGCACAAAAAATCATGCAAAAT
130 TTTGGTTAGAT-AA-AT--ATA---GATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAAC
*** * * *
63615 TGAGGTGGGTCCCGAAACGCGTTTTTTTAGC-CAAAAACCGTGATGGTTATAAACAATATATATG
188 TGACCCGGGCCCCGGAACGCG--TTTTTAACACAAAAACCGTGAT-G--AT--AC-----A-A--
* *
63679 ATTTCGGCT-AAAATTTAGCAAAAATTGA-ACCGAAAGATTTTTCCTCAATTTCTAGCGA-AACT
238 ATTTCGGCTAAAAATTT-GCAAAAATTGACA-CGAAATATTTTTCCTCAATTT-TAGCCACAA-T
*
63741 AATCATAA-A-A-AATATATA-AT--TT-AACGC
299 -ATCATAATATATAATATATATATAATTCAACTC
* * *
63768 CAAAAAAATTGAAAGCCTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATTAAT
1 CAAAAAGATTG-AAGAC-TTTTCACGCTTCTAATATCGTTTTT-CTATTTT-TTTCTAAATTAAT
* * * * * *
63833 TTCTGATTAACTCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATACAATGTGGATG
62 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * * * ** * *
63898 ATATTTGGTTAGATGAATATAGATATATTTTAAGGAGTCTTGGCGGCAAAAATCATACAAAAATG
127 AGATTTGGTTAGATAAATATAG--ATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTG
* * ** * * ** *
63963 ACTCGGGACCCCGG-ACAACGTTTTTCGCCAAAAAAATCGT--T-AT----GGTTCGGCTAAAAT
190 ACCCGGG-CCCCGGAAC-GCGTTTTT-AACACAAAAACCGTGATGATACAAATTTCGGCTAAAAA
* * * * *
64020 TTTGCAAAAATTGACCCGAAATATTTTT-TTCAATTTTTAGCCACAAT-TGACAATACTCATAAA
252 TTTGCAAAAATTGACACGAAATATTTTTCCTCAA-TTTTAGCCACAATATCATAATA-T-ATAAT
*
64083 AGAATATATAATTCAACGT-
314 A-TATATATAATTCAAC-TC
* * * * *
64102 CAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCATTTTTCTTTTTCTTTTTTACAAATTAAT
1 CAAAAAGATTGAA-GACTTTTCACGCTTCTAATATCGTTTTTCTATTT-TTTTCT--AAATTAAT
* * * * * * * * *
64167 TTCTAATTAAATAGAACCATGAATCAAATGCGCATAAAAACAAATCCTTAAATCCAATGTGCCTA
62 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
64232 AGATTTGGTTAGATAAATATAGATATTTCAAGGAGT-TTTGCCACCAAAAATCATGCAAAACTGA
127 AGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTG-CACCAAAAATCATGCAAAACTGA
64296 CCCAGGGCCCCGGAACGCGTTTTTAACACAAAAACCGTGATGATACACAATTTCGGCTAAAAATT
191 CCC-GGGCCCCGGAACGCGTTTTTAACACAAAAACCGTGATGATACA-AATTTCGGCTAAAAATT
*
64361 TGGAAAAATTGACACGAAATATTTTTCCTCAATATTTAGCCACAATACTCATAATATATATATAT
254 TGCAAAAATTGACACGAAATATTTTTCCTCAAT-TTTAGCCACAATA-TCATAATATATA-ATAT
64426 ATATATAATTCAACTC
316 ATATATAATTCAACTC
* * * *
64442 CAAAAAGATTGGAGTACTTTTCACGCTTTTAATATCGTTTTT-GATATTTTTCTAAATTAATTTC
1 CAAAAAGATTGAAG-ACTTTTCACGCTTCTAATATCGTTTTTCTATTTTTTTCTAAATTAATTTC
* * *
64506 TAATTAAATTGAAACAAGGTTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGA
65 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * *
64571 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAACT
130 TTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACT
64630 AAGCCGAGAC
Statistics
Matches: 700, Mismatches: 113, Indels: 109
0.76 0.12 0.12
Matches are distributed among these distances:
324 4 0.01
325 1 0.00
326 10 0.01
327 34 0.05
328 7 0.01
329 3 0.00
330 3 0.00
331 15 0.02
332 55 0.08
333 34 0.05
334 95 0.14
336 116 0.17
337 3 0.00
338 5 0.01
339 42 0.06
340 68 0.10
341 5 0.01
342 6 0.01
344 1 0.00
345 6 0.01
346 41 0.06
347 31 0.04
348 23 0.03
349 3 0.00
350 5 0.01
351 84 0.12
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.33
Consensus pattern (331 bp):
CAAAAAGATTGAAGACTTTTCACGCTTCTAATATCGTTTTTCTATTTTTTTCTAAATTAATTTCT
AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
TTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTGCACCAAAAATCATGCAAAACTGACCCGG
GCCCCGGAACGCGTTTTTAACACAAAAACCGTGATGATACAAATTTCGGCTAAAAATTTGCAAAA
ATTGACACGAAATATTTTTCCTCAATTTTAGCCACAATATCATAATATATAATATATATATAATT
CAACTC
Found at i:64764 original size:336 final size:334
Alignment explanation
Indices: 63327--64766 Score: 719
Period size: 336 Copynumber: 4.3 Consensus size: 334
63317 TGATGGTTAG
* * * * * * * * * * *
63327 TACACGATTTCGGCTAAAATTTTACAAAAATTGACCCAAAAGATATTTCCTCAATTTTTGGCTA-
1 TACACAATTTCGGCAAAAAATTTACAAAAAATGACACGAAATATTTTTCCTCAATATTTAGCCAC
* ** * * * * *
63391 AAATACTCAT-AAA-A-ATATATAATTTGACGTCAAAAAAATTGAAGGCCTTTTAACACTTCTAA
66 AAATAATCATAAAATATATATATAATTCAACGTCAAAAAGATTGAAGGACTTCTCACGCTTCTAA
* * * ** * * * *
63453 TATTATTTTTC-CT-TTTTTTC-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
131 TATCATTTTTCGATATCTTTTCTAAAATTAATTTCTAATTAAATAGAAACAAGAATCAAATGCGC
* * * *
63515 GTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTGATAT
196 ATAAAAACAAATCCTTAAATCCAATGTGCCTAAGATTTGATTAGAT-AA-AT--ATA---GATAT
* * * * *** ** * *
63580 TTCAAGGAGTCTTTG-CACAAAAAATCATGCAAAATTGA-GGTGGGTCCCGAAACGCGTTTTTTT
254 TTCAAGGAGT-TCTGCCACCAAAAATCATGCAAAACTAACCCAGGACCCCAAAACGCG-TTTTTA
*** *
63643 AGCCAAAAACCGTGATGGTTA
317 AAAAAAAAAACGTGAT-G--A
* * * *
63664 TAAACAATATATATGATTTCGGC-TAAAATTTAGCAAAAATTGA-ACCGAAAGATTTTTCCTCAA
1 T--AC-----ACA--ATTTCGGCAAAAAATTTA-CAAAAAATGACA-CGAAATATTTTTCCTCAA
* * * * * * *
63727 T-TTCTAGCGA-AACTAATCATAAAA-A-ATATATAATTTAACGCCAAAAAAATTGAAAGCCTTT
55 TATT-TAGCCACAAATAATCATAAAATATATATATAATTCAACGTCAAAAAGATTGAAGGAC-TT
* * * * * * * *
63788 TTCACGCTTCTAATATCGTTTTTC-CTAT-TTTATTTCCAAATTAATTTCTGATTAACTCGAAAC
118 CTCACGCTTCTAATATCATTTTTCGATATCTTT-TCT-AAAATTAATTTCTAATTAAATAGAAAC
* * * * * * * ** * * * *
63851 AAGATTTAGATACTCGTAAAAACAAATCCTTAAATACAATGTGGATGATATTTGGTTAGATGAAT
181 AAGAATCAAATGCGCATAAAAACAAATCCTTAAATCCAATGTGCCTAAGATTTGATTAGATAAAT
* * ** * * * * * *
63916 ATAGATATATTTTAAGGAG-TCTTGGCGGCAAAAATCATACAAAAATGACTCGGGACCCCGGACA
246 ATAG--ATATTTCAAGGAGTTC-TGCCACCAAAAATCATGCAAAACTAACCCAGGACCCC--AAA
*** *
63980 A--CGTTTTTCGCCAAAAAAATCGT--T-A
306 ACGCGTTTTT-AAAAAAAAAAACGTGATGA
** * * * * * * *
64005 T-----GGTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTT-TTCAATTTTTAGCCAC
1 TACACAATTTCGGCAAAAAATTTACAAAAAATGACACGAAATATTTTTCCTCAATATTTAGCCAC
* * *
64064 AATTGACAATACTCATAAAAGA-ATATATAATTCAACGTCAAAAAGATTGAAGGGCTTCTCACGC
66 -----A-AATAATCATAAAATATATATATAATTCAACGTCAAAAAGATTGAAGGACTTCTCACGC
** * * * *
64128 TTCTAATATCATTTTTCTTTTTCTTTTTTACAAATTAATTTCTAATTAAATAGAACCATGAATCA
125 TTCTAATATCATTTTTCGATATCTTTTCTA-AAATTAATTTCTAATTAAATAGAAACAAGAATCA
*
64193 AATGCGCATAAAAACAAATCCTTAAATCCAATGTGCCTAAGATTTGGTTAGATAAATATAGATAT
189 AATGCGCATAAAAACAAATCCTTAAATCCAATGTGCCTAAGATTTGATTAGATAAATATAGATAT
* * * ** *
64258 TTCAAGGAGTTTTGCCACCAAAAATCATGCAAAACTGACCCAGGGCCCCGGAACGCGTTTTTAAC
254 TTCAAGGAGTTCTGCCACCAAAAATCATGCAAAACTAACCCAGGACCCCAAAACGCGTTTTTAAA
* *
64323 ACAAAAACCGTGATGA
319 AAAAAAAACGTGATGA
* ** *
64339 TACACAATTTCGGCTAAAAATTTGGAAAAATTGACACGAAATATTTTTCCTCAATATTTAGCCAC
1 TACACAATTTCGGCAAAAAATTTACAAAAAATGACACGAAATATTTTTCCTCAATATTTAGCCAC
* * * * *
64404 AATACTCATAATATATATATATATATATAATTCAAC-TCCAAAAAGATTGGAGTACTTTTCACGC
66 AA-A-TAATCATA-A-A-ATATATATATAATTCAACGT-CAAAAAGATTGAAGGACTTCTCACGC
* * * ** *
64468 TTTTAATATCGTTTTT-GATAT-TTTTCT-AAATTAATTTCTAATTAAATTGAAACAAGGTTCAG
125 TTCTAATATCATTTTTCGATATCTTTTCTAAAATTAATTTCTAATTAAATAGAAACAAGAATCAA
* * * * * *
64530 ATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATATAGATATT
190 ATGCGCATAAAAACAAATCCTTAAATCCAATGTGCCTAAGATTTGATTAGATAAATATAGATATT
* * *
64595 TCAAGGAGTCTCTG-CGCCAAAAATCATGCAAAACTAAGCC-GAGACTCCAAAACGCGTTTTTAG
255 TCAAGGAGT-TCTGCCACCAAAAATCATGCAAAACTAACCCAG-GACCCCAAAACGCGTTTTTA-
*
64658 CCAAAAAAAAGTAACGTGATGGTTTG
317 --AAAAAAAA--AACGTGAT-G---A
** * * * * *
64684 TACATGATTTCGGCAAAAAATTTACAAAAAATGAC-CTAAAT-TTTTT-TTCAATTTTTGGCTA-
1 TACACAATTTCGGCAAAAAATTTACAAAAAATGACACGAAATATTTTTCCTCAATATTTAGCCAC
64745 AAATAATCATAAAATATATATA
66 AAATAATCATAAAATATATATA
64767 ATTTTACGCC
Statistics
Matches: 872, Mismatches: 161, Indels: 141
0.74 0.14 0.12
Matches are distributed among these distances:
326 10 0.01
327 29 0.03
328 6 0.01
330 2 0.00
331 10 0.01
332 49 0.06
333 37 0.04
334 115 0.13
335 6 0.01
336 149 0.17
337 6 0.01
338 7 0.01
339 56 0.06
340 65 0.07
341 11 0.01
342 12 0.01
343 5 0.01
344 8 0.01
345 41 0.05
346 82 0.09
347 52 0.06
348 27 0.03
349 6 0.01
350 1 0.00
351 80 0.09
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (334 bp):
TACACAATTTCGGCAAAAAATTTACAAAAAATGACACGAAATATTTTTCCTCAATATTTAGCCAC
AAATAATCATAAAATATATATATAATTCAACGTCAAAAAGATTGAAGGACTTCTCACGCTTCTAA
TATCATTTTTCGATATCTTTTCTAAAATTAATTTCTAATTAAATAGAAACAAGAATCAAATGCGC
ATAAAAACAAATCCTTAAATCCAATGTGCCTAAGATTTGATTAGATAAATATAGATATTTCAAGG
AGTTCTGCCACCAAAAATCATGCAAAACTAACCCAGGACCCCAAAACGCGTTTTTAAAAAAAAAA
ACGTGATGA
Found at i:68993 original size:48 final size:48
Alignment explanation
Indices: 68922--69062 Score: 273
Period size: 48 Copynumber: 2.9 Consensus size: 48
68912 AAGATTACAC
*
68922 CTTGTAACAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
68970 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
69018 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCA
1 CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCA
69063 AACAAGAGTT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 92 1.00
ACGTcount: A:0.45, C:0.09, G:0.26, T:0.21
Consensus pattern (48 bp):
CTTGTAAAAACAAGGGTGATGAAAAGTAAAAGATAGGGTTGATCACAA
Found at i:69037 original size:25 final size:26
Alignment explanation
Indices: 68956--69034 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
68946 AGTAAAAGAT
68956 AGGGTTGATCACAACTTGTAAAAACA
1 AGGGTTGATCACAACTTGTAAAAACA
* * *
68982 AGGG-TGATGA-AA--AGTAAAAGA-T
1 AGGGTTGATCACAACTTGTAAAA-ACA
69004 AGGGTTGATCACAACTTGTAAAAACA
1 AGGGTTGATCACAACTTGTAAAAACA
69030 AGGGT
1 AGGGT
69035 GATGAAAAGT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
22 10 0.24
23 6 0.15
24 4 0.10
25 6 0.15
26 15 0.37
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.22
Consensus pattern (26 bp):
AGGGTTGATCACAACTTGTAAAAACA
Found at i:69055 original size:22 final size:22
Alignment explanation
Indices: 68934--69056 Score: 88
Period size: 22 Copynumber: 5.2 Consensus size: 22
68924 TGTAACAACA
68934 AGGGTGATGAAAAGTAAAAGAT
1 AGGGTGATGAAAAGTAAAAGAT
* * *
68956 AGGGTTGATCACAACTTGTAAAA-ACA
1 AGGG-TGATGA-AA--AGTAAAAGA-T
68982 AGGGTGATGAAAAGTAAAAGAT
1 AGGGTGATGAAAAGTAAAAGAT
* * *
69004 AGGGTTGATCACAACTTGTAAAA-ACA
1 AGGG-TGATGA-AA--AGTAAAAGA-T
69030 AGGGTGATGAAAAGTAAAAGAT
1 AGGGTGATGAAAAGTAAAAGAT
69052 AGGGT
1 AGGGT
69057 TGATCAAACA
Statistics
Matches: 77, Mismatches: 12, Indels: 24
0.68 0.11 0.21
Matches are distributed among these distances:
22 25 0.32
23 12 0.16
24 8 0.10
25 12 0.16
26 20 0.26
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.20
Consensus pattern (22 bp):
AGGGTGATGAAAAGTAAAAGAT
Done.