Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000353.1 Hibiscus syriacus cultivar Beakdansim tig00000647_pilon, 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: 86557
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:13941 original size:29 final size:29
Alignment explanation
Indices: 13865--13971 Score: 85
Period size: 29 Copynumber: 3.7 Consensus size: 29
13855 AGAAATCTCA
* *
13865 AAACAAATCAGGG-AACAAATCTCATACAG
1 AAACAGATC-GGGAAACAAATCCCATACAG
* * * *
13894 -AACATATCGATG-AGCAAATCTCATACAG
1 AAACAGATCG-GGAAACAAATCCCATACAG
* *
13922 AAACAGATCGGGAAATAAATCCCATACAT
1 AAACAGATCGGGAAACAAATCCCATACAG
* *
13951 AAATAGATCGGGGAACAAATC
1 AAACAGATCGGGAAACAAATC
13972 ATGTACTAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
27 1 0.02
28 24 0.38
29 38 0.60
ACGTcount: A:0.48, C:0.20, G:0.16, T:0.17
Consensus pattern (29 bp):
AAACAGATCGGGAAACAAATCCCATACAG
Found at i:15549 original size:21 final size:21
Alignment explanation
Indices: 15523--15568 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
15513 TAATAAAAAA
15523 TTTATTTAAAATATT-ATTATT
1 TTTATTTAAAATATTAATT-TT
15544 TTTATTTAAAATATTAATTTT
1 TTTATTTAAAATATTAATTTT
15565 TTTA
1 TTTA
15569 ATATTTCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTATTTAAAATATTAATTTT
Found at i:23755 original size:21 final size:20
Alignment explanation
Indices: 23729--23767 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
23719 CGGGTCAAAT
*
23729 GAGATAAGATTTATCAAGTGA
1 GAGATAAGAGTTAT-AAGTGA
23750 GAGATAAGAGTTATAAGT
1 GAGATAAGAGTTATAAGT
23768 ATTGATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.44, C:0.03, G:0.26, T:0.28
Consensus pattern (20 bp):
GAGATAAGAGTTATAAGTGA
Found at i:24687 original size:36 final size:36
Alignment explanation
Indices: 24640--24780 Score: 246
Period size: 36 Copynumber: 3.9 Consensus size: 36
24630 TTGAGTATTT
* *
24640 ATATCAACTTTGGTACATTCATGTATCAATGTTATC
1 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
*
24676 ATATCATCTTTGGTACATTCGTGTATCAATGTTATC
1 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
*
24712 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATT
1 ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
24748 ATATCAGCTTTGGTACATTCGTGTATCAATGTT
1 ATATCAGCTTTGGTACATTCGTGTATCAATGTT
24781 CAGCACCGTT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 101 1.00
ACGTcount: A:0.26, C:0.16, G:0.15, T:0.43
Consensus pattern (36 bp):
ATATCAGCTTTGGTACATTCGTGTATCAATGTTATC
Found at i:25104 original size:28 final size:28
Alignment explanation
Indices: 25046--25106 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
25036 ATTATATGAT
* * * **
25046 ATGTTACAAATGTTGAGTATAAGATGGC
1 ATGTTACAAAGGTTAAGTACAAGATAAC
25074 ATGTTACAAAGGTTAAGTACAAGATAAC
1 ATGTTACAAAGGTTAAGTACAAGATAAC
25102 ATGTT
1 ATGTT
25107 TTAAATGGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (28 bp):
ATGTTACAAAGGTTAAGTACAAGATAAC
Found at i:26485 original size:9 final size:9
Alignment explanation
Indices: 26459--26543 Score: 71
Period size: 9 Copynumber: 9.0 Consensus size: 9
26449 GCTGGAAACT
*
26459 GGTTTAACC
1 GGTTTGACC
26468 GGTTCTGACC
1 GGTT-TGACC
26478 GGTTTGACC
1 GGTTTGACC
*
26487 GGTTTCGATC
1 GGTTT-GACC
* *
26497 AGTTCGAACC
1 GGTTTG-ACC
26507 GGTTTGACC
1 GGTTTGACC
*
26516 GGTCTGAACC
1 GGTTTG-ACC
*
26526 GGTTTGACT
1 GGTTTGACC
*
26535 GGTCTGACC
1 GGTTTGACC
26544 CGACCGACCG
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
9 32 0.53
10 28 0.47
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.31
Consensus pattern (9 bp):
GGTTTGACC
Found at i:26487 original size:19 final size:19
Alignment explanation
Indices: 26464--26541 Score: 79
Period size: 19 Copynumber: 4.1 Consensus size: 19
26454 AAACTGGTTT
*
26464 AACCGGTTCTGACCGGTTTG
1 AACCGGTT-TGACCGGTCTG
* *
26484 -ACCGGTTTCGATCAGT-TCG
1 AACCGGTTT-GACCGGTCT-G
26503 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
26522 AACCGGTTTGACTGGTCTG
1 AACCGGTTTGACCGGTCTG
26541 A
1 A
26542 CCCGACCGAC
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.04
19 38 0.78
20 9 0.18
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:26576 original size:22 final size:22
Alignment explanation
Indices: 26551--26593 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
26541 ACCCGACCGA
26551 CCGACCCGACCCGACCGTTGAC
1 CCGACCCGACCCGACCGTTGAC
* *
26573 CCGACCCGACCGGATCGTTGA
1 CCGACCCGACCCGACCGTTGA
26594 TCGTTGACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.44, G:0.26, T:0.12
Consensus pattern (22 bp):
CCGACCCGACCCGACCGTTGAC
Found at i:29121 original size:31 final size:31
Alignment explanation
Indices: 29077--29144 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
29067 TTATTAATTT
*
29077 TTTAAA-TCAATAAAATGCAAGAAAAAATAA
1 TTTAAAGTCAATAAAATGCAAGAAAAAAGAA
* * *
29107 TTTAAAGTGAATAAAATTCAATAAAAAAGAA
1 TTTAAAGTCAATAAAATGCAAGAAAAAAGAA
*
29138 TGTAAAG
1 TTTAAAG
29145 CTAAAAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.60, C:0.04, G:0.10, T:0.25
Consensus pattern (31 bp):
TTTAAAGTCAATAAAATGCAAGAAAAAAGAA
Found at i:29165 original size:38 final size:39
Alignment explanation
Indices: 29118--29194 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
29108 TTAAAGTGAA
29118 TAAAATTCAAT-AAAAAAGAATGTAAAGCTAAAAAATAT
1 TAAAATTCAATAAAAAAAGAATGTAAAGCTAAAAAATAT
* *
29156 TAAATTTCAATAAAAAAATAATGTAAAGCTAAAAAATAT
1 TAAAATTCAATAAAAAAAGAATGTAAAGCTAAAAAATAT
29195 CACCTCTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 10 0.28
39 26 0.72
ACGTcount: A:0.62, C:0.05, G:0.06, T:0.26
Consensus pattern (39 bp):
TAAAATTCAATAAAAAAAGAATGTAAAGCTAAAAAATAT
Found at i:29189 original size:18 final size:18
Alignment explanation
Indices: 29128--29193 Score: 55
Period size: 18 Copynumber: 3.5 Consensus size: 18
29118 TAAAATTCAA
*
29128 TAAAAAAGAATGTAAAGC
1 TAAAAAATAATGTAAAGC
*
29146 TAAAAAAT-AT-TAAATTTC
1 TAAAAAATAATGTAAA--GC
29164 AATAAAAAAATAATGTAAAGC
1 --T-AAAAAATAATGTAAAGC
29185 TAAAAAATA
1 TAAAAAATA
29194 TCACCTCTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
16 4 0.11
17 2 0.05
18 16 0.42
19 1 0.03
20 1 0.03
21 8 0.21
22 2 0.05
23 4 0.11
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.24
Consensus pattern (18 bp):
TAAAAAATAATGTAAAGC
Found at i:30625 original size:341 final size:339
Alignment explanation
Indices: 29261--31603 Score: 3408
Period size: 341 Copynumber: 7.0 Consensus size: 339
29251 ATATTAAATT
* * * *
29261 ATAATTTTATTAAAAATGAATAAACATTATTAATTGTTGTTAAAAAATAATAATTACTGAATAAC
1 ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAAT
*
29326 AATTCATTTGA-TCCTTCAATTGTAATTAAAAGTTTATTCTAATATTTTTTTATATTTTTAAACA
66 AATTCATTTGATTCC-TCAATTGTAATTAAAAGTTTATTTTAATA-TTTTTTATATTTTTAAACA
* **
29390 ATTAATTTTAAAATTCAATTAA-AATTTCAAAAATATATGAAATTTATAATTTTTTAAATTAT-A
129 ATTAATTTTAAAAATCAA-TAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAA
* *
29453 AA-A--TATT-TATCAT--CATCAT--TTTGTA-AAAA-AAATACTAGTTATAAATTTTTTATAC
193 AATATTTATTATATCATCACATCATCATTT-TATAAAATAAATACTAGTTATAAA-ATTTTATAA
* * * *
29508 AATTATTTATATTTTAAAATACTTACCCTCAAAGTTTTCATATACTAGATTATACGTATTCTATA
256 AATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTA
* *
29573 ATTTCATGGAAAAAATAAAA
321 ATTTCAT-GCAAAAATCAAA
* * * *
29593 ATAAATTTATTAAAAATGAATAAACAATATCAACTGTTGTTAAAAAATAATAATTAATGTATTAT
1 ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAAT
* * *
29658 AATTCATTTGATCCCTCAAATATAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
66 AATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
* *
29723 TAATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTAT-AAA-
131 TAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
29786 A--TATT-TATCAT--CATCATCATTTTATAAAATAAATACTAGTTATAAAACTTTTATAAAATT
196 ATTTATTATATCATCACATCATCATTTTATAAAATAAATACTAGTTATAAAA-TTTTATAAAATT
* * *
29846 ATTCATATTTTAAAATACTTGCTCTCAAAGTTTTTCTATACTAGATTATACGTATTGTGTAATTT
260 ATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTT
29911 CATGCAAAAATCAAA
325 CATGCAAAAATCAAA
* *
29926 ATAATTTTATTAAAAATGAATAAGCCTTATCAACTGTTGTT-AAAAATAATAATTAAT-ACATAA
1 ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGA-ATAA
* * *
29989 TAATTCATTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAATA-TTTTTATATTTTTAAATAA
65 TAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAA
* * *
30053 TTAATTTTAAAAGTCAACAAATTTTTT-AAAAATATTTGAAATTTATAATTTTTTAAATTATAAA
130 TTAATTTTAAAAATCAA-TAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAA
* * * *
30117 ATATTTATTAT-T-ATCATCATCATCATTTTGTAAAATAAATAATAGTTGTAAATTTTTTATAAA
194 ATATTTATTATATCATCA-CATCATCATTTTATAAAATAAATACTAGTTATAAA-ATTTTATAAA
* *
30180 ATTATTCATATTTTAAAATAATTACCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAA
257 ATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAA
30245 TTTCATGCAAAAATCAAA
322 TTTCATGCAAAAATCAAA
*
30263 ATAATTTTATTAAAAATGAATAAACATTATCAAGTGTTGTTAAAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAAT
* *
30328 AATTCATTTGATTCCTCAATTGTAATTAATATTTTATTTTAATATTTTTTATA-TTTTAAACAAT
66 AATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
30392 TAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
131 TAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
30457 ATTTATTATCATCATCAACATCATCATTTTATAAAATAAATACTAGTTATAGAAATTTTATAAAA
196 ATTTATTAT-ATCATC-ACATCATCATTTTATAAAATAAATACTAGTTATA-AAATTTTATAAAA
*
30522 TTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAAT
258 TTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAAT
*
30587 TTCATTCAAAAATCAAA
323 TTCATGCAAAAATCAAA
* *
30604 ATAATTTTATTAAAAATGAATAAACATTATCAATTTTTGTTAAAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAAT
30669 AATTCATTTGATTCCTCAATTGTAATTTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAA
66 AATTCATTTGATTCCTCAATTGTAA-TTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAA
* * *
30734 TTAATTTTAAAAGTCAA-ATTTTTTTTTAAAAATATATGAAATTTATAA--TTTTAAATTATAAA
130 TTAATTTTAAAAATCAATA-ATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAA
*
30796 ATATTTATTAT-T-ATCATCATCATCATTTTATAAAATAAATACTAGTTGTAAAAATTTTATAAA
194 ATATTTATTATATCATCA-CATCATCATTTTATAAAATAAATACTAGTTAT-AAAATTTTATAAA
* *
30859 ATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAA
257 ATTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAA
30924 TTTCATGCAAAAATCAAA
322 TTTCATGCAAAAATCAAA
* * *
30942 ATAATTTTATTAAAAATAAATAAACATTATCAACTATTGTTAAAAAATAACAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAAT
*
31007 AATTCATTTAATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
66 AATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
* * *
31072 TAATTTTTAAAATAAATAA-ATTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
131 TAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
*
31136 ATTTATTATCATCATCAACATCATCATTTTGTAAAATAAATACTAGTTATAAAATTTTTATAAAA
196 ATTTATTAT-ATCATC-ACATCATCATTTTATAAAATAAATACTAGTTATAAAA-TTTTATAAAA
* * *
31201 TTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCTTATACTAAATTATACGTATTGTGTAAT
258 TTATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAAT
*
31266 TTCATACAAAAATCAAA
323 TTCATGCAAAAATCAAA
* *
31283 ATAATTTTATTAAAAATAAATAAACATTATCAA---TTGTT-----GT--TAA--AA--AATAAT
1 ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAAT
* * *
31334 AATTCATTTGATTCCACAATTATAGTTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
66 AATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
*
31399 TAATTTTAAAAATCAATAATTTTTTCTAAAATATATGAAATTTATAATTTTTTAAATTAT-AAA-
131 TAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
*
31462 A--TATT-TATCAT--CATCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATT
196 ATTTATTATATCATCACATCATCATTTTATAAAATAAATACTAGTTATAAAA-TTTTATAAAATT
* * *
31522 ATTCATATTTTAAAATACTTACTCTTAAAGTTTTCCTATATTAGATTATACGTATTGTGTAATTT
260 ATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTT
*
31587 CATGCATAAATCAAA
325 CATGCAAAAATCAAA
31602 AT
1 AT
31604 TTATCGAGTT
Statistics
Matches: 1860, Mismatches: 110, Indels: 95
0.90 0.05 0.05
Matches are distributed among these distances:
319 122 0.07
322 5 0.00
323 1 0.00
324 4 0.00
326 1 0.00
327 87 0.05
328 38 0.02
329 2 0.00
330 3 0.00
331 164 0.09
332 169 0.09
333 58 0.03
334 90 0.05
335 5 0.00
336 26 0.01
337 219 0.12
338 376 0.20
339 11 0.01
340 6 0.00
341 389 0.21
342 31 0.02
343 53 0.03
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (339 bp):
ATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATGAATAAT
AATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAAT
TAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
ATTTATTATATCATCACATCATCATTTTATAAAATAAATACTAGTTATAAAATTTTATAAAATTA
TTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTC
ATGCAAAAATCAAA
Found at i:30906 original size:679 final size:672
Alignment explanation
Indices: 29261--31603 Score: 3471
Period size: 679 Copynumber: 3.5 Consensus size: 672
29251 ATATTAAATT
* * *
29261 ATAATTTTATTAAAAATGAATAAACATTATTAATTGTTGTTAAAAAATAATAATTACTGAATAAC
1 ATAATTTTATTAAAAATGAATAAACATTATCAATTGTTGTT-AAAAATAATAATTAAT-AATAAT
*
29326 AATTCATTTGA-TCCTTCAATTGTAATTAAAAGTTTATTCTAATATTTTTTTATATTTTTAAACA
64 AATTCATTTGATTCC-TCAATTGTAATTAAAAGTTTATTTTAATA-TTTTTTATATTTTTAAACA
* ** *
29390 ATTAATTTTAAAATTC-A-ATTAAAATTTCAAAAATATATGAAATTTATAATTTTTTAAATTATA
127 ATTAATTTTAAAAGTCAACATT-ATTTTTTAAAAATATATGAAATTTATAA-TTTTTAAATTATA
* *
29453 AAATATTTATCATCATCAT--TTTGTA-AAAA-AAATACTAGTTATAAATTTTTTATACAATTAT
190 AAATATTTATCATCATCATCATTT-TATAAAATAAATACTAGTTATAAAATTTTTATAAAATTAT
* * * *
29514 TTATATTTTAAAATACTTACCCTCAAAGTTTTCATATACTAGATTATACGTATTCTATAATTTCA
254 TCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCA
* * * *
29579 TGGAAAAAATAAAAATAAATTTATTAAAAATGAATAAACAATATCAACTGTTGTTAAAAAATAAT
319 T-GCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAAT
* * * * *
29644 AATTAATGTATTATAATTCATTTGATCCCTCAAATATAATTAAAAGTTTATTTTAATATTTTTTA
383 AATTAATGAATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTA
*
29709 TATTTTTAAACAATTAATTTTAAAAGTCAATAAATTTTTCAAAAATATATGAAATTTATAATTTT
448 TATTTTTAAACAATTAATTTTAAAAATCAAT-AATTTTTCAAAAATATATGAAATTTATAATTTT
29774 TTAAATTAT-AAA-A--TATT-T-ATCAT---CATCATCATTTTATAAAATAAATACTAGTTATA
512 TTAAATTATAAAATATTTATTATCATCATCAACATCATCATTTTATAAAATAAATACTAGTTATA
* * * *
29830 AAACTTTTATAAAATTATTCATATTTTAAAATACTTGCTCTCAAAGTTTTTCTATACTAGATTAT
577 AAACTTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTAT
*
29895 ACGTATTGTGTAATTTCATGCAAAAATCAAA
642 ACGTATTGTGTAATTTCATACAAAAATCAAA
* * *
29926 ATAATTTTATTAAAAATGAATAAGCCTTATCAACTGTTGTTAAAAATAATAATTAATACATAATA
1 ATAATTTTATTAAAAATGAATAAACATTATCAATTGTTGTTAAAAATAATAATTAATA-ATAATA
* * *
29991 ATTCATTTGATCCCTCAAATGTAATTAAAAGTTTATTTTAATA-TTTTTATATTTTTAAATAATT
65 ATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATT
* *
30055 AATTTTAAAAGTCAACA-AATTTTTTAAAAATATTTGAAATTTATAATTTTTTAAATTATAAAAT
130 AATTTTAAAAGTCAACATTATTTTTTAAAAATATATGAAATTTATAA-TTTTTAAATTAT-AAA-
* * * *
30119 ATTTATTATTATCATCATCATCATTTTGTAAAATAAATAATAGTTGTAAATTTTTTATAAAATTA
192 A--TA-T-TTATCATCATCATCATTTTATAAAATAAATACTAGTTATAAAATTTTTATAAAATTA
* *
30184 TTCATATTTTAAAATAATTACCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTTC
253 TTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTC
*
30249 ATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATCAAGTGTTGTTAAAAAATAAT
318 ATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAAT
* *
30314 AATTAATGAATAATAATTCATTTGATTCCTCAATTGTAATTAATATTTTATTTTAATATTTTTTA
383 AATTAATGAATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTA
30379 TA-TTTTAAACAATTAATTTTAAAAATCAATAATTTTTTCAAAAATATATGAAATTTATAATTTT
448 TATTTTTAAACAATTAATTTTAAAAATCAATAA-TTTTTCAAAAATATATGAAATTTATAATTTT
30443 TTAAATTATAAAATATTTATTATCATCATCAACATCATCATTTTATAAAATAAATACTAGTTATA
512 TTAAATTATAAAATATTTATTATCATCATCAACATCATCATTTTATAAAATAAATACTAGTTATA
30508 GAAA-TTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTA
577 -AAACTTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTA
*
30572 TACGTATTGTGTAATTTCATTCAAAAATCAAA
641 TACGTATTGTGTAATTTCATACAAAAATCAAA
*
30604 ATAATTTTATTAAAAATGAATAAACATTATCAATTTTTGTTAAAAAATAATAATTAATGAATAAT
1 ATAATTTTATTAAAAATGAATAAACATTATCAATTGTTGTT-AAAAATAATAATTAAT-AATAAT
30669 AATTCATTTGATTCCTCAATTGTAATTTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAA
64 AATTCATTTGATTCCTCAATTGTAA-TTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAA
*
30734 TTAATTTTAAAAGTCAA-ATTTTTTTTTAAAAATATATGAAATTTATAA-TTTTAAATTATAAAA
128 TTAATTTTAAAAGTCAACATTATTTTTTAAAAATATATGAAATTTATAATTTTTAAATTAT-AAA
* *
30797 TATTTATTATTATCATCATCATCATTTTATAAAATAAATACTAGTTGTAAAAATTTTATAAAATT
192 -A--TA-T-TTATCATCATCATCATTTTATAAAATAAATACTAGTTATAAAATTTTTATAAAATT
* *
30862 ATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTATATGTATTGTGTAATTT
252 ATTCATATTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTT
* *
30927 CATGCAAAAATCAAAATAATTTTATTAAAAATAAATAAACATTATCAACTATTGTTAAAAAATAA
317 CATGCAAAAATCAAAATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAA
* *
30992 CAATTAATGAATAATAATTCATTTAATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTT
382 TAATTAATGAATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTT
* * *
31057 ATATTTTTAAACAATTAATTTTTAAAATAAATAAATTTTCAAAAATATATGAAATTTATAATTTT
447 ATATTTTTAAACAATTAATTTTAAAAATCAATAATTTTTCAAAAATATATGAAATTTATAATTTT
*
31122 TTAAATTATAAAATATTTATTATCATCATCAACATCATCATTTTGTAAAATAAATACTAGTTATA
512 TTAAATTATAAAATATTTATTATCATCATCAACATCATCATTTTATAAAATAAATACTAGTTATA
* * *
31187 AAATTTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCTTATACTAAATTAT
577 AAACTTTTATAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTAT
31252 ACGTATTGTGTAATTTCATACAAAAATCAAA
642 ACGTATTGTGTAATTTCATACAAAAATCAAA
*
31283 ATAATTTTATTAAAAATAAATAAACATTATCAATTGTTG-------T--TAA--AA-AATAATAA
1 ATAATTTTATTAAAAATGAATAAACATTATCAATTGTTGTTAAAAATAATAATTAATAATAATAA
* * *
31336 TTCATTTGATTCCACAATTATAGTTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTA
66 TTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTA
* * *
31401 ATTTTAAAAATC-A-ATAATTTTTTCTAAAATATATGAAATTTATAATTTTTTAAATTATAAAAT
131 ATTTTAAAAGTCAACATTATTTTTT-AAAAATATATGAAATTTATAA-TTTTTAAATTATAAAAT
* *
31464 ATTTATCATCATCATCATTTTGTAAAATAAATACTAGTTATAAAACTTTTATAAAATTATTCATA
194 ATTTATCATCATCATCATTTTATAAAATAAATACTAGTTATAAAATTTTTATAAAATTATTCATA
* * * *
31529 TTTTAAAATACTTACTCTTAAAGTTTTCCTATATTAGATTATACGTATTGTGTAATTTCATGCAT
259 TTTTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGCAA
31594 AAATCAAAAT
324 AAATCAAAAT
31604 TTATCGAGTT
Statistics
Matches: 1552, Mismatches: 91, Indels: 75
0.90 0.05 0.04
Matches are distributed among these distances:
660 129 0.08
661 1 0.00
662 71 0.05
663 14 0.01
664 133 0.09
665 70 0.05
666 13 0.01
667 3 0.00
668 15 0.01
669 71 0.05
670 128 0.08
671 91 0.06
673 4 0.00
674 1 0.00
675 5 0.00
678 160 0.10
679 533 0.34
680 49 0.03
681 61 0.04
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (672 bp):
ATAATTTTATTAAAAATGAATAAACATTATCAATTGTTGTTAAAAATAATAATTAATAATAATAA
TTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTAAACAATTA
ATTTTAAAAGTCAACATTATTTTTTAAAAATATATGAAATTTATAATTTTTAAATTATAAAATAT
TTATCATCATCATCATTTTATAAAATAAATACTAGTTATAAAATTTTTATAAAATTATTCATATT
TTAAAATACTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGTGTAATTTCATGCAAAA
ATCAAAATAATTTTATTAAAAATGAATAAACATTATCAACTGTTGTTAAAAAATAATAATTAATG
AATAATAATTCATTTGATTCCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTTATATTTTTA
AACAATTAATTTTAAAAATCAATAATTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTAT
AAAATATTTATTATCATCATCAACATCATCATTTTATAAAATAAATACTAGTTATAAAACTTTTA
TAAAATTATTCATATTTTAAAATATTTACCCTCAAAGTTTTCCTATACTAGATTATACGTATTGT
GTAATTTCATACAAAAATCAAA
Found at i:36474 original size:24 final size:22
Alignment explanation
Indices: 36430--36479 Score: 55
Period size: 24 Copynumber: 2.2 Consensus size: 22
36420 TATAGCAGGG
* *
36430 TATTGTTCACGGTACTGTTTAT
1 TATTGTTCACGGTACTATTTAC
*
36452 TATTGTTCATACGGTATTATTTAC
1 TATTGTTC--ACGGTACTATTTAC
36476 TATT
1 TATT
36480 CATACCATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
24 15 0.65
ACGTcount: A:0.22, C:0.12, G:0.14, T:0.52
Consensus pattern (22 bp):
TATTGTTCACGGTACTATTTAC
Found at i:36502 original size:19 final size:21
Alignment explanation
Indices: 36455--36502 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
36445 TGTTTATTAT
**
36455 TGTTCATACGGTATTATTTAC
1 TGTTCATACCATATTATTTAC
*
36476 TATTCATACCATATT-TTT-C
1 TGTTCATACCATATTATTTAC
36495 TGTTCATA
1 TGTTCATA
36503 AAACGTATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 8 0.35
20 3 0.13
21 12 0.52
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (21 bp):
TGTTCATACCATATTATTTAC
Found at i:37599 original size:21 final size:21
Alignment explanation
Indices: 37573--37615 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37563 TTTTCGGGCT
* *
37573 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
37594 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
37615 A
1 A
37616 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:37675 original size:66 final size:68
Alignment explanation
Indices: 37595--37746 Score: 227
Period size: 67 Copynumber: 2.2 Consensus size: 68
37585 ACCCATTCAA
* *
37595 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
37659 -GG
66 GGG
* * *
37661 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
37726 GGGG
66 -GGG
*
37730 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
37747 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
66 26 0.34
67 33 0.43
69 18 0.23
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:38086 original size:29 final size:29
Alignment explanation
Indices: 38052--38123 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
38042 CATATTATGA
**
38052 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
38081 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
38110 TACATGACATGAAT
1 TACATGACATGAAT
38124 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:38478 original size:23 final size:22
Alignment explanation
Indices: 38418--38485 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
38408 TTATGGACAT
38418 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
38440 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
38462 AATTCTACAGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
38485 A
1 A
38486 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:44548 original size:21 final size:21
Alignment explanation
Indices: 44522--44564 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
44512 TTTTCGGGCT
* *
44522 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
44543 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
44564 A
1 A
44565 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:44639 original size:67 final size:67
Alignment explanation
Indices: 44544--44694 Score: 223
Period size: 67 Copynumber: 2.3 Consensus size: 67
44534 ACCCATTCAA
* * *
44544 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCTA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
44608 GGG
66 -GG
* * *
44611 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
44676 GG
66 GG
*
44678 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
44695 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
67 44 0.58
68 32 0.42
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:44683 original size:20 final size:20
Alignment explanation
Indices: 44658--44695 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
44648 GAATGCTTGA
*
44658 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
44678 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
44696 TGAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:45032 original size:29 final size:29
Alignment explanation
Indices: 44998--45069 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
44988 CATATTATGA
**
44998 TACATGACATGAATTTGTATTAAATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
*
45027 TACATGACATGAATTCATATTATATGTAT
1 TACATGACATGAATTCATATTAAATGTAT
45056 TACATGACATGAAT
1 TACATGACATGAAT
45070 ATGCAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (29 bp):
TACATGACATGAATTCATATTAAATGTAT
Found at i:45423 original size:23 final size:22
Alignment explanation
Indices: 45363--45428 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
45353 TTATGGACAT
45363 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
45385 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
45407 AATTCTACGGGGCACTTCGGTG
1 AATTCTAC-GGGCACTTCGGTG
45429 TATTTATACG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.70
23 13 0.30
ACGTcount: A:0.18, C:0.26, G:0.29, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:48612 original size:20 final size:20
Alignment explanation
Indices: 48567--48612 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
48557 ACGATTATTC
48567 TTATAATTTTTCTATCTAGA
1 TTATAATTTTTCTATCTAGA
* * * *
48587 TAATAATTTTTTTTTCTTGA
1 TTATAATTTTTCTATCTAGA
48607 TTATAA
1 TTATAA
48613 ATGTTTTTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (20 bp):
TTATAATTTTTCTATCTAGA
Found at i:49093 original size:15 final size:16
Alignment explanation
Indices: 49073--49105 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
49063 TGATCCCTCA
49073 TAATAAATATTAA-AG
1 TAATAAATATTAAGAG
*
49088 TAATAAATTTTAAGAG
1 TAATAAATATTAAGAG
49104 TA
1 TA
49106 TATTCATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (16 bp):
TAATAAATATTAAGAG
Found at i:79794 original size:27 final size:28
Alignment explanation
Indices: 79763--79825 Score: 110
Period size: 27 Copynumber: 2.3 Consensus size: 28
79753 TTCCATAACA
*
79763 AGTTTTGACTATTAGTT-CCGGACCTTG
1 AGTTTTGACTATTAGTTCCCGGACCTAG
79790 AGTTTTGACTATTAGTTCCCGGACCTAG
1 AGTTTTGACTATTAGTTCCCGGACCTAG
79818 AGTTTTGA
1 AGTTTTGA
79826 TGTTTGAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (28 bp):
AGTTTTGACTATTAGTTCCCGGACCTAG
Found at i:82172 original size:32 final size:32
Alignment explanation
Indices: 82136--82218 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
82126 TCATAATAGT
*
82136 TAAAATGATGATATAATATGTACTAAATTATC
1 TAAAATGATAATATAATATGTACTAAATTATC
* * ** *
82168 TAAAATAATAACATAATATGTGTTACATTATC
1 TAAAATGATAATATAATATGTACTAAATTATC
*
82200 TAAAATGATAATATGATAT
1 TAAAATGATAATATAATAT
82219 ATATTATGTC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.37
Consensus pattern (32 bp):
TAAAATGATAATATAATATGTACTAAATTATC
Found at i:84226 original size:21 final size:22
Alignment explanation
Indices: 84189--84230 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
84179 TGCTTATTTT
84189 TTAAAAAAAAATAATAATATAG
1 TTAAAAAAAAATAATAATATAG
*
84211 TTAATAAAAAAT-ATAATATA
1 TTAAAAAAAAATAATAATATA
84231 TAAAATATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
TTAAAAAAAAATAATAATATAG
Found at i:84237 original size:21 final size:22
Alignment explanation
Indices: 84190--84234 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
84180 GCTTATTTTT
84190 TAAA-AAAAAATAATAATATAG
1 TAAATAAAAAATAATAATATAG
*
84211 TTAATAAAAAAT-ATAATATA-
1 TAAATAAAAAATAATAATATAG
84231 TAAA
1 TAAA
84235 ATATGCTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 3 0.14
21 11 0.52
22 7 0.33
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
TAAATAAAAAATAATAATATAG
Found at i:84405 original size:16 final size:16
Alignment explanation
Indices: 84386--84421 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
84376 AATTCAATGT
84386 GATATAAATTAATAAA
1 GATATAAATTAATAAA
84402 GATATAAATTAATAAA
1 GATATAAATTAATAAA
84418 GATA
1 GATA
84422 ATTTGACGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (16 bp):
GATATAAATTAATAAA
Found at i:84503 original size:19 final size:19
Alignment explanation
Indices: 84479--84548 Score: 90
Period size: 19 Copynumber: 3.7 Consensus size: 19
84469 AGTCGGGTCG
*
84479 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGTTTAGACC
*
84498 GGTC-AACCGGTTCAGACC
1 GGTCAAACCGGTTTAGACC
*
84516 GGTCAAACCGG-TTCGAACC
1 GGTCAAACCGGTTTAG-ACC
84535 GGTCAAACCGGTTT
1 GGTCAAACCGGTTT
84549 TCCAGCAGCT
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
18 18 0.41
19 24 0.55
20 2 0.05
ACGTcount: A:0.23, C:0.30, G:0.27, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTTAGACC
Found at i:84516 original size:10 final size:10
Alignment explanation
Indices: 84486--84547 Score: 53
Period size: 9 Copynumber: 6.6 Consensus size: 10
84476 TCGGGTCAAC
*
84486 CCGGTTTAGA
1 CCGGTTCAGA
84496 CCGG-TCA-A
1 CCGGTTCAGA
84504 CCGGTTCAGA
1 CCGGTTCAGA
*
84514 CCGG-TCAAA
1 CCGGTTCAGA
84523 CCGGTTC-GAA
1 CCGGTTCAG-A
*
84533 CCGG-TCAAA
1 CCGGTTCAGA
84542 CCGGTT
1 CCGGTT
84548 TTCCAGCAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
8 5 0.12
9 20 0.48
10 17 0.40
ACGTcount: A:0.23, C:0.31, G:0.27, T:0.19
Consensus pattern (10 bp):
CCGGTTCAGA
Found at i:84527 original size:9 final size:9
Alignment explanation
Indices: 84495--84546 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
84485 CCCGGTTTAG
84495 ACCGGTC-A
1 ACCGGTCAA
*
84503 ACCGGTTCAG
1 ACCGG-TCAA
84513 ACCGGTCAA
1 ACCGGTCAA
*
84522 ACCGGTTCGA
1 ACCGG-TCAA
84532 ACCGGTCAA
1 ACCGGTCAA
84541 ACCGGT
1 ACCGGT
84547 TTTCCAGCAG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 5 0.14
9 19 0.51
10 13 0.35
ACGTcount: A:0.25, C:0.33, G:0.27, T:0.15
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:85257 original size:4 final size:4
Alignment explanation
Indices: 85248--85729 Score: 887
Period size: 4 Copynumber: 123.2 Consensus size: 4
85238 AATTTTATAA
85248 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85296 ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85342 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85390 ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85436 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85484 ATGT ATGT ATG- -TGT ATGT A-G- ATGT ATGT A-GT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85527 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85575 ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85622 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85670 ATGT ATGT ATGT ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
85717 ATGT ATGT ATGT A
1 ATGT ATGT ATGT A
85730 CCCCCTAGAC
Statistics
Matches: 467, Mismatches: 0, Indels: 22
0.96 0.00 0.04
Matches are distributed among these distances:
2 7 0.01
3 11 0.02
4 449 0.96
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Done.