Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007806.1 Hibiscus syriacus cultivar Beakdansim tig00110125_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: 416740
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:274882 original size:17 final size:17
Alignment explanation
Indices: 274860--274918 Score: 68
Period size: 17 Copynumber: 3.4 Consensus size: 17
274850 GTACTGAGTT
*
274860 AAAGAAAATTGAATTCA
1 AAAGAAAATTGAATTCG
274877 AAAGAAAAGTACTGAA-T-G
1 AAAGAAAA-T--TGAATTCG
274895 AAAGAAAATTGAATTCG
1 AAAGAAAATTGAATTCG
274912 AAAGAAA
1 AAAGAAA
274919 TGAAATAAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
15 4 0.11
16 1 0.03
17 17 0.47
18 9 0.25
19 1 0.03
20 4 0.11
ACGTcount: A:0.59, C:0.05, G:0.17, T:0.19
Consensus pattern (17 bp):
AAAGAAAATTGAATTCG
Found at i:274889 original size:35 final size:35
Alignment explanation
Indices: 274850--274918 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
274840 ATGAAACAAG
* *
274850 GTACTGAGTTAAAGAAAATTGAATTCAAAAGAAAA
1 GTACTGAATGAAAGAAAATTGAATTCAAAAGAAAA
*
274885 GTACTGAATGAAAGAAAATTGAATTCGAAAGAAA
1 GTACTGAATGAAAGAAAATTGAATTCAAAAGAAA
274919 TGAAATAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.22
Consensus pattern (35 bp):
GTACTGAATGAAAGAAAATTGAATTCAAAAGAAAA
Found at i:282814 original size:3 final size:3
Alignment explanation
Indices: 282800--282840 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
282790 TGGATCTAAA
*
282800 AAT AAA AAT AAT AATT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT A
282841 TTGAATGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:284209 original size:134 final size:134
Alignment explanation
Indices: 282993--284214 Score: 1328
Period size: 134 Copynumber: 9.1 Consensus size: 134
282983 ACTGTCACTT
* * * * *
282993 AGGGAATATCAGATAT-GGGTATGTTGA-TCTATTCCGCTATCACTCAGGGAAGATTGAATCAGG
1 AGGGAATATCAGATCTGGGGGA-GTTGATTC-ATTCTGCTGTCACTCAGGGAAGATTGAATCGGG
* * * *
283056 GTAGACTTGTTCTGCTGTCACTCAGGGAATACCAAATCTT-GAAATAGAGGGATATGTTTCACTT
64 GTAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAA-AGAGGGACATGTTCCGCTT
*
283120 TTTCTGA
128 CTTCTGA
* * * * *
283127 AGGAAATATCAGATATGGGGGAGTTGATCCATT-TCGCTTTCATTCAGGGAAGATTGAATCGGGG
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCT-GCTGTCACTCAGGGAAGATTGAATCGGGG
* * * * * * *
283191 CAGACTTGTTTTGCTATCACTTAGGGAATATCAAATCTTGGAAGAGATGGATC-TGTTCCTCTTC
65 TAGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGA-CATGTTCCGCTTC
283255 TTCTGA
129 TTCTGA
* * ** * *
283261 AGGGAATATCATATATGGGGGAGTTGACCCATTCTACTGTCACTCAGGGAAGATTGAATCGGGGC
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
* * * * * * **
283326 CGACTTGATCTGTTGTTACTCAGGGAATATCAAATCTTGGAAAAGAGGGACTTGTTTCATTTCTT
66 AGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
*
283391 TTGA
131 CTGA
** * * * **
283395 AGGGAATATTTGTTTTGGGGGAGTTGATTCATTCTGCTGTCACTGAGGGAAGATTGAATCGGGAC
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
* * * * * *
283460 AGACTTGTT-T-CATTATCACTTAGGGAATATCAAATCTTGGAAAAAAGGGAAATTTTTCGCTTC
66 AGACTTGTTCTGC--TGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTC
*
283523 TTCTAA
129 TTCTGA
* * * * ** ** *
283529 AGGGAACATCAAATCTGGGGGAATTGATCCATTCCACTGTCACTCAGGGAAGATTGAATCTAGGC
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
* * * *
283594 AGACTTGTTCTGCTGTCACTCATGGATTATCAAATCTTGGAAAAGAGGGACCTGTTCCGCTTTTT
66 AGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
283659 CTGA
131 CTGA
* * * *
283663 AGGGAATATCAAATCTGGGTGAGTTGATTCATTCTGCTATCACTCAGGAAAGATTGAATCGGGGT
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
* * * * * * * * *
283728 AGACTTGTTCCGTTGTCACTCATGTAATATCAAATCTTGAAAAAGAGAGACATATTCCACTTTTT
66 AGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
283793 CTGA
131 CTGA
*
283797 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTACTGTCACTCAGGGAAGATTGAATCGGGGT
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
* * * * * * * ** *
283862 AGACTTGTTCCGTTATTACTTAGGGAATATCAAATCTTGGAAAAGAGGAACATGCTCATCTTATT
66 AGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
283927 -TGA
131 CTGA
* * * *
283930 AGGGAATATCAGATATGAGGGAGTTCATCCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
* * * *
283995 AGACTTGTTCTACTGTCACTAAGGGATTATCAAATCTGGGAAAAGAGGGACATGTTCCGCTTCCT
66 AGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTT-CT
284060 T-TGA
130 TCTGA
* ** *
284064 AGGGAATATCATATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAACGAAGATTTAATCGGGGT
1 AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
* * * * * * *
284129 ATACTTATTCCGCTATCACTCAAGGAATATCAAATCTTAGAAAAGAGGGATATGTTCCGCTTCTT
66 AGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
*
284194 CTGG
131 CTGA
*
284198 AGGGAATATCATATCTG
1 AGGGAATATCAGATCTG
284215 CAAATTAAAC
Statistics
Matches: 913, Mismatches: 162, Indels: 26
0.83 0.15 0.02
Matches are distributed among these distances:
133 118 0.13
134 784 0.86
135 10 0.01
136 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.31
Consensus pattern (134 bp):
AGGGAATATCAGATCTGGGGGAGTTGATTCATTCTGCTGTCACTCAGGGAAGATTGAATCGGGGT
AGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAAAGAGGGACATGTTCCGCTTCTT
CTGA
Found at i:290358 original size:99 final size:99
Alignment explanation
Indices: 290187--290384 Score: 396
Period size: 99 Copynumber: 2.0 Consensus size: 99
290177 GTTCAATTAT
290187 TTAAATATCTCGAGACGAGACCTTAGATTCGATCTAATAATCTTTTCTCGATGAATTTAATTAAA
1 TTAAATATCTCGAGACGAGACCTTAGATTCGATCTAATAATCTTTTCTCGATGAATTTAATTAAA
290252 AAATGATCTTTTTCTTGATCCCTGAATTTTAAAA
66 AAATGATCTTTTTCTTGATCCCTGAATTTTAAAA
290286 TTAAATATCTCGAGACGAGACCTTAGATTCGATCTAATAATCTTTTCTCGATGAATTTAATTAAA
1 TTAAATATCTCGAGACGAGACCTTAGATTCGATCTAATAATCTTTTCTCGATGAATTTAATTAAA
290351 AAATGATCTTTTTCTTGATCCCTGAATTTTAAAA
66 AAATGATCTTTTTCTTGATCCCTGAATTTTAAAA
290385 ATGAAATCGA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 99 1.00
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.39
Consensus pattern (99 bp):
TTAAATATCTCGAGACGAGACCTTAGATTCGATCTAATAATCTTTTCTCGATGAATTTAATTAAA
AAATGATCTTTTTCTTGATCCCTGAATTTTAAAA
Found at i:290698 original size:28 final size:26
Alignment explanation
Indices: 290666--290736 Score: 79
Period size: 28 Copynumber: 2.6 Consensus size: 26
290656 ATGCCAAAAT
*
290666 TAAAATAAAAATAAAATATACAAGTGAC
1 TAAAATAAAATTAAAATAT-CAAGTG-C
* *
290694 TAAAATAAACATTTACAATATTAAGTGC
1 TAAAATAAA-A-TTAAAATATCAAGTGC
290722 TAAAATAAAATTAAA
1 TAAAATAAAATTAAA
290737 TAAAACATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 4 0.11
27 1 0.03
28 19 0.51
29 6 0.16
30 7 0.19
ACGTcount: A:0.61, C:0.07, G:0.06, T:0.27
Consensus pattern (26 bp):
TAAAATAAAATTAAAATATCAAGTGC
Found at i:292226 original size:3 final size:3
Alignment explanation
Indices: 292203--292255 Score: 70
Period size: 3 Copynumber: 17.3 Consensus size: 3
292193 GGATCTAAAA
* * *
292203 AAT AAA AAT ATT AATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAA
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
292249 AAT AAT A
1 AAT AAT A
292256 TCGAATGGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:296597 original size:140 final size:138
Alignment explanation
Indices: 296334--296721 Score: 440
Period size: 141 Copynumber: 2.8 Consensus size: 138
296324 CTTTTTAAAA
* * * * *
296334 TTAGAGAATAATTCGATGTGTCCTTCGCATTAAAAGGCCCAAGGGTCCACATTGATTATTCGATT
1 TTAG-GAATAATTCGATTTGGCATTCGCATTAAAATG-CCAAGGGTCCATATTGATTATTCGATT
* * *
296399 CCA-TAATTGGTAAAATTAATTAGGATTAACAATTAGAGCCTCCACTTTAGGCTGAATTTCACT-
64 -CAGTAATTGGTAAAAATGATTAGGATTAA-TATTAGAGCCTCCACTTTAGGCTGAATTTCA-TG
296462 TTAG-TCCTTTAAG
126 TTAGTTCC-TTAAG
* * * *
296475 TTAGGAATAATTCGATTTGGCATTCGTATTAAAATGCTCGAGGGACCATATTGATTATTCGATTT
1 TTAGGAATAATTCGATTTGGCATTCGCATTAAAATGC-CAAGGGTCCATATTGATTATTCGATTC
* * *
296540 AGTAATTGGATAAAAATGACTAGGATTAATATTAGAGCCTCCACTTTATGCTTAATTTCATGTTA
65 AGTAATTGG-TAAAAATGATTAGGATTAATATTAGAGCCTCCACTTTAGGCTGAATTTCATGTTA
*
296605 GTTCCTTAAT
129 GTTCCTTAAG
* * * * * *
296615 TTAGGGAATAATTCGATTTGGCTTTCACATTTAAATGGCCAAGGTTCCATGTTGATTATTCGAAT
1 TTA-GGAATAATTCGATTTGGCATTCGCATTAAAAT-GCCAAGGGTCCATATTGATTATTCGATT
* *
296680 CAGTAATTTGTTAAAATCGATTAGGATTAATATTAGAGCCTC
64 CAGTAATTGGTAAAAAT-GATTAGGATTAATATTAGAGCCTC
296722 AATTTTTATG
Statistics
Matches: 210, Mismatches: 29, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
139 3 0.01
140 102 0.49
141 103 0.49
142 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (138 bp):
TTAGGAATAATTCGATTTGGCATTCGCATTAAAATGCCAAGGGTCCATATTGATTATTCGATTCA
GTAATTGGTAAAAATGATTAGGATTAATATTAGAGCCTCCACTTTAGGCTGAATTTCATGTTAGT
TCCTTAAG
Found at i:299381 original size:21 final size:21
Alignment explanation
Indices: 299355--299396 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
299345 AATTCCAAAA
*
299355 TGCTACAGGGGTATCGATACC
1 TGCTACAGGGGTACCGATACC
299376 TGCTACAGGGGTACCGATACC
1 TGCTACAGGGGTACCGATACC
299397 GTTACTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.26, G:0.29, T:0.21
Consensus pattern (21 bp):
TGCTACAGGGGTACCGATACC
Found at i:300840 original size:3 final size:3
Alignment explanation
Indices: 300819--300859 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
300809 TGAAGAAAGG
* *
300819 GAA G-A GAA GAA AAA CAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
300860 CGAGGTAGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.02, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:302550 original size:21 final size:21
Alignment explanation
Indices: 302510--302549 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
302500 TGGTATCTTT
302510 TTAACAATTGATAATCTTTTG
1 TTAACAATTGATAATCTTTTG
*
302531 TTAACAATTGCT-ATCTTTT
1 TTAACAATTGATAATCTTTT
302550 TCATTAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.30, C:0.12, G:0.07, T:0.50
Consensus pattern (21 bp):
TTAACAATTGATAATCTTTTG
Found at i:302807 original size:20 final size:20
Alignment explanation
Indices: 302782--302831 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
302772 AGTAATTTAC
302782 ATAGTAATGATACTGTATGA
1 ATAGTAATGATACTGTATGA
*
302802 ATAGTACAT-ATACTGTTTGA
1 ATAGTA-ATGATACTGTATGA
302822 ATAGTAATGA
1 ATAGTAATGA
302832 ATAGTATCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 2 0.07
20 23 0.85
21 2 0.07
ACGTcount: A:0.40, C:0.06, G:0.18, T:0.36
Consensus pattern (20 bp):
ATAGTAATGATACTGTATGA
Found at i:302892 original size:21 final size:20
Alignment explanation
Indices: 302863--302906 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
302853 TCCAGAATGC
* *
302863 TACAGGGGTATCGATACCTGT
1 TACAAGGGTACCGATACC-GT
302884 TACAAGGGTACCGATACCGT
1 TACAAGGGTACCGATACCGT
302904 TAC
1 TAC
302907 TATTCATACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.25
Consensus pattern (20 bp):
TACAAGGGTACCGATACCGT
Found at i:304895 original size:36 final size:36
Alignment explanation
Indices: 304848--304951 Score: 117
Period size: 33 Copynumber: 3.0 Consensus size: 36
304838 GCTACCCCTA
*
304848 TATCTCACTTGAGATTATTTTCCTTAAAATAGATTG
1 TATCTCACTTGAGATTATTTTCCTTAAAATAAATTG
* *
304884 TATCTCACTTGAG---ATTGTCCTTAAAATAAATTT
1 TATCTCACTTGAGATTATTTTCCTTAAAATAAATTG
* * *
304917 TATCTCACTTGAAAGTT-TTTTTCTTAAAACAAATT
1 TATCTCACTTGAGA-TTATTTTCCTTAAAATAAATT
304952 TCTTCCTCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
33 29 0.51
36 28 0.49
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (36 bp):
TATCTCACTTGAGATTATTTTCCTTAAAATAAATTG
Found at i:304952 original size:36 final size:35
Alignment explanation
Indices: 304848--304952 Score: 108
Period size: 36 Copynumber: 3.0 Consensus size: 35
304838 GCTACCCCTA
* *
304848 TATCTCACTTG-AGATTATTTTCCTTAAAATAGATTG
1 TATCTCACTTGAAG-TT-TTTTCCTTAAAATAAATTT
* *
304884 TATCTCACTTG-AG-ATTGTCCTTAAAATAAATTT
1 TATCTCACTTGAAGTTTTTTCCTTAAAATAAATTT
* *
304917 TATCTCACTTGAAAGTTTTTTTCTTAAAACAAATTT
1 TATCTCACTTG-AAGTTTTTTCCTTAAAATAAATTT
304953 CTTCCTCACT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 27 0.47
35 2 0.03
36 29 0.50
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (35 bp):
TATCTCACTTGAAGTTTTTTCCTTAAAATAAATTT
Found at i:305538 original size:37 final size:39
Alignment explanation
Indices: 305469--305548 Score: 119
Period size: 37 Copynumber: 2.1 Consensus size: 39
305459 ATCGGACTAA
* * *
305469 AAATATTTGAGGGATAGTTTGAAGGTTGTTCGCACTTC-
1 AAATATTCGAGGGATAATTTGAAGGTTATTCGCACTTCG
305507 AAATATTCGAGGG-TAATTTGAAGGTTATTCGCACTTCG
1 AAATATTCGAGGGATAATTTGAAGGTTATTCGCACTTCG
305545 AAAT
1 AAAT
305549 CAAATCAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 22 0.58
38 16 0.42
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (39 bp):
AAATATTCGAGGGATAATTTGAAGGTTATTCGCACTTCG
Found at i:306543 original size:5 final size:5
Alignment explanation
Indices: 306533--306592 Score: 68
Period size: 5 Copynumber: 11.8 Consensus size: 5
306523 ATCAAAGACA
* *
306533 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAAT AGAACT -AGAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT A-AAAT AAAAT AAAAT AAAAT
*
306584 GAAAT AAAA
1 AAAAT AAAA
306593 CAAGATAATA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
4 2 0.04
5 36 0.78
6 8 0.17
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:307422 original size:32 final size:32
Alignment explanation
Indices: 307364--307454 Score: 139
Period size: 32 Copynumber: 2.8 Consensus size: 32
307354 TTAGTTTGCG
307364 CAATAAAATAAAATGTTAGTAA-GTTAGTAAGAA
1 CAATAAAATAAAA-GTTAG-AATGTTAGTAAGAA
* *
307397 CAATAAAGTAAAAGTTAGAATGTTAGTATGAA
1 CAATAAAATAAAAGTTAGAATGTTAGTAAGAA
307429 CAATAAAATAAAAGTTAGAATGTTAG
1 CAATAAAATAAAAGTTAGAATGTTAG
307455 CAAGTTAGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
31 2 0.04
32 40 0.74
33 12 0.22
ACGTcount: A:0.53, C:0.03, G:0.16, T:0.27
Consensus pattern (32 bp):
CAATAAAATAAAAGTTAGAATGTTAGTAAGAA
Found at i:307655 original size:21 final size:21
Alignment explanation
Indices: 307629--307677 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
307619 GATTGTACCC
307629 CGAATCGGGTCACCATAAGGT
1 CGAATCGGGTCACCATAAGGT
307650 CGAATCGGGTCACCATAAGGT
1 CGAATCGGGTCACCATAAGGT
307671 CGAATCG
1 CGAATCG
307678 AATATGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.29, C:0.24, G:0.29, T:0.18
Consensus pattern (21 bp):
CGAATCGGGTCACCATAAGGT
Found at i:317671 original size:3 final size:3
Alignment explanation
Indices: 317663--317734 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
317653 TCCCATTTCC
317663 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
317711 ATT ATT A-T ATT ATG ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
317735 ATAATAAATA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 64 0.97
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:318615 original size:28 final size:30
Alignment explanation
Indices: 318567--318632 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
318557 GGAAACTTAA
318567 AGAGAATGGAGAGCTTCTCTCTCTTTACAG
1 AGAGAATGGAGAGCTTCTCTCTCTTTACAG
* *
318597 AGAGAATGGATAGCTTCTCTCTCTTTAGAG
1 AGAGAATGGAGAGCTTCTCTCTCTTTACAG
318627 AGAGAA
1 AGAGAA
318633 ACAAAATGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (30 bp):
AGAGAATGGAGAGCTTCTCTCTCTTTACAG
Found at i:321880 original size:26 final size:27
Alignment explanation
Indices: 321816--321881 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
321806 GCATTTCTGC
*
321816 ATTTTTTGCATTTTCATTTTACATTCAA
1 ATTTTTT-CATTTGCATTTTACATTCAA
* * * *
321844 ATCTTTGCATTTGCA-TTTGCATTCGA
1 ATTTTTTCATTTGCATTTTACATTCAA
321870 ATTTTTTCATTT
1 ATTTTTTCATTT
321882 TTACATTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
26 19 0.61
27 7 0.23
28 5 0.16
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (27 bp):
ATTTTTTCATTTGCATTTTACATTCAA
Found at i:321890 original size:14 final size:14
Alignment explanation
Indices: 321873--321919 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
321863 CATTCGAATT
321873 TTTTCATTTTTACA
1 TTTTCATTTTTACA
*
321887 TTTT--TATTTACA
1 TTTTCATTTTTACA
*
321899 TTTTCATTTTTGCA
1 TTTTCATTTTTACA
321913 TTTTCAT
1 TTTTCAT
321920 CTTTGCATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 11 0.39
14 17 0.61
ACGTcount: A:0.19, C:0.13, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTCATTTTTACA
Found at i:321924 original size:14 final size:14
Alignment explanation
Indices: 321897--321927 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
321887 TTTTTATTTA
*
321897 CATTTTCATTTTTG
1 CATTTTCATCTTTG
321911 CATTTTCATCTTTG
1 CATTTTCATCTTTG
321925 CAT
1 CAT
321928 AATTACATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.16, C:0.19, G:0.06, T:0.58
Consensus pattern (14 bp):
CATTTTCATCTTTG
Found at i:326129 original size:123 final size:123
Alignment explanation
Indices: 325907--327221 Score: 1795
Period size: 123 Copynumber: 10.7 Consensus size: 123
325897 CACTCAATGG
* * * * * * *
325907 ATCAATATTTCAAAAAGGAGTCCATAATGAGAATAACTCATCTGATAATGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* *
325972 ATGAGAATAACTTGTTCAACCTTTTGCTCGACTCTATCGTAGAAGGAGATAGAGCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
*
326030 ATCAACATTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* * * * * *
326095 ATGAAAATAACTTGTTCAACCTTTTTCTCAACTCTATCGTATAAGGAGATAGAGCAGC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
* *
326153 ATCAACATTTCCAG-AGAGAGTTCATAATGAGAAGAACTCATCTGAGGAGAAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAG-GAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCAT
**
326217 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAATTAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAG-AGCAGC
* * *
326277 ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAAAAAAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* * *
326342 ATGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGAGCATC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
* * * *
326400 ATCAATATTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGATAAGGAAGAAGAAGTTCGTA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* * *
326465 ATAAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGATATAGAGCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
* * * *
326523 CTCAACATTTCCAGAAGAAGTTCATAATGAGAAGAACTCATCTAAGGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* * * * * *
326588 ATGAGAAGAACTTGTTCAAACTTTTTTTCTTGACTCTATTGCAGAATGAGATAGAGCAAC
66 ATGAGAAGAACTTGTTC-AAC-CTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
* * * *
326648 ATCAATATTTCCAGAAGGATTTCATATTGAGAAGAACTCATCTGAGGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* * *** * * * *
326713 ATGATAAGAACTTGTTCAACCTTTTTGTTCGACTCTATTAAAAAATGAGATAGAACAGA
66 ATGAGAAGAACTTGTTCAACC-TTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
** * * *
326772 ATCAACATTTTTAG-AGAGAGTTCATAATGAGAAGAACTCATATGAGAATGAAGAAAAAGTTCAT
1 ATCAACATTTCCAGAAG-GAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCAT
* * *
326836 AATGAGAAGAACTTTTTCAACCTTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAGC
65 AATGAGAAGAACTTGTTCAACC-TTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
326896 ATCAACATTTCCAG-A-GAGTTCATAATGAGAAGAACTCATCT---AA-GAATGAAGAAGTTCAT
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAA-GAAGAAGTTCAT
* * * * *
326955 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACCGAAGGATATAGATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
*
327014 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCT-AAAGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGA-AGGAAGAAGAAGTTCAT
* * * * *
327078 AATGAGAAGAACTTGTCCAACCTTTTGCTCGACTCTATCGCATAATGAGATAAATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
327137 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGA-AGAGGAAGAAGAAGTTCAT
1 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGA-AGGAAGAAGAAGTTCAT
327201 AATGAGAAGAACTTGTTCAAC
65 AATGAGAAGAACTTGTTCAAC
327222 TTTGCCTTAA
Statistics
Matches: 1064, Mismatches: 113, Indels: 30
0.88 0.09 0.02
Matches are distributed among these distances:
118 49 0.05
119 35 0.03
120 26 0.02
122 28 0.03
123 554 0.52
124 263 0.25
125 109 0.10
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (123 bp):
ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAGC
Found at i:326588 original size:370 final size:367
Alignment explanation
Indices: 325907--327221 Score: 1879
Period size: 370 Copynumber: 3.6 Consensus size: 367
325897 CACTCAATGG
* * * * * *
325907 ATCAATATTTCAAAAAGGAGTCCATAATGAGAATAACTCATCTGATAATGAAGAAGAAGTTCATA
1 ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* **
325972 ATGAGAATAACTTGTTCAACCTTTTGCTCGACTCTATCGTAGAAGGAGATAGAGCAGCATCAACA
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGAGCAGCATCAACA
326037 TTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAATGAA-A
131 TTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAAT-AAGA
* * * *
326101 ATAACTTGTTCAACCTTTTTCTCAACTCTATCGTATAAGGAGATAGAGCAGCATCAACATTTCCA
195 AGAACTTGTTCAACCTTTTGCTCAACTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCA
*
326166 GAGAGAGTTCATAATGAGAAGAACTCATCTGAGGAGAAAGAAGAAGTTCATAATGAGAAGAACTT
260 GAGA-AGTTCATAATGAGAAGAACTCATCTAAGGAG-AAGAAGAAGTTCATAATGAGAAGAACTT
* *
326231 GTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAATTAGC
323 GTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAG-ATCAAC
* *
326277 ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAAAAAAAGTTCATA
1 ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* * *
326342 ATGAGAAGAACTTGTTCAACCTTTTGCTCAACTCTATCACAGAAGGAGATAGAGCATCATCAATA
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGAGCAGCATCAACA
* *
326407 TTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGATAAGGAAGAAGAAGTTCGTAATAAGAA
131 TTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAATAAGAA
* * * *
326472 GAACTTGTTCAACCTTTTGCTCGACTCTATCGCAGAAGGATATAGAGCAACCTCAACATTTCCAG
196 GAACTTGTTCAACCTTTTGCTCAACTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCAG
326537 AAGAAGTTCATAATGAGAAGAACTCATCTAAGGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
261 -AGAAGTTCATAATGAGAAGAACTCATCTAAGGA-GAAGAAGAAGTTCATAATGAGAAGAACTTG
* * * * * *
326602 TTCAAACTTTTTTTCTTGACTCTATTGCAGAATGAGATAGAGCAAC
324 TTC-AAC-CTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* * *
326648 ATCAATATTTCCAGAAGGATTTCATATTGAGAAGAACTCATCTGAGGAGGAAGAAGAAGTTCATA
1 ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
* * * * * * * *
326713 ATGATAAGAACTTGTTCAACCTTTTTGTTCGACTCTATTAAAAAATGAGATAGAACAGAATCAAC
66 ATGAGAAGAACTTGTTCAACC-TTTTGCTCGACTCTATCACAGAAGGAGATAGAGCAGCATCAAC
* * * * *
326778 ATTTTTAG-AGAGAGTTCATAATGAGAAGAACTCATATGAGAATGAAGAAAAAGTTCATAATGAG
130 ATTTCTAGAAG-GAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAATAAG
* *
326842 AAGAACTTTTTCAACCTTTTTGCTCAACTCTATCGCAGAAGGAGATAGATCAGCATCAACATTTC
194 AAGAACTTGTTCAACC-TTTTGCTCAACTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTC
*
326907 CAGAG-AGTTCATAATGAGAAGAACTCATCTAA-GA-ATGAAGAAGTTCATAATGAGAAGAACTT
258 CAGAGAAGTTCATAATGAGAAGAACTCATCTAAGGAGAAGAAGAAGTTCATAATGAGAAGAACTT
* * *
326969 GTTCAACCTTTTGCTCGACTCTATCACCGAAGGATATAGATCAAC
323 GTTCAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
* *
327014 ATCAACATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCT-AAAGAGGAAGAAGAAGTTCAT
1 ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGA-AGGAAGAAGAAGTTCAT
* * * * * *
327078 AATGAGAAGAACTTGTCCAACCTTTTGCTCGACTCTATCGCATAATGAGATAAATCAGCATCAAC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGAGCAGCATCAAC
* *
327143 ATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGA-AGAGGAAGAAGAAGTTCATAATGAG
130 ATTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGA-AGGAAGAAGAAGTTCATAATAAG
327207 AAGAACTTGTTCAAC
194 AAGAACTTGTTCAAC
327222 TTTGCCTTAA
Statistics
Matches: 841, Mismatches: 93, Indels: 27
0.88 0.10 0.03
Matches are distributed among these distances:
364 1 0.00
365 104 0.12
366 108 0.13
367 3 0.00
368 31 0.04
369 2 0.00
370 296 0.35
371 119 0.14
372 131 0.16
373 46 0.05
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (367 bp):
ATCAATATTTCCAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGAGCAGCATCAACA
TTTCTAGAAGGAGTTCATAATGAGAAGAACTCATCTGAGAAGGAAGAAGAAGTTCATAATAAGAA
GAACTTGTTCAACCTTTTGCTCAACTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCAG
AGAAGTTCATAATGAGAAGAACTCATCTAAGGAGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
CAACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAAC
Found at i:329322 original size:61 final size:60
Alignment explanation
Indices: 329257--329450 Score: 194
Period size: 61 Copynumber: 3.2 Consensus size: 60
329247 ATAAATTGTT
* *
329257 TGTTGAAGATGACGTTGTTCCTTCTCGTTGACGAAATCGGGTCAATCTGGAGATAATTTGG
1 TGTTGAAGATGAC-TTGTTCCTTCTCGTTGAAGAAATCAGGTCAATCTGGAGATAATTTGG
* * * * * * * ** * *
329318 TGTTGAATATGACTATGGTCATCCAT-GTTGAAGAGATCTGGTCACT-TTCAGATAAATTGTT
1 TGTTGAAGATGACT-TGTTCCTTC-TCGTTGAAGAAATCAGGTCAATCTGGAGATAATTTG-G
*
329379 TGTTGAAGATGACATTGTTCCTTCTCGTTGAGGAAATCAGGTCAATCTGGAGATAATTTGG
1 TGTTGAAGATGAC-TTGTTCCTTCTCGTTGAAGAAATCAGGTCAATCTGGAGATAATTTGG
*
329440 TGTTAAAGATG
1 TGTTGAAGATG
329451 TTCTAGAAGT
Statistics
Matches: 102, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
60 12 0.12
61 78 0.76
62 12 0.12
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (60 bp):
TGTTGAAGATGACTTGTTCCTTCTCGTTGAAGAAATCAGGTCAATCTGGAGATAATTTGG
Found at i:329358 original size:122 final size:122
Alignment explanation
Indices: 329174--329446 Score: 424
Period size: 122 Copynumber: 2.2 Consensus size: 122
329164 GAGTACTTCG
* *
329174 AGGT-AATCTGGATATAATTTGGTGTTAAAAATGACACTACTCATCCATGTTGAAGAGTTCTGGA
1 AGGTCAATCTGGAGATAATTTGGTGTTAAAAATGACACTACTCATCCATGTTGAAGAGATCTGGA
* *
329238 CGCTTTCAGATAAATTGTTTGTTGAAGATGACGTTGTTCCTTCTCGTTGACGAAATC
66 CACTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCCTTCTCGTTGACGAAATC
* * * **
329295 GGGTCAATCTGGAGATAATTTGGTGTTGAATATGACTA-TGGTCATCCATGTTGAAGAGATCTGG
1 AGGTCAATCTGGAGATAATTTGGTGTTAAAAATGAC-ACTACTCATCCATGTTGAAGAGATCTGG
* *
329359 TCACTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCCTTCTCGTTGAGGAAATC
65 ACACTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCCTTCTCGTTGACGAAATC
329417 AGGTCAATCTGGAGATAATTTGGTGTTAAA
1 AGGTCAATCTGGAGATAATTTGGTGTTAAA
329447 GATGTTCTAG
Statistics
Matches: 137, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
121 3 0.02
122 133 0.97
123 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (122 bp):
AGGTCAATCTGGAGATAATTTGGTGTTAAAAATGACACTACTCATCCATGTTGAAGAGATCTGGA
CACTTTCAGATAAATTGTTTGTTGAAGATGACATTGTTCCTTCTCGTTGACGAAATC
Found at i:329627 original size:83 final size:83
Alignment explanation
Indices: 329486--329676 Score: 213
Period size: 83 Copynumber: 2.3 Consensus size: 83
329476 AGACAATACG
* * * * * * *
329486 ATTCCTTTGCGTTGAGGAAGTCTGATTGTCTAAGGATGACACTACTCATTCGCGTTGAGGAGATC
1 ATTCCTTCGTGTTGAGGAAGTCTGGTTGTCTAAGGATGACACTACTCATTCGCATTGAGAAAATA
* *
329551 TGATCGGTGGACGATATT
66 TGATCGATGGACGACATT
* * *
329569 ATTCCTTCGTGTTGAGGAAGTCTGGTTGTTTGAA-GATGACACTGCTCCTTCGCATTGAGAAAAT
1 ATTCCTTCGTGTTGAGGAAGTCTGGTTGTCT-AAGGATGACACTACTCATTCGCATTGAGAAAAT
*
329633 ATGGTCGATGGACGACATT
65 ATGATCGATGGACGACATT
* * * *
329652 TTTCTTTCATTTTGAGGAAGTCTGG
1 ATTCCTTCGTGTTGAGGAAGTCTGG
329677 CCGTTTTAAG
Statistics
Matches: 90, Mismatches: 17, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
83 88 0.98
84 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.27, T:0.35
Consensus pattern (83 bp):
ATTCCTTCGTGTTGAGGAAGTCTGGTTGTCTAAGGATGACACTACTCATTCGCATTGAGAAAATA
TGATCGATGGACGACATT
Found at i:330079 original size:104 final size:101
Alignment explanation
Indices: 329899--330137 Score: 244
Period size: 103 Copynumber: 2.3 Consensus size: 101
329889 GTGAGATAAC
* * * ** * * *
329899 ATTTTGTTTCGATTGAAACATTTTAGAATTTTTGTTTAAAGGGAAAATTGTCTCAAGTGAGACAA
1 ATTTTGTTTCAAGTGAAACAATTTCCAATTTTTGTTTAAAGGGAAAACTATCTCAAGCGAGACAA
* * * **
329964 AATTTGTTTTTAAGAAAAACAATCTCAAATGTTATCA
66 AATTAGGTTTT-AGAAAAACAATCTCAAACGAGATCA
* ** *
330001 ATTTTGTTTCTAGTGAAACAATTTCCAATTTGTGTGTTTTTAGGGAAAACTATCTTAAGCGAGAC
1 ATTTTGTTTCAAGTGAAACAATTTCCAATTT-T-TGTTTAAAGGGAAAACTATCTCAAGCGAGAC
* * * *
330066 GAAATTAGGTTTTAGGAAAACTATCTCAAGCGAGATCA
64 AAAATTAGGTTTTAGAAAAACAATCTCAAACGAGATCA
* *
330104 ATTTTGTTTCAAGTGAAACAATTTCAAAATTTTG
1 ATTTTGTTTCAAGTGAAACAATTTCCAATTTTTG
330138 GGAAGACTGT
Statistics
Matches: 112, Mismatches: 23, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
101 2 0.02
102 27 0.24
103 48 0.43
104 35 0.31
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (101 bp):
ATTTTGTTTCAAGTGAAACAATTTCCAATTTTTGTTTAAAGGGAAAACTATCTCAAGCGAGACAA
AATTAGGTTTTAGAAAAACAATCTCAAACGAGATCA
Found at i:330165 original size:58 final size:58
Alignment explanation
Indices: 330075--330188 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 58
330065 CGAAATTAGG
* * *
330075 TTTTAGGAAAACTATCTCAAGCGAGATCAATTTTGTTTCAAGTGAAACAATTTCAAAA
1 TTTTAGGAAAACTATCTCAAGCGAGAGCAATTTTGTTTCAAGAGAAACAATCTCAAAA
* * * *
330133 TTTTGGGAAGACTGTCTCAAGCGAG-GCAAATTTTGTTTCGAGAGAAACAATCTCAA
1 TTTTAGGAAAACTATCTCAAGCGAGAGC-AATTTTGTTTCAAGAGAAACAATCTCAA
330189 GGATTTGTGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
57 1 0.02
58 47 0.98
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (58 bp):
TTTTAGGAAAACTATCTCAAGCGAGAGCAATTTTGTTTCAAGAGAAACAATCTCAAAA
Found at i:333675 original size:15 final size:15
Alignment explanation
Indices: 333655--333704 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
333645 TTTCTATCTT
333655 TATTTCATTTCTTTC
1 TATTTCATTTCTTTC
*
333670 TATTTCCATTAC-TT-
1 TATTT-CATTTCTTTC
333684 TATTTCATTTCTTTC
1 TATTTCATTTCTTTC
333699 TATTTC
1 TATTTC
333705 CATTACTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 5 0.17
14 7 0.23
15 13 0.43
16 5 0.17
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTTCATTTCTTTC
Found at i:333685 original size:29 final size:29
Alignment explanation
Indices: 333652--333719 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
333642 TCTTTTCTAT
333652 CTTTATTTCATTTCTTTCTATTTCCATTA
1 CTTTATTTCATTTCTTTCTATTTCCATTA
333681 CTTTATTTCATTTCTTTCTATTTCCATTA
1 CTTTATTTCATTTCTTTCTATTTCCATTA
333710 CTTTATTTCA
1 CTTTATTTCA
333720 AGGACATCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (29 bp):
CTTTATTTCATTTCTTTCTATTTCCATTA
Found at i:333917 original size:16 final size:16
Alignment explanation
Indices: 333898--333932 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
333888 ATTGGAGTAC
333898 AAAAAGAAGAAGAAGAA
1 AAAAAGAA-AAGAAGAA
*
333915 AAAAAGAAAAGATGAA
1 AAAAAGAAAAGAAGAA
333931 AA
1 AA
333933 GAAAAAGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAAGAAGAA
Found at i:334076 original size:29 final size:29
Alignment explanation
Indices: 334036--334104 Score: 138
Period size: 29 Copynumber: 2.4 Consensus size: 29
334026 GATAACCTTA
334036 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
1 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
334065 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
1 TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
334094 TTGTTTCTTGA
1 TTGTTTCTTGA
334105 ATTGTAAGTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.22, C:0.07, G:0.29, T:0.42
Consensus pattern (29 bp):
TTGTTTCTTGAGAAAGGTTGCAGTAAGTG
Found at i:338277 original size:21 final size:21
Alignment explanation
Indices: 338236--338279 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
338226 AACCATCTCT
*
338236 TTTCTATCTTTATTTCATTTA
1 TTTCTATCTTTATTACATTTA
*
338257 TTTCTAT-TTTCATTACTTTTA
1 TTTCTATCTTT-ATTACATTTA
338278 TT
1 TT
338280 ATTACCCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 3 0.15
21 17 0.85
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTCTATCTTTATTACATTTA
Found at i:339573 original size:34 final size:36
Alignment explanation
Indices: 339524--339594 Score: 112
Period size: 35 Copynumber: 2.0 Consensus size: 36
339514 GTTTTCTCTC
339524 TTTCTTCTTT-TTTTTTTCTTTTTTT-TCCTTTGCTT
1 TTTCTTCTTTATTTTTTTCTTTTTTTCT-CTTTGCTT
339559 TTTC-TCTTTATTTTTTTCTTTTTTTCTCTTTGCTT
1 TTTCTTCTTTATTTTTTTCTTTTTTTCTCTTTGCTT
339594 T
1 T
339595 GATTTGATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
34 5 0.15
35 28 0.82
36 1 0.03
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (36 bp):
TTTCTTCTTTATTTTTTTCTTTTTTTCTCTTTGCTT
Found at i:343954 original size:16 final size:17
Alignment explanation
Indices: 343929--343970 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
343919 ATAATAATAA
*
343929 AAATAATAAAAAT-CAT
1 AAATATTAAAAATGCAT
343945 AAATATT-AAAATGCAT
1 AAATATTAAAAATGCAT
343961 AAAT-TTAAAA
1 AAATATTAAAA
343971 GTTAGGGAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 7 0.30
16 16 0.70
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.29
Consensus pattern (17 bp):
AAATATTAAAAATGCAT
Found at i:343955 original size:15 final size:15
Alignment explanation
Indices: 343937--343970 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
343927 AAAAATAATA
343937 AAAAT-CATAAATATT
1 AAAATGCATAAAT-TT
343952 AAAATGCATAAATTT
1 AAAATGCATAAATTT
343967 AAAA
1 AAAA
343971 GTTAGGGAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAATGCATAAATTT
Found at i:344141 original size:32 final size:32
Alignment explanation
Indices: 344095--344185 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
344085 TTTGCGCAAT
344095 AAAATAAAATGTTAGTAA-GTTAATAAGAACAAG
1 AAAATAAAA-GTTAG-AATGTTAATAAGAACAAG
* * * *
344128 AAAGTAAAAGTTAGAATGTTAGTATGAACAAT
1 AAAATAAAAGTTAGAATGTTAATAAGAACAAG
*
344160 AAAATAAAAGTTAGAATGTTAGTAAG
1 AAAATAAAAGTTAGAATGTTAATAAG
344186 TTAGAAAAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
31 2 0.04
32 41 0.80
33 8 0.16
ACGTcount: A:0.54, C:0.02, G:0.18, T:0.26
Consensus pattern (32 bp):
AAAATAAAAGTTAGAATGTTAATAAGAACAAG
Found at i:347384 original size:24 final size:24
Alignment explanation
Indices: 347356--347432 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
347346 AACCTTTTCA
347356 AAATTTACATACATAGTGGATTTT
1 AAATTTACATACATAGTGGATTTT
* * ** * * *
347380 AAA-TTAAATA-AAACCCCGAACTTA
1 AAATTTACATACATA--GTGGATTTT
347404 AAATTTACATACATAGTGGATTTT
1 AAATTTACATACATAGTGGATTTT
347428 AAATT
1 AAATT
347433 AAATAAAACC
Statistics
Matches: 35, Mismatches: 14, Indels: 8
0.61 0.25 0.14
Matches are distributed among these distances:
22 2 0.06
23 6 0.17
24 19 0.54
25 6 0.17
26 2 0.06
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (24 bp):
AAATTTACATACATAGTGGATTTT
Found at i:347410 original size:48 final size:48
Alignment explanation
Indices: 347353--347457 Score: 201
Period size: 48 Copynumber: 2.2 Consensus size: 48
347343 GATAACCTTT
347353 TCAAAATTTACATACATAGTGGATTTTAAATTAAATAAAACCCCGAAC
1 TCAAAATTTACATACATAGTGGATTTTAAATTAAATAAAACCCCGAAC
*
347401 TTAAAATTTACATACATAGTGGATTTTAAATTAAATAAAACCCCGAAC
1 TCAAAATTTACATACATAGTGGATTTTAAATTAAATAAAACCCCGAAC
347449 TCAAAATTT
1 TCAAAATTT
347458 CTAACTTTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (48 bp):
TCAAAATTTACATACATAGTGGATTTTAAATTAAATAAAACCCCGAAC
Found at i:347430 original size:25 final size:25
Alignment explanation
Indices: 347350--347430 Score: 60
Period size: 25 Copynumber: 3.3 Consensus size: 25
347340 ACCGATAACC
347350 TTTTCAAAATTTACATACATAGTGGA
1 TTTT-AAAATTTACATACATAGTGGA
* * ***
347376 TTTT-AAA-TTAAATA-AAACCCCGA
1 TTTTAAAATTTACATACATA-GTGGA
**
347399 ACTTAAAATTTACATACATAGTGGA
1 TTTTAAAATTTACATACATAGTGGA
347424 TTTTAAA
1 TTTTAAA
347431 TTAAATAAAA
Statistics
Matches: 37, Mismatches: 14, Indels: 9
0.62 0.23 0.15
Matches are distributed among these distances:
22 2 0.05
23 10 0.27
24 6 0.16
25 13 0.35
26 6 0.16
ACGTcount: A:0.43, C:0.12, G:0.09, T:0.36
Consensus pattern (25 bp):
TTTTAAAATTTACATACATAGTGGA
Found at i:355454 original size:21 final size:21
Alignment explanation
Indices: 355428--355467 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
355418 CCTCCTTTGA
*
355428 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
355449 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
355468 TGGGGTTTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:357425 original size:17 final size:17
Alignment explanation
Indices: 357400--357433 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
357390 TTCAACATTT
* *
357400 TGAATTGTTTGATTTTG
1 TGAACTGTTGGATTTTG
357417 TGAACTGTTGGATTTTG
1 TGAACTGTTGGATTTTG
357434 GATTTATGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.03, G:0.26, T:0.53
Consensus pattern (17 bp):
TGAACTGTTGGATTTTG
Found at i:358916 original size:17 final size:17
Alignment explanation
Indices: 358894--358939 Score: 92
Period size: 17 Copynumber: 2.7 Consensus size: 17
358884 ATTATTATTC
358894 AATATAAAATAATTTAA
1 AATATAAAATAATTTAA
358911 AATATAAAATAATTTAA
1 AATATAAAATAATTTAA
358928 AATATAAAATAA
1 AATATAAAATAA
358940 AAACATAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATAAAATAATTTAA
Found at i:361918 original size:76 final size:76
Alignment explanation
Indices: 361792--361944 Score: 279
Period size: 76 Copynumber: 2.0 Consensus size: 76
361782 TTCGATCCCC
*
361792 GATAATAAATCCATAATTTGACAAGATATTAAAGTTTTCAAAAATAATTCATGCTTAAAGAAATA
1 GATAATAAACCCATAATTTGACAAGATATTAAAGTTTTCAAAAATAATTCATGCTTAAAGAAATA
*
361857 GATGAGGATGG
66 GATGAGAATGG
*
361868 GATAATAAACCCATAATTTGACAAGATATTAAAGTTTTCAAAAATAATTCATGCTTAAAGAATTA
1 GATAATAAACCCATAATTTGACAAGATATTAAAGTTTTCAAAAATAATTCATGCTTAAAGAAATA
361933 GATGAGAATGG
66 GATGAGAATGG
361944 G
1 G
361945 TTGAATACGA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 74 1.00
ACGTcount: A:0.46, C:0.08, G:0.16, T:0.30
Consensus pattern (76 bp):
GATAATAAACCCATAATTTGACAAGATATTAAAGTTTTCAAAAATAATTCATGCTTAAAGAAATA
GATGAGAATGG
Found at i:363362 original size:18 final size:18
Alignment explanation
Indices: 363339--363384 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
363329 ACCGATCACA
*
363339 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCATTG
*
363357 ACCCGACCTGACCCATTG
1 ACCCGACCCGACCCATTG
363375 ACCCGACCCG
1 ACCCGACCCG
363385 TTGACCGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.20, C:0.50, G:0.20, T:0.11
Consensus pattern (18 bp):
ACCCGACCCGACCCATTG
Found at i:365737 original size:23 final size:24
Alignment explanation
Indices: 365703--365807 Score: 169
Period size: 23 Copynumber: 4.5 Consensus size: 24
365693 AATTATGTTA
*
365703 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
365727 TGATA-TTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
365750 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
365773 TGATACATGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
365797 TGATACTTGAC
1 TGATACTTGAC
365808 TTGAATTATG
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
23 44 0.59
24 31 0.41
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:367972 original size:13 final size:13
Alignment explanation
Indices: 367972--368020 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 13
367962 CCGTTGACCC
367972 GACCCGACCCGTT
1 GACCCGACCCGTT
367985 GACCCGACCGACCCGTT
1 GA--C--CCGACCCGTT
368002 GACCCGACCCGTT
1 GACCCGACCCGTT
368015 GACCCG
1 GACCCG
368021 TTGACCGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 18 0.56
15 2 0.06
17 12 0.38
ACGTcount: A:0.16, C:0.47, G:0.24, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:367973 original size:18 final size:18
Alignment explanation
Indices: 367950--368026 Score: 120
Period size: 18 Copynumber: 4.2 Consensus size: 18
367940 ACCGGTCACA
367950 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
367968 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
367986 ACCCGA-CCGACCCGTTG
1 ACCCGACCCGACCCGTTG
368003 ACCCGACCCGTTGACCCGTTG
1 ACCCGACCC---GACCCGTTG
368024 ACC
1 ACC
368027 GTTGACCGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.31
18 26 0.47
21 12 0.22
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:367988 original size:8 final size:8
Alignment explanation
Indices: 367977--368050 Score: 68
Period size: 8 Copynumber: 9.5 Consensus size: 8
367967 GACCCGACCC
367977 GACCCGTT
1 GACCCGTT
**
367985 GACCCGACC
1 GACCCG-TT
367994 GACCCGTT
1 GACCCGTT
368002 GACCC---
1 GACCCGTT
368007 GACCCGTT
1 GACCCGTT
368015 GACCCGTT
1 GACCCGTT
368023 GA-CCGTT
1 GACCCGTT
368030 GA-CCGTT
1 GACCCGTT
368037 GACCGGCGTT
1 GACC--CGTT
368047 GACC
1 GACC
368051 ATAGTTGACC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
5 5 0.09
7 14 0.25
8 22 0.40
9 6 0.11
10 8 0.15
ACGTcount: A:0.15, C:0.39, G:0.27, T:0.19
Consensus pattern (8 bp):
GACCCGTT
Found at i:368030 original size:7 final size:7
Alignment explanation
Indices: 368010--368041 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
368000 TTGACCCGAC
368010 CCGTTGA
1 CCGTTGA
368017 CCCGTTGA
1 -CCGTTGA
368025 CCGTTGA
1 CCGTTGA
368032 CCGTTGA
1 CCGTTGA
368039 CCG
1 CCG
368042 GCGTTGACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.12, C:0.34, G:0.28, T:0.25
Consensus pattern (7 bp):
CCGTTGA
Found at i:368040 original size:35 final size:35
Alignment explanation
Indices: 367950--368026 Score: 118
Period size: 35 Copynumber: 2.1 Consensus size: 35
367940 ACCGGTCACA
367950 ACCCGACCCGACCCGTTGACCCGACCCGACCCGTTG
1 ACCCGA-CCGACCCGTTGACCCGACCCGACCCGTTG
367986 ACCCGACCGACCCGTTGACCCGACCCGTTGACCCGTTG
1 ACCCGACCGACCCGTTGACCCGACCC---GACCCGTTG
368024 ACC
1 ACC
368027 GTTGACCGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
35 20 0.53
36 6 0.16
38 12 0.32
ACGTcount: A:0.17, C:0.48, G:0.22, T:0.13
Consensus pattern (35 bp):
ACCCGACCGACCCGTTGACCCGACCCGACCCGTTG
Found at i:370385 original size:23 final size:24
Alignment explanation
Indices: 370347--370428 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
370337 AATTCTATTA
*
370347 TGATACCTGACCTGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
*
370371 TGATA-TTGACATGGATTCTGATC
1 TGATACTTGACCTGGATTCTGATC
* *
370394 TGATACATGACCTGGATTCTGATA
1 TGATACTTGACCTGGATTCTGATC
370418 TGATACTTGAC
1 TGATACTTGAC
370429 TTGAATTATG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
23 21 0.41
24 30 0.59
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (24 bp):
TGATACTTGACCTGGATTCTGATC
Found at i:372131 original size:60 final size:59
Alignment explanation
Indices: 372040--372163 Score: 169
Period size: 60 Copynumber: 2.1 Consensus size: 59
372030 TGGGCATGAT
* * *
372040 GTTT-TCATATGATTTTCAAAGAATGAAATTTTTAAAAAATAAGAAAACAATTTTCAAA
1 GTTTCTCATATGATTTTCAAAAAATAAAATTTTTAAAAAATAAGAAAACAATTTCCAAA
* * * *
372098 GTTTCTCATTTGATTTTTAAAAAATTAAAATTTTTAAAAAGTAAGAAAACGATTTCCAAA
1 GTTTCTCATATGATTTTCAAAAAA-TAAAATTTTTAAAAAATAAGAAAACAATTTCCAAA
372158 GTTTCT
1 GTTTCT
372164 TACCCAATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 4 0.07
59 16 0.28
60 37 0.65
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (59 bp):
GTTTCTCATATGATTTTCAAAAAATAAAATTTTTAAAAAATAAGAAAACAATTTCCAAA
Found at i:373945 original size:36 final size:36
Alignment explanation
Indices: 373854--373961 Score: 119
Period size: 36 Copynumber: 3.0 Consensus size: 36
373844 GCCACCCCTA
* * * * * *
373854 TATCTCACTTGAGATTATTTCCCTTAAAATATATTG
1 TATCTCACTTGAGATTGTTTTCTTTAAAACAAATTT
*
373890 TATCTAACTTGAGATTGTTTTCTTTAAAACAAATTT
1 TATCTCACTTGAGATTGTTTTCTTTAAAACAAATTT
* *
373926 TATCTCACTTGAAAATG-TTTCTTTCAAAACAAATTT
1 TATCTCACTTGAGATTGTTTTCTTT-AAAACAAATTT
373962 CTTCCTCACT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
35 7 0.11
36 54 0.89
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (36 bp):
TATCTCACTTGAGATTGTTTTCTTTAAAACAAATTT
Found at i:374550 original size:37 final size:38
Alignment explanation
Indices: 374476--374550 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
374466 ACCGGACTAA
* * * *
374476 AAATATTTGAGGGATAATTTGAAGGTTGTTTGTGCTTC
1 AAATATTCGAGGGATAATTTGAAGGTTATTCGCGCTTC
*
374514 AAATATTCGAGGG-TAGTTTGAAGGTTATTCGCGCTTC
1 AAATATTCGAGGGATAATTTGAAGGTTATTCGCGCTTC
374551 GACATCAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 20 0.62
38 12 0.38
ACGTcount: A:0.25, C:0.09, G:0.27, T:0.39
Consensus pattern (38 bp):
AAATATTCGAGGGATAATTTGAAGGTTATTCGCGCTTC
Found at i:378944 original size:134 final size:135
Alignment explanation
Indices: 378685--379855 Score: 1164
Period size: 134 Copynumber: 8.4 Consensus size: 135
378675 CAGGGGGCGC
* * * * *
378685 GCCTTCTCTTTTTTTGTCAGAGAATAGGTTATAATTTCCCTATTATGTGTGATGTCCCCCGG-CA
1 GCCTTC-CCTTTTTTATCA-AGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCCGGTGA
* * *
378749 GGGCACTATTCATGTCAGTACCTATCATGTTTGGGGGGATGCAGCAATGTGGTTAAAGCGCATTT
64 -GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTT
378814 CAGGGGGT
128 CAGGGGGT
378822 GCCTTCCCTTTTTT-TC-AGAATAGGTTATAATTGCCCTATTTT-TCGTGATGTCCCCCCGGTGA
1 GCCTTCCCTTTTTTATCAAGAATAGGTTATAATTGCCCTATTTTGT-GTGATGT-CCCCCGGTGA
* * *
378884 GGCACTATTTATGTCAGTACCTATCATGTTTGAGGGGACGCAGCAATGTTGTTAAAGCGCATTTC
64 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTTC
*
378949 AGGGGGA
129 AGGGGGT
* * *
378956 GCGTATTTCAGGGGGTGCTCCTTCCCTTTTTTCAGAGAATAGGTTATAATTTCCCTATTTTGTGT
1 GC------C------TTC-CCTT---TTTTATCA-AGAATAGGTTATAATTGCCCTATTTTGTGT
* * * * * * *
379021 GATGTCCCCC-GTGAGGGCACTATTCATGTTAGTACCTATCATTTTTTAAGGGACACATCAATGC
49 GATGTCCCCCGGTGA-GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGT
* *
379085 GGTTAAAGTGCGTTTCA-GGGGT
113 GGTTAAAGCGCATTTCAGGGGGT
* * * * *
379107 -CGCTTTCCTTGTTTTGTC-AGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGCGG
1 GC-CTTCCCTT-TTTTATCAAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCCGGTGA
* * * * * *
379170 GGCATTATTAATGTCAGTACCTATCATGTTTAAGGGGACGTAGCAATGTCGTTAAAGCGCATTTC
64 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTTC
*
379235 AGGGGGC
129 AGGGGGT
* * **
379242 GCCTTCCC-TTTTTGTCAGAGAATAGGTTATAATTGCCATATTTTGTGTGATGTCCCCC-GACAG
1 GCCTTCCCTTTTTTATCA-AGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCCGGTGA-
* * * * *
379305 GGAACTATTCATGTCAGTACCTATCATGTTTTTAGGGGATGTAATAATGTGGTTAAAGCGCATTT
64 GGCACTATTCATGTCAGTACCTATCATG-TTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTT
379370 CAGGGGGCGT
128 CA-GGGG-GT
* * * *
379380 GCCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGTGG
1 GCCTTCCC-TTTTTTATCA-AGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCCGGTGA
* * * * * **
379445 GGAACTATTCTTGTCAGTACCTATCATGTTTGAGGGGACGCAATAATGTGCTTTAAGCGTGTTTC
64 GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTTC
379510 AGGGGGT
129 AGGGGGT
* * * * * *
379517 TCCTTTCCTTTTTTTGTCAGAGAATAGGTTATAATTACCCTATTTTGTGTCATGTCCCCCGG-AA
1 GCC-TTCCCTTTTTTATCA-AGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCCGGTGA
* * * *
379581 TGGCACTATTCATATCAGTACCTATCATGTTTGAGGGGACGCAATAATGTGGTTAAAGCACGTTT
64 -GGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTT
*
379646 CAGGGGGC
128 CAGGGGGT
* * * *
379654 ACCTTCCCTTTTTTTTATCAGAGAATAGGTTATAATTGCCTTATTTTGTGTCATGTCCCCTAGAG
1 GCCTTCCC--TTTTTTATCA-AGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCC-CG-G
* *
379719 TGA--CACTATTCATATGAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCAT
61 TGAGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCAT
379782 TTCAGGGGGCAT
126 TTCAGGGGG--T
* *
379794 GCCTTCCCTTTTTTTATCAGAGAATAGGTTATAAACT-CCCTATTTTGTGTCATGTCCCCCGG
1 GCCTTCCC-TTTTTTATCA-AGAATAGGTTAT-AATTGCCCTATTTTGTGTGATGTCCCCCGG
379856 AATGGCACTA
Statistics
Matches: 881, Mismatches: 107, Indels: 92
0.82 0.10 0.09
Matches are distributed among these distances:
132 1 0.00
133 38 0.04
134 169 0.19
135 77 0.09
136 51 0.06
137 130 0.15
138 134 0.15
139 78 0.09
140 86 0.10
141 2 0.00
145 1 0.00
146 2 0.00
147 4 0.00
150 5 0.01
151 10 0.01
152 60 0.07
153 32 0.04
154 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.36
Consensus pattern (135 bp):
GCCTTCCCTTTTTTATCAAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCCGGTGAGG
CACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTTCAG
GGGGT
Found at i:378963 original size:16 final size:16
Alignment explanation
Indices: 378939--378970 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
378929 ATGTTGTTAA
378939 AGCGCATTTCAGGGGG
1 AGCGCATTTCAGGGGG
*
378955 AGCGTATTTCAGGGGG
1 AGCGCATTTCAGGGGG
378971 TGCTCCTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.44, T:0.22
Consensus pattern (16 bp):
AGCGCATTTCAGGGGG
Found at i:379217 original size:286 final size:283
Alignment explanation
Indices: 378695--379866 Score: 1204
Period size: 286 Copynumber: 4.2 Consensus size: 283
378685 GCCTTCTCTT
* *
378695 TTTTTGTCAGAGAATAGGTTATAATTTCCCTATTATGTGTGATGTCCCCCGGCAGGGCACTATTC
1 TTTTTGTCAGAGAATAGGTTATAATTTCCCTATTTTGTGTGATGTCCCCCGGAAGGGCACTATTC
* ** * *
378760 ATGTCAGTACCTATCATGTTTGGGGGGATGCAGCAATGTGGTTAAAGCGCATTTCAGGGGG-TGC
66 ATGTCAGTACCTATCATGTTTGAGGGGACACA-TAATGTGGTTAAAGCGCATTTCAGGGGGCAGC
* *
378824 CTTCCC-TTTTTT-TCAGAATAGGTTATAATTGCCCTATTTT-TCGTGATGTCCCCCCGGTGAGG
130 CTTCCCTTTTTTTGTCAGAATAGGTTATAATTGCCCTATTTTGT-GTGATGT-CCCCTGGTGGGG
*
378886 CACTATTTATGTCAGTACCTATCATGTTTGAGGGGACGCAGCAATGTTGTTAAAGCGCATTTCAG
193 CACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAGCAATG-TGTTAAAGCGCATTTCA-
378951 GGGGAGCGTATTTCAGGGGGTGCTCCTTCCC
256 -GGGAGCGT-TTTCAGGGGGTG-TCCTTCCC
378982 TTTTT-TCAGAGAATAGGTTATAATTTCCCTATTTTGTGTGATGTCCCCCGTG-AGGGCACTATT
1 TTTTTGTCAGAGAATAGGTTATAATTTCCCTATTTTGTGTGATGTCCCCCG-GAAGGGCACTATT
* * * * * * * *
379045 CATGTTAGTACCTATCATTTTTTAAGGGACACATCAATGCGGTTAAAGTGCGTTTCAGGGGTC-G
65 CATGTCAGTACCTATCATGTTTGAGGGGACACAT-AATGTGGTTAAAGCGCATTTCAGGGGGCAG
* * *
379109 -CTTTCCTTGTTTTGTCAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGCGGGGC
129 CCTTCCCTTTTTTTGTCAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGTGGGGC
* * * *
379173 ATTATTAATGTCAGTACCTATCATGTTTAAGGGGACGTAGCAATGTCGTTAAAGCGCATTTCAGG
194 ACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAGCAATGT-GTTAAAGCGCATTTCAGG
379238 G-G-G----C-------G-CCTTCCC
258 GAGCGTTTTCAGGGGGTGTCCTTCCC
* * *
379250 TTTTTGTCAGAGAATAGGTTATAATTGCCATATTTTGTGTGATGTCCCCC-GACAGGGAACTATT
1 TTTTTGTCAGAGAATAGGTTATAATTTCCCTATTTTGTGTGATGTCCCCCGGA-AGGGCACTATT
* *
379314 CATGTCAGTACCTATCATGTTTTTAGGGGATGTA-ATAATGTGGTTAAAGCGCATTTCAGGGGGC
65 CATGTCAGTACCTATCATG-TTTGAGGGGA--CACATAATGTGGTTAAAGCGCATTTCAGGGGGC
* *
379378 GTGCCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGT
127 -AGCCTTCCCTTTTTTTG-T-CAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGT
* * * *
379443 GGGGAACTATTCTTGTCAGTACCTATCATGTTTGAGGGGA--C-GCAA-----TAATGTGC-TTT
189 GGGGCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAGCAATGTGTTAAAGCGCATTT
*
379499 -A---AGCGTGTTTCAGGGGGT-TCCTTTCCTT
254 CAGGGAGCGT-TTTCAGGGGGTGTCC-TTCC-C
* * *
379527 TTTTTGTCAGAGAATAGGTTATAATTACCCTATTTTGTGTCATGTCCCCCGGAATGGCACTATTC
1 TTTTTGTCAGAGAATAGGTTATAATTTCCCTATTTTGTGTGATGTCCCCCGGAAGGGCACTATTC
* * * *
379592 ATATCAGTACCTATCATGTTTGAGGGGACGCAATAATGTGGTTAAAGCACGTTTCAGGGGGCA-C
66 ATGTCAGTACCTATCATGTTTGAGGGGACAC-ATAATGTGGTTAAAGCGCATTTCAGGGGGCAGC
* * * * * *
379656 CTTCCCTTTTTTTTATCAGAGAATAGGTTATAATTGCCTTATTTTGTGTCATGTCCCCTAGAGTG
130 CTTCCC-TTTTTTTGTC--AGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGTGGG
* * * *
379721 ACACTATTCATATGAGTACCTATCATGTTTGAGGGGACGCAACAATGTGGTTAAAGCGCATTTCA
192 GCACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAGCAATGT-GTTAAAGCGCATTTCA
379786 GGG-G-G----CA-----TG-CCTTCCC
256 GGGAGCGTTTTCAGGGGGTGTCCTTCCC
* ** * *
379802 TTTTTTTATCAGAGAATAGGTTATAAACTCCCTATTTTGTGTCATGTCCCCCGGAATGGCACTAT
1 --TTTTTGTCAGAGAATAGGTTATAATTTCCCTATTTTGTGTGATGTCCCCCGGAAGGGCACTAT
379867 GTTGGAAATT
Statistics
Matches: 749, Mismatches: 78, Indels: 126
0.79 0.08 0.13
Matches are distributed among these distances:
262 1 0.00
263 1 0.00
264 1 0.00
265 3 0.00
266 6 0.01
267 1 0.00
268 13 0.02
269 69 0.09
270 34 0.05
271 2 0.00
272 6 0.01
273 12 0.02
274 9 0.01
275 159 0.21
276 45 0.06
277 138 0.18
278 5 0.01
282 3 0.00
283 1 0.00
284 9 0.01
285 9 0.01
286 178 0.24
287 42 0.06
288 2 0.00
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (283 bp):
TTTTTGTCAGAGAATAGGTTATAATTTCCCTATTTTGTGTGATGTCCCCCGGAAGGGCACTATTC
ATGTCAGTACCTATCATGTTTGAGGGGACACATAATGTGGTTAAAGCGCATTTCAGGGGGCAGCC
TTCCCTTTTTTTGTCAGAATAGGTTATAATTGCCCTATTTTGTGTGATGTCCCCTGGTGGGGCAC
TATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAGCAATGTGTTAAAGCGCATTTCAGGGAG
CGTTTTCAGGGGGTGTCCTTCCC
Found at i:379483 original size:275 final size:268
Alignment explanation
Indices: 378955--379866 Score: 1084
Period size: 275 Copynumber: 3.3 Consensus size: 268
378945 TTTCAGGGGG
* *
378955 AGCGTATTTCAGGGGGTGCTCCTTCCCTTTTT-TCAGAGAATAGGTTATAATTTCCCTATTTTGT
1 AGCGCATTTCA-GGGG-GCGCCTTCCCTTTTTGTCAGAGAATAGGTTATAA-TTCCCTATTTTGT
* * * *
379019 GTGATGTCCCCCGTGAGGGCACTATTCATGTTAGTACCTATCAT-TTTTTAAGGGA-CACATCAA
63 GTCATGTCCCCCG-AAGGGCACTATTCATGTCAGTACCTATCATGTTTTTAGGGGAGCA-AT-AA
* * * * * *
379082 TGCGGTTAAAGTGCGTTTCAGGGGTCG-CTTTCCTTGTTTTG-T-CAGAATAGGTTATAATTGCC
125 TGTGGTTAAAGCGCGTTTCAGGGGGCGCCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCC
* * * *
379144 CTATTTTGTGTGATGTCCCCTGGCGGGGCATTATTAATGTCAGTACCTATCATGTTTAAGGGGAC
190 CTATTTTGTGTGATGTCCCCTGG-GGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGAC
* *
379209 GTAGCAATGTCGTTAA
254 GCAACAATGT-GTTAA
*
379225 AGCGCATTTCAGGGGGCGCCTTCCCTTTTTGTCAGAGAATAGGTTATAATTGCCATATTTTGTGT
1 AGCGCATTTCAGGGGGCGCCTTCCCTTTTTGTCAGAGAATAGGTTATAATT-CCCTATTTTGTGT
* * *
379290 GATGTCCCCCGACAGGGAACTATTCATGTCAGTACCTATCATGTTTTTAGGGGATGTAATAATGT
65 CATGTCCCCCGA-AGGGCACTATTCATGTCAGTACCTATCATGTTTTTAGGGGA-GCAATAATGT
*
379355 GGTTAAAGCGCATTTCAGGGGGCGTGCCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCC
128 GGTTAAAGCGCGTTTCAGGGGGC--GCCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCC
*
379420 TATTTTGTGTGATGTCCCCTGGTGGGGAACTATTCTTGTCAGTACCTATCATGTTTGAGGGGACG
191 TATTTTGTGTGATGTCCCCTGG-GGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACG
* *
379485 CAATAATGTGCTTTA
255 CAACAATGTG-TTAA
** ** *
379500 AGCGTGTTTCAGGGGGTTCCTTTCCTTTTTTTGTCAGAGAATAGGTTATAATTACCCTATTTTGT
1 AGCGCATTTCAGGGGGCGCC-TTCC-CTTTTTGTCAGAGAATAGGTTATAATT-CCCTATTTTGT
* * *
379565 GTCATGTCCCCCGGAATGGCACTATTCATATCAGTACCTATCATG-TTTGAGGGGACGCAATAAT
63 GTCATGTCCCCC-GAAGGGCACTATTCATGTCAGTACCTATCATGTTTTTAGGGGA-GCAATAAT
* *
379629 GTGGTTAAAGCACGTTTCAGGGGGCACCTTCCCTTTTTTT-TATCAGAGAATAGGTTATAATTGC
126 GTGGTTAAAGCGCGTTTCAGGGGGCGCCTTCCCTTTTTTTGT-T-AGAGAATAGGTTATAATTGC
* * * * * * *
379693 CTTATTTTGTGTCATGTCCCCTAGAGTGACACTATTCATATGAGTACCTATCATGTTTGAGGGGA
189 CCTATTTTGTGTGATGTCCCCTGGGGGGA-ACTATTCATGTCAGTACCTATCATGTTTGAGGGGA
379758 CGCAACAATGTGGTTAA
253 CGCAACAATGT-GTTAA
* *
379775 AGCGCATTTCAGGGGGCATGCCTTCCCTTTTTTTATCAGAGAATAGGTTATAAACTCCCTATTTT
1 AGCGCATTTCAGGGGGC--GCCTTCCC--TTTTTGTCAGAGAATAGGTTAT-AATTCCCTATTTT
*
379840 GTGTCATGTCCCCCGGAATGGCACTAT
61 GTGTCATGTCCCCC-GAAGGGCACTAT
379867 GTTGGAAATT
Statistics
Matches: 559, Mismatches: 59, Indels: 41
0.85 0.09 0.06
Matches are distributed among these distances:
268 16 0.03
269 72 0.13
270 44 0.08
271 2 0.00
272 2 0.00
273 13 0.02
274 20 0.04
275 204 0.36
276 48 0.09
277 133 0.24
278 5 0.01
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (268 bp):
AGCGCATTTCAGGGGGCGCCTTCCCTTTTTGTCAGAGAATAGGTTATAATTCCCTATTTTGTGTC
ATGTCCCCCGAAGGGCACTATTCATGTCAGTACCTATCATGTTTTTAGGGGAGCAATAATGTGGT
TAAAGCGCGTTTCAGGGGGCGCCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTT
TGTGTGATGTCCCCTGGGGGGAACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAACAA
TGTGTTAA
Found at i:379732 original size:138 final size:137
Alignment explanation
Indices: 378955--379852 Score: 1023
Period size: 137 Copynumber: 6.6 Consensus size: 137
378945 TTTCAGGGGG
* * *
378955 AGCGTATTTCAGGGGGTGCTCCTTCCC--TTTTT-TCAGAGAATAGGTTATAATTTCCCTATTTT
1 AGCGCATTTCA-GGGG-GCACCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTTT
* * * * * *
379017 GTGTGATGTCCCCCGTGAGGG-CACTATTCATGTTAGTACCTATCATTTTTTAAGGGACAC-ATC
64 GTGTGATGTCCCCTG-GAGGGACACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAAT-
*
379080 AATGCGGTTAA
127 AATGTGGTTAA
* * * * * *
379091 AGTGCGTTTCAGGGGTC-GCTTTCCTTGTTTTGTC--AGAATAGGTTATAATTGCCCTATTTTGT
1 AGCGCATTTCAGGGGGCACCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTTTGT
* * * * * * **
379153 GTGATGTCCCCTGGCGGGGCATTATTAATGTCAGTACCTATCATGTTTAAGGGGACGTAGCAATG
66 GTGATGTCCCCTGGAGGGACACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAATG
*
379218 TCGTTAA
131 TGGTTAA
* *
379225 AGCGCATTTCAGGGGGCGCCTTCCC--TTTTTGTCAGAGAATAGGTTATAATTGCCATATTTTGT
1 AGCGCATTTCAGGGGGCACCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTTTGT
* * * * *
379288 GTGATGTCCCCCGACAGGGA-ACTATTCATGTCAGTACCTATCATGTTTTTAGGGGATGTAATAA
66 GTGATGTCCCCTG-GAGGGACACTATTCATGTCAGTACCTATCATG-TTTGAGGGGACGCAATAA
379352 TGTGGTTAA
129 TGTGGTTAA
* *
379361 AGCGCATTTCAGGGGGCGTGCCTTCCCTTTTTTTGTTAGAGAATAGGTTATAATTGCCCTATTTT
1 AGCGCATTTCAGGGGGC--ACCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTTT
* *
379426 GTGTGATGTCCCCTGGTGGGGA-ACTATTCTTGTCAGTACCTATCATGTTTGAGGGGACGCAATA
64 GTGTGATGTCCCCTGG-AGGGACACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATA
* *
379490 ATGTGCTTTA
128 ATGTGGTTAA
** ** * *
379500 AGCGTGTTTCAGGGGGTTCCTTTCCTTTTTTTGTCAGAGAATAGGTTATAATTACCCTATTTTGT
1 AGCGCATTTCAGGGGGCACCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTTTGT
* * * *
379565 GTCATGTCCCCCGGAATGG-CACTATTCATATCAGTACCTATCATGTTTGAGGGGACGCAATAAT
66 GTGATGTCCCCTGG-AGGGACACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAAT
379629 GTGGTTAA
130 GTGGTTAA
* * * *
379637 AGCACGTTTCAGGGGGCACCTTCCCTTTTTTTTATCAGAGAATAGGTTATAATTGCCTTATTTTG
1 AGCGCATTTCAGGGGGCACCTTCCC-TTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTTTG
* * * * * *
379702 TGTCATGTCCCCTAGAGTGACACTATTCATATGAGTACCTATCATGTTTGAGGGGACGCAACAAT
65 TGTGATGTCCCCTGGAGGGACACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAAT
379767 GTGGTTAA
130 GTGGTTAA
* *
379775 AGCGCATTTCAGGGGGCATGCCTTCCCTTTTTTTATCAGAGAATAGGTTATAAACT-CCCTATTT
1 AGCGCATTTCAGGGGGCA--CCTTCCCTTTTTTTGTCAGAGAATAGGTTAT-AATTGCCCTATTT
*
379839 TGTGTCATGTCCCC
63 TGTGTGATGTCCCC
379853 CGGAATGGCA
Statistics
Matches: 656, Mismatches: 85, Indels: 39
0.84 0.11 0.05
Matches are distributed among these distances:
133 16 0.02
134 94 0.14
135 75 0.11
136 52 0.08
137 128 0.20
138 124 0.19
139 81 0.12
140 86 0.13
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (137 bp):
AGCGCATTTCAGGGGGCACCTTCCCTTTTTTTGTCAGAGAATAGGTTATAATTGCCCTATTTTGT
GTGATGTCCCCTGGAGGGACACTATTCATGTCAGTACCTATCATGTTTGAGGGGACGCAATAATG
TGGTTAA
Found at i:380448 original size:21 final size:21
Alignment explanation
Indices: 380406--380448 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
380396 TTTAATAGGG
* **
380406 AAGTATCGATACCTCTTTAAC
1 AAGTATCGATACCCCTCAAAC
380427 AAGTATCGATACCCCTCAAAC
1 AAGTATCGATACCCCTCAAAC
380448 A
1 A
380449 TCAAATGCAA
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:0.37, C:0.28, G:0.09, T:0.26
Consensus pattern (21 bp):
AAGTATCGATACCCCTCAAAC
Found at i:381401 original size:21 final size:21
Alignment explanation
Indices: 381367--381417 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
381357 GGGTGTCATA
* *
381367 AAACCCTGCAGGCTGGGTATG
1 AAACCCTGCAGGCTAGGAATG
* **
381388 TAACCCTGTGGGCTAGGAATG
1 AAACCCTGCAGGCTAGGAATG
381409 AAACCCTGC
1 AAACCCTGC
381418 GGAGATGACA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (21 bp):
AAACCCTGCAGGCTAGGAATG
Found at i:381481 original size:42 final size:41
Alignment explanation
Indices: 381411--381497 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
381401 TAGGAATGAA
* *
381411 ACCCTGCGGAGATGACATATGAACTGGTGGGCTTGGCATAT
1 ACCCTGCGGAGATGACATATGAACTGGTGGGATGGGCATAT
** * * *
381452 ACCCTTGCGGAGATGGTATCTGAATTGGTGGGATGGGCATGT
1 ACCC-TGCGGAGATGACATATGAACTGGTGGGATGGGCATAT
381494 ACCC
1 ACCC
381498 CTGTGGCATC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 4 0.11
42 34 0.89
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.25
Consensus pattern (41 bp):
ACCCTGCGGAGATGACATATGAACTGGTGGGATGGGCATAT
Found at i:382072 original size:17 final size:17
Alignment explanation
Indices: 382050--382085 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
382040 AAACTGAAAC
382050 ATAAATATA-TAATTCTA
1 ATAAATATAGT-ATTCTA
382067 ATAAATATAGTATTCTA
1 ATAAATATAGTATTCTA
382084 AT
1 AT
382086 TATATCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.94
18 1 0.06
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.42
Consensus pattern (17 bp):
ATAAATATAGTATTCTA
Found at i:383205 original size:15 final size:16
Alignment explanation
Indices: 383185--383214 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
383175 CTATAGGCAA
383185 ACAAAT-ATAATTAAC
1 ACAAATAATAATTAAC
383200 ACAAATAATAATTAA
1 ACAAATAATAATTAA
383215 TTAATATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (16 bp):
ACAAATAATAATTAAC
Found at i:383221 original size:29 final size:29
Alignment explanation
Indices: 383187--383250 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
383177 ATAGGCAAAC
383187 AAATATAATTAACACAAATAATAATTA-AT
1 AAATATAATTAA-ACAAATAATAATTATAT
* * *
383216 TAATATATTTAAATAAATAATAATTATAT
1 AAATATAATTAAACAAATAATAATTATAT
383245 AAATAT
1 AAATAT
383251 TATTTTAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.43
29 17 0.57
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATATAATTAAACAAATAATAATTATAT
Found at i:383236 original size:21 final size:19
Alignment explanation
Indices: 383206--383249 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
383196 TAACACAAAT
* *
383206 AATAATTAATTAATATATTTA
1 AATAAATAA-TAAT-TATATA
383227 AATAAATAATAATTATATA
1 AATAAATAATAATTATATA
383246 AATA
1 AATA
383250 TTATTTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 4 0.19
21 8 0.38
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAATAATAATTATATA
Found at i:392416 original size:13 final size:13
Alignment explanation
Indices: 392395--392449 Score: 74
Period size: 13 Copynumber: 4.2 Consensus size: 13
392385 AATGACGCGC
*
392395 AATGAGCGTCATA
1 AATGCGCGTCATA
392408 AATGCGCGTCATA
1 AATGCGCGTCATA
* * *
392421 AATGTGTGTTATA
1 AATGCGCGTCATA
392434 AATGCGCGTCATA
1 AATGCGCGTCATA
392447 AAT
1 AAT
392450 TTATGACGCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (13 bp):
AATGCGCGTCATA
Found at i:392424 original size:26 final size:26
Alignment explanation
Indices: 392395--392449 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
392385 AATGACGCGC
392395 AATGAGCGTCATAAATGCGCGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
* * *
392421 AATGTGTGTTATAAATGCGCGTCATA
1 AATGAGCGTCATAAATGCGCGTCATA
392447 AAT
1 AAT
392450 TTATGACGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCGTCATA
Found at i:397533 original size:21 final size:20
Alignment explanation
Indices: 397500--397542 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
397490 TTGTTTTCTT
* *
397500 TTAAATTTATTTTCTTCGCTA
1 TTAAATATATTTT-TTCGATA
*
397521 TTAAATATGTTTTTTCGATA
1 TTAAATATATTTTTTCGATA
397541 TT
1 TT
397543 GTTGAATTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.58
Consensus pattern (20 bp):
TTAAATATATTTTTTCGATA
Found at i:400365 original size:15 final size:15
Alignment explanation
Indices: 400345--400374 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
400335 TTCTCATTTG
*
400345 ATTTTTAAAATTTAA
1 ATTTTTAAAAATTAA
400360 ATTTTTAAAAATTAA
1 ATTTTTAAAAATTAA
400375 GAAAACGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAAAAATTAA
Found at i:400486 original size:42 final size:42
Alignment explanation
Indices: 400418--400503 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
400408 TTACTAAAAC
* * * *
400418 GAGTAAGTCCTCTGGGCCATCAGTAAGTCTTTTGAGCATGAT
1 GAGTAAATCCTCTAGGCCATCAGTAAGTCTTTCGAGCAAGAT
* *
400460 GAGTAAATCCTCTAGGTCATCTGTAAGTCTTTCGAGCAAGAT
1 GAGTAAATCCTCTAGGCCATCAGTAAGTCTTTCGAGCAAGAT
400502 GA
1 GA
400504 TAAGTCTTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (42 bp):
GAGTAAATCCTCTAGGCCATCAGTAAGTCTTTCGAGCAAGAT
Found at i:402203 original size:36 final size:36
Alignment explanation
Indices: 402114--402219 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 36
402104 CACTCCTATT
* * * * *
402114 TCTCACTTGAGATTATTTTCCTTAAAATAAATTCTA
1 TCTCACTTGAAATTGTTTTCTTTAAAACAAATTTTA
402150 TCTCACTT-AAGATTGTTTTCTTTAAAACAAATTTTA
1 TCTCACTTGAA-ATTGTTTTCTTTAAAACAAATTTTA
* *
402186 TCTCACTTGAAAATG-TTTCTCTCAAAACAAATTT
1 TCTCACTTGAAATTGTTTTCT-TTAAAACAAATTT
402220 CTTCCTCACT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
35 6 0.10
36 52 0.87
37 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (36 bp):
TCTCACTTGAAATTGTTTTCTTTAAAACAAATTTTA
Found at i:402808 original size:37 final size:38
Alignment explanation
Indices: 402734--402808 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 38
402724 CCAGACTAAA
* * *
402734 AAATATTTGAGGGATAATTTGAAGGTTGTTCGTGCTTC
1 AAATATTCGAGGGATAATTTGAAGGTTATTCGCGCTTC
*
402772 AAATATTCGAGGG-TAGTTTGAAGGTTATTCGCGCTTC
1 AAATATTCGAGGGATAATTTGAAGGTTATTCGCGCTTC
402809 TACATCAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
37 21 0.64
38 12 0.36
ACGTcount: A:0.25, C:0.11, G:0.27, T:0.37
Consensus pattern (38 bp):
AAATATTCGAGGGATAATTTGAAGGTTATTCGCGCTTC
Found at i:403035 original size:3 final size:3
Alignment explanation
Indices: 403017--403066 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
403007 TTTTTCTATC
*
403017 TAT TTT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
403064 TAT
1 TAT
403067 AAATTATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:404016 original size:16 final size:16
Alignment explanation
Indices: 403995--404025 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
403985 ATAAATAAAT
403995 GAACATAAACGAACAC
1 GAACATAAACGAACAC
404011 GAACATAAACGAACA
1 GAACATAAACGAACA
404026 AATTTTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.23, G:0.13, T:0.06
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:404116 original size:16 final size:16
Alignment explanation
Indices: 404087--404153 Score: 84
Period size: 16 Copynumber: 4.3 Consensus size: 16
404077 CGTTCATTTA
404087 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
**
404101 ATAAATGCGCACGAAC
1 ATAAATGAACACGAAC
* *
404117 ATAAACGAACACGAAT
1 ATAAATGAACACGAAC
404133 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
404149 ATAAA
1 ATAAA
404154 CGTTGGAGAC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
14 6 0.14
16 37 0.86
ACGTcount: A:0.57, C:0.18, G:0.12, T:0.13
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:404131 original size:32 final size:32
Alignment explanation
Indices: 404095--404155 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
404085 TAATAAATAA
**
404095 ACGAACATAAATGCGCACGAACATAAACGAAC
1 ACGAACATAAATGAACACGAACATAAACGAAC
*
404127 ACGAATATAAATGAACACGAACATAAACG
1 ACGAACATAAATGAACACGAACATAAACG
404156 TTGGAGACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.52, C:0.21, G:0.15, T:0.11
Consensus pattern (32 bp):
ACGAACATAAATGAACACGAACATAAACGAAC
Found at i:405240 original size:10 final size:10
Alignment explanation
Indices: 405225--405272 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
405215 ATAAATGAAT
405225 GAACATAAAC
1 GAACATAAAC
405235 GAACATAACCGAAC
1 GAACAT-A---AAC
405249 GAACATAAAC
1 GAACATAAAC
*
405259 GAACATAACC
1 GAACATAAAC
405269 GAAC
1 GAAC
405273 GAACATAACT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
GAACATAAAC
Found at i:405249 original size:14 final size:14
Alignment explanation
Indices: 405232--405287 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
405222 AATGAACATA
405232 AACGAACATAACCG
1 AACGAACATAACCG
405246 AACGAACAT-A---
1 AACGAACATAACCG
405256 AACGAACATAACCG
1 AACGAACATAACCG
*
405270 AACGAACATAACTG
1 AACGAACATAACCG
405284 AACG
1 AACG
405288 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.52, C:0.25, G:0.14, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:405286 original size:24 final size:24
Alignment explanation
Indices: 405225--405280 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
405215 ATAAATGAAT
405225 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
405249 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
405273 GAACATAA
1 GAACATAA
405281 CTGAACGTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.55, C:0.23, G:0.12, T:0.09
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Done.