Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002748.1 Hibiscus syriacus cultivar Beakdansim tig00005659_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: 127885
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:475 original size:192 final size:198
Alignment explanation
Indices: 1--1185 Score: 1965
Period size: 193 Copynumber: 6.1 Consensus size: 198
1 ATCGACAC-TTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
**
65 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATAATTGTACCGGTTAGA
66 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTATAATTGTACCGGTTAGA
130 TTGAAAAA-TACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTATAT
130 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
192 ATGG
195 ATGG
196 ATCGACACTTTAT-GGTGC-CCCTG-TTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
* *
258 TATTAGTGTTGACACATTATTTAGACATATTCTCTCA-AAATA-AGTATAATTGTACCGGTTAGA
66 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAA-ACGGTATAATTGTACCGGTTAGA
321 TTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
130 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
385 AT-G
195 ATGG
*
388 ATTCAACACTTTATGGGTGCACCCTGTTTTCCATTCA-TCTGGAAAAC-AATATCGACAC-AACT
1 A-TCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACT
450 ATATTAGTGTCGACACA-TATTTAGAC--ATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
65 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTATAATTGTACCGGTTAG
512 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
129 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
577 TATGG
194 TATGG
*
582 ATCGACACTTTAT-GGTGCA-CCTTTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
645 TATTAGTGTCGACAC-TTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
66 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTATAATTGTACCGGTTAGA
709 TTG-AAAATTACATATTACATTATACTTTTGGGTTCG-TGATTTTGGGATCGACACTTTTTATAT
130 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
772 ATGG
195 ATGG
776 ATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAAC-AA-ATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
*
838 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAACCGGTATAATTGTA-CGGTTAGAT
66 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACGGTATAATTGTACCGGTTAGAT
*
902 TGAAAAATTAC-TATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTGTTTATATA
131 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
966 -GG
196 TGG
**
968 ATCGACACTTTATGGGTGCA-CCTG-TGGCCATTCATTCTGGAAAAC-AATATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
1030 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
66 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAA-CGGTATAATTGTACCGGTTAGA
*
1095 TTGAAAAATTACATA-TACATTATAATTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
130 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
1159 -T--
195 ATGG
1160 ATCGACACTTTAT-GGTGCACCCTGTT
1 ATCGACACTTTATGGGTGCACCCTGTT
1186 GGCCATATGT
Statistics
Matches: 944, Mismatches: 14, Indels: 66
0.92 0.01 0.06
Matches are distributed among these distances:
190 10 0.01
191 77 0.08
192 240 0.25
193 280 0.30
194 190 0.20
195 90 0.10
196 57 0.06
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (198 bp):
ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACGGTATAATTGTACCGGTTAGAT
TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
TGG
Found at i:725 original size:387 final size:392
Alignment explanation
Indices: 1--1185 Score: 2008
Period size: 387 Copynumber: 3.1 Consensus size: 392
1 ATCGACAC-TTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTA
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAAC-AATATCGACACAAACTA
***
65 TATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAATAAGTATAATTGTACCGGTTAGA
65 TATTAGTGTCGACACATTATTTAGACA-ATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGA
130 TTGAAAAA-TACATA-TACATTATACTTTTGGGTTCGATGATTTTGGGATCGACAC-TTTTATAT
129 TTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATAT
*
192 ATGGATCGACACTTTATGGTGCCCCTGTTTCCATTCATTCTGGAAAACAAATATCGACACAAACT
194 ATGGATCGACACTTTATGGTGCACCTGTTTCCATTCATTCTGGAAAACAAATATCGACACAAACT
* *
257 ATATTAGTGTTGACACATTATTTAGACATATTCTCTCA-AAATA--AGTATAATTGTACCGGTTA
259 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAA-ACCGGTATAATTGTACCGGTTA
319 GATTGAAAAATTACATATTACA-TATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
323 GATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTAT
383 ATATG
388 ATATG
*
388 ATTCAACACTTTATGGGTGCACCCTGTTTTCCATTCA-TCTGGAAAACAATATCGACAC-AACTA
1 A-TCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAATATCGACACAAACTA
451 TATTAGTGTCGACACA-TATTTAGAC-ATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
65 TATTAGTGTCGACACATTATTTAGACAATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
514 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
130 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
*
579 TGGATCGACACTTTATGGTGCACCTTTTTTCCATTCATTCTGGAAAACAAATATCGACACAAACT
195 TGGATCGACACTTTATGGTGCACC-TGTTTCCATTCATTCTGGAAAACAAATATCGACACAAACT
644 ATATTAGTGTCGACAC-TTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
259 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
708 ATTG-AAAATTACATATTACATTATACTTTTGGGTTCG-TGATTTTGGGATCGACACTTTTTATA
324 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
771 TATGG
389 TAT-G
776 ATCGACACTTTATGGGTGCACCCTG-TTTCCATTCATTCTGGAAAACAA-ATCGACACAAACTAT
1 ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAATATCGACACAAACTAT
839 ATTAGTGTCGACACATTATTTAGACATATTCTCTCAT-AAACCGGTATAATTGTA-CGGTTAGAT
66 ATTAGTGTCGACACATTATTTAGACA-ATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
*
902 TGAAAAATTAC-TATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTGTTTATATA
130 TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
**
966 -GGATCGACACTTTATGGGTGCACCTGTGGCCATTCATTCTGGAAAAC-AATATCGACACAAACT
195 TGGATCGACACTTTAT-GGTGCACCTGTTTCCATTCATTCTGGAAAACAAATATCGACACAAACT
1029 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
259 ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAG
*
1094 ATTGAAAAATTACATA-TACATTATAATTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
324 ATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATA
1158 T-T-
389 TATG
1160 ATCGACACTTTAT-GGTGCACCCTGTT
1 ATCGACACTTTATGGGTGCACCCTGTT
1186 GGCCATATGT
Statistics
Matches: 763, Mismatches: 14, Indels: 45
0.93 0.02 0.05
Matches are distributed among these distances:
383 53 0.07
384 20 0.03
385 81 0.11
386 201 0.26
387 268 0.35
388 86 0.11
389 44 0.06
390 10 0.01
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (392 bp):
ATCGACACTTTATGGGTGCACCCTGTTTTCCATTCATTCTGGAAAACAATATCGACACAAACTAT
ATTAGTGTCGACACATTATTTAGACAATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATT
GAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATAT
GGATCGACACTTTATGGTGCACCTGTTTCCATTCATTCTGGAAAACAAATATCGACACAAACTAT
ATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGAT
TGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATA
TG
Found at i:1342 original size:19 final size:18
Alignment explanation
Indices: 1300--1347 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1290 TTATATTCAC
*
1300 ATACAAAAATAAAATCGT
1 ATACAAAATTAAAATCGT
*
1318 AT-CAAAATTATAAATCTT
1 ATACAAAATTA-AAATCGT
1336 ATACAAAATTAA
1 ATACAAAATTAA
1348 CCCTACATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 7 0.27
18 11 0.42
19 8 0.31
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.29
Consensus pattern (18 bp):
ATACAAAATTAAAATCGT
Found at i:3156 original size:33 final size:33
Alignment explanation
Indices: 3119--3184 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3109 CATCTTAATA
* *
3119 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
* *
3152 TCACCCCTCAACACCTCTACTTCATTCACCACT
1 TCACCCCTCAACACCCCAACTTCATTCACCACT
3185 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCATTCACCACT
Found at i:3256 original size:19 final size:21
Alignment explanation
Indices: 3218--3257 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3208 CCCCTTATGC
*
3218 CTCTCGAGTGTATCTTCGACT
1 CTCTCGAGTGTATCTACGACT
3239 CTCTCGAGT-T-TCTACGACT
1 CTCTCGAGTGTATCTACGACT
3258 TGATCAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.15, C:0.30, G:0.17, T:0.38
Consensus pattern (21 bp):
CTCTCGAGTGTATCTACGACT
Found at i:5507 original size:17 final size:18
Alignment explanation
Indices: 5485--5527 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
5475 ATATATCCGG
5485 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
5502 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
5522 TATCAT
1 TATCAT
5528 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:5545 original size:20 final size:19
Alignment explanation
Indices: 5490--5536 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
5480 TCCGGTATCA
5490 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
5509 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
5530 TTTTACC
1 TTTTACC
5537 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:5684 original size:20 final size:20
Alignment explanation
Indices: 5658--5703 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
5648 CACTTTTAAA
5658 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
5677 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
5698 TTTACC
1 TTTACC
5704 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:9408 original size:21 final size:22
Alignment explanation
Indices: 9362--9419 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
9352 AATTTTTTTA
* * *
9362 TATAAAATTAAAAAAATAAAAT
1 TATAAATTTCAAAAAAGAAAAT
* *
9384 TATATATTTTAAAAAAGAAAA-
1 TATAAATTTCAAAAAAGAAAAT
9405 TATAAATTTCAAAAA
1 TATAAATTTCAAAAA
9420 TCTCAAAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.43
22 17 0.57
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (22 bp):
TATAAATTTCAAAAAAGAAAAT
Found at i:10588 original size:80 final size:80
Alignment explanation
Indices: 10455--10619 Score: 312
Period size: 80 Copynumber: 2.1 Consensus size: 80
10445 GCATAGGTTT
10455 AGAGTCCCCCACTAACTTGTTCTAAAATGATGCAAATATTGTTTTATTTGAGATAACAGCACTCA
1 AGAGTCCCCCACTAACTTGTTCTAAAATGATGCAAATATTGTTTTATTTGAGATAACAGCACTCA
*
10520 AAGTCCCTGATGAGC
66 AAATCCCTGATGAGC
*
10535 AGAGTCCCCCACTAACTTGTTCTAAAATTATGCAAATATTGTTTTATTTGAGATAACAGCACTCA
1 AGAGTCCCCCACTAACTTGTTCTAAAATGATGCAAATATTGTTTTATTTGAGATAACAGCACTCA
10600 AAATCCCTGATGAGC
66 AAATCCCTGATGAGC
10615 AGAGT
1 AGAGT
10620 ATATTTATCA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
80 83 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (80 bp):
AGAGTCCCCCACTAACTTGTTCTAAAATGATGCAAATATTGTTTTATTTGAGATAACAGCACTCA
AAATCCCTGATGAGC
Found at i:11228 original size:191 final size:193
Alignment explanation
Indices: 10895--11272 Score: 564
Period size: 191 Copynumber: 2.0 Consensus size: 193
10885 CCAATTCGAG
* *
10895 ATGACTATCCAGCTCAGTTGGTAGAGCACAAGGTTCTTAATCTTGAGGTCGTAGGATCGAGTCCC
1 ATGACCATCCAGCTCAGTTGGTAGAGCACAAGGTTCTTAACCTTGAGGTCGTAGGATCGAGTCCC
* * * * * *
10960 ACGGAGGACATTTTATAATTCAGAGGTCTTCTATGGAAGCTGTTCTCAACTTGGTATTGGGGGCA
66 ACGGAGGACATTTCATAATTCAGAGGTCTCCTACGGAAGCTGCTCTCAACCTAGTATTGGGGGCA
*
11025 GCCTACTATCTTACC-TC-CCTTTA-TCCCATTACATATGGGAACAAGAGACAACCATTTTGAA
131 GCCTACTATCTTACCTTCTCC-TTACCCCCATTACATATGGGAACAAGAGACAACCATTTTGAA
* * *
11086 ATGACCATTCAGCTCAGTTGGTAGAGCACAAGGTTCTTAACCTTGAGGTCGTGGGATCGAGTCTC
1 ATGACCATCCAGCTCAGTTGGTAGAGCACAAGGTTCTTAACCTTGAGGTCGTAGGATCGAGTCCC
* * * *
11151 ATGGAGGGCATTTCATAATTCGGAGGTCTCCTACGGAAGCTGCTCTCAACCTAGTGTTGGGGGCA
66 ACGGAGGACATTTCATAATTCAGAGGTCTCCTACGGAAGCTGCTCTCAACCTAGTATTGGGGGCA
* *
11216 GTCTACTATCTTACCTTCTCCTTACCCCCATTACATATGGGAACAAGGGACAACCAT
131 GCCTACTATCTTACCTTCTCCTTACCCCCATTACATATGGGAACAAGAGACAACCAT
11273 AATTTTATCC
Statistics
Matches: 166, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
191 129 0.78
192 5 0.03
193 32 0.19
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.29
Consensus pattern (193 bp):
ATGACCATCCAGCTCAGTTGGTAGAGCACAAGGTTCTTAACCTTGAGGTCGTAGGATCGAGTCCC
ACGGAGGACATTTCATAATTCAGAGGTCTCCTACGGAAGCTGCTCTCAACCTAGTATTGGGGGCA
GCCTACTATCTTACCTTCTCCTTACCCCCATTACATATGGGAACAAGAGACAACCATTTTGAA
Found at i:12388 original size:2 final size:2
Alignment explanation
Indices: 12381--12416 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12371 ACACCGCGTG
12381 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12417 AACATTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:18307 original size:19 final size:19
Alignment explanation
Indices: 18283--18322 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
18273 AACATATGAC
*
18283 ATTGAAATTTATTTAAATT
1 ATTGAAATTTAATTAAATT
*
18302 ATTGAAATTTAATTAATTT
1 ATTGAAATTTAATTAAATT
18321 AT
1 AT
18323 CAATAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
ATTGAAATTTAATTAAATT
Found at i:21373 original size:16 final size:16
Alignment explanation
Indices: 21352--21405 Score: 108
Period size: 16 Copynumber: 3.4 Consensus size: 16
21342 CGGAATTCCG
21352 GGTTTTGGATCGAAAC
1 GGTTTTGGATCGAAAC
21368 GGTTTTGGATCGAAAC
1 GGTTTTGGATCGAAAC
21384 GGTTTTGGATCGAAAC
1 GGTTTTGGATCGAAAC
21400 GGTTTT
1 GGTTTT
21406 CTTTGAACCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.22, C:0.11, G:0.31, T:0.35
Consensus pattern (16 bp):
GGTTTTGGATCGAAAC
Found at i:24438 original size:67 final size:67
Alignment explanation
Indices: 24330--24465 Score: 227
Period size: 67 Copynumber: 2.0 Consensus size: 67
24320 TGCAACAGTT
* *
24330 TCATACTGCCATCAACGTCCAGTTCATCATGGAAATCTTGCAGCCAGTACACTTCATGATGTTTA
1 TCATACTGCCATCAACGTCCAGTTCATCATAGAAATCTTGCAGCCAGTACACGTCATGATGTTTA
24395 AA
66 AA
* * *
24397 TCATACTGCCATCAATGTCTAGTTCATCATAGAAATCTTGCAGCCAGTGCACGTCATGATGTTTA
1 TCATACTGCCATCAACGTCCAGTTCATCATAGAAATCTTGCAGCCAGTACACGTCATGATGTTTA
24462 AA
66 AA
24464 TC
1 TC
24466 CGTCATGCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.31
Consensus pattern (67 bp):
TCATACTGCCATCAACGTCCAGTTCATCATAGAAATCTTGCAGCCAGTACACGTCATGATGTTTA
AA
Found at i:27428 original size:28 final size:28
Alignment explanation
Indices: 27383--27439 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
27373 GAGGGTATCA
27383 TACATACAACACGAGGGATGTCACATGC
1 TACATACAACACGAGGGATGTCACATGC
* * *
27411 TACATACTACAGGCGGGATGTCACATGC
1 TACATACAACACGAGGGATGTCACATGC
27439 T
1 T
27440 CAAAATTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (28 bp):
TACATACAACACGAGGGATGTCACATGC
Found at i:28695 original size:10 final size:10
Alignment explanation
Indices: 28665--28713 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
28655 GGTCTGCAAA
28665 AATAA-AATT
1 AATAATAATT
28674 AATAGA-AA-T
1 AATA-ATAATT
28683 AATAATAATT
1 AATAATAATT
28693 AATAATAA-T
1 AATAATAATT
28702 AATAAATAATT
1 AAT-AATAATT
28713 A
1 A
28714 TTATAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.03
9 15 0.43
10 17 0.49
11 2 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AATAATAATT
Found at i:28701 original size:16 final size:16
Alignment explanation
Indices: 28680--28721 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
28670 AATTAATAGA
*
28680 AATAATAATAATTAAT
1 AATAATAATAAATAAT
28696 AATAATAATAAATAAT
1 AATAATAATAAATAAT
* *
28712 TATTATAATA
1 AATAATAATA
28722 TATATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAATAATAAATAAT
Found at i:28719 original size:13 final size:13
Alignment explanation
Indices: 28679--28711 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28669 AAATTAATAG
28679 AAATAATAATAAT
1 AAATAATAATAAT
*
28692 TAATAATAATAAT
1 AAATAATAATAAT
28705 AAATAAT
1 AAATAAT
28712 TATTATAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:29811 original size:34 final size:34
Alignment explanation
Indices: 29773--29880 Score: 91
Period size: 34 Copynumber: 3.2 Consensus size: 34
29763 CCCCTTCTTT
29773 GTGAAGTTGAGCCTTGAATTGGATATCCTTCATC
1 GTGAAGTTGAGCCTTGAATTGGATATCCTTCATC
*** * * * *
29807 GTGAAGTT-AAAATCG---TAGATGA-CCAATTCGTT
1 GTGAAGTTGAGCCTTGAATTGGAT-ATCC--TTCATC
29839 GTGAAGTTGAGCCTTGAATTGGATATCCTTCATC
1 GTGAAGTTGAGCCTTGAATTGGATATCCTTCATC
29873 GTGAAGTT
1 GTGAAGTT
29881 AAAATCATAG
Statistics
Matches: 52, Mismatches: 14, Indels: 16
0.63 0.17 0.20
Matches are distributed among these distances:
30 6 0.12
31 1 0.02
32 12 0.23
33 6 0.12
34 20 0.38
35 1 0.02
36 6 0.12
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (34 bp):
GTGAAGTTGAGCCTTGAATTGGATATCCTTCATC
Found at i:29843 original size:66 final size:66
Alignment explanation
Indices: 29729--30455 Score: 491
Period size: 66 Copynumber: 11.4 Consensus size: 66
29719 GGTGGGCACA
* * * * *
29729 ATATCATTCGTCGTGAAGTTGAAATAGTGGATGGCCCCTTCTTTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
29794 G
66 G
* * * *
29795 ATATCCTTCATCGTGAAGTTAAAATCGTAGATGACCAATTCGTTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
29860 G
66 G
* * * * * *
29861 ATATCCTTCATCGTGAAGTTAAAATCATAGATGACTCATTCGTTGTGAAGTTGAACCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
29926 G
66 G
* * * * ** * * * *
29927 ATATCCTTCGTCATGAAGTTGAAA---T--ATAATCTA-AAG--ATGAATGTTGATG-GTGGGCA
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAA-GTTGA-GCCT-TGAA
*
29983 --CG
63 TTGG
* * *
29985 ATATCCTTCGTCGAGAAGTTGAAATCATGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
30050 G
66 G
* ** * ** * * *
30051 ATATCCTTCGTCGTGAAGTTGAAATCCAATCTAAAGA-TGAAT-ATTGCTG--G-TG-G----GC
1 ATATCCTTCGTCGTGAAGTTGAAAT-C-GT-GGATGACCCATTCGTTG-TGAAGTTGAGCCTTGA
*
30106 A--CG
62 ATTGG
* * * * * *
30109 ATATCATTCGTCGTGAAGTTGAAATCGTGGATGACCCCTTCTTTGTAAAATTGAGCCTTGAATTA
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
30174 G
66 G
* * * * ** * * * *
30175 ATAT-ATATCTTCGTGAAGTTGAAAT--T-CAT---CTA-AAG--ATGAATGTTGATG-GTGGGC
1 ATATCCT-TCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAA-GTTGA-GCCT-TGA
*
30229 A--CG
62 ATTGG
* * *
30232 ATATCCTTCGTCATTAAGTTGAAATCGTGGATGACCCCTTCGTTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
30297 G
66 G
* * * *
30298 ATATCCTTCGCCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTTGTGAAATTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
30363 G
66 G
* * *
30364 ATATCCTTCGTCGTGAAGTTGAAATAGTGGATGGCCTATTCGTTGTGAAGTTGAGCCTTGAATTG
1 ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
30429 G
66 G
* *
30430 ATATCCTTCGTCATGAAGTTCAAATC
1 ATATCCTTCGTCGTGAAGTTGAAATC
30456 CAATCTAAAG
Statistics
Matches: 507, Mismatches: 107, Indels: 94
0.72 0.15 0.13
Matches are distributed among these distances:
55 3 0.01
56 3 0.01
57 27 0.05
58 58 0.11
59 12 0.02
60 9 0.02
61 5 0.01
63 8 0.02
64 12 0.02
65 16 0.03
66 342 0.67
67 4 0.01
68 5 0.01
69 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (66 bp):
ATATCCTTCGTCGTGAAGTTGAAATCGTGGATGACCCATTCGTTGTGAAGTTGAGCCTTGAATTG
G
Found at i:30032 original size:124 final size:124
Alignment explanation
Indices: 29639--30472 Score: 810
Period size: 124 Copynumber: 6.6 Consensus size: 124
29629 GTTGACAGAC
* * * *
29639 ACCCCTTCGCTGTGAAGTTGAGCTTTGAATTGGATAT-CTTCGTTGTGAAGTTGAAATCCAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCT
* * * *
29703 AAAGATGGATGTTGCTGGTGGGCACAATATCATTCGTCGTGAAGTTGAAAT-AGTGGATG
66 AAAGATGAATGTTGATGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCA-TGGATG
* * * *
29762 GCCCCTTCTTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCATCGTGAAGTTAAAATCGTAGAT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC-TA-AT
* * * * * * * * *
29827 GACCAATTCGTTGTGAA-GTTGA-GCCT-TGAATTGGATATCCTTCATCGTGAAGTTAAAATCAT
64 --CTAA--AG--ATGAATGTTGATG-GTGGGCA--CGATATCCTTCGTCGTGAAGTTGAAATCAT
*
29889 AGATG
120 GGATG
* * * * *
29894 ACTCATTCGTTGTGAAGTTGAACCTTGAATTGGATATCCTTCGTCATGAAGTTGAAATATAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCT
*
29959 AAAGATGAATGTTGATGGTGGGCACGATATCCTTCGTCGAGAAGTTGAAATCATGGATG
66 AAAGATGAATGTTGATGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATG
*
30018 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCT
* * * *
30083 AAAGATGAATATTGCTGGTGGGCACGATATCATTCGTCGTGAAGTTGAAATCGTGGATG
66 AAAGATGAATGTTGATGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATG
* * * * * * *
30142 ACCCCTTCTTTGTAAAATTGAGCCTTGAATTAGATAT-ATATCTTCGTGAAGTTGAAAT-TCATC
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCT-TCGTCGTGAAGTTGAAATCTAATC
* * *
30205 TAAAGATGAATGTTGATGGTGGGCACGATATCCTTCGTCATTAAGTTGAAATCGTGGATG
65 TAAAGATGAATGTTGATGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATG
* *
30265 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGCCGTGAAGTTGAAATCGTGGAT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC-T-AAT
** * * * * * *
30330 GGCCCCT-TCGTTGTGAA-ATTGA-GCCT-TGAATTGGATATCCTTCGTCGTGAAGTTGAAAT-A
64 -----CTAAAG--ATGAATGTTGATG-GTGGGCA--CGATATCCTTCGTCGTGAAGTTGAAATCA
30390 GTGGATG
119 -TGGATG
* ** * * *
30397 GCCTATTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCATGAAGTTCAAATCCAATCT
1 ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCT
*
30462 AAAGATAAATG
66 AAAGATGAATG
30473 GTGCTTCGAG
Statistics
Matches: 579, Mismatches: 98, Indels: 66
0.78 0.13 0.09
Matches are distributed among these distances:
123 141 0.24
124 219 0.38
125 10 0.02
126 9 0.02
128 6 0.01
130 12 0.02
131 14 0.02
132 167 0.29
133 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (124 bp):
ACCCCTTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAATCT
AAAGATGAATGTTGATGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATCATGGATG
Found at i:30283 original size:32 final size:32
Alignment explanation
Indices: 30247--30417 Score: 89
Period size: 32 Copynumber: 5.2 Consensus size: 32
30237 CTTCGTCATT
30247 AAGTTGAAATCGTGGATGACCCCTTCGTTGTG
1 AAGTTGAAATCGTGGATGACCCCTTCGTTGTG
** * * **
30279 AAGTTGAGCCTTGAATTGGAT-A-TCCTTCGCCGTG
1 AAGTTGA-AATCG---TGGATGACCCCTTCGTTGTG
*
30313 AAGTTGAAATCGTGGATGGCCCCTTCGTTGTG
1 AAGTTGAAATCGTGGATGACCCCTTCGTTGTG
* ** * * *
30345 AAATTGAGCCTTGAATTGGAT-A-TCCTTCGTCGTG
1 AAGTTGA-AATCG---TGGATGACCCCTTCGTTGTG
* * **
30379 AAGTTGAAATAGTGGATGGCCTATTCGTTGTG
1 AAGTTGAAATCGTGGATGACCCCTTCGTTGTG
30411 AAGTTGA
1 AAGTTGA
30418 GCCTTGAATT
Statistics
Matches: 98, Mismatches: 29, Indels: 24
0.65 0.19 0.16
Matches are distributed among these distances:
30 10 0.10
32 37 0.38
33 8 0.08
34 32 0.33
35 1 0.01
36 10 0.10
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (32 bp):
AAGTTGAAATCGTGGATGACCCCTTCGTTGTG
Found at i:30314 original size:34 final size:34
Alignment explanation
Indices: 30268--30449 Score: 135
Period size: 34 Copynumber: 5.5 Consensus size: 34
30258 GTGGATGACC
*
30268 CCTTCGTTGTGAAGTTGAGCCTTGAATTGGATAT
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
* ** * * **
30302 CCTTCGCCGTGAAGTTGAAATCGTGGA-TGG--CC
1 CCTTCGTCGTGAAGTTG-AGCCTTGAATTGGATAT
* *
30334 CCTTCGTTGTGAAATTGAGCCTTGAATTGGATAT
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
** * **
30368 CCTTCGTCGTGAAGTTGA--AAT--AGTGGATGG
1 CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
*
30398 CCTATTCGTTGTGAAGTTGAGCCTTGAATTGGATAT
1 CC--TTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
*
30434 CCTTCGTCATGAAGTT
1 CCTTCGTCGTGAAGTT
30450 CAAATCCAAT
Statistics
Matches: 106, Mismatches: 32, Indels: 20
0.67 0.20 0.13
Matches are distributed among these distances:
30 8 0.08
31 5 0.05
32 33 0.31
34 47 0.44
35 5 0.05
36 8 0.08
ACGTcount: A:0.21, C:0.17, G:0.27, T:0.35
Consensus pattern (34 bp):
CCTTCGTCGTGAAGTTGAGCCTTGAATTGGATAT
Found at i:33605 original size:65 final size:63
Alignment explanation
Indices: 33483--33692 Score: 212
Period size: 65 Copynumber: 3.3 Consensus size: 63
33473 TTTATCAAAG
* * *
33483 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAATTG-AACATCGAATGC
1 TGATGCATCGATGCA-CAA-CCATGCATCGATGCACTCAGGATATT---TTGAAATATCGAATGC
33545 ATT
61 ATT
* *
33548 TCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGAAAATATCGAATGCAT
1 TGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-AAATATCGAATGCAT
33612 T
63 T
* * * * **
33613 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAATATCTAATGCGCT
1 TGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGAAATATCGAATGCATT
33677 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
33693 TCGTAGTGCA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 1 0.01
63 3 0.02
64 46 0.37
65 69 0.56
66 5 0.04
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (63 bp):
TGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGAAATATCGAATGCATT
Found at i:34961 original size:21 final size:21
Alignment explanation
Indices: 34935--34979 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
34925 GATTTCTGGG
*
34935 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
34956 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
34977 CAA
1 CAA
34980 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:35446 original size:20 final size:22
Alignment explanation
Indices: 35406--35462 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
35396 TGAATGTGTG
*
35406 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
35428 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
35448 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
35463 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:36028 original size:31 final size:31
Alignment explanation
Indices: 35990--36176 Score: 313
Period size: 31 Copynumber: 6.0 Consensus size: 31
35980 AGGGTCGAGG
35990 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
36021 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
36052 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
36083 GTTTACCTATGTTCTTCGGGACATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
36114 GTTTACCTATGTTCTTCGGGACATATGGATT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
36145 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
36176 G
1 G
36177 GTCCTTCGGG
Statistics
Matches: 147, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 146 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:36962 original size:2 final size:2
Alignment explanation
Indices: 36955--37009 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
36945 GAGTTATGAG
36955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36997 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
37010 GATAGATGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:39537 original size:21 final size:21
Alignment explanation
Indices: 39511--39555 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
39501 GATTTCTGGG
*
39511 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
39532 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
39553 CAA
1 CAA
39556 ACGAACAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:40023 original size:20 final size:22
Alignment explanation
Indices: 39983--40039 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
39973 TGAATGTGTG
*
39983 ATATGTTATGATGATATAAACC
1 ATATGATATGATGATATAAACC
*
40005 ATATGATATGAT-A-ATAAACT
1 ATATGATATGATGATATAAACC
40025 ATATGAATATG-TGAT
1 ATATG-ATATGATGAT
40040 TATGAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 12 0.40
21 7 0.23
22 11 0.37
ACGTcount: A:0.44, C:0.05, G:0.14, T:0.37
Consensus pattern (22 bp):
ATATGATATGATGATATAAACC
Found at i:40608 original size:31 final size:31
Alignment explanation
Indices: 40569--40724 Score: 269
Period size: 31 Copynumber: 5.0 Consensus size: 31
40559 AGGGTCGAGG
40569 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
40600 ATTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
40631 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
40662 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
40693 GTTTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
40724 G
1 G
40725 GTCCTTCGGG
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 119 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:41602 original size:2 final size:2
Alignment explanation
Indices: 41595--41619 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41585 ATCTTTTAAA
41595 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
41620 CCCCTATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:43800 original size:36 final size:36
Alignment explanation
Indices: 43753--43830 Score: 138
Period size: 36 Copynumber: 2.2 Consensus size: 36
43743 GATAAATTAT
43753 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
*
43789 AATCTACATATCTATGGTTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGTTGATTCTTTTATCACTTA
*
43825 ATTCTA
1 AATCTA
43831 GAACTTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.46
Consensus pattern (36 bp):
AATCTACATATCCATGGTTGATTCTTTTATCACTTA
Found at i:46604 original size:24 final size:24
Alignment explanation
Indices: 46575--46681 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
46565 AAACAGAGAT
*
46575 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
46599 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
46623 GTTAGGAATCAGAACATATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
46647 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
46671 ATCAGAAATCA
1 ATCAGAAATCA
46682 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:46681 original size:48 final size:48
Alignment explanation
Indices: 46575--46683 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 48
46565 AAACAGAGAT
* * *
46575 ATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
46623 GTTAGGAATCAGAACATATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
46671 ATCAGAAATCAGA
1 ATCAGAAATCAGA
46684 TAAAATATTC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:49281 original size:23 final size:22
Alignment explanation
Indices: 49230--49288 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 22
49220 AGTCAATGGT
*
49230 CAAT-GGGTCGGGTCGGGTTAA
1 CAATCGGGTCGGGTCGGGTCAA
**
49251 CGGGTCGGGTCGGGTCGGGTCAA
1 C-AATCGGGTCGGGTCGGGTCAA
*
49274 GCAATCGGTTCGGGT
1 -CAATCGGGTCGGGT
49289 TGTAACCGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 1 0.03
22 1 0.03
23 26 0.90
24 1 0.03
ACGTcount: A:0.14, C:0.19, G:0.46, T:0.22
Consensus pattern (22 bp):
CAATCGGGTCGGGTCGGGTCAA
Found at i:51379 original size:24 final size:24
Alignment explanation
Indices: 51351--51457 Score: 97
Period size: 24 Copynumber: 4.5 Consensus size: 24
51341 AAACGAAGAT
*
51351 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
51375 ATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * * *
51399 GTTAGGAATCAGAACATATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
51423 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
51447 ATCAGAAATCA
1 ATCAGAAATCA
51458 GATAAAATAT
Statistics
Matches: 60, Mismatches: 23, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:51457 original size:48 final size:48
Alignment explanation
Indices: 51351--51459 Score: 137
Period size: 48 Copynumber: 2.3 Consensus size: 48
51341 AAACGAAGAT
* * *
51351 ATCAGAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAG
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
51399 GTTAGGAATCAGAACATATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
51447 ATCAGAAATCAGA
1 ATCAGAAATCAGA
51460 TAAAATATTC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAGAACATAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:53363 original size:36 final size:36
Alignment explanation
Indices: 53316--53388 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
53306 GATAAATTAT
53316 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
53352 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
1 AATCTACATATCCATGGCTGATTCTTTTATCACTTA
53388 A
1 A
53389 TTTCAGAACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.41
Consensus pattern (36 bp):
AATCTACATATCCATGGCTGATTCTTTTATCACTTA
Found at i:59956 original size:19 final size:19
Alignment explanation
Indices: 59932--59984 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
59922 AAATGCATTT
59932 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
59951 CATGCATCGATGCACATAC
1 CATGCATCGATGCACATAC
59970 CATGCATCGATGCAC
1 CATGCATCGATGCAC
59985 TCTGGCTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (19 bp):
CATGCATCGATGCACATAC
Found at i:61781 original size:16 final size:15
Alignment explanation
Indices: 61757--61788 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
61747 AACATCTTTT
61757 AAAAACATTTTTAAG
1 AAAAACATTTTTAAG
61772 AAAAATCATTTTTAAG
1 AAAAA-CATTTTTAAG
61788 A
1 A
61789 CCAAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (15 bp):
AAAAACATTTTTAAG
Found at i:61938 original size:12 final size:12
Alignment explanation
Indices: 61921--61945 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
61911 GATTGTGAAC
61921 ATTAAAATTTAA
1 ATTAAAATTTAA
61933 ATTAAAATTTAA
1 ATTAAAATTTAA
61945 A
1 A
61946 AACCCGACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
ATTAAAATTTAA
Found at i:63281 original size:19 final size:19
Alignment explanation
Indices: 63252--63305 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
63242 GGCCTGCAAA
63252 AATAA-AATTAATATAAAT
1 AATAATAATTAATATAAAT
63270 AATAATAATTAATA-ATAAT
1 AATAATAATTAATATA-AAT
* *
63289 AATAATTATTATTATAA
1 AATAATAATTAATATAA
63306 TATATATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 6 0.19
19 24 0.77
20 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAATAATTAATATAAAT
Found at i:63285 original size:13 final size:13
Alignment explanation
Indices: 63267--63291 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63257 AATTAATATA
63267 AATAATAATAATT
1 AATAATAATAATT
63280 AATAATAATAAT
1 AATAATAATAAT
63292 AATTATTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AATAATAATAATT
Found at i:66363 original size:29 final size:29
Alignment explanation
Indices: 66320--66402 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
66310 CTCACCTAAC
* *
66320 TAAATTGATGTAAGCAATGCCATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
66350 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
66379 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
66403 ATTGGGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:69686 original size:23 final size:23
Alignment explanation
Indices: 69653--69720 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
69643 ATTATTATAT
69653 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
69676 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* ** *
69699 GCCACTTTGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
69721 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:76432 original size:23 final size:23
Alignment explanation
Indices: 76398--76461 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
76388 TTATTATATA
76398 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
76421 AT-GCACTCCGGTGCAATTCTACG
1 -TGGCACTACGGTGCAATTCTACG
*
76444 TGGCACTTCGGTGCAATT
1 TGGCACTACGGTGCAATT
76462 ATACAAGTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 1 0.03
23 35 0.95
24 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.25, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:76924 original size:2 final size:2
Alignment explanation
Indices: 76917--76960 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
76907 ACTTATACAC
76917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76959 AT
1 AT
76961 TATCGTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:81193 original size:419 final size:425
Alignment explanation
Indices: 80402--81252 Score: 1480
Period size: 419 Copynumber: 2.0 Consensus size: 425
80392 ATGTTTAGTT
80402 GCATAAGCTCTGCTTTGTCCTCTTGCTGAACCTTCTTTCTCTGTGAAGTTCTTATTTACAGTCTG
1 GCATAAGCTCTGCTTTGTCCTCTTGCTGAACCTTCTTTCTCTGTGAAGTTCTTATTTACAGTCTG
*
80467 AGGCTTTCCATGCAACCTCCAATATTTCTCTTTGGTGTGAAGAGATTTTTTACAGTAATTACACC
66 AGGCTTTCCATGCAACCTCCAACATTTCTCTTTGGTGTGAAGAGATTTTTTACAGTAATTACACC
* *
80532 ATAAGGAGTCCTTGTTAGCCTTCCTTGTTCCTTCTTTACCTTTAATATTCTACTGCTCTAGACAA
131 ATAAGGAGTCCTTGTTAG-C--CC-T-TTCCTTCTTTA-CTTTAATATTATACTGCTCCAGACAA
80597 TTTGGTCCCTCAGGAACAGCCCTGGTAACCAAGGCCGAGCTTTCTACTTGATTATTTTCAACCAC
190 TTTGGTCCCTCAGGAACAGCCCTGGTAACCAAGGCCGAGCTTTCTACTTGATTATTTTCAACCAC
*
80662 CATCACTCCTCTTCTTCATTCTTTAGCACGAATGATAGCAATAGTTTCATTCAGTGATTATTTAA
255 CATCACTCCTCTTCTTCATTCTTCAGCACGAATGATAGCAATAGTTTCATTCAGTGATTATTTAA
*
80727 CGGAAGTGGATTGGATTTTGAGGCCTTTTTCTGCCCCTTCATTTTTCAGTTCATTGGTTGGGGAA
320 CGGAAGTGGATTAGATTTTGAGGCCTTTTTCTGCCCCTTCATTTTTCAGTTCATTGGTTGGGGAA
80792 ATAGGGGCCTTAGTTACAGCTAAGGACATTATGATGAGATG
385 ATAGGGGCCTTAGTTACAGCTAAGGACATTATGATGAGATG
* *
80833 GCATAAGCTCTGCTTTGTCCTCTTGTTGAACCTTCTTTCTCTGTGAAGTTCTTATTTGCAGTCTG
1 GCATAAGCTCTGCTTTGTCCTCTTGCTGAACCTTCTTTCTCTGTGAAGTTCTTATTTACAGTCTG
*
80898 AGGCTTTCCATGCAACCTCCAACATTTCTCTTTGGTGTGACGAGATTTTTTA-AGTAATTACACC
66 AGGCTTTCCATGCAACCTCCAACATTTCTCTTTGGTGTGAAGAGATTTTTTACAGTAATTACACC
*
80962 ATAAGGAGTCCTTGTTAG-CC-TT-CTT-TTT-CTTTAATATTATGCTGCTCCAGACAATTTGGT
131 ATAAGGAGTCCTTGTTAGCCCTTTCCTTCTTTACTTTAATATTATACTGCTCCAGACAATTTGGT
81022 CCCTCAGGAACAGCCCTGGTAACCAAGGCCGAGCTTTCTACTTGATTATTTTCAACCACCATCAC
196 CCCTCAGGAACAGCCCTGGTAACCAAGGCCGAGCTTTCTACTTGATTATTTTCAACCACCATCAC
* *
81087 TCCTCTTCTTCATTCTTCAGCACGAATGATAGCAATAGTTTCATTCAGTGATTGTTTAACGGCAG
261 TCCTCTTCTTCATTCTTCAGCACGAATGATAGCAATAGTTTCATTCAGTGATTATTTAACGGAAG
*
81152 TGGATTAGATTTTGAGGCCTTTTTCTGCCCCTTCGTTTTTCAGTTCATTGGTTGGGGAAATAGGG
326 TGGATTAGATTTTGAGGCCTTTTTCTGCCCCTTCATTTTTCAGTTCATTGGTTGGGGAAATAGGG
* *
81217 GCCTTAGTTACTGCTAAGGACATTATGGTGAGATG
391 GCCTTAGTTACAGCTAAGGACATTATGATGAGATG
81252 G
1 G
81253 ATCCCTAGGA
Statistics
Matches: 406, Mismatches: 14, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
419 253 0.62
421 3 0.01
422 3 0.01
423 2 0.00
426 2 0.00
430 30 0.07
431 113 0.28
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (425 bp):
GCATAAGCTCTGCTTTGTCCTCTTGCTGAACCTTCTTTCTCTGTGAAGTTCTTATTTACAGTCTG
AGGCTTTCCATGCAACCTCCAACATTTCTCTTTGGTGTGAAGAGATTTTTTACAGTAATTACACC
ATAAGGAGTCCTTGTTAGCCCTTTCCTTCTTTACTTTAATATTATACTGCTCCAGACAATTTGGT
CCCTCAGGAACAGCCCTGGTAACCAAGGCCGAGCTTTCTACTTGATTATTTTCAACCACCATCAC
TCCTCTTCTTCATTCTTCAGCACGAATGATAGCAATAGTTTCATTCAGTGATTATTTAACGGAAG
TGGATTAGATTTTGAGGCCTTTTTCTGCCCCTTCATTTTTCAGTTCATTGGTTGGGGAAATAGGG
GCCTTAGTTACAGCTAAGGACATTATGATGAGATG
Found at i:81813 original size:22 final size:22
Alignment explanation
Indices: 81622--81810 Score: 272
Period size: 22 Copynumber: 8.6 Consensus size: 22
81612 AATATATTTT
* *
81622 TTTTAAAATAAATAAATACATA
1 TTTTAAAATAAATCAATCCATA
81644 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
81666 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
**
81688 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
81710 TTTTAAAATAAACCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
81732 TTTTAAAATAAATCAAACCATA
1 TTTTAAAATAAATCAATCCATA
81754 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
***
81776 TTTTAAAATAAATTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
81798 TTTTAAAATAAAT
1 TTTTAAAATAAAT
81811 TTTAAAATAG
Statistics
Matches: 150, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
21 3 0.02
22 143 0.95
23 4 0.03
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:81827 original size:11 final size:12
Alignment explanation
Indices: 81775--81836 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
81765 ATCAATCCAT
81775 ATTTTAAAATAA
1 ATTTTAAAATAA
***
81787 ATTTTTCCAT--
1 ATTTTAAAATAA
81797 ATTTTAAAATAA
1 ATTTTAAAATAA
*
81809 ATTTTAAAATAG
1 ATTTTAAAATAA
81821 A-TTT-AAAT-A
1 ATTTTAAAATAA
81830 ATTTTAA
1 ATTTTAA
81837 TTTCTTTGAA
Statistics
Matches: 38, Mismatches: 8, Indels: 9
0.69 0.15 0.16
Matches are distributed among these distances:
9 1 0.03
10 14 0.37
11 4 0.11
12 19 0.50
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:87033 original size:47 final size:47
Alignment explanation
Indices: 86964--87064 Score: 193
Period size: 47 Copynumber: 2.1 Consensus size: 47
86954 GGAGGAGGAC
86964 ATATGTTCCTTTCATAATCTTTGCAGATATAGAGGTATGATCTGGCT
1 ATATGTTCCTTTCATAATCTTTGCAGATATAGAGGTATGATCTGGCT
87011 ATATGTTCCTTTCATAATCTTTGCAGATATAGAGGTATGATCTGGCT
1 ATATGTTCCTTTCATAATCTTTGCAGATATAGAGGTATGATCTGGCT
*
87058 ATTTGTT
1 ATATGTT
87065 GGGTCTATGT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 53 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.43
Consensus pattern (47 bp):
ATATGTTCCTTTCATAATCTTTGCAGATATAGAGGTATGATCTGGCT
Found at i:100279 original size:16 final size:16
Alignment explanation
Indices: 100260--100309 Score: 91
Period size: 16 Copynumber: 3.1 Consensus size: 16
100250 TGGACTTTGG
*
100260 AGGGTTGAAACTTGAA
1 AGGGTTAAAACTTGAA
100276 AGGGTTAAAACTTGAA
1 AGGGTTAAAACTTGAA
100292 AGGGTTAAAACTTGAA
1 AGGGTTAAAACTTGAA
100308 AG
1 AG
100310 AGGTAAGCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.28, T:0.24
Consensus pattern (16 bp):
AGGGTTAAAACTTGAA
Found at i:105665 original size:21 final size:23
Alignment explanation
Indices: 105617--105674 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
105607 TATTAGTAAA
* *
105617 ATAACAAATTAGGTAGCGCTTAT
1 ATAATAAAATAGGTAGCGCTTAT
**
105640 ATAATGTAATAGGTAGCGC-T-T
1 ATAATAAAATAGGTAGCGCTTAT
105661 ATAATAAAATAGGT
1 ATAATAAAATAGGT
105675 TAATTACTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 13 0.45
22 1 0.03
23 15 0.52
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (23 bp):
ATAATAAAATAGGTAGCGCTTAT
Found at i:105711 original size:83 final size:85
Alignment explanation
Indices: 105616--105833 Score: 325
Period size: 87 Copynumber: 2.6 Consensus size: 85
105606 TTATTAGTAA
*
105616 AATAACAAATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAATAAAATAGGTTAATTA
1 AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAATAAAATAGGTTAATTA
*
105681 CT-GAAACATTATTAA-CAC
66 CTAGAAACATTATCAAGCAC
* *
105699 AATAACATATTAGATTA-CGTTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGGTTAA
1 AATAACATATTAG-GTAGCGCTTATATAATGTAATAGGTAGCGC-T-TATAATAAAATAGGTTAA
105763 TTACTAGAAACATTATCAAGCAC
63 TTACTAGAAACATTATCAAGCAC
* * *
105786 AATAACATATTAGGTAGTGCTTATATAATGTAATAGGTAACGTTTATA
1 AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATA
105834 TTGACATATT
Statistics
Matches: 120, Mismatches: 9, Indels: 10
0.86 0.06 0.07
Matches are distributed among these distances:
83 37 0.31
84 3 0.03
85 27 0.22
86 15 0.12
87 38 0.32
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (85 bp):
AATAACATATTAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAATAAAATAGGTTAATTA
CTAGAAACATTATCAAGCAC
Found at i:105955 original size:14 final size:14
Alignment explanation
Indices: 105887--105959 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
105877 ATTGTAAATT
105887 TATTTTAATAA-AA
1 TATTTTAATAATAA
** *
105900 TATAATAATCATAA
1 TATTTTAATAATAA
* * *
105914 TTTTTTATTTATAA
1 TATTTTAATAATAA
* *
105928 AATTATAGAT-ATAA
1 TATTTTA-ATAATAA
105942 TATTTTAATAATAA
1 TATTTTAATAATAA
105956 TATT
1 TATT
105960 GACATAGATA
Statistics
Matches: 43, Mismatches: 14, Indels: 5
0.69 0.23 0.08
Matches are distributed among these distances:
13 10 0.23
14 32 0.74
15 1 0.02
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (14 bp):
TATTTTAATAATAA
Found at i:105955 original size:28 final size:28
Alignment explanation
Indices: 105887--105955 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
105877 ATTGTAAATT
*
105887 TATTTTAATAA-AATATAATAATCATAA
1 TATTTTAATAATAAAATAATAATCATAA
* * * *
105914 TTTTTTATTTATAAAATTATAGAT-ATAA
1 TATTTTAATAATAAAATAATA-ATCATAA
105942 TATTTTAATAATAA
1 TATTTTAATAATAA
105956 TATTGACATA
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
27 8 0.25
28 22 0.69
29 2 0.06
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
TATTTTAATAATAAAATAATAATCATAA
Found at i:106042 original size:24 final size:25
Alignment explanation
Indices: 105974--106042 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
105964 TAGATAATAT
*
105974 TAAATAA-ATTATTCTAATATT-TTAA
1 TAAATAATATTA-T-TATTATTATTAA
105999 -AAATAATATTATTATT-TTATTAA
1 TAAATAATATTATTATTATTATTAA
106022 TAAATAATATTATT-TTATTAT
1 TAAATAATATTATTATTATTAT
106043 ATTTGATGCT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.23
24 24 0.62
25 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTATTAA
Found at i:106443 original size:92 final size:92
Alignment explanation
Indices: 106340--106899 Score: 865
Period size: 92 Copynumber: 6.1 Consensus size: 92
106330 TCGGTAAAAT
*
106340 CGGTAAAAAAATAACAAAATCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
1 CGGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
*
106405 AAAAGGATCGATATTTTACAATATAAC
66 AAAAGGATCGATACTTTACAATATAAC
** **** *
106432 CGGTAAAAAAATAACAAAACCGAAAAATAAATTT---TTATATATTGAAAGTATCGATCCTTTTA
1 CGGTAAAAAAATAACAAAACCG--GTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTA
*
106494 TAAAAAGGATCGATATTTTACAATATAAC
64 TAAAAAGGATCGATACTTTACAATATAAC
*
106523 CTGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
1 CGGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
* *
106588 AAAATGATCGATATTTTACAATATAAC
66 AAAAGGATCGATACTTTACAATATAAC
106615 CGGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
1 CGGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
106680 AAAAGGATCGATACTTTACAATATAAC
66 AAAAGGATCGATACTTTACAATATAAC
** * * *
106707 ATGTAAAAAAATAACAAAATCGGTAGCGTTTTACCTGATATATTGAAAGTATCGATCCTTTTATA
1 CGGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
106772 AAAAGGATCGATACTTTACAATATAAC
66 AAAAGGATCGATACTTTACAATATAAC
** *
106799 AAGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTATA
1 CGGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
* *
106864 AAAATGATAGATACTTTACAATATAAC
66 AAAAGGATCGATACTTTACAATATAAC
*
106891 AGGTAAAAA
1 CGGTAAAAA
106900 TGACAAAACC
Statistics
Matches: 432, Mismatches: 31, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
89 4 0.01
91 77 0.18
92 347 0.80
94 4 0.01
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.30
Consensus pattern (92 bp):
CGGTAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTATA
AAAAGGATCGATACTTTACAATATAAC
Found at i:110722 original size:183 final size:184
Alignment explanation
Indices: 110021--110736 Score: 1301
Period size: 184 Copynumber: 3.9 Consensus size: 184
110011 GCGTTACTGA
110021 AAAGTATG-GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
1 AAAGTA-GCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
* *
110085 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCAATGTTTT
65 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
110150 TTCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
130 TTCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
*
110205 AAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
1 AAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
110270 TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
66 TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
* * *
110335 TTAATCGACACTTTTTGAAAGGGTATCGACACTTTTTTCATCCATTCTGGATAT
131 TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
* *
110389 AAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCAAAAAATCGG
1 AAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
* *
110454 TATATCTATACCGGTTATATTACAAAATTACTTATTACATTATAATTATGGGTTCCGATATTTTT
66 TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
*
110519 TCAATCGACACTTTTTGAAAAGGTATCGACACTGTTTTCATCCATTCTGGACAT
131 TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
110573 AAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATT-TCTCATAAAACCGG
1 AAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
110637 TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
66 TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
*
110702 TCAATCGACACTTTTTGAAAATGTATCGACACTTT
131 TCAATCGACACTTTTTGAAAAGGTATCGACACTTT
110737 ATGTTGATAT
Statistics
Matches: 510, Mismatches: 21, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
183 108 0.21
184 402 0.79
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.36
Consensus pattern (184 bp):
AAAGTAGCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
Found at i:112109 original size:3 final size:3
Alignment explanation
Indices: 112101--112155 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
112091 ACTTCTTTGG
* * *
112101 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC TTC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
112149 ATC ATC A
1 ATC ATC A
112156 GCTTCATCTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:112160 original size:12 final size:12
Alignment explanation
Indices: 112101--112168 Score: 91
Period size: 12 Copynumber: 5.7 Consensus size: 12
112091 ACTTCTTTGG
*
112101 ATCATCATCATC
1 ATCATCATCTTC
*
112113 ATCATCATCATC
1 ATCATCATCTTC
112125 ATCATCATCTTC
1 ATCATCATCTTC
*
112137 ATCGTCATCTTC
1 ATCATCATCTTC
*
112149 ATCATCAGCTTC
1 ATCATCATCTTC
*
112161 ATCTTCAT
1 ATCATCAT
112169 TGACCGCTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 50 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.38
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:114241 original size:19 final size:21
Alignment explanation
Indices: 114184--114236 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
114174 TGATGTTTTT
*
114184 GGGATCAACACCTTTTATATA
1 GGGATCGACACCTTTTATATA
114205 GGGATCGACACCTTTTATATA
1 GGGATCGACACCTTTTATATA
*
114226 TGGATCGACAC
1 GGGATCGACAC
114237 TTTATGGTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (21 bp):
GGGATCGACACCTTTTATATA
Found at i:114373 original size:220 final size:220
Alignment explanation
Indices: 113985--114435 Score: 724
Period size: 220 Copynumber: 2.0 Consensus size: 220
113975 CGATGTTTCT
*
113985 GGGATTGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
1 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
*
114050 GACCAATAGTATCGACACAAAATTAAAAAGTGTTGATACATATTATATACCTAATCTCTCTAAAA
66 GACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCTAAAA
* * * * *
114115 CCGGTATACTTATACCGGTTATATTGAAAATTTACCTATTACATTATACTTATGGGTTTTGATGT
131 CCAGTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATAGGTTTCGATGT
*
114180 TTTTGGGATCAACACCTTTTATATA
196 TTCTGGGATCAACACCTTTTATATA
*
114205 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATT-TT
1 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
*
114269 TACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAA
66 GACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTC-TAAA
* * * *
114334 ATCAGTATACTTATACCTGTTAGATTGAAAAATTACCTATTACTTTATATTTATAGGTTTCGATG
130 ACCAGTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATAGGTTTCGATG
** *
114399 TTTCTGGGATTGACACTTTTTATATA
195 TTTCTGGGATCAACACCTTTTATATA
*
114425 TGGATCGACAC
1 GGGATCGACAC
114436 TTTATGGTTG
Statistics
Matches: 212, Mismatches: 18, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
219 59 0.28
220 153 0.72
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (220 bp):
GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
GACCAATAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCTAAAA
CCAGTATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATAGGTTTCGATGT
TTCTGGGATCAACACCTTTTATATA
Found at i:114676 original size:199 final size:200
Alignment explanation
Indices: 113656--114858 Score: 1772
Period size: 200 Copynumber: 5.9 Consensus size: 200
113646 ATATTTAAAT
* * * *
113656 TAGTATCGACACAAAATTAAAAAGTGTCGATACATA-TATTACATCTATTATCTCATAAAACCAG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTA-TACACCTAATCTCTCATAAAACCGG
*
113720 TATACTTATACCGATTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
* *
113785 GGGATCGACACTTTTTATATATGGATCGACACTTTATAGTTGCACCCTGTTTGCCATTCATTCTG
130 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
113850 GACCAA
195 GACCAA
113856 TAGTATCGACACAAAATTAAAAAGTGTCGATACATA-TATTACACCTAATCTCTCATAAAACCGG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTA-TACACCTAATCTCTCATAAAACCGG
*
113920 TATACTTATACCTGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
*
113985 GGGATTGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
130 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
114050 GACCAA
195 GACCAA
* *
114056 TAGTATCGACACAAAATTAAAAAGTGTTGATACATATTATATACCTAATCTCTC-TAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATACACCTAATCTCTCATAAAACCGGT
* * * *
114120 ATACTTATACCGGTTATATTGAAAATTTACCTATTACATTATACTTATGGGTTTTGATGTTTTTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
*
114185 GGATCAACACCTTTTATATAGGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCAC
131 GGAT------C-----------GA-C-AC-CTTTT-ATATATGGATCGACACTTTATGGTTGCAC
**
114250 CCTGTTTGCCATTCATT-TTTACCAA
175 CCTGTTTGCCATTCATTCTGGACCAA
* * *
114275 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAATCAGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATACACCTAATCTCTCATAAAACCGGT
* * * *
114340 ATACTTATACCTGTTAGATTGAAAAATTACCTATTACTTTATATTTATAGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * * * *
114405 GGATTGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTAG
131 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
114470 A-CAA
196 ACCAA
*
114474 TAGTATTGACACAAAATTAAAAAGTGTCGATACATA-TATTACACCTAATCTCTCATAAAACCGG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTA-TACACCTAATCTCTCATAAAACCGG
*
114538 TATACTT-TACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
* *
114602 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTGCCATTTATTCTG
130 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
114667 GACCAA
195 GACCAA
* *
114673 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCACTCATAAAACCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATACACCTAATCTCTCATAAAACCGGT
*
114738 ATACTTATACCGGTTAGATTGAAAAATTACCTATTATATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* ** *
114803 GGATCGATATTTTTTATATATAGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
114859 ATTGTAAATT
Statistics
Matches: 913, Mismatches: 62, Indels: 56
0.89 0.06 0.05
Matches are distributed among these distances:
198 116 0.13
199 253 0.28
200 354 0.39
201 4 0.00
202 1 0.00
203 2 0.00
216 2 0.00
217 1 0.00
218 2 0.00
219 63 0.07
220 115 0.13
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (200 bp):
TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATACACCTAATCTCTCATAAAACCGGT
ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
ACCAA
Found at i:115114 original size:19 final size:19
Alignment explanation
Indices: 115090--115136 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
115080 ACATTCACAT
115090 ACAAAATTATAAATCGTAC
1 ACAAAATTATAAATCGTAC
* *
115109 ACAAAATTATAAATCTTAT
1 ACAAAATTATAAATCGTAC
115128 ACAAAATTA
1 ACAAAATTA
115137 ACCCTACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.30
Consensus pattern (19 bp):
ACAAAATTATAAATCGTAC
Found at i:116719 original size:12 final size:12
Alignment explanation
Indices: 116702--116754 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
116692 TCCTCCTCAT
116702 TTCTTCCATCTC
1 TTCTTCCATCTC
* *
116714 TTCTT-CTTCTT
1 TTCTTCCATCTC
* * *
116725 TTCCTCCCTCTT
1 TTCTTCCATCTC
116737 TTCTTCCATCTC
1 TTCTTCCATCTC
116749 TTCTTC
1 TTCTTC
116755 TTCCTCCTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
11 8 0.24
12 25 0.76
ACGTcount: A:0.04, C:0.40, G:0.00, T:0.57
Consensus pattern (12 bp):
TTCTTCCATCTC
Found at i:116736 original size:15 final size:16
Alignment explanation
Indices: 116718--116761 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
116708 CATCTCTTCT
116718 TCTTCTT-TTCCTCCC
1 TCTTCTTCTTCCTCCC
116733 TCTT-TTCTTCCAT--C
1 TCTTCTTCTTCC-TCCC
116747 TCTTCTTCTTCCTCC
1 TCTTCTTCTTCCTCC
116762 TCTATTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
14 8 0.33
15 15 0.62
16 1 0.04
ACGTcount: A:0.02, C:0.43, G:0.00, T:0.55
Consensus pattern (16 bp):
TCTTCTTCTTCCTCCC
Found at i:116742 original size:35 final size:34
Alignment explanation
Indices: 116691--116757 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
116681 ATCGACTTCC
116691 TTCCTCCTCATTTCTTCCATCTCTTCTTCTTCTT
1 TTCCTCCTCATTTCTTCCATCTCTTCTTCTTCTT
*
116725 TTCCTCCCTCTTTTCTTCCATCTCTTCTTCTTC
1 TTCCT-CCTCATTTCTTCCATCTCTTCTTCTTC
116758 CTCCTCTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 5 0.16
35 26 0.84
ACGTcount: A:0.04, C:0.40, G:0.00, T:0.55
Consensus pattern (34 bp):
TTCCTCCTCATTTCTTCCATCTCTTCTTCTTCTT
Found at i:117089 original size:21 final size:21
Alignment explanation
Indices: 117063--117124 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
117053 CTTATGCCTG
* * *
117063 TCAAGTGTATCTTCGACTCTC
1 TCAAGTTTCTCTTCGACTCTA
*
117084 TCAAGTTTCTCTTTGACTCTA
1 TCAAGTTTCTCTTCGACTCTA
117105 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTCTCTTCGACTCT
117125 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.11, T:0.44
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCTA
Found at i:118207 original size:28 final size:27
Alignment explanation
Indices: 118151--118209 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 27
118141 ACCCTTCTCC
*
118151 TTAAGGTGTTTAGTTAATTTCACCTTT
1 TTAAGGTGTTTAGTTAATTTCACCCTT
118178 TTAAGGTG-TTAGTTAATGATTCACCCTT
1 TTAAGGTGTTTAGTTAAT--TTCACCCTT
118206 TTAA
1 TTAA
118210 TGCTGCATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 9 0.31
27 8 0.28
28 12 0.41
ACGTcount: A:0.25, C:0.12, G:0.15, T:0.47
Consensus pattern (27 bp):
TTAAGGTGTTTAGTTAATTTCACCCTT
Found at i:119587 original size:181 final size:182
Alignment explanation
Indices: 119362--119833 Score: 759
Period size: 181 Copynumber: 2.6 Consensus size: 182
119352 CGTACTTACG
*
119362 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATATCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
119427 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGATACTTTAT
66 TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
*
119492 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * *
119543 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTGCCGGTTTCATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
*
119608 TATCATATTTTTACTTGTTATATCGTTGTGGATCGATACA-TTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
* *
119672 AGGTGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTGTCGATCCTTATATT
131 AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
* * * * * **
119724 AAAGTACCGACACTTTAAATATATCTGGTACCGCTTTACCGGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
119789 TGTCATAGTTTTACATGTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTT
119834 AATTTGGATC
Statistics
Matches: 267, Mismatches: 22, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
180 70 0.26
181 193 0.72
182 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACATGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
AGGCGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTGTCGATCCTTATATT
Found at i:120771 original size:23 final size:23
Alignment explanation
Indices: 120740--120783 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
120730 TTTTCTTAAT
120740 ATAAAAAAATAA-ATATTAATAAA
1 ATAAAAAAA-AATATATTAATAAA
*
120763 ATAATAAAAAATATATTAATA
1 ATAAAAAAAAATATATTAATA
120784 TATATAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
ATAAAAAAAAATATATTAATAAA
Found at i:121049 original size:2 final size:2
Alignment explanation
Indices: 121042--121092 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
121032 ATTTAAACAA
*
121042 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
121084 AT AT AT AT A
1 AT AT AT AT A
121093 ATAATAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:121223 original size:29 final size:30
Alignment explanation
Indices: 121169--121227 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
121159 ATTGCAATTA
121169 AATAGTGACTAAAACATATAAAATTAAAAT
1 AATAGTGACTAAAACATATAAAATTAAAAT
* *
121199 AATAG-GATTAAAATATA-AAATATTAAAAT
1 AATAGTGACTAAAACATATAAA-ATTAAAAT
121228 TTACAGCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 18 0.69
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (30 bp):
AATAGTGACTAAAACATATAAAATTAAAAT
Found at i:122424 original size:23 final size:23
Alignment explanation
Indices: 122388--122456 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
122378 CACCACAGCT
* *
122388 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
* * * *
122411 CGTAGAATTACACCGTAGTACCG
1 CGTAGAAATACACCGAAGTGCCA
*
122434 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCA
122457 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.17
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCA
Found at i:122927 original size:2 final size:2
Alignment explanation
Indices: 122920--122984 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
122910 ATTCATCTTC
122920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122962 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
122985 CATTTTTCCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:124115 original size:19 final size:19
Alignment explanation
Indices: 124091--124140 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
124081 CCTTAACATG
124091 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
124110 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
124129 TGCATCGATGCA
1 TGCATCGATGCA
124141 TTAATTGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:125899 original size:3 final size:3
Alignment explanation
Indices: 125891--125935 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
125881 TATTTATTTA
* *
125891 AAT AAT AAT AAT AAT AAT AAT GTAT AAT AAT AAT AAT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AA
125936 AAGCAAACTG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 35 0.95
4 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:126241 original size:45 final size:45
Alignment explanation
Indices: 126177--126299 Score: 212
Period size: 45 Copynumber: 2.8 Consensus size: 45
126167 CTCGAAGGCT
* *
126177 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCTGAAGA
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGA
*
126222 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGA
126267 TTTTGAAAACATCATGCACTGAAGGACTT-CAGA
1 TTTTGAAAACATCATGCACTGAAGGACTTACAGA
126300 GTTTCATCTT
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 4 0.05
45 71 0.95
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGA
Done.