Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008433.1 Hibiscus syriacus cultivar Beakdansim tig00111231_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: 451884
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:384422 original size:41 final size:41
Alignment explanation
Indices: 384384--384891 Score: 432
Period size: 41 Copynumber: 12.2 Consensus size: 41
384374 CATTTTTTCA
* *
384384 ACAAACGCCGTAAAAGAGTAGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * *
384425 ACAAACGCCGCTAAAGACTCA-TAATTTAGTGGCATTTTTAT
1 ACAAACGCCGTTAAAGACT-AGTACTTTAGTGGCGTTTTTAT
* * * *
384466 ACAAACGCCGTTATAGAATTGTACTTTAGTGGTGTTTTTAT
1 ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * * * *
384507 ACAAACGTCGTTATACA-TATGTACTATAGTGGCGTTTGTGTTT
1 ACAAACGCCGTTAAAGACTA-GTACTTTAGTGGCGTTT-T-TAT
* *
384550 AAAAACGCCGTTAAAGACTCA-TAATTTAGTGGCGTTTTTAT
1 ACAAACGCCGTTAAAGACT-AGTACTTTAGTGGCGTTTTTAT
*
384591 ACAAATGCCGTTAAAGACTCA-TACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGTTAAAGACT-AGTACTTTAGTGGCGTTTTTAT
* * ** *
384632 ACAAACTCCGCTAAAGACGCGTACTTTAGTGGCATTTTTAT
1 ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * * * * *
384673 TCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
1 ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTT-T-TAT
* * * * *
384716 ACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTAT
1 ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * * * * * *
384757 ACAAATGCCGCTAAAGGCCCA-TACTTTATTGACATTTTTAT
1 ACAAACGCCGTTAAA-GACTAGTACTTTAGTGGCGTTTTTAT
* *
384798 ACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTAT
1 ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTTTTAT
* * * * * * * *
384839 TCAAACGTCGCTATACACTTGTACTATAGTGGCGTTTGTGTTT
1 ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTT-T-TAT
384882 ACAAACGCCG
1 ACAAACGCCG
384892 CAAGTTTACA
Statistics
Matches: 371, Mismatches: 82, Indels: 26
0.77 0.17 0.05
Matches are distributed among these distances:
40 3 0.01
41 289 0.78
42 8 0.02
43 69 0.19
44 1 0.00
45 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (41 bp):
ACAAACGCCGTTAAAGACTAGTACTTTAGTGGCGTTTTTAT
Found at i:384580 original size:166 final size:166
Alignment explanation
Indices: 384384--384891 Score: 732
Period size: 166 Copynumber: 3.1 Consensus size: 166
384374 CATTTTTTCA
* * * *
384384 ACAAACGCCGTAAAAGAGT-AGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATA
1 ACAAACGCCGTTAAAGACTCA-TAATTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCATA
* * * * * * *
384448 ATTTAGTGGCATTTTTATACAAACGCCGTTATAGAATTGTACTTTAGTGGTGTTTTTATACAAAC
65 CTTTAGTGGCATTTTTATACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAAC
384513 GTCGTTATACA-TATGTACTATAGTGGCGTTTGTGTTT
130 GTCGTTATACACT-TGTACTATAGTGGCGTTTGTGTTT
* *
384550 AAAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATACAAATGCCGTTAAAGACTCATAC
1 ACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCATAC
* * * * *
384615 TTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACGCGTACTTTAGTGGCATTTTTATTCAAACG
66 TTTAGTGGCATTTTTATACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACG
*
384680 CCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
131 TCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
* * * * * *
384716 ACAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAATGCCGCTAAAGGCCCATAC
1 ACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCATAC
* *
384781 TTTATTGACATTTTTATACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACG
66 TTTAGTGGCATTTTTATACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACG
*
384846 TCGCTATACACTTGTACTATAGTGGCGTTTGTGTTT
131 TCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
384882 ACAAACGCCG
1 ACAAACGCCG
384892 CAAGTTTACA
Statistics
Matches: 304, Mismatches: 36, Indels: 4
0.88 0.10 0.01
Matches are distributed among these distances:
166 302 0.99
167 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (166 bp):
ACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATACAAATGCCGCTAAAGACTCATAC
TTTAGTGGCATTTTTATACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACG
TCGTTATACACTTGTACTATAGTGGCGTTTGTGTTT
Found at i:384656 original size:125 final size:123
Alignment explanation
Indices: 384404--384875 Score: 462
Period size: 125 Copynumber: 3.8 Consensus size: 123
384394 TAAAAGAGTA
* * *
384404 GTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACA
1 GTACTTTAGTGGCATTTTTATACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATACA
* * * * * * * * *
384469 AACGCCGTTATAGAATTGTACTTTAGTGGTGTTTTTATACAAACGT-CGTTATACATAT
66 AACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAAC-TCCGCTAAAGACAC
* * * *
384527 GTACTATAGTGGCGTTTGTGTTTAAAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATA
1 GTACTTTAGTGGCATTT-T-TATACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATA
* * *
384592 CAAATGCCGTTAAAGACTCATACTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACGC
64 CAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACAC
* * * ** * * *
384652 GTACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTTTA
1 GTACTTTAGTGGCATTTTTATACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTT-T-TATA
* * * * * *
384717 CAAACGTCGCTAAAGACTCGTAATTTAGTGGCATTTTTATACAAA-TGCCGCTAAAGGCCC
64 CAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACT-CCGCTAAAGACAC
* * * * * * *
384777 ATACTTTATTGACATTTTTATACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATTCA
1 GTACTTTAGTGGCATTTTTATACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATACA
* * * * * *
384842 AACGTCGCTATACACTTGTACTATAGTGGCGTTT
66 AACGCCGTTAAAGACTCGTACTTTAGTGGCGTTT
384876 GTGTTTACAA
Statistics
Matches: 289, Mismatches: 54, Indels: 12
0.81 0.15 0.03
Matches are distributed among these distances:
123 79 0.27
124 6 0.02
125 204 0.71
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (123 bp):
GTACTTTAGTGGCATTTTTATACAAACGCCGTTAAAGACTCATAATTTAGTGGCGTTTTTATACA
AACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACTCCGCTAAAGACAC
Found at i:384871 original size:207 final size:207
Alignment explanation
Indices: 384384--384891 Score: 576
Period size: 207 Copynumber: 2.4 Consensus size: 207
384374 CATTTTTTCA
* * * * * *
384384 ACAAACGCCGTAAAAGAGTAGTACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAA
1 ACAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTAC
* * *
384449 TTTAGTGGCATTTTTATACAAACGCCGTTATAGAATTGTACTTTAGTGGTGTTTTTATACAAACG
66 TTTAGTGGCATTTTTATACAAACGCCGTTATACAATTGTACTATAGTGGCGTTTTTATACAAACG
* * * * * * *
384514 TCGTTATACATATGTACTATAGTGGCGTTTGTGTTTAAAAACGCCGTTAAAGACTCATAATTTAG
131 TCGCTATACAGATGTAATATAGTGGCATTTGTGTATAAAAACGCCGCTAAAGACCCATAATTTAG
* *
384579 TGGCGTTTTTAT
196 TGACATTTTTAT
* * *
384591 ACAAATGCCGTTAAAGACTCATACTTTAGTGGCGTTTTTATACAAAC-TCCGCTAAAGACGCGTA
1 ACAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGT-CGCTAAAGACTCGTA
* * *
384655 CTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTTTACAA
65 CTTTAGTGGCATTTTTATACAAACGCCGTTATACAATTGTACTATAGTGGCGTTT-T-TATACAA
* * * * *
384720 ACGTCGCTA-A-AGACTCGTAATTTAGTGGCATTT-T-TATACAAATGCCGCTAAAGGCCCATAC
128 ACGTCGCTATACAGA-T-GTAATATAGTGGCATTTGTGTATAAAAACGCCGCTAAAGACCCATAA
*
384781 TTTATTGACATTTTTAT
191 TTTAGTGACATTTTTAT
* * * * *
384798 ACAAACACCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATTCAAACGTCGCTATACACTTGTAC
1 ACAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTAC
* * *
384863 TATAGTGGCGTTTGTGTTTACAAACGCCG
66 TTTAGTGGCATTT-T-TATACAAACGCCG
384892 CAAGTTTACA
Statistics
Matches: 251, Mismatches: 42, Indels: 14
0.82 0.14 0.05
Matches are distributed among these distances:
207 206 0.82
208 6 0.02
209 39 0.16
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (207 bp):
ACAAACGCCGTTAAAGACTCGTACTTTAGTGGCGTTTTTATACAAACGTCGCTAAAGACTCGTAC
TTTAGTGGCATTTTTATACAAACGCCGTTATACAATTGTACTATAGTGGCGTTTTTATACAAACG
TCGCTATACAGATGTAATATAGTGGCATTTGTGTATAAAAACGCCGCTAAAGACCCATAATTTAG
TGACATTTTTAT
Found at i:388495 original size:43 final size:42
Alignment explanation
Indices: 388436--388745 Score: 247
Period size: 43 Copynumber: 7.3 Consensus size: 42
388426 TGTTTGTATC
*
388436 CAAAAACGTCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTT
1 CAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTT-TGTT
* * * *
388479 CAAAAACACCGTTATAGGTCTGACATTTTGCGGCGTTTGTGTC
1 CAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTT-TGTT
* * *
388522 CAAAAACGCCACTATAGGTCTGACCTTTTACGGCG-TTTGTT
1 CAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTTGTT
* * * *
388563 CTAAGAACGCCAG-TATATGTCTTA-TCTTTTGCGGTG-TTTGTAT
1 C-AAAAACGCC-GCTATAGGTCTGACT-TTTTGCGGCGTTTTGT-T
* * *
388606 CCAAAAACACCGCTATAGATCTGACTTTTTGCAGCGTTTT-TT
1 -CAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTTGTT
* ** * * *
388648 CTAGAAACGCCGCTATATATCATAACTTTTTGCGGTGTTTAT-TC
1 C-AAAAACGCCGCTATAGGTC-TGACTTTTTGCGGCGTTT-TGTT
* * *
388692 CAAAAACGCCGCTATAGATATCGACTTTTTGTGGCG-TTTGTT
1 CAAAAACGCCGCTATAGGTCT-GACTTTTTGCGGCGTTTTGTT
388734 CAAAAAACGCCG
1 C-AAAAACGCCG
388746 TAATAGATAT
Statistics
Matches: 214, Mismatches: 39, Indels: 28
0.76 0.14 0.10
Matches are distributed among these distances:
41 6 0.03
42 55 0.26
43 145 0.68
44 8 0.04
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (42 bp):
CAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTTGTT
Found at i:388622 original size:85 final size:85
Alignment explanation
Indices: 388422--388745 Score: 350
Period size: 85 Copynumber: 3.8 Consensus size: 85
388412 AAGGTAATTA
* *
388422 GCGGTGTTTGTATCCAAAAACGTCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGT-TCAAAAAC
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGT-TCT-AAAAAC
* * * *
388486 ACCGTTATAGGTCTGACATTTT
64 GCCGCTATATGTCTTACATTTT
* * * * * * *
388508 GCGGCGTTTGTGTCCAAAAACGCCACTATAGGTCTGACCTTTTACGGCGTTTGTTCTAAGAACGC
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTTCTAAAAACGC
388573 CAG-TATATGTCTTATC-TTTT
66 C-GCTATATGTCTTA-CATTTT
* * * *
388593 GCGGTGTTTGTATCCAAAAACACCGCTATAGATCTGACTTTTTGCAGCGTTTTTTCTAGAAACGC
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTTCTAAAAACGC
* * *
388658 CGCTATATATCATAACTTTTT
66 CGCTATATGTC-TTACATTTT
* * * *
388679 GCGGTGTTTAT-TCCAAAAACGCCGCTATAGATATCGACTTTTTGTGGCGTTTGTTCAAAAAACG
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCT-GACTTTTTGCGGCGTTTGTTCTAAAAACG
388743 CCG
65 CCG
388746 TAATAGATAT
Statistics
Matches: 200, Mismatches: 31, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
84 1 0.00
85 105 0.52
86 94 0.47
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (85 bp):
GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTTCTAAAAACGC
CGCTATATGTCTTACATTTT
Found at i:388700 original size:128 final size:128
Alignment explanation
Indices: 388422--388741 Score: 324
Period size: 128 Copynumber: 2.5 Consensus size: 128
388412 AAGGTAATTA
* * *
388422 GCGGTGTTTGTATCCAAAAACGTCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTCAAAAACA
1 GCGGTGTTTGT-TCCAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTATCCAAAAACA
* * * * *
388487 CCGTTATAGGTCTGACATTTTGCGGCGTTTGTGTCCAAAAACGCCACTATAGGTCTGACCTTTT
65 CCGCTATAGATCTGACATTTTGCAGCGTTTGTGTCCAAAAACGCCACTATAGATCTAACCTTTT
* * * * * * *
388551 ACGGCGTTTGTTCTAAGAACGCCAG-TATATGTCTTA-TCTTTTGCGGTGTTTGTATCCAAAAAC
1 GCGGTGTTTGTTCCAAAAACGCC-GCTATAGGTCTGACT-TTTTGCGGCGTTTGTATCCAAAAAC
* * * * * * *
388614 ACCGCTATAGATCTGACTTTTTGCAGCGTTT-TTTCTAGAAACGCCGCTATATATCATAACTTTT
64 ACCGCTATAGATCTGACATTTTGCAGCGTTTGTGTCCAAAAACGCCACTATAGATC-TAACCTTT
388678 T
128 T
* * * * *
388679 GCGGTGTTTATTCCAAAAACGCCGCTATAGATATCGACTTTTTGTGGCGTTTGT-TCAAAAAAC
1 GCGGTGTTTGTTCCAAAAACGCCGCTATAGGTCT-GACTTTTTGCGGCGTTTGTATCCAAAAAC
388742 GCCGTAATAG
Statistics
Matches: 151, Mismatches: 34, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
127 20 0.13
128 106 0.70
129 24 0.16
130 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (128 bp):
GCGGTGTTTGTTCCAAAAACGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTATCCAAAAACAC
CGCTATAGATCTGACATTTTGCAGCGTTTGTGTCCAAAAACGCCACTATAGATCTAACCTTTT
Found at i:388767 original size:86 final size:85
Alignment explanation
Indices: 388422--388768 Score: 328
Period size: 86 Copynumber: 4.0 Consensus size: 85
388412 AAGGTAATTA
* *
388422 GCGGTGTTTGTATCCAAAAACGTCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGT-TCAAAAAC
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGT-TCT-AAAAAC
* * * *
388486 ACCGTTATAGGT-CTGACATTTT
64 GCCG-TATAGATATTGACCTTTT
* * * * * * *
388508 GCGGCGTTTGTGTCCAAAAACGCCACTATAGGTCTGACCTTTTACGGCGTTTGTTCTAAGAACGC
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTTCTAAAAACGC
* *
388573 CAGTATATG-TCTT-ATCTTTT
66 C-GTATA-GATATTGACCTTTT
* * * *
388593 GCGGTGTTTGTATCCAAAAACACCGCTATAGATCTGACTTTTTGCAGCGTTTTTTCTAGAAACGC
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTTCTAAAAACGC
* * *
388658 CGCTATATATCA-TAACTTTTT
66 CG-TATAGAT-ATTGACCTTTT
* * * *
388679 GCGGTGTTTAT-TCCAAAAACGCCGCTATAGATATCGACTTTTTGTGGCGTTTGTTCAAAAAACG
1 GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCT-GACTTTTTGCGGCGTTTGTTCTAAAAACG
*
388743 CCGTAATAGATATTGACCTATT
65 CCGT-ATAGATATTGACCTTTT
388765 GCGG
1 GCGG
388769 CATTTTTTGT
Statistics
Matches: 212, Mismatches: 38, Indels: 22
0.78 0.14 0.08
Matches are distributed among these distances:
84 1 0.00
85 102 0.48
86 109 0.51
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.35
Consensus pattern (85 bp):
GCGGTGTTTGTATCCAAAAACGCCGCTATAGATCTGACTTTTTGCGGCGTTTGTTCTAAAAACGC
CGTATAGATATTGACCTTTT
Found at i:389122 original size:20 final size:20
Alignment explanation
Indices: 389097--389152 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
389087 TGAAATGAAA
389097 ATCGCAACGAGAGAATAACT
1 ATCGCAACGAGAGAATAACT
389117 ATCGCAATGCG-GA-AATAACT
1 ATCGCAA--CGAGAGAATAACT
*
389137 ATCGTAACGAGAGAAT
1 ATCGCAACGAGAGAAT
389153 CGCAACGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 23 0.74
21 2 0.06
22 2 0.06
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (20 bp):
ATCGCAACGAGAGAATAACT
Found at i:389181 original size:33 final size:33
Alignment explanation
Indices: 389137--389214 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
389127 GGAAATAACT
* ** *
389137 ATCGTAACGAGAGAATCGCAACGTGATATGAAA
1 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
389170 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
1 ATCGCAACGAGAGAATCGCAACACGAAATGAAA
*
389203 ATCGCAATGAGA
1 ATCGCAACGAGA
389215 TTTTGGTTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACACGAAATGAAA
Found at i:389245 original size:14 final size:14
Alignment explanation
Indices: 389226--389282 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
389216 TTTGGTTTCG
389226 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
389240 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
389259 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
389273 CGTTGCGATT
1 CGTTGCGATT
389283 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:389258 original size:33 final size:33
Alignment explanation
Indices: 389221--389290 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
389211 GAGATTTTGG
389221 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
*
389254 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
389287 TTTC
1 TTTC
389291 TCTCGTTGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTATCTCGTTGCGATTTTCA
Found at i:389293 original size:21 final size:20
Alignment explanation
Indices: 389274--389345 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
389264 CGATTCTCTC
389274 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
389294 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
*
389315 GTTGCGATTTTTATTTTCAT
1 GTTGCGATTTTCATTTTCAT
389335 GTTGCGATTTT
1 GTTGCGATTTT
389346 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:390425 original size:22 final size:22
Alignment explanation
Indices: 390394--390465 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
390384 CTGAGTGGCA
*
390394 TATGAAATTTGCCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
390417 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
* *
390439 TATG-AGTGGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
390460 TATGAA
1 TATGAA
390466 ACCCTCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 19 0.44
22 21 0.49
23 3 0.07
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:390452 original size:21 final size:21
Alignment explanation
Indices: 390406--390464 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
390396 TGAAATTTGC
* * *
390406 CCCGAAGGACCTGTGAATTTGT
1 CCCGAAGGACCTATG-AGTGGT
390428 CCCGAAGGACCTATGAGTGGT
1 CCCGAAGGACCTATGAGTGGT
390449 CCCGAAGGACCTATGA
1 CCCGAAGGACCTATGA
390465 AACCCTCGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.25, C:0.25, G:0.29, T:0.20
Consensus pattern (21 bp):
CCCGAAGGACCTATGAGTGGT
Found at i:391040 original size:64 final size:63
Alignment explanation
Indices: 390907--391062 Score: 156
Period size: 64 Copynumber: 2.4 Consensus size: 63
390897 TAATGAAGGT
* ** ** *
390907 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTTTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGACGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
* *
390971 ATGCATCGATGCATGACTTATGCATCGACGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGACGCA-TAAAATGCATTCGATGTTT-TATTATTAAAGA
391033 G
63 G
*
391034 AGTGCATCGATGCATTACAAATGCATCGA
1 A-TGCATCGATGCA-TACTAATGCATCGA
391063 TACACCTTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 69 0.88
65 6 0.08
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGACGCATAAAATGCATTCGATGTTTTATTATTAAAGAG
Found at i:394849 original size:84 final size:84
Alignment explanation
Indices: 394708--394875 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
394698 AAATACATCG
*
394708 GGAAACTCTGTGACTATGGAAATTTCTTCAATTCTTTTCTCCTTGGTTCTAATATCCAACACATT
1 GGAAACGCTGTGACTATGGAAATTTCTTCAATTCTTTTCTCCTTGGTTCTAATATCCAACACATT
394773 AGCAATGAACCCTTGACAT
66 AGCAATGAACCCTTGACAT
394792 GGAAACGCTGTGACTATGGAAATTTCTTCAATTCTTTTCTCCTTGGTTCTAATATCCAACACATT
1 GGAAACGCTGTGACTATGGAAATTTCTTCAATTCTTTTCTCCTTGGTTCTAATATCCAACACATT
394857 AGCAATGAACCCTTGACAT
66 AGCAATGAACCCTTGACAT
394876 CCCTGTAGTA
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.35
Consensus pattern (84 bp):
GGAAACGCTGTGACTATGGAAATTTCTTCAATTCTTTTCTCCTTGGTTCTAATATCCAACACATT
AGCAATGAACCCTTGACAT
Found at i:397377 original size:22 final size:22
Alignment explanation
Indices: 397346--397417 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
397336 CTGAGTGGCA
397346 TATGAAATTTGTCCCGAAGGACC
1 TATG-AATTTGTCCCGAAGGACC
*
397369 TGTGAATTTGTCCCGAAGGACC
1 TATGAATTTGTCCCGAAGGACC
* * *
397391 TATG-AGTGGTCCCGAAAGACC
1 TATGAATTTGTCCCGAAGGACC
397412 TATGAA
1 TATGAA
397418 ACCCTCGACT
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 18 0.42
22 22 0.51
23 3 0.07
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (22 bp):
TATGAATTTGTCCCGAAGGACC
Found at i:397404 original size:21 final size:21
Alignment explanation
Indices: 397356--397416 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
397346 TATGAAATTT
* * *
397356 GTCCCGAAGGACCTGTGAATTT
1 GTCCCGAAGGACCTATG-AGTG
397378 GTCCCGAAGGACCTATGAGTG
1 GTCCCGAAGGACCTATGAGTG
*
397399 GTCCCGAAAGACCTATGA
1 GTCCCGAAGGACCTATGA
397417 AACCCTCGAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.21
Consensus pattern (21 bp):
GTCCCGAAGGACCTATGAGTG
Found at i:397992 original size:64 final size:63
Alignment explanation
Indices: 397859--398015 Score: 158
Period size: 64 Copynumber: 2.4 Consensus size: 63
397849 TAATGAAGGT
* * * ** *
397859 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCA-TACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
* *
397923 ATGCATCGATGCATGACTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATT-TTAAA-A
1 ATGCATCGATGCAT-ACTAATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATTAAAGA
397985 G
63 G
*
397986 AGTGCATCGATGCATTACAAATGCATCGAT
1 A-TGCATCGATGCA-TACTAATGCATCGAT
398016 ACACCTTCAA
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCATACTAATGCATCGATGCATAAAATGCATTCGATGTTCTATTATTAAAGAG
Found at i:399020 original size:20 final size:20
Alignment explanation
Indices: 398995--399196 Score: 187
Period size: 20 Copynumber: 9.9 Consensus size: 20
398985 TTTAAAAATC
398995 GCGTTGCGATTTACGGATAT
1 GCGTTGCGATTTACGGATAT
*
399015 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAT
* *
399035 GTCGTTGCGATTTACAGATAC
1 G-CGTTGCGATTTACGGATAT
* *
399056 GCATTGCGATTTACGTAT-T
1 GCGTTGCGATTTACGGATAT
* *
399075 CTCGTTGCGATTTACGTAT-T
1 -GCGTTGCGATTTACGGATAT
* *
399095 CTCGTTGCGATTTACGGATAC
1 -GCGTTGCGATTTACGGATAT
*
399116 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAT
* *
399136 GTCGTTGCGATTTATGGATAC
1 G-CGTTGCGATTTACGGATAT
* *
399157 GCGTTACGATTTACGGATAC
1 GCGTTGCGATTTACGGATAT
399177 GCGTTGCGATTTTACGGATA
1 GCGTTGCGA-TTTACGGATA
399197 CTCGTATTGA
Statistics
Matches: 152, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
20 108 0.71
21 44 0.29
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.38
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAT
Found at i:399130 original size:61 final size:60
Alignment explanation
Indices: 398994--399201 Score: 256
Period size: 61 Copynumber: 3.4 Consensus size: 60
398984 CTTTAAAAAT
* * *
398994 CGCGTTGCGATTTACGGATAT-GCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGAT-TCTCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
* *
399055 CGCATTGCGATTTACGTATTCTCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATTCTCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
* * * * * * *
399115 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTATGGATACGCGTTACGATTTACGGATA
1 CGCGTTGCGA-TTTACGGATTCTCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
*
399176 CGCGTTGCGATTTTACGGATACTCGT
1 CGCGTTGCGA-TTTACGGATTCTCGT
399202 ATTGATAGTC
Statistics
Matches: 130, Mismatches: 15, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
60 38 0.29
61 92 0.71
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATTCTCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:399171 original size:101 final size:101
Alignment explanation
Indices: 398996--399188 Score: 314
Period size: 101 Copynumber: 1.9 Consensus size: 101
398986 TTAAAAATCG
*
398996 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCATT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCATT
* * * *
399061 GCGATTTACGTATTCTCGTTGCGATTTACGTATTCT
66 ACGATTTACGGATACGCGTTGCGATTTACGTATTCT
** *
399097 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTATGGATACGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCATT
399162 ACGATTTACGGATACGCGTTGCGATTT
66 ACGATTTACGGATACGCGTTGCGATTT
399189 TACGGATACT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 84 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (101 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACAGATACGCATT
ACGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:399221 original size:61 final size:61
Alignment explanation
Indices: 398994--399230 Score: 191
Period size: 61 Copynumber: 3.9 Consensus size: 61
398984 CTTTAAAAAT
* * * * *
398994 CGCGTTGCGA-TTTACGGATA-TGCGTTGCGATTTTACGTAT-TGTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTTACGGATACT-CGTTGCGA-TTCATGAATACG-CGTTGCGATTTACGGATA
* * * * * * * *
399055 CGCATTGCGA-TTTACGTATTCTCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTCATGAATACGCGTTGCGATTTACGGATA
* ** * * *
399115 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTATGGATACGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTTACGGATACTCGTTGCGATTCATGAATACGCGTTGCGATTTACGGATA
*
399176 CGCGTTGCGATTTTACGGATACTCGTAT-TGATAGTCA-GAAT-CGCGTTGCGATTTA
1 CGCGTTGCGATTTTACGGATACTCGT-TGCGAT--TCATGAATACGCGTTGCGATTTA
399231 TAAGTTCGCG
Statistics
Matches: 150, Mismatches: 20, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
60 35 0.23
61 108 0.72
62 5 0.03
63 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (61 bp):
CGCGTTGCGATTTTACGGATACTCGTTGCGATTCATGAATACGCGTTGCGATTTACGGATA
Found at i:399241 original size:20 final size:20
Alignment explanation
Indices: 399216--399268 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 20
399206 ATAGTCAGAA
399216 TCGCGTTGCGA-TTT-ATAAGT
1 TCGCGTTGCGATTTTCAT-A-T
399236 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
399256 TCGCGTTGCGATT
1 TCGCGTTGCGATT
399269 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 25 0.81
21 4 0.13
22 2 0.06
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:400490 original size:228 final size:227
Alignment explanation
Indices: 400091--400998 Score: 848
Period size: 228 Copynumber: 4.0 Consensus size: 227
400081 CTACATCCCT
* * * * * * * * *
400091 CCACGAAGCCTGAGCACAAGGTGAAGCGTAGACTCTTTCTGTATATTGTAATCAGCAAGGGTCCT
1 CCACGAAGACGGAGCACAAGATGAAGAGTCGACTCCTTCTGAATATTATAATCAGCAA-GGTAC-
* * * * * * * * *
400156 G-CCATCTTCCAGCTGCTTCCCTGCGAAAATCAACCTCTGTTGGTCTGGAGGAATCCCTTCCTTA
64 GACCATCTTCAAGCTGCTTCCCGGCGAAGATCAATCGCTGTTGGTCCGGAGGGATGCCTTCCTTG
* * * * * * * * * *
400220 TCCTGGATTTTCGCCTTCACATTGTCGATCGTATCGGAGCTTTCTACCTCAAGGGTAATTGTTTT
129 TCCTGAATCTTCGCCTTGACATTATCGATGGTGTCGGAGCTTTCCACCTCAAGAGTGATTGTCTT
* *
400285 TCCGGTCAAGGTTTTAACAAAGATCTGCATGCCA
194 GCCGGTTAAGGTTTTAACAAAGATCTGCATGCCA
* * * * * * *
400319 CCACGAAGCCTGAGCACAAGGTGAAGAGTCGATTCCTTCTGAATATTGTAATCGGCCAAGGTGCG
1 CCACGAAGACGGAGCACAAGATGAAGAGTCGACTCCTTCTGAATATTATAATCAG-CAAGGTACG
* *
400384 ACCATCGTCTAA-CTGCTTCCCGGCGAAGATCAATCGCTGCTGGTCCGGAGGGATGCCTTCCTTG
65 ACCATCTTC-AAGCTGCTTCCCGGCGAAGATCAATCGCTGTTGGTCCGGAGGGATGCCTTCCTTG
* * * * * *
400448 TCCTGAATCTTGGCCTTGACATTGTCTATGGTGTCAGAGCTTTCCACTTCAAGAGTGATGGTCTT
129 TCCTGAATCTTCGCCTTGACATTATCGATGGTGTCGGAGCTTTCCACCTCAAGAGTGATTGTCTT
* * *
400513 GCCGGTTAGGGTTTTAACGAAGATCTGCATACCA
194 GCCGGTTAAGGTTTTAACAAAGATCTGCATGCCA
* * * * * * * *
400547 CCACGGAGACGGAGGACTAGATGTAGTGTCGATTCCTTCTGAATGTTATAATCAGCGAGAGTACG
1 CCACGAAGACGGAGCACAAGATGAAGAGTCGACTCCTTCTGAATATTATAATCAGCAAG-GTACG
* * * * * * *
400612 GCCGTCTTCAAGTTGCTTGCCGGCGAAGATCAATCGTTGTTGGTCCGGAGGTATGCCTTCTTTGT
65 ACCATCTTCAAGCTGCTTCCCGGCGAAGATCAATCGCTGTTGGTCCGGAGGGATGCCTTCCTTGT
* * * * * *
400677 CCTGAATCTTCGCCTTGACGTTATCGATGGTGTCCGAGCTTTCGACTTCAAGAGTTATAGTCTTG
130 CCTGAATCTTCGCCTTGACATTATCGATGGTGTCGGAGCTTTCCACCTCAAGAGTGATTGTCTTG
* *
400742 CCGGTTAAGGTTTTGACGAAGATCTGCATGCCA
195 CCGGTTAAGGTTTTAACAAAGATCTGCATGCCA
* * * * * * * * * *
400775 CCGCGGAGACGGAGAACCAGATGGAGAGTCGACTCCTTCTGGATGTTATAGTCGGCGAGGGTACG
1 CCACGAAGACGGAGCACAAGATGAAGAGTCGACTCCTTCTGAATATTATAATCAGC-AAGGTACG
* * * * * * *
400840 ACCGTCTTCAAGTTGCTTTCCGGCGAAGATCAATCGTTGTTGATCGGGAGGGATACCTTCCTTGT
65 ACCATCTTCAAGCTGCTTCCCGGCGAAGATCAATCGCTGTTGGTCCGGAGGGATGCCTTCCTTGT
* * * * * * * *
400905 CTTGAATCTTGGACTTGACGTTATCGATGGTGTCGGAGCTCTCCACCTCGAGGGTGATTGTTTTG
130 CCTGAATCTTCGCCTTGACATTATCGATGGTGTCGGAGCTTTCCACCTCAAGAGTGATTGTCTTG
* * * *
400970 CCGGTGAGGGTCTTCACAAAGATCTGCAT
195 CCGGTTAAGGTTTTAACAAAGATCTGCAT
400999 CTTCAACGAA
Statistics
Matches: 569, Mismatches: 105, Indels: 12
0.83 0.15 0.02
Matches are distributed among these distances:
227 6 0.01
228 558 0.98
229 5 0.01
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.29
Consensus pattern (227 bp):
CCACGAAGACGGAGCACAAGATGAAGAGTCGACTCCTTCTGAATATTATAATCAGCAAGGTACGA
CCATCTTCAAGCTGCTTCCCGGCGAAGATCAATCGCTGTTGGTCCGGAGGGATGCCTTCCTTGTC
CTGAATCTTCGCCTTGACATTATCGATGGTGTCGGAGCTTTCCACCTCAAGAGTGATTGTCTTGC
CGGTTAAGGTTTTAACAAAGATCTGCATGCCA
Found at i:407371 original size:18 final size:18
Alignment explanation
Indices: 407350--407385 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
407340 TATTTTATTT
407350 AGTTTTAAAATTTAAATG
1 AGTTTTAAAATTTAAATG
407368 AGTTTTAAAATTTAAATG
1 AGTTTTAAAATTTAAATG
407386 GGCAGTGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
AGTTTTAAAATTTAAATG
Found at i:407447 original size:2 final size:2
Alignment explanation
Indices: 407435--407467 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
407425 GTGGCTGAGT
407435 TA TA T- TA TA TA TA TA TA TA TA T- TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
407468 GTATTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:407457 original size:17 final size:17
Alignment explanation
Indices: 407435--407467 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
407425 GTGGCTGAGT
407435 TATATTATATATATATA
1 TATATTATATATATATA
407452 TATATTATATATATAT
1 TATATTATATATATAT
407468 GTATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTATATATATATA
Found at i:407460 original size:15 final size:15
Alignment explanation
Indices: 407442--407472 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
407432 AGTTATATTA
407442 TATATATATATATAT
1 TATATATATATATAT
*
407457 TATATATATATGTAT
1 TATATATATATATAT
407472 T
1 T
407473 TAATTCGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
TATATATATATATAT
Found at i:423365 original size:30 final size:30
Alignment explanation
Indices: 423329--423400 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
423319 CCCGAAGGAC
* *
423329 CTATCCAGAGGTCACAAGGAACCTCGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
423359 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
423389 CTGTCCATAGGT
1 CTATCCAGAGGT
423401 TCCGAAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:423425 original size:31 final size:31
Alignment explanation
Indices: 423387--423572 Score: 179
Period size: 31 Copynumber: 6.0 Consensus size: 31
423377 GATCCTCGGC
* *
423387 AACTGTCCATAGGTTCCGAAGAACCTAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
**
423418 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCGAAGAACATAGGTA
*
423449 TACTGTCCATATG-TCTCGAA-AGACATAGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
*
423480 ATTCTGTCCATATGTTCC-ATAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGA-AGAACATAGGTA
*
423512 TACTGTCCATATG-TCTCGAA-AGAC--AGGTA
1 AACTGTCCATATGTTC-CGAAGA-ACATAGGTA
* *
423541 ATTCTGTCCATATGTTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCGAAGAACATAGGTA
423573 TACCCTCAAC
Statistics
Matches: 127, Mismatches: 14, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
29 5 0.04
30 22 0.17
31 69 0.54
32 28 0.22
33 3 0.02
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (31 bp):
AACTGTCCATATGTTCCGAAGAACATAGGTA
Found at i:423503 original size:63 final size:62
Alignment explanation
Indices: 423411--423575 Score: 280
Period size: 63 Copynumber: 2.7 Consensus size: 62
423401 TCCGAAGAAC
* *
423411 CTAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGA
1 CTAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGA
423472 CATAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGA
1 C-TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGA
*
423535 C-AGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 CTAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATAC
423576 CCTCAACTCT
Statistics
Matches: 99, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
61 40 0.40
62 7 0.07
63 52 0.53
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (62 bp):
CTAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGA
Found at i:428355 original size:30 final size:30
Alignment explanation
Indices: 428319--428390 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
428309 CCCGAAGGAC
* * *
428319 CTATCCAGAGGTCACAAGGAACCTTGGTAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* *
428349 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
*
428379 CTATCCATAGGT
1 CTATCCAGAGGT
428391 TCCGAAGAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:428485 original size:63 final size:63
Alignment explanation
Indices: 428402--428567 Score: 298
Period size: 63 Copynumber: 2.7 Consensus size: 63
428392 CCGAAGAACC
* *
428402 TAGGTAA-ACTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
428464 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
1 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
*
428527 TAGGTAATTCTGTCCATATGTTCCGTAGAACATAGGTATAC
1 TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATAC
428568 CCTCAACTCT
Statistics
Matches: 100, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.07
63 93 0.93
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (63 bp):
TAGGTAATTCTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGACA
Found at i:428560 original size:32 final size:32
Alignment explanation
Indices: 428382--428564 Score: 200
Period size: 31 Copynumber: 5.8 Consensus size: 32
428372 TCGGCAACTA
* * *
428382 TCCATAGGTTCCGAAGAACCTAGGTAA-ACTG
1 TCCATATGTTCCGTAGAACATAGGTAATACTG
*
428413 TCCATATGTTCCTTAGAACATAGGT-ATACTG
1 TCCATATGTTCCGTAGAACATAGGTAATACTG
* *
428444 TCCATATG-TCTCG-AAAGACATAGGTAATTCTG
1 TCCATATGTTC-CGTAGA-ACATAGGTAATACTG
*
428476 TCCATATGTTCCATAGAACATAGGT-ATACTG
1 TCCATATGTTCCGTAGAACATAGGTAATACTG
* *
428507 TCCATATG-TCTCG-AAAGACATAGGTAATTCTG
1 TCCATATGTTC-CGTAGA-ACATAGGTAATACTG
428539 TCCATATGTTCCGTAGAACATAGGTA
1 TCCATATGTTCCGTAGAACATAGGTA
428565 TACCCTCAAC
Statistics
Matches: 127, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
30 9 0.07
31 64 0.50
32 46 0.36
33 8 0.06
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (32 bp):
TCCATATGTTCCGTAGAACATAGGTAATACTG
Found at i:437201 original size:14 final size:13
Alignment explanation
Indices: 437182--437224 Score: 59
Period size: 14 Copynumber: 3.2 Consensus size: 13
437172 ATTTAGATAC
437182 ATTTTATATTTTGT
1 ATTTTATATTTT-T
437196 ATTTTATAGTTTTT
1 ATTTTATA-TTTTT
*
437210 ATTTTTTATTTTT
1 ATTTTATATTTTT
437223 AT
1 AT
437225 AAAAATGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 7 0.26
14 16 0.59
15 4 0.15
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (13 bp):
ATTTTATATTTTT
Found at i:438763 original size:30 final size:28
Alignment explanation
Indices: 438729--438788 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
438719 ATAAAATAAT
438729 ATTTAAT-TATCAAATATTATATTTTTATTA
1 ATTTAATCT-TCAAATA-T-TATTTTTATTA
* *
438759 ATTTAGTCTTTAAATATTATTTTTATTA
1 ATTTAATCTTCAAATATTATTTTTATTA
438787 AT
1 AT
438789 ATTTTGGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 13 0.48
29 1 0.04
30 12 0.44
31 1 0.04
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTAATCTTCAAATATTATTTTTATTA
Found at i:439150 original size:30 final size:31
Alignment explanation
Indices: 439079--439150 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
439069 GAAAAAAAAA
* *
439079 TTAGGTACTTATTTTGATCAAAAAGATAATT
1 TTAGGTACTTATTTTGATCAAAAAAATAACT
* *
439110 TTAAGTACTTATTTTGAAT-AAAAAAAT-GCT
1 TTAGGTACTTATTTTG-ATCAAAAAAATAACT
439140 TTAGGTACTTA
1 TTAGGTACTTA
439151 AATGAAAATG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 11 0.31
31 22 0.63
32 2 0.06
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (31 bp):
TTAGGTACTTATTTTGATCAAAAAAATAACT
Found at i:445665 original size:309 final size:311
Alignment explanation
Indices: 445074--445704 Score: 1070
Period size: 309 Copynumber: 2.0 Consensus size: 311
445064 TTAGATTGCT
* *
445074 ACATGTAAAAAAATGGTTTTTTTGTCCAATATCTCACTTGAGGTAAATTATTTAGCTCAATAGAC
1 ACAT-TAAAAAAATGGGTTTTTTGTCCAATATCTCACTTGAGGTAAATCATTTAGCTCAATAGAC
*
445139 TATCAAAGAATTTAATTTATAATCTACGACATTTGCTACAGTAAAGAGCAAACTTGTCACATTGG
65 CATCAAAGAATTTAATTTATAATCTACGACATTTGCTACAGTAAAGAGCAAACTTGTCAC--TGG
*
445204 GTGATGAGTTTGTTTGGAAATATTTTTTAATGGACCATGTATTTGGGTCCCATATGGGCCAATAT
128 GTGATGAGTTTGTTTGGAAATATTTTTTAATGGACCAGGTATTTGGGTCCCATATGGGCCAATAT
*
445269 TTAATATATTCACTGGGACTTGTCACTTCAACGTGACGAGTCTATTGAGAATTTAAATTTTTTAA
193 TTAATATATTCACTGAGACTTGTCACTTCAACGTGACGAGTCTATTGAGAATTTAAATTTTTTAA
*
445334 TTCATTAAATAATTTTAAGAAAGAAAAAAATT-AAAAAAATTAAACGAACTAGTC
258 TTCATTAAATAATTTAAAGAAAG-AAAAAATTAAAAAAAATTAAACGAACTAGTC
*
445388 ACATTAAAAAAATGGGTTTTTTGTCCAATATCTCATTTGAGGTAAATCATTTAGCTCAATAGACC
1 ACATTAAAAAAATGGGTTTTTTGTCCAATATCTCACTTGAGGTAAATCATTTAGCTCAATAGACC
* * *
445453 ATCAAAGAATTTAATTTGTAATCTATGACATTTGTTACAGTAAAGAGCAAACTTGTCAC-GGGTG
66 ATCAAAGAATTTAATTTATAATCTACGACATTTGCTACAGTAAAGAGCAAACTTGTCACTGGGTG
*
445517 ATGAGTTTGTTTGGAAATA-TTTTTAATGGTCCAGGTATTTGGGTCCCATATGGGCCAATATTTA
131 ATGAGTTTGTTTGGAAATATTTTTTAATGGACCAGGTATTTGGGTCCCATATGGGCCAATATTTA
* *
445581 ATATATTCACTGAGACTTGTCACTTTAATGTGACGAGTCTATTGAGAATTTAAATTTTTTAATTC
196 ATATATTCACTGAGACTTGTCACTTCAACGTGACGAGTCTATTGAGAATTTAAATTTTTTAATTC
* *
445646 ATTAAATAATTTAAAGAAAGAAAAAATTAAAAAAAATTAAATGAACTCGTC
261 ATTAAATAATTTAAAGAAAGAAAAAATTAAAAAAAATTAAACGAACTAGTC
445697 ACATTAAA
1 ACATTAAA
445705 GTAACAAGTT
Statistics
Matches: 301, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
308 8 0.03
309 152 0.50
310 24 0.08
313 113 0.38
314 4 0.01
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (311 bp):
ACATTAAAAAAATGGGTTTTTTGTCCAATATCTCACTTGAGGTAAATCATTTAGCTCAATAGACC
ATCAAAGAATTTAATTTATAATCTACGACATTTGCTACAGTAAAGAGCAAACTTGTCACTGGGTG
ATGAGTTTGTTTGGAAATATTTTTTAATGGACCAGGTATTTGGGTCCCATATGGGCCAATATTTA
ATATATTCACTGAGACTTGTCACTTCAACGTGACGAGTCTATTGAGAATTTAAATTTTTTAATTC
ATTAAATAATTTAAAGAAAGAAAAAATTAAAAAAAATTAAACGAACTAGTC
Found at i:449448 original size:13 final size:14
Alignment explanation
Indices: 449430--449464 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
449420 TTATTTAAGT
*
449430 TTTTTTAA-TATTA
1 TTTTTTAATTAATA
449443 TTTTTTAATTAATA
1 TTTTTTAATTAATA
449457 TTTTTTAA
1 TTTTTTAA
449465 ACTATATCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTTAATTAATA
Found at i:450743 original size:44 final size:45
Alignment explanation
Indices: 450635--450814 Score: 198
Period size: 44 Copynumber: 4.1 Consensus size: 45
450625 TAATTTTATA
* * * *
450635 ACACTTACTCCGGCTCTCGGTTTTAAC-TTA-AAGTACCCATCTCCG
1 ACACTTACTCCGACTCTCGGTTTT-ACTTTAGTA-TATCTATCTCCG
*
450680 --ACTTACTCCGGCTCTCGG-TTTACTTTAGTATATCTATCTCCG
1 ACACTTACTCCGACTCTCGGTTTTACTTTAGTATATCTATCTCCG
450722 ACACTTACTCCGACTCTCGGTTTTTACTTTAG--TATCTATCTCCG
1 ACACTTACTCCGACTCTCGG-TTTTACTTTAGTATATCTATCTCCG
* *
450766 ACACTTACTCCGACTCTCGGTTTTTACTTAAGTA-A-CCATCTCCG
1 ACACTTACTCCGACTCTCGG-TTTTACTTTAGTATATCTATCTCCG
450810 ACACT
1 ACACT
450815 CGTGACTTGA
Statistics
Matches: 121, Mismatches: 6, Indels: 17
0.84 0.04 0.12
Matches are distributed among these distances:
41 2 0.02
42 16 0.13
43 19 0.16
44 73 0.60
45 1 0.01
46 10 0.08
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (45 bp):
ACACTTACTCCGACTCTCGGTTTTACTTTAGTATATCTATCTCCG
Found at i:450786 original size:88 final size:86
Alignment explanation
Indices: 450635--450814 Score: 229
Period size: 88 Copynumber: 2.1 Consensus size: 86
450625 TAATTTTATA
* *
450635 ACACTTACTCCGGCTCTCGGTTTTAACTTAAAGTACCCATCTCCGACTTACTCCGGCTCTCGG-T
1 ACACTTACTCCGACTCTCGGTTTTAACTTAAAGTACCCATCTCCGACTTACTCCGACTCTCGGTT
* *
450699 TTACTTTAGTATATCTATCTCCG
66 TTACTTAAGTA-A-CCATCTCCG
* * * *
450722 ACACTTACTCCGACTCTCGGTTTTTACTT-TAGTATCTATCTCCGACACTTACTCCGACTCTCGG
1 ACACTTACTCCGACTCTCGGTTTTAACTTAAAGTACCCATCTCCG--ACTTACTCCGACTCTCGG
450786 TTTTTACTTAAGTAACCATCTCCG
64 -TTTTACTTAAGTAACCATCTCCG
450810 ACACT
1 ACACT
450815 CGTGACTTGA
Statistics
Matches: 81, Mismatches: 8, Indels: 7
0.84 0.08 0.07
Matches are distributed among these distances:
86 12 0.15
87 27 0.33
88 30 0.37
89 1 0.01
90 11 0.14
ACGTcount: A:0.21, C:0.31, G:0.12, T:0.36
Consensus pattern (86 bp):
ACACTTACTCCGACTCTCGGTTTTAACTTAAAGTACCCATCTCCGACTTACTCCGACTCTCGGTT
TTACTTAAGTAACCATCTCCG
Done.