Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002276.1 Hibiscus syriacus cultivar Beakdansim tig00004630_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: 831455
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:530289 original size:11 final size:11
Alignment explanation
Indices: 530242--530289 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
530232 TTTCCTTTCT
*
530242 TTTTTTTATTA
1 TTTTTGTATTA
*
530253 TTCTTGTATTA
1 TTTTTGTATTA
*
530264 TTACTTGTATTA
1 TT-TTTGTATTA
*
530276 TTTTTATATTA
1 TTTTTGTATTA
530287 TTT
1 TTT
530290 ATTTTGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.21, C:0.04, G:0.04, T:0.71
Consensus pattern (11 bp):
TTTTTGTATTA
Found at i:530519 original size:2 final size:2
Alignment explanation
Indices: 530514--530553 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
530504 ATTTTACTAT
530514 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
530554 TCTACACAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:531353 original size:37 final size:37
Alignment explanation
Indices: 531296--531399 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
531286 AATGATCGTC
*
531296 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
531333 TTGCTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* *
531370 CTACTATGATTTAAACTCCT-AAGATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
531400 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
36 9 0.15
37 50 0.85
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:532172 original size:20 final size:22
Alignment explanation
Indices: 532147--532186 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
532137 AGTCGTATAT
532147 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
532167 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
532187 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:532238 original size:20 final size:21
Alignment explanation
Indices: 532213--532254 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
532203 CCCAGAATAG
532213 AGGGAATCG-TACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
532233 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
532254 A
1 A
532255 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:532316 original size:21 final size:21
Alignment explanation
Indices: 532290--532329 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
532280 CTGTTGAACA
532290 GGGGGGAATCGATACCCCCGG
1 GGGGGGAATCGATACCCCCGG
*
532311 GGGGGGAATCGGTACCCCC
1 GGGGGGAATCGATACCCCC
532330 TGGACATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.30, G:0.42, T:0.10
Consensus pattern (21 bp):
GGGGGGAATCGATACCCCCGG
Found at i:532389 original size:19 final size:19
Alignment explanation
Indices: 532365--532424 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
532355 AACCTGCAGA
532365 GGGTATCTGTACCCCCTGG
1 GGGTATCTGTACCCCCTGG
* *
532384 GGGTATCTGTACCTCTTGGGG
1 GGGTATCTGTACCCCCT--GG
* *
532405 GGGAATCTATACCCCCTGG
1 GGGTATCTGTACCCCCTGG
532424 G
1 G
532425 CAATCTTGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.55
21 15 0.45
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.27
Consensus pattern (19 bp):
GGGTATCTGTACCCCCTGG
Found at i:532545 original size:29 final size:32
Alignment explanation
Indices: 532513--532573 Score: 101
Period size: 29 Copynumber: 2.0 Consensus size: 32
532503 AAACTTTGAA
532513 TAAATTCAATT-AAGTCC-AAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAAACCATTTTG
532542 TAAATTCAATTCAAGTCCAAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAAACCATTTTG
532574 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 11 0.38
30 6 0.21
31 5 0.17
32 7 0.24
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (32 bp):
TAAATTCAATTCAAGTCCAAAAAACCATTTTG
Found at i:534739 original size:33 final size:30
Alignment explanation
Indices: 534690--534755 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 30
534680 CCTTACAAAC
534690 TCCTAGTTTTCCGGGCTAAACTAGAACCTT
1 TCCTAGTTTTCCGGGCTAAACTAGAACCTT
*
534720 TCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCTAG-TTTT-C-CGGGCTAAACTAGAACCTT
534753 TCC
1 TCC
534756 CCTTTACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 6 0.19
31 4 0.12
32 1 0.03
33 21 0.66
ACGTcount: A:0.23, C:0.29, G:0.17, T:0.32
Consensus pattern (30 bp):
TCCTAGTTTTCCGGGCTAAACTAGAACCTT
Found at i:534993 original size:20 final size:22
Alignment explanation
Indices: 534968--535007 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
534958 AGTCGTATAT
534968 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
534988 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
535008 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:535059 original size:21 final size:21
Alignment explanation
Indices: 535035--535077 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
535025 CCCAGAATAG
535035 AGGGAATC-AGTACCCCTTCAT
1 AGGGAATCGA-TACCCCTTCAT
535056 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
535077 A
1 A
535078 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:535139 original size:21 final size:21
Alignment explanation
Indices: 535113--535156 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
535103 CTGTTGAACA
*
535113 GGGGGGGAATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
535134 GGGGGGAAATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
535155 GG
1 GG
535157 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (21 bp):
GGGGGGAAATCGGTACCCCCT
Found at i:535215 original size:20 final size:20
Alignment explanation
Indices: 535190--535252 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
535180 AAAACCTGCA
535190 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
*
535210 GGGGGTATCTGTACCCCTTGG
1 GGGGGTATCTGTACCCCCT-G
* *
535231 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
535251 GG
1 GG
535253 CAATCTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:535233 original size:21 final size:21
Alignment explanation
Indices: 535190--535252 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
535180 AAAACCTGCA
535190 GGGGGTATCTGTACCCCCT-G
1 GGGGGTATCTGTACCCCCTGG
*
535210 GGGGGTATCTGTACCCCTTGG
1 GGGGGTATCTGTACCCCCTGG
* *
535231 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
535252 G
1 G
535253 CAATCTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:535374 original size:29 final size:31
Alignment explanation
Indices: 535342--535401 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
535332 AAACTTTGAA
535342 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
535371 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
535402 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:535864 original size:27 final size:28
Alignment explanation
Indices: 535811--535861 Score: 81
Period size: 25 Copynumber: 1.9 Consensus size: 28
535801 TTATTCTACT
535811 TATTTATATTATATATGTATATTTTTAA
1 TATTTATATTATATATGTATATTTTTAA
535839 TATTT-TATTAT-TAT-TATATTTTT
1 TATTTATATTATATATGTATATTTTT
535862 TTACTTTCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 9 0.39
26 3 0.13
27 6 0.26
28 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTAA
Found at i:535902 original size:12 final size:11
Alignment explanation
Indices: 535880--535920 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
535870 TCTTTCTTTT
535880 TATTATTCTTG
1 TATTATTCTTG
535891 TATTATTACTTG
1 TATTATT-CTTG
* *
535903 TATTATTTTTA
1 TATTATTCTTG
535914 TATTATT
1 TATTATT
535921 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:536140 original size:2 final size:2
Alignment explanation
Indices: 536135--536183 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
536125 ATTTTACTAT
536135 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
536177 TA TA TA T
1 TA TA TA T
536184 TTTACACAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:536528 original size:23 final size:23
Alignment explanation
Indices: 536502--536553 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
536492 TATTTGTTTA
* *
536502 TTTTTATTTTTTTTTCATT-TTCT
1 TTTTTATATATTTTT-ATTATTCT
*
536525 TTTTTATATATTTTTATTATTTT
1 TTTTTATATATTTTTATTATTCT
536548 TTTTTA
1 TTTTTA
536554 CTTACTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 3 0.12
23 22 0.88
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (23 bp):
TTTTTATATATTTTTATTATTCT
Found at i:536973 original size:37 final size:37
Alignment explanation
Indices: 536920--537024 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
536910 AATGATCGTC
536920 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
536957 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
536994 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
537025 TCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:537587 original size:21 final size:21
Alignment explanation
Indices: 537563--537603 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
537553 TCTTTGCATT
*
537563 TTATTTTTATATTACTATTAA
1 TTATTATTATATTACTATTAA
*
537584 TTATTATTATTTTACTATTA
1 TTATTATTATATTACTATTA
537604 TATTTTCCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATTATTATATTACTATTAA
Found at i:537651 original size:21 final size:21
Alignment explanation
Indices: 537626--537670 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
537616 ATTCTAATTA
537626 TTTATATATATATGTA-TATTT
1 TTTATATATATAT-TATTATTT
* *
537647 TTTATTTTTATATTATTATTT
1 TTTATATATATATTATTATTT
537668 TTT
1 TTT
537671 CCTTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTATATATATATTATTATTT
Found at i:537709 original size:12 final size:11
Alignment explanation
Indices: 537685--537714 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
537675 TCTTTTTTTT
537685 TATTATTCTTG
1 TATTATTCTTG
537696 TATTATTACTTG
1 TATTATT-CTTG
537708 TATTATT
1 TATTATT
537715 TTATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:537944 original size:2 final size:2
Alignment explanation
Indices: 537939--537995 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
537929 ATTTTACTAT
*
537939 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
537981 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
537996 TCTACACAAG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:538322 original size:10 final size:11
Alignment explanation
Indices: 538243--538322 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
538233 AATTTATATA
538243 TATTTACTTTTT
1 TATTTA-TTTTT
*
538255 TATTTATTTTA
1 TATTTATTTTT
* * *
538266 TATATATATAT
1 TATTTATTTTT
538277 TATTCGTATTTTGT
1 TATT--TATTTT-T
538291 TA-TTATTATTT
1 TATTTATT-TTT
*
538302 TGTTTATTTTT
1 TATTTATTTTT
538313 TATTTATTTT
1 TATTTATTTT
538323 CTTTTTCATT
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
11 32 0.60
12 13 0.25
13 5 0.09
14 3 0.06
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.71
Consensus pattern (11 bp):
TATTTATTTTT
Found at i:538362 original size:28 final size:27
Alignment explanation
Indices: 538293--538362 Score: 63
Period size: 28 Copynumber: 2.5 Consensus size: 27
538283 TATTTTGTTA
*
538293 TTATTATTTTGTTTATTTTTTATTTATT
1 TTATTATTTT-TTTATTTTTTATATATT
*
538321 TTCTT-TTTCATTTTCA-TTTTTATATATT
1 TTATTATTT--TTTT-ATTTTTTATATATT
538349 TTATTATTTGTTTT
1 TTATTATTT-TTTT
538363 TTACTTACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
27 3 0.09
28 26 0.76
29 5 0.15
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.76
Consensus pattern (27 bp):
TTATTATTTTTTTATTTTTTATATATT
Found at i:538789 original size:37 final size:37
Alignment explanation
Indices: 538732--538836 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
538722 AATGATCGTC
*
538732 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
538769 TTGCTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* *
538806 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
538837 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:539366 original size:34 final size:32
Alignment explanation
Indices: 539313--539382 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
539303 CCTTACAAAC
* * *
539313 TCCCTAGTTTTTCCGGGCTAAACTGGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
539345 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
539379 TCCC
1 TCCC
539383 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:539685 original size:21 final size:21
Alignment explanation
Indices: 539661--539703 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
539651 CCCAGAATAG
*
539661 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
539682 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
539703 A
1 A
539704 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:539780 original size:20 final size:19
Alignment explanation
Indices: 539740--539776 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
539730 TGTTGAAAAG
539740 GGGGGGAATCGATACCCCT
1 GGGGGGAATCGATACCCCT
*
539759 GGGGGGAATCGGTACCCC
1 GGGGGGAATCGATACCCC
539777 CTGGACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.27, G:0.41, T:0.14
Consensus pattern (19 bp):
GGGGGGAATCGATACCCCT
Found at i:539856 original size:19 final size:20
Alignment explanation
Indices: 539816--539876 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
539806 AACCTGCAGA
539816 GGGTATCTGTACCCCCTGGG
1 GGGTATCTGTACCCCCTGGG
*
539836 GGGTATCTGTACCCCTTGGGG
1 GGGTATCTGTACCCCCT-GGG
* *
539857 GGGAATCTATACCCCCTGGG
1 GGGTATCTGTACCCCCTGGG
539877 CAATCTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 19 0.53
21 17 0.47
ACGTcount: A:0.13, C:0.28, G:0.34, T:0.25
Consensus pattern (20 bp):
GGGTATCTGTACCCCCTGGG
Found at i:539859 original size:21 final size:21
Alignment explanation
Indices: 539816--539876 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
539806 AACCTGCAGA
539816 GGGTATCTGTACCCCCT-GGG
1 GGGTATCTGTACCCCCTGGGG
*
539836 GGGTATCTGTACCCCTTGGGG
1 GGGTATCTGTACCCCCTGGGG
* *
539857 GGGAATCTATACCCCCTGGG
1 GGGTATCTGTACCCCCTGGG
539877 CAATCTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.13, C:0.28, G:0.34, T:0.25
Consensus pattern (21 bp):
GGGTATCTGTACCCCCTGGGG
Found at i:539998 original size:29 final size:31
Alignment explanation
Indices: 539966--540025 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
539956 AAACTTTGAA
539966 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
539995 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
540026 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:542234 original size:34 final size:32
Alignment explanation
Indices: 542181--542250 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
542171 CCTTACAAAC
*
542181 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
542213 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
542247 TCCC
1 TCCC
542251 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:542487 original size:20 final size:22
Alignment explanation
Indices: 542462--542501 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
542452 AGTCGTATAT
542462 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
542482 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
542502 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:542568 original size:21 final size:22
Alignment explanation
Indices: 542529--542572 Score: 65
Period size: 21 Copynumber: 2.0 Consensus size: 22
542519 CCCAAAATAG
542529 AGGGAATCAGTACCCCCTTCAT
1 AGGGAATCAGTACCCCCTTCAT
542551 AGGGAATC-GATA-CCCCTTCAT
1 AGGGAATCAG-TACCCCCTTCAT
542572 A
1 A
542573 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.30, C:0.30, G:0.18, T:0.23
Consensus pattern (22 bp):
AGGGAATCAGTACCCCCTTCAT
Found at i:542634 original size:21 final size:21
Alignment explanation
Indices: 542608--542651 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
542598 CTGTTGAACA
*
542608 GGGGGGGAATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
542629 GGGGGGAAATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
542650 GG
1 GG
542652 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (21 bp):
GGGGGGAAATCGGTACCCCCT
Found at i:542710 original size:20 final size:20
Alignment explanation
Indices: 542685--542747 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
542675 AAAACCTGCA
542685 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
*
542705 GGGGGTATCTGTACCCCTTGG
1 GGGGGTATCTGTACCCCCT-G
* *
542726 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
542746 GG
1 GG
542748 CAATCTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:542728 original size:21 final size:21
Alignment explanation
Indices: 542685--542747 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
542675 AAAACCTGCA
542685 GGGGGTATCTGTACCCCCT-G
1 GGGGGTATCTGTACCCCCTGG
*
542705 GGGGGTATCTGTACCCCTTGG
1 GGGGGTATCTGTACCCCCTGG
* *
542726 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
542747 G
1 G
542748 CAATCTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:542869 original size:29 final size:31
Alignment explanation
Indices: 542837--542896 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
542827 AAACTTTGAA
542837 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
542866 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
542897 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:543388 original size:12 final size:11
Alignment explanation
Indices: 543366--543406 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
543356 TCTTTCTTTT
543366 TATTATTCTTG
1 TATTATTCTTG
543377 TATTATTACTTG
1 TATTATT-CTTG
* *
543389 TATTATTTTTA
1 TATTATTCTTG
543400 TATTATT
1 TATTATT
543407 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:543625 original size:2 final size:2
Alignment explanation
Indices: 543620--543652 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
543610 ATTTTACTAT
543620 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
543653 TTACACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:544449 original size:37 final size:37
Alignment explanation
Indices: 544396--544500 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
544386 AATGATCGTC
544396 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
544433 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
544470 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
544501 TCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:545072 original size:21 final size:21
Alignment explanation
Indices: 545014--545082 Score: 79
Period size: 21 Copynumber: 3.3 Consensus size: 21
545004 ACCCAATATA
* *
545014 TATATTTATT-TTCTTTGCTTT
1 TATATTTATTATT-TTTACTAT
* *
545035 TTTATTT-TTATTATTACTAT
1 TATATTTATTATTTTTACTAT
545055 TATATTTATTATTTTTACTAT
1 TATATTTATTATTTTTACTAT
545076 TATATTT
1 TATATTT
545083 TCCTTTTATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 13 0.32
21 27 0.68
ACGTcount: A:0.23, C:0.06, G:0.01, T:0.70
Consensus pattern (21 bp):
TATATTTATTATTTTTACTAT
Found at i:545183 original size:12 final size:11
Alignment explanation
Indices: 545159--545188 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
545149 TTTCTTTTTT
545159 TATTATTCTTG
1 TATTATTCTTG
545170 TATTATTACTTG
1 TATTATT-CTTG
545182 TATTATT
1 TATTATT
545189 TATATTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.07, G:0.07, T:0.63
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:545374 original size:30 final size:28
Alignment explanation
Indices: 545334--545392 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 28
545324 TATATTTTTC
545334 TATTAATTTTCTATATTTTATATT-ATATTA
1 TATTAATTTTCT-T-TTTT-TATTGATATTA
*
545364 TATTTATTTTCTTTTTTTATTGATATTA
1 TATTAATTTTCTTTTTTTATTGATATTA
545392 T
1 T
545393 TGTTGTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 4 0.15
28 11 0.41
29 1 0.04
30 11 0.41
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (28 bp):
TATTAATTTTCTTTTTTTATTGATATTA
Found at i:545423 original size:2 final size:2
Alignment explanation
Indices: 545418--545460 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
545408 ATTTTACTAT
545418 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
545460 T
1 T
545461 TCTACACAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:546259 original size:37 final size:37
Alignment explanation
Indices: 546202--546306 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
546192 AATGATCGTC
*
546202 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
546239 TTGCTATGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
* *
546276 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTATGATTCAAACTCCTAAAAATAGGAT
546307 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTATGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:546837 original size:34 final size:32
Alignment explanation
Indices: 546784--546853 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
546774 CCTTACAAAC
* * *
546784 TCCCTAGTTTTTCCGGGCTAAACTGGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
546816 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
546850 TCCC
1 TCCC
546854 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 5 0.16
34 20 0.62
ACGTcount: A:0.21, C:0.30, G:0.17, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:547093 original size:20 final size:22
Alignment explanation
Indices: 547068--547107 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
547058 AGTCGTATAT
547068 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
547088 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
547108 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:547159 original size:21 final size:21
Alignment explanation
Indices: 547135--547177 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
547125 CCCAGAATAG
*
547135 AGGGAATCGGTACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
547156 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
547177 A
1 A
547178 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:547239 original size:21 final size:21
Alignment explanation
Indices: 547213--547256 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
547203 CTGTTGAAAA
547213 GGGGGGGAATCGATACCCCCT
1 GGGGGGGAATCGATACCCCCT
*
547234 GGGGGGGAATCGGTACCCCCT
1 GGGGGGGAATCGATACCCCCT
547255 GG
1 GG
547257 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.27, G:0.43, T:0.14
Consensus pattern (21 bp):
GGGGGGGAATCGATACCCCCT
Found at i:547332 original size:19 final size:20
Alignment explanation
Indices: 547292--547334 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
547282 AACCTGCAGA
547292 GGGTATATGTACCCCCTGGG
1 GGGTATATGTACCCCCTGGG
* *
547312 GGGTATCTGTACCCCTTGGG
1 GGGTATATGTACCCCCTGGG
547332 GGG
1 GGG
547335 GAATCTATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.12, C:0.23, G:0.40, T:0.26
Consensus pattern (20 bp):
GGGTATATGTACCCCCTGGG
Found at i:547335 original size:21 final size:21
Alignment explanation
Indices: 547292--547352 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
547282 AACCTGCAGA
*
547292 GGGTATATGTACCCCCT-GGG
1 GGGTATCTGTACCCCCTGGGG
*
547312 GGGTATCTGTACCCCTTGGGG
1 GGGTATCTGTACCCCCTGGGG
* *
547333 GGGAATCTATACCCCCTGGG
1 GGGTATCTGTACCCCCTGGG
547353 CAATCTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
20 15 0.43
21 20 0.57
ACGTcount: A:0.15, C:0.26, G:0.34, T:0.25
Consensus pattern (21 bp):
GGGTATCTGTACCCCCTGGGG
Found at i:547474 original size:29 final size:31
Alignment explanation
Indices: 547442--547501 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
547432 AAACTTTGAA
547442 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
547471 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
547502 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:549966 original size:20 final size:22
Alignment explanation
Indices: 549941--549980 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
549931 AGTCGTATAT
549941 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
549961 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
549981 TATACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:550032 original size:21 final size:21
Alignment explanation
Indices: 550008--550050 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
549998 CCCAGAATAG
550008 AGGGAATC-AGTACCCCTTCAT
1 AGGGAATCGA-TACCCCTTCAT
550029 AGGGAATCGATACCCCTTCAT
1 AGGGAATCGATACCCCTTCAT
550050 A
1 A
550051 ATATTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (21 bp):
AGGGAATCGATACCCCTTCAT
Found at i:550111 original size:20 final size:21
Alignment explanation
Indices: 550086--550128 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
550076 CTGTTGAACA
550086 GGGGGG-AATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
550106 GGGGGGAAATCGGTACCCCCT
1 GGGGGGAAATCGGTACCCCCT
550127 GG
1 GG
550129 ACATTCTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.16, C:0.28, G:0.42, T:0.14
Consensus pattern (21 bp):
GGGGGGAAATCGGTACCCCCT
Found at i:550187 original size:20 final size:20
Alignment explanation
Indices: 550162--550224 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
550152 AAAACCTGCA
550162 GGGGGTATCTGTACCCCCTG
1 GGGGGTATCTGTACCCCCTG
*
550182 GGGGGTATCTGTACCCCTTGG
1 GGGGGTATCTGTACCCCCT-G
* *
550203 GGGGGAATCTATACCCCCTG
1 GGGGGTATCTGTACCCCCTG
550223 GG
1 GG
550225 CAATCTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
20 21 0.55
21 17 0.45
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGTATCTGTACCCCCTG
Found at i:550205 original size:21 final size:21
Alignment explanation
Indices: 550162--550224 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
550152 AAAACCTGCA
550162 GGGGGTATCTGTACCCCCT-G
1 GGGGGTATCTGTACCCCCTGG
*
550182 GGGGGTATCTGTACCCCTTGG
1 GGGGGTATCTGTACCCCCTGG
* *
550203 GGGGGAATCTATACCCCCTGG
1 GGGGGTATCTGTACCCCCTGG
550224 G
1 G
550225 CAATCTTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.13, C:0.27, G:0.37, T:0.24
Consensus pattern (21 bp):
GGGGGTATCTGTACCCCCTGG
Found at i:550346 original size:29 final size:31
Alignment explanation
Indices: 550314--550373 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
550304 AAACTTTGAA
550314 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
550343 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
550374 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:550814 original size:22 final size:23
Alignment explanation
Indices: 550788--550831 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
550778 CTACTTATTT
550788 ATATTATA-TATGTA-TATTTTTA
1 ATATTATATTAT-TATTATTTTTA
*
550810 ATATTTTATTATTATTATTTTT
1 ATATTATATTATTATTATTTTT
550832 TTACTTTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (23 bp):
ATATTATATTATTATTATTTTTA
Found at i:550866 original size:11 final size:9
Alignment explanation
Indices: 550815--550878 Score: 51
Period size: 9 Copynumber: 6.8 Consensus size: 9
550805 TTTTAATATT
*
550815 TTATTATTA
1 TTATTTTTA
550824 TTATTTTT-
1 TTATTTTTA
550832 TTACTTTCTCT-
1 TTA-TTT-T-TA
*
550843 TTCTTTTTA
1 TTATTTTTA
550852 TTATTCTTGTA
1 TTATT-TT-TA
550863 TTATTTTTA
1 TTATTTTTA
550872 TTATTTT
1 TTATTTT
550879 ATTTTGTTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.09
9 24 0.52
10 8 0.17
11 10 0.22
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (9 bp):
TTATTTTTA
Found at i:551161 original size:2 final size:2
Alignment explanation
Indices: 551097--551142 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
551087 ATTTTACTAT
551097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
551138 TA TA T
1 TA TA T
551143 TTACACAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:551909 original size:37 final size:38
Alignment explanation
Indices: 551868--551970 Score: 136
Period size: 37 Copynumber: 2.7 Consensus size: 38
551858 GATCGTCCTA
* **
551868 CTAGGATTCAAACTCCTAAAAATATGATAGAATT-TTG
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
*
551905 CTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAC
1 CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
* * *
551943 CTATGATTTAAACTCCTAAAGATAGGAT
1 CTAGGATTCAAACTCCTAAAAATAGGAT
551971 CACAAGCACT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
37 32 0.55
38 26 0.45
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (38 bp):
CTAGGATTCAAACTCCTAAAAATAGGATAGAATTCTAC
Found at i:552543 original size:11 final size:11
Alignment explanation
Indices: 552527--552563 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
552517 TTTGCATTTC
552527 TATATTACTAT
1 TATATTACTAT
552538 TATATT--TAT
1 TATATTACTAT
*
552547 TATTTTACTAT
1 TATATTACTAT
552558 TATATT
1 TATATT
552564 TTCCTTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.36
11 14 0.64
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (11 bp):
TATATTACTAT
Found at i:552615 original size:13 final size:13
Alignment explanation
Indices: 552547--552615 Score: 50
Period size: 13 Copynumber: 5.1 Consensus size: 13
552537 TTATATTTAT
*
552547 TATTTTACTATTA
1 TATTTTATTATTA
*
552560 TATTTTCCTTATTA
1 TATTTT-ATTATTA
*
552574 TACTTATATTA-TA
1 TA-TTTTATTATTA
* *
552587 TATGTATATTTTTTA
1 TAT-TTTA-TTATTA
552602 TATTTTATTATTA
1 TATTTTATTATTA
552615 T
1 T
552616 TATATTTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
12 1 0.02
13 20 0.45
14 15 0.34
15 8 0.18
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (13 bp):
TATTTTATTATTA
Found at i:552664 original size:12 final size:11
Alignment explanation
Indices: 552642--552681 Score: 55
Period size: 12 Copynumber: 3.6 Consensus size: 11
552632 TCTTTCTTTT
552642 TATTATTCTTG
1 TATTATTCTTG
552653 TATTATTACTTG
1 TATTATT-CTTG
*
552665 TATTATT-TTA
1 TATTATTCTTG
552675 TATTATT
1 TATTATT
552682 ATTTTGTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 9 0.33
11 7 0.26
12 11 0.41
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:552681 original size:22 final size:23
Alignment explanation
Indices: 552642--552701 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
552632 TCTTTCTTTT
*
552642 TATTATTCTTGTATTATTA-CTTG
1 TATTATT-TTATATTATTATCTTG
*
552665 TATTATTTTATATTATTATTTTG
1 TATTATTTTATATTATTATCTTG
*
552688 TATATATATTATAT
1 TAT-TATTTTATAT
552702 ATGCGTATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.31
23 13 0.41
24 9 0.28
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.63
Consensus pattern (23 bp):
TATTATTTTATATTATTATCTTG
Found at i:552833 original size:21 final size:20
Alignment explanation
Indices: 552795--552842 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
552785 ATATTATACA
552795 TATATTTTCTATTAATTT-T
1 TATATTTTCTATTAATTTAT
552814 CTATATTTT-TATTATCATTTAT
1 -TATATTTTCTATTA--ATTTAT
552836 TATATTT
1 TATATTT
552843 ATTTTCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.20
20 8 0.32
21 11 0.44
22 1 0.04
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (20 bp):
TATATTTTCTATTAATTTAT
Found at i:552901 original size:2 final size:2
Alignment explanation
Indices: 552894--552932 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
552884 TACTATTATT
*
552894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
552933 TCTAACAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:553711 original size:37 final size:37
Alignment explanation
Indices: 553658--553762 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
553648 AATGATCGTC
553658 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
553695 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
553732 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
553763 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:554326 original size:20 final size:20
Alignment explanation
Indices: 554303--554342 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
554293 ATTTTCTTTG
*
554303 TATTCTATTATTT-CTATTAT
1 TATTATATT-TTTACTATTAT
554323 TATTATATTTTTACTATTAT
1 TATTATATTTTTACTATTAT
554343 ATTTTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.17
20 15 0.83
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
TATTATATTTTTACTATTAT
Found at i:554414 original size:27 final size:28
Alignment explanation
Indices: 554362--554413 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
554352 TTATTCTACT
554362 TATTTATATTATATATGTATATTTTTTA
1 TATTTATATTATATATGTATATTTTTTA
554390 TATTT-TATTAT-TAT-TATATTTTTT
1 TATTTATATTATATATGTATATTTTTT
554414 TACTTTCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 10 0.42
26 3 0.12
27 6 0.25
28 5 0.21
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (28 bp):
TATTTATATTATATATGTATATTTTTTA
Found at i:554453 original size:12 final size:11
Alignment explanation
Indices: 554431--554471 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
554421 TCTTTCTTTT
554431 TATTATTCTTG
1 TATTATTCTTG
554442 TATTATTACTTG
1 TATTATT-CTTG
* *
554454 TATTATTTTTA
1 TATTATTCTTG
554465 TATTATT
1 TATTATT
554472 TATTTTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:555012 original size:22 final size:21
Alignment explanation
Indices: 554978--555019 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
554968 TTATTCGTAC
554978 TTTGTATTATTATTTTGTTTA
1 TTTGTATTATTATTTTGTTTA
*
554999 TTTGTTTTATTTATTTTGTTT
1 TTTGTATTA-TTATTTTGTTT
555020 TTCATTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.14, C:0.00, G:0.10, T:0.76
Consensus pattern (21 bp):
TTTGTATTATTATTTTGTTTA
Found at i:555470 original size:37 final size:37
Alignment explanation
Indices: 555426--555521 Score: 138
Period size: 37 Copynumber: 2.6 Consensus size: 37
555416 ATAATCGTCC
*
555426 TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTA
* * *
555463 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTA
* *
555500 TACTATGATTTAAACTCCTAAA
1 TACTAGGATTCAAACTCCTAAA
555522 GATATGATCC
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAAGATAGAATTA
Found at i:556164 original size:24 final size:22
Alignment explanation
Indices: 556137--556188 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 22
556127 TTTATTCTAC
556137 TTATTTATATTATATATGTATATT
1 TTATTTATATTAT-TAT-TATATT
556161 TTATATT-TATTATTATTATATT
1 TTAT-TTATATTATTATTATATT
556183 TT-TTTA
1 TTATTTA
556189 CTTTCTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.08
21 1 0.04
22 8 0.31
23 3 0.12
24 10 0.38
25 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (22 bp):
TTATTTATATTATTATTATATT
Found at i:556179 original size:15 final size:14
Alignment explanation
Indices: 556138--556183 Score: 60
Period size: 13 Copynumber: 3.4 Consensus size: 14
556128 TTATTCTACT
556138 TATTTATATTA-TA
1 TATTTATATTATTA
*
556151 TATGTATATT-TTA
1 TATTTATATTATTA
556164 TATTTATTATTATTA
1 TATTTA-TATTATTA
556179 TATTT
1 TATTT
556184 TTTTACTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 16 0.57
14 4 0.14
15 8 0.29
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TATTTATATTATTA
Found at i:556226 original size:12 final size:11
Alignment explanation
Indices: 556204--556244 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
556194 TCTTTCTTTT
556204 TATTATTCTTG
1 TATTATTCTTG
556215 TATTATTACTTG
1 TATTATT-CTTG
* *
556227 TATTATTTTTA
1 TATTATTCTTG
556238 TATTATT
1 TATTATT
556245 TATTTTGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:556837 original size:30 final size:30
Alignment explanation
Indices: 556764--556837 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
556754 TACTTTGTTA
*
556764 TTATTATTT-TGTTTATTTGTTTTATTTATT
1 TTATTATTTAT-TTTATTTGTTTTATATATT
* *
556794 TTCTT-TTTCATTTTCTTT-TTTATATATATT
1 TTATTATTT-ATTTTATTTGTTT-TATATATT
556824 TTATTATTTATTTT
1 TTATTATTTATTTT
556838 TTTACTTACT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
29 6 0.17
30 26 0.72
31 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.76
Consensus pattern (30 bp):
TTATTATTTATTTTATTTGTTTTATATATT
Found at i:557263 original size:37 final size:37
Alignment explanation
Indices: 557210--557306 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
557200 AATGATCGTC
557210 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
557247 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
557284 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
557307 GATAAGATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:557896 original size:52 final size:49
Alignment explanation
Indices: 557832--557939 Score: 132
Period size: 52 Copynumber: 2.1 Consensus size: 49
557822 TACCCATATA
*
557832 TATATTTATTTT-CTTTGCATTTTA-TTATTATATTATATTAT-TATTATTTT
1 TATATTTATTTTCCTTT--ATTCTACTTATTATATTATA-TATGTA-TATTTT
557882 TACTATTATATTTTCCTTTATTCTACTTATTATATTATATATGTATATTTT
1 TA-TATT-TATTTTCCTTTATTCTACTTATTATATTATATATGTATATTTT
557933 TATATTT
1 TATATTT
557940 TATTATTATA
Statistics
Matches: 52, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
49 1 0.02
50 6 0.12
51 20 0.38
52 21 0.40
53 4 0.08
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (49 bp):
TATATTTATTTTCCTTTATTCTACTTATTATATTATATATGTATATTTT
Found at i:557937 original size:21 final size:21
Alignment explanation
Indices: 557911--557954 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
557901 ATTCTACTTA
557911 TTATATTATA-TATGTATATTT
1 TTATATTATATTAT-TATATTT
*
557932 TTATATTTTATTATTATATTT
1 TTATATTATATTATTATATTT
557953 TT
1 TT
557955 TTACTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TTATATTATATTATTATATTT
Found at i:557996 original size:12 final size:11
Alignment explanation
Indices: 557966--558001 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
557956 TACTTTCTCT
*
557966 TTCTTTTATTA
1 TTCTTGTATTA
557977 TTCTTGTATTA
1 TTCTTGTATTA
557988 TTACTTGTATTA
1 TT-CTTGTATTA
558000 TT
1 TT
558002 TTATATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.19, C:0.08, G:0.06, T:0.67
Consensus pattern (11 bp):
TTCTTGTATTA
Found at i:558019 original size:2 final size:2
Alignment explanation
Indices: 558014--558040 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
558004 ATATATTTTT
558014 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
558041 GCGTATGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:558137 original size:19 final size:19
Alignment explanation
Indices: 558115--558182 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 19
558105 TTTTAAGTGC
558115 TATATTTTATAATATTATA
1 TATATTTTATAATATTATA
* *
558134 TATATTTTTCTATTAATTTTCTA
1 TATA--TTT-TA-TAATATTATA
*
558157 TAT-TTTTATTATATTATA
1 TATATTTTATAATATTATA
558175 TTATATTT
1 -TATATTT
558183 CTTTTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
18 7 0.18
19 9 0.24
20 6 0.16
21 3 0.08
22 2 0.05
23 11 0.29
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATTTTATAATATTATA
Found at i:558142 original size:41 final size:44
Alignment explanation
Indices: 558097--558191 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 44
558087 AAATATTTGG
558097 TTTTTTTATTTTAA-GTGCTATA-TTTTATAATATTATA-TATA
1 TTTTTTTATTTTAATGTGCTATATTTTTATAATATTATATTATA
* * * *
558138 TTTTTCTA--TTAATTTTCTATATTTTTATTATATTATATTATA
1 TTTTTTTATTTTAATGTGCTATATTTTTATAATATTATATTATA
*
558180 TTTCTTT-TTTTA
1 TTTTTTTATTTTA
558192 TTGATATTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
39 4 0.09
40 6 0.14
41 21 0.49
42 9 0.21
43 3 0.07
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.66
Consensus pattern (44 bp):
TTTTTTTATTTTAATGTGCTATATTTTTATAATATTATATTATA
Found at i:558150 original size:23 final size:23
Alignment explanation
Indices: 558124--558201 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 23
558114 CTATATTTTA
*
558124 TAATATTATATATATTTTTCTAT
1 TAATATTATATATATTTTTATAT
* * *
558147 TAATTTTCTATATTTTTATTATAT
1 TAATATTATATATATTT-TTATAT
* * *
558171 T-ATATTATATTTCTTTTTTTAT
1 TAATATTATATATATTTTTATAT
*
558193 TGATATTAT
1 TAATATTAT
558202 TGTTGTTATA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
22 6 0.14
23 32 0.73
24 6 0.14
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (23 bp):
TAATATTATATATATTTTTATAT
Found at i:558179 original size:21 final size:21
Alignment explanation
Indices: 558115--558201 Score: 67
Period size: 21 Copynumber: 4.1 Consensus size: 21
558105 TTTTAAGTGC
*
558115 TATA-TTTTATAATATTATA-
1 TATATTTTTATTATATTATAT
558134 TATATTTTTCTATTA-ATT-T-T
1 TATA-TTTT-TATTATATTATAT
558154 CTATATTTTTATTATATTATAT
1 -TATATTTTTATTATATTATAT
* *
558176 TATATTTCTTTTTTTATTGATAT
1 TATATTT-TTATTATATT-ATAT
558199 TAT
1 TAT
558202 TGTTGTTATA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
19 9 0.16
20 8 0.15
21 18 0.33
22 13 0.24
23 7 0.13
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (21 bp):
TATATTTTTATTATATTATAT
Found at i:558227 original size:2 final size:2
Alignment explanation
Indices: 558222--558254 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
558212 TACATTTTAC
558222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
558255 TCTATACAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:558608 original size:25 final size:26
Alignment explanation
Indices: 558580--558638 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 26
558570 TTTCTTTTTC
558580 ATTTTCTTTTTTA-TATA-TATTTTAT
1 ATTTTCTTTTTTACT-TACTATTTTAT
*
558605 A-TTTGTTTTTTACTTACTATTTTAT
1 ATTTTCTTTTTTACTTACTATTTTAT
* *
558630 CTTTGCTTT
1 ATTTTCTTT
558639 CTTCATTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
24 12 0.44
25 10 0.37
26 5 0.19
ACGTcount: A:0.19, C:0.08, G:0.03, T:0.69
Consensus pattern (26 bp):
ATTTTCTTTTTTACTTACTATTTTAT
Found at i:559032 original size:37 final size:37
Alignment explanation
Indices: 558979--559075 Score: 149
Period size: 37 Copynumber: 2.6 Consensus size: 37
558969 AATGATCGTC
558979 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
559016 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
559053 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
559076 GATAAGATCC
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:559715 original size:21 final size:22
Alignment explanation
Indices: 559690--559735 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
559680 ATTCTACTTA
559690 TTTATATTATA-TATGTA-TATT
1 TTTATATTATATTAT-TATTATT
*
559711 TTTATATTTTATTATTATTATT
1 TTTATATTATATTATTATTATT
559733 TTT
1 TTT
559736 TTTACTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATATTATATTATTATTATT
Found at i:559795 original size:11 final size:11
Alignment explanation
Indices: 559748--559794 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
559738 TACTTTCTCT
*
559748 TTCTTTTATTA
1 TTCTTGTATTA
559759 TTCTTGTATTA
1 TTCTTGTATTA
559770 TTACTTGTATTA
1 TT-CTTGTATTA
* *
559782 TTTTTATATTA
1 TTCTTGTATTA
559793 TT
1 TT
559795 TATTTGTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
11 21 0.66
12 11 0.34
ACGTcount: A:0.21, C:0.06, G:0.04, T:0.68
Consensus pattern (11 bp):
TTCTTGTATTA
Found at i:560008 original size:2 final size:2
Alignment explanation
Indices: 560003--560043 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
559993 ATTTTACTAT
560003 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
560044 TCTACACAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:560285 original size:18 final size:17
Alignment explanation
Indices: 560258--560291 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
560248 GTCATTTAAT
560258 TTATTAATTTATATTTAC
1 TTATTAATTTAT-TTTAC
*
560276 TTATTTATTTATTTTA
1 TTATTAATTTATTTTA
560292 TATATATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTAATTTATTTTAC
Found at i:560386 original size:26 final size:26
Alignment explanation
Indices: 560359--560407 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
560349 TTCTTTTCAT
560359 TTTCTTTTTTA-TATA-TATTTTATTA
1 TTTCTTTTTTACT-TACTATTTTATTA
*
560384 TTTGTTTTTTACTTACTATTTTAT
1 TTTCTTTTTTACTTACTATTTTAT
560408 CTTTGCTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.71
Consensus pattern (26 bp):
TTTCTTTTTTACTTACTATTTTATTA
Found at i:561573 original size:20 final size:20
Alignment explanation
Indices: 561533--561573 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
561523 ACCTTACTAA
*
561533 CTCTTTTCATTTTTTTTCAT
1 CTCTTTTCATTTTTTTCCAT
561553 CTCTTTT-ATTTTATTTCCAT
1 CTCTTTTCATTTT-TTTCCAT
561573 C
1 C
561574 ATCTACATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (20 bp):
CTCTTTTCATTTTTTTCCAT
Found at i:562703 original size:21 final size:21
Alignment explanation
Indices: 562677--562720 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
562667 ATTTCTGGGA
* *
562677 AAGGGGAATCGGTACCCATTC
1 AAGGGGAACCGATACCCATTC
*
562698 AAGGGGAACCGATACCCCTTC
1 AAGGGGAACCGATACCCATTC
562719 AA
1 AA
562721 ACGAACAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (21 bp):
AAGGGGAACCGATACCCATTC
Found at i:563318 original size:18 final size:18
Alignment explanation
Indices: 563295--563329 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
563285 TTAGGAGATT
563295 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
563313 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
563330 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:563570 original size:2 final size:2
Alignment explanation
Indices: 563563--563614 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
563553 AATCTTGAGG
*
563563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
563605 AT AT AT AT AT
1 AT AT AT AT AT
563615 GAAATGAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:564416 original size:23 final size:23
Alignment explanation
Indices: 564372--564416 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
564362 ATCATTATAT
*
564372 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
564395 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
564417 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:567495 original size:20 final size:20
Alignment explanation
Indices: 567470--567512 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
567460 GATTTCTGGG
* *
567470 CAAGGGAATCGGTACCCATT
1 CAAGGGAACCGATACCCATT
*
567490 CAAGGGAACCGATACCCCTT
1 CAAGGGAACCGATACCCATT
567510 CAA
1 CAA
567513 ACGAACAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.30, G:0.21, T:0.16
Consensus pattern (20 bp):
CAAGGGAACCGATACCCATT
Found at i:568352 original size:2 final size:2
Alignment explanation
Indices: 568345--568370 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
568335 AATCTTGAGG
568345 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
568371 GAAATGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:569171 original size:23 final size:23
Alignment explanation
Indices: 569127--569171 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
569117 ATCATTATAT
*
569127 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
569150 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
569172 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:571202 original size:21 final size:21
Alignment explanation
Indices: 571176--571220 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
571166 GATTTCTGGG
* *
571176 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
571197 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
571218 CAA
1 CAA
571221 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:571833 original size:18 final size:18
Alignment explanation
Indices: 571801--571835 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
571791 TTAGGAGATT
*
571801 TGAACATAGATGATAAGA
1 TGAACATAGAAGATAAGA
*
571819 TGAACATATAAGATAAG
1 TGAACATAGAAGATAAG
571836 CTAGATGGGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (18 bp):
TGAACATAGAAGATAAGA
Found at i:572074 original size:2 final size:2
Alignment explanation
Indices: 572067--572108 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
572057 AATCTTGAGG
*
572067 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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
572109 GAAATGAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:572911 original size:23 final size:23
Alignment explanation
Indices: 572867--572911 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
572857 ATCATTATAT
*
572867 GGCACTACAGTGCAATTCTACGG
1 GGCACTACAGTGCAATTATACGG
* * *
572890 GGCACTTCGGTGCATTTATACG
1 GGCACTACAGTGCAATTATACG
572912 AGCCAAAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACAGTGCAATTATACGG
Found at i:573287 original size:12 final size:12
Alignment explanation
Indices: 573270--573355 Score: 57
Period size: 12 Copynumber: 6.8 Consensus size: 12
573260 TTTTTATTAC
573270 TATTATATTTAT
1 TATTATATTTAT
* *
573282 TATTATTTTTAC
1 TATTATATTTAT
573294 TATTATATTT-T
1 TATTATATTTAT
* *
573305 CCTTTTATACTTATT
1 --TATTATATTTA-T
*
573320 TATATATATATAT
1 TAT-TATATTTAT
* *
573333 TTTTTTATTTTAT
1 TATTATA-TTTAT
573346 TATTATATTT
1 TATTATATTT
573356 TTTTACTTTC
Statistics
Matches: 54, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
12 25 0.46
13 22 0.41
14 6 0.11
15 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATATTTAT
Found at i:573354 original size:21 final size:23
Alignment explanation
Indices: 573318--573360 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
573308 TTTATACTTA
573318 TTTATATATATATATTTTTTTAT
1 TTTATATATATATATTTTTTTAT
573341 TTTAT-TAT-TATATTTTTTTA
1 TTTATATATATATATTTTTTTA
573361 CTTTCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTATATATATATATTTTTTTAT
Found at i:573399 original size:12 final size:11
Alignment explanation
Indices: 573369--573413 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
573359 TACTTTCTCT
*
573369 TTCTTTTATTA
1 TTCTTGTATTA
573380 TTCTTGTATTA
1 TTCTTGTATTA
573391 TTACTTGTATTA
1 TT-CTTGTATTA
573403 TT-TT-TATTA
1 TTCTTGTATTA
573412 TT
1 TT
573414 TATTTTCCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
9 7 0.22
10 2 0.06
11 12 0.38
12 11 0.34
ACGTcount: A:0.20, C:0.07, G:0.04, T:0.69
Consensus pattern (11 bp):
TTCTTGTATTA
Found at i:574016 original size:30 final size:30
Alignment explanation
Indices: 573943--574016 Score: 73
Period size: 30 Copynumber: 2.5 Consensus size: 30
573933 TACTTTGTTA
*
573943 TTATTATTT-TGTTTATTTGTTTTATTTATT
1 TTATTATTTAT-TTTATTTGTTTTATATATT
* *
573973 TTCTT-TTTCATTTTCTTT-TTTATATATATT
1 TTATTATTT-ATTTTATTTGTTT-TATATATT
574003 TTATTATTTATTTT
1 TTATTATTTATTTT
574017 TTTACTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
29 6 0.17
30 26 0.72
31 4 0.11
ACGTcount: A:0.18, C:0.04, G:0.03, T:0.76
Consensus pattern (30 bp):
TTATTATTTATTTTATTTGTTTTATATATT
Found at i:574481 original size:37 final size:36
Alignment explanation
Indices: 574389--574482 Score: 120
Period size: 37 Copynumber: 2.6 Consensus size: 36
574379 AATGATCGTC
574389 CTACTAGGATTC-AACTCCT-AAAATAGGATGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATGAATT
* * *
574423 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT-GAATT
* *
574460 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
574483 GATAAGATCC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
34 10 0.20
35 7 0.14
36 10 0.20
37 23 0.46
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATGAATT
Found at i:575181 original size:12 final size:11
Alignment explanation
Indices: 575159--575199 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
575149 TCTTTCTTTT
575159 TATTATTCTTG
1 TATTATTCTTG
575170 TATTATTACTTG
1 TATTATT-CTTG
* *
575182 TATTATTTTTA
1 TATTATTCTTG
575193 TATTATT
1 TATTATT
575200 TATTTGCTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:575425 original size:2 final size:2
Alignment explanation
Indices: 575420--575454 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
575410 ATTTTACTAT
575420 TA TA TA TA TA TA TA TA TA TA TA TA 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
575455 TCTATACAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:576237 original size:37 final size:37
Alignment explanation
Indices: 576184--576280 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
576174 AATGATCGTC
576184 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * * * *
576221 TTGCTAGGATTCAAACTCTTAAAAATATGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* *
576258 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
576281 GATAAGATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:577016 original size:2 final size:2
Alignment explanation
Indices: 577009--577075 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
576999 TTTATTTTGT
577009 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
*
577051 TA TA TA GA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
577076 GCGTATGTAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:577210 original size:21 final size:20
Alignment explanation
Indices: 577159--577213 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
577149 ATATTATAAT
577159 ATTATCATATATTTTCTATTA
1 ATTAT-ATATATTTTCTATTA
* *
577180 ATTTTCTATATTTT-TATTA
1 ATTATATATATTTTCTATTA
577199 TCATTATATATATTT
1 --ATTATATATATTT
577214 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.18
20 8 0.29
21 15 0.54
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTATATATATTTTCTATTA
Done.