Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001034.1 Hibiscus syriacus cultivar Beakdansim tig00002056_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: 94551
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:4396 original size:81 final size:80
Alignment explanation
Indices: 4010--5006 Score: 900
Period size: 81 Copynumber: 12.2 Consensus size: 80
4000 ATTTGTCAAT
* *
4010 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCTAAGGCACATCATTTGCAGCATATCTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
4075 AGAAGGGTTATCTGC
66 AGAAGGGTTATCTGC
* * * * * * * *
4090 CAAAGACC-CCTGAGTTTGATTACACTCAGCTTCG-GGGCACATCATTTACAGCATAACTCAAGG
1 CAAAGACCTTC-GAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTTGCAGCATAACTTAAGT
* *
4153 CTAGAAGGGTTATATGTCAC
64 CGAGAAGGGTTATCTG---C
* * * *
4173 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGC--AACTTAAGTCT
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
* *
4236 ATAAGGGTTGTCTGCC
66 AGAAGGGTTATCTG-C
* * * * *
4252 AACAAAAGACATTTGAGTTCTACTACGCTCAGCTC-AACGGCACATCATTTGCAACATAGCTTAA
1 --C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCGAA-GGCACATCATTTGCAGCATAACTTAA
* *
4316 GTCGAGAAGGGCTATATGC
62 GTCGAGAAGGGTTATCTGC
** * * * * *
4335 CAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACACCATTTGCAGCATAACTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTTGCAGCATAACTTAAGTC
4400 GAGAAGGGTTATCTGC
65 GAGAAGGGTTATCTGC
* * *
4416 CAATAAAAGACCTTTGAGTTCGACTACGCTCAGCTC-AACGACACATCATTTGCAGCATAGCTTA
1 C----AAAGACCTTCGAGTTCGACTACGCTCAGCTCGAA-GGCACATCATTTGCAGCATAACTTA
* *
4480 AGTCGAGAATGGCTATCTGC
61 AGTCGAGAAGGGTTATCTGC
** * * * * * *
4500 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCG-AGAGCACATTATTTACAGCATAACTCAAGG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAG-GCACATCATTTGCAGCATAACTTAAGT
*
4564 CTAGAAGGGTTATCTATGAC
64 CGAGAAGGGTTATC--TG-C
* * * * * *
4584 CAAAAGACCTTTGAGTTCGACTACGTTCAGCTCTAAGGCACATCATTTACAGTATAGCTTAAGTC
1 C-AAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTC
*
4649 GAGAAGGGTTATTTGC
65 GAGAAGGGTTATCTGC
** * * *
4665 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTTGCAGCATAACTTAAGTC
* **
4730 AAGAAGGGTTATGCCAC
65 GAGAAGGGTTAT-CTGC
* * * *
4747 CAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
* * *
4812 AGAATGGCTATCTTC
66 AGAAGGGTTATCTGC
* * * * * * * *
4827 CAAAGACC-CCTGAGTTCGATTACACTCAGCTTCGAGGGCACATAATTTACAGCATAACTCAAGG
1 CAAAGACCTTC-GAGTTCGACTACGCTCAGC-TCGAAGGCACATCATTTGCAGCATAACTTAAGT
* *
4891 CTAGAAGGGTTATCTATTAC
64 CGAGAAGGGTTATC---TGC
* * * **
4911 CAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCATTTGCAGCATGGCTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
*
4976 AGAAGGGCTATCTGC
66 AGAAGGGTTATCTGC
4991 C--A-ACCTTCGAGTTCGA
1 CAAAGACCTTCGAGTTCGA
5007 TTATATTCAA
Statistics
Matches: 726, Mismatches: 155, Indels: 75
0.76 0.16 0.08
Matches are distributed among these distances:
77 13 0.02
78 1 0.00
79 2 0.00
80 160 0.22
81 223 0.31
82 72 0.10
83 80 0.11
84 126 0.17
85 49 0.07
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (80 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCGAAGGCACATCATTTGCAGCATAACTTAAGTCG
AGAAGGGTTATCTGC
Found at i:4396 original size:165 final size:164
Alignment explanation
Indices: 4010--4993 Score: 1101
Period size: 165 Copynumber: 6.0 Consensus size: 164
4000 ATTTGTCAAT
** * * * * * *
4010 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCTAAGGCACATCATTTGCAGCATATCTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTC
* ** * * * **
4074 GAGAAGGGTTATCTG-C--C-AAAGACCCCTGAGTTTGATTACACTCAGCTTCGGGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAAGGCACATCAT
* * * * * * *
4135 TTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCAC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG---C
** * * * * * **
4173 CAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCATATCATTTGTAGC--AACTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTC
* * * *
4235 TATAAGGGTTGTCTGCCAACAAAAGACATTTGAGTTCTACTACGCTCAGCTCAACGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCAT
* *
4300 TTGCAACATAGCTTAAGTCGAGAAGGGCTATATGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
* * *
4335 CAAAGACCCCCGAGTTTGATTACACTCAGCTTCGAGGGCACACCATTTGCAGCATAACTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTC
* * *
4400 GAGAAGGGTTATCTGCCAATAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCAT
*
4465 TTGCAGCATAGCTTAAGTCGAGAATGGCTATCTGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
* * * *
4500 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGAGCACATTATTTACAGCATAACTCAAGGC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTC
*** * *
4565 TAGAAGGGTTATCTATGACCAAAAGACCTTTGAGTTCGACTACGTTCAGCTCTAAGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTC-AAGGCACATCAT
* * * *
4630 TTACAGTATAGCTTAAGTCGAGAAGGGTTATTTGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
*
4665 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTC
* * *
4730 AAGAAGGGTTA--TGCC-ACCAAAGACCTTTGAGTTCGACTATGCTCAGCTCCAAGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCAT
* * * *
4792 TTGCAGCACAACTTAAGTCGAGAATGGCTATCTTC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
* * * *
4827 CAAAGACCCCTGAGTTCGATTACACTCAGCTTCGAGGGCACATAATTTACAGCATAACTCAAGGC
1 CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTC
*** * * * *
4892 TAGAAGGGTTATCT-ATTACCAAAGACCTTCGAGTTTGACTACGTTCAGCTCCAAGGCACATCAT
66 TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCAT
*
4956 TTGCAGCATGGCTTAAGTCGAGAAGGGCTATCTGC
130 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
4991 CAA
1 CAA
4994 CCTTCGAGTT
Statistics
Matches: 707, Mismatches: 101, Indels: 25
0.85 0.12 0.03
Matches are distributed among these distances:
161 21 0.03
162 165 0.23
163 68 0.10
164 80 0.11
165 371 0.52
166 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (164 bp):
CAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTTAAGTC
TAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
Found at i:4590 original size:330 final size:324
Alignment explanation
Indices: 3968--4993 Score: 1213
Period size: 330 Copynumber: 3.1 Consensus size: 324
3958 TTTAAGATAA
* * * * ** *
3968 CATTTGCAATATAGCTCAAGACAAGAAGGGCTATTTGTCAATCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAACATAGCTTAAGTCGAGAAGGGCTATTTG-C---CAAAGACCCCCGAGTTCGATTAC
* * * *
4033 GCTCAGC-TCTAAGGCACATCATTTGCAGCATATCTTAAGTCGAGAAGGGTTATCTGCC-AAAGA
62 ACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGA
** * * * ** * * * * *
4096 CCCCTGAGTTTGATTACACTCAGCTTCGGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGG
127 CCTTTGAGTTCGACTACGCTCAGC-TCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAATG
* * ** * * * * * * **
4161 GTTATATGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGTAGC-
191 GCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGCACATAATTTACAGCA
* * * * ** * * *
4225 -AACTTAAGTCTATAAGGGTTGTCTGCCAACAAAAGACATTTGAGTTCTACTACGCTCAGCTCAA
253 TAACTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTTGAGTTCTACTACGTTCAGCTCAA
4289 CGGCACAT
318 -GGCACAT
* *
4297 CATTTGCAACATAGCTTAAGTCGAGAAGGGCTATATGCCAAAGACCCCCGAGTTTGATTACACTC
1 CATTTGCAACATAGCTTAAGTCGAGAAGGGCTATTTGCCAAAGACCCCCGAGTTCGATTACACTC
*
4362 AGCTTCGAGGGCACACCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAATAAAAGAC
66 AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC---AAAAGAC
* *
4427 CTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCATAGCTTAAGTCGAGAATGG
128 CTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCATTTGCAGCATAACTTAAGTCGAGAATGG
*
4492 CTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGAGCACATTATTTACAGCATAA
192 CTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAG-GCACATAATTTACAGCATAA
* *
4557 CTCAAGGCTAGAAGGGTTATCTATGACCAAAAGACCTTTGAGTTCGACTACGTTCAGCTCTAAGG
256 CTCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTTGAGTTCTACTACGTTCAGCTC-AAGG
4622 CACAT
320 CACAT
* ** *
4627 CATTTACAGTATAGCTTAAGTCGAGAAGGGTTATTTGCCAAAGACCCCCGAGTTCGATTACACTC
1 CATTTGCAACATAGCTTAAGTCGAGAAGGGCTATTTGCCAAAGACCCCCGAGTTCGATTACACTC
*
4692 AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTA--TGCCACCAAAGACC
66 AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA--AAAGACC
* *
4755 TTTGAGTTCGACTATGCTCAGCTCCAAGGCACATCATTTGCAGCACAACTTAAGTCGAGAATGGC
129 TTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAATGGC
* *
4820 TATCTTCCAAAGACCCCTGAGTTCGATTACACTCAGCTTCGAGGGCACATAATTTACAGCATAAC
193 TATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGA-GGCACATAATTTACAGCATAAC
* *
4885 TCAAGGCTAGAAGGGTTATCTATTACC-AAAGACCTTCGAGTT-TGACTACGTTCAGCTCCAAGG
257 TCAAGGCTAGAAGGGTTATCTATCACCAAAAGACCTTTGAGTTCT-ACTACGTTCAGCT-CAAGG
4948 CACAT
320 CACAT
* * *
4953 CATTTGCAGCATGGCTTAAGTCGAGAAGGGCTATCTGCCAA
1 CATTTGCAACATAGCTTAAGTCGAGAAGGGCTATTTGCCAA
4994 CCTTCGAGTT
Statistics
Matches: 607, Mismatches: 74, Indels: 35
0.85 0.10 0.05
Matches are distributed among these distances:
325 26 0.04
326 119 0.20
327 182 0.30
328 21 0.03
329 34 0.06
330 223 0.37
331 2 0.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.25
Consensus pattern (324 bp):
CATTTGCAACATAGCTTAAGTCGAGAAGGGCTATTTGCCAAAGACCCCCGAGTTCGATTACACTC
AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAAAAGACCTT
TGAGTTCGACTACGCTCAGCTCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAATGGCTAT
CTGCCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGCACATAATTTACAGCATAACTCAA
GGCTAGAAGGGTTATCTATCACCAAAAGACCTTTGAGTTCTACTACGTTCAGCTCAAGGCACAT
Found at i:6367 original size:6 final size:6
Alignment explanation
Indices: 6343--6405 Score: 56
Period size: 6 Copynumber: 10.0 Consensus size: 6
6333 AATTTAACAA
* * *
6343 TTTATT ATTATT ATTATT TTTATT TCTATT TGATT-TT TTTATTCT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT T--TTATT TTTA-T-T TTTATT
6394 TTTATT TTTATT
1 TTTATT TTTATT
6406 CTTAATTTCA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
5 2 0.04
6 35 0.73
7 5 0.10
8 6 0.12
ACGTcount: A:0.19, C:0.03, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:6394 original size:16 final size:16
Alignment explanation
Indices: 6343--6467 Score: 58
Period size: 16 Copynumber: 7.4 Consensus size: 16
6333 AATTTAACAA
*
6343 TTTATTATTATTATTATT
1 TTTATTCTT-TTATT-TT
6361 TTTATTTCTATTTGATTTT
1 TTTA-TTCT-TTT-ATTTT
6380 TTTATTCTTTTATTTT
1 TTTATTCTTTTATTTT
* * *
6396 TATTTTTATTCTTAATTTCA
1 T-TTATTCTT-TT-ATTT-T
*
6416 CTTA-TC-TTTA-TTT
1 TTTATTCTTTTATTTT
*
6429 TTTATTATTGTTATTTT
1 TTTATTCTT-TTATTTT
** *
6446 AATATTCTTTTATTTA
1 TTTATTCTTTTATTTT
6462 TTTATT
1 TTTATT
6468 TATTTAATTA
Statistics
Matches: 80, Mismatches: 16, Indels: 24
0.67 0.13 0.20
Matches are distributed among these distances:
13 3 0.04
14 3 0.04
15 2 0.03
16 21 0.26
17 19 0.24
18 11 0.14
19 17 0.21
20 4 0.05
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.72
Consensus pattern (16 bp):
TTTATTCTTTTATTTT
Found at i:6548 original size:25 final size:25
Alignment explanation
Indices: 6499--6550 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
6489 TTTGACCTAA
* **
6499 TTTTCTTTTTATTTATTTTTCTTTT
1 TTTTCTTTTGATTTATTTTAATTTT
6524 TTTTCTTTTGATTTATTTTAATTTT
1 TTTTCTTTTGATTTATTTTAATTTT
6549 TT
1 TT
6551 ACTTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.81
Consensus pattern (25 bp):
TTTTCTTTTGATTTATTTTAATTTT
Found at i:6561 original size:3 final size:3
Alignment explanation
Indices: 6553--6584 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
6543 AATTTTTTAC
6553 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6585 TTTCCTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:7038 original size:23 final size:23
Alignment explanation
Indices: 7009--7058 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
6999 ACCAAACATG
* *
7009 AAAATATAGATTCTATTTTCATA
1 AAAATATAGATTATATTCTCATA
7032 AAAATATAGATTATATTCTCATA
1 AAAATATAGATTATATTCTCATA
7055 AAAA
1 AAAA
7059 ATCTCATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.04, T:0.38
Consensus pattern (23 bp):
AAAATATAGATTATATTCTCATA
Found at i:19009 original size:2 final size:2
Alignment explanation
Indices: 19002--19026 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18992 TTCCAACACC
19002 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
19027 ATTCGATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:30974 original size:19 final size:20
Alignment explanation
Indices: 30952--30992 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
30942 CTTGTTTTCT
30952 TAAAAAATTTAAAT-TTTTA
1 TAAAAAATTTAAATATTTTA
* *
30971 TAAATAATTTAAGTATTTTA
1 TAAAAAATTTAAATATTTTA
30991 TA
1 TA
30993 TTAATATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
TAAAAAATTTAAATATTTTA
Found at i:37783 original size:21 final size:21
Alignment explanation
Indices: 37741--37783 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
37731 TTTCTGGGCT
*
37741 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
37762 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
37783 A
1 A
37784 ACGAATATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:37836 original size:20 final size:20
Alignment explanation
Indices: 37811--37848 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
37801 GAACGCTAGA
*
37811 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
37831 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
37849 TAATAAATTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:37860 original size:15 final size:15
Alignment explanation
Indices: 37840--37870 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
37830 GGGGGAACCG
37840 ATTCCCCCATAATAA
1 ATTCCCCCATAATAA
37855 ATTCCCCCATAATAA
1 ATTCCCCCATAATAA
37870 A
1 A
37871 AAAAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
ATTCCCCCATAATAA
Found at i:38527 original size:103 final size:103
Alignment explanation
Indices: 38343--38560 Score: 355
Period size: 103 Copynumber: 2.1 Consensus size: 103
38333 GCAGAGGGTC
* * * * *
38343 TATGTGGTCATTCGGGACATATATATATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACCTCC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAGATCTCGTGAGACACATAC
*
38408 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
* * *
38446 TATGTTGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGATCTCGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAGATCTCGTGAGACACATAC
38511 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
38549 TATGTGGTCCTT
1 TATGTGGTCCTT
38561 ATGGAAATTA
Statistics
Matches: 105, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATATATTCTTTGGAACATGTGTGAGATCTCGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:38603 original size:23 final size:23
Alignment explanation
Indices: 38577--38628 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
38567 ATTATTATAT
*
38577 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTAAGC
* *
38600 GGCACTCCGGTGCAATTCTAAGT
1 GGCACTACGGTGCAATTCTAAGC
38623 GGCACT
1 GGCACT
38629 TAGCTGCAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.21, C:0.29, G:0.27, T:0.23
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTAAGC
Found at i:38636 original size:23 final size:23
Alignment explanation
Indices: 38587--38639 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
38577 GGCACTACGG
* * *
38587 TGCAATTCTACGCGGCACTCCGG
1 TGCAATTCTAAGCGGCACTCAGC
* *
38610 TGCAATTCTAAGTGGCACTTAGC
1 TGCAATTCTAAGCGGCACTCAGC
38633 TGCAATT
1 TGCAATT
38640 ATACGAGCTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TGCAATTCTAAGCGGCACTCAGC
Found at i:39372 original size:29 final size:29
Alignment explanation
Indices: 39353--39423 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
39343 TCGTCGGGCA
39353 TGCATGGCGACCTCTTTGGTCGCCCGGAG
1 TGCATGGCGACCTCTTTGGTCGCCCGGAG
**** **
39382 TGCATGGCGACCTAGGAGGTCGCTGGGAG
1 TGCATGGCGACCTCTTTGGTCGCCCGGAG
39411 TGCATGGCGACCT
1 TGCATGGCGACCT
39424 ATGGGTTGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.14, C:0.27, G:0.38, T:0.21
Consensus pattern (29 bp):
TGCATGGCGACCTCTTTGGTCGCCCGGAG
Found at i:39764 original size:2 final size:2
Alignment explanation
Indices: 39757--39782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
39747 TATAATATTC
39757 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
39783 TAATTATCTC
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:43805 original size:12 final size:12
Alignment explanation
Indices: 43788--43829 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
43778 AGTTTTGAAA
43788 ATAAAAATTAAT
1 ATAAAAATTAAT
* *
43800 ATAAAAA-GAAA
1 ATAAAAATTAAT
43811 ATAAAAATTAAT
1 ATAAAAATTAAT
43823 ATAAAAA
1 ATAAAAA
43830 GAATAGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (12 bp):
ATAAAAATTAAT
Found at i:43810 original size:23 final size:23
Alignment explanation
Indices: 43784--43832 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
43774 AATGAGTTTT
43784 GAAAATAAAAATTAATATAAAAA
1 GAAAATAAAAATTAATATAAAAA
43807 GAAAATAAAAATTAATATAAAAA
1 GAAAATAAAAATTAATATAAAAA
43830 GAA
1 GAA
43833 TAGAAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (23 bp):
GAAAATAAAAATTAATATAAAAA
Found at i:43834 original size:11 final size:11
Alignment explanation
Indices: 43797--43850 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
43787 AATAAAAATT
43797 AATATAAAAAG
1 AATATAAAAAG
* *
43808 AAAATAAAAATT
1 AATATAAAAA-G
43820 AATATAAAAAG
1 AATATAAAAAG
*
43831 AATAGAAAAGAG
1 AATATAAAA-AG
43843 AAATATAA
1 -AATATAA
43851 TTTTTTATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 17 0.50
12 11 0.32
13 6 0.18
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.19
Consensus pattern (11 bp):
AATATAAAAAG
Found at i:43839 original size:23 final size:23
Alignment explanation
Indices: 43784--43839 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
43774 AATGAGTTTT
*
43784 GAAAATAAAAATTAATATAAAAA
1 GAAAAGAAAAATTAATATAAAAA
*
43807 GAAAATAAAAATTAATATAAAAA
1 GAAAAGAAAAATTAATATAAAAA
*
43830 GAATAGAAAA
1 GAAAAGAAAA
43840 GAGAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (23 bp):
GAAAAGAAAAATTAATATAAAAA
Found at i:45771 original size:23 final size:23
Alignment explanation
Indices: 45728--45771 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
45718 ACATATTAGG
* **
45728 TAGCGCTTGTATAATGTAATATA
1 TAGCGCTTATATAATAAAATATA
45751 TAGCGCTTATATAATAAAATA
1 TAGCGCTTATATAATAAAATA
45772 GGCATTTAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (23 bp):
TAGCGCTTATATAATAAAATATA
Found at i:45848 original size:87 final size:86
Alignment explanation
Indices: 45688--45849 Score: 238
Period size: 87 Copynumber: 1.9 Consensus size: 86
45678 TATGTTTTAT
*
45688 CATTTAACCAGAAATTTATCAAGTACAATAACATATTAGGTAGCGCTTGTATAATGTAATATATA
1 CATTTAACCAGAAATTTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATATATA
* *
45753 GCGCTTATATAATAAAATAGG
66 ACACTTATATAATAAAATAGG
*
45774 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAG-GACTTATATAATGTAATA-A
1 CATTTAACCAGAAAT-TTATCAAGTACAATAACATATTAGGTAGCG-CTTATATAATGTAATATA
*
45837 GTAACATTTATAT
64 -TAACACTTATAT
45850 TGACCTATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
86 16 0.24
87 52 0.76
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (86 bp):
CATTTAACCAGAAATTTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATATATA
ACACTTATATAATAAAATAGG
Found at i:46368 original size:200 final size:199
Alignment explanation
Indices: 45844--46571 Score: 927
Period size: 199 Copynumber: 3.7 Consensus size: 199
45834 TAAGTAACAT
* * * * *
45844 TTATATTGACCTATTTTCTAAGT-AAACATG-TATATTTATACCGGTAACATTGCAAATTTACAT
1 TTATGTTGACCTATTTTCTAA-TAAAAC-CGATATATTTATACCGGTTACATTGTAAATTTACCT
* * *
45907 ATTACATTATAATTATTGGTTTCGATGTTTTTTTGGATCGATACAATTT--TAAATGTATCGACA
64 ATTACATTATAATTATCGGTTTCGATG-TTTTTGGGATCGATAC-TTTTAATAAATGTATCGACA
* * * * * * *
45970 CTTTATGCTTGCACTTCGTTGGGCATTCATTCTGGAAAAAAGTATCGACACAAACTTAAAAAGTG
127 CTATATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAATTTAACAAGTG
*
46035 TTGATACA
192 TCGATACA
* * * * *
46043 TTAT-TTAGACCTATTTTCTTATAAAACCGGTATATCTATACTGGGTACATTGTAAATTTACCTA
1 TTATGTT-GACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTA
* * * *
46107 TCACATTGTAATTTTC-GTTTCGATATTTTTGGGATCGATACTTTTAATAAATGTATCGACACTA
65 TTACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTA
* *
46171 TATGCGTGCACCCCGTTTGGCATTCATTATGGACAAAATGTATCGACACAAATTTAACAAGTGTC
130 TATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAA-GTATCGACACAAATTTAACAAGTGTC
*
46236 GATACT
194 GATACA
* * *
46242 TTATGCTGACCTATTTTCTCATAAAATCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
*
46307 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTT
66 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTAT
* **
46372 ATGTGTGCACCTCGTTTGGGCATTCATTCTGGACAATAAGTATCGACACAAATTCCACAAGTGTC
131 ATGCGTGCACCTCGTTT-GGCATTCATTCTGGACAA-AAGTATCGACACAAATTTAACAAGTGTC
46437 GATACA
194 GATACA
* * * * *
46443 TTATGTTGACATGTTTTCTAAT-TAACCGATATATTTATACCAGTTACATTGTTAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
* *
46507 TACATTATAATTATTGGTTTCGATTTTTTTGGG-TCGATACTTTTAGA-AAATGTATCGACAC-A
66 TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTA-ATAAATGTATCGACACTA
46569 TAT
130 TAT
46572 TTAAGTGGTT
Statistics
Matches: 463, Mismatches: 55, Indels: 23
0.86 0.10 0.04
Matches are distributed among these distances:
196 3 0.01
197 15 0.03
198 63 0.14
199 183 0.40
200 133 0.29
201 64 0.14
202 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (199 bp):
TTATGTTGACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTAT
ATGCGTGCACCTCGTTTGGCATTCATTCTGGACAAAAGTATCGACACAAATTTAACAAGTGTCGA
TACA
Found at i:48597 original size:21 final size:22
Alignment explanation
Indices: 48562--48602 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
48552 AACACGCGAT
48562 ATTTAAAAATGTATCGACACAA
1 ATTTAAAAATGTATCGACACAA
48584 ATTTAAAAAT-TATCGACAC
1 ATTTAAAAATGTATCGACAC
48603 TTTATGCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.29
Consensus pattern (22 bp):
ATTTAAAAATGTATCGACACAA
Found at i:48954 original size:203 final size:203
Alignment explanation
Indices: 48634--49183 Score: 739
Period size: 200 Copynumber: 2.7 Consensus size: 203
48624 ATAAAACCAG
* * *
48634 TATATTTATACCGGTTACATTGGAAATTTACCTATTACATTATAA-T-T-ATGA--GTTTCGAAG
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAATTATCGTTTCGATG
*
48694 TTTTTGAGATCGATACTTTTTAAAAATATATCGACACTTTATGAGTGCACCCTTTTGGGCATTCC
66 TTTTTG-GATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTCC
* * * *
48759 TTCTAGACAAAAAATATCGACACAAAATACACAA-GT-GATACATTTTGTAGACCTATTCTCTCA
130 TTCTAGACAAAAAGTATCGACACAAAATACAAAAGGTCGATACATTATGTAGACATATTCTCTCA
*
48822 TAAAATTGA
195 TAAAATCGA
* *
48831 TATATTTATGCCGGTTACATTGTAAATTTACCTATTACATTATAATTATAATTATTCATTTCGAT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAATTA-TCGTTTCGAT
* *
48896 GTTTTTGTGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTC
65 GTTTTTG-GATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTC
* * *
48961 ATTCTTGACAAAAAGTATCGACACAAATTACAAAAGTGTCGATACATTATGTAGACATATTCTCT
129 CTTCTAGACAAAAAGTATCGACACAAAATACAAAAG-GTCGATACATTATGTAGACATATTCTCT
* *
49026 CATAAGATCGG
193 CATAAAATCGA
* *
49037 TATAGTTATACCTGTTACATTGTAAATTTACCTATTAC------ATTATAATTATCGGTTTCGAT
1 TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAATTATC-GTTTCGAT
* * *
49096 GTTTTTAGGATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCTTTTTGGGCATTC
65 GTTTTT-GGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTC
*
49161 CTTCTGGACAAAAAGTATCGACA
129 CTTCTAGACAAAAAGTATCGACA
49184 GATTCTAAAA
Statistics
Matches: 313, Mismatches: 29, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
197 43 0.14
198 1 0.00
199 3 0.01
200 100 0.32
201 1 0.00
203 97 0.31
205 2 0.01
206 66 0.21
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (203 bp):
TATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATAATTATCGTTTCGATG
TTTTTGGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGCATTCCT
TCTAGACAAAAAGTATCGACACAAAATACAAAAGGTCGATACATTATGTAGACATATTCTCTCAT
AAAATCGA
Found at i:49155 original size:200 final size:197
Alignment explanation
Indices: 48624--49183 Score: 757
Period size: 203 Copynumber: 2.8 Consensus size: 197
48614 CTATTTTGTT
* * *
48624 ATAAAACCAGTATATTTATACCGGTTACATTGGAAATTTACCTATTACATTATAATTAT-GAGTT
1 ATAAAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCG-GTT
* *
48688 TCGAAGTTTTTGAGATCGATACTTTTTAAAAATATATCGACACTTTATGAGTGCACCCTTTTGGG
65 TCGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGG
* * * *
48753 CATTCCTTCTAGACAAAAAATATCGACACAAAATACACAAGTGATACATTTTGTAGACCTATTCT
130 CATTCCTTCTAGACAAAAAGTATCGACACAAAATACAAAAGTGATACATTATGTAGACATATTCT
48818 CTC
195 CTC
* * *
48821 ATAAAATTGATATATTTATGCCGGTTACATTGTAAATTTACCTATTACATTATAATTATAATTAT
1 ATAAAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAC------ATTATAATTA-
* * * *
48886 TC-ATTTCGATGTTTTTGTGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCT
59 TCGGTTTCGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCT
* * *
48950 TTTGGGCATTCATTCTTGACAAAAAGTATCGACACAAATTACAAAAGTGTCGATACATTATGTAG
124 TTTGGGCATTCCTTCTAGACAAAAAGTATCGACACAAAATACAAAA--GT-GATACATTATGTAG
49015 ACATATTCTCTC
186 ACATATTCTCTC
* * *
49027 ATAAGATCGGTATAGTTATACCTGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTT
1 ATAAAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTT
* * *
49092 CGATGTTTTT-AGGATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCTTTTTGGG
66 CGATGTTTTTGA-GATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGG
*
49156 CATTCCTTCTGGACAAAAAGTATCGACA
130 CATTCCTTCTAGACAAAAAGTATCGACA
49184 GATTCTAAAA
Statistics
Matches: 317, Mismatches: 33, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
197 42 0.13
199 2 0.01
200 97 0.31
203 107 0.34
204 1 0.00
205 2 0.01
206 66 0.21
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (197 bp):
ATAAAATCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTT
CGATGTTTTTGAGATCGATACTTTTTAAAAATGTATCGACACTTTATGAGTGCACCCTTTTGGGC
ATTCCTTCTAGACAAAAAGTATCGACACAAAATACAAAAGTGATACATTATGTAGACATATTCTC
TC
Found at i:49521 original size:159 final size:159
Alignment explanation
Indices: 49232--49528 Score: 531
Period size: 159 Copynumber: 1.9 Consensus size: 159
49222 GTTTCGATGT
49232 TTTTGGGATCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGCACCCTTTTGGGCATTCAT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGCACCCTTTTGGGCATTCAT
*
49297 TATGGACAAAAAGTATCAACACAAATTACAAAAGTGTCGATACATTACGTAGACCTATTCTCTCA
66 TATGGACAAAAAGTATCAACACAAATTACAAAAATGTCGATACATTACGTAGACCTATTCTCTCA
49362 TAAAACCGATTATATTATAGGTTTCAATA
131 TAAAACCGATTATATTATAGGTTTCAATA
*
49391 TTTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCCTTTTGGGCATTCAT
1 TTTTGGGATCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGCACCCTTTTGGGCATTCAT
* * * * *
49456 TCTGGACAAAAAGTATCGACACAAATTCCAAAAATGTCGATATATTATGTAGACCTATTCTCTCA
66 TATGGACAAAAAGTATCAACACAAATTACAAAAATGTCGATACATTACGTAGACCTATTCTCTCA
49521 TAAAACCG
131 TAAAACCG
49529 GTATAGTTGT
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
159 131 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (159 bp):
TTTTGGGATCGATACTTTTTATAAATGTATCGAAACTTTATGCGTGCACCCTTTTGGGCATTCAT
TATGGACAAAAAGTATCAACACAAATTACAAAAATGTCGATACATTACGTAGACCTATTCTCTCA
TAAAACCGATTATATTATAGGTTTCAATA
Found at i:50094 original size:19 final size:19
Alignment explanation
Indices: 50070--50118 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
50060 TTACATTCAC
50070 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
**
50089 ATACAAAATTATAAATTTT
1 ATACAAAATTATAAATCGT
*
50108 ATACATAATTA
1 ATACAAAATTA
50119 ACCCCACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.53, C:0.08, G:0.02, T:0.37
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:53141 original size:16 final size:18
Alignment explanation
Indices: 53111--53145 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
53101 ATGACTTGGT
53111 TATATGTCATATGAAATA
1 TATATGTCATATGAAATA
53129 TATATG-CAT-TGAAATA
1 TATATGTCATATGAAATA
53145 T
1 T
53146 CATGATCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (18 bp):
TATATGTCATATGAAATA
Found at i:53787 original size:18 final size:18
Alignment explanation
Indices: 53764--53802 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
53754 TCCTCCTCAT
*
53764 TTCCTCCATTTTTTATTC
1 TTCCTCCATCTTTTATTC
*
53782 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTATTC
53800 TTC
1 TTC
53803 ATATTTTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.33, G:0.00, T:0.59
Consensus pattern (18 bp):
TTCCTCCATCTTTTATTC
Found at i:54500 original size:22 final size:23
Alignment explanation
Indices: 54472--54527 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
54462 AACCTGCATT
*
54472 TATAATAAAAT-TTATCATTTTA
1 TATAATAAAATACTATCATTTTA
*
54494 TATAATAACTATACTATCATTTTA
1 TATAATAA-AATACTATCATTTTA
*
54518 TATAAAAAAA
1 TATAATAAAA
54528 CAAAAACGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.29
23 3 0.11
24 17 0.61
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATAAAATACTATCATTTTA
Found at i:56786 original size:182 final size:182
Alignment explanation
Indices: 56474--57294 Score: 1067
Period size: 182 Copynumber: 4.5 Consensus size: 182
56464 TACGCGTACT
* * * **
56474 TATTAAAGTATTGACACTTTCAATATATTCGGTAGCTCTTTACTGGTTTTGTCATTTCGAGACAT
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCG
*
56539 GTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTATCATAAAGTATTGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTATCATAAAGTATCGACACT
*
56604 TTATAGGTGCTAAAACTGTTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
* *
56656 TATTAAAGTATCGACACTTTTAATATATCCGGTAGCTCTTTACCGGTTTTTTCATTTCGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCG
* * *
56721 ATTTTGTCATATTTTTACCTATTATATCGTTATGGATCGATACATTATCATAAAATATCGACACT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTATCATAAAGTATCGACACT
* *
56786 TTATAGGCGCTAAAACTATTTCTCTTTTAAATTCCCAAAGTGTCGATACTTA
131 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
*
56838 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCGGTTTTGTC-TTTCCGAGACC
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTT-CGAGACC
* ** * * *
56902 GGTTTTGTCATATTTTTACCTGTTGTATCGTTATAAATCGATACATTTTTATAAAGTATTGACAC
65 GGTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTATCATAAAGTATCGACAC
*
56967 TTTATAGGCACTAAAACTGTTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
130 TTTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
* * * * * *
57020 TATTAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTATCGGTGTTGTCTTTTTGAGACCG
1 TATTAAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCG
* * * * * * * *
57085 GTTTTGTCATTTTTTTAACTGTTGTATCGTTATGGATCGATATATTTTTATAAAGTATCGATATT
66 GTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTATCATAAAGTATCGACACT
* ** * * * *
57150 TTATAGGTGCTATTATTGCTTCTCTTTTAAATTCACAAAGTGTCGATATTTA
131 TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
** * * * * * *
57202 T-TTCAATCTAATCGATACTTTCAACATATTCGATAACGT-TTTACTGGTTTTGTCATAATT--A
1 TATT-AAAGT-ATCGACACTTTCAATATATCCGGTAGC-TCTTTACCGGTTTTGTCAT--TTCGA
* * *
57263 AACCGATTTTGTCATATTTTTATCTGTTATAT
61 GACCGGTTTTGTCATATTTTTACCTGTTATAT
57295 TGATATAAAT
Statistics
Matches: 564, Mismatches: 68, Indels: 13
0.87 0.11 0.02
Matches are distributed among these distances:
181 5 0.01
182 492 0.87
183 65 0.12
185 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TATTAAAGTATCGACACTTTCAATATATCCGGTAGCTCTTTACCGGTTTTGTCATTTCGAGACCG
GTTTTGTCATATTTTTACCTGTTATATCGTTATGGATCGATACATTATCATAAAGTATCGACACT
TTATAGGCGCTAAAACTGTTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
Found at i:59983 original size:23 final size:23
Alignment explanation
Indices: 59957--60018 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
59947 TTCGTTTTTA
*
59957 TTTATTGTTCACGAACATGTTCG
1 TTTATTGTTCACGAACATATTCG
* * **
59980 TTTAATATTCACGAATGTATTCG
1 TTTATTGTTCACGAACATATTCG
*
60003 TTTATATGTTTACGAA
1 TTTAT-TGTTCACGAA
60019 TGTGTTCATT
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
23 22 0.73
24 8 0.27
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (23 bp):
TTTATTGTTCACGAACATATTCG
Found at i:60021 original size:24 final size:23
Alignment explanation
Indices: 59976--60030 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
59966 CACGAACATG
59976 TTCGTTTAATATTCACGAATGTA
1 TTCGTTTAATATTCACGAATGTA
* * *
59999 TTCGTTTATATGTTTACGAATGTG
1 TTCGTTTA-ATATTCACGAATGTA
*
60023 TTCATTTA
1 TTCGTTTA
60031 GAGTTCACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 8 0.30
24 19 0.70
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (23 bp):
TTCGTTTAATATTCACGAATGTA
Found at i:60050 original size:23 final size:23
Alignment explanation
Indices: 60024--60100 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
60014 ACGAATGTGT
* *
60024 TCATTTAGAGTTCACTAATATGC
1 TCATTTAGAGTTCACGAACATGC
* *
60047 TCATTTAGAATTCACGAACATGT
1 TCATTTAGAGTTCACGAACATGC
* * *
60070 TCATTTAGAGTTAATGAGCATGC
1 TCATTTAGAGTTCACGAACATGC
*
60093 TCGTTTAG
1 TCATTTAG
60101 TATTTGTTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (23 bp):
TCATTTAGAGTTCACGAACATGC
Found at i:60525 original size:17 final size:17
Alignment explanation
Indices: 60503--60537 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
60493 GAAAAATAGT
60503 TAGTTATACATATAAAA
1 TAGTTATACATATAAAA
**
60520 TAGTTATATGTATAAAA
1 TAGTTATACATATAAAA
60537 T
1 T
60538 GTAACATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.09, T:0.40
Consensus pattern (17 bp):
TAGTTATACATATAAAA
Found at i:64272 original size:74 final size:74
Alignment explanation
Indices: 64187--64336 Score: 273
Period size: 74 Copynumber: 2.0 Consensus size: 74
64177 TATACAAGGA
* * *
64187 ATGAAATTTAATATGATTTGGTCTTAACTACTTTTATGAGAAAACAATGATCTACTATAAATGTA
1 ATGAAATTTAATATGATTTGGTCTTAACCACTTATATGAAAAAACAATGATCTACTATAAATGTA
64252 AAGATTTGT
66 AAGATTTGT
64261 ATGAAATTTAATATGATTTGGTCTTAACCACTTATATGAAAAAACAATGATCTACTATAAATGTA
1 ATGAAATTTAATATGATTTGGTCTTAACCACTTATATGAAAAAACAATGATCTACTATAAATGTA
64326 AAGATTTGT
66 AAGATTTGT
64335 AT
1 AT
64337 CACAAAGAGT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.38
Consensus pattern (74 bp):
ATGAAATTTAATATGATTTGGTCTTAACCACTTATATGAAAAAACAATGATCTACTATAAATGTA
AAGATTTGT
Found at i:69763 original size:2 final size:2
Alignment explanation
Indices: 69756--69783 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
69746 TAAAAAGACG
69756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69784 TTAGAGAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71073 original size:5 final size:6
Alignment explanation
Indices: 71055--71079 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
71045 TTCCTTCCAA
71055 TTATTT TTATTT TTATTT TTATTT T
1 TTATTT TTATTT TTATTT TTATTT T
71080 GAGAATAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:92786 original size:38 final size:39
Alignment explanation
Indices: 92738--92814 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 39
92728 AATCAAGCTG
* *
92738 ATTCTACTTCTTCACTTTGAGTTTACGGAATAGATTGTA
1 ATTCTACTTCTTCACTTCGAGTTTACAGAATAGATTGTA
92777 ATTCT-CTTCTTCACTTCGAGTTTACAGAATAGATTGTA
1 ATTCTACTTCTTCACTTCGAGTTTACAGAATAGATTGTA
92815 TTAACCTTGG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 31 0.86
39 5 0.14
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.43
Consensus pattern (39 bp):
ATTCTACTTCTTCACTTCGAGTTTACAGAATAGATTGTA
Done.