Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009110.1 Hibiscus syriacus cultivar Beakdansim tig00112584_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: 291768
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
File 2 of 2
Found at i:232172 original size:7 final size:7
Alignment explanation
Indices: 232135--232190 Score: 62
Period size: 7 Copynumber: 7.9 Consensus size: 7
232125 AAAAAAAAAG
232135 AATAATA
1 AATAATA
*
232142 AATACT-
1 AATAATA
232148 AATAATAA
1 AATAAT-A
232156 AATAAATA
1 AAT-AATA
232164 AATAATA
1 AATAATA
232171 AATAA-A
1 AATAATA
232177 TAATAATA
1 -AATAATA
232185 AATAAT
1 AATAAT
232191 GTATTATCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
6 6 0.14
7 25 0.60
8 8 0.19
9 3 0.07
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (7 bp):
AATAATA
Found at i:232760 original size:33 final size:32
Alignment explanation
Indices: 232734--232800 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 32
232724 CAAATGCTTC
232734 GGTTTTAGTGTTTCAAATGGACTCAAATACGTT
1 GGTTTTAGTGTTTC-AATGGACTCAAATACGTT
*
232767 GGTTTTAGTGTTTCAATAGGACTCAAGTACGTT
1 GGTTTTAGTGTTTCAAT-GGACTCAAATACGTT
232800 G
1 G
232801 ATTTATTTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 3 0.09
33 29 0.91
ACGTcount: A:0.25, C:0.12, G:0.24, T:0.39
Consensus pattern (32 bp):
GGTTTTAGTGTTTCAATGGACTCAAATACGTT
Found at i:232862 original size:3 final size:3
Alignment explanation
Indices: 232854--232900 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
232844 GGCCTGCAAA
232854 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AA- ATAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT A-AT AAT AAT AAT
232899 AA
1 AA
232901 AATGTTTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 3 0.08
3 33 0.82
4 4 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:233980 original size:24 final size:22
Alignment explanation
Indices: 233940--234016 Score: 67
Period size: 24 Copynumber: 3.6 Consensus size: 22
233930 ATGCAATTAA
233940 TGCATCGATGCA---TAAGGAG
1 TGCATCGATGCACTGTAAGGAG
233959 TGCATCGATGCACATGTTAAGG-G
1 TGCATCGATGCAC-TG-TAAGGAG
* *
233982 ATGCATCGATACACTGT-A-GAA
1 -TGCATCGATGCACTGTAAGGAG
234003 TGCATCGATGCACT
1 TGCATCGATGCACT
234017 TCAAGGGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
19 12 0.25
20 14 0.29
21 1 0.02
22 1 0.02
23 3 0.06
24 17 0.35
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (22 bp):
TGCATCGATGCACTGTAAGGAG
Found at i:235644 original size:23 final size:23
Alignment explanation
Indices: 235554--235636 Score: 121
Period size: 23 Copynumber: 3.6 Consensus size: 23
235544 CATTTTATAT
*
235554 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCAGTGCAATTCTACGC
*
235577 GGCACTTCAGTGTAATTCTACGC
1 GGCACTTCAGTGCAATTCTACGC
* *
235600 GGCATTTCAGTGCAATTCTACGT
1 GGCACTTCAGTGCAATTCTACGC
*
235623 GGCACTTCGGTGCA
1 GGCACTTCAGTGCA
235637 TTTATACGAG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.19, C:0.27, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTCTACGC
Found at i:237188 original size:15 final size:15
Alignment explanation
Indices: 237168--237262 Score: 190
Period size: 15 Copynumber: 6.3 Consensus size: 15
237158 TCGTAGGACC
237168 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
237183 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
237198 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
237213 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
237228 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
237243 ACTACGTCCCGAAGG
1 ACTACGTCCCGAAGG
237258 ACTAC
1 ACTAC
237263 AATACCCTCG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 80 1.00
ACGTcount: A:0.27, C:0.34, G:0.25, T:0.14
Consensus pattern (15 bp):
ACTACGTCCCGAAGG
Found at i:237939 original size:34 final size:35
Alignment explanation
Indices: 237871--237939 Score: 106
Period size: 34 Copynumber: 2.0 Consensus size: 35
237861 TTCATTTAGG
237871 GGGGAATCGATACCTCCCCAGGGGAATCTATTCCC
1 GGGGAATCGATACCTCCCCAGGGGAATCTATTCCC
*
237906 GGGGAATCGATA-C-CCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCTCCCCA-GGGGAATCTATTCCC
237940 CCTGCACATA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 5 0.16
34 15 0.47
35 12 0.38
ACGTcount: A:0.22, C:0.30, G:0.29, T:0.19
Consensus pattern (35 bp):
GGGGAATCGATACCTCCCCAGGGGAATCTATTCCC
Found at i:244669 original size:34 final size:34
Alignment explanation
Indices: 244626--244693 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
244616 TTTCATTTAG
244626 GGGGAATCGATACCCCCCA-GGGGAATCTGTTCCC
1 GGGGAATCGATA-CCCCCAGGGGGAATCTGTTCCC
244660 GGGGAATCGATACCCCCAGGGGGAATCTGTTCCC
1 GGGGAATCGATACCCCCAGGGGGAATCTGTTCCC
244694 CCTGCACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 6 0.18
34 27 0.82
ACGTcount: A:0.21, C:0.31, G:0.31, T:0.18
Consensus pattern (34 bp):
GGGGAATCGATACCCCCAGGGGGAATCTGTTCCC
Found at i:244684 original size:19 final size:18
Alignment explanation
Indices: 244626--244686 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 18
244616 TTTCATTTAG
244626 GGGGAATCGATACCCCCCA
1 GGGGAATCGATA-CCCCCA
*
244645 GGGGAATCTG-T--TCCC-
1 GGGGAATC-GATACCCCCA
244660 GGGGAATCGATACCCCCA
1 GGGGAATCGATACCCCCA
244678 GGGGGAATC
1 -GGGGAATC
244687 TGTTCCCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
14 1 0.03
15 9 0.26
16 3 0.09
17 3 0.09
19 17 0.50
20 1 0.03
ACGTcount: A:0.23, C:0.30, G:0.33, T:0.15
Consensus pattern (18 bp):
GGGGAATCGATACCCCCA
Found at i:244694 original size:19 final size:18
Alignment explanation
Indices: 244639--244695 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
244629 GAATCGATAC
244639 CCCCCAGGGGAATCTGTT
1 CCCCCAGGGGAATCTGTT
*
244657 --CCC-GGGGAATC-GATA
1 CCCCCAGGGGAATCTG-TT
244672 CCCCCAGGGGGAATCTGTT
1 CCCCCA-GGGGAATCTGTT
244691 CCCCC
1 CCCCC
244696 TGCACATACT
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
14 1 0.03
15 9 0.29
16 3 0.10
17 3 0.10
19 14 0.45
20 1 0.03
ACGTcount: A:0.18, C:0.37, G:0.28, T:0.18
Consensus pattern (18 bp):
CCCCCAGGGGAATCTGTT
Found at i:245668 original size:83 final size:83
Alignment explanation
Indices: 245505--245833 Score: 426
Period size: 83 Copynumber: 4.0 Consensus size: 83
245495 GGTCTTTGGC
* ** * * *
245505 AGATAGCCCTTCTTTCCTTGAGCTATGCTGTAAATGATGGTGCCTTTGAGCTGAACGTAATCAAA
1 AGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGAT-GTGCCTTGGAGCTGAGCGTAGTCAAA
*
245570 CTCGAAGGTCTTTGTTAAA
65 CTCGAAGGTCTTTGTTGAA
*
245589 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAAC
1 AGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAAC
245654 TCGAAGGTCTTTGTTGGAA
66 TCGAAGGTCTTTGTT-GAA
* * * * * * * * *
245673 A-ATAACCCTTCTCGACTTAAGCCATGCTGCAAATGATGTACCTTTGAGCTGAGCGTGGTCGAAC
1 AGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAAC
* **
245737 TTGAAGGTCTTTGTTGGC
66 TCGAAGGTCTTTGTTGAA
* * *
245755 AGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCTTGGAGCTGAGCGTAGTCAAAC
1 AGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAAC
245820 TCGAAGGTCTTTGT
66 TCGAAGGTCTTTGT
245834 GTTTCAAGAG
Statistics
Matches: 209, Mismatches: 34, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
82 2 0.01
83 170 0.81
84 37 0.18
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (83 bp):
AGATAACCCTTCTAGCCTTGAGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAAC
TCGAAGGTCTTTGTTGAA
Found at i:245745 original size:166 final size:167
Alignment explanation
Indices: 245529--245833 Score: 495
Period size: 166 Copynumber: 1.8 Consensus size: 167
245519 TCCTTGAGCT
* *
245529 ATGCTGTAAATGATGGTGCCTTTGAGCTGAACGTAATCAAACTCGAAGGTCTTTGTTAAAAGATA
1 ATGCTGCAAATGATGGTACCTTTGAGCTGAACGTAATCAAACTCGAAGGTCTTTGTTAAAAGATA
*
245594 ACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAA
66 ACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAA
245659 GGTCTTTGTTGGAAAATAACCCTTCTCGACTTAAGCC
131 GGTCTTTGTTGGAAAATAACCCTTCTCGACTTAAGCC
* ** * * ***
245696 ATGCTGCAAATGAT-GTACCTTTGAGCTGAGCGTGGTCGAACTTGAAGGTCTTTGTTGGCAGATA
1 ATGCTGCAAATGATGGTACCTTTGAGCTGAACGTAATCAAACTCGAAGGTCTTTGTTAAAAGATA
*
245760 ACCCTTCTAGCCTTGAGTTATGTTGTAAATAATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAA
66 ACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAA
245825 GGTCTTTGT
131 GGTCTTTGT
245834 GTTTCAAGAG
Statistics
Matches: 126, Mismatches: 12, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
166 113 0.90
167 13 0.10
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (167 bp):
ATGCTGCAAATGATGGTACCTTTGAGCTGAACGTAATCAAACTCGAAGGTCTTTGTTAAAAGATA
ACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAA
GGTCTTTGTTGGAAAATAACCCTTCTCGACTTAAGCC
Found at i:245973 original size:37 final size:37
Alignment explanation
Indices: 245926--246077 Score: 153
Period size: 37 Copynumber: 4.3 Consensus size: 37
245916 AGGTTTTTTG
* *
245926 TGTTTCAAGAGAAACTGTCTCCAGAGAGGCAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
245963 TGTTTCAAGAGAAACATAT-TC-A-A-AG-----ATTGG
1 TGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAATT-T
*
245993 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* *
246030 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
246066 TGTTTCAAGAGA
1 TGTTTCAAGAGA
246078 GATGACCCCT
Statistics
Matches: 96, Mismatches: 8, Indels: 23
0.76 0.06 0.18
Matches are distributed among these distances:
29 5 0.05
30 17 0.18
31 1 0.01
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 14 0.15
37 49 0.51
38 4 0.04
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:246073 original size:21 final size:21
Alignment explanation
Indices: 246012--246079 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
246002 AGAAACTGTC
246012 TCAAGAGAGACAAAACTTTGTT
1 TCAAGAGAGACAAAA-TTTGTT
*
246034 TCAAG-G-G---AAA-TTGTC
1 TCAAGAGAGACAAAATTTGTT
246049 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
246070 TCAAGAGAGA
1 TCAAGAGAGA
246080 TGACCCCTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
15 9 0.24
16 1 0.03
17 4 0.11
20 4 0.11
21 15 0.39
22 5 0.13
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:246781 original size:110 final size:110
Alignment explanation
Indices: 246640--246837 Score: 333
Period size: 110 Copynumber: 1.8 Consensus size: 110
246630 ACTAGGAAAT
* *
246640 TGTTTGTTGACAGCCAGCCGCCCCTTTGCTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAATAT
1 TGTTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATAT
* *
246705 TCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGG
66 TCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGG
* * *
246750 TGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTTGAGTCCAATAT
1 TGTTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATAT
246815 TCTTCGCTGTGAAGTTAAAATTG
66 TCTTCGCTGTGAAGTTAAAATTG
246838 GCTATGAAAC
Statistics
Matches: 81, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
110 81 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (110 bp):
TGTTTGTTGACAGCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCCAATAT
TCTTCGCTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAAAGG
Found at i:251052 original size:3 final size:3
Alignment explanation
Indices: 251046--251114 Score: 61
Period size: 3 Copynumber: 21.3 Consensus size: 3
251036 GAAAAAAATG
251046 AAT AAT AAAT AAT AA- AAT AAT AAT AA- AAT AAAT AAAT AAT AAT AAAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT -AAT
251093 AAAT AAAT AAT AAT AAAT AAT A
1 -AAT -AAT AAT AAT -AAT AAT A
251115 TATTATCATT
Statistics
Matches: 60, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.07
3 32 0.53
4 24 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:251067 original size:11 final size:10
Alignment explanation
Indices: 251041--251114 Score: 88
Period size: 10 Copynumber: 7.8 Consensus size: 10
251031 AAAAAGAAAA
251041 AAATGAATAAT
1 AAAT-AATAAT
251052 AAATAAT-A-
1 AAATAATAAT
251060 AAATAATAAT
1 AAATAATAAT
251070 -AA-AATAAAT
1 AAATAAT-AAT
251079 AAATAATAAT
1 AAATAATAAT
251089 AAAT-A-AAT
1 AAATAATAAT
251097 AAATAATAAT
1 AAATAATAAT
251107 AAATAATA
1 AAATAATA
251115 TATTATCATT
Statistics
Matches: 56, Mismatches: 0, Indels: 15
0.79 0.00 0.21
Matches are distributed among these distances:
8 17 0.30
9 9 0.16
10 23 0.41
11 7 0.12
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.27
Consensus pattern (10 bp):
AAATAATAAT
Found at i:251069 original size:18 final size:18
Alignment explanation
Indices: 251041--251112 Score: 110
Period size: 18 Copynumber: 3.9 Consensus size: 18
251031 AAAAAGAAAA
251041 AAATGAATAATAAAT-AAT
1 AAAT-AATAATAAATAAAT
251059 AAAATAATAATAAAATAAAT
1 -AAATAATAAT-AAATAAAT
251079 AAATAATAATAAATAAAT
1 AAATAATAATAAATAAAT
251097 AAATAATAATAAATAA
1 AAATAATAATAAATAA
251113 TATATTATCA
Statistics
Matches: 51, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
18 30 0.59
19 18 0.35
20 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.01, T:0.26
Consensus pattern (18 bp):
AAATAATAATAAATAAAT
Found at i:251080 original size:4 final size:4
Alignment explanation
Indices: 251049--251112 Score: 61
Period size: 4 Copynumber: 17.2 Consensus size: 4
251039 AAAAATGAAT
251049 AATA AAT- AATA AA-A TAAT- AATAA AATA AATA AAT- AAT- AATA AATA
1 AATA AATA AATA AATA -AATA AAT-A AATA AATA AATA AATA AATA AATA
251094 AATA AAT- AAT- AATA AATA A
1 AATA AATA AATA AATA AATA A
251113 TATATTATCA
Statistics
Matches: 53, Mismatches: 0, Indels: 14
0.79 0.00 0.21
Matches are distributed among these distances:
3 19 0.36
4 31 0.58
5 3 0.06
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:251090 original size:37 final size:38
Alignment explanation
Indices: 251032--251109 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 38
251022 ATGTTAAACA
251032 AAAAGAAAAAAATGAATAATAAAT-AATAAAATAATAAT
1 AAAAGAAAAAAATGAATAATAAATAAAT-AAATAATAAT
* *
251070 AAAATAAATAAAT-AATAATAAATAAATAAATAATAAT
1 AAAAGAAAAAAATGAATAATAAATAAATAAATAATAAT
251107 AAA
1 AAA
251110 TAATATATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
37 23 0.62
38 14 0.38
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (38 bp):
AAAAGAAAAAAATGAATAATAAATAAATAAATAATAAT
Found at i:251693 original size:33 final size:33
Alignment explanation
Indices: 251652--251720 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
251642 ACTCAAATCT
*
251652 TTGGTTTTAGTGTTAT-AATATGACCCAAATACG
1 TTGGTTTTAGTGTT-TCAATAGGACCCAAATACG
*
251685 TTGGTTTTAGTGTTTCAATAGGACTCAAATACG
1 TTGGTTTTAGTGTTTCAATAGGACCCAAATACG
251718 TTG
1 TTG
251721 ATTTATTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 1 0.03
33 32 0.97
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.41
Consensus pattern (33 bp):
TTGGTTTTAGTGTTTCAATAGGACCCAAATACG
Found at i:251797 original size:13 final size:14
Alignment explanation
Indices: 251769--251800 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
251759 TGTGGGACCT
251769 ATAAAAATAATAAA
1 ATAAAAATAATAAA
251783 ATAAAAATAAT-AA
1 ATAAAAATAATAAA
251796 ATAAA
1 ATAAA
251801 TAAATATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
ATAAAAATAATAAA
Found at i:251801 original size:17 final size:17
Alignment explanation
Indices: 251769--251818 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
251759 TGTGGGACCT
251769 ATAAAAATAAT--A-AA
1 ATAAAAATAATAAATAA
251783 ATAAAAATAATAAATAA
1 ATAAAAATAATAAATAA
*
251800 ATAAATATAATATAATAA
1 ATAAAAATAATA-AATAA
251818 A
1 A
251819 ATATTTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 11 0.35
16 1 0.03
17 13 0.42
18 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATAATAAATAA
Found at i:252492 original size:3 final size:3
Alignment explanation
Indices: 252484--252531 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
252474 TTATTTATTT
252484 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
252532 TATATTTAGC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:253086 original size:11 final size:11
Alignment explanation
Indices: 253070--253094 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
253060 GATCTGATTC
253070 AACCCAACCCG
1 AACCCAACCCG
253081 AACCCAACCCG
1 AACCCAACCCG
253092 AAC
1 AAC
253095 TTATACTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.52, G:0.08, T:0.00
Consensus pattern (11 bp):
AACCCAACCCG
Found at i:255554 original size:167 final size:170
Alignment explanation
Indices: 255217--255555 Score: 404
Period size: 167 Copynumber: 2.0 Consensus size: 170
255207 ATTCCAATCG
* * * * *
255217 ATATTGTGCATTCTTAAACATATATCCAGTCATCATAACACTGTACATGAGTTGTGCAAGATTTT
1 ATATTGTGCATTCTTAAACACATATCCAGTAATCATAACACTATACATGAGTTGTACAAGATTCT
*
255282 CGGCAACCTAAAGGAGAAAATCAAAGAAATCCAAATGATTGTCTAAACCAACAATGGTCAAGTTC
66 CAGCAACCTAAAGGAGAAAATCAAAGAAATCCAAATGATTGTCTAAACCAACAATGGTCAAGTTC
* * * *
255347 AATAACACTAATAAACATGAACAAAATAGAACCGAAGAAC
131 AATAACACTAACAAACACGAACAAAATAGAAACAAAGAAC
* * * *
255387 ATATTTTGCATTCTTAAACACATATCTAGTAATCATAACACTATACATTAGTTTTACAAGA-TCT
1 ATATTGTGCATTCTTAAACACATATCCAGTAATCATAACACTATACATGAGTTGTACAAGATTCT
* ** *
255451 CAGCAACCTAAA-GTG-AAATCAAAGAGCTCCTAATGATTGTCTAAACCAAC-A-GG-CACTTAG
66 CAGCAACCTAAAGGAGAAAATCAAAGAAATCCAAATGATTGTCTAAACCAACAATGGTCA---AG
* * *
255511 TTCAATAACACTAACAATC-CGAGTCAAAATCGAAACAAAGAAC
128 TTCAATAACACTAACAAACACGA-ACAAAATAGAAACAAAGAAC
255554 AT
1 AT
255556 CTATTATCAC
Statistics
Matches: 144, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
164 2 0.01
165 2 0.01
166 3 0.02
167 69 0.48
168 2 0.01
169 13 0.09
170 53 0.37
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.25
Consensus pattern (170 bp):
ATATTGTGCATTCTTAAACACATATCCAGTAATCATAACACTATACATGAGTTGTACAAGATTCT
CAGCAACCTAAAGGAGAAAATCAAAGAAATCCAAATGATTGTCTAAACCAACAATGGTCAAGTTC
AATAACACTAACAAACACGAACAAAATAGAAACAAAGAAC
Found at i:273586 original size:38 final size:38
Alignment explanation
Indices: 273543--273662 Score: 129
Period size: 38 Copynumber: 3.2 Consensus size: 38
273533 AATAAAAAAA
273543 ATATATTAAGTTATTTGTATACAACTTTTATTACATATAT
1 ATATATTAAGTTATTTGTATACAACTTTTATTA-A-ATAT
* *** * * *
273583 ATATATATAAATTATAAATA-ATAA--TTTAATAAAAAT
1 ATATAT-TAAGTTATTTGTATACAACTTTTATTAAATAT
273619 ATATATTAAGTTATTTGTATACAACTTTTATTAAATAT
1 ATATATTAAGTTATTTGTATACAACTTTTATTAAATAT
273657 ATATAT
1 ATATAT
273663 ATAAATATAA
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
35 9 0.15
36 12 0.19
37 1 0.02
38 22 0.35
40 9 0.15
41 9 0.15
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (38 bp):
ATATATTAAGTTATTTGTATACAACTTTTATTAAATAT
Found at i:273623 original size:76 final size:73
Alignment explanation
Indices: 273537--273683 Score: 258
Period size: 76 Copynumber: 2.0 Consensus size: 73
273527 ATAAAAAATA
273537 AAAAAAATATATTAAGTTATTTGTATACAACTTTTATTACATATATATATATATAAATTATAAAT
1 AAAAAAATATATTAAGTTATTTGTATACAACTTTTATTA-A-ATATATATATATAAA-TATAAAT
273602 AATAATTTAAT
63 AATAATTTAAT
*
273613 AAAAATATATATTAAGTTATTTGTATACAACTTTTATTAAATATATATATATAAATATAAATAAT
1 AAAAAAATATATTAAGTTATTTGTATACAACTTTTATTAAATATATATATATAAATATAAATAAT
273678 AATTTA
66 AATTTA
273684 TTAAGTTATT
Statistics
Matches: 70, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
73 16 0.23
74 15 0.21
75 1 0.01
76 38 0.54
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (73 bp):
AAAAAAATATATTAAGTTATTTGTATACAACTTTTATTAAATATATATATATAAATATAAATAAT
AATTTAAT
Found at i:277544 original size:263 final size:260
Alignment explanation
Indices: 277065--277568 Score: 796
Period size: 263 Copynumber: 1.9 Consensus size: 260
277055 ACGGGCCAAT
* *
277065 ACTGATAGTTTAGGTACTAAACGCGTTAAGTTTTAAATGGTGGGATATTAAAATGAAACAAAAAC
1 ACTGATAGTTTAGGTACTAAACGCGTTAAGTTTTAAACGGTGGGATACTAAAATGAAACAAAAAC
* *
277130 TAAACGTTAGGCATGAATTTGAAAAAATCAAAATATTAGGTACTAAAACAAACTATGATAGTTTA
66 TAAACGTTAGACATGAATTTGAAAAAATCAAAATATTAGGTACTAAAACAAACAATGATAGTTTA
** ** *
277195 GGTACTAAATGTGTAGTTTGTCAATTTTTTGCATAATGCTAAATTGAGTTAATTACATCATATGT
131 GGTACTAAATGCATAGTTTACCAATTTTTTGCATAATGCTAAATTGAGTTAATTACATCATATAT
277260 CCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAATGTTCCAAATTCATCCCTAA
196 CCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAATGTTCCAAATTCATCCCTAA
277325 ACTGATAGTTTAGGTACTAAACGC-TCTAAGTTTTAAACGGTGGGATACTAAAATGAAACAAAAA
1 ACTGATAGTTTAGGTACTAAACGCGT-TAAGTTTTAAACGGTGGGATACTAAAATGAAACAAAAA
* ** ** *
277389 TTAAACGTTAGACATGGTTTTGAAAAAATTGAAATA-TAGGTACTAAAACAAACCAAAATTTATA
65 CTAAACGTTAGACATGAATTTGAAAAAATCAAAATATTAGGTACTAAAACAAA-C--AA-TGATA
*
277453 GTTTAGGTACTAAATGCATAGTTTACCCATTTTTTGCATAATGCTAAATTGAGTTAATTACATCA
126 GTTTAGGTACTAAATGCATAGTTTACCAATTTTTTGCATAATGCTAAATTGAGTTAATTACATCA
*
277518 TATATCCTCAAAATATGACTAACATTTTAAATTGGTCCCTAAACTTTAAAT
191 TATATCCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAAT
277569 TAGTCCCCAA
Statistics
Matches: 222, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
259 17 0.08
260 91 0.41
262 1 0.00
263 113 0.51
ACGTcount: A:0.40, C:0.13, G:0.14, T:0.33
Consensus pattern (260 bp):
ACTGATAGTTTAGGTACTAAACGCGTTAAGTTTTAAACGGTGGGATACTAAAATGAAACAAAAAC
TAAACGTTAGACATGAATTTGAAAAAATCAAAATATTAGGTACTAAAACAAACAATGATAGTTTA
GGTACTAAATGCATAGTTTACCAATTTTTTGCATAATGCTAAATTGAGTTAATTACATCATATAT
CCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAATGTTCCAAATTCATCCCTAA
Found at i:277698 original size:137 final size:137
Alignment explanation
Indices: 277452--277718 Score: 473
Period size: 137 Copynumber: 1.9 Consensus size: 137
277442 CAAAATTTAT
277452 AGTTTAGGTACTAAATGCATAGTTTACCCATTTTTTGCATAATGCTAAATTGAGTTAATTACATC
1 AGTTTAGGTACTAAATGCATAGTTTACCCATTTTTTGCATAATGCTAAATTGAGTTAATTACATC
*
277517 ATATATCCTCAAAATATGACTAACATTTTAAATTGGTCCCTAAACTTTAAATTAGTCCCCAAAAT
66 ATATATCCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAATTAGTCCCCAAAAT
277582 TTTTAAA
131 TTTTAAA
* *
277589 AGTTTAGGTACTAAATGCGTAGTTT-GCCATTTTTTTGCATAATGCTAAATTGAGTTAATTACAT
1 AGTTTAGGTACTAAATGCATAGTTTACCCA-TTTTTTGCATAATGCTAAATTGAGTTAATTACAT
* *
277653 CATATGTCCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAATTAGTCCTCAAAA
65 CATATATCCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAATTAGTCCCCAAAA
277718 T
130 T
277719 ATGTTCCAAA
Statistics
Matches: 124, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
136 3 0.02
137 121 0.98
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (137 bp):
AGTTTAGGTACTAAATGCATAGTTTACCCATTTTTTGCATAATGCTAAATTGAGTTAATTACATC
ATATATCCTCAAAATATGACCAACATTTTAAATTGGTCCCTAAACTTTAAATTAGTCCCCAAAAT
TTTTAAA
Found at i:277789 original size:55 final size:55
Alignment explanation
Indices: 277729--277832 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 55
277719 ATGTTCCAAA
277729 TTCATCCGT-AAACTATAACCA-TCATTCTAAATTAGTCCCCAAACTTTTTAAAAGT
1 TTCAT-CGTCAAACTATAA-CATTCATTCTAAATTAGTCCCCAAACTTTTTAAAAGT
* * *
277784 TTCATCTTCAAACTATGACATTCATTTTAAATTAGTCCCCAAACTTTTT
1 TTCATCGTCAAACTATAACATTCATTCTAAATTAGTCCCCAAACTTTTT
277833 GAGCATTCCA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
54 4 0.09
55 40 0.91
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (55 bp):
TTCATCGTCAAACTATAACATTCATTCTAAATTAGTCCCCAAACTTTTTAAAAGT
Found at i:278145 original size:60 final size:60
Alignment explanation
Indices: 278011--278147 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
278001 GAAAGTTTGG
* * *
278011 GGACCAATTTAAAAAGAGTGTCATAGTTCACGGATGAAATTAGAATATTAAAAAGTCTAG
1 GGACCAATTTAAAATGAGAGTCATAGTTCACGGATGAAATTAGAATATTAAAAAGTCTAA
* * * *
278071 GGACTAATTTAAAATGAGAGTCATAGTTC-GGGAATGAAATT-GAAATATTCAAAAGTTTAA
1 GGACCAATTTAAAATGAGAGTCATAGTTCACGG-ATGAAATTAG-AATATTAAAAAGTCTAA
**
278131 GGACCGGTTTAAAATGA
1 GGACCAATTTAAAATGA
278148 AGATTATAGT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 3 0.05
60 62 0.95
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (60 bp):
GGACCAATTTAAAATGAGAGTCATAGTTCACGGATGAAATTAGAATATTAAAAAGTCTAA
Found at i:283429 original size:36 final size:36
Alignment explanation
Indices: 283382--283453 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
283372 TCAAGAAGAG
283382 AATGGTTCCATCATTATGAACCTGTCTCAGGAGGAT
1 AATGGTTCCATCATTATGAACCTGTCTCAGGAGGAT
283418 AATGGTTCCATCATTATGAACCTGTCTCAGGAGGAT
1 AATGGTTCCATCATTATGAACCTGTCTCAGGAGGAT
283454 CTGTGTATAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (36 bp):
AATGGTTCCATCATTATGAACCTGTCTCAGGAGGAT
Done.