Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005078.1 Hibiscus syriacus cultivar Beakdansim tig00011407_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: 106783
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:15678 original size:12 final size:12
Alignment explanation
Indices: 15661--15685 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15651 AGTCACTCGT
15661 CCATAACCACAA
1 CCATAACCACAA
15673 CCATAACCACAA
1 CCATAACCACAA
15685 C
1 C
15686 TCGGCCTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.44, G:0.00, T:0.08
Consensus pattern (12 bp):
CCATAACCACAA
Found at i:34246 original size:19 final size:19
Alignment explanation
Indices: 34224--34264 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
34214 CCCAACCAAG
34224 TCAGACCGGTCCAACCGGT
1 TCAGACCGGTCCAACCGGT
* **
34243 TCAGACTGGTTTAACCGGT
1 TCAGACCGGTCCAACCGGT
34262 TCA
1 TCA
34265 ATATACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.24
Consensus pattern (19 bp):
TCAGACCGGTCCAACCGGT
Found at i:36513 original size:31 final size:31
Alignment explanation
Indices: 36478--36579 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
36468 GTCCATAAGA
36478 AATTATCAGTCGATGCTGAACCGATACAAGG
1 AATTATCAGTCGATGCTGAACCGATACAAGG
** * *
36509 AATTATCAG-CAGCGGCTGAACCTGCCAGAGATAGG
1 AATTATCAGTC-GATGCTGAACC-G--ATACA-AGG
* * *
36544 AATTACCAGTCGGTGCTGAACCTATACAAGG
1 AATTATCAGTCGATGCTGAACCGATACAAGG
36575 AATTA
1 AATTA
36580 CTAGCAACGA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
30 1 0.02
31 26 0.47
32 4 0.07
34 3 0.05
35 20 0.36
36 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (31 bp):
AATTATCAGTCGATGCTGAACCGATACAAGG
Found at i:36594 original size:66 final size:66
Alignment explanation
Indices: 36478--36604 Score: 193
Period size: 66 Copynumber: 1.9 Consensus size: 66
36468 GTCCATAAGA
* * *
36478 AATTATCAGTCGATGCTGAACCGATACAAGGAATTATCAGCAGCGGCTGAACCTGCCAGAGATAG
1 AATTACCAGTCGATGCTGAACCGATACAAGGAATTATCAGCAACGACTGAACCTGCCAGAGATAG
36543 G
66 G
* *
36544 AATTACCAGTCGGTGCTGAACCTATACAAGGAATTA-CTAGCAACGACTGAACCTGCCAGAG
1 AATTACCAGTCGATGCTGAACCGATACAAGGAATTATC-AGCAACGACTGAACCTGCCAGAG
36605 TCTTCATACC
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 1 0.02
66 54 0.98
ACGTcount: A:0.34, C:0.23, G:0.24, T:0.20
Consensus pattern (66 bp):
AATTACCAGTCGATGCTGAACCGATACAAGGAATTATCAGCAACGACTGAACCTGCCAGAGATAG
G
Found at i:44750 original size:381 final size:381
Alignment explanation
Indices: 44047--44755 Score: 1319
Period size: 381 Copynumber: 1.9 Consensus size: 381
44037 TAATTGAATT
* * *
44047 TAAAATTCAATTAATAAGAAATCCTAAAATTGTCATTAATGAATCATGATAATTACCATTTTCCA
1 TAAAATTCAATTAATAAGAAATCCTAAAATTATCATTAATGAATCATGATAATTACCACTTGCCA
44112 TTGAAATATCTTCCATCAAAACATATCATAGTCAAAGATGAACCAACTTGAGGTTGATTTTCTAC
66 TTGAAATATCTTCCATCAAAACATATCATAGTCAAAGATGAACCAACTTGAGGTTGATTTTCTAC
* *
44177 TTTTTCCATGCAATTTTCAAATATTTTAATTTAGTCGCCAATTTTTCCAATTCAACTAAGTAGTG
131 TTTTGCCATGCAATTTTCAAATATTTTAATTTAGTCACCAATTTTTCCAATTCAACTAAGTAGTG
* *
44242 AAAATTAACTTCAATTCCATTGATCCATGCTAAATTGCACTATTCTAAAACATTGAAATAATATT
196 AAAATTAACTTCAATTCCACTGATCCATGCTAAATTGCACTATTCTAAAACATGGAAATAATATT
44307 TCCAACATTTATCTAACATCCTTCAAATTTTAGTGAAATTCTGGTTCGATCTGATATCTGATTTC
261 TCCAACATTTATCTAACATCCTTCAAATTTTAGTGAAATTCTGGTTCGATCTGATATCTGATTTC
44372 TTATGGGACTTTACTATTTTATATCTTTTAATACAAATCCCTAATCAAAATTATGA
326 TTATGGGACTTTACTATTTTATATCTTTTAATACAAATCCCTAATCAAAATTATGA
44428 TAAAATTCAATTAATAAGAAATCCTAAAATTATCATTAATGAATCATGATAATTACCACTTGCCA
1 TAAAATTCAATTAATAAGAAATCCTAAAATTATCATTAATGAATCATGATAATTACCACTTGCCA
*
44493 TTGAAATATCTTCCATCAAAACATATCATAGTTAAAGATGAACCAACTTGAGGTTGATTTTCTAC
66 TTGAAATATCTTCCATCAAAACATATCATAGTCAAAGATGAACCAACTTGAGGTTGATTTTCTAC
44558 TTTTGCCATGCAATTTTCAAATATTTTAATTTAGTCACCAATTTTTCCAATTCAACTAAGTAGTG
131 TTTTGCCATGCAATTTTCAAATATTTTAATTTAGTCACCAATTTTTCCAATTCAACTAAGTAGTG
* * *
44623 AAAATTAACTTCAATTCTACTGATCCATGCTAAATTTCACTATTCTAAAATATGGAAATAATATT
196 AAAATTAACTTCAATTCCACTGATCCATGCTAAATTGCACTATTCTAAAACATGGAAATAATATT
44688 TCCAACATTTATCTAACATCCTTCAAATTTTAGTGAAATTCTGGTTCGATCTGATATCTGATTTC
261 TCCAACATTTATCTAACATCCTTCAAATTTTAGTGAAATTCTGGTTCGATCTGATATCTGATTTC
44753 TTA
326 TTA
44756 AAGGGCATGC
Statistics
Matches: 317, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
381 317 1.00
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (381 bp):
TAAAATTCAATTAATAAGAAATCCTAAAATTATCATTAATGAATCATGATAATTACCACTTGCCA
TTGAAATATCTTCCATCAAAACATATCATAGTCAAAGATGAACCAACTTGAGGTTGATTTTCTAC
TTTTGCCATGCAATTTTCAAATATTTTAATTTAGTCACCAATTTTTCCAATTCAACTAAGTAGTG
AAAATTAACTTCAATTCCACTGATCCATGCTAAATTGCACTATTCTAAAACATGGAAATAATATT
TCCAACATTTATCTAACATCCTTCAAATTTTAGTGAAATTCTGGTTCGATCTGATATCTGATTTC
TTATGGGACTTTACTATTTTATATCTTTTAATACAAATCCCTAATCAAAATTATGA
Found at i:50205 original size:21 final size:21
Alignment explanation
Indices: 50163--50215 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
50153 ATTCTGACTA
50163 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
50184 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
* *
50205 TTGCAATGCGA
1 TCGCATTGCGA
50216 ATACGTAAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:50232 original size:20 final size:20
Alignment explanation
Indices: 50207--50330 Score: 137
Period size: 20 Copynumber: 6.2 Consensus size: 20
50197 TTCCTAATTT
*
50207 GCAATGCGAATACGTAAATC
1 GCAATGCGATTACGTAAATC
* *
50227 GCAATGCGAATTAGGAAAATC
1 GCAATGCG-ATTACGTAAATC
50248 GCAATGCGATTACGTAAATC
1 GCAATGCGATTACGTAAATC
* *
50268 GCATTGCGATTACGT-ATTC
1 GCAATGCGATTACGTAAATC
*
50287 GCATTGCGATTTACGT-AATC
1 GCAATGCGA-TTACGTAAATC
*
50307 GCATTGCGATTTA-GTAAATC
1 GCAATGCGA-TTACGTAAATC
50327 GCAA
1 GCAA
50331 CGAGATTCTG
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
19 14 0.15
20 61 0.66
21 17 0.18
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (20 bp):
GCAATGCGATTACGTAAATC
Found at i:51244 original size:24 final size:24
Alignment explanation
Indices: 51193--51246 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
51183 GTATTCGAAA
*
51193 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
51217 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
51241 TTTGAT
1 TTTGAT
51247 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:53786 original size:20 final size:20
Alignment explanation
Indices: 53719--53814 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
53709 GGCATTCATT
*
53719 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
53739 TGAC-ATTCGCAATCATC-TTAA
1 TGACTA-TCGCAA-C-GCGGAAA
*
53760 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
53780 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
53799 TGAAAATCGCAACGCG
1 TGACTATCGCAACGCG
53815 AATTTAGTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
19 18 0.31
20 26 0.45
21 12 0.21
22 2 0.03
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:53800 original size:19 final size:19
Alignment explanation
Indices: 53758--53816 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
53748 CAATCATCTT
*
53758 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
53778 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
53797 AATGAAAATCGCAACGCGA
1 AATGACTATCGCAACGCGA
53816 A
1 A
53817 TTTAGTTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:53913 original size:38 final size:38
Alignment explanation
Indices: 53841--53914 Score: 121
Period size: 38 Copynumber: 1.9 Consensus size: 38
53831 GCGATTTTTT
* **
53841 CGTTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCG
53879 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTT
1 CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTT
53915 TTGCCTTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (38 bp):
CGTTGCGATTTTCATTTCGCATTGCGATAGTCATTTCG
Found at i:53914 original size:19 final size:19
Alignment explanation
Indices: 53822--53906 Score: 126
Period size: 19 Copynumber: 4.7 Consensus size: 19
53812 GCGAATTTAG
53822 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
53838 TTT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
53855 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
53874 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
53893 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
53907 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
14 8 0.13
15 3 0.05
16 3 0.05
17 3 0.05
19 46 0.73
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:54031 original size:14 final size:14
Alignment explanation
Indices: 54012--54048 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
54002 CATCAATTAA
54012 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
54026 ACAAATCATCTTTT
1 ACAAATCAACTTTT
54040 ACAAATCAA
1 ACAAATCAA
54049 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:56189 original size:94 final size:94
Alignment explanation
Indices: 56076--56346 Score: 380
Period size: 94 Copynumber: 3.0 Consensus size: 94
56066 GCATTACTTC
* *
56076 AACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
56141 ATTGGCAGCAAACGAACAAATTTACTTTA
66 ATTGGCAGCAAACGAACAAATTTACTTTA
56170 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
1 AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
* * *
56235 ATTGGCAGC-AAC---CGAATATAC-TTC
66 ATTGGCAGCAAACGAACAAATTTACTTTA
*
56259 AACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGTTTAGCAG
1 AACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAG
* * * *
56320 TATTGGCAACAACCGAATAAATTTACT
65 AATTGGCAGCAAACGAACAAATTTACT
56347 AAGCAATCTA
Statistics
Matches: 159, Mismatches: 12, Indels: 15
0.85 0.06 0.08
Matches are distributed among these distances:
86 24 0.15
87 2 0.01
89 18 0.11
90 40 0.25
93 3 0.02
94 72 0.45
ACGTcount: A:0.49, C:0.18, G:0.13, T:0.20
Consensus pattern (94 bp):
AACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGCAGA
ATTGGCAGCAAACGAACAAATTTACTTTA
Found at i:57172 original size:21 final size:22
Alignment explanation
Indices: 57130--57172 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
57120 AATAACAAAC
*
57130 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
57152 ATTA-TAATT-TTAAAAATATTA
1 ATTAGTAATTGTTAAAAA-ATTA
57173 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:58045 original size:20 final size:20
Alignment explanation
Indices: 58020--58062 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
58010 TTTTGGTTAA
58020 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
58040 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
58060 AAT
1 AAT
58063 CGCAACACGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.14, G:0.23, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:58085 original size:33 final size:34
Alignment explanation
Indices: 58026--58100 Score: 118
Period size: 33 Copynumber: 2.2 Consensus size: 34
58016 TTAAAATGAA
*
58026 AATCGCAACGAGAGAATGAAAATCGCAACGAGAG
1 AATCGCAACGAGAGAATAAAAATCGCAACGAGAG
58060 AATCGCAAC-ACGA-AATAAAAATCGCAACGAGAG
1 AATCGCAACGA-GAGAATAAAAATCGCAACGAGAG
58093 AATCGCAA
1 AATCGCAA
58101 TGCGATTTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 28 0.72
34 11 0.28
ACGTcount: A:0.49, C:0.20, G:0.21, T:0.09
Consensus pattern (34 bp):
AATCGCAACGAGAGAATAAAAATCGCAACGAGAG
Found at i:58741 original size:20 final size:20
Alignment explanation
Indices: 58718--58805 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
58708 TCAGATACGT
58718 ATTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
* *
58738 ATTGCGATTTTCCTAATTCGC
1 ATTGCGATTTACGT-ATTCGC
* *
58759 ATTGCGATTTACTTAATCGC
1 ATTGCGATTTACGTATTCGC
*
58779 GTTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTATTCGC
58799 ATTGCGA
1 ATTGCGA
58806 ATTAGGAAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 40 0.69
21 18 0.31
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (20 bp):
ATTGCGATTTACGTATTCGC
Found at i:58770 original size:41 final size:40
Alignment explanation
Indices: 58718--58805 Score: 122
Period size: 41 Copynumber: 2.2 Consensus size: 40
58708 TCAGATACGT
* *
58718 ATTGCGATTTACGTATTCGCATTGCGATTTTCCTAATTCGC
1 ATTGCGATTTACGTAATCGCATTGCGATTTACCT-ATTCGC
* * *
58759 ATTGCGATTTACTTAATCGCGTTGCGATTTACGTATTCGC
1 ATTGCGATTTACGTAATCGCATTGCGATTTACCTATTCGC
58799 ATTGCGA
1 ATTGCGA
58806 ATTAGGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 13 0.31
41 29 0.69
ACGTcount: A:0.20, C:0.20, G:0.19, T:0.40
Consensus pattern (40 bp):
ATTGCGATTTACGTAATCGCATTGCGATTTACCTATTCGC
Found at i:58826 original size:21 final size:21
Alignment explanation
Indices: 58802--58847 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
58792 TATTCGCATT
58802 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
58823 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
58844 GCGA
1 GCGA
58848 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:59635 original size:19 final size:20
Alignment explanation
Indices: 59606--59645 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
59596 AAATAAAATA
* *
59606 ATATATTAAAATTTTATTTT
1 ATATATTAAAAGTTTAATTT
59626 ATAT-TTAAAAGTTTAATTT
1 ATATATTAAAAGTTTAATTT
59645 A
1 A
59646 GCTCTAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
ATATATTAAAAGTTTAATTT
Found at i:59644 original size:20 final size:20
Alignment explanation
Indices: 59606--59644 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
59596 AAATAAAATA
*
59606 ATATATTAAAATTTTATTTT
1 ATATATTAAAATTTAATTTT
59626 ATAT-TTAAAAGTTTAATTT
1 ATATATTAAAA-TTTAATTT
59645 AGCTCTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATATATTAAAATTTAATTTT
Found at i:60667 original size:24 final size:25
Alignment explanation
Indices: 60640--60686 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
60630 TTGTTTTTAT
*
60640 TTTAATTACT-TAACTTTCAAATAA
1 TTTAATAACTCTAACTTTCAAATAA
60664 TTTAATAACTCTAACTTTCAAAT
1 TTTAATAACTCTAACTTTCAAAT
60687 TTATTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTAATAACTCTAACTTTCAAATAA
Found at i:61865 original size:23 final size:22
Alignment explanation
Indices: 61839--61882 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
61829 ATTAATTTTC
*
61839 TTTAAAAAAATCTTAAAATTCCT
1 TTTAAAAAAATC-CAAAATTCCT
61862 TTTAAAAAAATCCAAAATTCC
1 TTTAAAAAAATCCAAAATTCC
61883 AAAAAAAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (22 bp):
TTTAAAAAAATCCAAAATTCCT
Found at i:70701 original size:29 final size:29
Alignment explanation
Indices: 70669--70724 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
70659 TTATCTCCTC
70669 ACTTAT-ATTCTAATCATTAAAATTTAATT
1 ACTTATAATT-TAATCATTAAAATTTAATT
* * *
70698 ACTTTTAATTTAATCATTCAACTTTAA
1 ACTTATAATTTAATCATTAAAATTTAA
70725 ATATTAAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (29 bp):
ACTTATAATTTAATCATTAAAATTTAATT
Found at i:71500 original size:66 final size:66
Alignment explanation
Indices: 71394--71517 Score: 203
Period size: 66 Copynumber: 1.9 Consensus size: 66
71384 TAGGTCCATA
*
71394 AGGAATTATCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTGCCAGAGA
1 AGGAATTACCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTGCCAGAGA
71459 T
66 T
* * * *
71460 AGGAATTGCCAGTCGGTGTTGAACCTATATAAGGAATTACCAGCATCGACTGAACCTG
1 AGGAATTACCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTG
71518 TAAGAGTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (66 bp):
AGGAATTACCAGTCGGTGTTGAACCTATACAAGAAATTACCAGCAGCGACTGAACCTGCCAGAGA
T
Found at i:73538 original size:5 final size:5
Alignment explanation
Indices: 73528--73553 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
73518 TATTATTATT
73528 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
73554 TTTTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:76248 original size:17 final size:18
Alignment explanation
Indices: 76213--76249 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
76203 TTTCACCTAT
76213 AATTATTAAAAAAATTAA
1 AATTATTAAAAAAATTAA
76231 AATTA-TAAAATAAA-TAA
1 AATTATTAAAA-AAATTAA
76248 AA
1 AA
76250 CAATATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATTATTAAAAAAATTAA
Found at i:76293 original size:19 final size:19
Alignment explanation
Indices: 76271--76323 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
76261 TAATTTTCAC
* *
76271 TAATTCAAATAATATAAAT
1 TAATTAAAATAATATAAAA
* * *
76290 TAATTTAAGTAATTTAAAA
1 TAATTAAAATAATATAAAA
*
76309 TAAATAAAATAATAT
1 TAATTAAAATAATAT
76324 TTTTTTTGGG
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
TAATTAAAATAATATAAAA
Found at i:78436 original size:1 final size:1
Alignment explanation
Indices: 78430--78466 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
78420 GCTTATTACC
* *
78430 TTTTTTTCTTTTCTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
78467 GCTCCCTTGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:79894 original size:30 final size:30
Alignment explanation
Indices: 79858--80102 Score: 302
Period size: 30 Copynumber: 8.2 Consensus size: 30
79848 GTAGGTCAAC
* *
79858 CCTTTAAGTTTATATTTTTACTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
*
79888 CCTTTAA-TTT-TATGTTTTTGCTATTTTAAT
1 CCTTTAAGTTTCTAT-TTTTT-CTATTTTAGT
*
79918 CTTTTAAGTTTCTATTTTTT-TATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
* * * *
79947 CCTTTAAATTTTTGTTTTTTCTTTTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
*
79977 CCTTTAAGTTTTTATTTTTTCTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
80007 CCTTTAAGTTTCTA-TTTTTCTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
*
80036 CCTTTAACTTTCTATTTTTTCTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGT
* * *
80066 CCCTTAAGTTCCTATTTTTGT-TATTTTGGT
1 CCTTTAAGTTTCTATTTTT-TCTATTTTAGT
*
80096 CCATTAA
1 CCTTTAA
80103 ATCATTGAGT
Statistics
Matches: 189, Mismatches: 19, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.02
29 59 0.31
30 115 0.61
31 9 0.05
32 3 0.02
ACGTcount: A:0.18, C:0.12, G:0.07, T:0.63
Consensus pattern (30 bp):
CCTTTAAGTTTCTATTTTTTCTATTTTAGT
Found at i:79965 original size:89 final size:88
Alignment explanation
Indices: 79858--80092 Score: 303
Period size: 89 Copynumber: 2.6 Consensus size: 88
79848 GTAGGTCAAC
* * *
79858 CCTTTAAGTTTATATTTTTACTATTTTAGTCCTTTAA-TTTTATGTTTTTGCTATTTTAATCTTT
1 CCTTTAAATTTATATTTTTTCTATTTTAGTCCTTTAAGTTTTAT-TTTTT-CTATTTTAATCCTT
*
79922 TAAGTTTCTATTTTTTTATTTTAGT
64 TAAGTTTCTATTTTTCTATTTTAGT
* * * *
79947 CCTTTAAATTTTTGTTTTTTCTTTTTTAGTCCTTTAAGTTTTTATTTTTTCTATTTTAGTCCTTT
1 CCTTTAAATTTATATTTTTTCTATTTTAGTCCTTTAAG-TTTTATTTTTTCTATTTTAATCCTTT
80012 AAGTTTCTATTTTTCTATTTTAGT
65 AAGTTTCTATTTTTCTATTTTAGT
* * * *
80036 CCTTTAACTTTCTATTTTTTCTATTTTAGTCCCTTAAGTTCCTATTTTTGT-TATTTT
1 CCTTTAAATTTATATTTTTTCTATTTTAGTCCTTTAAGTT-TTATTTTT-TCTATTTT
80093 GGTCCATTAA
Statistics
Matches: 128, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
88 2 0.02
89 114 0.89
90 6 0.05
91 6 0.05
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.64
Consensus pattern (88 bp):
CCTTTAAATTTATATTTTTTCTATTTTAGTCCTTTAAGTTTTATTTTTTCTATTTTAATCCTTTA
AGTTTCTATTTTTCTATTTTAGT
Found at i:80073 original size:59 final size:60
Alignment explanation
Indices: 79858--80102 Score: 305
Period size: 59 Copynumber: 4.1 Consensus size: 60
79848 GTAGGTCAAC
* * * * * *
79858 CCTTTAAGTTTATATTTTTACTATTTTAGTCCTTTAATTTTATGTTTTTGCTATTTTAAT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
* * * * * *
79918 CTTTTAAGTTTCTATTTTTT-TATTTTAGTCCTTTAAATTTTTGTTTTTTCTTTTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
*
79977 CCTTTAAGTTTTTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTT-CTATTTTAGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
* * * * *
80036 CCTTTAACTTTCTATTTTTTCTATTTTAGTCCCTTAAGTTCCTATTTTTGTTATTTTGGT
1 CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
*
80096 CCATTAA
1 CCTTTAA
80103 ATCATTGAGT
Statistics
Matches: 162, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
59 106 0.65
60 56 0.35
ACGTcount: A:0.18, C:0.12, G:0.07, T:0.63
Consensus pattern (60 bp):
CCTTTAAGTTTCTATTTTTTCTATTTTAGTCCTTTAAGTTTCTATTTTTGCTATTTTAGT
Found at i:85564 original size:29 final size:28
Alignment explanation
Indices: 85532--85587 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
85522 ATTTCAAAAT
85532 TATA-ATTATGAAA-AAAATATTAATTTA
1 TATATATTAT-AAATAAAATATTAATTTA
*
85559 TATATATTATAAATAAAATATTTATTTA
1 TATATATTATAAATAAAATATTAATTTA
85587 T
1 T
85588 TTAGAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 7 0.27
28 19 0.73
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TATATATTATAAATAAAATATTAATTTA
Found at i:85682 original size:20 final size:19
Alignment explanation
Indices: 85643--85684 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
85633 TTTCTTCGAT
85643 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
85662 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
85682 ATT
1 ATT
85685 TATAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:85700 original size:120 final size:118
Alignment explanation
Indices: 85550--85787 Score: 293
Period size: 120 Copynumber: 2.0 Consensus size: 118
85540 TGAAAAAAAT
* * * *
85550 ATTAATTTATATATATTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAA-GGACTTCTA
1 ATTAATATATATATATTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGG-CATCCA
* *
85614 AGTGCCTTAAGACAGCTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACA
65 AGTGCCTTAAGACAGC-CATTTCTT-AATATTAAAAAATAAATAAAT-ATTAAAACA
**
85671 ATTAATATATA-AT-TTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGCATCCA
1 ATTAATATATATATATTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGCATCCA
* ** * *
85734 ATTGTTTTAAGACTGCCATTTCTTAATATTGAAAAATAAATAAATATTAAAACA
65 AGTGCCTTAAGACAGCCATTTCTTAATATTAAAAAATAAATAAATATTAAAACA
85788 GGATTAAAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
117 9 0.09
118 19 0.19
119 11 0.11
120 51 0.50
121 12 0.12
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (118 bp):
ATTAATATATATATATTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGGCATCCAA
GTGCCTTAAGACAGCCATTTCTTAATATTAAAAAATAAATAAATATTAAAACA
Found at i:85847 original size:22 final size:22
Alignment explanation
Indices: 85822--85864 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
85812 TAAATAAGAT
85822 TTTAATAAATAAATAAATATTA
1 TTTAATAAATAAATAAATATTA
* * *
85844 TTTATTATATAAATATATATT
1 TTTAATAAATAAATAAATATT
85865 TATGGCTAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATAAATAAATAAATATTA
Found at i:85877 original size:22 final size:18
Alignment explanation
Indices: 85831--85867 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
85821 TTTTAATAAA
85831 TAAATAAATATTATTTAT
1 TAAATAAATATTATTTAT
*
85849 TATATAAATATATATTTAT
1 TAAATAAATAT-TATTTAT
85868 GGCTAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAATAAATATTATTTAT
Found at i:87657 original size:76 final size:76
Alignment explanation
Indices: 87531--88474 Score: 1629
Period size: 76 Copynumber: 12.4 Consensus size: 76
87521 AGGTCCTAAA
* * *
87531 AAACATCATGCACTGAAGGGA-TTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGTA-GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
*
87595 AAGGTTTTTTGG
65 AAGGCTTTTTGG
* * *
87607 AAACATGATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
87672 AGGCTTTTTGG
66 AGGCTTTTTGG
*
87683 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
87748 AGGATTTTTGG
66 AGGCTTTTTGG
87759 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
87824 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
87836 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
87901 AGGCTTTTTGG
66 AGGCTTTTTGG
*
87912 AAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
87977 AGGCTTTTTGG
66 AGGCTTTTTGG
*
87988 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
88053 AAGGCTTTTTGG
65 AAGGCTTTTTGG
* * *
88065 AAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCTGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
88130 AGGCTTTTTGG
66 AGGCTTTTTGG
*
88141 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
88206 AGGCTTTTTGG
66 AGGCTTTTTGG
*
88217 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
*
88282 AGGCTTTTTTG
66 AGGCTTTTTGG
*
88293 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAAAAAGCTCCCGA
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
88358 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
88369 AAACATCATGCACTATAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
88434 AAGGCTTTTTGG
65 AAGGCTTTTTGG
*
88446 AAACATCATGCACTGCAGGACTTACAGAT
1 AAACATCATGCACTGTAGGACTTACAGAT
88475 ATGAGAAATA
Statistics
Matches: 828, Mismatches: 36, Indels: 7
0.95 0.04 0.01
Matches are distributed among these distances:
75 3 0.00
76 626 0.76
77 199 0.24
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (76 bp):
AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGG
Found at i:87931 original size:229 final size:228
Alignment explanation
Indices: 87531--88474 Score: 1629
Period size: 229 Copynumber: 4.1 Consensus size: 228
87521 AGGTCCTAAA
* * *
87531 AAACATCATGCACTGAAGGGA-TTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGCA-GGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCG
* * * *
87595 AAGGTTTTTTGGAAACATGATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCA
*
87660 AAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
*
87725 TGAAAACATCAAAAAGCTCCCGAAGGATTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
*
87759 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
*
87824 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCA
*
87889 AAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
87954 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
87988 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCG
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCCG
* *
88053 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACATATGACCCTAAGGCTTTGAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCA
* *
88118 AAAAGCTCCTGAAGGCTTTTTGGAAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
88183 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
* *
88217 AAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGATTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
* * * *
88282 AGGCTTTTTTGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAATATCAA
66 AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAA
*
88347 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
*
88412 AAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGG
196 GAAAACAT-CAAAAAGCTCCCGAAGGCTTTTTGG
88446 AAACATCATGCACTGCAGGACTTACAGAT
1 AAACATCATGCACTGCAGGACTTACAGAT
88475 ATGAGAAATA
Statistics
Matches: 688, Mismatches: 25, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
227 3 0.00
228 188 0.27
229 497 0.72
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (228 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTAAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:88122 original size:305 final size:305
Alignment explanation
Indices: 87531--88474 Score: 1667
Period size: 305 Copynumber: 3.1 Consensus size: 305
87521 AGGTCCTAAA
*
87531 AAACATCATGCACTGAAGGGA-TTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCG
1 AAACATCATGCACTGCA-GGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCG
* * * *
87595 AAGGTTTTTTGGAAACATGATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCA
65 AAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGATTTGAAAACATCA
*
87660 AAAAGCTCCCGAAGGCTTTTTGGAAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
130 AAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTT
*
87725 TGAAAACATCAAAAAGCTCCCGAAGGATTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA
195 TGAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA
87790 CCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGG
260 CCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGG
87836 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
* *
87901 AGGCTTTTTGGAAATATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGATTTGAAAACATCAA
*
87966 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
* *
88031 GAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGCAGGACTTACATATGA
196 GAAAACAT-CAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGA
*
88096 CCCTAAGGCTTTGAAAACAT-CAAAAAGCTCCTGAAGGCTTTTTGG
260 CCCTAAGGCTTTGAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGG
* * * *
88141 AAACATCATGCATTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
88206 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGATTTGAAAACATCAA
66 AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGATTTGAAAACATCAA
*
88271 AAAGCTCCCGAAGGCTTTTTTGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
131 AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
* *
88336 GAAAATATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTATAGGACTTACAGATGAC
196 GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGAC
*
88401 CCTAAGGCTTTAAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGG
261 CCTAAGGCTTTGAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGG
88446 AAACATCATGCACTGCAGGACTTACAGAT
1 AAACATCATGCACTGCAGGACTTACAGAT
88475 ATGAGAAATA
Statistics
Matches: 608, Mismatches: 28, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
304 75 0.12
305 460 0.76
306 73 0.12
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (305 bp):
AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTAAAAACATCAAAAAGCTCCCGA
AGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGATTTGAAAACATCAA
AAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTT
GAAAACATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGTAGGACTTACAGATGAC
CCTAAGGCTTTGAAAACATCCAAAAAGCTCCCGAAGGCTTTTTGG
Found at i:93960 original size:10 final size:9
Alignment explanation
Indices: 93945--94034 Score: 50
Period size: 8 Copynumber: 10.6 Consensus size: 9
93935 CCCCTTTTTC
*
93945 TTTTTCCCT
1 TTTTTTCCT
93954 TTTTTTCC-
1 TTTTTTCCT
93962 TTTTTT-CT
1 TTTTTTCCT
*
93970 CATTTTT-CT
1 -TTTTTTCCT
*
93979 TTTTTTCAT
1 TTTTTTCCT
*
93988 CTTTTTCC-
1 TTTTTTCCT
93996 TTTTTT-CT
1 TTTTTTCCT
**
94004 CATTTTCC-
1 TTTTTTCCT
*
94012 TTTTTTCAT
1 TTTTTTCCT
94021 CTTTTTT-CT
1 -TTTTTTCCT
94030 TTTTT
1 TTTTT
94035 CTTTCTTTGC
Statistics
Matches: 61, Mismatches: 13, Indels: 15
0.69 0.15 0.17
Matches are distributed among these distances:
7 2 0.03
8 30 0.49
9 23 0.38
10 6 0.10
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTTCCT
Found at i:93975 original size:17 final size:16
Alignment explanation
Indices: 93955--94036 Score: 110
Period size: 17 Copynumber: 4.9 Consensus size: 16
93945 TTTTTCCCTT
93955 TTTTTCCTTTTTTCTC
1 TTTTTCCTTTTTTCTC
*
93971 ATTTTTCTTTTTTTCATC
1 -TTTTTCCTTTTTTC-TC
93989 TTTTTCCTTTTTTCTC
1 TTTTTCCTTTTTTCTC
*
94005 ATTTTCCTTTTTTCATC
1 TTTTTCCTTTTTTC-TC
*
94022 TTTTTTCTTTTTTCT
1 TTTTTCCTTTTTTCT
94037 TTCTTTGCTG
Statistics
Matches: 58, Mismatches: 5, Indels: 5
0.85 0.07 0.07
Matches are distributed among these distances:
16 16 0.28
17 40 0.69
18 2 0.03
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTCCTTTTTTCTC
Found at i:93977 original size:33 final size:33
Alignment explanation
Indices: 93939--94036 Score: 135
Period size: 34 Copynumber: 2.9 Consensus size: 33
93929 ATTTCTCCCC
* *
93939 TTTTTCTTTTTCCCTTTTTTTCCTTTTTTCTCA
1 TTTTTCTTTTTTCATTTTTTTCCTTTTTTCTCA
*
93972 TTTTTCTTTTTTTCATCTTTTTCCTTTTTTCTCA
1 TTTTTC-TTTTTTCATTTTTTTCCTTTTTTCTCA
*
94006 TTTTCCTTTTTTCATCTTTTTT-CTTTTTTCT
1 TTTTTCTTTTTTCAT-TTTTTTCCTTTTTTCT
94037 TTCTTTGCTG
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
33 24 0.41
34 34 0.59
ACGTcount: A:0.04, C:0.21, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTTCTTTTTTCATTTTTTTCCTTTTTTCTCA
Found at i:93993 original size:34 final size:33
Alignment explanation
Indices: 93955--94036 Score: 137
Period size: 33 Copynumber: 2.5 Consensus size: 33
93945 TTTTTCCCTT
*
93955 TTTTTCCTTTTTTCTCATTTTTCTTTTTTTCATC
1 TTTTTCCTTTTTTCTCA-TTTTCCTTTTTTCATC
93989 TTTTTCCTTTTTTCTCATTTTCCTTTTTTCATC
1 TTTTTCCTTTTTTCTCATTTTCCTTTTTTCATC
*
94022 TTTTTTCTTTTTTCT
1 TTTTTCCTTTTTTCT
94037 TTCTTTGCTG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 29 0.63
34 17 0.37
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (33 bp):
TTTTTCCTTTTTTCTCATTTTCCTTTTTTCATC
Found at i:96936 original size:36 final size:36
Alignment explanation
Indices: 96859--96942 Score: 91
Period size: 36 Copynumber: 2.3 Consensus size: 36
96849 GTAAATGCGA
* *
96859 AAATGCATAA-ATGAAAAAATAAGAATGCAAATTGTG
1 AAATGCA-AAGATGAAAAAATAAGAATACAAAATGTG
* *
96895 TAATGCAAAGATGTAAAAAGTAAGAATACAAAATG-G
1 AAATGCAAAGATG-AAAAAATAAGAATACAAAATGTG
*
96931 AAATGCACAGAT
1 AAATGCAAAGAT
96943 ACAAAATGTA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
35 2 0.05
36 20 0.50
37 18 0.45
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.20
Consensus pattern (36 bp):
AAATGCAAAGATGAAAAAATAAGAATACAAAATGTG
Found at i:99187 original size:22 final size:21
Alignment explanation
Indices: 99159--99199 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
99149 TTAATACCTG
*
99159 AATAAAATAAATAAATAATATT
1 AATAAAAT-AATAAAAAATATT
99181 AATAAAATAATAAAAAATA
1 AATAAAATAATAAAAAATA
99200 ATAAGTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (21 bp):
AATAAAATAATAAAAAATATT
Found at i:99202 original size:13 final size:13
Alignment explanation
Indices: 99159--99213 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 13
99149 TTAATACCTG
99159 AATAA-AATAAATA
1 AATAATAATAAA-A
*
99172 AATAATATTAATAA
1 AATAATAATAA-AA
99186 AATAATAA-AAAA
1 AATAATAATAAAA
99198 TAATAAGTAATAAAA
1 -AATAA-TAATAAAA
99213 A
1 A
99214 TTTGAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 2 0.06
13 12 0.34
14 16 0.46
15 5 0.14
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
AATAATAATAAAA
Found at i:99208 original size:25 final size:25
Alignment explanation
Indices: 99164--99212 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
99154 ACCTGAATAA
*
99164 AATAAATAAATAATATTAATAAAAT
1 AATAAATAAATAATAGTAATAAAAT
99189 AATAAA-AAATAATAAGTAATAAAA
1 AATAAATAAATAAT-AGTAATAAAA
99213 ATTTGAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
AATAAATAAATAATAGTAATAAAAT
Found at i:99835 original size:20 final size:19
Alignment explanation
Indices: 99796--99847 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
99786 TTTCTTCGAT
99796 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
99815 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
99835 ATTTATAAAATAA
1 A-TTAAAAAATAA
99848 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:99948 original size:120 final size:121
Alignment explanation
Indices: 99717--99941 Score: 298
Period size: 120 Copynumber: 1.9 Consensus size: 121
99707 TTAATTTATA
* * *
99717 TATATAAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGCCTTAAGACAG
1 TATATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACTACTAGGTGCCTTAAGACAG
*
99782 CTCTTTTCTTCGATATTAAAAAATAAATAAATAATTAAAACAATTAATATATAATT
66 CTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATAATT
* * * **
99838 TATA-AAATAAGATATTTATTTATTTAAAAATATTAGAAAATAGACATAC-AGTTGTTTTAAGAC
1 TATATAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-AGAC-TACTAGGTGCCTTAAGAC
* *
99901 TGCTC-TTTCTT-AATATTGAAAAATAAATAAAT-ATTAAAACA
64 AGCTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACA
99942 TGATTAAAAT
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
118 9 0.10
119 19 0.21
120 39 0.43
121 22 0.24
122 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (121 bp):
TATATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAAGACTACTAGGTGCCTTAAGACAG
CTCTTTTCTTCAATATTAAAAAATAAATAAATAATTAAAACAATTAATATATAATT
Found at i:100010 original size:2 final size:2
Alignment explanation
Indices: 99992--100034 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
99982 AGTAAAATAA
* *
99992 AT AT AT TT AT -T AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
100033 AT
1 AT
100035 GGCTAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:101531 original size:24 final size:24
Alignment explanation
Indices: 101473--101535 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
101463 GGGTTTTATT
* *
101473 TAATTT-AATAATATATTATAATAA
1 TAATTTAAATAAT-TTTTAAAATAA
*
101497 TAA-TAATAATAATTTTTAAAATAA
1 TAATTTA-AATAATTTTTAAAATAA
101521 TAATTTAAATAATTT
1 TAATTTAAATAATTT
101536 AAGTAAATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
23 1 0.03
24 23 0.72
25 8 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAATTTAAATAATTTTTAAAATAA
Done.