Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003950.1 Hibiscus syriacus cultivar Beakdansim tig00008538_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: 111806
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:10948 original size:33 final size:33
Alignment explanation
Indices: 10906--10976 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
10896 TGAGGAGTCC
10906 AATATTAGCGGCTTGGAATAGTATATTTTCCCA
1 AATATTAGCGGCTTGGAATAGTATATTTTCCCA
10939 AATATTAGCGGCTTGGAATAGTATATTTTCCCA
1 AATATTAGCGGCTTGGAATAGTATATTTTCCCA
10972 AATAT
1 AATAT
10977 CAAAGGGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (33 bp):
AATATTAGCGGCTTGGAATAGTATATTTTCCCA
Found at i:13578 original size:30 final size:30
Alignment explanation
Indices: 13515--13579 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
13505 AATAAGGTTT
***
13515 TTTGGCCCAATAAGGCACCCTCCGTAATTA
1 TTTGGCCCAATAAGGCACCCTCAAAAATTA
*
13545 TTTGGCCCAATAGGGCA-CCTCAAAAATTAA
1 TTTGGCCCAATAAGGCACCCTCAAAAATT-A
13575 TTTGG
1 TTTGG
13580 GATCTACGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 8 0.27
30 22 0.73
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (30 bp):
TTTGGCCCAATAAGGCACCCTCAAAAATTA
Found at i:17152 original size:18 final size:18
Alignment explanation
Indices: 17129--17163 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
17119 AGGGTTCTAC
*
17129 GTGGTCCTTTGGGACATA
1 GTGGTCCTTCGGGACATA
17147 GTGGTCCTTCGGGACAT
1 GTGGTCCTTCGGGACAT
17164 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.20, G:0.34, T:0.31
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:25470 original size:95 final size:92
Alignment explanation
Indices: 25267--25491 Score: 217
Period size: 95 Copynumber: 2.4 Consensus size: 92
25257 CCCAAGCAAT
* * *
25267 GGGGTATCGATACCATGGTAAGGGTATCGATACCAGTAAACATTGAATCTAAATTGGGTATTGAT
1 GGGGTATCGATACCATGGTAAGGGTATCGATACCAGT-AACATTGAAGCTAAATTAGGTATCGAT
25332 ACCTATAGGGGGTATCAGTACCATAGCATA
65 A-CTATAGGGGGTATCAGTACCATA-CATA
** * *
25362 GGGGTATTTATACCATGGTGAGGGTATCGATACCAAGCT-AC-TTCGAAGCTAATTTAGGTATCG
1 GGGGTATCGATACCATGGTAAGGGTATCGATACC-AG-TAACATT-GAAGCTAAATTAGGTATCG
*
25425 ATA-TATTAAGGGGGTATC-GATACCCTA-ATA
63 ATACTA-T-AGGGGGTATCAG-TACCATACATA
* *
25455 GGGTAGTATCGATACCATAAGCAAGGGTATCGATACC
1 GGG--GTATCGATACCAT-GGTAAGGGTATCGATACC
25492 TAAGGGCCAA
Statistics
Matches: 108, Mismatches: 13, Indels: 17
0.78 0.09 0.12
Matches are distributed among these distances:
93 8 0.07
94 4 0.04
95 78 0.72
96 17 0.16
97 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (92 bp):
GGGGTATCGATACCATGGTAAGGGTATCGATACCAGTAACATTGAAGCTAAATTAGGTATCGATA
CTATAGGGGGTATCAGTACCATACATA
Found at i:26066 original size:79 final size:79
Alignment explanation
Indices: 25904--26066 Score: 220
Period size: 79 Copynumber: 2.1 Consensus size: 79
25894 AAACGAATGT
25904 AAAAGAATAATGCATATGGGTGAATTATGGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
1 AAAAGAATAATGCATATGGGTGAATTATGGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
* * *
25969 TACATTGTCAGCAT
66 TACATTATCAACAG
* * * ** *
25983 AAAAGAATAATGCATATGTGTGCATTATTGGCATGAAAGGATGCCATATTTGAAAT-TCATATGG
1 AAAAGAATAATGCATATGGGTGAATTATGGGCATGAAAGGATGCCATAGCTAAAATGT-ATATGG
*
26047 GTGCATTATCAACAG
65 GTACATTATCAACAG
26062 AAAAG
1 AAAAG
26067 TATGCTAAAG
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
78 1 0.01
79 72 0.99
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.28
Consensus pattern (79 bp):
AAAAGAATAATGCATATGGGTGAATTATGGGCATGAAAGGATGCCATAGCTAAAATGTATATGGG
TACATTATCAACAG
Found at i:26081 original size:45 final size:45
Alignment explanation
Indices: 26032--26291 Score: 369
Period size: 45 Copynumber: 5.8 Consensus size: 45
26022 GATGCCATAT
* * *
26032 TTGAAAT-TCATATGGGTGCATTATCAACAGAAAAGTATGCTAAAG
1 TTGAAATGT-ATATGGGTACATTATCAACAGAAAAGTATACTATAG
* * * * * *
26077 TTGAAATGCATATGGGTGCATTGTCAATAGAAAAGTATGCTAGAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
*
26122 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATGG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
* *
26167 TTGAAATGTATATGGGTACATTATCAACATAAAAGTATACTATGG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
*
26212 TTGAAATGTATATGGGTACATTATCAACATAAAAGTATACTATAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
* *
26257 TTGAAATGCATATGGGTGCATTATCAACAGAAAAG
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAG
26292 ATGTTAGAAT
Statistics
Matches: 198, Mismatches: 16, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 198 1.00
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (45 bp):
TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACTATAG
Found at i:32430 original size:16 final size:17
Alignment explanation
Indices: 32409--32453 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
32399 TCATTTTCTT
32409 AGTTTGAGAGTTTTA-A
1 AGTTTGAGAGTTTTACA
*
32425 AGTTTGAAAG-TTTACA
1 AGTTTGAGAGTTTTACA
*
32441 CGTTTGAGAGTTT
1 AGTTTGAGAGTTT
32454 GAGATTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 18 0.75
17 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.42
Consensus pattern (17 bp):
AGTTTGAGAGTTTTACA
Found at i:32664 original size:83 final size:83
Alignment explanation
Indices: 32567--32755 Score: 263
Period size: 83 Copynumber: 2.3 Consensus size: 83
32557 ATAATGGAAC
* * * * * *
32567 ACGCCCCTTTCATTTTTGGATGAGATGGAACACTATGACATGATATATATTCTCTTAATAAT-AT
1 ACGCACCTTTCA-TTTCGGATGAGATGGAACACTATGAAATGACATAGATTCTCTAAATAATAAT
*
32631 GGAAAATGCTTCCCTTGGA
65 GGAAAATGCTTCCATTGGA
* * *
32650 ATGCACCTTTCATTTCAGATGGGATGGAACACTATGAAATGACATAGATTCTCTAAATAATAATG
1 ACGCACCTTTCATTTCGGATGAGATGGAACACTATGAAATGACATAGATTCTCTAAATAATAATG
32715 GAAAATGCTTCCATTGGA
66 GAAAATGCTTCCATTGGA
*
32733 ACGCGCCTTTCATTTCGGATGAG
1 ACGCACCTTTCATTTCGGATGAG
32756 CTGAATAATA
Statistics
Matches: 91, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
82 42 0.46
83 49 0.54
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (83 bp):
ACGCACCTTTCATTTCGGATGAGATGGAACACTATGAAATGACATAGATTCTCTAAATAATAATG
GAAAATGCTTCCATTGGA
Found at i:32764 original size:54 final size:54
Alignment explanation
Indices: 32705--32807 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 54
32695 AGATTCTCTA
** * *
32705 AATAATAATGGAAAATGCTTCCATTGGAACGCGCCTTTCATTTCGGATGAGCTG
1 AATAATAATAAAAAATGCTTCCACTGGAACACGCCTTTCATTTCGGATGAGCTG
* *
32759 AATAATAATAAAAAATGCTTCCACTGGAACATGCCTTTCATTTTGGATG
1 AATAATAATAAAAAATGCTTCCACTGGAACACGCCTTTCATTTCGGATG
32808 GGATGGAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 43 1.00
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (54 bp):
AATAATAATAAAAAATGCTTCCACTGGAACACGCCTTTCATTTCGGATGAGCTG
Found at i:32849 original size:83 final size:83
Alignment explanation
Indices: 32756--33092 Score: 406
Period size: 83 Copynumber: 4.1 Consensus size: 83
32746 TTCGGATGAG
** * * *
32756 CTGAATAATAATAAAAAATGCTTCCACTGGAACATGCCTTTCATTTTGGATGGGATGGAACACAA
1 CTGAATAATAATGGAAAATGCTTCCCCTGGAACACGCCTTTCATTTTGGATGGGATGGAACACTA
* *
32821 TGACACGACAGAGATTCT
66 TGACATGACAAAGATTCT
* * *
32839 CTGAATAATAATGGAAAATGCTTCCCCTGGAA-ATCGTCTTTTATTTCGGATGGGATGGAACACT
1 CTGAATAATAATGGAAAATGCTTCCCCTGGAACA-CGCCTTTCATTTTGGATGGGATGGAACACT
* *
32903 ATGACATGGCAAATATTCT
65 ATGACATGACAAAGATTCT
* * * * *
32922 CTAAATAATAATGGAAAATACTTCCCCTGGAATACGCCTTTCATTTTGGATTGGATGAAACACTA
1 CTGAATAATAATGGAAAATGCTTCCCCTGGAACACGCCTTTCATTTTGGATGGGATGGAACACTA
* * *
32987 CGACATGGCAGAGATTCT
66 TGACATGACAAAGATTCT
* * * * * **
33005 CTGAATAATAATGGAAAATGTTTCCCTTGGAGCGCGCCCTTCATTTTGGATGGGAAAGAACACTA
1 CTGAATAATAATGGAAAATGCTTCCCCTGGAACACGCCTTTCATTTTGGATGGGATGGAACACTA
*
33070 TGACATGACAAATATTCT
66 TGACATGACAAAGATTCT
33088 CTGAA
1 CTGAA
33093 AATGGGAAAA
Statistics
Matches: 214, Mismatches: 38, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
82 1 0.00
83 212 0.99
84 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (83 bp):
CTGAATAATAATGGAAAATGCTTCCCCTGGAACACGCCTTTCATTTTGGATGGGATGGAACACTA
TGACATGACAAAGATTCT
Found at i:32962 original size:220 final size:220
Alignment explanation
Indices: 32572--32972 Score: 572
Period size: 220 Copynumber: 1.8 Consensus size: 220
32562 GGAACACGCC
* * * * * *
32572 CCTTTCATTTTTGGATGAGATGGAACACTATGACATGATATATATTCTCTTAATAATATGGAAAA
1 CCTTTCATTTTTGGATGAGATGGAACACAATGACACGACAGAGATTCTCTGAATAATATGGAAAA
* *
32637 TGCTTCCCTTGGAATGCACCTTTCATTTCAGATGGGATGGAACACTATGAAATGACATAGATTCT
66 TGCTTCCCCTGGAATGCACCTTTCATTTCAGATGGGATGGAACACTATGAAATGACAAAGATTCT
* * *
32702 CTAAATAATAATGGAAAATGCTTCCATTGGAACGCGCCTTTCATTTCGGATGAGCTGAATAATAA
131 CTAAATAATAATGGAAAATACTTCCACTGGAACACGCCTTTCATTTCGGATGAGCTGAATAATAA
32767 TAAAAAATGCTTCCACTGGAACATG
196 TAAAAAATGCTTCCACTGGAACATG
*
32792 CCTTTCA-TTTTGGATGGGATGGAACACAATGACACGACAGAGATTCTCTGAATAATAATGGAAA
1 CCTTTCATTTTTGGATGAGATGGAACACAATGACACGACAGAGATTCTCTGAATAAT-ATGGAAA
** * * * * *
32856 ATGCTTCCCCTGGAAAT-CGTCTTTTATTTCGGATGGGATGGAACACTATGACATGGCAAATATT
65 ATGCTTCCCCTGG-AATGCACCTTTCATTTCAGATGGGATGGAACACTATGAAATGACAAAGATT
* * *
32920 CTCTAAATAATAATGGAAAATACTTCCCCTGGAATACGCCTTTCATTTTGGAT
129 CTCTAAATAATAATGGAAAATACTTCCACTGGAACACGCCTTTCATTTCGGAT
32973 TGGATGAAAC
Statistics
Matches: 157, Mismatches: 22, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
219 42 0.27
220 112 0.71
221 3 0.02
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (220 bp):
CCTTTCATTTTTGGATGAGATGGAACACAATGACACGACAGAGATTCTCTGAATAATATGGAAAA
TGCTTCCCCTGGAATGCACCTTTCATTTCAGATGGGATGGAACACTATGAAATGACAAAGATTCT
CTAAATAATAATGGAAAATACTTCCACTGGAACACGCCTTTCATTTCGGATGAGCTGAATAATAA
TAAAAAATGCTTCCACTGGAACATG
Found at i:35799 original size:164 final size:164
Alignment explanation
Indices: 35528--35856 Score: 471
Period size: 164 Copynumber: 2.0 Consensus size: 164
35518 AATTGACTCT
* * * * *
35528 ATCCTAGCTACGGGCGCATAAGTTTCATCAAATTCTATTCATTTTTCTTTAGTATACCTTTGAGC
1 ATCCTAGCTACGGGCGCATAAGTTTCATCAAAATATATTCATTCTTCTTAAGTATACCCTTGAGC
* * * * *
35593 AACAAGTCTAGCCTTTTTCCTCACTATGTTATCACTTTCATCTAATTTATTCCTAAATA-GACAT
66 AACAAGTCCAACCTTGTTCCTCACGATGTTACCACTTTCATCTAATTTATTCCTAAATACG-CAT
* * *
35657 TTAGTACCTATAGTAGGTTTGTCACTAGGCCTTTC
130 TTAATACCTATAGTAGATTTGTCACTAGACCTTTC
* * *
35692 ATCCTAGCTACGGGTGCATAAGTTTCATTAAAATATATTCCTTCTTCTTAAGTATACCCTTGAGC
1 ATCCTAGCTACGGGCGCATAAGTTTCATCAAAATATATTCATTCTTCTTAAGTATACCCTTGAGC
*
35757 AACAAGTCCAACCTTGTTCTTCACGATGTTACCACTTTCATCTAATTTATTCCTAAATACGCATT
66 AACAAGTCCAACCTTGTTCCTCACGATGTTACCACTTTCATCTAATTTATTCCTAAATACGCATT
* *
35822 TAATACCTATAGTAGATTTTTCATTAGACCTTTC
131 TAATACCTATAGTAGATTTGTCACTAGACCTTTC
35856 A
1 A
35857 ACTAACATCC
Statistics
Matches: 145, Mismatches: 19, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
164 144 0.99
165 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.39
Consensus pattern (164 bp):
ATCCTAGCTACGGGCGCATAAGTTTCATCAAAATATATTCATTCTTCTTAAGTATACCCTTGAGC
AACAAGTCCAACCTTGTTCCTCACGATGTTACCACTTTCATCTAATTTATTCCTAAATACGCATT
TAATACCTATAGTAGATTTGTCACTAGACCTTTC
Found at i:42973 original size:10 final size:10
Alignment explanation
Indices: 42958--42990 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
42948 ATAAGATACA
42958 TGAAATGGGT
1 TGAAATGGGT
42968 TGAAATGGGT
1 TGAAATGGGT
*
42978 TGAGATGGGT
1 TGAAATGGGT
42988 TGA
1 TGA
42991 CATGTCGGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.42, T:0.30
Consensus pattern (10 bp):
TGAAATGGGT
Found at i:47432 original size:3 final size:3
Alignment explanation
Indices: 47424--47464 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
47414 AATTGTAAAT
47424 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
47465 TTATAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:47725 original size:40 final size:43
Alignment explanation
Indices: 47628--47740 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 43
47618 GTTGGAGTCC
*
47628 ACACTGCTCATACGTGATGAAGAGATCTGGTCGTTTAAAAGTG
1 ACACTGCTCATACGTGATGAAGAGATCTGGTCGTGTAAAAGTG
* * **
47671 ACAC-GACTCCTACGTGATGAGGAGATCTGGTCG-GT-GGA-TG
1 ACACTG-CTCATACGTGATGAAGAGATCTGGTCGTGTAAAAGTG
*
47711 ACACTGCTCATACGTGATGAAGAGTTCTGG
1 ACACTGCTCATACGTGATGAAGAGATCTGG
47741 CCATCTTTAG
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
40 27 0.45
41 2 0.03
42 2 0.03
43 29 0.48
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.26
Consensus pattern (43 bp):
ACACTGCTCATACGTGATGAAGAGATCTGGTCGTGTAAAAGTG
Found at i:47862 original size:40 final size:40
Alignment explanation
Indices: 47762--47997 Score: 186
Period size: 40 Copynumber: 5.6 Consensus size: 40
47752 AAGGGTGATA
* * * *
47762 ACACGGTTCCTACGCGATGAGGATGACTGGTAATCTAGGGGTG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGG---TCTAGGGATG
* * * *
47805 ACACGGCTCCTATGTGATGAGGAGGTCTGGTCTATGAATG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGGTCTAGGGATG
* * *
47845 ACACGGTTCCTACGTGATGAGGATGGTATGCCATCTTTAGGATGATA
1 ACACGGTTCCTACGTGATGAGGA-GGTCTG--GTC--TAGG--GATG
* * *
47892 ACACAGTTCCTACGTGATGAGGATGG-CTGGTTATATAGGGTTG
1 ACACGGTTCCTACGTGATGAGGA-GGTCTGG---TCTAGGGATG
* *
47935 ACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATG
1 ACACGGTTCCTACGTGATGAGGAGGTCTGGTCTAGGGATG
*
47975 ACACGATTCCTACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
47998 TGGCTGACCA
Statistics
Matches: 154, Mismatches: 28, Indels: 25
0.74 0.14 0.12
Matches are distributed among these distances:
40 56 0.36
41 5 0.03
42 2 0.01
43 54 0.35
45 7 0.05
46 2 0.01
47 28 0.18
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.26
Consensus pattern (40 bp):
ACACGGTTCCTACGTGATGAGGAGGTCTGGTCTAGGGATG
Found at i:47952 original size:130 final size:132
Alignment explanation
Indices: 47668--48015 Score: 452
Period size: 130 Copynumber: 2.6 Consensus size: 132
47658 TCGTTTAAAA
* * * * * * *
47668 GTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGTGGATGACACTGCTCATACGTGATGAAG
1 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACGGTTCCTACGTGATGAGG
* * *
47733 A-GTTCTGGCCATCTTTAGGAAGGGTGATAACACGGTTCCTACGCGATGAGGATGACTGGTAATC
66 ATGGTCT-GCCATCTTTAGGAA--GTGATAACACAGTTCCTACGCGATGAGGATGACTGGTAATA
47797 TAGGG
128 TAGGG
* * *
47802 GTGACACGGCTCCTATGTGATGAGGAGGTCTGGTCTATGAATGACACGGTTCCTACGTGATGAGG
1 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACGGTTCCTACGTGATGAGG
* * * *
47867 ATGGTATGCCATCTTTAGG-A-TGATAACACAGTTCCTACGTGATGAGGATGGCTGGTTATATAG
66 ATGGTCTGCCATCTTTAGGAAGTGATAACACAGTTCCTACGCGATGAGGATGACTGGTAATATAG
47930 GG
131 GG
* * *
47932 TTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGAGGGATGACACGATTCCTACGTGATGAGG
1 GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACGGTTCCTACGTGATGAGG
47997 ATGG-CTGACCATCTTTAGG
66 ATGGTCTG-CCATCTTTAGG
48016 GATTATGGTT
Statistics
Matches: 188, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
129 2 0.01
130 114 0.61
133 1 0.01
134 68 0.36
135 3 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (132 bp):
GTGACACGGCTCCTACGTGATGAGGAGGTCTGGTCGATGGATGACACGGTTCCTACGTGATGAGG
ATGGTCTGCCATCTTTAGGAAGTGATAACACAGTTCCTACGCGATGAGGATGACTGGTAATATAG
GG
Found at i:48102 original size:30 final size:28
Alignment explanation
Indices: 48028--48102 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
48018 TTATGGTTTT
48028 AAGAGAAACTGACTCAAAGATTTGCTTC
1 AAGAGAAACTGACTCAAAGATTTGCTTC
* * * *
48056 AAAAGAAACAGGCTCAAAGATATATGTTTC
1 AAGAGAAACTGACTCAAAGAT-T-TGCTTC
* *
48086 ATGAGAAACTGTCTCAA
1 AAGAGAAACTGACTCAA
48103 GGGAAACAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
28 18 0.49
29 1 0.03
30 18 0.49
ACGTcount: A:0.43, C:0.16, G:0.17, T:0.24
Consensus pattern (28 bp):
AAGAGAAACTGACTCAAAGATTTGCTTC
Found at i:48979 original size:2 final size:2
Alignment explanation
Indices: 48974--48998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
48964 TATGTATATA
48974 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
48999 AAGGAAAATG
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:50012 original size:2 final size:2
Alignment explanation
Indices: 50005--50047 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
49995 ATCTTTATTG
50005 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50047 T
1 T
50048 TATGGCTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54105 original size:30 final size:30
Alignment explanation
Indices: 54003--54223 Score: 144
Period size: 30 Copynumber: 7.2 Consensus size: 30
53993 TTAATAAAAT
* *
54003 AAGGAACT-AAATAGTAATAAACAGAAATTTA
1 AAGG-ACTAAAATAATAA-AAACAGAAAGTTA
* * * *
54034 CAGGACTAAAACAACAAAAACAGAAAATTA
1 AAGGACTAAAATAATAAAAACAGAAAGTTA
* *
54064 AATGACTAAAATAATAAAAATAGAAAGTTA
1 AAGGACTAAAATAATAAAAACAGAAAGTTA
* * *
54094 AAGGATTAAAAT-AGAAAAATAGAAAGTTAA
1 AAGGACTAAAATAATAAAAACAGAAAGTT-A
* * *
54124 AATG-CTAAGCTAAATTATAAATACAGAAAGTTA
1 AAGGACT-A---AAATAATAAAAACAGAAAGTTA
* * * * * *
54157 AAGGACCACAATAACAAATACAAAAATTTA
1 AAGGACTAAAATAATAAAAACAGAAAGTTA
* *
54187 AAGGACTAAAATAGTAAAAACA-AACATTTA
1 AAGGACTAAAATAATAAAAACAGAA-AGTTA
54217 AAGGACT
1 AAGGACT
54224 CAATCATAAA
Statistics
Matches: 150, Mismatches: 31, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
29 18 0.12
30 100 0.67
31 9 0.06
33 9 0.06
34 14 0.09
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.20
Consensus pattern (30 bp):
AAGGACTAAAATAATAAAAACAGAAAGTTA
Found at i:58798 original size:9 final size:9
Alignment explanation
Indices: 58784--58809 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
58774 TGACGGAGCT
58784 GGAGGCGAA
1 GGAGGCGAA
58793 GGAGGCGAA
1 GGAGGCGAA
58802 GGAGGCGA
1 GGAGGCGA
58810 CAACGAGGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.58, T:0.00
Consensus pattern (9 bp):
GGAGGCGAA
Found at i:61471 original size:20 final size:19
Alignment explanation
Indices: 61448--61493 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
61438 CGATATAACA
61448 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
61468 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
*
61488 GATAAA
1 GGTAAA
61494 GCGCTACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.54, C:0.11, G:0.15, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:63841 original size:33 final size:33
Alignment explanation
Indices: 63804--63869 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
63794 AAATAGATGG
* *
63804 AGTGGTGAAAGAAGTAGAGGTGTTGATGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
*
63837 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
63870 TCTTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.00, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:66783 original size:194 final size:198
Alignment explanation
Indices: 66361--66861 Score: 599
Period size: 194 Copynumber: 2.5 Consensus size: 198
66351 TAACGACCCA
** * *
66361 AAAAACATCGAAATTCATAATTATAGTGTAATGGGTAATTTTTCAATATAACCGGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTT-AATATAACCGGTATAAATATA
* * * * * * *
66426 CCGGTTTTATGA-AAAATATGTCTACAACATTTATTGACACTTATTAGTATTGTTTCGATACTTT
65 CTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTATTAATATTGTTTCGATAATTT
*
66490 GTGTCCAGAATGGATGCCAAAAAGGGGAAACCTACAAAGTGTCGATACATCTATTAAAAGTATCA
130 GTGTCCAGAATGGATGCCAAAAAGGGGAAACCTACAAAGTGACGATACATCTA-TAAAAGTATCA
66555 ATCCC
194 ATCCC
*
66560 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAACCGGTATACATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTT-TAATATAACCGGTATAAATATA
* *
66625 CTGGTTTTATGAGAGAATAGGTCTATAATATGTATCGACACTTATTAATATTGTGTT-GATAATT
65 CTGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTATTAATATTGT-TTCGATAATT
* * ** * ** *
66689 TTTGTCCATAATTTATGCCAAAAAGGGTG-AACGC-ATAAAGT-AC-AT-TTTC-A-AAAAGTGT
129 TGTGTCCAGAATGGATGCCAAAAAGGG-GAAAC-CTACAAAGTGACGATACATCTATAAAAGTAT
*
66747 CGATCCC
192 CAATCCC
** * *
66754 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAACCAGTATAAATATA
1 AAAAACATCGAAACCCATAATTATAATGTAATAGGT-AATTTTTAATATAACCGGTATAAATATA
*
66819 -TCGGTTTTATGAGAGAATAGGTATACAACATGTATCGACACTT
65 CT-GGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTT
66862 TGTTGAAAAA
Statistics
Matches: 263, Mismatches: 32, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
193 1 0.00
194 105 0.40
195 5 0.02
196 1 0.00
197 2 0.01
198 2 0.01
199 70 0.27
200 73 0.28
201 4 0.02
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.33
Consensus pattern (198 bp):
AAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTTAATATAACCGGTATAAATATAC
TGGTTTTATGAGAGAATAGGTCTACAACATGTATCGACACTTATTAATATTGTTTCGATAATTTG
TGTCCAGAATGGATGCCAAAAAGGGGAAACCTACAAAGTGACGATACATCTATAAAAGTATCAAT
CCC
Found at i:70009 original size:23 final size:23
Alignment explanation
Indices: 69980--70027 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
69970 AAATAGGTCA
* *
69980 ATATAAGCGCTACCTATTATATT
1 ATATAAGAGCTACCTAATATATT
*
70003 ATATAAGAGCTACCTAATATGTT
1 ATATAAGAGCTACCTAATATATT
70026 AT
1 AT
70028 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.38
Consensus pattern (23 bp):
ATATAAGAGCTACCTAATATATT
Found at i:70084 original size:23 final size:23
Alignment explanation
Indices: 70054--70105 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
70044 TCCGGTCAAA
* *
70054 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATACAAACGC
*
70077 TACCTATTATATTATACAAACGC
1 TACCTATTACATTATACAAACGC
70100 TACCTA
1 TACCTA
70106 ATATGTTATT
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:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATACAAACGC
Found at i:70085 original size:87 final size:86
Alignment explanation
Indices: 69980--70140 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 86
69970 AAATAGGTCA
*
69980 ATATAAGCGCTACCTATTATATTATATAAGA-GCTACCTAATATGTTATTGTACTTGATAATATT
1 ATATAAGCGCTACCTATTATATTATACAA-ACGCTACCTAATATGTTATTGTACTTGATAATATT
70044 TCCGGTCAAATACCTATTACATT
65 TCCGGT-AAATACCTATTACATT
70067 ATATAAGCGCTACCTATTATATTATACAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTATATTATACAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
*
70132 TCGGTAAAT
66 CCGGTAAAT
70141 GATATAATAT
Statistics
Matches: 71, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
86 5 0.07
87 66 0.93
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.39
Consensus pattern (86 bp):
ATATAAGCGCTACCTATTATATTATACAAACGCTACCTAATATGTTATTGTACTTGATAATATTT
CCGGTAAATACCTATTACATT
Found at i:70114 original size:23 final size:23
Alignment explanation
Indices: 70054--70114 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
70044 TCCGGTCAAA
* * * *
70054 TACCTATTACATTATATAAGCGC
1 TACCTAATATATTATACAAACGC
*
70077 TACCTATTATATTATACAAACGC
1 TACCTAATATATTATACAAACGC
*
70100 TACCTAATATGTTAT
1 TACCTAATATATTAT
70115 TGTACTTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (23 bp):
TACCTAATATATTATACAAACGC
Found at i:70815 original size:72 final size:73
Alignment explanation
Indices: 70669--70816 Score: 194
Period size: 72 Copynumber: 2.0 Consensus size: 73
70659 CTTGAATTTG
* * * *
70669 AAATAAAATAATTGAAGTTCGACTCGACTCGTAAGCTCAAGAGCATAAAATTTTCAAGCTTGGCT
1 AAATAAAATAATTGAAGCTCGACTCCACTCGAAAGCTCAAGAGCATAAAATTTTCAAGCTTGACT
* *
70734 TAAATTCA
66 CAAAATCA
*
70742 AAATAAAA-AATTGAAGCTCGACTCCACTCGAAAGCTCACGAG-ATTAAAATTTTCAAGCTCT-A
1 AAATAAAATAATTGAAGCTCGACTCCACTCGAAAGCTCAAGAGCA-TAAAATTTTCAAGCT-TGA
70804 CTCAAAATCA
64 CTCAAAATCA
70814 AAA
1 AAA
70817 AATTGAAGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
71 1 0.02
72 56 0.85
73 9 0.14
ACGTcount: A:0.43, C:0.19, G:0.13, T:0.26
Consensus pattern (73 bp):
AAATAAAATAATTGAAGCTCGACTCCACTCGAAAGCTCAAGAGCATAAAATTTTCAAGCTTGACT
CAAAATCA
Found at i:71302 original size:52 final size:52
Alignment explanation
Indices: 71224--71329 Score: 212
Period size: 52 Copynumber: 2.0 Consensus size: 52
71214 ATTAGAGGCT
71224 TTGTTAAAGGTAAACTAAAATATTAAAAACAGCTTTATATCAAATATAATAA
1 TTGTTAAAGGTAAACTAAAATATTAAAAACAGCTTTATATCAAATATAATAA
71276 TTGTTAAAGGTAAACTAAAATATTAAAAACAGCTTTATATCAAATATAATAA
1 TTGTTAAAGGTAAACTAAAATATTAAAAACAGCTTTATATCAAATATAATAA
71328 TT
1 TT
71330 AATAACGATA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.34
Consensus pattern (52 bp):
TTGTTAAAGGTAAACTAAAATATTAAAAACAGCTTTATATCAAATATAATAA
Found at i:72066 original size:67 final size:67
Alignment explanation
Indices: 71992--72123 Score: 210
Period size: 67 Copynumber: 2.0 Consensus size: 67
71982 TTTTTGTTTT
* * *
71992 TTCTCACTGAAATTTTAAAAGTAACAAATTGATCACTAACATTATTGATTTATAATAAATTGATC
1 TTCTCACTGAAATTTTAAAAATAACAAATTGATCACTAACATTATTAAATTATAATAAATTGATC
72057 AG
66 AG
* * *
72059 TTCTCACTTAAGTTTTAAAAATAACAAATTGATCACTAATATTATTAAATTATAATAAATTGATC
1 TTCTCACTGAAATTTTAAAAATAACAAATTGATCACTAACATTATTAAATTATAATAAATTGATC
72124 GGTTGACGTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
67 59 1.00
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (67 bp):
TTCTCACTGAAATTTTAAAAATAACAAATTGATCACTAACATTATTAAATTATAATAAATTGATC
AG
Found at i:80202 original size:16 final size:17
Alignment explanation
Indices: 80181--80220 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
80171 AATCACCGGT
*
80181 GATTTATATATTTATC-
1 GATTTATATATTGATCA
80197 GATTTA-ATATTGATCA
1 GATTTATATATTGATCA
80213 GA-TTATAT
1 GATTTATAT
80221 TTTTTGATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (17 bp):
GATTTATATATTGATCA
Found at i:80373 original size:50 final size:50
Alignment explanation
Indices: 80251--80373 Score: 131
Period size: 50 Copynumber: 2.5 Consensus size: 50
80241 GCAGTAAAGT
* * * * * *
80251 GCGTCCCTTGAAT-CGCGTTATACGTTGATTTGGTGTCACGTGGGTATAGC
1 GCGTCCCCTG-ATCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGC
* ** *
80301 GCGCCCCCTGCCCCGTGATATACGGTGATCTGGCGCCACGTGGGTATAGC
1 GCGTCCCCTGATCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGC
*
80351 GCGTCCCCTGATCCGCGCTATAC
1 GCGTCCCCTGATCCGCGATATAC
80374 CTGGGTATCT
Statistics
Matches: 57, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.15, C:0.30, G:0.29, T:0.26
Consensus pattern (50 bp):
GCGTCCCCTGATCCGCGATATACGGTGATCTGGCGCCACGTGGGTATAGC
Found at i:80517 original size:20 final size:19
Alignment explanation
Indices: 80484--80525 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
80474 TTTTATCACA
*
80484 CTAAATTCTATCAAATTCT
1 CTAAATTCTATCAAATACT
*
80503 CTAAATTTCTCTCAAATACT
1 CTAAA-TTCTATCAAATACT
80523 CTA
1 CTA
80526 TCTTTTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (19 bp):
CTAAATTCTATCAAATACT
Found at i:80844 original size:111 final size:111
Alignment explanation
Indices: 80650--80982 Score: 612
Period size: 111 Copynumber: 3.0 Consensus size: 111
80640 TGAAAATCAT
* *
80650 ATATCTCTACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
80715 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
80761 ATATCTCGACACTTTGTTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
80826 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
80872 ATATCTCGACATTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
80937 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
80983 TTTTTGTAAT
Statistics
Matches: 215, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 215 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:85587 original size:50 final size:50
Alignment explanation
Indices: 85511--85637 Score: 164
Period size: 50 Copynumber: 2.5 Consensus size: 50
85501 CCCTACGTGA
* ** * *
85511 CGTATAGCGCAGATCAGGGGGGGCGCTATACCCACGTGGCGCCAGATCAC
1 CGTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
* *
85561 CGTATATCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAG
1 CGTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
** *
85611 CGTATAGCGCGGTTCAGGGGGCACGCT
1 CGTATAGCGCGGGGCAGGGGGCGCGCT
85638 TTACTGCTAC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.20, C:0.29, G:0.36, T:0.15
Consensus pattern (50 bp):
CGTATAGCGCGGGGCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAC
Found at i:87896 original size:21 final size:21
Alignment explanation
Indices: 87872--87961 Score: 117
Period size: 21 Copynumber: 4.3 Consensus size: 21
87862 GTCGGCCCAA
* *
87872 ATGCCACTACATCCATTTCAG
1 ATGCCACTACAACCAGTTCAG
* *
87893 ATGCCACCACAACCGGTTCAG
1 ATGCCACTACAACCAGTTCAG
* *
87914 ATGCCACTACATCCATTTCAG
1 ATGCCACTACAACCAGTTCAG
*
87935 ATGCCACTACAACCGGTTCAG
1 ATGCCACTACAACCAGTTCAG
87956 ATGCCA
1 ATGCCA
87962 TTACCGTAGG
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.22
Consensus pattern (21 bp):
ATGCCACTACAACCAGTTCAG
Found at i:87918 original size:42 final size:42
Alignment explanation
Indices: 87872--87961 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
87862 GTCGGCCCAA
87872 ATGCCACTACATCCATTTCAGATGCCACCACAACCGGTTCAG
1 ATGCCACTACATCCATTTCAGATGCCACCACAACCGGTTCAG
*
87914 ATGCCACTACATCCATTTCAGATGCCACTACAACCGGTTCAG
1 ATGCCACTACATCCATTTCAGATGCCACCACAACCGGTTCAG
87956 ATGCCA
1 ATGCCA
87962 TTACCGTAGG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.29, C:0.34, G:0.14, T:0.22
Consensus pattern (42 bp):
ATGCCACTACATCCATTTCAGATGCCACCACAACCGGTTCAG
Found at i:88459 original size:13 final size:14
Alignment explanation
Indices: 88418--88476 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 14
88408 ATGTTTTTAT
*
88418 TATTTAATTATTTG
1 TATTTAATTGTTTG
* *
88432 AATTGT-ATAGTTTG
1 TATT-TAATTGTTTG
88446 TATTTAA-TGTTTG
1 TATTTAATTGTTTG
*
88459 TATTTAATTGTTTT
1 TATTTAATTGTTTG
88473 TATT
1 TATT
88477 ATTTAGCTTG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
13 13 0.36
14 22 0.61
15 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.63
Consensus pattern (14 bp):
TATTTAATTGTTTG
Found at i:88476 original size:14 final size:13
Alignment explanation
Indices: 88441--88476 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
88431 GAATTGTATA
88441 GTTTGTATTTAAT
1 GTTTGTATTTAAT
88454 GTTTGTATTTAATT
1 GTTTGTATTTAA-T
*
88468 GTTTTTATT
1 GTTTGTATT
88477 ATTTAGCTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.14, T:0.67
Consensus pattern (13 bp):
GTTTGTATTTAAT
Found at i:92026 original size:17 final size:18
Alignment explanation
Indices: 91987--92027 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
91977 ATTTTATGAG
91987 GTAAAAAATGATATTATT
1 GTAAAAAATGATATTATT
92005 GTAAAAAAT-ATAATTATT
1 GTAAAAAATGAT-ATTATT
92023 -TAAAA
1 GTAAAA
92028 TTTTGAGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (18 bp):
GTAAAAAATGATATTATT
Found at i:92160 original size:30 final size:30
Alignment explanation
Indices: 92117--92174 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
92107 ATTATATTTT
*
92117 ATATAAATTAATATGATAATTAT-TTAAAA
1 ATATAAATTAATATAATAATTATATTAAAA
92146 ATATAAATTTAATATAATAATTATATTAA
1 ATATAAA-TTAATATAATAATTATATTAA
92175 TTACATGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 7 0.27
30 15 0.58
31 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
ATATAAATTAATATAATAATTATATTAAAA
Found at i:93222 original size:50 final size:49
Alignment explanation
Indices: 93140--93326 Score: 196
Period size: 50 Copynumber: 3.8 Consensus size: 49
93130 TTTAACAATT
* * * * * *
93140 AACACATACTTACACCGATGTAAGTATATACATCTCCAAATCTAAAAATA
1 AACATATATTTACACTGGTGTAAGTATGTACATCTCC-AACCTAAAAATA
* * * *
93190 AACATATATTTATACTAGTATAAGTATGTACATCTCCCAGCCTAAAAATA
1 AACATATATTTACACTGGTGTAAGTATGTACATCT-CCAACCTAAAAATA
* *
93240 AACATATACTCACA-TCGGTGTAAGTATGTACATCTCTCAACCTAAAAATA
1 AACATATATTTACACT-GGTGTAAGTATGTACATCTC-CAACCTAAAAATA
* * *
93290 AACACATATTTACACCGGTGTAAGTATGCACATCTCC
1 AACATATATTTACACTGGTGTAAGTATGTACATCTCC
93327 CAATATTTTA
Statistics
Matches: 112, Mismatches: 21, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
49 3 0.03
50 107 0.96
51 2 0.02
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (49 bp):
AACATATATTTACACTGGTGTAAGTATGTACATCTCCAACCTAAAAATA
Found at i:93323 original size:100 final size:100
Alignment explanation
Indices: 93140--93328 Score: 254
Period size: 100 Copynumber: 1.9 Consensus size: 100
93130 TTTAACAATT
* * * *
93140 AACACATACTTACACCGATGTAAGTATATACATCTCCAAATCTAAAAATAAACATATATTTATAC
1 AACACATACTCACACCGATGTAAGTATATACATCTCCAAACCTAAAAATAAACACATATTTACAC
* *
93205 TAGTATAAGTATGTACATCTCCCAGCCTAAAAATA
66 CAGTATAAGTATGCACATCTCCCAGCCTAAAAATA
* * * *
93240 AACATATACTCACATCGGTGTAAGTATGTACATCTCTC-AACCTAAAAATAAACACATATTTACA
1 AACACATACTCACACCGATGTAAGTATATACATCTC-CAAACCTAAAAATAAACACATATTTACA
* *
93304 CCGGTGTAAGTATGCACATCTCCCA
65 CCAGTATAAGTATGCACATCTCCCA
93329 ATATTTTAGA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
100 75 0.99
101 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (100 bp):
AACACATACTCACACCGATGTAAGTATATACATCTCCAAACCTAAAAATAAACACATATTTACAC
CAGTATAAGTATGCACATCTCCCAGCCTAAAAATA
Found at i:95426 original size:20 final size:22
Alignment explanation
Indices: 95403--95442 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
95393 TCCTTCATGT
95403 TTTTAATTT-TTATA-ATTTCG
1 TTTTAATTTCTTATATATTTCG
*
95423 TTTTATTTTCTTATATATTT
1 TTTTAATTTCTTATATATTT
95443 ACTTCATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (22 bp):
TTTTAATTTCTTATATATTTCG
Found at i:98585 original size:12 final size:11
Alignment explanation
Indices: 98551--98588 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 11
98541 GCAAATGATG
98551 TAAAAT-ATTC
1 TAAAATAATTC
*
98561 TAAAATAAATC
1 TAAAATAATTC
98572 TAAATATAATTC
1 TAAA-ATAATTC
98584 TAAAA
1 TAAAA
98589 ATGCTAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 6 0.25
11 8 0.33
12 10 0.42
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAATAATTC
Found at i:100114 original size:21 final size:21
Alignment explanation
Indices: 100088--100210 Score: 151
Period size: 21 Copynumber: 5.8 Consensus size: 21
100078 AGGGTGTCAA
100088 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACTCCTGC
*
100109 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACTCCTGC
*
100130 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACTCCTGC
*
100151 AGTGCATCCATGCACTTTCCAT-T
1 AGTGCATCCATGCAC--TCC-TGC
* * *
100174 AGTGCATCGATGAAC-CATGC
1 AGTGCATCCATGCACTCCTGC
100194 AGTGCATCCATGCACTC
1 AGTGCATCCATGCACTC
100211 TATTTCGAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
19 1 0.01
20 14 0.16
21 57 0.65
23 15 0.17
24 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACTCCTGC
Found at i:100669 original size:34 final size:33
Alignment explanation
Indices: 100630--100695 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
100620 GTAAAGGGGA
*
100630 AAAGGTTCTAG-CTAAGCCCGTGTAAAAGCTAGGG
1 AAAGGTTCTAGTCTAA-CCCGTG-AAAAACTAGGG
*
100664 AAAGGTTCTAGTTTAACCCGTGAAAAACTAGG
1 AAAGGTTCTAGTCTAACCCGTGAAAAACTAGG
100696 AAGTTGTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 9 0.31
34 17 0.59
35 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (33 bp):
AAAGGTTCTAGTCTAACCCGTGAAAAACTAGGG
Found at i:103012 original size:21 final size:21
Alignment explanation
Indices: 102986--103151 Score: 182
Period size: 21 Copynumber: 7.9 Consensus size: 21
102976 AGGGTGTCAA
102986 AGTGCATCCATGCACTCCTGT
1 AGTGCATCCATGCACTCCTGT
103007 AGTGCATCCATGCACTCCTGT
1 AGTGCATCCATGCACTCCTGT
*
103028 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACTCCTGT
*
103049 AGTTCATCCATGCA--CCTGT
1 AGTGCATCCATGCACTCCTGT
103068 GCAGTGCATCCATGCA--CCTGT
1 --AGTGCATCCATGCACTCCTGT
103089 GCAGTGCATCCATGCACCTGCCAT-T
1 --AGTGCATCCATGCA-CT-CC-TGT
* * *
103114 AGTGCATCGATGCAC-CATGC
1 AGTGCATCCATGCACTCCTGT
103134 AGTGCATCCATGCACTCC
1 AGTGCATCCATGCACTCC
103152 ATTTCGAATG
Statistics
Matches: 128, Mismatches: 8, Indels: 18
0.83 0.05 0.12
Matches are distributed among these distances:
19 6 0.05
20 15 0.12
21 89 0.70
22 1 0.01
23 13 0.10
25 3 0.02
26 1 0.01
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCACTCCTGT
Done.