Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005954.1 Hibiscus syriacus cultivar Beakdansim tig00013986_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: 85164
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1407 original size:69 final size:70
Alignment explanation
Indices: 1296--1437 Score: 277
Period size: 69 Copynumber: 2.0 Consensus size: 70
1286 CCAGTGCACT
1296 AGGGAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCAC-TTGCTAAAGTTTG
1 AGGGAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTTG
1360 TGTTG
66 TGTTG
1365 AGGGAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTTG
1 AGGGAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTTG
1430 TGTTG
66 TGTTG
1435 AGG
1 AGG
1438 TTGATGTTAA
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 51 0.71
70 21 0.29
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (70 bp):
AGGGAACCAATCTCCATGGACTCTTTCACTGCTTCTAAAACTAGATTGCACTTTGCTAAAGTTTG
TGTTG
Found at i:8029 original size:31 final size:31
Alignment explanation
Indices: 7994--8058 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
7984 TCAACCGTTA
*
7994 AAATTATCAGTTTTGGTCAGTTTTAGTACCT
1 AAATTATCAGTTTTGGTCAGTTTTAATACCT
*
8025 AAATTATCAGTTTTGGTCGGTTTTAATACCT
1 AAATTATCAGTTTTGGTCAGTTTTAATACCT
8056 AAA
1 AAA
8059 CTTTTAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.43
Consensus pattern (31 bp):
AAATTATCAGTTTTGGTCAGTTTTAATACCT
Found at i:16128 original size:16 final size:16
Alignment explanation
Indices: 16107--16137 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
16097 TCGCCGACCG
16107 AATTCACTATTCATGA
1 AATTCACTATTCATGA
16123 AATTCACTATTCATG
1 AATTCACTATTCATG
16138 TGAATAGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
AATTCACTATTCATGA
Found at i:29265 original size:308 final size:306
Alignment explanation
Indices: 28697--29316 Score: 1222
Period size: 308 Copynumber: 2.0 Consensus size: 306
28687 ATTATGTTGC
28697 ATTTGCAGGCAAAGCTGAATGAGGCATTAGCTGGAACTGTTGAAGCACTTTTAGATGGAGCTAAT
1 ATTTGCAGGCAAAGCTGAATGAGGCATTAGCTGGAACTGTTGAAGCACTTTTAGATGGAGCTAAT
28762 GATGAGACATGGCCCTCAATAAAGAAAATTCTCCACCGTGAAACTGATTCAGCATTTCTGGACTC
66 GATGAGACATGGCCCTCAATAAAGAAAATTCTCCACCGTGAAACTGATTCAGCATTTCTGGACTC
28827 TCCAGAGCCCTTTTGGTTTTGACATGGATGTGGAAACCAAGGAGAAGATGCTATCGAGTCTACAG
131 TCCAGAGCCCTTTTGGTTTTGACATGGATGTGGAAACCAAGGAGAAGATGCTATCGAGTCTACAG
28892 GATTATGCAAGAGGTGTGGTTGAAGCAAAAGCAAGAGAAGAAGCTGGAAGGGTATTGATTCGTAT
196 GATTATGCAAGAGGTGTGGTTGAAGCAAAAGCAAGAGAAGAAGCTGGAAGGGTATTGATTCGTAT
28957 GAAGGACAGGTAATAACATATTTCAATGCTTGAGTTAATCGGTTTG
261 GAAGGACAGGTAATAACATATTTCAATGCTTGAGTTAATCGGTTTG
29003 ATTTGCAGGCAAAGCTGAATGAGGCATTAGCTGGAACTGTTGAAGCACTTTTAGATGGAGCTAAT
1 ATTTGCAGGCAAAGCTGAATGAGGCATTAGCTGGAACTGTTGAAGCACTTTTAGATGGAGCTAAT
29068 GATGAGACATGGCCCTCAATAAAGAAAATTCTCCACCGTGAAACTGATTCAGCCATTTCTGGACT
66 GATGAGACATGGCCCTCAATAAAGAAAATTCTCCACCGTGAAACTGATTCAG-CATTTCTGGACT
29133 CTCCAGAGCCCTTTCTGGTTTTGACATGGATGTGGAAACCAAGGAGAAGATGCTATCGAGTCTAC
130 CTCCAGAGCCCTTT-TGGTTTTGACATGGATGTGGAAACCAAGGAGAAGATGCTATCGAGTCTAC
29198 AGGATTATGCAAGAGGTGTGGTTGAAGCAAAAGCAAGAGAAGAAGCTGGAAGGGTATTGATTCGT
194 AGGATTATGCAAGAGGTGTGGTTGAAGCAAAAGCAAGAGAAGAAGCTGGAAGGGTATTGATTCGT
29263 ATGAAGGACAGGTAATAACATATTTCAATGCTTGAGTTAATCGGTTTG
259 ATGAAGGACAGGTAATAACATATTTCAATGCTTGAGTTAATCGGTTTG
29311 ATTTGC
1 ATTTGC
29317 TAGACATTAT
Statistics
Matches: 312, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
306 117 0.38
307 26 0.08
308 169 0.54
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (306 bp):
ATTTGCAGGCAAAGCTGAATGAGGCATTAGCTGGAACTGTTGAAGCACTTTTAGATGGAGCTAAT
GATGAGACATGGCCCTCAATAAAGAAAATTCTCCACCGTGAAACTGATTCAGCATTTCTGGACTC
TCCAGAGCCCTTTTGGTTTTGACATGGATGTGGAAACCAAGGAGAAGATGCTATCGAGTCTACAG
GATTATGCAAGAGGTGTGGTTGAAGCAAAAGCAAGAGAAGAAGCTGGAAGGGTATTGATTCGTAT
GAAGGACAGGTAATAACATATTTCAATGCTTGAGTTAATCGGTTTG
Found at i:32573 original size:2 final size:2
Alignment explanation
Indices: 32566--32606 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
32556 TGTTTTCCTA
32566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32607 CGTGATAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:32865 original size:30 final size:30
Alignment explanation
Indices: 32831--32905 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
32821 GTCAAACGAC
*
32831 TTAATTGATTTAAATT-TTAAATTTAATGA-T
1 TTAATTGATTTAAATTCTT-AATTTAA-AATT
**
32861 TTAATTGAAATAAATTCTTAATTTAAAATT
1 TTAATTGATTTAAATTCTTAATTTAAAATT
32891 TTAATTGATTGTAAA
1 TTAATTGATT-TAAA
32906 AAAATAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
29 1 0.03
30 30 0.81
31 6 0.16
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (30 bp):
TTAATTGATTTAAATTCTTAATTTAAAATT
Found at i:34411 original size:24 final size:24
Alignment explanation
Indices: 34371--34419 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
34361 TGATTCGAAT
34371 AGAAGGAGAAAAAAATAAAAGAAA
1 AGAAGGAGAAAAAAATAAAAGAAA
* *
34395 AGAAGGA-AGAAATAATAAGAGAAA
1 AGAAGGAGA-AAAAAATAAAAGAAA
34419 A
1 A
34420 TAATAGATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.71, C:0.00, G:0.22, T:0.06
Consensus pattern (24 bp):
AGAAGGAGAAAAAAATAAAAGAAA
Found at i:35813 original size:17 final size:18
Alignment explanation
Indices: 35787--35826 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
35777 TATTATTGAA
*
35787 AATAACTTTTATC-TTTT
1 AATAAATTTTATCATTTT
35804 AATAAATTTTATCAATTTT
1 AATAAATTTTATC-ATTTT
35823 AATA
1 AATA
35827 TGTTAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
19 8 0.40
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (18 bp):
AATAAATTTTATCATTTT
Found at i:38365 original size:29 final size:29
Alignment explanation
Indices: 38322--38404 Score: 121
Period size: 29 Copynumber: 2.8 Consensus size: 29
38312 CTCACCTAAC
*
38322 TAAATTGATGTAAGCAATGACATCATTACT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
38352 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
38381 TAAATGATGTAAGTAATGATATCA
1 TAAATGATGTAAGCAATGACATCA
38405 ATTTAGTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 44 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:41785 original size:15 final size:15
Alignment explanation
Indices: 41765--41794 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41755 CTTTCTTATA
41765 GTTGTTGTTGGAATT
1 GTTGTTGTTGGAATT
*
41780 GTTGTTGTTGTAATT
1 GTTGTTGTTGGAATT
41795 TCAGCCTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.30, T:0.57
Consensus pattern (15 bp):
GTTGTTGTTGGAATT
Found at i:43114 original size:29 final size:30
Alignment explanation
Indices: 43071--43150 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
43061 CTCACCTAAC
*
43071 TAAATTGATGTAAGCAATGACAAT-ATTACT
1 TAAA-TGATGTAAGCAATGACAATCATTAAT
* *
43101 TAAATGATGTAAGCAATGGC-ATCTTTAAT
1 TAAATGATGTAAGCAATGACAATCATTAAT
**
43130 TAAATGATGTAATTAATGACA
1 TAAATGATGTAAGCAATGACA
43151 TCAATTTAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 2 0.05
29 36 0.86
30 4 0.10
ACGTcount: A:0.42, C:0.09, G:0.15, T:0.34
Consensus pattern (30 bp):
TAAATGATGTAAGCAATGACAATCATTAAT
Found at i:44739 original size:3 final size:3
Alignment explanation
Indices: 44733--44780 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
44723 TCCTTACAAC
44733 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
44781 GTATGTTTGA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55685 original size:14 final size:14
Alignment explanation
Indices: 55666--55698 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55656 ATCCCCAAAA
55666 CTTAAATCA-TAAAT
1 CTTAAA-CACTAAAT
55680 CTTAAACACTAAAT
1 CTTAAACACTAAAT
55694 CTTAA
1 CTTAA
55699 TTTAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (14 bp):
CTTAAACACTAAAT
Found at i:57392 original size:201 final size:199
Alignment explanation
Indices: 56722--57456 Score: 754
Period size: 200 Copynumber: 3.6 Consensus size: 199
56712 TAGGTAGCAC
* * * * *
56722 TTATATTGACCTATTTTTTGAAGT-AAACCGATATATTTATACCGGTAACATTGCAAATTTACCT
1 TTATGTTGACCTATTTTCT-AA-TAAAACCGGTATATTTATACCGGTTACATTGGAAATTTACCT
* * * * * *
56786 ATTATATTATTATTACCGGTTTCGATGTTTTTTTAGATCGATATAATTT-TAAATGTATCGACAT
64 ATTACATTATAATTATCGGTTTCGATGTTTTTGTAGATCGATAT-TTTTATAAATGTATCGACAC
* * * * * *
56850 TTTATGCTTGCACCTGGTTGGGAATTCATATTTCATTCTGGAAAAAAGTATCGACACAAACTAAC
128 TTTATGCGTGCACCTCGTT-TG--TGC--A-TTCATTCTGGACAAAAGTATCGACACAAATTAAC
56915 AAAGTGTCGATACA
187 -AAGTGTCGATACA
* * *
56929 TTAT-TTAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGAAAATTTACCTA
1 TTATGTT-GACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGGAAATTTACCTA
* * ** *
56993 TTACATTATACTTATGGGTTTCGATGTTTCCG-GGATCGATATTTTTATAAATGTATCGACACTT
65 TTACATTATAATTATCGGTTTCGATGTTTTTGTAGATCGATATTTTTATAAATGTATCGACACTT
* * * * *
57057 TATG-GTTGTACC-C-TTTTTGGCATTCATTCTGTACCAAAAGTATCGACACAAATTTAGCAAGC
130 TATGCG-TGCACCTCGTTTGT-GCATTCATTCTGGA-CAAAAGTATCGACACAAA-TTAACAAGT
*
57119 GTCGATACT
191 GTCGATACA
* * * *
57128 TTATGCTGACCTATTTT-TATCATAAAACCGGTATATTTATATCTGTTACATTGTAAATTTACCT
1 TTATGTTGACCTATTTTCTA--ATAAAACCGGTATATTTATACCGGTTACATTGGAAATTTACCT
*
57192 AATACATTATAATTATCGGTTTCGATGTTTTTGT-GATCGATACTTTTTAATAAATGTATCGACA
64 ATTACATTATAATTATCGGTTTCGATGTTTTTGTAGATCGATA-TTTTT-ATAAATGTATCGACA
* *
57256 CTTTATGCGTGCACCTCGTTTGTGCATTCATCCTGGACAATAAGTATCGACACAAATTCCACAAG
127 CTTTATGCGTGCACCTCGTTTGTGCATTCATTCTGGACAA-AAGTATCGACACAAATT-AACAAG
57321 TGTCGATACA
190 TGTCGATACA
* * * *
57331 TTATGTTGACCTGTTTTCTAAT-TAACCGGTATATTTATATCGGTTACATTGGTAATTTACCTAT
1 TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGGAAATTTACCTAT
** * * * * *
57395 TACATTATAATTATTAGTTTTGATGTTTTT-TGGGTCGATACTTGTATAAAATGTATCGACAC
66 TACATTATAATTATCGGTTTCGATGTTTTTGTAGATCGATATTTTTAT-AAATGTATCGACAC
57457 ATATTTAGGT
Statistics
Matches: 446, Mismatches: 61, Indels: 49
0.80 0.11 0.09
Matches are distributed among these distances:
198 11 0.02
199 44 0.10
200 99 0.22
201 77 0.17
202 34 0.08
203 58 0.13
204 9 0.02
205 35 0.08
206 65 0.15
207 14 0.03
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (199 bp):
TTATGTTGACCTATTTTCTAATAAAACCGGTATATTTATACCGGTTACATTGGAAATTTACCTAT
TACATTATAATTATCGGTTTCGATGTTTTTGTAGATCGATATTTTTATAAATGTATCGACACTTT
ATGCGTGCACCTCGTTTGTGCATTCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGA
TACA
Found at i:60204 original size:177 final size:177
Alignment explanation
Indices: 59908--60263 Score: 570
Period size: 177 Copynumber: 2.0 Consensus size: 177
59898 ATATTAAAAA
* * * *
59908 ATTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGATCGATACTATTTGAAAATGTAT
1 ATTACCTATTACATTATAATTATGGGTTTCGATATTTTCGGGATCAACACTATTTGAAAATGTAT
* * *
59973 CGACACTTTGTGCGTTCATCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAA-ATTTA
66 CGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAATATTAA
*
60037 TATAGTGTCGATACATGTTATAGACCTATTATCTCATAAAACCGGTAT
131 GA-AGTGTCGATACATGTTATAGACCTATTATCTCATAAAACCGGTAT
* *
60085 ATTACCTATTACATTATAATTATGGGTTTCGATATTTTCGGGATCAACACTTTTTGAATATGTAT
1 ATTACCTATTACATTATAATTATGGGTTTCGATATTTTCGGGATCAACACTATTTGAAAATGTAT
* * *
60150 CGACACTTTATGCGTTCACCCTTTTTGGCATCTATTTTGGACAAAAATTATCGACACAATATTAA
66 CGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAATATTAA
*
60215 GAAGTGTCGATACATGTTATAGACCTATTCTCTCATAAAACCGGTAT
131 GAAGTGTCGATACATGTTATAGACCTATTATCTCATAAAACCGGTAT
60262 AT
1 AT
60264 GTATACCGGT
Statistics
Matches: 164, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
177 159 0.97
178 5 0.03
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (177 bp):
ATTACCTATTACATTATAATTATGGGTTTCGATATTTTCGGGATCAACACTATTTGAAAATGTAT
CGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAATATTAA
GAAGTGTCGATACATGTTATAGACCTATTATCTCATAAAACCGGTAT
Found at i:63307 original size:24 final size:25
Alignment explanation
Indices: 63280--63332 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
63270 ATGTAGTTCA
63280 TCGGGATAAA-TTCTACGCGGTC-CT
1 TCGGGATAAATTTCTACGCGG-CACT
*
63304 TCGGGATAAATTTCTATGCGGCACT
1 TCGGGATAAATTTCTACGCGGCACT
63329 TCGG
1 TCGG
63333 TGCAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 11 0.42
25 15 0.58
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (25 bp):
TCGGGATAAATTTCTACGCGGCACT
Found at i:66004 original size:3 final size:3
Alignment explanation
Indices: 65996--66041 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
65986 GTTTGGATCG
* * * *
65996 TCA TCA TCA TCA TCA TCA TCA TCT TCA TCG TCA TCT TCA TCT TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
66042 TGACCGCTTG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.24, C:0.33, G:0.02, T:0.41
Consensus pattern (3 bp):
TCA
Found at i:66013 original size:12 final size:12
Alignment explanation
Indices: 65996--66041 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
65986 GTTTGGATCG
*
65996 TCATCATCATCA
1 TCATCATCATCT
66008 TCATCATCATCT
1 TCATCATCATCT
*
66020 TCATCGTCATCT
1 TCATCATCATCT
*
66032 TCATCTTCAT
1 TCATCATCAT
66042 TGACCGCTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.24, C:0.33, G:0.02, T:0.41
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:67872 original size:21 final size:21
Alignment explanation
Indices: 67842--67894 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
67832 TGTTTCTGGG
67842 ATCGATACTTTTTATAAATAT
1 ATCGATACTTTTTATAAATAT
*
67863 ATCGACACTTTTTATAAATAT
1 ATCGATACTTTTTATAAATAT
67884 ATCGATACTTT
1 ATCGATACTTT
67895 ATGGTTGCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (21 bp):
ATCGATACTTTTTATAAATAT
Found at i:68033 original size:221 final size:221
Alignment explanation
Indices: 67642--68478 Score: 798
Period size: 200 Copynumber: 4.0 Consensus size: 221
67632 ATTTTCTGGG
* * *
67642 ATCGATACTTTTTATAAATGGATCGATACTTTATAGTTGCACTCTTTTTGGCATTCATTATGGAC
1 ATCGACACTTTTTATAAATAGATCGATACTTTATAGTTGCACCCTTTTTGGCATTCATTATGGAC
*
67707 CAAAAGTATCGATACAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAACC
66 CAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAACC
* *
67772 GGTAAATTTATACTGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
131 GATAAATTTATACCGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
67837 CTGGGATCGATACTTTTTATAAATAT
196 CTGGGATCGATACTTTTTATAAATAT
* * * *
67863 ATCGACACTTTTTATAAATATATCGATACTTTATGGTTGCACCCTTTTTTGCATTCATTCTGGAC
1 ATCGACACTTTTTATAAATAGATCGATACTTTATAGTTGCACCCTTTTTGGCATTCATTATGGAC
* *
67928 CAAAAGTATCGACACAAAATTAAAAAG-GTTCGATACATGTTGTAGACCTATTCTCTCGTAAAAC
66 CAAAAGTATCGACACAAAATTAAAAAGTG-TCGATACATGTTGTAAACATATTCTCTCGTAAAAC
* * *
67992 CGATACATTTATACCGGTTACATTAAAAATTTACTTATTACATTATACTTATGGGTTTCGATGTT
130 CGATAAATTTATACCGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTT
*
68057 TCTTGGATCGATACTTTTTATAAATGGAT
195 TCTGGGATCGATACTTTTTATAAAT--AT
** * * ** * * * * *
68086 AT--ACAC--TTTAT-GGTTG--C-A-CCTTT-T--TTGGCATTCATTTTGG-A-CCA-AAAGTA
1 ATCGACACTTTTTATAAATAGATCGATACTTTATAGTT-GCACCCTTTTTGGCATTCATTATGGA
* * *
68136 TC----G-A-C-A-AAAA-ATTAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCGTAAAAC
65 CCAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAAC
* * * *
68192 CGATAAATTTATATCGGTTACATTGAAAATTTACCTATTGCATTATACTTATGGGTTTCGATGTT
130 CGATAAATTTATACCGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTT
* **
68257 TTTGGGATCGATACTTTTTATAAATGG
195 TCTGGGATCGATACTTTTTATAAATAT
** * ** * * * * * *
68284 ATCGACAC--TTTAT-GGTTG--C-ACCCTTT-T--TGGCA--TTTATTCTGG-A-CCA-AAAGT
1 ATCGACACTTTTTATAAATAGATCGATACTTTATAGTTGCACCCTT-TT-TGGCATTCATTATGG
* * *
68335 ATC----G-A-C-ACA-AAA-TTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAA
64 ACCAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAA
* * *
68391 CCGGTAAATTTATACCGGTTACATTGAAAAATTACCTATTGCATTATACTTATGGGTTTCGATGT
129 CCGATAAATTTATACCGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGT
68456 TTCTGGGATCGATACTTTTTATA
194 TTCTGGGATCGATACTTTTTATA
68479 TATGGATCGA
Statistics
Matches: 554, Mismatches: 50, Indels: 45
0.85 0.08 0.07
Matches are distributed among these distances:
198 3 0.01
199 2 0.00
200 293 0.53
201 12 0.02
202 1 0.00
203 1 0.00
204 1 0.00
205 1 0.00
209 3 0.01
210 2 0.00
211 3 0.01
212 9 0.02
213 1 0.00
214 4 0.01
215 1 0.00
216 1 0.00
218 1 0.00
219 5 0.01
220 1 0.00
221 205 0.37
223 4 0.01
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (221 bp):
ATCGACACTTTTTATAAATAGATCGATACTTTATAGTTGCACCCTTTTTGGCATTCATTATGGAC
CAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAACC
GATAAATTTATACCGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTT
CTGGGATCGATACTTTTTATAAATAT
Found at i:68404 original size:400 final size:405
Alignment explanation
Indices: 67512--68490 Score: 1447
Period size: 421 Copynumber: 2.4 Consensus size: 405
67502 TATTTAAATT
*
67512 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
* * * *
67577 TATTTATACCGTTTACATTGAAAAATTACCTATTATATTATACTTATGTGTTTCGAT-TTTCTGG
66 AATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
* *
67641 GATCGATACTTTTTATAAATGGATCGATACTTTATAGTTGCACTCTTTTTGGCATTCATTATGGA
131 GATCGATACTTTTTATAAATGGATAGACACTTTATAGTTGCACTCTTTTTGGCATTCATTATGGA
* *
67706 CCAAAAGTATCGATACAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAAC
196 CCAAAAGTATCGACAAAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAAC
*
67771 CGGTAAATTTATACTGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTT
261 CGATAAATTTATACTGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTT
* *
67836 TCTGGGATCGATACTTTTTATAAATATATCGACACTTTTTATAAATATATCGATACTTTATGGTT
326 TCTGGGATCGATACTTTTTAT-AATATATCG---------------AGATCGACACTTTATGGTT
*
67901 GCACCCTTTTTTGCATTCATTCTGGACCAAA
375 GCACCCTTTTTGGCATTCATTCTGGACCAAA
*
67932 AGTATCGACACAAAATTAAAAAG-GTTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGAT
1 AGTATCGACACAAAATTAAAAAGTG-TCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGT
* *
67996 ACATTTATACCGGTTACATT-AAAAATTTACTTATTACATTATACTTATGGGTTTCGATGTTTCT
65 AAATTTATACCGGTTACATTGAAAAA-TTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
* * * *
68060 TGGATCGATACTTTTTATAAATGGATATACACTTTATGGTTGCAC-CTTTTTTGGCATTCATTTT
129 GGGATCGATACTTTTTATAAATGGATAGACACTTTATAGTTGCACTC-TTTTTGGCATTCATTAT
*
68124 GGACCAAAAGTATCGACAAAAAATTAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCGTAA
193 GGACCAAAAGTATCGACAAAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAA
* * *
68189 AACCGATAAATTTATA-TCGGTTACATTGAAAATTTACCTATTGCATTATACTTATGGGTTTCGA
258 AACCGATAAATTTATACT-GGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGA
*
68253 TGTTTTTGGGATCGATACTTTTTAT-A-A-AT-G-GATCGACACTTTATGGTTGCACCCTTTTTG
322 TGTTTCTGGGATCGATACTTTTTATAATATATCGAGATCGACACTTTATGGTTGCACCCTTTTTG
*
68313 GCATTTATTCTGGACCAAA
387 GCATTCATTCTGGACCAAA
68332 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
*
68397 AATTTATACCGGTTACATTGAAAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTTCTGG
66 AATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
* *
68462 GATCGATACTTTTTATATATGGATCGACA
131 GATCGATACTTTTTATAAATGGATAGACA
68491 TATAAGCTTA
Statistics
Matches: 519, Mismatches: 33, Indels: 34
0.89 0.06 0.06
Matches are distributed among these distances:
400 188 0.36
401 6 0.01
416 1 0.00
417 2 0.00
418 1 0.00
419 7 0.01
420 109 0.21
421 205 0.39
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.38
Consensus pattern (405 bp):
AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACCGGTA
AATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
GATCGATACTTTTTATAAATGGATAGACACTTTATAGTTGCACTCTTTTTGGCATTCATTATGGA
CCAAAAGTATCGACAAAAAATTAAAAAGTGTCGATACATGTTGTAAACATATTCTCTCGTAAAAC
CGATAAATTTATACTGGTTACATTAAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTT
TCTGGGATCGATACTTTTTATAATATATCGAGATCGACACTTTATGGTTGCACCCTTTTTGGCAT
TCATTCTGGACCAAA
Found at i:68486 original size:200 final size:200
Alignment explanation
Indices: 67863--68490 Score: 1035
Period size: 200 Copynumber: 3.1 Consensus size: 200
67853 TTATAAATAT
* ** * *
67863 ATCGACACTTTTTATAAATATATCGATACTTTATGGTTGCACCCTTTTTTGCATTCATTCTGGAC
1 ATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGAC
67928 CAAAAGTATCGACACAAAATTAAAAAG-GTTCGATACATGTTGTAGACCTATTCTCTCGTAAAAC
66 CAAAAGTATCGACACAAAATTAAAAAGTG-TCGATACATGTTGTAGACCTATTCTCTCGTAAAAC
* * *
67992 CGATACATTTATACCGGTTACATT-AAAAATTTACTTATTACATTATACTTATGGGTTTCGATGT
130 CGATAAATTTATACCGGTTACATTGAAAAA-TTACCTATTGCATTATACTTATGGGTTTCGATGT
*
68056 TTCTTGG
194 TTCTGGG
** * *
68063 ATCGATACTTTTTATAAATGGATATACACTTTATGGTTGCACCTTTTTTGGCATTCATTTTGGAC
1 ATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGAC
* *
68128 CAAAAGTATCGACAAAAAATTAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCGTAAAACC
66 CAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACC
* *
68193 GATAAATTTATATCGGTTACATTGAAAATTTACCTATTGCATTATACTTATGGGTTTCGATGTTT
131 GATAAATTTATACCGGTTACATTGAAAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTT
*
68258 TTGGG
196 CTGGG
*
68263 ATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTTATTCTGGAC
1 ATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGAC
68328 CAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACC
66 CAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACC
*
68393 GGTAAATTTATACCGGTTACATTGAAAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTT
131 GATAAATTTATACCGGTTACATTGAAAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTT
68458 CTGGG
196 CTGGG
*
68463 ATCGATACTTTTTATATATGGATCGACA
1 ATCGATACTTTTTATAAATGGATCGACA
68491 TATAAGCTTA
Statistics
Matches: 396, Mismatches: 30, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
200 391 0.99
201 5 0.01
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (200 bp):
ATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGAC
CAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAACC
GATAAATTTATACCGGTTACATTGAAAAATTACCTATTGCATTATACTTATGGGTTTCGATGTTT
CTGGG
Found at i:69347 original size:4 final size:4
Alignment explanation
Indices: 69338--70017 Score: 1328
Period size: 4 Copynumber: 170.2 Consensus size: 4
69328 AATGCCCTTT
69338 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69386 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69434 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69482 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69530 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69578 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
69626 CATA C--A CAGA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69672 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69720 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69768 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69816 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69864 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69912 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
69960 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
70008 CCATA CATA C
1 -CATA CATA C
70018 CTCTCTTAGC
Statistics
Matches: 672, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
2 2 0.00
4 666 0.99
5 4 0.01
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:71031 original size:16 final size:16
Alignment explanation
Indices: 70983--71032 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
70973 TCCTCCTCAT
70983 TTCTTCTATATTTTCTTC
1 TTCTTC-ATATTTT-TTC
* * *
71001 TTCTTCCTCTCTTTTC
1 TTCTTCATATTTTTTC
71017 TTCTTCATATTTTTTC
1 TTCTTCATATTTTTTC
71033 AGATCATCGT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 16 0.62
17 4 0.15
18 6 0.23
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (16 bp):
TTCTTCATATTTTTTC
Found at i:73798 original size:20 final size:19
Alignment explanation
Indices: 73753--73810 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
73743 CCGGTAGCAC
*
73753 TTTACTGGTTTTATCATTT
1 TTTACCGGTTTTATCATTT
* *
73772 TGATACCGGTTTTTTCATATT
1 T-TTACCGGTTTTATCAT-TT
* *
73793 TTTACCTGTTATATCATT
1 TTTACCGGTTTTATCATT
73811 ATGGATCGAT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
19 2 0.07
20 25 0.83
21 3 0.10
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (19 bp):
TTTACCGGTTTTATCATTT
Found at i:73900 original size:182 final size:181
Alignment explanation
Indices: 73593--74011 Score: 619
Period size: 182 Copynumber: 2.3 Consensus size: 181
73583 GGTAGCGCTT
* *
73593 TACCGGTTTTATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCATTATGGATCGATACATTTTTATAAAGTATCG
73658 ACACTTTATAAGCGTTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
66 ACACTTTATAAGCGTTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
* * * *
73723 TACCGACACTTTAAATATATCCGGTAGCA-CTTTACTGGTTTTATCATTTTGA
131 TACCGACACGTTAAATATATCCGGTAG-AGCTTTACCGGTATTATC-TTTTCA
*
73775 TACCGGTTTTTTCATATTTTTACCTGTTATATCATTATGGATCGATACATTTTTATAAAGTATCG
1 TACCGGTTTTATCATATTTTTACCTGTTATATCATTATGGATCGATACATTTTTATAAAGTATCG
* * *
73840 ACACTTTATAGGCGTTAAAACT-TATTCTCTTTTAAATTCACAAAGTGTCGATCCTTATATTAGA
66 ACACTTTATAAGCGTTAAAACTGT-TTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAA
* * * *
73904 GTATCGACACGTTCAATATATCTGGTAGAGCTTTACCGGTATTGTCTTTTCA
130 GTACCGACACGTTAAATATATCCGGTAGAGCTTTACCGGTATTATCTTTTCA
* * *
73956 TAACAGGTTTTATCATATTTTTACTTGTTATATTGA-TATGGATCGATACATTTTTA
1 T-ACCGGTTTTATCATATTTTTACCTGTTATA-TCATTATGGATCGATACATTTTTA
74012 ATTTGGATCG
Statistics
Matches: 215, Mismatches: 18, Indels: 8
0.89 0.07 0.03
Matches are distributed among these distances:
181 8 0.04
182 205 0.95
183 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (181 bp):
TACCGGTTTTATCATATTTTTACCTGTTATATCATTATGGATCGATACATTTTTATAAAGTATCG
ACACTTTATAAGCGTTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATACTTATATTAAAG
TACCGACACGTTAAATATATCCGGTAGAGCTTTACCGGTATTATCTTTTCA
Found at i:76428 original size:8 final size:9
Alignment explanation
Indices: 76407--76440 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
76397 TGTACCTATT
76407 TTTTTCTTC
1 TTTTTCTTC
76416 TTTTTCTTC
1 TTTTTCTTC
*
76425 TTTTTCCTC
1 TTTTTCTTC
76434 TGTTTTC
1 T-TTTTC
76441 CCTTTTCCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.74
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:83818 original size:25 final size:25
Alignment explanation
Indices: 83784--83833 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
83774 AAAAACATAA
83784 GTAAACTCAGAATTTCTTCTGTCAT
1 GTAAACTCAGAATTTCTTCTGTCAT
83809 GTAAACTCAGAATTTCTTCTGTCAT
1 GTAAACTCAGAATTTCTTCTGTCAT
83834 TCACCAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (25 bp):
GTAAACTCAGAATTTCTTCTGTCAT
Done.