Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007878.1 Hibiscus syriacus cultivar Beakdansim tig00110254_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: 246905
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:194826 original size:21 final size:21
Alignment explanation
Indices: 194802--194855 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
194792 TCCACTGCTA
194802 TGCTCTCCCATCCCACCACTT
1 TGCTCTCCCATCCCACCACTT
194823 TGCTCTCCCATCCCACCACTT
1 TGCTCTCCCATCCCACCACTT
194844 TGCTCTCCCATC
1 TGCTCTCCCATC
194856 TTTGCTGGGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.13, C:0.52, G:0.06, T:0.30
Consensus pattern (21 bp):
TGCTCTCCCATCCCACCACTT
Found at i:195691 original size:21 final size:21
Alignment explanation
Indices: 195658--195705 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
195648 AGGCAAAATT
195658 ATAAGATTATAAAT-AAATAGAA
1 ATAA-ATTATAAATAAAATA-AA
*
195680 ATAAATTTTAAATAAAATAAA
1 ATAAATTATAAATAAAATAAA
195701 ATAAA
1 ATAAA
195706 ATTGTATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (21 bp):
ATAAATTATAAATAAAATAAA
Found at i:195721 original size:5 final size:5
Alignment explanation
Indices: 195715--195803 Score: 70
Period size: 5 Copynumber: 17.8 Consensus size: 5
195705 AATTGTATTA
* * * * * *
195715 TTATA TTATG TTATG TTATG TTATG CTATG CTATG CTATG CTATG CTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
* * * * * *
195765 CTATG CTATG CTATG CTATG CTATG TTATG TTATA TTAT
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTAT
195804 ATTGACAACC
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 80 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.49
Consensus pattern (5 bp):
TTATG
Found at i:195733 original size:10 final size:10
Alignment explanation
Indices: 195721--195794 Score: 112
Period size: 10 Copynumber: 7.4 Consensus size: 10
195711 ATTATTATAT
* *
195721 TATGTTATGT
1 TATGCTATGC
*
195731 TATGTTATGC
1 TATGCTATGC
195741 TATGCTATGC
1 TATGCTATGC
195751 TATGCTATGC
1 TATGCTATGC
195761 TATGCTATGC
1 TATGCTATGC
195771 TATGCTATGC
1 TATGCTATGC
*
195781 TATGCTATGT
1 TATGCTATGC
195791 TATG
1 TATG
195795 TTATATTATA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 61 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (10 bp):
TATGCTATGC
Found at i:195738 original size:15 final size:15
Alignment explanation
Indices: 195721--195794 Score: 112
Period size: 15 Copynumber: 4.9 Consensus size: 15
195711 ATTATTATAT
* * *
195721 TATGTTATGTTATGT
1 TATGCTATGCTATGC
195736 TATGCTATGCTATGC
1 TATGCTATGCTATGC
195751 TATGCTATGCTATGC
1 TATGCTATGCTATGC
195766 TATGCTATGCTATGC
1 TATGCTATGCTATGC
*
195781 TATGCTATGTTATG
1 TATGCTATGCTATG
195795 TTATATTATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 55 1.00
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (15 bp):
TATGCTATGCTATGC
Found at i:195913 original size:5 final size:5
Alignment explanation
Indices: 195903--196210 Score: 238
Period size: 5 Copynumber: 61.6 Consensus size: 5
195893 AATTTCTTTA
* * * * * * * *
195903 TATGT TATGT TGTGT TGTGT TGTGT TGTGT TGTGT TGTGT TGTGT TGTGT
1 TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT
* * * * * * * * *
195953 TGTGT TGTGT TGTGT TCTGC TATGC TATGT TATGT TGTGT TGTGT TGTGT
1 TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT
* * * * *
196003 TATGT TCTGC TATGC TATGT TATGT TATGC TATGT TATGC TATGT TATGT
1 TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT
* * * * * *
196053 TATGT TATGC TATGT TATGT TATGT TATGC TATAT TATGC TATGC TATGC
1 TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT
* * * * * *
196103 TATGC TATGC TATGT TATGC TATGT TATGT TATGT TATGC TATGC TATGC
1 TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT
* * * * * * *
196153 TATGA TATGC TATGC TATGT TATGC TATGC TATGC TATGC TATGT TATGT
1 TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT TATGT
*
196203 TATAT TAT
1 TATGT TAT
196211 ATTGACAACC
Statistics
Matches: 271, Mismatches: 32, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 271 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (5 bp):
TATGT
Found at i:196016 original size:10 final size:10
Alignment explanation
Indices: 195965--196201 Score: 267
Period size: 10 Copynumber: 23.7 Consensus size: 10
195955 TGTTGTGTTG
*
195965 TGTTCTGCTA
1 TGTTATGCTA
* *
195975 TGCTATGTTA
1 TGTTATGCTA
* * *
195985 TGTTGTGTTG
1 TGTTATGCTA
* *
195995 TGTTGTGTTA
1 TGTTATGCTA
*
196005 TGTTCTGCTA
1 TGTTATGCTA
* *
196015 TGCTATGTTA
1 TGTTATGCTA
196025 TGTTATGCTA
1 TGTTATGCTA
196035 TGTTATGCTA
1 TGTTATGCTA
*
196045 TGTTATGTTA
1 TGTTATGCTA
196055 TGTTATGCTA
1 TGTTATGCTA
*
196065 TGTTATGTTA
1 TGTTATGCTA
196075 TGTTATGCTA
1 TGTTATGCTA
*
196085 TATTATGCTA
1 TGTTATGCTA
*
196095 TGCTATGCTA
1 TGTTATGCTA
*
196105 TGCTATGCTA
1 TGTTATGCTA
196115 TGTTATGCTA
1 TGTTATGCTA
*
196125 TGTTATGTTA
1 TGTTATGCTA
196135 TGTTATGCTA
1 TGTTATGCTA
*
196145 TGCTATGCTA
1 TGTTATGCTA
*
196155 TGATATGCTA
1 TGTTATGCTA
* *
196165 TGCTATGTTA
1 TGTTATGCTA
*
196175 TGCTATGCTA
1 TGTTATGCTA
*
196185 TGCTATGCTA
1 TGTTATGCTA
196195 TGTTATG
1 TGTTATG
196202 TTATATTATA
Statistics
Matches: 197, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 197 1.00
ACGTcount: A:0.19, C:0.11, G:0.21, T:0.50
Consensus pattern (10 bp):
TGTTATGCTA
Found at i:198398 original size:14 final size:15
Alignment explanation
Indices: 198371--198399 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
198361 ATATCCACGT
198371 GGAGAAAGAAGGAAA
1 GGAGAAAGAAGGAAA
198386 GGAGAAA-AAGGAAA
1 GGAGAAAGAAGGAAA
198400 TATCTGGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
GGAGAAAGAAGGAAA
Found at i:198537 original size:37 final size:37
Alignment explanation
Indices: 198487--198559 Score: 146
Period size: 37 Copynumber: 2.0 Consensus size: 37
198477 ATTTTTGCAC
198487 TTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAAAA
1 TTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAAAA
198524 TTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAAA
1 TTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAAA
198560 GCTTAAGGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (37 bp):
TTTAGTTACGGTTTTGATTCTTGAGGTACTAAGAAAA
Found at i:199081 original size:22 final size:22
Alignment explanation
Indices: 199031--199089 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
199021 ACCATATGGA
* *
199031 AGAGGTATCGGTA--CTTGGAT
1 AGAGGTATCGGTACCCTAGCAT
199051 AG-GGTATCGGTACCCTAGCAT
1 AGAGGTATCGGTACCCTAGCAT
199072 AGAGGTATCGGTACCCTA
1 AGAGGTATCGGTACCCTA
199090 AGGGTAGTAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 10 0.29
20 2 0.06
21 7 0.21
22 15 0.44
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (22 bp):
AGAGGTATCGGTACCCTAGCAT
Found at i:200644 original size:18 final size:18
Alignment explanation
Indices: 200621--200672 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
200611 TATGTGATAT
200621 GTGGTCCTTC-GGAACATA
1 GTGGTCCTTCAGG-ACATA
*
200639 GTGGTCCTTCAGGGCATA
1 GTGGTCCTTCAGGACATA
200657 GTGGTCCTTCAGGACA
1 GTGGTCCTTCAGGACA
200673 AATTTTACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
18 29 0.94
19 2 0.06
ACGTcount: A:0.19, C:0.23, G:0.31, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCAGGACATA
Found at i:210884 original size:24 final size:24
Alignment explanation
Indices: 210855--210932 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
210845 TAGTACTGAT
210855 ACAAAAATGTAACATATGCATTAA
1 ACAAAAATGTAACATATGCATTAA
* * ** * *
210879 ACAAAATTG-ATCGATAACCATCAT
1 ACAAAAATGTAAC-ATATGCATTAA
*
210903 ACGAAAATGTAA-ACTATGCATTAA
1 ACAAAAATGTAACA-TATGCATTAA
210927 ACAAAA
1 ACAAAA
210933 TCATTCAATA
Statistics
Matches: 37, Mismatches: 14, Indels: 6
0.65 0.25 0.11
Matches are distributed among these distances:
23 3 0.08
24 33 0.89
25 1 0.03
ACGTcount: A:0.53, C:0.15, G:0.09, T:0.23
Consensus pattern (24 bp):
ACAAAAATGTAACATATGCATTAA
Found at i:212025 original size:55 final size:55
Alignment explanation
Indices: 211957--212153 Score: 317
Period size: 55 Copynumber: 3.6 Consensus size: 55
211947 ATTGTTTGAG
211957 TGTGTATCAGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGCAATT
1 TGTGTATCAGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGCAATT
* * *
212012 TGTGTATCGGTACACTGAGAAGTGTATCGATACACTCAAAACATCGAATGTC-ATT
1 TGTGTATCAGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATG-CAATT
* *
212067 TGTGTATCGGTACACTGAGGAGTGTATCGATACCCT-CAAACATCGAATGCAATT
1 TGTGTATCAGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGCAATT
*
212121 TGTGTATCAGTACACTAAGGAGTGTATCGATAC
1 TGTGTATCAGTACACTGAGGAGTGTATCGATAC
212154 CCCCCAGTTA
Statistics
Matches: 132, Mismatches: 8, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
53 1 0.01
54 46 0.35
55 84 0.64
56 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.28
Consensus pattern (55 bp):
TGTGTATCAGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGCAATT
Found at i:218744 original size:20 final size:20
Alignment explanation
Indices: 218719--218793 Score: 150
Period size: 20 Copynumber: 3.8 Consensus size: 20
218709 TTGTATGAGT
218719 GTGTATCGGTACACTGAGGA
1 GTGTATCGGTACACTGAGGA
218739 GTGTATCGGTACACTGAGGA
1 GTGTATCGGTACACTGAGGA
218759 GTGTATCGGTACACTGAGGA
1 GTGTATCGGTACACTGAGGA
218779 GTGTATCGGTACACT
1 GTGTATCGGTACACT
218794 CCAAACATCG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.24, C:0.16, G:0.33, T:0.27
Consensus pattern (20 bp):
GTGTATCGGTACACTGAGGA
Found at i:218828 original size:55 final size:55
Alignment explanation
Indices: 218759--218940 Score: 285
Period size: 55 Copynumber: 3.3 Consensus size: 55
218749 ACACTGAGGA
*
218759 GTGTATCGGTACACTGAGGAGTGTATCGGTACACTCCAAACATCGAATGAAATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
* * **
218814 GTGTATCGGTACACTGAGGAGTGTATTGATACACTCAAAACATCGAATGTCATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
* * *
218869 GTGTATCGGTACACTGAGGAGTGTATCGATAC-CTTCAAACATTGAATGCAATTT
1 GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
218923 GTGTATCGGTACACTGAG
1 GTGTATCGGTACACTGAG
218941 TGTACCGATA
Statistics
Matches: 116, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
54 35 0.30
55 81 0.70
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (55 bp):
GTGTATCGGTACACTGAGGAGTGTATCGATACACTCCAAACATCGAATGAAATTT
Found at i:219341 original size:21 final size:21
Alignment explanation
Indices: 219299--219348 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
219289 GTGTTAGGAA
* * *
219299 AATATGAGCTTTGAACAGGTG
1 AATATGAACTTCGAACAAGTG
*
219320 AATATGAACTTCGAATAAGTG
1 AATATGAACTTCGAACAAGTG
*
219341 AATGTGAA
1 AATATGAA
219349 TATACTCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (21 bp):
AATATGAACTTCGAACAAGTG
Found at i:219530 original size:23 final size:22
Alignment explanation
Indices: 219503--219582 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 22
219493 CCGGGATAAA
* *
219503 TATGTGGCACTTCGGTGCAACC
1 TATGTGGCACTTCGATGCAAAC
219525 TTATGTGGCACTTCGATGCAAAC
1 -TATGTGGCACTTCGATGCAAAC
*
219548 TATGTGGTC-CTTC-AAG-ACAAC
1 TATGTGG-CACTTCGATGCA-AAC
219569 TATGTGGCACTTCG
1 TATGTGGCACTTCG
219583 GTATAAATTA
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
20 2 0.04
21 16 0.32
22 11 0.22
23 21 0.42
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.30
Consensus pattern (22 bp):
TATGTGGCACTTCGATGCAAAC
Found at i:221052 original size:23 final size:23
Alignment explanation
Indices: 220960--221051 Score: 130
Period size: 23 Copynumber: 4.0 Consensus size: 23
220950 CACCACAGCT
*
220960 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
220983 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
* *
221006 CGTAGAATTACACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
221029 TGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
221052 TATAATAATG
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 62 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:222731 original size:22 final size:20
Alignment explanation
Indices: 222678--222732 Score: 56
Period size: 22 Copynumber: 2.6 Consensus size: 20
222668 TTCAGACTAA
222678 ATAGTATTGATACTCATCCT
1 ATAGTATTGATACTCATCCT
* * * *
222698 ACAGTATCGATACTTCCTTTCT
1 ATAGTATTGATAC-T-CATCCT
222720 ATAGTATTGATAC
1 ATAGTATTGATAC
222733 CTACTTCGGT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 11 0.41
21 1 0.04
22 15 0.56
ACGTcount: A:0.29, C:0.20, G:0.11, T:0.40
Consensus pattern (20 bp):
ATAGTATTGATACTCATCCT
Found at i:223081 original size:20 final size:21
Alignment explanation
Indices: 223038--223081 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
223028 AAACTAACTT
** *
223038 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
223059 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
223079 ACA
1 ACA
223082 CTCAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:224586 original size:2 final size:2
Alignment explanation
Indices: 224579--224623 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
224569 CATATTTAAA
224579 AT AT AT AT AT AT AT 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
224621 AT A
1 AT A
224624 CACTCTATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:227040 original size:54 final size:55
Alignment explanation
Indices: 226898--227398 Score: 693
Period size: 54 Copynumber: 9.3 Consensus size: 55
226888 GAACTTGAAG
* *
226898 AATCTTCATCAATCGTGTCTGCTCCCTATTTCC-TCAGAGAGTATAAGACCCAAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTA-TTCCTTCAGAGAGTATAAGACTCGAAC
* * * *
226953 AATCTTCAACAAATCTTGTCTGCTCCCTATTCCTTCAGAGAATATAAGACCCG-AC
1 AATCTTCATC-AATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
* *
227008 AATCTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTTGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
* * *
227063 AATCTTCA--AATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
* * ** *
227116 -ATCTTCAACAGTCGTGTCTGCTCCCTATTTATGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
227170 AAT-TTCATCAATCGTGTCTGC-CCC--TTCCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
* *
227221 AATCTTCATCAAT-GTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
* *
227275 AATCTTCAACAATCGTGTCTGCTCCCCATTCCTTCAGAGAG--TAAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
* *
227328 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
*
227383 AATCTTCAACAATCGT
1 AATCTTCATCAATCGT
227399 TTGGAAACCT
Statistics
Matches: 399, Mismatches: 34, Indels: 26
0.87 0.07 0.06
Matches are distributed among these distances:
51 35 0.09
52 19 0.05
53 93 0.23
54 132 0.33
55 86 0.22
56 34 0.09
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (55 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAC
Found at i:227138 original size:107 final size:108
Alignment explanation
Indices: 226898--227391 Score: 682
Period size: 107 Copynumber: 4.6 Consensus size: 108
226888 GAACTTGAAG
* * *
226898 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTT---C
* * *
226963 AAATCTTGTCTGCTCCCTATTCCTTCAGAGAATATAAGAC-CCGAC
63 AAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCCAAC
* * *
227008 AATCTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCAAA
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAA
* *
227073 TCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCCAAC
66 TCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCCAAC
* * * *
227116 -ATCTTCAACAGTCGTGTCTGCTCCCTATTTATGCAGAGAGTATAAGACTCGAACAAT-TTCATC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCA--
*
227179 AATCGTGTCTGC-CCC--TTCCTTCAGAGAGTATAAGACTCGAAC
64 AATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCCAAC
*
227221 AATCTTCATCAAT-GTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATCTTCAAC
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTC-A-
* *
227285 AATCGTGTCTGCTCCCCATTCCTTCAGAGAG--TAAGACTCGAAC
64 AATCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCCAAC
*
227328 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAACAATCTTCAA
1 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
227392 CAATCGTTTG
Statistics
Matches: 348, Mismatches: 26, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
105 67 0.19
106 31 0.09
107 120 0.34
108 62 0.18
109 13 0.04
110 55 0.16
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (108 bp):
AATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAAA
TCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCCAAC
Found at i:227300 original size:267 final size:269
Alignment explanation
Indices: 226902--227398 Score: 763
Period size: 267 Copynumber: 1.8 Consensus size: 269
226892 TTGAAGAATC
226902 TTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAAT
1 TTCATCAATCGTGTCTGCTCCC--TTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAAT
* * *
226967 CTTGTCTGCTCCCTATTCCTTCAGAGAATATAAGACCCGACAATCTTCATCAATCGTGTCTGCTC
64 CGTGTCTGCTCCCTATTCCTGCAGAGAATATAAGACCCGACAATCTTCAACAATCGTGTCTGCTC
*
227032 CCCATTCCTTCAGAGAGTATAAGACTTGAACAATCTTCA-AATCGTGTCTGCTCCCTATTTCTGC
129 CCCATTCCTTCAGAGAG--TAAGACTCGAACAATCTTCACAATCGTGTCTGCTCCCTATTTCTGC
*
227096 AGAGAGTATAAGACTCCAAC-ATCTTCAACAGTCGTGTCTGCTCCCTATTTATGCAGAGAGTATA
192 AGAGAGTATAAGACTCCAACAATCTTCAACAATCGTGTCTGCTCCCTATTTATGCAGAGAGTATA
227160 AGACTCGAACAAT
257 AGACTCGAACAAT
* * *
227173 TTCATCAATCGTGTCTGC-CCC-TTCCTTCAGAGAGTATAAGACTCGAACAATCTTCATC-AAT-
1 TTCATCAATCGTGTCTGCTCCCTTTCC-TCAGAGAGTATAAGACCCAAACAATCTTCAACAAATC
* * *
227234 GTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTC
65 GTGTCTGCTCCCTATTCCTGCAGAGAATATAAGACCCG-ACAATCTTCAACAATCGTGTCTGCTC
*
227299 CCCATTCCTTCAGAGAGTAAGACTCGAACAATCTTCATCAATCGTGTCTGCTCCCTATTTCTTCA
129 CCCATTCCTTCAGAGAGTAAGACTCGAACAATCTTCA-CAATCGTGTCTGCTCCCTATTTCTGCA
* *
227364 GAGAGTATGAGACTCGAACAATCTTCAACAATCGT
193 GAGAGTATAAGACTCCAACAATCTTCAACAATCGT
227399 TTGGAAACCT
Statistics
Matches: 207, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
265 19 0.09
266 33 0.16
267 91 0.44
268 43 0.21
270 3 0.01
271 18 0.09
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (269 bp):
TTCATCAATCGTGTCTGCTCCCTTTCCTCAGAGAGTATAAGACCCAAACAATCTTCAACAAATCG
TGTCTGCTCCCTATTCCTGCAGAGAATATAAGACCCGACAATCTTCAACAATCGTGTCTGCTCCC
CATTCCTTCAGAGAGTAAGACTCGAACAATCTTCACAATCGTGTCTGCTCCCTATTTCTGCAGAG
AGTATAAGACTCCAACAATCTTCAACAATCGTGTCTGCTCCCTATTTATGCAGAGAGTATAAGAC
TCGAACAAT
Found at i:231844 original size:8 final size:8
Alignment explanation
Indices: 231831--231858 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
231821 AAAAGAAGAT
231831 ATATATAC
1 ATATATAC
231839 ATATATAC
1 ATATATAC
231847 ATATATAC
1 ATATATAC
231855 ATAT
1 ATAT
231859 GGGAGAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Done.