Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007116.1 Hibiscus syriacus cultivar Beakdansim tig00018601_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: 73145
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3448 original size:13 final size:13
Alignment explanation
Indices: 3430--3456 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3420 AGCAATTTAA
3430 AATGAATCTATTG
1 AATGAATCTATTG
3443 AATGAATCTATTG
1 AATGAATCTATTG
3456 A
1 A
3457 CTGTTATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
AATGAATCTATTG
Found at i:31729 original size:20 final size:21
Alignment explanation
Indices: 31704--31755 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
31694 ATTCAATCAA
31704 TATCGATACCAAT-G-AGGTAG
1 TATCGATACCAATGGTAGG-AG
*
31724 TATCGATACC-ATGGTAGGGG
1 TATCGATACCAATGGTAGGAG
31744 TATCGATACCAA
1 TATCGATACCAA
31756 GCATCATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 2 0.07
20 22 0.79
21 4 0.14
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (21 bp):
TATCGATACCAATGGTAGGAG
Found at i:31822 original size:75 final size:73
Alignment explanation
Indices: 31743--31902 Score: 178
Period size: 73 Copynumber: 2.2 Consensus size: 73
31733 CATGGTAGGG
* * * * *
31743 GTATCGATACCAAGCATCATCGAAGCTAAAAATTAG-TATCGATACCGAAGGGGGTATTAGTACC
1 GTATCGATACCAAGAAACATC-AAACT--AAATTAGATATCGATACCGAAAGGGGTATCAGTACC
* *
31807 ATAGTATGGTA
63 ATAGTATAGAA
* * * *
31818 GTATCGATACCAGGAAACATCAAACTAAATTTGATATCGATATCGAAAGGGGTATCGGTACCATA
1 GTATCGATACCAAGAAACATCAAACTAAATTAGATATCGATACCGAAAGGGGTATCAGTACCATA
31883 GTATAGAA
66 GTATAGAA
*
31891 GTATCGGTACCA
1 GTATCGATACCA
31903 GGATAGCAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
72 6 0.08
73 44 0.61
74 4 0.06
75 18 0.25
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (73 bp):
GTATCGATACCAAGAAACATCAAACTAAATTAGATATCGATACCGAAAGGGGTATCAGTACCATA
GTATAGAA
Found at i:31915 original size:20 final size:21
Alignment explanation
Indices: 31869--31908 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
31859 ATCGAAAGGG
*
31869 GTATCGGTACCATAGTATAGAA
1 GTATCGGTACCA-AGGATAGAA
31891 GTATCGGTACC-AGGATAG
1 GTATCGGTACCAAGGATAG
31909 CAATATCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (21 bp):
GTATCGGTACCAAGGATAGAA
Found at i:32240 original size:54 final size:54
Alignment explanation
Indices: 32180--33899 Score: 2034
Period size: 54 Copynumber: 31.9 Consensus size: 54
32170 TACCAAATAG
* * * *
32180 GCACTAATTGTGCATTTCATGGAATTCATCATATGTGGATGAATAATCGTTTCAA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC-A
* * * *
32235 G-ACTAAGTGTACATTTCACGGAATTCTTCTTATGTGGATGAATAACGGTTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * ** * *
32287 GACATTAAGTGTGCATTTCACGGAATTCATCATATGTGGATGAATAGTCATTTCG
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * * *
32342 GCACTAAGTGTGGATTTCATGGAATTTATCCCATGTGGATAAAAAACCGTTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * ** *
32395 GACACTAAGTGTGCTTTTCACGAAATTCATCCTATATGGATGAATATTCGTTTCG
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * ** *
32450 GCACTAACTGTGCATTTCACAGAATTCATCCTATGTGGATGAATGATTGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * **
32504 GCACTAAGTATGCATTCCACAGAATTCATATTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * *
32558 GCACTATGTGCGCATTTCACGAAATTCATCCTATGGGGATGAATAACCATTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
32612 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
32666 ACACTAAGTGTTCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
*
32720 GCAATAAGTGT-CATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
32773 ACACTAAGTGGGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGCTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * *
32827 GAACTAAATGCGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
*** * * **
32881 GCACTAAGTGTGCATTT-ATTAAAATTCATCCTATAT-GATGAATAACTGTTTTG
1 GCACTAAGTGTGCATTTCA-CGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
32934 GCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACAGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * *
32988 GCACTAAGTGTGCATTTCACGGAATTTATCCTATGTGGATGAATAGCTGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * *
33042 GCAAC-AAGTGTGCATTTCAAGAAATTCATCCTACGTGGATGAATAACCGTTTCG
1 GC-ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
33096 GCACTAAGTTTTCATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * *
33150 GCACTAAGTGTGCATTTAACGGAATTCATCCTATGTGGATGAGTAATCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
*
33204 GCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
33258 ACA-TAAGTGAGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * ** *
33311 GAACTTAA-TGCGCATTTCACAAAATTCATCCTATGTGGATGAATAACCATTTCA
1 GCAC-TAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * **
33365 GCACTAAGTGTGCATTT-ATCAGAATTCATCCTATGTGGATGAATAACTGTTTTG
1 GCACTAAGTGTGCATTTCA-CGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* *
33419 GCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTAA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * **
33473 GCACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAACTGTTTTG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * *
33527 GCAAC-AAGTGTACATTTCACGAAATTCATCCTACGTGGATGAATAACCGTTTCG
1 GC-ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* *
33581 GCACTAAGTTTGCATTTCAC-GAATTCATCATATGTGGATGAATAACCGTTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * *
33634 GCACTAAGTGTGCATTTCAC-AAATTCATCCTATGTGGATGAGA-AATCGCTTCA
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGA-ATAACCGTTTCA
* * * *
33687 GCACTAAGTGTGCATTTCGCCGAATTCATCCTATGTGGATGAATAATCGTTTCT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * **
33741 GCACCAAGTGTGTATTTCACAGAATTCATCGTATGTGGATGAATAACAATTTC-
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * * **
33794 GACACTAAGTGTGCAATCCACAGAATTCATCATGA-GTTGATGAATAACCGTACCA
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCT-ATGTGGATGAATAACCGTTTCA
* * * * * *
33849 GCACTATGTGTGCAAATCCACAGAATTCATCATGAT-TTGATGAATAACCGT
1 GCACTAAGTGTGC-ATTTCACGGAATTCATCCT-ATGTGGATGAATAACCGT
33900 ACATGCACTA
Statistics
Matches: 1442, Mismatches: 197, Indels: 52
0.85 0.12 0.03
Matches are distributed among these distances:
52 1 0.00
53 247 0.17
54 1145 0.79
55 49 0.03
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (54 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
Found at i:32885 original size:323 final size:324
Alignment explanation
Indices: 32180--33862 Score: 2066
Period size: 323 Copynumber: 5.2 Consensus size: 324
32170 TACCAAATAG
* * * *
32180 GCACTAATTGTGCATTTCATGGAATTCATCATATGTGGATGAATAATCGTTTCAAG-ACTAAGTG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC-AGCACTAAGTG
* * * * * *
32244 TACATTTCACGGAATTCTTCTTATGTGGATGAATAACGGTTTC-GACATTAAGTGTGCATTTCAC
65 TGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAG-CACTAAGTGTGCATTTCAC
* ** * * * * *
32308 GGAATTCATCATATGTGGATGAATAGTCATTTCGGCACTAAGTGTGGATTTCATGGAATTTATCC
129 GGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACGGAATTCATCC
* * * * * * *
32373 CATGTGGATAAAAAACCGTTTCGACACTAAGTGTGCTTTTCACGAAATTCATCCTATATGGATGA
194 TATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGA
** * * * **
32438 ATATTCGTTTCGGCACTAACTGTGCATTTCACAGAATTCATCCTATGTGGATGAATGATTGTTTC
259 ATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
*
32503 G
324 A
* * * ** * *
32504 GCACTAAGTATGCATTCCACAGAATTCATATTATGTGGATGAATAACCGTTTCAGCACTATGTGC
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGT
* *
32569 GCATTTCACGAAATTCATCCTATGGGGATGAATAACCATTTCAGCACTAAGTGTGCATTTCACGG
66 GCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACGG
* *
32634 AATTCATCCTATGTGGATGAATAACCGTTTCAACACTAAGTGTTCATTTCACGGAATTCATCCTA
131 AATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCTA
*
32699 TGTGGATGAATAACCGTTTCGGCAATAAGTGT-CATTTCACGGAATTCATCCTATGTGGATGAAT
196 TGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAAT
** * *
32763 AACCGTTTCAACACTAAGTGGGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGCTTCA
261 AACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
* * * * *
32827 GAACTAAATGCGCATTTCACGAAATTCATCCTATGTGGATGAATAACCATTTCAGCACTAAGTGT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGT
** * * ** *
32892 GCATTT-ATTAAAATTCATCCTATAT-GATGAATAACTGTTTTGGCACTAAGTGTGCATTTCACA
66 GCATTTCA-CGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACG
* * *
32955 GAATTCATCCTATGTGGATGAATAACAGTTTCGGCACTAAGTGTGCATTTCACGGAATTTATCCT
130 GAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCT
* * * * *
33020 ATGTGGATGAATAGCTGTTTCGGCAAC-AAGTGTGCATTTCAAGAAATTCATCCTACGTGGATGA
195 ATGTGGATGAATAACCGTTTCGGC-ACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGA
* * *
33084 ATAACCGTTTCGGCACTAAGTTTTCATTTTACGGAATTCATCCTATGTGGATGAATAACCGTTTC
259 ATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
33149 A
324 A
* * * *
33150 GCACTAAGTGTGCATTTAACGGAATTCATCCTATGTGGATGAGTAATCGTTTCGGCACTAAGTGT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGT
* *
33215 GCATTTCAC-AGAATTCATCCTATGTGGATGAATAACCGTTTCAACA-TAAGTGAGCATTTCACG
66 GCATTTCACGA-AATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACG
* * * **
33278 GAATTCATCCTATGTGGATGAATAACCGTTTCGGAACTTAA-TGCGCATTTCACAAAATTCATCC
130 GAATTCATCCTATGTGGATGAATAACCGTTTCAGCAC-TAAGTGTGCATTTCACGGAATTCATCC
* * *
33342 TATGTGGATGAATAACCATTTCAGCACTAAGTGTGCATTT-ATCAGAATTCATCCTATGTGGATG
194 TATGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCA-CGGAATTCATCCTATGTGGATG
* * *
33406 AATAACTGTTTTGGCACTAAGTGTGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTT
258 AATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTT
*
33471 AA
323 CA
* * **
33473 GCACTAAGTGTGCATTTCACGGAATTCATCCTATATGGATGAATAACTGTTTTGGCAAC-AAGTG
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGC-ACTAAGTG
* * * *
33537 TACATTTCACGAAATTCATCCTACGTGGATGAATAACCGTTTCGGCACTAAGTTTGCATTTCAC-
65 TGCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACG
* *
33601 GAATTCATCATATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCAC-AAATTCATCCT
130 GAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCT
* * * * *
33665 ATGTGGATGAGA-AATCGCTTCAGCACTAAGTGTGCATTTCGCCGAATTCATCCTATGTGGATGA
195 ATGTGGATGA-ATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGA
* * * * * * **
33729 ATAATCGTTTCTGCACCAAGTGTGTATTTCACAGAATTCATCGTATGTGGATGAATAACAATTTC
259 ATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTC
33794 -
324 A
* * * * * ** *
33794 GACACTAAGTGTGCAATCCACAGAATTCATCATGA-GTTGATGAATAACCGTACCAGCACTATGT
1 G-CACTAAGTGTGCATTTCACGGAATTCATCCT-ATGTGGATGAATAACCGTTTCAGCACTAAGT
33858 GTGCA
64 GTGCA
33863 AATCCACAGA
Statistics
Matches: 1168, Mismatches: 171, Indels: 42
0.85 0.12 0.03
Matches are distributed among these distances:
321 3 0.00
322 298 0.26
323 640 0.55
324 226 0.19
325 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.33
Consensus pattern (324 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGT
GCATTTCACGAAATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACGG
AATTCATCCTATGTGGATGAATAACCGTTTCAGCACTAAGTGTGCATTTCACGGAATTCATCCTA
TGTGGATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAAT
AACCGTTTCGGCACTAAGTGTGCATTTCACGGAATTCATCCTATGTGGATGAATAACCGTTTCA
Found at i:33257 original size:26 final size:26
Alignment explanation
Indices: 33228--33309 Score: 60
Period size: 26 Copynumber: 3.1 Consensus size: 26
33218 TTTCACAGAA
33228 TTCATCCTATGTGGATGAATAACCGT
1 TTCATCCTATGTGGATGAATAACCGT
* * * * * * *
33254 TTCAACATAAGT-GA-GCATTTCACGGAA
1 TTCATCCTATGTGGATG-A-ATAACCG-T
33281 TTCATCCTATGTGGATGAATAACCGT
1 TTCATCCTATGTGGATGAATAACCGT
33307 TTC
1 TTC
33310 GGAACTTAAT
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
24 1 0.03
25 3 0.08
26 16 0.43
27 13 0.35
28 3 0.08
29 1 0.03
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (26 bp):
TTCATCCTATGTGGATGAATAACCGT
Found at i:33889 original size:55 final size:55
Alignment explanation
Indices: 33796--34110 Score: 379
Period size: 55 Copynumber: 5.8 Consensus size: 55
33786 ACAATTTCGA
*
33796 CACTAAGTGTGC-AATCCACAGAATTCATCATGAGTTGATGAATAACCGTACCA-G
1 CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA-CATG
*
33850 CACTATGTGTGCAAATCCACAGAATTCATCATGATTTGATGAATAACCGTACATG
1 CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATG
* * * * *
33905 CACTATGTTTGCAAATCAACAAAATTTATCATGAGTTGATGAATAACCGTACCA-A
1 CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTA-CATG
* * * * *
33960 CATTATGTGTGCAAATCAAC-GAATTCGTCATGATTTGATGAATAACCATACATG
1 CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATG
* * * * *
34014 CACTATGTGTGAAAATCCACAGAATTCATCTTGAGTTGATAAATAATCGTACAGG
1 CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATG
* * * **
34069 CACGATGTTTGC-AACCCATGGAATTCATCATGAGTTGATGAA
1 CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAA
34111 CTACCATATA
Statistics
Matches: 222, Mismatches: 34, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
53 2 0.01
54 80 0.36
55 138 0.62
56 2 0.01
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.29
Consensus pattern (55 bp):
CACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACATG
Found at i:33918 original size:109 final size:108
Alignment explanation
Indices: 33796--34135 Score: 407
Period size: 109 Copynumber: 3.1 Consensus size: 108
33786 ACAATTTCGA
*
33796 CACTAAGTGTGCAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACCAGCACTATGTGTG
1 CACTATGTGTGCAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACCAGCACTATGTGTG
*
33861 CAAATCCACAGAATTCATCATGATTTGATGAATAACCGTACATG
66 CAAATCCAC-GAATTCATCATGATTTGATGAATAACCATACATG
* * * * * *
33905 CACTATGTTTGCAAATCAACAAAATTTATCATGAGTTGATGAATAACCGTACCAACATTATGTGT
1 CACTATGTGTGC-AATCCACAGAATTCATCATGAGTTGATGAATAACCGTACCAGCACTATGTGT
* *
33970 GCAAATCAACGAATTCGTCATGATTTGATGAATAACCATACATG
65 GCAAATCCACGAATTCATCATGATTTGATGAATAACCATACATG
* * * * * *
34014 CACTATGTGTGAAAATCCACAGAATTCATCTTGAGTTGATAAATAATCGTA-CAGGCACGATGTT
1 CACTATGTGTG-CAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACCA-GCACTATGTG
* * * * *
34078 TGC-AACCCATGGAATTCATCATGAGTTGATGAACT-ACCATATAGG
64 TGCAAATCCA-CGAATTCATCATGATTTGATGAA-TAACCATACATG
*
34123 CACTAAGTGTGCA
1 CACTATGTGTGCA
34136 TCTAAATAAA
Statistics
Matches: 195, Mismatches: 31, Indels: 11
0.82 0.13 0.05
Matches are distributed among these distances:
108 7 0.04
109 131 0.67
110 57 0.29
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (108 bp):
CACTATGTGTGCAATCCACAGAATTCATCATGAGTTGATGAATAACCGTACCAGCACTATGTGTG
CAAATCCACGAATTCATCATGATTTGATGAATAACCATACATG
Found at i:34411 original size:81 final size:80
Alignment explanation
Indices: 34275--34434 Score: 180
Period size: 81 Copynumber: 2.0 Consensus size: 80
34265 GGTCCAAAAT
* ** * * * * *
34275 AAAAGAATAATGGTCTAACTATGCAATTGGTAGAAAGGTTCCAATTATGCCAGTTAGATGAACGG
1 AAAAGAATAAGGGTCTAACTATGCAATTGACAGAAAAGTTCCAAATATGCAAGTTAAATGAAAGG
*
34340 TTAAACACCGTTGAGC
66 CTAAACACC-TTGAGC
*
34356 AAAAGAATAAGGGAT-TAACTATGCATTTGACAGAAAAGTGT-CAAATATGCAAGTTAAATGAAA
1 AAAAGAATAAGGG-TCTAACTATGCAATTGACAGAAAAGT-TCCAAATATGCAAGTTAAATGAAA
*
34419 GGCTAAATACCTTGAG
64 GGCTAAACACCTTGAG
34435 GTAGAAGAAT
Statistics
Matches: 66, Mismatches: 11, Indels: 5
0.80 0.13 0.06
Matches are distributed among these distances:
80 5 0.08
81 59 0.89
82 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.25
Consensus pattern (80 bp):
AAAAGAATAAGGGTCTAACTATGCAATTGACAGAAAAGTTCCAAATATGCAAGTTAAATGAAAGG
CTAAACACCTTGAGC
Found at i:35682 original size:45 final size:45
Alignment explanation
Indices: 35631--35904 Score: 433
Period size: 45 Copynumber: 6.1 Consensus size: 45
35621 GGAAGGAATT
* *
35631 CATATGGGTGCATTACCAACAGAAAAGTATTCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATG
* *
35676 CATATGGGTGCATTATCAACAGAAAAATATGATATAGTTGAAATG
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATG
* *
35721 CATATGGGTGCA-TATCAACAGAAAAGTATGCTATAATTGAAATA
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATG
* * *
35765 CATATGGGTGCATCATCAACAGAAAAGTATGCTATTGTTAAAATG
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATG
*
35810 TATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATG
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATG
*
35855 CATATGGGTGCATTATCAACATAAAAGTATGCTATAGTTGAAAATG
1 CATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTG-AAATG
35901 CATA
1 CATA
35905 ATGGTTCATT
Statistics
Matches: 208, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
44 40 0.19
45 159 0.76
46 9 0.04
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (45 bp):
CATATGGGTGCATTATCAACAGAAAAGTATGCTATAGTTGAAATG
Found at i:46831 original size:13 final size:14
Alignment explanation
Indices: 46800--46831 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
46790 TATACTTCGG
46800 TGGAAGCGGTCGTT
1 TGGAAGCGGTCGTT
46814 TGGAAGCGGTCG-T
1 TGGAAGCGGTCGTT
46827 TGGAA
1 TGGAA
46832 AACTGCTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.19, C:0.12, G:0.44, T:0.25
Consensus pattern (14 bp):
TGGAAGCGGTCGTT
Found at i:49985 original size:54 final size:54
Alignment explanation
Indices: 49901--50098 Score: 200
Period size: 54 Copynumber: 3.7 Consensus size: 54
49891 CATCACACAT
* * ** * *
49901 AATTCATAATGAGTTTATGAATGACTGTATCGGTACTATATGTGCAACCAACAG
1 AATTCATAATAAGTTTATGAATTACCATATCGGCACTATGTGTGCAACCAACAG
* * * * * * *
49955 AATTCATAATGAGTTTGTGAATTACCGTATCGACACTATGTGTTCAACCCACAT
1 AATTCATAATAAGTTTATGAATTACCATATCGGCACTATGTGTGCAACCAACAG
* * * * * **
50009 AATTCATAACAAGTTTGTGAATTACCATATCTGCAC-ATGTGTGCAATCTATGG
1 AATTCATAATAAGTTTATGAATTACCATATCGGCACTATGTGTGCAACCAACAG
*
50062 AATTCATAATAAGTTTATGAATTTCCATATCGGCACT
1 AATTCATAATAAGTTTATGAATTACCATATCGGCACT
50099 TAGGCACAAC
Statistics
Matches: 119, Mismatches: 24, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
53 43 0.36
54 76 0.64
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (54 bp):
AATTCATAATAAGTTTATGAATTACCATATCGGCACTATGTGTGCAACCAACAG
Found at i:56401 original size:108 final size:108
Alignment explanation
Indices: 56209--56412 Score: 275
Period size: 108 Copynumber: 1.9 Consensus size: 108
56199 TACTATTGAA
* * * *
56209 ACTATGTGTGTAACCCAAGGAGTTCATAATGAATTTATGCATGACCGTATCGGCACTATGTGTGC
1 ACTATGTGTGCAACCCAAGGAATTCATAATGAATTTATGCATGACCGTATCAGCACTATGTGTCC
* *
56274 AACCCATATAATTCATAATGAGTTTATGAATGACCGTATCGAC
66 AACCCACAGAATTCATAATGAGTTTATGAATGACCGTATCGAC
** * *
56317 ACTATGTGTGCAACCCACTGAATTCATAAT-AAGTTTGTGCATTACCGTATCAGCACTATGTGTC
1 ACTATGTGTGCAACCCAAGGAATTCATAATGAA-TTTATGCATGACCGTATCAGCACTATGTGTC
* * *
56381 CAACTCACAGAATTCGTAATGAGTTTGTGAAT
65 CAACCCACAGAATTCATAATGAGTTTATGAAT
56413 TACCTTATGT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
107 2 0.02
108 80 0.98
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (108 bp):
ACTATGTGTGCAACCCAAGGAATTCATAATGAATTTATGCATGACCGTATCAGCACTATGTGTCC
AACCCACAGAATTCATAATGAGTTTATGAATGACCGTATCGAC
Found at i:56406 original size:54 final size:53
Alignment explanation
Indices: 56209--56412 Score: 230
Period size: 54 Copynumber: 3.8 Consensus size: 53
56199 TACTATTGAA
* * * *
56209 ACTATGTGTGTAACCCA-AGGAGTTCATAATGAATTTATGCATGACCGTATCGGC
1 ACTATGTGTGCAACCCACA-GAATTCATAATGAGTTTATGAATGACCGTATC-GC
* *
56263 ACTATGTGTGCAACCCATATAATTCATAATGAGTTTATGAATGACCGTATCGAC
1 ACTATGTGTGCAACCCACAGAATTCATAATGAGTTTATGAATGACCGTATCG-C
* * * * *
56317 ACTATGTGTGCAACCCACTGAATTCATAATAAGTTTGTGCATTACCGTATCAGC
1 ACTATGTGTGCAACCCACAGAATTCATAATGAGTTTATGAATGACCGTATC-GC
* * * *
56371 ACTATGTGTCCAACTCACAGAATTCGTAATGAGTTTGTGAAT
1 ACTATGTGTGCAACCCACAGAATTCATAATGAGTTTATGAAT
56413 TACCTTATGT
Statistics
Matches: 129, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
53 1 0.01
54 126 0.98
55 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (53 bp):
ACTATGTGTGCAACCCACAGAATTCATAATGAGTTTATGAATGACCGTATCGC
Found at i:64866 original size:14 final size:13
Alignment explanation
Indices: 64830--64858 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
64820 TCGATTGTGC
64830 CTATGT-AATGGA
1 CTATGTAAATGGA
64842 CTATGTAAATGGA
1 CTATGTAAATGGA
64855 CTAT
1 CTAT
64859 TTTAAATGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (13 bp):
CTATGTAAATGGA
Found at i:64872 original size:32 final size:32
Alignment explanation
Indices: 64836--64906 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
64826 GTGCCTATGT
64836 AATGGACTATGTAAATGGACTATTTTAAATGC
1 AATGGACTATGTAAATGGACTATTTTAAATGC
* *
64868 AATGGACTATGTAAATTGACTCTTTTAAATGC
1 AATGGACTATGTAAATGGACTATTTTAAATGC
64900 AATGGAC
1 AATGGAC
64907 CTTTATTTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (32 bp):
AATGGACTATGTAAATGGACTATTTTAAATGC
Found at i:65006 original size:15 final size:15
Alignment explanation
Indices: 64986--65033 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
64976 GACTACTATT
64986 TATAATATGCAACTA
1 TATAATATGCAACTA
*
65001 TATAATATGCTACTA
1 TATAATATGCAACTA
* *
65016 TATAACAT-AAACTA
1 TATAATATGCAACTA
65030 TATA
1 TATA
65034 GTATACTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 8 0.28
15 21 0.72
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (15 bp):
TATAATATGCAACTA
Found at i:65019 original size:17 final size:17
Alignment explanation
Indices: 64978--65019 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
64968 TTTAACATGA
*
64978 CTACTATTTATAATATG
1 CTACTATATATAATATG
*
64995 CAAC--TATATAATATG
1 CTACTATATATAATATG
65010 CTACTATATA
1 CTACTATATA
65020 ACATAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 4
0.74 0.11 0.15
Matches are distributed among these distances:
15 13 0.65
17 7 0.35
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.40
Consensus pattern (17 bp):
CTACTATATATAATATG
Found at i:65113 original size:28 final size:30
Alignment explanation
Indices: 65081--65166 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 30
65071 ACTATTTAAA
*
65081 ACATGCAACTATTATTTAATAT-TA-TATG
1 ACATGCAACTATTATTTAATATGTACTATC
*
65109 ACATGCAAATGCAATTATATTTAATATGTACTATC
1 ACATGC-AA--CTA-T-TATTTAATATGTACTATC
*
65144 ACATGCAATTATTATTTAATATG
1 ACATGCAACTATTATTTAATATG
65167 CAACCACCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
28 6 0.13
29 2 0.04
30 11 0.23
31 3 0.06
32 2 0.04
33 10 0.21
34 4 0.09
35 9 0.19
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.41
Consensus pattern (30 bp):
ACATGCAACTATTATTTAATATGTACTATC
Done.