Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009336.1 Hibiscus syriacus cultivar Beakdansim tig00113104_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: 78682
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:4816 original size:23 final size:23
Alignment explanation
Indices: 4785--4829 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4775 TACCACAGTT
*
4785 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
*
4808 CGTAGAAATGCACCTAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
4830 ATATAAGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:16948 original size:20 final size:20
Alignment explanation
Indices: 16925--16974 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
16915 GATGCTACTG
16925 ATTTGGTGTTGATATTGCTA
1 ATTTGGTGTTGATATTGCTA
* *
16945 ATTTAGTGCTGATATTGCTA
1 ATTTGGTGTTGATATTGCTA
*
16965 ATTTGTTGTT
1 ATTTGGTGTT
16975 ATTAATGTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (20 bp):
ATTTGGTGTTGATATTGCTA
Found at i:20402 original size:54 final size:54
Alignment explanation
Indices: 20344--20730 Score: 544
Period size: 54 Copynumber: 7.2 Consensus size: 54
20334 CTATAGTTTT
* * * * *
20344 CACACATAGTGCCAAAATGGTGATTCATCAATATATGATGAATTTCGTGGCTTG
1 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTCGTGGGTTG
* *
20398 CACACTTAGTGCCAAAACGGTGATTCATCAATATATGATGAATTTCGTGGGTTG
1 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTCGTGGGTTG
* * *
20452 CACACTTAGTGCCGAAACGGTAATTCATCAACATATGATGAATTCCATGGGTTG
1 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTCGTGGGTTG
* * ** * ** *
20506 CACACTTAGTACTGAAATAGTGATTCATCAATATATGATGAA-TTCTGTGGACTA
1 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTC-GTGGGTTG
*
20560 CACACTTAGTGCCGAAATGGTGATTCATCAACATATGATGAA-TTCTGTGGGTTG
1 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTC-GTGGGTTG
* *
20614 CACACTTAGTGTCGAAACGGTGATTCATCAACATATGATGAATTTCATGGGTTG
1 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTCGTGGGTTG
*
20668 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTCCGTGGGTTG
1 CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTCGTGGGTTG
20722 CACACTTAG
1 CACACTTAG
20731 ATCCTATTTG
Statistics
Matches: 299, Mismatches: 32, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
53 2 0.01
54 294 0.98
55 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.30
Consensus pattern (54 bp):
CACACTTAGTGCCGAAACGGTGATTCATCAACATATGATGAATTTCGTGGGTTG
Found at i:27371 original size:54 final size:54
Alignment explanation
Indices: 27311--27882 Score: 810
Period size: 54 Copynumber: 10.6 Consensus size: 54
27301 ACTCATAAAA
* * * *
27311 ATATTATGAATTATGT-GGTTAGCACACATAGTGCCAAAACGGTGATTCATTAAC
1 ATATGATGAATTCTGTGGGTT-GCACACTTAGTGCCAAAACGGTGATTCATCAAC
* *
27365 ATATTATGAATTCTGTGGGTTGCACACTTAGTACCAAAACGGTGATTCATCAAC
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
* * * *
27419 ATATGATGAATTCTATGGGTTGCACACTTAGTGCCGAAAGGGTGATTCATCAAT
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
*
27473 ATATGATGAATT-TCGTGGGTTGCACACTTAGTGCCAAAACCGTGATTCATCAAC
1 ATATGATGAATTCT-GTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
* * * *
27527 ATATGATGAATTTTGTGGGTTGCCCACTTAGTGTCGAAACGGTGATTCATCAAC
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
* * * *
27581 ATATGATGAATTCTGTGGGTTGCACAGTTAGTGCCGAAATGGTGATTTATCAAC
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
* * *
27635 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCGAAATGGTGATTCATCAAT
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
* * *
27689 ATTTGATGAATTTTGTGGGTTGCACACTTAGTGCCAAAATGGTGATTCATCAAC
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
* * *
27743 ATATGATGAATTCCGTGGGTTGTACACTTAGTGCCGAAAA-GGTGATTCATAAAC
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCC-AAAACGGTGATTCATCAAC
*
27797 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCGAAACGGTGATTCATCAAC
1 ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
*
27851 ATATAATGAATT-TCGTGGGTTGCACACTTAGT
1 ATATGATGAATTCT-GTGGGTTGCACACTTAGT
27883 TCCTATTTGG
Statistics
Matches: 470, Mismatches: 42, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
53 5 0.01
54 456 0.97
55 9 0.02
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (54 bp):
ATATGATGAATTCTGTGGGTTGCACACTTAGTGCCAAAACGGTGATTCATCAAC
Found at i:28254 original size:22 final size:23
Alignment explanation
Indices: 28216--28260 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
28206 ATTAGTATCG
* *
28216 ATACTCATACTATGGTATCGATA
1 ATACTCATACTAGGGTACCGATA
28239 ATACT-ATACTAGGGTACCGATA
1 ATACTCATACTAGGGTACCGATA
28261 CTCTATCACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (23 bp):
ATACTCATACTAGGGTACCGATA
Found at i:35161 original size:5 final size:5
Alignment explanation
Indices: 35148--35216 Score: 57
Period size: 5 Copynumber: 13.0 Consensus size: 5
35138 GAGGCAACCC
* * ***
35148 ATTTC ATTTT ATTTT CATTTT TTTTAT ATTTT ATTTT ATTTT ATCAG ATGCTTT
1 ATTTT ATTTT ATTTT -ATTTT ATTT-T ATTTT ATTTT ATTTT ATTTT AT--TTT
35202 ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT
35217 TCTCTAAACA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
5 40 0.78
6 9 0.18
7 2 0.04
ACGTcount: A:0.20, C:0.06, G:0.03, T:0.71
Consensus pattern (5 bp):
ATTTT
Found at i:35165 original size:11 final size:11
Alignment explanation
Indices: 35149--35191 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
35139 AGGCAACCCA
35149 TTTCATTTTAT
1 TTTCATTTTAT
35160 TTTCATTTT-T
1 TTTCATTTTAT
*
35170 TTTATATTTTAT
1 TTT-CATTTTAT
35182 TTT-ATTTTAT
1 TTTCATTTTAT
35192 CAGATGCTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 11 0.38
11 14 0.48
12 4 0.14
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTCATTTTAT
Found at i:35179 original size:17 final size:17
Alignment explanation
Indices: 35148--35191 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
35138 GAGGCAACCC
* *
35148 ATTTCATTTTAT-TTTC
1 ATTTTATTTTATATTTT
35164 ATTTT-TTTTATATTTT
1 ATTTTATTTTATATTTT
35180 ATTTTATTTTAT
1 ATTTTATTTTAT
35192 CAGATGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 6 0.25
16 12 0.50
17 6 0.25
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTATTTTATATTTT
Found at i:37446 original size:19 final size:19
Alignment explanation
Indices: 37400--37443 Score: 72
Period size: 18 Copynumber: 2.4 Consensus size: 19
37390 CTTTAATTTG
*
37400 TTTATTTAATTATTTTTCT
1 TTTATTTAATTATTTATCT
37419 TTTATTTAATTA-TTATCT
1 TTTATTTAATTATTTATCT
37437 TTTATTT
1 TTTATTT
37444 TAAAACAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTATTTATCT
Found at i:37546 original size:35 final size:36
Alignment explanation
Indices: 37479--37546 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 36
37469 TTTAAATTTA
* *
37479 TTACTATTAATATTTATTATTATATTTTTTTTCTTT
1 TTACTATTAATATTTATTATTATATATCTTTTCTTT
*
37515 TTACTATTTAT-TTTATT-TTAATATATCTTTTC
1 TTACTATTAATATTTATTATT-ATATATCTTTTC
37547 AACTTCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 2 0.07
35 16 0.57
36 10 0.36
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (36 bp):
TTACTATTAATATTTATTATTATATATCTTTTCTTT
Found at i:49358 original size:45 final size:45
Alignment explanation
Indices: 49285--49547 Score: 214
Period size: 45 Copynumber: 5.9 Consensus size: 45
49275 TTGAAGGAAT
* *
49285 AGTCAATC-TTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGA
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
* * * * *
49329 AGTCAACCTTTTAGTGGTGTTGTTCTTGACTTTCTCGTGGAGAGA
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
* * ** * * *
49374 AGTAAATCTTTCAGTTTTG-TCTTCATTGACTTTCTCGAGAAGATG-
1 AGTCAATCTTTTAGTGATGTTATTC-TTGACTTTCTCGTGAA-AAGA
* * * *
49419 AGTCAATCTTTTAGTGATGTCATTTTTGACTTTCTCGTGAAGAGG
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
* * * * *
49464 AGTCAATCTTTTAGTGCTATCATTCTTTACTTTCTGGT-AAAGAGA
1 AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAA-AGA
* *
49509 AATCAATCTTTCT-GT-ATTGTGATTCTTGACTTTCTCGTG
1 AGTCAATCTTT-TAGTGA-TGTTATTCTTGACTTTCTCGTG
49548 TAGATGAGTT
Statistics
Matches: 170, Mismatches: 40, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
44 14 0.08
45 152 0.89
46 4 0.02
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (45 bp):
AGTCAATCTTTTAGTGATGTTATTCTTGACTTTCTCGTGAAAAGA
Found at i:49472 original size:90 final size:89
Alignment explanation
Indices: 49285--49547 Score: 241
Period size: 90 Copynumber: 2.9 Consensus size: 89
49275 TTGAAGGAAT
* * *
49285 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGGTGTT
1 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGAGAAAAGAAGTCAACCTTTTAGTGATGTC
* *
49350 GTTCTTGACTTTCTCGTGGAGAGA
66 ATTCTTGACTTTCTCGTGAAGAGA
* ** * *
49374 AGTAAATCTTTCAGTTTTGTC-TTCATTGACTTTCTCGAGAAGATG-AGTCAATCTTTTAGTGAT
1 AGTCAATCTTT-AGTGATGTCATT-ATTGACTTTCTCGAGAA-AAGAAGTCAACCTTTTAGTGAT
* *
49437 GTCATTTTTGACTTTCTCGTGAAGAGG
63 GTCATTCTTGACTTTCTCGTGAAGAGA
* * * * * *
49464 AGTCAATCTTTTAGTGCTATCATTCTTTACTTTCT-G-GTAAAGAGAAATCAATCTTTCT-GT-A
1 AGTCAATC-TTTAGTGATGTCATTATTGACTTTCTCGAG-AAA-AGAAGTCAACCTTT-TAGTGA
*
49525 TTGTGATTCTTGACTTTCTCGTG
62 -TGTCATTCTTGACTTTCTCGTG
49548 TAGATGAGTT
Statistics
Matches: 142, Mismatches: 22, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
88 2 0.01
89 17 0.12
90 115 0.81
91 8 0.06
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.42
Consensus pattern (89 bp):
AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGAGAAAAGAAGTCAACCTTTTAGTGATGTC
ATTCTTGACTTTCTCGTGAAGAGA
Found at i:49538 original size:135 final size:134
Alignment explanation
Indices: 49285--49556 Score: 348
Period size: 135 Copynumber: 2.0 Consensus size: 134
49275 TTGAAGGAAT
* * *
49285 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGGTGTT
1 AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGCTATC
* ** * * *
49350 GTTCTTGACTTTCTCGTGGAGAGAAGTAAATCTTTCAGTTTTGTCTTCATTGACTTTCTCGAGAA
66 ATTCTTGACTTTCTCGTAAAGAGAAATAAATCTTTCAGTATTGTATTCATTGACTTTCTCGAGAA
49415 GATG
131 GATG
* * * *
49419 AGTCAATCTTTTAGTGATGTCATTTTTGACTTTCTCGTGAAGAGGAGTCAATCTTTTAGTGCTAT
1 AGTCAATC-TTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGCTAT
* * * * *
49484 CATTCTTTACTTTCTGGTAAAGAGAAATCAATCTTTCTGTATTGTGATTC-TTGACTTTCTCGTG
65 CATTCTTGACTTTCTCGTAAAGAGAAATAAATCTTTCAGTATTGT-ATTCATTGACTTTCTCGAG
*
49548 TAGATG
129 AAGATG
49554 AGT
1 AGT
49557 TAACCTGTCT
Statistics
Matches: 117, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
134 8 0.07
135 106 0.91
136 3 0.03
ACGTcount: A:0.24, C:0.15, G:0.20, T:0.42
Consensus pattern (134 bp):
AGTCAATCTTTAGTGATGTCATTATTGACTTTCTCGTGAAAAGAAGTCAACCTTTTAGTGCTATC
ATTCTTGACTTTCTCGTAAAGAGAAATAAATCTTTCAGTATTGTATTCATTGACTTTCTCGAGAA
GATG
Found at i:50362 original size:55 final size:54
Alignment explanation
Indices: 50277--50930 Score: 686
Period size: 55 Copynumber: 12.0 Consensus size: 54
50267 AATCACATTC
* *
50277 GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCACCTTCTAAAGATTTTT
1 GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
* * * * *
50331 GTAGTCTTATCTCCCTAAAAGAAAAGTGGAGCACACCTATCTTCCAAATATTTTT
1 G-AGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
* **** *
50386 CGAGTCTTATCTCCCTGAAAGAAGAGTGGAGAAGATTTGTCTACCAAAGATTTTT
1 -GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
* * * * *
50441 -TGTCTTATCTCCCTAAAAGAAAAGTGGAGCAGACCTATCTTCCAAAGATTTATC
1 GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT-TT
** * *
50495 GAGTCTTATCTCATTGAAAGAAGAGTGGAGCAGACCCGTCTTACAAAGATTTTT
1 GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
* ** * * *
50549 CGAGTCTTATATCTTTCAAAGAAGAGTGGAGCAGACCCTTCTTACAAAGATTTTTT
1 -GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGA-TTTTT
* * * * * * * *
50605 GAGTCTTATCTCCCGGAGAGAATAGTGGAGTAGGCTCGTCTTCCAAATATTTTT
1 GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
* * *
50659 CGAGGCTTATCTCCCTGAAAGAAGAGTGGAGCATG-CCCACCTTTCAAAGAATTTTT
1 -GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCA-GACCCATCTTCCAAAG-ATTTTT
* * * **
50715 GAGTCTTATCTCCCTGAAAGAAGAGTGGATCATAGCTTTCTTCCAAAGATTTTTT
1 GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGA-TTTTT
* * *
50770 GAGTCTTATATCCCTGAAAGAAGAGTCGAGCAGACCCATCTTCCAAATATTTTT
1 GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
* * * ** *
50824 CAAGTCTTATCTCCCTGAAAGTAGAGTGGAGCATACTTATCTTCCATAGATTTTT
1 -GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
*
50879 CTAGT-TTCATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAA-ATTT
1 -GAGTCTT-ATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTT
50931 ATCTGACTAC
Statistics
Matches: 495, Mismatches: 92, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
53 43 0.09
54 20 0.04
55 419 0.85
56 13 0.03
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (54 bp):
GAGTCTTATCTCCCTGAAAGAAGAGTGGAGCAGACCCATCTTCCAAAGATTTTT
Found at i:63695 original size:21 final size:20
Alignment explanation
Indices: 63655--63697 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
63645 TAATTCCTTA
*
63655 TTTTTCATTATTTTTGTTAT
1 TTTTTCATTATGTTTGTTAT
63675 TTTTTACATGTATGTTT-TTAT
1 TTTTT-CAT-TATGTTTGTTAT
63696 TT
1 TT
63698 CGATCATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.16, C:0.05, G:0.07, T:0.72
Consensus pattern (20 bp):
TTTTTCATTATGTTTGTTAT
Found at i:64582 original size:19 final size:19
Alignment explanation
Indices: 64558--64603 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
64548 TATTGGATGA
64558 CTTGATGCAGCTAGCCATG
1 CTTGATGCAGCTAGCCATG
64577 CTTGATGCAGCTAGCCATG
1 CTTGATGCAGCTAGCCATG
64596 CTTGATGC
1 CTTGATGC
64604 TGGTTATAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (19 bp):
CTTGATGCAGCTAGCCATG
Found at i:65687 original size:45 final size:45
Alignment explanation
Indices: 65638--65772 Score: 171
Period size: 45 Copynumber: 3.0 Consensus size: 45
65628 TTAAAAAAAG
*
65638 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAACTCCAACATA
1 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
* ** ** * * *
65683 GTCTTAAGTTATAAGTTGGGTAATGCTAATAAGAGTTCCAATATA
1 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
* *
65728 CTCTTAGGGAATAAGATGGGTAATGCTGGTAATAGCTCCAACATA
1 GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
65773 ATGAGAGAAA
Statistics
Matches: 71, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 71 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (45 bp):
GTCTTAGGGAATAAGTTGGGTAATGCTGGTAATAGCTCCAACATA
Found at i:76419 original size:41 final size:41
Alignment explanation
Indices: 76374--76541 Score: 178
Period size: 41 Copynumber: 4.1 Consensus size: 41
76364 TTATATCTTT
*
76374 ACAATTCTATTCAATTCAATCATAGCAGCATGCAATAATTC
1 ACAATTCTATTCAATTCAATCATGGCAGCATGCAATAATTC
* *
76415 ACAATTCGATTCAATTCAATCATGGCAGCATACAATAATTC
1 ACAATTCTATTCAATTCAATCATGGCAGCATGCAATAATTC
* * * *
76456 ACAATTCAACTT-AATTCGATCATGGTAGCATGCAATAATCC
1 ACAATTCTA-TTCAATTCAATCATGGCAGCATGCAATAATTC
* ** * * * *
76497 ATAATT-TAATTCAATTCGGTCATGGAAACATGCATTTATTC
1 ACAATTCT-ATTCAATTCAATCATGGCAGCATGCAATAATTC
76538 ACAA
1 ACAA
76542 ACCAATTCAA
Statistics
Matches: 107, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.02
41 103 0.96
42 2 0.02
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (41 bp):
ACAATTCTATTCAATTCAATCATGGCAGCATGCAATAATTC
Found at i:76568 original size:41 final size:41
Alignment explanation
Indices: 76518--76595 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
76508 CAATTCGGTC
*
76518 ATGGAAACATGCATTTATTCACAAACCAATTCAATTATACT
1 ATGGAAACATGCATTAATTCACAAACCAATTCAATTATACT
* * * *
76559 ATGGTAACATGTATTAATTCCCAATCCAATTCAATTA
1 ATGGAAACATGCATTAATTCACAAACCAATTCAATTA
76596 AAGCAAGGCA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (41 bp):
ATGGAAACATGCATTAATTCACAAACCAATTCAATTATACT
Done.