Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008024.1 Hibiscus syriacus cultivar Beakdansim tig00110499_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: 1023309
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:972710 original size:3 final size:3
Alignment explanation
Indices: 972639--972699 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
972629 ATTTTTGTTT
*
972639 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA ATA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
972684 -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
972700 AATAATTATT
Statistics
Matches: 53, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
2 6 0.11
3 44 0.83
4 3 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:977289 original size:21 final size:22
Alignment explanation
Indices: 977244--977316 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
977234 CATACATGCA
*
977244 TTTACATTTTGTATCTGTGCAT
1 TTTACATTTTGTATCTGTACAT
*
977266 TTT-CATTTTGTATTCT-TACTT
1 TTTACATTTTGTA-TCTGTACAT
* *
977287 TTTACATCTTTGAAT-TGCACAT
1 TTTACAT-TTTGTATCTGTACAT
*
977309 TTTGCATT
1 TTTACATT
977317 CTTATTTTTG
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
21 17 0.41
22 19 0.46
23 5 0.12
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.56
Consensus pattern (22 bp):
TTTACATTTTGTATCTGTACAT
Found at i:981692 original size:22 final size:22
Alignment explanation
Indices: 981666--981742 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
981656 ATCTACACTC
981666 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
981688 TTCAAAGATGATAGATTCTATT
1 TTCAAAGATGATAGATTCTCTT
*
981710 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
981732 TTCAAAGATGA
1 TTCAAAGATGA
981743 AAGCTTTATT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:982616 original size:76 final size:76
Alignment explanation
Indices: 982418--983141 Score: 1307
Period size: 76 Copynumber: 9.6 Consensus size: 76
982408 CTATTTCCAA
982418 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
982483 AGCCTTA----
66 AGCCTTAGGGT
982490 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
982555 AGCCTTAGGGT
66 AGCCTTAGGGT
982566 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
982631 AGCCTTAGGGT
66 AGCCTTAGGGT
982642 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
982707 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
982718 CATCTGGAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
982783 AGCCTTAGGGT
66 AGCCTTAGGGT
982794 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
982859 AGCCTTAGGGT
66 AGCCTTAGGGT
*
982870 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
982935 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
982946 CATCTGTAAGTCCTACAGTGCACGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTCTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
983011 AGCCTTAGGGT
66 AGCCTTAGGGT
983022 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
983087 AGCCTTAGGGT
66 AGCCTTAGGGT
** * * *
983098 CATCTGTAAGTCCTTTAGTGCATCATATTTTC-AAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
983142 TCATCTGTAA
Statistics
Matches: 631, Mismatches: 17, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
72 72 0.11
74 8 0.01
75 4 0.01
76 547 0.87
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:983144 original size:45 final size:45
Alignment explanation
Indices: 983080--983176 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
983070 CTTTTTGATG
* * *
983080 TTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTTTAGTGCATCATA
1 TTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATCATA
* * *
983125 TTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATTATG
1 TTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATCATA
983170 TTTTCAA
1 TTTTCAA
983177 CATTTCCATC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (45 bp):
TTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATCATA
Found at i:983326 original size:15 final size:14
Alignment explanation
Indices: 983308--983383 Score: 65
Period size: 15 Copynumber: 5.7 Consensus size: 14
983298 TTTTGTTTTT
983308 ATTATTATTATTAAA
1 ATTATTATTATT-AA
983323 ATTATTATTATT-A
1 ATTATTATTATTAA
* *
983336 A-TAATATTATATAT
1 ATTATTATTAT-TAA
983350 ATTATTA-TATT--
1 ATTATTATTATTAA
983361 A-TATTATTATTAA
1 ATTATTATTATTAA
*
983374 ATAATTATTA
1 ATTATTATTA
983384 CAAGCCCAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 5 0.10
11 5 0.10
12 8 0.16
13 5 0.10
14 11 0.22
15 16 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATTATTATTAA
Found at i:983343 original size:24 final size:25
Alignment explanation
Indices: 983306--983383 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 25
983296 ATTTTTGTTT
*
983306 TTATTATTATTATTA-AAATTATTA
1 TTATTAATATTATTATAAATTATTA
*
983330 TTATTAATAATATTATATATATTATTA
1 TTATTAATATTATTATA-A-ATTATTA
*
983357 -TATT-ATATTATTATTAAATAATTA
1 TTATTAATATTATTA-TAAATTATTA
983381 TTA
1 TTA
983384 CAAGCCCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
24 19 0.42
25 12 0.27
26 7 0.16
27 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATTAATATTATTATAAATTATTA
Found at i:983353 original size:27 final size:25
Alignment explanation
Indices: 983306--983383 Score: 81
Period size: 27 Copynumber: 3.1 Consensus size: 25
983296 ATTTTTGTTT
983306 TTATTAT--TATTATTAAAATTATTA
1 TTATTATAATATTATT-AAATTATTA
*
983330 TTATTAATAATATTATATATATTATTA
1 TTATT-ATAATATTAT-TAAATTATTA
* *
983357 -TATTATATTATTATTAAATAATTA
1 TTATTATAATATTATTAAATTATTA
983381 TTA
1 TTA
983384 CAAGCCCAGA
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
24 13 0.29
25 13 0.29
26 4 0.09
27 14 0.31
28 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TTATTATAATATTATTAAATTATTA
Found at i:983383 original size:3 final size:3
Alignment explanation
Indices: 983306--983372 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
983296 ATTTTTGTTT
** * *
983306 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA ATA ATA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
983351 TTA TTA -TA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
983373 AATAATTATT
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 6 0.11
3 45 0.83
4 3 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:984694 original size:29 final size:28
Alignment explanation
Indices: 984644--984712 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
984634 TTTTTACAAG
*
984644 TTTTATTTATTTTAAATATATAGTTTTAA
1 TTTTATTTATTTTAAATATATA-TGTTAA
* *
984673 TTTTATTTATTGTTTAGT-TATATGTTAA
1 TTTTATTTATT-TTAAATATATATGTTAA
*
984701 TTTTATATATTT
1 TTTTATTTATTT
984713 ACTTTTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 1 0.03
28 15 0.43
29 15 0.43
30 4 0.11
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (28 bp):
TTTTATTTATTTTAAATATATATGTTAA
Found at i:984721 original size:48 final size:47
Alignment explanation
Indices: 984622--984728 Score: 117
Period size: 49 Copynumber: 2.2 Consensus size: 47
984612 ACTAATTTCA
* * *
984622 AATTTTATTTATTTTTTACAAGTTTTATTTATTTTAAATATATAGTTTT
1 AATTTTATTTATTGTTT--AAGTTATATTTATTTTAAATATATACTTTT
* *
984671 AATTTTATTTATTGTTT-AGTTATATGTTAATTTTATATATTTACTTTT
1 AATTTTATTTATTGTTTAAGTTATAT-TT-ATTTTAAATATATACTTTT
984719 AATTATTATT
1 AATT-TTATT
984729 ACTATTATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
46 7 0.14
47 2 0.04
48 20 0.40
49 21 0.42
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (47 bp):
AATTTTATTTATTGTTTAAGTTATATTTATTTTAAATATATACTTTT
Found at i:986846 original size:11 final size:11
Alignment explanation
Indices: 986815--986857 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
986805 ATTTAACAAC
986815 ATTATTTATTATT
1 ATTA-TTATTA-T
986828 ATTATTATTAT
1 ATTATTATTAT
* *
986839 ATTCTTATAAT
1 ATTATTATTAT
986850 ATTATTAT
1 ATTATTAT
986858 GTTATTAGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
12 6 0.22
13 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:996916 original size:22 final size:21
Alignment explanation
Indices: 996877--996926 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
996867 AAGAGAAAGT
**
996877 AAAAGAATTTTAACAAAACCC
1 AAAAGAATTTTAACAAAAAAC
996898 AAAAGAACTTTTATA-AAAAAAC
1 AAAAGAA-TTTTA-ACAAAAAAC
996920 AAAAGAA
1 AAAAGAA
996927 AGGAGTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 7 0.28
22 17 0.68
23 1 0.04
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (21 bp):
AAAAGAATTTTAACAAAAAAC
Found at i:997872 original size:18 final size:19
Alignment explanation
Indices: 997840--997877 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
997830 AGTCCACGTG
* *
997840 ATAAACAGAATTAAATCAA
1 ATAAACAGAAATAAAACAA
997859 ATAAA-AGAAATAAAACAA
1 ATAAACAGAAATAAAACAA
997877 A
1 A
997878 CTACAAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.71, C:0.08, G:0.05, T:0.16
Consensus pattern (19 bp):
ATAAACAGAAATAAAACAA
Found at i:997923 original size:14 final size:13
Alignment explanation
Indices: 997892--997929 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
997882 AAGCAACAAA
997892 TTTTGTTTTTTCC
1 TTTTGTTTTTTCC
*
997905 CTTTGTTTTTCTCC
1 TTTTGTTTTT-TCC
997919 TTTTGTTTTTT
1 TTTTGTTTTTT
997930 TTTCCGATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTGTTTTTTCC
Found at i:999705 original size:7 final size:7
Alignment explanation
Indices: 999689--999719 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
999679 AATTCAAGAA
999689 AAATAA-
1 AAATAAT
999695 AAATAAT
1 AAATAAT
999702 AAATAAT
1 AAATAAT
999709 AAATAAT
1 AAATAAT
999716 AAAT
1 AAAT
999720 CAAAGAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:1000060 original size:32 final size:32
Alignment explanation
Indices: 1000019--1000091 Score: 110
Period size: 32 Copynumber: 2.3 Consensus size: 32
1000009 TAAAAGGTCC
* * *
1000019 AGTCAGCACGAGGAAGATTATGGAAGCAGCCT
1 AGTCAGCACGAAGAAGATTATAGAAGCAACCT
*
1000051 AGTCAGCACGAAGAAGATTCTAGAAGCAACCT
1 AGTCAGCACGAAGAAGATTATAGAAGCAACCT
1000083 AGTCAGCAC
1 AGTCAGCAC
1000092 AATCTGAGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.22, G:0.26, T:0.15
Consensus pattern (32 bp):
AGTCAGCACGAAGAAGATTATAGAAGCAACCT
Found at i:1001233 original size:143 final size:143
Alignment explanation
Indices: 1001068--1001350 Score: 485
Period size: 143 Copynumber: 2.0 Consensus size: 143
1001058 AAATTATCAA
*
1001068 GTCCTTATGGATCGACCCTCTTTCACTATACTATTCTCAATTTTATTTATTTTATTTTGAAGAGG
1 GTCCTTAAGGATCGACCCTCTTTCACTATACTATTCTCAATTTTATTTATTTTATTTTGAAGAGG
*
1001133 ATTTATTTTATTTTTACGAGTAAAACGACGCTGTTCATCCAGACTACAGGTTTTGCTAGAGACAT
66 ATTTATTTTATTTTGACGAGTAAAACGACGCTGTTCATCCAGACTACAGGTTTTGCTAGAGACAT
1001198 TTTCACTTCACAC
131 TTTCACTTCACAC
*
1001211 GTCCTTAAGGATCGACCCTCTTTCACTATACTATTCTCCATTTTATTTATTTTATTTTGAAGAGG
1 GTCCTTAAGGATCGACCCTCTTTCACTATACTATTCTCAATTTTATTTATTTTATTTTGAAGAGG
* * * * * *
1001276 ATTTATTTTATTTTGACGATTAAAACGACGTTTTTCGTCCAGATTACAGGTTTTGCTTGAGACAT
66 ATTTATTTTATTTTGACGAGTAAAACGACGCTGTTCATCCAGACTACAGGTTTTGCTAGAGACAT
1001341 TTTCACTTCA
131 TTTCACTTCA
1001351 TATGCTTTTT
Statistics
Matches: 131, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
143 131 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (143 bp):
GTCCTTAAGGATCGACCCTCTTTCACTATACTATTCTCAATTTTATTTATTTTATTTTGAAGAGG
ATTTATTTTATTTTGACGAGTAAAACGACGCTGTTCATCCAGACTACAGGTTTTGCTAGAGACAT
TTTCACTTCACAC
Found at i:1006523 original size:17 final size:17
Alignment explanation
Indices: 1006501--1006550 Score: 93
Period size: 17 Copynumber: 3.0 Consensus size: 17
1006491 GGCAATTAGA
1006501 ATGTTATTAGCATTTAC
1 ATGTTATTAGCATTTAC
1006518 ATGTTATTAGCATTTAC
1 ATGTTATTAGCATTTAC
1006535 ATGTTATTAGC-TTTAC
1 ATGTTATTAGCATTTAC
1006551 TTTATATCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.15
17 28 0.85
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (17 bp):
ATGTTATTAGCATTTAC
Found at i:1011512 original size:31 final size:30
Alignment explanation
Indices: 1011474--1011623 Score: 126
Period size: 31 Copynumber: 4.9 Consensus size: 30
1011464 GGGCCTAAGA
* *
1011474 GCCTACCCAAGAAAGTTCTCAAGGCCACGTG
1 GCCTACCCAAGAAAGATCTCAGGGCCACG-G
* * *
1011505 GCCTACCCAATAAAGATCTCAGGGCCGCAAG
1 GCCTACCCAAGAAAGATCTCAGGGCCAC-GG
* * *
1011536 GCCTACTCAAGAATGATCTTAGGGCCACAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCAC-GG
*
1011567 GCCTACCCAAGAAAAATC-CAAGGGTCGCA-GG
1 GCCTACCCAAGAAAGATCTC-AGGG-C-CACGG
*
1011598 GCCTACCCAAGAATA-ATCTCGGGGCC
1 GCCTACCCAAGAA-AGATCTCAGGGCC
1011624 GCAAAGCCTA
Statistics
Matches: 97, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
29 1 0.01
30 1 0.01
31 90 0.93
32 3 0.03
33 2 0.02
ACGTcount: A:0.31, C:0.31, G:0.24, T:0.15
Consensus pattern (30 bp):
GCCTACCCAAGAAAGATCTCAGGGCCACGG
Found at i:1011623 original size:62 final size:62
Alignment explanation
Indices: 1011474--1011641 Score: 162
Period size: 62 Copynumber: 2.7 Consensus size: 62
1011464 GGGCCTAAGA
* * * *
1011474 GCCTACCCAAGAA-AGTTCTCAAGGCCAC-GTGGCCTACCCAATAAAGATCTCAGGGCCGCAAG
1 GCCTACCCAAGAATA-ATCTCAGGGCCACAG-GGCCTACCCAAGAAAAATCTCAGGGCCGCAAG
* * * * *
1011536 GCCTACTCAAGAATGATCTTAGGGCCACAGGGCCTACCCAAGAAAAATC-CAAGGGTCGCAGG
1 GCCTACCCAAGAATAATCTCAGGGCCACAGGGCCTACCCAAGAAAAATCTC-AGGGCCGCAAG
* * ** *
1011598 GCCTACCCAAGAATAATCTCGGGGCCGCAAAGCCTACTCAAGAA
1 GCCTACCCAAGAATAATCTCAGGGCCACAGGGCCTACCCAAGAA
1011642 TCACATTAGG
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
61 1 0.01
62 84 0.98
63 1 0.01
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.14
Consensus pattern (62 bp):
GCCTACCCAAGAATAATCTCAGGGCCACAGGGCCTACCCAAGAAAAATCTCAGGGCCGCAAG
Found at i:1011633 original size:31 final size:31
Alignment explanation
Indices: 1011504--1011642 Score: 138
Period size: 31 Copynumber: 4.5 Consensus size: 31
1011494 AAGGCCACGT
*
1011504 GGCCTACCCAATAA-AGATCTCAGGGCCGCAA
1 GGCCTACCCAAGAATA-ATCTCAGGGCCGCAA
* * * * *
1011535 GGCCTACTCAAGAATGATCTTAGGGCCACAG
1 GGCCTACCCAAGAATAATCTCAGGGCCGCAA
* * *
1011566 GGCCTACCCAAGAAAAATC-CAAGGGTCGCAG
1 GGCCTACCCAAGAATAATCTC-AGGGCCGCAA
*
1011597 GGCCTACCCAAGAATAATCTCGGGGCCGCAA
1 GGCCTACCCAAGAATAATCTCAGGGCCGCAA
* *
1011628 AGCCTACTCAAGAAT
1 GGCCTACCCAAGAAT
1011643 CACATTAGGT
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.14
Consensus pattern (31 bp):
GGCCTACCCAAGAATAATCTCAGGGCCGCAA
Found at i:1014072 original size:22 final size:23
Alignment explanation
Indices: 1014046--1014104 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
1014036 CCCGAAAAAC
*
1014046 GTCAATGGTCGGTCAACGA-CCA
1 GTCAACGGTCGGTCAACGATCCA
* *
1014068 GTCAACGGT-GGCCAACGATCTA
1 GTCAACGGTCGGTCAACGATCCA
1014090 GTCAACGG-CGGTCAA
1 GTCAACGGTCGGTCAA
1014105 AGCGGTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
21 8 0.26
22 23 0.74
ACGTcount: A:0.27, C:0.27, G:0.29, T:0.17
Consensus pattern (23 bp):
GTCAACGGTCGGTCAACGATCCA
Done.