Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009436.1 Hibiscus syriacus cultivar Beakdansim tig00113494_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: 78693
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:64 original size:17 final size:18
Alignment explanation
Indices: 50--86 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
40 AATTGAATAG
50 ATATTGAAATCGAATATA
1 ATATTGAAATCGAATATA
*
68 ATTTTGAAATCGAATATA
1 ATATTGAAATCGAATATA
86 A
1 A
87 AATCTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.11, T:0.35
Consensus pattern (18 bp):
ATATTGAAATCGAATATA
Found at i:7053 original size:9 final size:9
Alignment explanation
Indices: 7039--7137 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
7029 CTGCTAGAAA
7039 ACCGGTTTG
1 ACCGGTTTG
*
7048 ACCGGTTTTCA
1 ACCGG-TTT-G
*
7059 ACCGATTTCG
1 ACCGGTTT-G
7069 ACCGGTTTG
1 ACCGGTTTG
*
7078 AAGCGGTTTG
1 -ACCGGTTTG
*
7088 ACCGGTTCG
1 ACCGGTTTG
**
7097 AAGTGGTTTG
1 -ACCGGTTTG
*
7107 ACCGGTCTG
1 ACCGGTTTG
7116 AACCGGTTTG
1 -ACCGGTTTG
*
7126 ACCGGTCTG
1 ACCGGTTTG
7135 ACC
1 ACC
7138 CGACCCGACC
Statistics
Matches: 70, Mismatches: 15, Indels: 10
0.74 0.16 0.11
Matches are distributed among these distances:
9 30 0.43
10 36 0.51
11 4 0.06
ACGTcount: A:0.16, C:0.24, G:0.30, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:7092 original size:19 final size:19
Alignment explanation
Indices: 7038--7131 Score: 107
Period size: 19 Copynumber: 4.8 Consensus size: 19
7028 GCTGCTAGAA
*
7038 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGG-TTTG
*
7058 AACCGATTTCGACCGGTTTG
1 AACCGGTTT-GACCGGTTTG
* *
7078 AAGCGGTTTGACCGGTTCG
1 AACCGGTTTGACCGGTTTG
** *
7097 AAGTGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTTTG
7116 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
7132 CTGACCCGAC
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
19 39 0.62
20 18 0.29
21 6 0.10
ACGTcount: A:0.17, C:0.22, G:0.31, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTTTG
Found at i:14388 original size:19 final size:20
Alignment explanation
Indices: 14337--14415 Score: 74
Period size: 19 Copynumber: 4.0 Consensus size: 20
14327 GCTGCTGGAA
* *
14337 AACCGGTTTGACCGGTTTTC
1 AACCGGTTTGACCGGTTCTG
*
14357 AACCTGTTTTGACCGGTTC-G
1 AACC-GGTTTGACCGGTTCTG
** *
14377 AAGTGGTTTGACAGG-TCTG
1 AACCGGTTTGACCGGTTCTG
14396 AACCGGTTTGACCGG-TCTG
1 AACCGGTTTGACCGGTTCTG
14415 A
1 A
14416 CCCGACCCTA
Statistics
Matches: 47, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
18 2 0.04
19 27 0.57
20 6 0.13
21 12 0.26
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.32
Consensus pattern (20 bp):
AACCGGTTTGACCGGTTCTG
Found at i:14458 original size:17 final size:17
Alignment explanation
Indices: 14433--14470 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
14423 CTACTGACCC
14433 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
*
14450 GACCTGACCCGACCGTT
1 GACCCGACCCGACCGTT
14467 GACC
1 GACC
14471 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:21563 original size:13 final size:13
Alignment explanation
Indices: 21542--21578 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
21532 GACCGGTCAC
*
21542 GACCTGACCCGTT
1 GACCCGACCCGTT
21555 GACCCGACCCGTT
1 GACCCGACCCGTT
*
21568 GACCCGGCCCG
1 GACCCGACCCG
21579 ACCGTTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.46, G:0.27, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:21638 original size:29 final size:29
Alignment explanation
Indices: 21596--21733 Score: 188
Period size: 29 Copynumber: 4.8 Consensus size: 29
21586 ACCGTTGATC
*
21596 GGTGCTATTTTGGTAAATAATTCAATTTT
1 GGTGCTATTTTGGTAAATAATTCAGTTTT
*
21625 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTTTGGTAAATAATTCAGTTTT
*
21654 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTTTGGTAAATAATTCAGTTTT
* * *
21683 GGTGCTATTCTT-GTATATAATTCGGTTTA
1 GGTGCTATT-TTGGTAAATAATTCAGTTTT
* *
21712 GGTGCTATTATGGTAATTAATT
1 GGTGCTATTTTGGTAAATAATT
21734 TGAAATGGGT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
28 1 0.01
29 94 0.98
30 1 0.01
ACGTcount: A:0.24, C:0.08, G:0.21, T:0.47
Consensus pattern (29 bp):
GGTGCTATTTTGGTAAATAATTCAGTTTT
Found at i:21745 original size:58 final size:58
Alignment explanation
Indices: 21596--21756 Score: 175
Period size: 58 Copynumber: 2.8 Consensus size: 58
21586 ACCGTTGATC
* * * *
21596 GGTGCTATTTTGGTAAATAATTCA-ATTTTGGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTATGGTAAATAATTCAGA-ATGGGTGCTATTTTGGTAAATAATTCGGTTTA
* ** * *
21654 GGTGCTATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTT-GTATATAATTCGGTTTA
1 GGTGCTATTATGGTAAATAATTCAGAATGGGTGCTATT-TTGGTAAATAATTCGGTTTA
* *
21712 GGTGCTATTATGGTAATTAATT-TGAAATGGGTGCTATTTTGGTAA
1 GGTGCTATTATGGTAAATAATTCAG-AATGGGTGCTATTTTGGTAA
21757 TTATTTTAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
57 3 0.03
58 83 0.94
59 2 0.02
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (58 bp):
GGTGCTATTATGGTAAATAATTCAGAATGGGTGCTATTTTGGTAAATAATTCGGTTTA
Found at i:21745 original size:87 final size:87
Alignment explanation
Indices: 21596--21756 Score: 198
Period size: 87 Copynumber: 1.9 Consensus size: 87
21586 ACCGTTGATC
* * *** *
21596 GGTGCTATTTTGGTAAATAATTCAATTTTGGTGCTATTTTGGTAAATAATTCGGTTTTGGTGCTA
1 GGTGCTATTTTGGTAAATAATTCAATTTAGGTGCTATTATGGTAAATAATTCGAAATGGGTGCTA
21661 TTCTGGTAAATAATTCAGTTTT
66 TTCTGGTAAATAATTCAGTTTT
* ** * *
21683 GGTGCTATTCTT-GTATATAATTCGGTTTAGGTGCTATTATGGTAATTAATTTGAAATGGGTGCT
1 GGTGCTATT-TTGGTAAATAATTCAATTTAGGTGCTATTATGGTAAATAATTCGAAATGGGTGCT
*
21747 ATTTTGGTAA
65 ATTCTGGTAA
21757 TTATTTTAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
87 59 0.97
88 2 0.03
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.46
Consensus pattern (87 bp):
GGTGCTATTTTGGTAAATAATTCAATTTAGGTGCTATTATGGTAAATAATTCGAAATGGGTGCTA
TTCTGGTAAATAATTCAGTTTT
Found at i:21772 original size:29 final size:29
Alignment explanation
Indices: 21712--21772 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
21702 ATTCGGTTTA
* *
21712 GGTGCTATTATGGTAATTAATTTGAAATG
1 GGTGCTATTATGGTAATTAATTTAAAAAG
* *
21741 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTATGGTAATTAATTTAAAAAG
21770 GGT
1 GGT
21773 CTTCTTTGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.03, G:0.25, T:0.43
Consensus pattern (29 bp):
GGTGCTATTATGGTAATTAATTTAAAAAG
Found at i:29048 original size:5 final size:5
Alignment explanation
Indices: 28985--29037 Score: 52
Period size: 5 Copynumber: 9.4 Consensus size: 5
28975 TGACCGATCA
28985 CGACC CGACC CGTTGACC CGACC CGACC CATTGACC CGACC CGACC CGACC
1 CGACC CGACC C---GACC CGACC CGACC C---GACC CGACC CGACC CGACC
29036 CG
1 CG
29038 TTGACCCGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
5 32 0.76
8 10 0.24
ACGTcount: A:0.19, C:0.53, G:0.21, T:0.08
Consensus pattern (5 bp):
CGACC
Found at i:29048 original size:18 final size:18
Alignment explanation
Indices: 28985--29032 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
28975 TGACCGATCA
28985 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
29003 CGACCCGACCCATTGACC
1 CGACCCGACCCGTTGACC
29021 CGACCCGACCCG
1 CGACCCGACCCG
29033 ACCCGTTGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.19, C:0.52, G:0.21, T:0.08
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:29048 original size:23 final size:20
Alignment explanation
Indices: 28985--29037 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 20
28975 TGACCGATCA
28985 CGACCCGACCCGTTGACCCGACC
1 CGACCCGACCC---GACCCGACC
29008 CGACCCATTGACCCGACCCGACC
1 CGACCC---GACCCGACCCGACC
29031 CGACCCG
1 CGACCCG
29038 TTGACCCGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
20 1 0.04
23 21 0.78
26 5 0.19
ACGTcount: A:0.19, C:0.53, G:0.21, T:0.08
Consensus pattern (20 bp):
CGACCCGACCCGACCCGACC
Found at i:29098 original size:29 final size:29
Alignment explanation
Indices: 29056--29194 Score: 181
Period size: 29 Copynumber: 4.8 Consensus size: 29
29046 ACCGTTGACC
* * *
29056 GGTGCTATTTTGGTAAGTAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
29085 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
* *
29114 GGTGGTATTTTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
* * *
29143 GGTGCTATTCTAGTAAATAATTCGGTTTA
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
* *
29172 GGTGCT-TTCTGATAATTAATTCA
1 GGTGCTATTCTGGTAAATAATTCA
29195 AAATGGGTGC
Statistics
Matches: 96, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
28 13 0.14
29 83 0.86
ACGTcount: A:0.24, C:0.09, G:0.22, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:29226 original size:29 final size:29
Alignment explanation
Indices: 29172--29238 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
29162 ATTCGGTTTA
* *
29172 GGTGCT-TTCTGATAATTAATTCAAAATG
1 GGTGCTATTTTGATAATTAATTCAAAAAG
* *
29200 GGTGCTATTTTGATAATTATTTTAAAAAG
1 GGTGCTATTTTGATAATTAATTCAAAAAG
*
29229 GGTGTTATTT
1 GGTGCTATTT
29239 ATGTAAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.45
Consensus pattern (29 bp):
GGTGCTATTTTGATAATTAATTCAAAAAG
Found at i:30692 original size:17 final size:17
Alignment explanation
Indices: 30654--30692 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
30644 GATAGTATAA
*
30654 TTTATTTATAATTTCAT
1 TTTATTTATAATGTCAT
* *
30671 GTTATTTATAATGTGAT
1 TTTATTTATAATGTCAT
30688 TTTAT
1 TTTAT
30693 ATTGATGGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.03, G:0.08, T:0.62
Consensus pattern (17 bp):
TTTATTTATAATGTCAT
Found at i:38031 original size:33 final size:33
Alignment explanation
Indices: 37985--38080 Score: 120
Period size: 33 Copynumber: 2.9 Consensus size: 33
37975 TAAAGGTTGA
* *
37985 GAATACTCAACATCCGTATGGTACTAGGAACAG
1 GAATACTCCACATCCGTACGGTACTAGGAACAG
* * * *
38018 GAATACTCCACATCCATACAGCACTAGGAACAT
1 GAATACTCCACATCCGTACGGTACTAGGAACAG
* *
38051 GAATATTACACATCCGTACGGTACTAGGAA
1 GAATACTCCACATCCGTACGGTACTAGGAA
38081 GATGACTAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (33 bp):
GAATACTCCACATCCGTACGGTACTAGGAACAG
Found at i:49504 original size:21 final size:22
Alignment explanation
Indices: 49480--49524 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
49470 ATAAGGGAGA
49480 TATTGATACT-CTTAGCCTAGG
1 TATTGATACTCCTTAGCCTAGG
*
49501 TATTGATACTCCTTAGTCTAGG
1 TATTGATACTCCTTAGCCTAGG
49523 TA
1 TA
49525 GTTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (22 bp):
TATTGATACTCCTTAGCCTAGG
Found at i:50796 original size:21 final size:20
Alignment explanation
Indices: 50770--50810 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
50760 AGACCCCAAA
50770 AGAAGAATAAAGAAAAATAAT
1 AGAAGAA-AAAGAAAAATAAT
*
50791 AGAAGAACAAGAAAAATAAT
1 AGAAGAAAAAGAAAAATAAT
50811 GAGATAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.71, C:0.02, G:0.15, T:0.12
Consensus pattern (20 bp):
AGAAGAAAAAGAAAAATAAT
Found at i:60646 original size:21 final size:21
Alignment explanation
Indices: 60622--60661 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60612 TTCTTTAGTC
* *
60622 TCTGACTGTTAAAAGTTATCA
1 TCTGACTATTAAAAATTATCA
60643 TCTGACTATTAAAAATTAT
1 TCTGACTATTAAAAATTAT
60662 AAAATGATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (21 bp):
TCTGACTATTAAAAATTATCA
Found at i:62073 original size:2 final size:2
Alignment explanation
Indices: 62066--62097 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
62056 AACCGTATGA
62066 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
62098 AACAAAAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:64082 original size:3 final size:3
Alignment explanation
Indices: 64076--64109 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
64066 TATGTAACAT
64076 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
64110 TTTATAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:64448 original size:55 final size:54
Alignment explanation
Indices: 64401--64594 Score: 277
Period size: 55 Copynumber: 3.6 Consensus size: 54
64391 CCCTTTTTCT
* *
64401 TTCAGGGAGTAT-AGAACTCAAAC-ATCTTCAACACTCGTGTCTGTTCCCTATTCC
1 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACA-TCGTGTCTGTTCCCTATTCC
*
64455 TTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCT-TCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAAC-ATCGTGTCTGT-TCCCTATTCC
* *
64510 TTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAAC-ATCGTGTCTGTTCCCTATTCC
64565 TTCAGAGAGTATAAGACTCGAACAATCTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTC
64595 TTCTTATGGG
Statistics
Matches: 127, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
54 18 0.14
55 108 0.85
56 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (54 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACATCGTGTCTGTTCCCTATTCC
Found at i:64613 original size:55 final size:55
Alignment explanation
Indices: 64401--64641 Score: 269
Period size: 55 Copynumber: 4.4 Consensus size: 55
64391 CCCTTTTTCT
* * **
64401 TTCAGGGAGTAT-AGAACTCAAAC-ATCTTCAAC-ACTCGTGTCTGTTCCCTATTCC
1 TTCAGAGAGTATAAG-ACTCGAACAATCTTCAACTA-TCGTGTCTACTCCCTATTCC
* * *
64455 TTCAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTTCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTCTACTCCCTATTCC
* *
64510 TTTAGAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTCTGCTCCCTATTCC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTCTACTCCCTATTCC
** * * *
64565 TTCAGAGAGTATAAGACTCGAACAATCTTCTTCTTAT-GGGT-TCACTCCCTCTTTC
1 TTCAGAGAGTATAAGACTCGAACAATCTTCAAC-TATCGTGTCT-ACTCCCTATTCC
64620 TTCAGAGAGTAT-AGAACTCGAA
1 TTCAGAGAGTATAAG-ACTCGAA
64642 TATCTTCTTC
Statistics
Matches: 165, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
54 20 0.12
55 141 0.85
56 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (55 bp):
TTCAGAGAGTATAAGACTCGAACAATCTTCAACTATCGTGTCTACTCCCTATTCC
Found at i:64613 original size:110 final size:108
Alignment explanation
Indices: 64360--64756 Score: 347
Period size: 110 Copynumber: 3.6 Consensus size: 108
64350 GAAGTATGGA
* * ** * * *
64360 ACTCGAACAGTCTTCTGCCAATGGGTTCGTTCCCTTTTTCTTTCAGGGAGTATAGAACTCAAACA
1 ACTCGAACAATCTTCT-ACAATGGGTTCACTCCCTATTTCTTT-AGAGAGTATAGAACTCGAACA
*
64425 TCTTCAACACTCGTGTCTGTTCCCTATTCCTTCAGAGAGTATAAG
64 TCTTCAACACTCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * *
64470 ACTTGAACAATCTTCAACAAT-CGTGTCTTCTCCCTATTCCTTTAGAGAGTATA-AGACTCGAAC
1 ACTCGAACAATCTTCTACAATGGGT-TC-ACTCCCTATTTCTTTAGAGAGTATAGA-ACTCGAAC
64533 AATCTTCAACTA-TCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
63 -ATCTTCAAC-ACTCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
* * * * *
64580 ACTCGAACAATCTTCTTCTTATGGGTTCACTCCCTCTTTCTTCAGAGAGTATAGAACTCGAATAT
1 ACTCGAACAATCTTCTAC-AATGGGTTCACTCCCTATTTCTTTAGAGAGTATAGAACTCGAACAT
** ** * * * * *
64645 CTTCTTCAAACAG-GTTTGCTCCCTCTTTC-TCTAGGGAGTATAAA
65 CTTCAACACTC-GTGTCTGCTCCCTATTCCTTC-AGAGAGTATAAG
* * * * * * *
64689 ACTCGGAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCTAGGGAGTATAGAACTCGAACAT
1 ACTCGAACAATCTTCTAC-AATGGGTTCACTCCCTATTTCTTTAGAGAGTATAGAACTCGAACAT
64753 CTTC
65 CTTC
64757 TTCTGCTTCA
Statistics
Matches: 237, Mismatches: 39, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
108 58 0.24
109 60 0.25
110 111 0.47
111 6 0.03
112 2 0.01
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.34
Consensus pattern (108 bp):
ACTCGAACAATCTTCTACAATGGGTTCACTCCCTATTTCTTTAGAGAGTATAGAACTCGAACATC
TTCAACACTCGTGTCTGCTCCCTATTCCTTCAGAGAGTATAAG
Found at i:64671 original size:54 final size:54
Alignment explanation
Indices: 64568--64759 Score: 244
Period size: 54 Copynumber: 3.5 Consensus size: 54
64558 CTATTCCTTC
** * *
64568 AGAGAGTATA-AGACTCGAACAATCTTCTTCTTATGGGTTCACTCCCTCTTTCT-T
1 AGAGAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
64622 CAGAGAGTATAGAACTCGAATATCTTCTTCAAACAGGTTTGCTCCCTCTTTCTCT
1 -AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
* * *
64677 AGGGAGTATAAAACTCGGACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
1 AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
*
64731 AGGGAGTATAGAACTCGAACATCTTCTTC
1 AGAGAGTATAGAACTCGAACATCTTCTTC
64760 TGCTTCACTA
Statistics
Matches: 120, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
54 101 0.84
55 18 0.15
56 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (54 bp):
AGAGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCTTTCTCT
Found at i:77155 original size:7 final size:7
Alignment explanation
Indices: 77136--77168 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
77126 AAACCGTATG
77136 AATATAT
1 AATATAT
77143 -ATATAT
1 AATATAT
77149 AATATAT
1 AATATAT
77156 AATATAT
1 AATATAT
*
77163 CATATA
1 AATATA
77169 AACAAAGATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATAT
Done.