Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002217.1 Hibiscus syriacus cultivar Beakdansim tig00004512_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: 61734
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:573 original size:14 final size:15
Alignment explanation
Indices: 554--585 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
544 TATTCCGATA
554 ATTTTAAAA-AAATT
1 ATTTTAAAATAAATT
568 ATTTTAAAATAAATT
1 ATTTTAAAATAAATT
583 ATT
1 ATT
586 GTATTTACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTTAAAATAAATT
Found at i:4802 original size:24 final size:24
Alignment explanation
Indices: 4750--4802 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
4740 TAGGTTTAAT
*
4750 TAATAGTACACCACATTAAAACAA
1 TAATAGTACACAACATTAAAACAA
* * * *
4774 CAATAGTACATAACATTATAATAA
1 TAATAGTACACAACATTAAAACAA
4798 TAATA
1 TAATA
4803 ATAATAATAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.55, C:0.15, G:0.04, T:0.26
Consensus pattern (24 bp):
TAATAGTACACAACATTAAAACAA
Found at i:7887 original size:77 final size:77
Alignment explanation
Indices: 7795--7952 Score: 316
Period size: 77 Copynumber: 2.1 Consensus size: 77
7785 GCTAACCCTA
7795 GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAGCAGTGTCAGCAATACACTTGTACTCA
1 GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAGCAGTGTCAGCAATACACTTGTACTCA
7860 GCTTCCATTATG
66 GCTTCCATTATG
7872 GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAGCAGTGTCAGCAATACACTTGTACTCA
1 GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAGCAGTGTCAGCAATACACTTGTACTCA
7937 GCTTCCATTATG
66 GCTTCCATTATG
7949 GATC
1 GATC
7953 TGGACACTGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.27
Consensus pattern (77 bp):
GATCAGCAAGTAAGGCACTTACCCATGTTACTTCAGCAGCAGTGTCAGCAATACACTTGTACTCA
GCTTCCATTATG
Found at i:12798 original size:28 final size:30
Alignment explanation
Indices: 12762--12831 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 30
12752 GGTAAGATAT
12762 AATTAATCATAGGAAAT-G-TACAAAATA-
1 AATTAATCATAGGAAATGGATACAAAATAG
12789 ATATTAATCATAGGAAATGGGATACAAAATAG
1 A-ATTAATCATAGGAAAT-GGATACAAAATAG
12821 AATTAATCATA
1 AATTAATCATA
12832 AAAGAAATGA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
27 1 0.03
28 16 0.42
30 1 0.03
31 19 0.50
32 1 0.03
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (30 bp):
AATTAATCATAGGAAATGGATACAAAATAG
Found at i:19019 original size:30 final size:30
Alignment explanation
Indices: 18950--19017 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
18940 CATGGTCCCC
18950 TAAAATTTT-AAAAATCATAATTTAGACCGT
1 TAAAATTTTAAAAAAT-ATAATTTAGACCGT
*
18980 TAAAATTTTAAAAAAT-TAATTT-GACCCTT
1 TAAAATTTTAAAAAATATAATTTAGA-CCGT
19009 TAAAATTTT
1 TAAAATTTT
19018 TAGAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
28 2 0.06
29 18 0.51
30 9 0.26
31 6 0.17
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (30 bp):
TAAAATTTTAAAAAATATAATTTAGACCGT
Found at i:23246 original size:2 final size:2
Alignment explanation
Indices: 23241--23275 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
23231 ATAAAAAATA
23241 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23276 AGAAAATCAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25037 original size:256 final size:256
Alignment explanation
Indices: 24601--25446 Score: 1096
Period size: 255 Copynumber: 3.3 Consensus size: 256
24591 TTCCTCATGA
* * * * * *
24601 TTGAGTCGATCTTGGATGACTTGAGCATGAT-TTCCTTTATCGTGAAGTTGAAATCTAGCTCGAA
1 TTGAGTCGATATTGGGTGATTTAAGCATGATATT-CTTTATCGTGAAGTTGAAATCAAGCTCAAA
* * * * *
24665 CTCTGAACCAGAAAGTAGTTCCTCATTATTGAGTTAACCTAAATCACAATTGATTTTTGGGTCTT
65 ATCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGA-TTTTGGGTCTT
* *
24730 CTTCTAGTCCAATATCATTCATC-GTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
129 ATTCTAGTCCAATATCCTT-ATCTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
* *
24794 GCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCATGGCCGACTCCTTCTTTGTGAAG
193 GCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * * *
24858 TTAAGTTGATATTGGGTGATTTAAGCATGATATTCTTTGTTGTGAAGTTGAAATCAAGCTCAAAA
1 TTGAGTCGATATTGGGTGATTTAAGCATGATATTCTTTATCGTGAAGTTGAAATCAAGCTCAAAA
* * * * * *
24923 TCTGAACTGGAAAGTAGCTCCCCGTTGTTGAGTTAAGCTAAATTACATTTGATTTTGGGTCTTAT
66 TCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGATTTTGGGTCTTAT
* *
24988 TCTAGTCCAATATCCTTAGCTGTGAAGTTAAAATTTGACTTGAAGACCTTGGTTTAAAAATTA-C
131 TCTAGTCCAATATCCTTATCTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAA-TAGC
* * * * *
25052 TCCCTGAGCAC-ATATCCTTTATTATAAAGTTGAAATCGTGGTCGACTCCTTCGTTGTGAAG
195 TCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * * * *
25113 TTGAGTCGATCTTGGGTGATTTGAA-CATGATATACTTCATCGTGAAGTTGAAAACAAGGTCAAA
1 TTGAGTCGATATTGGGTGATTT-AAGCATGATATTCTTTATCGTGAAGTTGAAATCAAGCTCAAA
* * * *
25177 ATCTGAACTGGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCGCAATTGATTTTGGGTATTT
65 ATCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGATTTTGGGTCTTA
* *
25242 TTCTAGTCCAATA-CCTT-TCGTCGTGAAGTTGAAATTTGGCTTGAAGACCTTGGTTTGAAAATA
130 TTCTAGTCCAATATCCTTATC-T-GTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
* * * *
25305 GCTCCATGAGCATGATATCTTTCATCATGAAGTTGAAATTGTGGCCGACTCCTTCGCTGTGAAG
193 GCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * * * *
25369 TTGAGTCGATATTGGATGATTTGAGTATGATA-TCATTTTTCGTGAAGTTGAAATCAAGCTCGAA
1 TTGAGTCGATATTGGGTGATTTAAGCATGATATTC-TTTATCGTGAAGTTGAAATCAAGCTCAAA
25433 ATCTGAACTAGAAA
65 ATCTGAACTAGAAA
25447 ATGGCTTATT
Statistics
Matches: 507, Mismatches: 72, Indels: 21
0.85 0.12 0.04
Matches are distributed among these distances:
253 1 0.00
254 7 0.01
255 216 0.43
256 185 0.36
257 96 0.19
258 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (256 bp):
TTGAGTCGATATTGGGTGATTTAAGCATGATATTCTTTATCGTGAAGTTGAAATCAAGCTCAAAA
TCTGAACTAGAAAGTAGATCCTCATTGTTGAGTTAAGCTAAATCACAATTGATTTTGGGTCTTAT
TCTAGTCCAATATCCTTATCTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATAGCT
CCATGAGCACGATATCCTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
Found at i:25533 original size:256 final size:252
Alignment explanation
Indices: 24601--25549 Score: 941
Period size: 256 Copynumber: 3.7 Consensus size: 252
24591 TTCCTCATGA
* * * * * * * * *
24601 TTGAGTCGATCTTGGATGACTTGAGCATGATTTCCTTTATCGTGAAGTTGAAATCTAGCTCGAAC
1 TTGAGTCGATATTGGGTGATTTGAGCATGATATCATTTTTCGTGAAGTTGAAATCAAGCTCAAAA
** * * * **
24666 TCTGAACCAGAAAGTAGTTCCTCATT-ATTGAGTTAACCTAAATCACAATTGATTTTTGGGTCT-
66 TCTGAACTGGAAAGT-G--GCTCATTGTTTGAGTTAAGCTAAATTGCAATTGA-TTTTGGGTCTA
* * *
24729 TCTTCTAGTCCAATATCATTCATCGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
127 T-TT-TAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
* * *
24794 GCTCCATGAGCACGATATCCTTCATCATGAAGTTGAAATCATGGCCGACTCCTTCTTTGTGAAG
190 GCTCCATGAGCA-GATATCTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * *
24858 TTAAGTTGATATTGGGTGATTTAAGCATGATATTC-TTTGTT-GTGAAGTTGAAATCAAGCTCAA
1 TTGAGTCGATATTGGGTGATTTGAGCATGATA-TCATTT-TTCGTGAAGTTGAAATCAAGCTCAA
* * * *
24921 AATCTGAACTGGAAAGTAGCTCCCCGTTG-TTGAGTTAAGCTAAATTACATTTGATTTTGGGTCT
64 AATCTGAACTGGAAAGTGGCT---CATTGTTTGAGTTAAGCTAAATTGCAATTGATTTTGGGTC-
* * * *
24985 TATTCTAGTCCAATATCCTTAGCTGTGAAGTTAAAATTTGACTTGAAGACCTTGGTTTAAAAATT
125 TATTTTAGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAA-T
* * * * *
25050 A-CTCCCTGAGCACATATCCTTT-ATTATAAAGTTGAAATCGTGGTCGACTCCTTCGTTGTGAAG
189 AGCTCCATGAGCAGATAT-CTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * ** * *
25113 TTGAGTCGATCTTGGGTGATTTGAACATGATAT-ACTTCATCGTGAAGTTGAAAACAAGGTCAAA
1 TTGAGTCGATATTGGGTGATTTGAGCATGATATCA-TTTTTCGTGAAGTTGAAATCAAGCTCAAA
* * * *
25177 ATCTGAACTGGAAAGTAGATCCTCATTG-TTGAGTTAAGCTAAATCGCAATTGATTTTGGGTATT
65 ATCTGAACTGGAAAGT-G--GCTCATTGTTTGAGTTAAGCTAAATTGCAATTGATTTTGGGTCTA
* * *
25241 TTTCTAGTCCAATA-CCTTTCGTCGTGAAGTTGAAATTTGGCTTGAAGACCTTGGTTTGAAAATA
127 TTT-TAGTCCAATATCC-TTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATA
* *
25305 GCTCCATGAGCATGATATCTTTCATCATGAAGTTGAAATTGTGGCCGACTCCTTCGCTGTGAAG
190 GCTCCATGAGCA-GATATCTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
* * *
25369 TTGAGTCGATATTGGATGATTTGAGTATGATATCATTTTTCGTGAAGTTGAAATCAAGCTCGAAA
1 TTGAGTCGATATTGGGTGATTTGAGCATGATATCATTTTTCGTGAAGTTGAAATCAAGCTCAAAA
* * * ** * * * * *
25434 TCTGAACTAGAAAATGGCTTATTGTTATCGAGTTGAA-CTAGTTTGTAGTTGATTTCGGATCTCC
66 TCTGAACTGGAAAGTGGCTCATTGTT-T-GAGTT-AAGCTAAATTGCAATTGATTTTGGGTCT-A
* * * *
25498 TTTTAG-CCTAATATCCTTCGTTATGAAGTTGAAATTCGGCTTGAACACCTTG
127 TTTTAGTCC-AATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTG
25550 ATGATAGCTC
Statistics
Matches: 572, Mismatches: 91, Indels: 59
0.79 0.13 0.08
Matches are distributed among these distances:
253 6 0.01
254 12 0.02
255 207 0.36
256 242 0.42
257 99 0.17
258 6 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (252 bp):
TTGAGTCGATATTGGGTGATTTGAGCATGATATCATTTTTCGTGAAGTTGAAATCAAGCTCAAAA
TCTGAACTGGAAAGTGGCTCATTGTTTGAGTTAAGCTAAATTGCAATTGATTTTGGGTCTATTTT
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTTGACTTGAAGACCTTGGTTTAAAAATAGCTCCA
TGAGCAGATATCTTTCATCATGAAGTTGAAATCGTGGCCGACTCCTTCGTTGTGAAG
Found at i:37437 original size:15 final size:15
Alignment explanation
Indices: 37417--37450 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
37407 TCAAGATTAT
**
37417 TTAAACATATGTATA
1 TTAAACATACATATA
37432 TTAAACATACATATA
1 TTAAACATACATATA
37447 TTAA
1 TTAA
37451 CTCTAGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (15 bp):
TTAAACATACATATA
Found at i:41852 original size:22 final size:21
Alignment explanation
Indices: 41804--41852 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
41794 AAAAATAAAA
*
41804 ATAAAAACAAAGAAAACTTTG
1 ATAAAAAAAAAGAAAACTTTG
* *
41825 AAAAAAAGAAAAGAAAACTTTT
1 ATAAAAA-AAAAGAAAACTTTG
41847 ATAAAA
1 ATAAAA
41853 CTCAAAGCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.18
Consensus pattern (21 bp):
ATAAAAAAAAAGAAAACTTTG
Found at i:45778 original size:10 final size:9
Alignment explanation
Indices: 45747--45776 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
45737 ATTTTATACA
45747 TTACATTCT
1 TTACATTCT
45756 TTATCATTCT
1 TTA-CATTCT
45766 TTACATTCT
1 TTACATTCT
45775 TT
1 TT
45777 TATTTTACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (9 bp):
TTACATTCT
Found at i:46897 original size:64 final size:65
Alignment explanation
Indices: 46792--46956 Score: 203
Period size: 64 Copynumber: 2.6 Consensus size: 65
46782 TTTCAAAGTA
* **
46792 GTGTACCAATGCACCA-ATCAATGCATCGATGCA-TCCTTGAATAAATTGAATTTCGAATGCATT
1 GTGTACCAATGCA-CAGA-CCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATT
46855 TT
64 TT
* * * **
46857 GTGTACCGATGCACA-AGGCATGCATCAATGCACTCC-TGAATATTTTGAACATCGAATGCATTT
1 GTGTACCAATGCACAGA-CCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTT
46920 T
65 T
46921 GTGTACCAATGCACAGACCATGCATCGATGCACTCC
1 GTGTACCAATGCACAGACCATGCATCGATGCACTCC
46957 AGCTTGTTTG
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 70 0.81
65 16 0.19
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (65 bp):
GTGTACCAATGCACAGACCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTT
Found at i:48941 original size:21 final size:21
Alignment explanation
Indices: 48917--48956 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
48907 AAGACTTTAT
48917 TTTCAAAATAT-AAAAATGATA
1 TTTCAAAAT-TGAAAAATGATA
48938 TTTCAAAATTGAAAAATGA
1 TTTCAAAATTGAAAAATGA
48957 AAATAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.33
Consensus pattern (21 bp):
TTTCAAAATTGAAAAATGATA
Found at i:52847 original size:23 final size:22
Alignment explanation
Indices: 52767--52844 Score: 79
Period size: 23 Copynumber: 3.5 Consensus size: 22
52757 ACTAGCTAGT
*
52767 GCATCGATGCATCCCTTGAATGT
1 GCATCGATGCAT-CCTTGAATGA
* *
52790 GCATCGATACAT-CATGAA-GA
1 GCATCGATGCATCCTTGAATGA
*
52810 TGCACCGATGCACTCCTTGAATGA
1 -GCATCGATGCA-TCCTTGAATGA
52834 GCATCGATGCA
1 GCATCGATGCA
52845 CTCTGCTGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 14 0.32
22 1 0.02
23 26 0.59
24 2 0.05
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (22 bp):
GCATCGATGCATCCTTGAATGA
Found at i:55576 original size:64 final size:65
Alignment explanation
Indices: 55426--55589 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 65
55416 TTCAAAGTAG
* * * **
55426 TGTACCGATGCACCAATCAATGCATCGAAGCA-TCCTTGAATAAATTGAATTTCGAATGCATTTT
1 TGTACCGATGCA-CAAGCCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTT
*
55490 G
65 A
* * **
55491 TGTACCGATGTACAAGGCATGCATCGATGCACTCC-TGAATATTTTGAACATCGAATGCATTTTA
1 TGTACCGATGCACAAGCCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTTA
* *
55555 TGTACCGATGCAC-AGACCATGCATCTATGTACTCC
1 TGTACCGATGCACAAG-CCATGCATCGATGCACTCC
55590 AGCTTGTTTG
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
63 2 0.02
64 67 0.81
65 14 0.17
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (65 bp):
TGTACCGATGCACAAGCCATGCATCGATGCACTCCTTGAATAAATTGAACATCGAATGCATTTTA
Found at i:57188 original size:14 final size:14
Alignment explanation
Indices: 57156--57187 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
57146 AAAAGAACAG
57156 GAAAAAT-AAAAAT
1 GAAAAATGAAAAAT
57169 GAAAAATGAAAAA-
1 GAAAAATGAAAAAT
57182 GAAAAA
1 GAAAAA
57188 AAGAAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (14 bp):
GAAAAATGAAAAAT
Found at i:57215 original size:34 final size:35
Alignment explanation
Indices: 57123--57228 Score: 89
Period size: 34 Copynumber: 3.1 Consensus size: 35
57113 CTAAAGAGGA
* * *
57123 AAAAAGAAAA-AAAAAA-GAACAA-GAAAAGAACAGG
1 AAAAATAAAATAAAAAATGAAAAAGGAAAA-AATA-G
*
57157 AAAAATAAAAATGAAAAATGAAAAA-GAAAAAA-AG
1 AAAAAT-AAAATAAAAAATGAAAAAGGAAAAAATAG
57191 AAAAAT-AAATAAAAAATGGAAAAAAGGAAAAAATAG
1 AAAAATAAAATAAAAAAT-G-AAAAAGGAAAAAATAG
57227 AA
1 AA
57229 GGAAGAAAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
32 10 0.16
33 1 0.02
34 17 0.28
35 12 0.20
36 11 0.18
37 10 0.16
ACGTcount: A:0.77, C:0.02, G:0.14, T:0.07
Consensus pattern (35 bp):
AAAAATAAAATAAAAAATGAAAAAGGAAAAAATAG
Found at i:59831 original size:117 final size:118
Alignment explanation
Indices: 59622--59835 Score: 333
Period size: 117 Copynumber: 1.8 Consensus size: 118
59612 TCCATTATAG
* * * *
59622 AAGGAGGTGGATCATCATTTCCAATGGAGGGGTTTATAATGAGAAGAACTCGTCCGATGAGGGAG
1 AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
* *
59687 AAGAAGTTCATAATGAGATGAACTTGTTCAACTTTTGTTCGAATACATCACAA
66 AAGAAGTTCATAATGAGAAGAAATTGTTCAACTTTTGTTCGAATACATCACAA
* *
59740 AAGGAGGTGGATCAAT-ATTTCCAGTGGA-GAGTTCATAATGAGAAGAACTCATTCGATAAGGGA
1 AAGGAGGTGGATC-ATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGA
59803 GAAGAAGTTCATAATGAGAAGAAATTGTTCAAC
65 GAAGAAGTTCATAATGAGAAGAAATTGTTCAAC
59836 CTTAGCTCGA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
117 61 0.70
118 24 0.28
119 2 0.02
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (118 bp):
AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
AAGAAGTTCATAATGAGAAGAAATTGTTCAACTTTTGTTCGAATACATCACAA
Found at i:59832 original size:20 final size:19
Alignment explanation
Indices: 59770--59833 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
59760 CCAGTGGAGA
*
59770 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAAAT
* *
59789 CATTCGATAAGGGAGAAG-AA-
1 -GTTC-ATAA-TGAGAAGAAAT
59809 GTTCATAATGAGAAGAAATT
1 GTTCATAATGAGAAGAAA-T
59829 GTTCA
1 GTTCA
59834 ACCTTAGCTC
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
17 6 0.18
18 6 0.18
19 3 0.09
20 8 0.24
21 5 0.15
22 6 0.18
ACGTcount: A:0.42, C:0.09, G:0.23, T:0.25
Consensus pattern (19 bp):
GTTCATAATGAGAAGAAAT
Found at i:59861 original size:117 final size:118
Alignment explanation
Indices: 59622--59862 Score: 324
Period size: 117 Copynumber: 2.1 Consensus size: 118
59612 TCCATTATAG
* * * *
59622 AAGGAGGTGGATCATCATTTCCAATGGAGGGGTTTATAATGAGAAGAACTCGTCCGATGAGGGAG
1 AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
* * * * * *
59687 AAGAAGTTCATAATGAGATGAACTTGTTCAACTTTTGTTCGAATACATCACAA
66 AAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTAGCTCGAATACAACACAA
* *
59740 AAGGAGGTGGATCAAT-ATTTCCAGTGGA-GAGTTCATAATGAGAAGAACTCATTCGATAAGGGA
1 AAGGAGGTGGATC-ATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGA
* * *
59803 GAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTAGCTCGATTCCAACACAT
65 GAAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTAGCTCGAATACAACACAA
59857 AAGGAG
1 AAGGAG
59863 TTAGAATAGC
Statistics
Matches: 107, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
117 81 0.76
118 24 0.22
119 2 0.02
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (118 bp):
AAGGAGGTGGATCATCATTTCCAATGGAGGAGTTCATAATGAGAAGAACTCATCCGATAAGGGAG
AAGAAGTTCATAATGAGAAGAAATTGTTCAACCTTAGCTCGAATACAACACAA
Found at i:60326 original size:117 final size:118
Alignment explanation
Indices: 60049--60668 Score: 629
Period size: 117 Copynumber: 5.3 Consensus size: 118
60039 TCATCACTTC
* * * * *
60049 GTTCGAATCCATCACAGGAGGATG-TGGATCAA-AATTTCTAATGGGAGAGTTCATAATGAGAAG
1 GTTCGATTCCATCACAAGAGGA-GATGGATCAACATTTTC-AATGGAAGGGTTCATAATGAGAAG
* *
60112 AACTCATCCGAAGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
64 AACTCATCTGAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * * ** * *
60167 GTTCAAATCCATCA-TAGAATAAGGTGTATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGA
1 GTTCGATTCCATCACAAG-AGGAGATGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGA
* * *
60231 ACTAAT-TGAATGTGGGAGAAGAAGTTTATAATGA-AAGAACTTGTTCAACCTTT
65 ACTCATCTGAA-GAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
** *
60284 GTTCGATTCCATCACCGGAGTAGATGGAAT-AACATTTTCAATGGAAGGGTTCATAATGAGAAGA
1 GTTCGATTCCATCACAAGAGGAGATGG-ATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGA
* * *
60348 AC-CATCTGAAGAGGGAGAAAAACGTTAATAATGAGAAGAAC-TGTTTAACCTTT
65 ACTCATCTGAAGAGGGAGAAGAA-GTTCATAATGAGAAGAACTTGTTCAACCTTT
* * * * * * * * * *
60401 ATTTGATTCAATCACAGGAGGAGGTAGATCAACA-TTCCAATGGGAGAGTTCATAATGTA-TAGA
1 GTTCGATTCCATCACAAGAGGAGATGGATCAACATTTTCAATGGAAGGGTTCATAATG-AGAAGA
* * **
60464 ACTCATCCGACGAGGGAGAAGAAGGACATAATGAGAAGAACTTGTTCAACCTTT
65 ACTCATCTGAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
* * * *
60518 GTTCGAATCCATCACAAAAGGCGGTGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
1 GTTCGATTCCATCACAAGAGGAGATGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
* * *
60583 CTTAT-TCAATGAGGGAGAAGAAGTTCATAAT-ATGAAGAACTTGTTCAACCTTA
66 CTCATCTGAA-GAGGGAGAAGAAGTTCATAATGA-GAAGAACTTGTTCAACCTTT
* *
60636 GCTT-GATTCCATCACATA-AGGAGTTGGAACAAC
1 G-TTCGATTCCATCACA-AGAGGAGATGGATCAAC
60669 TCTGACCTTG
Statistics
Matches: 415, Mismatches: 68, Indels: 38
0.80 0.13 0.07
Matches are distributed among these distances:
116 54 0.13
117 184 0.44
118 169 0.41
119 8 0.02
ACGTcount: A:0.37, C:0.14, G:0.23, T:0.26
Consensus pattern (118 bp):
GTTCGATTCCATCACAAGAGGAGATGGATCAACATTTTCAATGGAAGGGTTCATAATGAGAAGAA
CTCATCTGAAGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
Found at i:60836 original size:40 final size:40
Alignment explanation
Indices: 60643--60854 Score: 187
Period size: 40 Copynumber: 5.2 Consensus size: 40
60633 TTAGCTTGAT
* *
60643 TCCATCACATAAGGAGTTGGAACAAC-TCTGACCTTGGCACA
1 TCCATCACATAAGGAGTTGGATCAACATC--ACCTTGGCTCA
* * * * *
60684 TCCATCGCATAAGGAGTTGGATCATCATCATCATT-TCTATCG
1 TCCATCACATAAGGAGTTGGATCAACATCA-CCTTGGC--TCA
** * * ** *
60726 TCCATCACATAAGGAGTTTAATCAACATTATCATTTTCCCA
1 TCCATCACATAAGGAGTTGGATCAACATCA-CCTTGGCTCA
*
60767 TCCAT-ACATAAGAAGTTGGATCAACATCACCTTGGCTCA
1 TCCATCACATAAGGAGTTGGATCAACATCACCTTGGCTCA
* *
60806 TCCATCACATAAGGAGTTGGATCAGCATCACCTTGGGTCA
1 TCCATCACATAAGGAGTTGGATCAACATCACCTTGGCTCA
*
60846 ACCATCACA
1 TCCATCACA
60855 ATGGGAGTAG
Statistics
Matches: 139, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
39 11 0.08
40 61 0.44
41 32 0.23
42 33 0.24
43 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (40 bp):
TCCATCACATAAGGAGTTGGATCAACATCACCTTGGCTCA
Found at i:61243 original size:12 final size:12
Alignment explanation
Indices: 61226--61269 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
61216 AACCGAACTT
61226 AAACCAAGACCC
1 AAACCAAGACCC
61238 AAACCAAGACCC
1 AAACCAAGACCC
* *
61250 AAACCCAGGCCC
1 AAACCAAGACCC
61262 AAAACCAA
1 -AAACCAA
61270 ATCCCTAGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.50, C:0.41, G:0.09, T:0.00
Consensus pattern (12 bp):
AAACCAAGACCC
Done.