Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001389.1 Hibiscus syriacus cultivar Beakdansim tig00002710_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: 67953
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:7032 original size:59 final size:59
Alignment explanation
Indices: 6940--7058 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
6930 CACTGCCATC
6940 TATCTCAGACAGATTGACAACCTTAATACGTTATCTAGATCTTGGAGGACATGGTTAGG
1 TATCTCAGACAGATTGACAACCTTAATACGTTATCTAGATCTTGGAGGACATGGTTAGG
6999 TATCTCAGACAGATTGACAACCTTAATACGTTATCTAGATCTTGGAGGACATGGTTAGG
1 TATCTCAGACAGATTGACAACCTTAATACGTTATCTAGATCTTGGAGGACATGGTTAGG
7058 T
1 T
7059 GCACCATCTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (59 bp):
TATCTCAGACAGATTGACAACCTTAATACGTTATCTAGATCTTGGAGGACATGGTTAGG
Found at i:7034 original size:31 final size:31
Alignment explanation
Indices: 6940--7034 Score: 74
Period size: 31 Copynumber: 3.2 Consensus size: 31
6930 CACTGCCATC
6940 TATCTCAGACAGATTGACAACCTTAATACGT
1 TATCTCAGACAGATTGACAACCTTAATACGT
** * *** *
6971 TATCT-AGATC---TTGGAGGACATGGTTA-GG
1 TATCTCAGA-CAGATT-GACAACCTTAATACGT
6999 TATCTCAGACAGATTGACAACCTTAATACGT
1 TATCTCAGACAGATTGACAACCTTAATACGT
7030 TATCT
1 TATCT
7035 AGATCTTGGA
Statistics
Matches: 43, Mismatches: 14, Indels: 14
0.61 0.20 0.20
Matches are distributed among these distances:
28 9 0.21
29 10 0.23
30 10 0.23
31 14 0.33
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (31 bp):
TATCTCAGACAGATTGACAACCTTAATACGT
Found at i:21306 original size:2 final size:2
Alignment explanation
Indices: 21299--21328 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21289 TCAACCAAAG
21299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21329 TAATCTAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26320 original size:2 final size:2
Alignment explanation
Indices: 26313--26339 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26303 TTCAATATCC
26313 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 A
26340 CAAGTCAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:32541 original size:2 final size:2
Alignment explanation
Indices: 32536--32636 Score: 202
Period size: 2 Copynumber: 50.5 Consensus size: 2
32526 GGAAGAAAAA
32536 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
32578 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
32620 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
32637 AGGGTATTCA
Statistics
Matches: 99, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 99 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37950 original size:10 final size:10
Alignment explanation
Indices: 37929--37973 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
37919 CGTCTGTTTT
*
37929 TCTGTTGTTC
1 TCTGTTGCTC
*
37939 TCCGTTGCTC
1 TCTGTTGCTC
* *
37949 TCTGTGGCTG
1 TCTGTTGCTC
37959 TCTGTTGCTC
1 TCTGTTGCTC
37969 TCTGT
1 TCTGT
37974 CCTTCTGGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.00, C:0.27, G:0.24, T:0.49
Consensus pattern (10 bp):
TCTGTTGCTC
Found at i:38437 original size:3 final size:3
Alignment explanation
Indices: 38429--38532 Score: 154
Period size: 3 Copynumber: 34.0 Consensus size: 3
38419 TTATTTATTA
* *
38429 AAT AAT AAT AAT ATAT ATT AAT AAT AAT AAT AAAT ACT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
* *
38476 AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38524 AAT AAT AAT
1 AAT AAT AAT
38533 TTTAAATGAA
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
3 85 0.93
4 6 0.07
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:38816 original size:76 final size:76
Alignment explanation
Indices: 38657--39298 Score: 1153
Period size: 76 Copynumber: 8.5 Consensus size: 76
38647 GATGGAAATG
* * * *
38657 TTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
38722 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
38734 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38799 CCCGAAGGCTT
66 CCCGAAGGCTT
38810 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38874 CCCGAAGGCTT
66 CCCGAAGGCTT
*
38885 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38950 CCCGAAGGCTT
66 CCCGAAGGCTT
38961 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39026 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
39037 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39102 CCCGAAGGCTT
66 CCCGAAGGCTT
* * *
39113 TTTAGAAACATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39177 CCCGAAGGCTT
66 CCCGAAGGCTT
39188 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39253 CCCGAAGGCTT
66 CCCGAAGGCTT
39264 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
39299 TAAGAAATAG
Statistics
Matches: 549, Mismatches: 14, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
75 147 0.27
76 360 0.66
77 42 0.08
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:38938 original size:151 final size:152
Alignment explanation
Indices: 38657--39298 Score: 1153
Period size: 151 Copynumber: 4.2 Consensus size: 152
38647 GATGGAAATG
* * * *
38657 TTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
*
38722 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
38787 CATCAAAAAGCTCCCGAAGGCTT
130 CATCAAAAAGCTCCCGAAGGCTT
38810 TTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
38874 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
38939 ATTAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
38961 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
* *
39026 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
39091 ATTAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
* * *
39113 TTTAGAAACATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39177 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
39242 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
39264 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
39299 TAAGAAATAG
Statistics
Matches: 472, Mismatches: 16, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
151 285 0.60
152 154 0.33
153 33 0.07
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (152 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTT
Found at i:39058 original size:227 final size:228
Alignment explanation
Indices: 38657--39298 Score: 1171
Period size: 227 Copynumber: 2.8 Consensus size: 228
38647 GATGGAAATG
* *
38657 TTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCAAAAAGC
*
38722 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
38787 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGA-CCGAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
38851 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
195 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
* * *
38885 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATTAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
38950 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
39015 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
* *
39080 GTTTTGAAAACATTAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
39113 TTTAGAAACATCATGCACTGAAGGGCTTACAGATGA-CCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
39177 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
39242 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
39299 TAAGAAATAG
Statistics
Matches: 399, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
227 287 0.72
228 112 0.28
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.22
Consensus pattern (228 bp):
TTTGGAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:39997 original size:21 final size:22
Alignment explanation
Indices: 39964--40042 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
39954 CATAAAGCTT
* *
39964 TCATTTTTGAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
* * *
39986 TCATCTTTAAAAAGAAAATTTG
1 TCATCTTTAAAAAGAGAATCTA
* **
40008 TCATC-TTGAAGTGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
*
40029 TTATCTTTAAAAAG
1 TCATCTTTAAAAAG
40043 TGCAGATGTA
Statistics
Matches: 41, Mismatches: 15, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
21 14 0.34
22 27 0.66
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.37
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:42776 original size:114 final size:112
Alignment explanation
Indices: 42576--42883 Score: 450
Period size: 114 Copynumber: 2.8 Consensus size: 112
42566 GATCATGCAG
* ** *
42576 TTCATTTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATTTTTCAAATCCAATGATTAGTTCTGGGGTT-CTACC-AACCAGATCAGATAACTCAAAGA
*
42641 ATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
64 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
42690 TTCATTTTTCAAATCCAATGATTAGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATTTTTCAAATCCAATGATTAGTTCTGGGGTTC-TACC-AACCAGATCAGATAACTCAAAGA
*
42755 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
64 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
*
42804 TTCATCTTTCAAATCCAATGATTAGATTCT---G---T-CCAACCAGATCAGATAACTCAAAGAA
1 TTCATTTTTCAAATCCAATGATTAG-TTCTGGGGTTCTACCAACCAGATCAGATAACTCAAAGAA
42862 CACTTCCAGAAGATGCTATTGG
65 CACTTCCAGAAGATGCTATTGG
42884 CAAATTACAT
Statistics
Matches: 182, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
106 46 0.25
107 2 0.01
108 1 0.01
112 1 0.01
113 1 0.01
114 128 0.70
115 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (112 bp):
TTCATTTTTCAAATCCAATGATTAGTTCTGGGGTTCTACCAACCAGATCAGATAACTCAAAGAAC
ACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:49812 original size:13 final size:15
Alignment explanation
Indices: 49790--49826 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
49780 TTTGACAGAA
49790 AAAT-AAATAC-TG-
1 AAATAAAATACTTGC
49802 AAATAAAATACTTGC
1 AAATAAAATACTTGC
49817 AAATAAAATA
1 AAATAAAATA
49827 AAACATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.18
13 6 0.27
14 2 0.09
15 10 0.45
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.24
Consensus pattern (15 bp):
AAATAAAATACTTGC
Found at i:51703 original size:10 final size:10
Alignment explanation
Indices: 51682--51726 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
51672 CGTCTGTTTT
*
51682 TCTGTTGTTC
1 TCTGTTGCTC
*
51692 TCCGTTGCTC
1 TCTGTTGCTC
* *
51702 TCTGTGGCTG
1 TCTGTTGCTC
51712 TCTGTTGCTC
1 TCTGTTGCTC
51722 TCTGT
1 TCTGT
51727 CCTTCTGGTT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.00, C:0.27, G:0.24, T:0.49
Consensus pattern (10 bp):
TCTGTTGCTC
Found at i:52187 original size:3 final size:3
Alignment explanation
Indices: 52179--52285 Score: 169
Period size: 3 Copynumber: 35.0 Consensus size: 3
52169 TTATTTATTA
* *
52179 AAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAAT ACT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
*
52226 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52274 AAT AAT AAT AAT
1 AAT AAT AAT AAT
52286 TTTAAATGAA
Statistics
Matches: 96, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
3 90 0.94
4 6 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:53270 original size:60 final size:60
Alignment explanation
Indices: 53196--53553 Score: 536
Period size: 60 Copynumber: 6.0 Consensus size: 60
53186 ATCTGTTCTG
* * *
53196 ATCTTCCATATTGGAGTCCTAGATCTTAGTGGTCTAGGATAAGTCTTTATGGATGCCTGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCTGT
* * * * *
53256 GTCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGCTAAGTCCATATAGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCTGT
* * *
53316 ATCTTCCATATTGGATTCCTATATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCTAT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCTGT
** *
53376 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGATTAT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCTGT
* * * *
53436 ATCTTCCATATTAGACTCCTAGATCTTAGTGATCTAGGGTAAGTCTTTATGGATGCATGT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCTGT
* *
53496 ATCTTCCATATTGGACTCATAGATCTTAGTGATCTAGGGTAAGTCCTTATGGATGCCT
1 ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCT
53554 ATTCTGGGGT
Statistics
Matches: 269, Mismatches: 29, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 269 1.00
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (60 bp):
ATCTTCCATATTGGACTCCTAGATCTTAGTGGTCTAGGGTAAGTCCTTATGGATGCCTGT
Found at i:56754 original size:27 final size:27
Alignment explanation
Indices: 56698--56753 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
56688 CTCGCATAAG
* *
56698 AAATTACAAAAATACCCTTATGGGGTA
1 AAATTACAAAAATACCATTATGCGGTA
*
56725 AAATTACAAAAATA-CATTATGCTGTA
1 AAATTACAAAAATACCATTATGCGGTA
56751 AAA
1 AAA
56754 AGACCAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.50, C:0.12, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACAAAAATACCATTATGCGGTA
Found at i:59507 original size:18 final size:16
Alignment explanation
Indices: 59471--59501 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59461 ATGTGCTTTG
59471 ATATATAAGTATTTTA
1 ATATATAAGTATTTTA
59487 ATATATAAGTATTTT
1 ATATATAAGTATTTT
59502 TTAATAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATATAAGTATTTTA
Found at i:61950 original size:2 final size:2
Alignment explanation
Indices: 61943--61975 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
61933 TTTTTCGTTG
61943 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 A
61976 ATCCTTCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62766 original size:434 final size:427
Alignment explanation
Indices: 61959--62835 Score: 1488
Period size: 434 Copynumber: 2.0 Consensus size: 427
61949 ATATATATAT
* *
61959 ATATATATATATATATAATCCTTCAAATACGATACACGTGGTGATGACGAAATGGGTGATGGAAT
1 ATATATATATATATATAA-CCTTAAAATACGATACACGTGGTGATGACGAAATGAGTGATGGAAT
62024 GTTAGAGTAAGAATGCAATACTGCAGAGAATTGAGTTTGACCATGAACGATATTAAAAATTTTAT
65 GTTAGAGTAAGAATGCAATACTGCAGAGAATTGAGTTTGACCATGAACGATATTAAAAATTTTAT
62089 ACTTGGCAAAGATGAAAAAAAAATTGTGTGGGGAATAATTCTTAAATATAAAAGTTACAAATAAT
130 ACTTGGCAAAGATGAAAAAAAAATTGTGTGGGGAATAATTCTTAAATATAAAAGTTACAAATAAT
* * *
62154 TACTGTTGATCAAGTTTATGTTCACTTTCAAATATGCATATGAATTTTTATTGGTTAGCTTTTCA
195 TACTGTTGATCAAGTTTATATTCAATTTCAAATATGCATATGAATTTTTATTGGTTAGATTTTCA
*
62219 ATTTATTATTCAAATAAAATATTATAAAATTTCAATTAGAGTTGATCTGATAATATCAACTTTTT
260 ATTTATTATTCAAATAAAAAATTATAAAATTTCAATTAGAGTTGATCTGATAATATCAACTTTTT
* *
62284 TTAAGATAAAATAAGTTTGAATCACATTCGATTATGTAAAATTGTGGTCAAATTAGGTTCATGTT
325 TAAAGATAAAATAAGTTTGAATCACATTCGATTATGTAAAAGTGTGGTCAAATTAGGTTCATGTT
*
62349 TAGGAAGAAAAATTTCTGACTGGACTTAGCTTAGAATA
390 TAGGAAGAAAAATTTCTGACTCGACTTAGCTTAGAATA
62387 ATATATATATATATAT-ACACTTAAAATACGATACACGTGGTGATGACGAAATGAGTGATGGAAT
1 ATATATATATATATATAAC-CTTAAAATACGATACACGTGGTGATGACGAAATGAGTGATGGAAT
* *
62451 GTTAGAGTAAGAATGCAATACTGCGGATAATTGAGTTTGACCATGAACGATATTAAAAATTTTAT
65 GTTAGAGTAAGAATGCAATACTGCAGAGAATTGAGTTTGACCATGAACGATATTAAAAATTTTAT
62516 ACTTGGCAAAGATGAAAAAAATATAATTTTTTGTGTGGGGAATAATTCTTAAATATAAAAGTTAC
130 ACTTGGCAAAGATG-AAAAAA-A-AA----TTGTGTGGGGAATAATTCTTAAATATAAAAGTTAC
*
62581 AAATAATTACTGTTGATTAAGTTTATATTCAATTTCAAATATGCATATGAATTTTTATTGGTTAG
188 AAATAATTACTGTTGATCAAGTTTATATTCAATTTCAAATATGCATATGAATTTTTATTGGTTAG
* *
62646 ATTTTTAATTTATTATTCAAATAAAAAATTATAAAATTTTAATTAGAGTTGATCTGATAATATCA
253 ATTTTCAATTTATTATTCAAATAAAAAATTATAAAATTTCAATTAGAGTTGATCTGATAATATCA
* *
62711 ACTTTTTTAAAGA-AAAGTTGAGTTTGAATCACATTCGATTATGTAAAAGTGTGGTCAAATTAGG
318 ACTTTTTTAAAGATAAA-ATAAGTTTGAATCACATTCGATTATGTAAAAGTGTGGTCAAATTAGG
* *
62775 TTCATGTTTAGGATGAAAAATTTCTGACTCGACTTGGCTTAGAATA
382 TTCATGTTTAGGAAGAAAAATTTCTGACTCGACTTAGCTTAGAATA
62821 ATATATATATATATA
1 ATATATATATATATA
62836 GATAATTTTT
Statistics
Matches: 422, Mismatches: 18, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
426 1 0.00
427 121 0.29
428 22 0.05
429 1 0.00
430 2 0.00
433 3 0.01
434 272 0.64
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (427 bp):
ATATATATATATATATAACCTTAAAATACGATACACGTGGTGATGACGAAATGAGTGATGGAATG
TTAGAGTAAGAATGCAATACTGCAGAGAATTGAGTTTGACCATGAACGATATTAAAAATTTTATA
CTTGGCAAAGATGAAAAAAAAATTGTGTGGGGAATAATTCTTAAATATAAAAGTTACAAATAATT
ACTGTTGATCAAGTTTATATTCAATTTCAAATATGCATATGAATTTTTATTGGTTAGATTTTCAA
TTTATTATTCAAATAAAAAATTATAAAATTTCAATTAGAGTTGATCTGATAATATCAACTTTTTT
AAAGATAAAATAAGTTTGAATCACATTCGATTATGTAAAAGTGTGGTCAAATTAGGTTCATGTTT
AGGAAGAAAAATTTCTGACTCGACTTAGCTTAGAATA
Found at i:65502 original size:3 final size:3
Alignment explanation
Indices: 65494--65542 Score: 55
Period size: 3 Copynumber: 16.3 Consensus size: 3
65484 TTTATATGTA
* * *
65494 AAT AAT AAT AAA AAT AAT ATTT TAT AAT AAT AAT AAT -AT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
65539 AAT A
1 AAT A
65543 TTTAATAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.92
4 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:66010 original size:41 final size:40
Alignment explanation
Indices: 65937--66015 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
65927 CTGATGGTGA
* *
65937 TCCAACTCCTTATAAGTGGATAAGCTAAGGTCGGTGTTGT
1 TCCAACTCCTTATAAGTGGATAAGCCAAGGTCGATGTTGT
** *
65977 TCCAACTCCTTATGTGATGGATGAGCCAAGGTCGATGTT
1 TCCAACTCCTTATAAG-TGGATAAGCCAAGGTCGATGTT
66016 CTTCTCATTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 14 0.42
41 19 0.58
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (40 bp):
TCCAACTCCTTATAAGTGGATAAGCCAAGGTCGATGTTGT
Found at i:67361 original size:8 final size:8
Alignment explanation
Indices: 67344--67400 Score: 68
Period size: 8 Copynumber: 7.5 Consensus size: 8
67334 TGAACCCTCA
67344 TTTTCAATT
1 TTTTC-ATT
67353 TTTTCA--
1 TTTTCATT
67359 TTTTCATT
1 TTTTCATT
67367 TTTT-ATT
1 TTTTCATT
*
67374 TTTTTATT
1 TTTTCATT
67382 TTTTCA-T
1 TTTTCATT
67389 TTTTCATT
1 TTTTCATT
67397 TTTT
1 TTTT
67401 TATTCTCTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
6 6 0.14
7 14 0.33
8 18 0.42
9 5 0.12
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:67361 original size:15 final size:15
Alignment explanation
Indices: 67344--67400 Score: 73
Period size: 15 Copynumber: 3.8 Consensus size: 15
67334 TGAACCCTCA
67344 TTTTCAATTTTTTCA-
1 TTTTC-ATTTTTTCAT
67359 TTTTCATTTTTT-ATT
1 TTTTCATTTTTTCA-T
*
67374 TTTTTATTTTTTCAT
1 TTTTCATTTTTTCAT
67389 TTTTCATTTTTT
1 TTTTCATTTTTT
67401 TATTCTCTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
13 1 0.03
14 7 0.19
15 28 0.76
16 1 0.03
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCATTTTTTCAT
Found at i:67362 original size:7 final size:7
Alignment explanation
Indices: 67352--67399 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
67342 CATTTTCAAT
67352 TTTTTCA
1 TTTTTCA
67359 -TTTTCA
1 TTTTTCA
*
67365 TTTTTTA
1 TTTTTCA
*
67372 TTTTTTTA
1 -TTTTTCA
67380 TTTTTTCA
1 -TTTTTCA
67388 TTTTTCA
1 TTTTTCA
67395 TTTTT
1 TTTTT
67400 TTATTCTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 6 0.16
7 17 0.46
8 14 0.38
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.79
Consensus pattern (7 bp):
TTTTTCA
Found at i:67377 original size:23 final size:23
Alignment explanation
Indices: 67344--67403 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
67334 TGAACCCTCA
* *
67344 TTTTCAATTTTTT-CATTTTCAT
1 TTTTCATTTTTTTATATTTTCAT
* *
67366 TTTTTATTTTTTTATTTTTTCAT
1 TTTTCATTTTTTTATATTTTCAT
67389 TTTTCATTTTTTTAT
1 TTTTCATTTTTTTAT
67404 TCTCTTTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 11 0.34
23 21 0.66
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCATTTTTTTATATTTTCAT
Found at i:67404 original size:23 final size:23
Alignment explanation
Indices: 67359--67404 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
67349 AATTTTTTCA
*
67359 TTTTCATTTTTTATTTTTTTATT
1 TTTTCATTTTTCATTTTTTTATT
67382 TTTTCATTTTTCATTTTTTTATT
1 TTTTCATTTTTCATTTTTTTATT
67405 CTCTTTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTCATTTTTCATTTTTTTATT
Found at i:67414 original size:23 final size:20
Alignment explanation
Indices: 67350--67414 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 20
67340 CTCATTTTCA
* *
67350 ATTTTTTCATTTTCATTTTTT
1 ATTTTTTTATTTT-TTTTTTT
67371 ATTTTTTTATTTTTTCATTTTT
1 ATTTTTTTATTTTTT--TTTTT
*
67393 CATTTTTTTATTCTCTTTTTTT
1 -ATTTTTTTATT-TTTTTTTTT
67415 CTAAGCATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
20 1 0.03
21 12 0.32
22 10 0.27
23 11 0.30
24 3 0.08
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (20 bp):
ATTTTTTTATTTTTTTTTTT
Done.