Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003244.1 Hibiscus syriacus cultivar Beakdansim tig00006821_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: 84644
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:9111 original size:19 final size:20
Alignment explanation
Indices: 9085--9132 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
9075 TATATATTTT
* *
9085 TAAAATTTGACACCCCAAAA
1 TAAATTTTGACACCACAAAA
9105 TAAATTTTTGACACCACAAAA
1 TAAA-TTTTGACACCACAAAA
9126 T-AATTTT
1 TAAATTTT
9133 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 4 0.16
20 6 0.24
21 15 0.60
ACGTcount: A:0.46, C:0.19, G:0.04, T:0.31
Consensus pattern (20 bp):
TAAATTTTGACACCACAAAA
Found at i:9132 original size:20 final size:21
Alignment explanation
Indices: 9090--9134 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
9080 ATTTTTAAAA
*
9090 TTTGACACCCCAAAATAAATT
1 TTTGACACCACAAAATAAATT
*
9111 TTTGACACCACAAAATAATTT
1 TTTGACACCACAAAATAAATT
9132 TTT
1 TTT
9135 TTAAATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.36
Consensus pattern (21 bp):
TTTGACACCACAAAATAAATT
Found at i:15381 original size:2 final size:2
Alignment explanation
Indices: 15376--15409 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15366 AATAATGTAC
15376 AT AT 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 AT AT
15410 TTCTTCTTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18036 original size:17 final size:18
Alignment explanation
Indices: 18014--18051 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
18004 TTTTCTTTTT
18014 GGTAAAATTAATTT-AAG
1 GGTAAAATTAATTTAAAG
18031 GGTAAAATTAATTTAAAG
1 GGTAAAATTAATTTAAAG
18049 GGT
1 GGT
18052 TAACTACATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (18 bp):
GGTAAAATTAATTTAAAG
Found at i:21259 original size:20 final size:20
Alignment explanation
Indices: 21234--21290 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
21224 TTTTCCGACT
21234 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
21254 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
21274 ATCGCAATGCGAGTATG
1 ATCGCAATGCGAATATG
21291 ACTATCGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:21297 original size:20 final size:20
Alignment explanation
Indices: 21274--21387 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
21264 GAATATGTAA
* *
21274 ATCGCAATGCGAGTATGACT
1 ATCGCAATGCGATTCTGACT
* *
21294 ATCGCAACGCGATTCTGACC
1 ATCGCAATGCGATTCTGACT
* *
21314 ATCGCAACGAGATTCTGACT
1 ATCGCAATGCGATTCTGACT
21334 ATCGCAACT-CGATTCTGACT
1 ATCGCAA-TGCGATTCTGACT
* * * *
21354 GTCGCAACGTGATGCTGACT
1 ATCGCAATGCGATTCTGACT
21374 ATCGCAATGCGATT
1 ATCGCAATGCGATT
21388 TTCAAAGCGT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGATTCTGACT
Found at i:21318 original size:40 final size:39
Alignment explanation
Indices: 21289--21387 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 39
21279 AATGCGAGTA
21289 TGACTATCGCAACGCGATTCTGACCATCGCAACGAGATTC
1 TGACTATCGCAACGCGATTCTGACCATCGCAACGAGA-TC
* ** *
21329 TGACTATCGCAACTCGATTCTGACTGTCGCAACGTGATGC
1 TGACTATCGCAACGCGATTCTGACCATCGCAACGAGAT-C
*
21369 TGACTATCGCAATGCGATT
1 TGACTATCGCAACGCGATT
21388 TTCAAAGCGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 1 0.02
40 51 0.98
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.26
Consensus pattern (39 bp):
TGACTATCGCAACGCGATTCTGACCATCGCAACGAGATC
Found at i:21587 original size:22 final size:22
Alignment explanation
Indices: 21562--21604 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
21552 GGCGACATCC
21562 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
21584 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
21605 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:22055 original size:20 final size:20
Alignment explanation
Indices: 21981--22055 Score: 64
Period size: 20 Copynumber: 3.8 Consensus size: 20
21971 AGAATCGCAA
21981 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTAAGTTTCGCGT
* * *
22000 TGCGATAGTCAA-ATTCGCGT
1 TGCGAT-TTTAAGTTTCGCGT
* * * *
22020 TGTGATTTTCATTTTCGTGT
1 TGCGATTTTAAGTTTCGCGT
22040 TGCGATTTTAAGTTTC
1 TGCGATTTTAAGTTTC
22056 AGAAACTATT
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
19 8 0.20
20 32 0.78
21 1 0.02
ACGTcount: A:0.16, C:0.15, G:0.23, T:0.47
Consensus pattern (20 bp):
TGCGATTTTAAGTTTCGCGT
Found at i:23532 original size:24 final size:24
Alignment explanation
Indices: 23498--23553 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
23488 CTGAAACATC
*
23498 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAATTCCGAGTATTGACCAAG
*
23522 ATCAAATTCCGGGTATTGACCAAG
1 ATCAAATTCCGAGTATTGACCAAG
23546 ATCAAATT
1 ATCAAATT
23554 TCGAATACCG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCGAGTATTGACCAAG
Found at i:24408 original size:20 final size:20
Alignment explanation
Indices: 24372--24477 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
24362 AAAATTTAGT
24372 GTTGCGACAGT-AGAATCGC
1 GTTGCGACAGTCAGAATCGC
24391 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
24411 GTTGCGACAGTTAGAATCGC
1 GTTGCGACAGTCAGAATCGC
*
24431 GTTGCGATAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
* * * *
24451 ATTGCGATAGGCATAATCGC
1 GTTGCGACAGTCAGAATCGC
*
24471 ATTGCGA
1 GTTGCGA
24478 TTTACATATT
Statistics
Matches: 80, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
19 11 0.14
20 69 0.86
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.24
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:24478 original size:20 final size:20
Alignment explanation
Indices: 24425--24520 Score: 93
Period size: 20 Copynumber: 4.8 Consensus size: 20
24415 CGACAGTTAG
* * *
24425 AATCGCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGACAT
*
24445 AATCGCATTGCGATAGGCAT
1 AATCGCATTGCGATAGACAT
**
24465 AATCGCATTGCGATTTACAT
1 AATCGCATTGCGATAGACAT
* **
24485 ATTCGCATTGCGATTTACAT
1 AATCGCATTGCGATAGACAT
* *
24505 ATTTGCATTGCGATAG
1 AATCGCATTGCGATAG
24521 TCGGAAAATC
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (20 bp):
AATCGCATTGCGATAGACAT
Found at i:30841 original size:34 final size:34
Alignment explanation
Indices: 30796--30863 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
30786 CTGCCTGAAT
*
30796 GAGCTGCAATGCAATCTTATCGTGATGAAGCGAA
1 GAGCTGAAATGCAATCTTATCGTGATGAAGCGAA
*
30830 GAGCTGAAATGCAATCTTGTCGTGATGAAGCGAA
1 GAGCTGAAATGCAATCTTATCGTGATGAAGCGAA
30864 CTTGGGCGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (34 bp):
GAGCTGAAATGCAATCTTATCGTGATGAAGCGAA
Found at i:31681 original size:36 final size:35
Alignment explanation
Indices: 31599--31682 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 35
31589 TGGCTAGTTC
* *
31599 TCAAGGTCGGATGGAGGGTGTATATTTTTAGTGAA
1 TCAAGGTCGGATGGAGGGTGTATATTTTGAGTCAA
** *
31634 TCTAAACTCGGATGGAGGGTGTATATTTTCGGGTCAA
1 TC-AAGGTCGGATGGAGGGTGTATATTTT-GAGTCAA
31671 GTC-AGGTCGGAT
1 -TCAAGGTCGGAT
31683 TGACTAAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
35 2 0.05
36 31 0.79
37 4 0.10
38 2 0.05
ACGTcount: A:0.24, C:0.11, G:0.33, T:0.32
Consensus pattern (35 bp):
TCAAGGTCGGATGGAGGGTGTATATTTTGAGTCAA
Found at i:32964 original size:184 final size:182
Alignment explanation
Indices: 32642--33027 Score: 616
Period size: 185 Copynumber: 2.1 Consensus size: 182
32632 ATTAAATTTT
* *
32642 AAATATTAAATATATTATATATAACATATGGCTCAACCCAAACTATTTAAAACTCAATTAATAAT
1 AAATATTAAATATATTATATATAACATATGGCTCAACCCAAACCATTTAAAACCCAATTAATAAT
* * * **
32707 TTAAGATCTAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAATTTTATATAATTTTTT
66 TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATATTATATAAAATTTT
*
32772 TATTTTATAATTATATATTATTTAAATTAATTGTAACATGTTTTTTT-AATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTAT-A-AT-TTTTTTTGAATTAAA
*
32826 AAATATTAAATATATTATATATAACATATGGGCTCATCCCAAACCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATAT-GGCTCAACCCAAACCATTTAAAACCCAATTAATAA
32891 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAA-ATTATATAAAATTT
65 TTTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATATTATATAAAATTT
32955 TTATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTTGAATTAAA
130 TTATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTTGAATTAAA
* *
33008 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
33028 AATTAGAAAA
Statistics
Matches: 189, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
181 15 0.08
182 19 0.10
183 1 0.01
184 74 0.39
185 80 0.42
ACGTcount: A:0.45, C:0.08, G:0.03, T:0.44
Consensus pattern (182 bp):
AAATATTAAATATATTATATATAACATATGGCTCAACCCAAACCATTTAAAACCCAATTAATAAT
TTAAGATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAATATTATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAATTTTTTTTGAATTAAA
Found at i:33042 original size:26 final size:25
Alignment explanation
Indices: 32984--33043 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
32974 TATTTAAATT
* * *
32984 AATTATAATTTTTTTTGAATTAAAA
1 AATTTTAATTTTTTATAAATTAAAA
*
33009 AATATTTAATTTTTATATAAATTAGAA
1 AAT-TTTAATTTTT-TATAAATTAAAA
33036 AATTTTAA
1 AATTTTAA
33044 AAAAAATCGG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 3 0.10
26 14 0.48
27 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
AATTTTAATTTTTTATAAATTAAAA
Found at i:36517 original size:60 final size:59
Alignment explanation
Indices: 36450--36621 Score: 272
Period size: 59 Copynumber: 2.9 Consensus size: 59
36440 ATAGTCGGGT
36450 GACCATTTTGTAACTTTTAATAGTCGGGGGACTCAACAAAGCAACATCCTATAATCCAAA
1 GACCATTTTGTAACTTTTAATAGTC-GGGGACTCAACAAAGCAACATCCTATAATCCAAA
* *
36510 GACCATTTTGTAACTTTTAATAGTCGGTGACTCAACAAAACAACATCCTATAATCCAAA
1 GACCATTTTGTAACTTTTAATAGTCGGGGACTCAACAAAGCAACATCCTATAATCCAAA
** * *
36569 GACCATTTTGTAACTTTTAATAGTTAAGGGACTCAATAAAGCAACGTCCTATA
1 GACCATTTTGTAACTTTTAATAG-TCGGGGACTCAACAAAGCAACATCCTATA
36622 GTCGAGGAGC
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
59 55 0.53
60 48 0.47
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.29
Consensus pattern (59 bp):
GACCATTTTGTAACTTTTAATAGTCGGGGACTCAACAAAGCAACATCCTATAATCCAAA
Found at i:37578 original size:59 final size:58
Alignment explanation
Indices: 37477--37594 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 58
37467 GACCATTTTA
* *
37477 TAACTTTTAATAGTCGAGGGACTCAACAAAGAAACACTCTATAGTCAGAGGATCATTTG
1 TAACTTTTAATAGTCAAGGGACTCAACAAAGAAACACCCTATAGTC-GAGGATCATTTG
* * * * * *
37536 TAACTTTTTATATTCAAGGGACTTAATAAAGCAATACCCTATAGTCGAGGATCATTTG
1 TAACTTTTAATAGTCAAGGGACTCAACAAAGAAACACCCTATAGTCGAGGATCATTTG
37594 T
1 T
37595 GTACTTCACC
Statistics
Matches: 51, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 13 0.25
59 38 0.75
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (58 bp):
TAACTTTTAATAGTCAAGGGACTCAACAAAGAAACACCCTATAGTCGAGGATCATTTG
Found at i:40107 original size:42 final size:42
Alignment explanation
Indices: 40061--40142 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
40051 TGTATCATCC
*
40061 ACCCGAATCCGA-TCTGACCCGAAAATT-TTTATCCTCCACTTG
1 ACCCGAAT-CGACTC-GACCCGAAAATTCTATATCCTCCACTTG
* * *
40103 ACCCGACTTGACTCGATCCGAAAATTCTATATCCTCCACT
1 ACCCGAATCGACTCGACCCGAAAATTCTATATCCTCCACT
40143 GTACTCCAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
41 13 0.38
42 21 0.62
ACGTcount: A:0.27, C:0.34, G:0.11, T:0.28
Consensus pattern (42 bp):
ACCCGAATCGACTCGACCCGAAAATTCTATATCCTCCACTTG
Found at i:44165 original size:78 final size:78
Alignment explanation
Indices: 44022--44165 Score: 191
Period size: 78 Copynumber: 1.8 Consensus size: 78
44012 CAAAAACCAA
* * * * * * *
44022 AAACTATAAACTACGACTTAGGGTTTATAGTTTAGGGTTTTAAATTAAGGGTATGATATAGAATG
1 AAACTATAAACCACAACATAGGGTTTATAATTTAGGATTTTAAATTAAGGATATGATATAAAATG
44087 AAACACATACCCT
66 AAACACATACCCT
* *
44100 AAACTATAAACCATAACATAGGGTTTATAATTTAGGATTTTAAATT-AGGAATATGGTATAAAAT
1 AAACTATAAACCACAACATAGGGTTTATAATTTAGGATTTTAAATTAAGG-ATATGATATAAAAT
44164 GA
65 GA
44166 TGCAATTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 3 0.05
78 53 0.95
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.33
Consensus pattern (78 bp):
AAACTATAAACCACAACATAGGGTTTATAATTTAGGATTTTAAATTAAGGATATGATATAAAATG
AAACACATACCCT
Found at i:45983 original size:25 final size:23
Alignment explanation
Indices: 45935--45995 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
45925 TATATAAAGT
45935 AATAATAAAAATAAATAAATATA
1 AATAATAAAAATAAATAAATATA
*
45958 ATTATAATAAAAATAAATAGGA-ATA
1 A--ATAATAAAAATAAATA-AATATA
45983 AATAATAAAAATA
1 AATAATAAAAATA
45996 GCAAAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 13 0.38
25 20 0.59
26 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (23 bp):
AATAATAAAAATAAATAAATATA
Found at i:47434 original size:105 final size:105
Alignment explanation
Indices: 47225--47895 Score: 1128
Period size: 105 Copynumber: 6.4 Consensus size: 105
47215 GTGCTGTTTT
* * **
47225 GAGTTCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGACA-TTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA-ATTTGAGAA-ACGTTTGTTGACA
** * *** *
47289 GTCAGCGGTCCCTTCGTGGTGAAGTTGAACTTGTACTGTCTT
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
47331 GAGTCCAAAATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGTTGGAGAAAGGTTTGGTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
*
47396 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
47436 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
47501 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
47541 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
47606 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
47646 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
*
47711 CAGCGGTCACTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
47751 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAATTTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
47816 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
47856 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
47896 GGTAAAACCT
Statistics
Matches: 537, Mismatches: 27, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
105 493 0.92
106 44 0.08
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAATTTGAGAAACGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:48737 original size:8 final size:8
Alignment explanation
Indices: 48724--48772 Score: 62
Period size: 8 Copynumber: 5.6 Consensus size: 8
48714 CGTTCTTCTC
48724 TTTTTGTT
1 TTTTTGTT
48732 TTTTTGTTTTT
1 TTTTTG---TT
48743 TTTTTGTT
1 TTTTTGTT
48751 TTTTTGTT
1 TTTTTGTT
48759 TTTTGTGTT
1 TTTT-TGTT
48768 TTTTT
1 TTTTT
48773 TCAACTTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
8 21 0.57
9 8 0.22
11 8 0.22
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (8 bp):
TTTTTGTT
Found at i:48746 original size:11 final size:11
Alignment explanation
Indices: 48730--48755 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
48720 TCTCTTTTTG
48730 TTTTTTTGTTT
1 TTTTTTTGTTT
48741 TTTTTTTGTTT
1 TTTTTTTGTTT
48752 TTTT
1 TTTT
48756 GTTTTTTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTGTTT
Found at i:48748 original size:19 final size:19
Alignment explanation
Indices: 48724--48762 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
48714 CGTTCTTCTC
48724 TTTTTGTTTTTTTGTTTTT
1 TTTTTGTTTTTTTGTTTTT
48743 TTTTTGTTTTTTTGTTTTT
1 TTTTTGTTTTTTTGTTTTT
48762 T
1 T
48763 GTGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (19 bp):
TTTTTGTTTTTTTGTTTTT
Found at i:48773 original size:19 final size:19
Alignment explanation
Indices: 48727--48772 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
48717 TCTTCTCTTT
*
48727 TTGTTTTTTTGTTTTTTTT
1 TTGTTTTTTTGTTTTTTTG
48746 TTGTTTTTTTG-TTTTTTG
1 TTGTTTTTTTGTTTTTTTG
48764 -TGTTTTTTT
1 TTGTTTTTTT
48773 TCAACTTAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 9 0.35
18 6 0.23
19 11 0.42
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (19 bp):
TTGTTTTTTTGTTTTTTTG
Found at i:58221 original size:10 final size:10
Alignment explanation
Indices: 58196--58229 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
58186 AAGGTTAGTA
*
58196 AAATAGAAAT
1 AAATAAAAAT
*
58206 AGATAAAAAT
1 AAATAAAAAT
58216 AAATAAAAAT
1 AAATAAAAAT
58226 AAAT
1 AAAT
58230 GGTAAATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:59519 original size:25 final size:23
Alignment explanation
Indices: 59471--59531 Score: 79
Period size: 25 Copynumber: 2.6 Consensus size: 23
59461 TATATAAAGT
59471 AATAATAAAAATAAATAAATATA
1 AATAATAAAAATAAATAAATATA
*
59494 ATTATAATAAAAATAAATAGGA-ATA
1 A--ATAATAAAAATAAATA-AATATA
59519 AATAATAAAAATA
1 AATAATAAAAATA
59532 GCAAAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
23 13 0.38
25 20 0.59
26 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.26
Consensus pattern (23 bp):
AATAATAAAAATAAATAAATATA
Found at i:75817 original size:102 final size:102
Alignment explanation
Indices: 75636--76027 Score: 511
Period size: 102 Copynumber: 3.8 Consensus size: 102
75626 CTGAACGAGC
* * * * * *
75636 GGAGGTGGTGGAAACACCAATGGAGTACTTGGTGCCAAGGATGGTAAATGTTCTTCGATAGAGAA
1 GGAGATGGTGGCAACACCAATGGAATACTTGGAGCCAAGGATGGTAAATGTTCTTCAATAGGGAA
* * *
75701 TGGTGGCGGAGCTGTATTTTGGGTTTGCACGGATTGA
66 TGGTAGCGGAGCTGTATTTTGGGTTTGCGCGGATGGA
* *
75738 GGAGATGGTGGCAACACCAATGGAGTACTTGGTGCCAAGGATGGTAAATGTTCTTCAATAGGGAA
1 GGAGATGGTGGCAACACCAATGGAATACTTGGAGCCAAGGATGGTAAATGTTCTTCAATAGGGAA
75803 TGGTAGCGGAGCTGTATTTT-GGTTTCGCGCGGATGGA
66 TGGTAGCGGAGCTGTATTTTGGGTTT-GCGCGGATGGA
* * *
75840 GGAGGTGGTGGCAACACCACTGGAATGCTTGGAGCCAAGGATGGTAAATGTTCTTCAATAGGGAA
1 GGAGATGGTGGCAACACCAATGGAATACTTGGAGCCAAGGATGGTAAATGTTCTTCAATAGGGAA
* * * * *
75905 TGGT-GACGGAGCTATATTTCGAGTTCGCGTGGATGGA
66 TGGTAG-CGGAGCTGTATTTTGGGTTTGCGCGGATGGA
* ** *
75942 GGAGATGGTGGCAACACTACCGGAATACTTGGAGCCAAGGATGGTAAATGTTCTTCAATAGGGAC
1 GGAGATGGTGGCAACACCAATGGAATACTTGGAGCCAAGGATGGTAAATGTTCTTCAATAGGGAA
**
76007 T-AAAGGCGGAGCTGTATTTTG
66 TGGTA-GCGGAGCTGTATTTTG
76028 CGGCATTGGT
Statistics
Matches: 259, Mismatches: 26, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
101 6 0.02
102 249 0.96
103 4 0.02
ACGTcount: A:0.26, C:0.14, G:0.35, T:0.26
Consensus pattern (102 bp):
GGAGATGGTGGCAACACCAATGGAATACTTGGAGCCAAGGATGGTAAATGTTCTTCAATAGGGAA
TGGTAGCGGAGCTGTATTTTGGGTTTGCGCGGATGGA
Found at i:77720 original size:4 final size:4
Alignment explanation
Indices: 77707--77761 Score: 103
Period size: 4 Copynumber: 14.0 Consensus size: 4
77697 ATCAACCAAA
77707 TCTT TC-T TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
77754 TCTT TCTT
1 TCTT TCTT
77762 GATGATCTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 3 0.06
4 47 0.94
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TCTT
Found at i:79240 original size:30 final size:30
Alignment explanation
Indices: 79204--79265 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
79194 TTTTGAAGAA
* * *
79204 AAAAATTTAAAGTTTAAGTGCTAAACGGAT
1 AAAAATTGAAAGTTTAAGTACTAAACGCAT
*
79234 AAAAATTGATAGTTTAAGTACTAAACGCAT
1 AAAAATTGAAAGTTTAAGTACTAAACGCAT
79264 AA
1 AA
79266 TTTACCATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.29
Consensus pattern (30 bp):
AAAAATTGAAAGTTTAAGTACTAAACGCAT
Found at i:80955 original size:15 final size:15
Alignment explanation
Indices: 80935--80965 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
80925 GTAAAAAAAA
*
80935 AATCCGACTCAATAC
1 AATCCGACCCAATAC
80950 AATCCGACCCAATAC
1 AATCCGACCCAATAC
80965 A
1 A
80966 TGACGTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.35, G:0.06, T:0.16
Consensus pattern (15 bp):
AATCCGACCCAATAC
Found at i:82085 original size:60 final size:60
Alignment explanation
Indices: 81972--82088 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
81962 ATGTGAATAC
* * *
81972 ATATAATTTGGGATGAAATTGAAATGTTGAAAATGTTTCAAGACCAATTTAGAATGAAGG
1 ATATAATTTGGGATGAAACTAAAATGTTCAAAATGTTTCAAGACCAATTTAGAATGAAGG
* * * *
82032 ATATATTTTGGAGATGAAACTAAAATGTTCAAAAT-TTTGAGGACTAATTTAGAATGA
1 ATATAATTTGG-GATGAAACTAAAATGTTCAAAATGTTTCAAGACCAATTTAGAATGA
82089 TAGTAGTAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 29 0.59
61 20 0.41
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (60 bp):
ATATAATTTGGGATGAAACTAAAATGTTCAAAATGTTTCAAGACCAATTTAGAATGAAGG
Done.