Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003500.1 Hibiscus syriacus cultivar Beakdansim tig00007398_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: 121336
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:8758 original size:29 final size:29
Alignment explanation
Indices: 8702--8769 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
8692 TATGCATAAG
* **
8702 TAAATTCATCATTTATAATGCATCACCAA
1 TAAATGCATCATTTATAACACATCACCAA
* *
8731 TAAATGCATCATTTATAGCACATTACCAA
1 TAAATGCATCATTTATAACACATCACCAA
8760 TAATATGCAT
1 TAA-ATGCAT
8770 TCGAATTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (29 bp):
TAAATGCATCATTTATAACACATCACCAA
Found at i:15865 original size:8 final size:8
Alignment explanation
Indices: 15843--15902 Score: 59
Period size: 8 Copynumber: 7.1 Consensus size: 8
15833 TTACACTTAA
*
15843 AAAAAAGG
1 AAAAAATG
15851 AAAAAATG
1 AAAAAATG
15859 AAAAAATG
1 AAAAAATG
15867 ATGGAAAAATG
1 A---AAAAATG
*
15878 AAAAAAAG
1 AAAAAATG
15886 AAAAAAT-
1 AAAAAATG
15893 AAATAAATG
1 AAA-AAATG
15902 A
1 A
15903 GGGTTCAAGA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
7 3 0.07
8 32 0.73
9 1 0.02
11 8 0.18
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (8 bp):
AAAAAATG
Found at i:17157 original size:135 final size:134
Alignment explanation
Indices: 16911--17157 Score: 345
Period size: 135 Copynumber: 1.8 Consensus size: 134
16901 ATTATCGCTA
**
16911 TAAAATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTAATTAGATCTCCTCATCA
1 TAAAATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTAACCAGATCTCCTCATCA
** *
16976 CGTAGGAGTCGTGTCACCCCTAGATAACCAGACATCCTCATCACGTAGGAACCGTGTTATCGCCC
66 CGTAGGAACCGTGTCACCCCTAGACAACCAGACATCCTCATCACGTAGGAACCGTGTTATCGCCC
17041 TTCC
131 TTCC
* * *
17045 TAAAGATGGCCAATAACTCTTCATCACGTATGAGCAGTGTCAT-CCCTCGACCAGATTTCCTCAT
1 TAAA-ATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCT-AACCAGATCTCCTCAT
* * * *
17109 CACGTAGGAACCGTGTCACCCTTAGACGACCCGA-ACTCTTCATCACGTA
64 CACGTAGGAACCGTGTCACCCCTAGACAACCAGACA-TCCTCATCACGTA
17158 TGAGCATGTC
Statistics
Matches: 98, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
134 9 0.09
135 89 0.91
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (134 bp):
TAAAATGGCCAAGAACTCTTCATCACGTATGAGCAGTGTCATCCCCTAACCAGATCTCCTCATCA
CGTAGGAACCGTGTCACCCCTAGACAACCAGACATCCTCATCACGTAGGAACCGTGTTATCGCCC
TTCC
Found at i:17344 original size:3 final size:3
Alignment explanation
Indices: 17331--17380 Score: 66
Period size: 3 Copynumber: 16.3 Consensus size: 3
17321 ATTTTAATTC
*
17331 ATT ACT ATT ATT ATT -TT AATT ATT ATT ATTT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT A-TT ATT ATT ATT ATT ATT
17377 ATT A
1 ATT A
17381 ATACAAATGG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 35 0.83
4 5 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:17378 original size:22 final size:22
Alignment explanation
Indices: 17320--17380 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
17310 GAGTCTTTTC
*
17320 TATTTTAATTCATTACTA-TTAT
1 TATTTTAATT-ATTATTATTTAT
17342 TATTTTAATTATTATTATTTAT
1 TATTTTAATTATTATTATTTAT
17364 TATTATT-ATTATTATTA
1 TATT-TTAATTATTATTA
17381 ATACAAATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 6 0.17
22 28 0.78
23 2 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (22 bp):
TATTTTAATTATTATTATTTAT
Found at i:20958 original size:23 final size:22
Alignment explanation
Indices: 20914--20958 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
20904 ATGTTTATAT
* *
20914 AAATTTTAATATAATAATAATA
1 AAATATTAATATAATAAAAATA
*
20936 AAATATTAATTATTATAAAAATA
1 AAATATTAA-TATAATAAAAATA
20959 TACAACTCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAATATTAATATAATAAAAATA
Found at i:33957 original size:4 final size:4
Alignment explanation
Indices: 33948--34289 Score: 684
Period size: 4 Copynumber: 85.5 Consensus size: 4
33938 TCATTTCTGA
33948 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
33996 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34044 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34092 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34140 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34188 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34236 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34284 ATGT AT
1 ATGT AT
34290 ATACATGCAT
Statistics
Matches: 338, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 338 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:41770 original size:15 final size:15
Alignment explanation
Indices: 41728--41770 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
41718 ATACGATAAC
*
41728 AAAACAATATTTCGTT
1 AAAA-AATATTTTGTT
41744 AAAAAATATTTTGTT
1 AAAAAATATTTTGTT
41759 AAAAAATATTTT
1 AAAAAATATTTT
41771 ATGGTTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 22 0.85
16 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (15 bp):
AAAAAATATTTTGTT
Found at i:45394 original size:52 final size:52
Alignment explanation
Indices: 45328--45433 Score: 194
Period size: 52 Copynumber: 2.0 Consensus size: 52
45318 CTCTTTGTTG
* *
45328 AATATTTAGACCCTAAGATCTAATATGTGAACTTTAGTTGCTTTGGTGGTCA
1 AATATTTAGACCCTAAGATCTAATATGTGAACTTTAGTTGCTTTAGTAGTCA
45380 AATATTTAGACCCTAAGATCTAATATGTGAACTTTAGTTGCTTTAGTAGTCA
1 AATATTTAGACCCTAAGATCTAATATGTGAACTTTAGTTGCTTTAGTAGTCA
45432 AA
1 AA
45434 CGAACCGTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (52 bp):
AATATTTAGACCCTAAGATCTAATATGTGAACTTTAGTTGCTTTAGTAGTCA
Found at i:53219 original size:56 final size:56
Alignment explanation
Indices: 53145--53438 Score: 267
Period size: 56 Copynumber: 5.3 Consensus size: 56
53135 ACTACAACCG
*
53145 AGAAACTGACACCTCTGTGTAGTTAAAAATGACTGAGCACCTCTGTGCTTCAGTAT
1 AGAAACTGACACCTCTGTGTAGTTAAAAATGATTGAGCACCTCTGTGCTTCAGTAT
* * * * * * * *
53201 AGAATCTGGCACCTCTGTGCT--TT-ATAATGATTAAGCACCTATGTTCTTCAATAG
1 AGAAACTGACACCTCTGTG-TAGTTAAAAATGATTGAGCACCTCTGTGCTTCAGTAT
* * * *
53255 ACAAACTGACACCTATGTGCAGTTAAAAATGATTGGGCACCTCTGTGCTTCAGTAT
1 AGAAACTGACACCTCTGTGTAGTTAAAAATGATTGAGCACCTCTGTGCTTCAGTAT
* * * * * * * *
53311 AGAATCTAACACCTC--TGTACTTTATAATGATTGAGTACCTCCGTGCTTCAATCA-
1 AGAAACTGACACCTCTGTGTAGTTAAAAATGATTGAGCACCTCTGTGCTTCAGT-AT
* * * * * *
53365 AAAAACTGACACCTTTGTGCAGTTAAAAATGACTGAGTACCTCTGTGCTTCAGTCT
1 AGAAACTGACACCTCTGTGTAGTTAAAAATGATTGAGCACCTCTGTGCTTCAGTAT
* *
53421 AGAATCTGACACATCTGT
1 AGAAACTGACACCTCTGT
53439 ATTTTTAATG
Statistics
Matches: 181, Mismatches: 49, Indels: 16
0.74 0.20 0.07
Matches are distributed among these distances:
54 79 0.44
55 5 0.03
56 96 0.53
57 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (56 bp):
AGAAACTGACACCTCTGTGTAGTTAAAAATGATTGAGCACCTCTGTGCTTCAGTAT
Found at i:53250 original size:54 final size:54
Alignment explanation
Indices: 53145--53521 Score: 233
Period size: 54 Copynumber: 6.9 Consensus size: 54
53135 ACTACAACCG
* * * *
53145 AGAAACTGACACCTCTGTG-TAGTTAAAAATGACTGAGCACCTCTGTGCTTCAGTAT
1 AGAATCTGACACCTCTGTGCT--TT-ATAATGATTAAGCACCTCTGTGCTTCAGTAT
* * * * *
53201 AGAATCTGGCACCTCTGTGCTTTATAATGATTAAGCACCTATGTTCTTCAATAG
1 AGAATCTGACACCTCTGTGCTTTATAATGATTAAGCACCTCTGTGCTTCAGTAT
* * * * * **
53255 ACAAACTGACACCTATGTGCAGTTAAAAATGATTGGGCACCTCTGTGCTTCAGTAT
1 AGAATCTGACACCTCTGTGC--TTTATAATGATTAAGCACCTCTGTGCTTCAGTAT
* * * * * *
53311 AGAATCTAACACCTCTGTACTTTATAATGATTGAGTACCTCCGTGCTTCAATCA-
1 AGAATCTGACACCTCTGTGCTTTATAATGATTAAGCACCTCTGTGCTTCAGT-AT
* * * * * * * * *
53365 AAAAACTGACACCTTTGTGCAGTTAAAAATGACTGAGTACCTCTGTGCTTCAGTCT
1 AGAATCTGACACCTCTGTGC--TTTATAATGATTAAGCACCTCTGTGCTTCAGTAT
* * * ** * * *
53421 AGAATCTGACACATCTGT-ATTTTTAATGATCGAGCACCTCTATGTTTCAATAT
1 AGAATCTGACACCTCTGTGCTTTATAATGATTAAGCACCTCTGTGCTTCAGTAT
* * ** *
53474 AGGATCTAGA-ACCTATGTGCTTTAGGATGATTGAA-CACCTTTGTGCTT
1 AGAATCT-GACACCTCTGTGCTTTATAATGATT-AAGCACCTCTGTGCTT
53522 TGACAAACGA
Statistics
Matches: 241, Mismatches: 70, Indels: 22
0.72 0.21 0.07
Matches are distributed among these distances:
53 36 0.15
54 101 0.42
55 4 0.02
56 99 0.41
57 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (54 bp):
AGAATCTGACACCTCTGTGCTTTATAATGATTAAGCACCTCTGTGCTTCAGTAT
Found at i:53317 original size:110 final size:110
Alignment explanation
Indices: 53147--53459 Score: 423
Period size: 110 Copynumber: 2.9 Consensus size: 110
53137 TACAACCGAG
* * *
53147 AAACTGACACCTCTGTGTAGTTAAAAATGACTGAGCACCTCTGTGCTTCAGTATAGAATCTGGCA
1 AAACTGACACCTATGTGCAGTTAAAAATGACTGAGCACCTCTGTGCTTCAGTATAGAATCTGACA
* * * *
53212 CCTCTGTGCTTTATAATGATTAAGCACCTATGTTCTTCAAT-AGAC
66 CCTCTGTACTTTATAATGATTAAGCACCTACGTGCTTCAATCA-AA
* * *
53257 AAACTGACACCTATGTGCAGTTAAAAATGATTGGGCACCTCTGTGCTTCAGTATAGAATCTAACA
1 AAACTGACACCTATGTGCAGTTAAAAATGACTGAGCACCTCTGTGCTTCAGTATAGAATCTGACA
* * *
53322 CCTCTGTACTTTATAATGATTGAGTACCTCCGTGCTTCAATCAAA
66 CCTCTGTACTTTATAATGATTAAGCACCTACGTGCTTCAATCAAA
* * *
53367 AAACTGACACCTTTGTGCAGTTAAAAATGACTGAGTACCTCTGTGCTTCAGTCTAGAATCTGACA
1 AAACTGACACCTATGTGCAGTTAAAAATGACTGAGCACCTCTGTGCTTCAGTATAGAATCTGACA
* * **
53432 CATCTGTA-TTTTTAATGATCGAGCACCT
66 CCTCTGTACTTTATAATGATTAAGCACCT
53460 CTATGTTTCA
Statistics
Matches: 179, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
109 17 0.09
110 161 0.90
111 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.32
Consensus pattern (110 bp):
AAACTGACACCTATGTGCAGTTAAAAATGACTGAGCACCTCTGTGCTTCAGTATAGAATCTGACA
CCTCTGTACTTTATAATGATTAAGCACCTACGTGCTTCAATCAAA
Found at i:64404 original size:24 final size:24
Alignment explanation
Indices: 64355--64412 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
64345 AAATCAACAT
* *
64355 ACAATCCGATTCAACAAAAATGTTC
1 ACAATCTGATTCAAC-AAAATATTC
64380 ACAATCTGATTCAATC-AAATATTC
1 ACAATCTGATTCAA-CAAAATATTC
*
64404 ACAGTCTGA
1 ACAATCTGA
64413 CTAAATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.52
25 13 0.45
26 1 0.03
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (24 bp):
ACAATCTGATTCAACAAAATATTC
Found at i:70940 original size:29 final size:29
Alignment explanation
Indices: 70879--70964 Score: 102
Period size: 29 Copynumber: 3.0 Consensus size: 29
70869 CCCAACCCAT
* ****
70879 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
*
70908 AGGTCGCCATGCACTCCGGGCGACCAAGG
1 AGGTCGCCATGCACTCCCGGCGACCAAGG
70937 AGGTCGCCATGCA-TGCCCGGCGACCAAG
1 AGGTCGCCATGCACT-CCCGGCGACCAAG
70965 CTTTTAACCC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
28 1 0.02
29 48 0.98
ACGTcount: A:0.20, C:0.38, G:0.29, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGGCGACCAAGG
Found at i:71169 original size:29 final size:29
Alignment explanation
Indices: 71107--71191 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
71097 CAAGGAGACA
* *
71107 AGGTCG-CCGGACGTGCATGGCGACCTCCT
1 AGGTCGCCCGGA-GTGCATGGCGACCTACG
* *
71136 TGGTCGCCCGGAGTGCATGGCGACCTAGG
1 AGGTCGCCCGGAGTGCATGGCGACCTACG
**
71165 AGGTCGCTGGGAGTGCATGGCGACCTA
1 AGGTCGCCCGGAGTGCATGGCGACCTA
71192 TGGGTTGGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 43 0.90
30 5 0.10
ACGTcount: A:0.15, C:0.28, G:0.39, T:0.18
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACG
Found at i:72323 original size:23 final size:23
Alignment explanation
Indices: 72297--72343 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
72287 ATCAAATATC
*
72297 ACATGTCATAATCTGATTAGATA
1 ACATGTCACAATCTGATTAGATA
72320 ACATGTCACAATCTGATTAGATA
1 ACATGTCACAATCTGATTAGATA
72343 A
1 A
72344 AATTTTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (23 bp):
ACATGTCACAATCTGATTAGATA
Found at i:97299 original size:26 final size:26
Alignment explanation
Indices: 97263--97318 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
97253 AATTGCTTGC
*
97263 CTGATAGCATTAGTTACACCACCTTT
1 CTGATAACATTAGTTACACCACCTTT
97289 CTGATAACATTAGTTACACCACCTTT
1 CTGATAACATTAGTTACACCACCTTT
97315 CTGA
1 CTGA
97319 ATGGGCTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.34
Consensus pattern (26 bp):
CTGATAACATTAGTTACACCACCTTT
Found at i:98994 original size:30 final size:30
Alignment explanation
Indices: 98960--99048 Score: 142
Period size: 30 Copynumber: 3.0 Consensus size: 30
98950 CACAAATCGG
*
98960 TCACTCATGTAATCGTTTGTTACAAAATGA
1 TCACTCACGTAATCGTTTGTTACAAAATGA
98990 TCACTCACGTAATCGTTTGTTACAAAATGA
1 TCACTCACGTAATCGTTTGTTACAAAATGA
* * *
99020 TCACTAACGTTACCGTTTGTTACAAAATG
1 TCACTCACGTAATCGTTTGTTACAAAATG
99049 GTTACTCGAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (30 bp):
TCACTCACGTAATCGTTTGTTACAAAATGA
Found at i:99136 original size:3 final size:3
Alignment explanation
Indices: 99128--99217 Score: 173
Period size: 3 Copynumber: 30.3 Consensus size: 3
99118 CTACTGACTC
99128 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
99176 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-T TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
99218 TCTATCAAAG
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:99300 original size:7 final size:7
Alignment explanation
Indices: 99288--99319 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
99278 CCATTTCAAG
99288 GCCTTTT
1 GCCTTTT
99295 GCCTTTT
1 GCCTTTT
99302 GCCTTTT
1 GCCTTTT
99309 -CC-TTT
1 GCCTTTT
99314 GCCTTT
1 GCCTTT
99320 GCCCATCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
5 3 0.13
6 4 0.17
7 16 0.70
ACGTcount: A:0.00, C:0.31, G:0.12, T:0.56
Consensus pattern (7 bp):
GCCTTTT
Found at i:99998 original size:30 final size:30
Alignment explanation
Indices: 99958--100016 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
99948 GTTAACGTGG
*
99958 AGTGATCATTTTATAACAAACGATAATGTT
1 AGTGACCATTTTATAACAAACGATAATGTT
* *
99988 AGTGACCATTTTGTAACAAATGATAATGT
1 AGTGACCATTTTATAACAAACGATAATGT
100017 GACTATTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (30 bp):
AGTGACCATTTTATAACAAACGATAATGTT
Found at i:100414 original size:167 final size:164
Alignment explanation
Indices: 100040--100511 Score: 584
Period size: 167 Copynumber: 2.8 Consensus size: 164
100030 GTTTACCCTT
* * *** * *
100040 AGCCAAACATTTGTGATCATTGGTGTAATTTACCTGTTATAATTCACATAATAATTTATCATCAT
1 AGCCAAACATTAGTGACCATTAACGTAATTTACCTTTTATAATTCACATAATAATCTATCAT-AT
* *** *
100105 CGATACTCATTAGCCCGACATTCCCTGACGTGTGTTTAGGCCACGAGCCAATGGTTCAATATTTC
65 CGATACTCATTAGCCCGACATTTCCTGA-GTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTC
* *
100170 ATTTCCATTTCAAACATCAATGGTGAACTAACACTT
129 ATTTCCATTTCAAACATCAATAGTGAACTAACACTA
* * * *
100206 AGCCAAACATTAGTGACCATTGATGTAGTTTACCCTTTATAATTCACATAATAATCTATCACTAT
1 AGCCAAACATTAGTGACCATTAACGTAATTTACCTTTTATAATTCACATAATAATCTATCA-TAT
* * * * * * *
100271 CAATACTCATTAGCCTGACATTTCCTTAATGTGTTTAGGCCATGAGCTACCAGTTCACTGTTTCA
65 CGATACTCATTAGCCCGACATTTCCTGAGTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTCA
*
100336 TTTCCATTTCAAATATCAATAGTGAAAACTAACACTA
130 TTTCCATTTCAAACATCAATAGTG--AACTAACACTA
* *
100373 AGCCAAATATTAGTGACCATTAACGTAATTTACCTTTTATAATTCACATAATGATCTATCATTAT
1 AGCCAAACATTAGTGACCATTAACGTAATTTACCTTTTATAATTCACATAATAATCTATCA-TAT
* * * * *
100438 CGATACTCATTAGCCCCACATTTCCAGGCGTGTGTTTAGGCCACGAACCACCAGTTCATTGTTTC
65 CGATACTCATTAGCCCGACATTTCC-TGAGTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTC
100503 ATTTCCATT
129 ATTTCCATT
100512 CTACGCGCAC
Statistics
Matches: 262, Mismatches: 40, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
165 51 0.19
166 80 0.31
167 91 0.35
168 40 0.15
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (164 bp):
AGCCAAACATTAGTGACCATTAACGTAATTTACCTTTTATAATTCACATAATAATCTATCATATC
GATACTCATTAGCCCGACATTTCCTGAGTGTGTTTAGGCCACGAGCCACCAGTTCAATGTTTCAT
TTCCATTTCAAACATCAATAGTGAACTAACACTA
Found at i:102481 original size:19 final size:20
Alignment explanation
Indices: 102457--102507 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
102447 AATGACCAAT
102457 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
102476 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
102496 AAAATCGCAACG
1 AAAATCGCAACG
102508 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:102501 original size:20 final size:20
Alignment explanation
Indices: 102457--102734 Score: 148
Period size: 20 Copynumber: 13.6 Consensus size: 20
102447 AATGACCAAT
* *
102457 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
102476 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
102496 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
102516 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
102536 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
102557 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
102580 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
102600 TGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
102620 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
102643 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
102663 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
102683 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
102703 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
102723 AAAATCGCAACG
1 AAAATCGCAACG
102735 TTAAAAAGAA
Statistics
Matches: 206, Mismatches: 41, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
19 17 0.08
20 146 0.71
21 14 0.07
23 29 0.14
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:102644 original size:63 final size:63
Alignment explanation
Indices: 102561--102732 Score: 233
Period size: 63 Copynumber: 2.8 Consensus size: 63
102551 GCTTCCAAGT
** * *
102561 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTGAGAGAG
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAA
*
102624 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAA
* * * * *
102687 TCGCAATGCGA-TT-G-AGAGAATCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAA
102733 CGTTAAAAAG
Statistics
Matches: 98, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
60 27 0.28
61 1 0.01
62 2 0.02
63 68 0.69
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (63 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGACTGAGAGAA
Found at i:102729 original size:40 final size:40
Alignment explanation
Indices: 102602--102732 Score: 181
Period size: 40 Copynumber: 3.2 Consensus size: 40
102592 CGATTGATTG
*
102602 AATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTT---AGAA
* * * * *
102645 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
102685 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
1 AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
102725 AATCGCAA
1 AATCGCAA
102733 CGTTAAAAAG
Statistics
Matches: 77, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 46 0.60
43 31 0.40
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (40 bp):
AATCGCAATGCGATTGAGAGAATCGCAACGCGATTTAGAA
Found at i:102744 original size:20 final size:20
Alignment explanation
Indices: 102721--102764 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
102711 AACGCGATTT
*
102721 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
102741 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
102761 AGAA
1 AGAA
102765 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:102853 original size:6 final size:6
Alignment explanation
Indices: 102842--102873 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
102832 GACACGTATT
102842 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
102874 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:103621 original size:6 final size:6
Alignment explanation
Indices: 103559--103665 Score: 144
Period size: 5 Copynumber: 19.5 Consensus size: 6
103549 TCTCGTCTCG
103559 GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG- GGTCG-
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
103599 GGTCG- GGTCGT -GTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
103645 GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGT
103666 AATACGTGTC
Statistics
Matches: 100, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
5 50 0.50
6 50 0.50
ACGTcount: A:0.00, C:0.18, G:0.54, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:103768 original size:20 final size:20
Alignment explanation
Indices: 103743--103786 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
103733 TTTTTAACTA
*
103743 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
103763 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
103783 TTCT
1 TTCT
103787 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:103796 original size:20 final size:20
Alignment explanation
Indices: 103773--103967 Score: 85
Period size: 20 Copynumber: 9.6 Consensus size: 20
103763 TTCTTTTTAA
103773 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
*** *
103793 CGTTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
103813 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
103833 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
103856 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
103877 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
103895 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
103917 CGTTGCGATTTTC-ATAATCG
1 CGTTGCGATTTTCTA-AATCG
103937 CGTTGCGATTTTGCT--ATCG
1 CGTTGCGATTTT-CTAAATCG
103956 CGTTGCGATTTT
1 CGTTGCGATTTT
103968 ATTGGTCATT
Statistics
Matches: 136, Mismatches: 28, Indels: 23
0.73 0.15 0.12
Matches are distributed among these distances:
18 2 0.01
19 16 0.12
20 87 0.64
21 14 0.10
22 4 0.03
23 13 0.10
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:103957 original size:19 final size:20
Alignment explanation
Indices: 103917--103967 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
103907 TTCTTTTTAA
103917 CGTTGCGATTTTCATAATCG
1 CGTTGCGATTTTCATAATCG
103937 CGTTGCGATTTTGC-T-ATCG
1 CGTTGCGATTTT-CATAATCG
103956 CGTTGCGATTTT
1 CGTTGCGATTTT
103968 ATTGGTCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.53
20 13 0.43
21 1 0.03
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCATAATCG
Found at i:104278 original size:15 final size:16
Alignment explanation
Indices: 104258--104290 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
104248 TAAAATATAA
104258 TATTCTC-AATAATCT
1 TATTCTCTAATAATCT
*
104273 TATTCTCTGATAATCT
1 TATTCTCTAATAATCT
104289 TA
1 TA
104291 CAATAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.30, C:0.18, G:0.03, T:0.48
Consensus pattern (16 bp):
TATTCTCTAATAATCT
Found at i:104440 original size:21 final size:20
Alignment explanation
Indices: 104409--104450 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
104399 AGTACCAAAC
104409 TCTTCTCTCTCTATTT-CTTT
1 TCTTCTCTCTCT-TTTGCTTT
104429 TCTTCTTCTCTCTTTTGCTTT
1 TCTTC-TCTCTCTTTTGCTTT
104450 T
1 T
104451 GCATGCACAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (20 bp):
TCTTCTCTCTCTTTTGCTTT
Found at i:111275 original size:22 final size:22
Alignment explanation
Indices: 111247--111303 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
111237 ATCTTCTATT
111247 GTTTAGGGTTTT-GAACTTAAGG
1 GTTTAGGGTTTTAG-ACTTAAGG
*
111269 GTTTAGGGGTTTAGACTTAAGG
1 GTTTAGGGTTTTAGACTTAAGG
*
111291 GTTTAAGGTTTTA
1 GTTTAGGGTTTTA
111304 AGCTAGGTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.42
Consensus pattern (22 bp):
GTTTAGGGTTTTAGACTTAAGG
Done.