Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002956.1 Hibiscus syriacus cultivar Beakdansim tig00006107_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: 86079
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:710 original size:20 final size:21
Alignment explanation
Indices: 677--736 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
667 TTTTTTTATT
*
677 TTTTTTTCATTTTATTCT-TTGA
1 TTTTTTT-ATTTTATT-TACTGA
699 TTTTTTTA-TTTATTTACTGA
1 TTTTTTTATTTTATTTACTGA
719 TTTTTTTAGTCTTTATTT
1 TTTTTTTA-T-TTTATTT
737 CTTTTTTTAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 1 0.03
20 17 0.52
21 1 0.03
22 7 0.21
23 7 0.21
ACGTcount: A:0.15, C:0.07, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTTTTATTTTATTTACTGA
Found at i:4915 original size:64 final size:64
Alignment explanation
Indices: 4843--5011 Score: 207
Period size: 64 Copynumber: 2.6 Consensus size: 64
4833 CGATACATTG
** **
4843 GTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGTAATTTGTGCATCGATGCATA
1 GTAGTGCATCGATGCATC-CCATTAATAATAAA-ACATCGAATGTAATCGGTGCATCGATGCATA
4906 A
64 A
* * *
4907 GTAGTGCATCTATGCATCCCATTAATAGTGAAACATCGAATGTAATCGGTGCATCGATGCATAA
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATCGGTGCATCGATGCATAA
* * **
4971 GGAGTGCATCGATGCATCCCAGTAATAATACTACATCGAAT
1 GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAAT
5012 ACCTTTTATG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
64 84 0.94
65 5 0.06
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (64 bp):
GTAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGTAATCGGTGCATCGATGCATAA
Found at i:5379 original size:12 final size:12
Alignment explanation
Indices: 5361--5396 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5351 TATATGTGTT
5361 CATGTGATATGA
1 CATGTGATATGA
*
5373 TATGTGATATGA
1 CATGTGATATGA
*
5385 CCTGTGATATGA
1 CATGTGATATGA
5397 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:5464 original size:29 final size:29
Alignment explanation
Indices: 5416--5514 Score: 164
Period size: 29 Copynumber: 3.4 Consensus size: 29
5406 ATGAAGTGAT
* *
5416 ATGAGATACATGATCCCAAGAGAAATGAC
1 ATGAGCTACATGATCACAAGAGAAATGAC
*
5445 ATTAGCTACATGATCACAAGAGAAATGAC
1 ATGAGCTACATGATCACAAGAGAAATGAC
5474 ATGAGCTACATGATCACAAGAGAAATGAC
1 ATGAGCTACATGATCACAAGAGAAATGAC
5503 ATGAG-TACATGA
1 ATGAGCTACATGA
5515 ACATATGAAA
Statistics
Matches: 66, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
28 7 0.11
29 59 0.89
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.19
Consensus pattern (29 bp):
ATGAGCTACATGATCACAAGAGAAATGAC
Found at i:11834 original size:64 final size:64
Alignment explanation
Indices: 11765--11919 Score: 190
Period size: 64 Copynumber: 2.4 Consensus size: 64
11755 GAATGTGAAC
* ** **
11765 CGATGCATTGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAGACATCGAATGCAATTTGTGCA
1 CGATGCATAGGTAGTGCATCGATGCATC-CCATTAACAATAAA-ACATCGAATGCAATCGGTGCA
11828 T
64 T
* * *
11829 CGATGCATAAGTAGTGCATCGATGCATCCCATTAACAGTGAAACATCGAATGCAATCGGTGCAT
1 CGATGCATAGGTAGTGCATCGATGCATCCCATTAACAATAAAACATCGAATGCAATCGGTGCAT
11893 CGATGCATAAGG-AGTGCATCGATGCAT
1 CGATGCAT-AGGTAGTGCATCGATGCAT
11920 AAGGAGTGCA
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 72 0.91
65 7 0.09
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (64 bp):
CGATGCATAGGTAGTGCATCGATGCATCCCATTAACAATAAAACATCGAATGCAATCGGTGCAT
Found at i:11911 original size:19 final size:19
Alignment explanation
Indices: 11887--11938 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
11877 AATGCAATCG
11887 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
11906 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
11925 GTGCATCGATGCAT
1 GTGCATCGATGCAT
11939 CCCAACAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCATAAGGA
Found at i:12330 original size:12 final size:12
Alignment explanation
Indices: 12312--12347 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
12302 TATATGTGTT
12312 CATGTGATATGA
1 CATGTGATATGA
*
12324 TATGTGATATGA
1 CATGTGATATGA
*
12336 CCTGTGATATGA
1 CATGTGATATGA
12348 GAACATGATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:12389 original size:17 final size:17
Alignment explanation
Indices: 12369--12447 Score: 52
Period size: 17 Copynumber: 5.2 Consensus size: 17
12359 GAAGTGATAT
12369 GAGATACATGATCACAA
1 GAGATACATGATCACAA
*
12386 GAGA-A-ATG---ACAT
1 GAGATACATGATCACAA
*
12398 GAGCTACATGATCACAA
1 GAGATACATGATCACAA
*
12415 GAGA-A-ATG---ACAT
1 GAGATACATGATCACAA
*
12427 GAGCTACATGATCACAA
1 GAGATACATGATCACAA
12444 GAGA
1 GAGA
12448 AATGACATGA
Statistics
Matches: 44, Mismatches: 8, Indels: 20
0.61 0.11 0.28
Matches are distributed among these distances:
12 12 0.27
13 2 0.05
14 6 0.14
15 6 0.14
16 2 0.05
17 16 0.36
ACGTcount: A:0.46, C:0.16, G:0.22, T:0.16
Consensus pattern (17 bp):
GAGATACATGATCACAA
Found at i:12409 original size:29 final size:29
Alignment explanation
Indices: 12367--12465 Score: 182
Period size: 29 Copynumber: 3.4 Consensus size: 29
12357 ATGAAGTGAT
*
12367 ATGAGATACATGATCACAAGAGAAATGAC
1 ATGAGCTACATGATCACAAGAGAAATGAC
12396 ATGAGCTACATGATCACAAGAGAAATGAC
1 ATGAGCTACATGATCACAAGAGAAATGAC
12425 ATGAGCTACATGATCACAAGAGAAATGAC
1 ATGAGCTACATGATCACAAGAGAAATGAC
12454 ATGAG-TACATGA
1 ATGAGCTACATGA
12466 ACATATGAAA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
28 7 0.10
29 62 0.90
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (29 bp):
ATGAGCTACATGATCACAAGAGAAATGAC
Found at i:15537 original size:164 final size:163
Alignment explanation
Indices: 15214--16206 Score: 1154
Period size: 164 Copynumber: 6.0 Consensus size: 163
15204 CTAGTGCCAA
* * ** * * * *
15214 CAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCATATCATTTGCAACATAGCTCAAGGCA
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCG
* * *
15279 AGAAGGGATATTTTCCAACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGACACATCATT
66 AGAAGGGCTATCTT----CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
*
15344 TACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAC
127 TACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
* * *
15381 TAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGTAGTATAGCTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCG
* * * * * *
15446 AGAAGGGTTATCTATTAACGACTCTCGAGTTCGATTACACTCAGCTTCAAGAGCACATCA-TTAG
66 AGAAGGGCTATCT-TCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA-
* * * *
15510 TAGCATAACTTAA-GTTGAGAAGGGTTATCTGCCAAC
129 CAGCATAACTCAAGGCT-AGAAGGGTTATCTGTC-AC
* *
15546 CAAAGACCTTTGAGTTCGACTACGGTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCG
* * *
15611 AGAAGGGCTATCTTCCAAAGACCCTCGAGTTCAATTACACTCAGCTTCGAGGGTATATCATTTAC
66 AGAAGGGCTATCTT-CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTAC
* *
15676 AGCATAACTCAAGGCTAGAAGAGTTATTTGTCAC
130 AGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
* * * * *
15710 CAAAGACCTTCGAGTTTGACTACGCTCAGCTCTAAGACACATTATTTG-ATGTATAGCTTAAGTC
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA-GTATAACTTAAGTC
* * * *
15774 GATAAGGGCTATCTGCCAAAGACTCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTG
65 GAGAAGGGCTATCT-TCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
* * * * *
15839 CAGCATAACTTAAGTCGAGAAGGGTTATATGCCAAC
129 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-AC
* * *
15875 CAAAGACCTTTGAGCTT-GATTACGCTCAGCTCCAAGGCACATCATTTGTAGTATAACTTAAGTC
1 CAAAGACCTTCGAG-TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTC
* * * *
15939 GATAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACATAATTTA
65 GAGAAGGGCTATCT-TCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
*
16004 CAACATAACTCAAGGCTAGAAGGGTTATCTGTCAC
129 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
* *
16039 CAAAGACCTTCGAGTTCAACTACGCTCAGCTTCAAGGCACATCATTTGCAGTATAACTTAAGTCG
1 CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCG
* * * * *
16104 AGAAGGGCTATCTGCCAACTGAAGA-CCTCCGAGTTCGATTACATTCAAC-TC-AGAGGCAAACC
66 AGAAGGGCTATCT-TC-A---AAGACCCT-CGAGTTCGATTACACTCAGCTTCGAG-GGCACATC
* * *
16166 AAATTTACAACATAGCTCAAGGCAAGAAGGGTTATCTGTCA
124 --ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCA
16207 ATAAATTTTT
Statistics
Matches: 713, Mismatches: 92, Indels: 40
0.84 0.11 0.05
Matches are distributed among these distances:
163 8 0.01
164 280 0.39
165 279 0.39
166 10 0.01
167 77 0.11
168 22 0.03
169 37 0.05
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (163 bp):
CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACTTAAGTCG
AGAAGGGCTATCTTCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA
GCATAACTCAAGGCTAGAAGGGTTATCTGTCAC
Found at i:15815 original size:329 final size:329
Alignment explanation
Indices: 15208--16121 Score: 1334
Period size: 329 Copynumber: 2.8 Consensus size: 329
15198 TCAAAGCTAG
* * * ** *
15208 TGCCAA-CAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCATATCATTTGCAACATAGCT
1 TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACT
* * * * * *
15272 CAAGGCAAGAAGGGATATTTTCCAACAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGACA
66 TAAGTCGAGAAGGGCTATCTT-C--CAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCA
*
15337 CATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACTAAAGACCTTCGAGTTCGACT
128 CATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACT
* * *** *
15402 ACGCTCAGCTCCAAGGCACATCATTTG-TAGTATAGCTTAAGTCGAGAAGGGTTATCTATTAACG
193 ACGCTCAGCTCTAAGGCACATCATTTGAT-GTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAG
* *
15466 ACTCTCGAGTTCGATTACACTCAGCTTCAAGAGCACATCATTAGTAGCATAACTTAAGTTGAGAA
257 ACTCTCGAGTTCGATTACACTCAGCTTCAAGAGCACATCATTAGCAGCATAACTTAAGTCGAGAA
*
15531 GGGTTATC
322 GGGTTATA
*
15539 TGCCAACCAAAGACCTTTGAGTTCGACTACGGTCAGCTCCAAGGCACATCATTTGCAGTATAACT
1 TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACT
* * *
15604 TAAGTCGAGAAGGGCTATCTTCCAAAGACCCTCGAGTTCAATTACACTCAGCTTCGAGGGTATAT
66 TAAGTCGAGAAGGGCTATCTTCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
* * * *
15669 CATTTACAGCATAACTCAAGGCTAGAAGAGTTATTTGTCACCAAAGACCTTCGAGTTTGACTACG
131 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
* * *
15734 CTCAGCTCTAAGACACATTATTTGATGTATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACTC
196 CTCAGCTCTAAGGCACATCATTTGATGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTC
* * *
15799 TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGT
261 TCGAGTTCGATTACACTCAGCTTCAAGAGCACATCATTAGCAGCATAACTTAAGTCGAGAAGGGT
15864 TATA
326 TATA
* *
15868 TGCCAACCAAAGACCTTTGAGCTT-GATTACGCTCAGCTCCAAGGCACATCATTTGTAGTATAAC
1 TGCCAACCAAAGACCTTTGAG-TTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAAC
* * *
15932 TTAAGTCGATAAGGGCTATCTGCCAAAGACCCTCGAGTTTGATTACACTCAGCTTCGAGGGCACA
65 TTAAGTCGAGAAGGGCTATCTTCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACA
* *
15997 TAATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCAACTAC
130 TCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTAC
*
16062 GCTCAGCT-TCAAGGCACATCATTTGCA-GTATAACTTAAGTCGAGAAGGGCTATCTGCCAA
195 GCTCAGCTCT-AAGGCACATCATTTG-ATGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
16122 CTGAAGACCT
Statistics
Matches: 524, Mismatches: 54, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
328 1 0.00
329 444 0.85
330 4 0.01
331 7 0.01
332 68 0.13
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (329 bp):
TGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGTATAACT
TAAGTCGAGAAGGGCTATCTTCCAAAGACCCTCGAGTTCGATTACACTCAGCTTCGAGGGCACAT
CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACG
CTCAGCTCTAAGGCACATCATTTGATGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACTC
TCGAGTTCGATTACACTCAGCTTCAAGAGCACATCATTAGCAGCATAACTTAAGTCGAGAAGGGT
TATA
Found at i:16846 original size:73 final size:69
Alignment explanation
Indices: 16764--17120 Score: 204
Period size: 72 Copynumber: 5.1 Consensus size: 69
16754 AGTAATATAG
* *
16764 TATAATTTTTGAAAATGTTTTTGAAAACTATAATATATAGTTTTCAAAAAATATTTTTTGAAATA
1 TATAGTTTTT-AAAACGTTTTTGAAAACTATAATATATAG-TTTC-AAAAATATTTTTTGAAATA
16829 TATATTA
63 TATATTA
* **
16836 TATAGTTTTTTAAAACGTTTTTGAAAACTTATATACAATATATAAGTTTC-AAAACA-TTTTAAA
1 TATAG-TTTTTAAAACGTTTTTGAAAAC---TAT--AATATAT-AGTTTCAAAAATATTTTTTGA
*
16899 AATTATATAGTA
59 AA-TATATATTA
* * * * *
16911 TATAGTTTTCAAATA--ATTTTGAAAA-TATAATATATAGTTTAAAAAAACATTTTTGGAAAATT
1 TATAGTTTTTAAA-ACGTTTTTGAAAACTATAATATATAGTTT-CAAAAATATTTTTTG-AAA--
*
16973 TATATAATA
61 TATATATTA
* * * * **
16982 TATAGTTTTAAAAAAACATTTTGGAAAACT-TAA-ATA-ATTTTTTTAAAATCA-TTTTTGAAA-
1 TATAGTTTT--TAAAACGTTTTTGAAAACTATAATATATA-GTTTCAAAAAT-ATTTTTTGAAAT
*
17042 ACTATATAA
62 A-TATATTA
* * *
17051 TATAGTTTTGAAAAAGTTTTT--AAA-TATAATATATAGTTT-AAAGAT-TTTTTTGAAACATAT
1 TATAGTTTTTAAAACGTTTTTGAAAACTATAATATATAGTTTCAAAAATATTTTTTG-AA-ATAT
17111 ATATTA
64 ATATTA
17117 TATA
1 TATA
17121 TTATTATTAA
Statistics
Matches: 226, Mismatches: 30, Indels: 64
0.71 0.09 0.20
Matches are distributed among these distances:
64 7 0.03
65 12 0.05
66 22 0.10
67 17 0.08
68 7 0.03
69 21 0.09
70 3 0.01
71 21 0.09
72 31 0.14
73 24 0.11
74 25 0.11
75 23 0.10
77 11 0.05
78 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (69 bp):
TATAGTTTTTAAAACGTTTTTGAAAACTATAATATATAGTTTCAAAAATATTTTTTGAAATATAT
ATTA
Found at i:16978 original size:39 final size:36
Alignment explanation
Indices: 16792--17019 Score: 148
Period size: 39 Copynumber: 6.2 Consensus size: 36
16782 TTTTGAAAAC
**
16792 TATAATATATAGTTTTCAAAAAATATTTTTTG-AAA-TA
1 TATAATATATAG-TTT-AAAAAA-ACATTTTGAAAATTA
* *** *
16829 TATATTATATAGTTTTTTAAAACGTTTTTGAAAACTTA
1 TATAATATATAGTTTAAAAAAAC-ATTTTGAAAA-TTA
* *
16867 TATACAATATATAAGTTT--CAAAACATTTTAAAAATTA
1 TAT--AATATAT-AGTTTAAAAAAACATTTTGAAAATTA
* ** *
16904 TATAGTATATAGTTTTCAAATA-ATTTTG-AAA--A
1 TATAATATATAGTTTAAAAAAACATTTTGAAAATTA
16936 TATAATATATAGTTTAAAAAAACATTTTTGGAAAATTTA
1 TATAATATATAGTTTAAAAAAACA-TTTT-GAAAA-TTA
16975 TATAATATATAGTTTTAAAAAAACATTTTGGAAAACTTA
1 TATAATATATAG-TTTAAAAAAACATTTT-GAAAA-TTA
*
17014 AATAAT
1 TATAAT
17020 TTTTTTAAAA
Statistics
Matches: 155, Mismatches: 19, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
32 19 0.12
33 1 0.01
34 13 0.08
35 21 0.14
36 12 0.08
37 17 0.11
38 13 0.08
39 36 0.23
40 18 0.12
41 5 0.03
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.43
Consensus pattern (36 bp):
TATAATATATAGTTTAAAAAAACATTTTGAAAATTA
Found at i:16987 original size:71 final size:68
Alignment explanation
Indices: 16886--17092 Score: 185
Period size: 71 Copynumber: 3.0 Consensus size: 68
16876 TATAAGTTTC
* * *
16886 AAAACA-TTTTAAAAATTATATAGTATATAGTTTTCAAATAATTTTGAAAATATAATATATAGTT
1 AAAACATTTTTGAAAATTATATAATATATAGTTTT-AAAAAATTTTGAAAATATAATATATAGTT
16950 TAAA
65 TAAA
16954 AAAACATTTTTGGAAAATTTATATAATATATAGTTTTAAAAAAACATTTTGGAAAACT-TAA-AT
1 AAAACATTTTT-GAAAA-TTATATAATATATAGTTTT--AAAAA-ATTTT-GAAAA-TATAATAT
* **
17017 A-ATTTTTTTA
59 ATA-GTTTAAA
* * * *
17027 AAATCATTTTTGAAAACTATAT-A-ATATAGTTTTGAAAAAGTTTT-TAAATATAATATATAGTT
1 AAAACATTTTTGAAAATTATATAATATATAGTTTT-AAAAAATTTTGAAAATATAATATATAGTT
17089 TAAA
65 TAAA
17093 GATTTTTTTG
Statistics
Matches: 113, Mismatches: 15, Indels: 24
0.74 0.10 0.16
Matches are distributed among these distances:
64 1 0.01
65 6 0.05
66 7 0.06
67 5 0.04
68 11 0.10
69 14 0.12
70 5 0.04
71 23 0.20
72 10 0.09
73 22 0.19
74 8 0.07
75 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (68 bp):
AAAACATTTTTGAAAATTATATAATATATAGTTTTAAAAAATTTTGAAAATATAATATATAGTTT
AAA
Found at i:17146 original size:10 final size:10
Alignment explanation
Indices: 17133--17194 Score: 72
Period size: 10 Copynumber: 6.3 Consensus size: 10
17123 ATTATTAATA
17133 TTTATTTCAT
1 TTTATTTCAT
*
17143 TTTATTTTAT
1 TTTATTTCAT
17153 TTTATTTCAT
1 TTTATTTCAT
*
17163 TTCATTTCAT
1 TTTATTTCAT
* *
17173 GTTA-TTAAT
1 TTTATTTCAT
*
17182 TTAATTTCAT
1 TTTATTTCAT
17192 TTT
1 TTT
17195 TTGTCAGGGT
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
9 6 0.15
10 35 0.85
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTATTTCAT
Found at i:17147 original size:20 final size:20
Alignment explanation
Indices: 17124--17164 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17114 TTATATATTA
17124 TTATTA-ATATTTATTTCATT
1 TTATTATAT-TTTATTTCATT
*
17144 TTATTTTATTTTATTTCATT
1 TTATTATATTTTATTTCATT
17164 T
1 T
17165 CATTTCATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
TTATTATATTTTATTTCATT
Found at i:18295 original size:4 final size:4
Alignment explanation
Indices: 18280--18400 Score: 61
Period size: 4 Copynumber: 29.2 Consensus size: 4
18270 TTCAAAATAA
* * *
18280 TATT TTTT TATT TATT TAATT T-TT TCCTT TTTT TATTT TCATTT TATT
1 TATT TATT TATT TATT T-ATT TATT T-ATT TATT TA-TT T-A-TT TATT
* * * * * *
18328 TCTT TGATT TATTT CTATT TATT TAAT GATT T-TT TA-G TCTT TATT T-CT
1 TATT T-ATT TA-TT -TATT TATT TATT TATT TATT TATT TATT TATT TATT
18376 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
18401 TTCTATCTAA
Statistics
Matches: 90, Mismatches: 16, Indels: 22
0.70 0.12 0.17
Matches are distributed among these distances:
3 9 0.10
4 56 0.62
5 18 0.20
6 7 0.08
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:18304 original size:19 final size:19
Alignment explanation
Indices: 18277--18420 Score: 59
Period size: 19 Copynumber: 7.6 Consensus size: 19
18267 ACTTTCAAAA
*
18277 TAATATTTTTTTATTTATT
1 TAATTTTTTTTTATTTATT
**
18296 TAATTTTTTCCT-TTT-TT
1 TAATTTTTTTTTATTTATT
* *
18313 T-ATTTTCATTTTATTTCTT
1 TAATTTT-TTTTTATTTATT
* * *
18332 TGATTTATTTCTATTTATT
1 TAATTTTTTTTTATTTATT
** * *
18351 TAATGATTTTTTA-GTCTT
1 TAATTTTTTTTTATTTATT
*
18369 T-ATTTCTTATTTATTTATT
1 TAATTT-TTTTTTATTTATT
*
18388 T-ATTTATTTATTT-TTCTATC
1 TAATTT-TTT-TTTATT-TATT
18408 TAATATTTTTTTT
1 TAAT-TTTTTTTT
18421 GCCTTTGTCA
Statistics
Matches: 90, Mismatches: 25, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
16 5 0.06
17 7 0.08
18 16 0.18
19 41 0.46
20 14 0.16
21 5 0.06
22 2 0.02
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (19 bp):
TAATTTTTTTTTATTTATT
Found at i:18342 original size:23 final size:22
Alignment explanation
Indices: 18280--18400 Score: 76
Period size: 22 Copynumber: 5.6 Consensus size: 22
18270 TTCAAAATAA
* *
18280 TATTTTTTTATTTATTTAATTT
1 TATTTCTTTATTTATTTCATTT
* *
18302 T-TTCCTTTTTTTATTTTCATTT
1 TATTTCTTTATTTA-TTTCATTT
18324 TATTTCTTTGATTTATTTC-TATT
1 TATTTCTTT-ATTTATTTCAT-TT
** *
18347 TATTTAATGATTT-TTT-AGTCTT
1 TATTTCTTTATTTATTTCA-T-TT
18369 TATTTC-TTATTTATTT-A-TT
1 TATTTCTTTATTTATTTCATTT
*
18388 TATTTATTTATTT
1 TATTTCTTTATTT
18401 TTCTATCTAA
Statistics
Matches: 78, Mismatches: 13, Indels: 18
0.72 0.12 0.17
Matches are distributed among these distances:
19 7 0.09
20 6 0.08
21 17 0.22
22 26 0.33
23 18 0.23
24 4 0.05
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTTCTTTATTTATTTCATTT
Found at i:25747 original size:3 final size:3
Alignment explanation
Indices: 25741--25806 Score: 98
Period size: 3 Copynumber: 22.0 Consensus size: 3
25731 TTTACTCATT
* *
25741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
25789 -TA TATA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA
25807 AAAAAATAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.04
3 52 0.91
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:27988 original size:32 final size:30
Alignment explanation
Indices: 27918--27988 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
27908 TCTTTTCAAA
*
27918 ATTTTTTTTATATATATACTTATTATTTTC
1 ATTTTATTTATATATATACTTATTATTTTC
** * *
27948 ATAGTATTTATATATTTTCTTATTAATATTTC
1 ATTTTATTTATATATATACTTATT-AT-TTTC
27980 ATTTTATTT
1 ATTTTATTT
27989 GCAAGTATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
30 19 0.59
31 2 0.06
32 11 0.34
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (30 bp):
ATTTTATTTATATATATACTTATTATTTTC
Found at i:31289 original size:15 final size:15
Alignment explanation
Indices: 31269--31300 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
31259 ATCAATACCT
31269 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
31284 TTTTGCATACATTCA
1 TTTTGCATACATGCA
31299 TT
1 TT
31301 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:38993 original size:16 final size:17
Alignment explanation
Indices: 38967--39029 Score: 67
Period size: 16 Copynumber: 3.7 Consensus size: 17
38957 TTTGAATACA
*
38967 ATTCTATTTATTTTAAG
1 ATTCAATTTATTTTAAG
*
38984 -TTCAATTTA-TTTGAG
1 ATTCAATTTATTTTAAG
*
38999 ATTCAATTTATTTTCGAAA
1 ATTCAATTTATTTT--AAG
39018 ATTCAATTTATT
1 ATTCAATTTATT
39030 CTTCTATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 5 0.13
16 17 0.45
17 3 0.08
19 13 0.34
ACGTcount: A:0.32, C:0.08, G:0.06, T:0.54
Consensus pattern (17 bp):
ATTCAATTTATTTTAAG
Found at i:40230 original size:92 final size:92
Alignment explanation
Indices: 40070--40250 Score: 301
Period size: 92 Copynumber: 2.0 Consensus size: 92
40060 AAAATCAATC
*
40070 ATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
* *
40135 GGTTTGGTAT-GAACCACAGAACCAGTT
66 GGTTTGATATAAAACC-CAGAACCAGTT
* *
40162 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTCTCTGATTT
1 ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
40227 GGTTTGATATAAAACCCAGAACCA
66 GGTTTGATATAAAACCCAGAACCA
40251 ATCATTGGAA
Statistics
Matches: 83, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 79 0.95
93 4 0.05
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (92 bp):
ATTGAATTTGGAAGAGGAATGTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
GGTTTGATATAAAACCCAGAACCAGTT
Found at i:41158 original size:113 final size:113
Alignment explanation
Indices: 40996--41637 Score: 1027
Period size: 113 Copynumber: 5.7 Consensus size: 113
40986 TGTCAGTTAC
*
40996 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
41061 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
41109 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
41174 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
* *
41222 AGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATAAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* *
41287 AACCTTTTGCTCAAATCCATCACTTGATGGATTAGTTTTGCCAGAGAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
41335 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* *
41400 AACCTTTTGCTCAAATCCATCATTTGATGGATCAGCTTCT-CCAGAAAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTT-TGCCAGAGAA
* *
41448 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAAAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
* ** * * * **
41513 AACCTTTTGTTTGAATTCATCATTTGATGGATCAGCATCCCCA-ATGAAA
66 AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGA-G-AA
* * * **
41562 GAGTTCATAATGAGAAAAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 -AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
*
41627 CGACCTTTTGC
65 CAACCTTTTGC
41638 ATGACTCTAT
Statistics
Matches: 497, Mismatches: 27, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
112 1 0.00
113 425 0.86
114 3 0.01
115 68 0.14
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
AACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTGCCAGAGAA
Found at i:41980 original size:3 final size:3
Alignment explanation
Indices: 41974--42027 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
41964 TTTACTCATT
*
41974 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
42019 TTA TTA TTA
1 TTA TTA TTA
42028 AAAAAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:44939 original size:2 final size:2
Alignment explanation
Indices: 44932--44959 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
44922 TTATCTTTTA
44932 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
44960 TATCTACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45174 original size:21 final size:21
Alignment explanation
Indices: 45150--45190 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
45140 CCGAACTATT
45150 AATGTTATATG-AATTTATATG
1 AATGTTA-ATGTAATTTATATG
*
45171 AATGTTAATGTTATTTATAT
1 AATGTTAATGTAATTTATAT
45191 TTTATCACCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (21 bp):
AATGTTAATGTAATTTATATG
Found at i:54867 original size:6 final size:6
Alignment explanation
Indices: 54856--54885 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
54846 GACTGCTTCT
*
54856 GAAAGG GAAAGG GAAAGG GAAAGA GAAAGG
1 GAAAGG GAAAGG GAAAGG GAAAGG GAAAGG
54886 AATTTCTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:58330 original size:20 final size:22
Alignment explanation
Indices: 58293--58336 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
58283 TATGAACAAA
*
58293 TTTAAAAATGTTATGTC-TCAT
1 TTTAAAAATGTTAGGTCTTCAT
*
58314 TTTAAAAGT-TTAGGTCTTCAT
1 TTTAAAAATGTTAGGTCTTCAT
58335 TT
1 TT
58337 ATCCATATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (22 bp):
TTTAAAAATGTTAGGTCTTCAT
Found at i:59902 original size:8 final size:8
Alignment explanation
Indices: 59891--59924 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
59881 GGAAAATGAA
59891 AGGGATTG
1 AGGGATTG
59899 AGGGATTG
1 AGGGATTG
59907 AGGGATTG
1 AGGGATTG
59915 AGGGA-TG
1 AGGGATTG
59922 AGG
1 AGG
59925 CTACGAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.19
8 21 0.81
ACGTcount: A:0.26, C:0.00, G:0.53, T:0.21
Consensus pattern (8 bp):
AGGGATTG
Found at i:67469 original size:2 final size:2
Alignment explanation
Indices: 67462--67511 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
67452 GCTATGGGTC
67462 AT AT AT AT 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 AT AT AT AT
67504 AT AT AT AT
1 AT AT AT AT
67512 TCATGGTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80051 original size:2 final size:2
Alignment explanation
Indices: 80044--80087 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
80034 GGCATTAAAG
80044 AT AT AT AT 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 AT AT AT AT
80086 AT
1 AT
80088 TTTAAACATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.