Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001480.1 Hibiscus syriacus cultivar Beakdansim tig00002873_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: 157423
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:129190 original size:91 final size:90
Alignment explanation
Indices: 129013--129199 Score: 304
Period size: 91 Copynumber: 2.0 Consensus size: 90
129003 ATATTTCAAA
*
129013 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTA
129078 GCAGAATTGGCAGCAACCGAATAAATTT
63 GCAGAATTGGCAGCAACCGAATAAATTT
129106 ACTTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAG
1 ACTTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAG
*
129170 CAGTATTGGCAGCAACCGAATAAATTT
64 CAGAATTGGCAGCAACCGAATAAATTT
129197 ACT
1 ACT
129200 AAGCAATCTA
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.47
93 21 0.23
95 27 0.30
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (90 bp):
ACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
GAATTGGCAGCAACCGAATAAATTT
Found at i:129402 original size:63 final size:63
Alignment explanation
Indices: 129343--129484 Score: 151
Period size: 63 Copynumber: 2.3 Consensus size: 63
129333 CTTAGAGCGG
* * * *
129343 CAACCTCAC-CACGTAAAGTAGACACCTCCGCACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTC-CTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* * * *** *
129406 CGATCTCCTCACGCAAGGCATTGACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTAC
1 CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
* *
129469 CGATCTCCTCACGCAA
1 CAACCTCCTCACGCAA
129485 GGCATTGACC
Statistics
Matches: 69, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
62 1 0.01
63 68 0.99
ACGTcount: A:0.26, C:0.37, G:0.18, T:0.19
Consensus pattern (63 bp):
CAACCTCCTCACGCAAAGCAGACACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGCAC
Found at i:129485 original size:63 final size:63
Alignment explanation
Indices: 129366--129496 Score: 253
Period size: 63 Copynumber: 2.1 Consensus size: 63
129356 TAAAGTAGAC
*
129366 ACCTCCGCACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
129429 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
1 ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
129492 ACCTC
1 ACCTC
129497 ATCACGTAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
63 67 1.00
ACGTcount: A:0.23, C:0.37, G:0.19, T:0.21
Consensus pattern (63 bp):
ACCTCCACACGCCATGCACCATCGTTATCGCGTAGAGTACCGATCTCCTCACGCAAGGCATTG
Found at i:131014 original size:33 final size:33
Alignment explanation
Indices: 130972--131036 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
130962 ACGAGATAAT
**
130972 GAGAATCGCAACGCGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAACGA
131005 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGAAAATCGCAACG
131037 CGAAATGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAACGA
Found at i:131031 original size:52 final size:52
Alignment explanation
Indices: 130955--131091 Score: 211
Period size: 52 Copynumber: 2.6 Consensus size: 52
130945 TTGAAATGAA
* * **
130955 AATCGCAACGAGATAATGAGAATCGCAACGCGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
131008 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
* *
131060 AATCGCAACGCGAAATGAAAATCACAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
131092 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 66 0.85
53 12 0.15
ACGTcount: A:0.45, C:0.21, G:0.23, T:0.12
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:131091 original size:19 final size:19
Alignment explanation
Indices: 130947--131082 Score: 139
Period size: 19 Copynumber: 7.6 Consensus size: 19
130937 TCTTTTGGTT
*
130947 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
130966 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
130986 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
131003 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
131019 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
131038 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
131055 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
131071 GAAATGAAAATC
1 GAAATGAAAATC
131083 ACAATGCGAT
Statistics
Matches: 97, Mismatches: 9, Indels: 22
0.76 0.07 0.17
Matches are distributed among these distances:
14 19 0.20
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 49 0.51
20 17 0.18
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:131109 original size:19 final size:19
Alignment explanation
Indices: 131087--131131 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
131077 AAAATCACAA
*
131087 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
131106 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
131125 TGCGATT
1 TGCGATT
131132 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:131709 original size:20 final size:20
Alignment explanation
Indices: 131685--131817 Score: 153
Period size: 20 Copynumber: 6.7 Consensus size: 20
131675 CGCTATGTAA
* * *
131685 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
131705 ATCGC-TTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
131724 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
131745 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
131765 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
131785 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
131805 ATCGCATTGCGAT
1 ATCGCATTGCGAT
131818 TTTCCCAATT
Statistics
Matches: 99, Mismatches: 10, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
19 20 0.20
20 65 0.66
21 12 0.12
22 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:131857 original size:81 final size:80
Alignment explanation
Indices: 131685--131838 Score: 193
Period size: 81 Copynumber: 1.9 Consensus size: 80
131675 CGCTATGTAA
* * * ** *
131685 ATCGCGTTGCGAAAGTCAGAATCGCTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGC
1 ATCGCATTGCGAAAGTCAGAATCGCTTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGC
131750 ATTGCGATAGTAAGT
66 ATTGCGATAGTAAGT
* * *
131765 ATCGCATTGCGATAGTCAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TC
1 ATCGCATTGCGAAAGTCAGAATCGC-TTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATC
*
131829 GCGTTGCGAT
64 GCATTGCGAT
131839 TTACTTATTC
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
80 22 0.35
81 38 0.61
82 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.32
Consensus pattern (80 bp):
ATCGCATTGCGAAAGTCAGAATCGCTTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGC
ATTGCGATAGTAAGT
Found at i:135428 original size:28 final size:26
Alignment explanation
Indices: 135383--135449 Score: 62
Period size: 26 Copynumber: 2.5 Consensus size: 26
135373 TGTATAGCAT
*
135383 ATATGATATTATACATAATAATTTCAAAA
1 ATAT-ATAATATACAT-A-AATTTCAAAA
* **
135412 ATATATAATATATATAAATTTTGAAA
1 ATATATAATATACATAAATTTCAAAA
*
135438 ATATATAGTATA
1 ATATATAATATA
135450 GTTTTTGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 19 0.58
27 1 0.03
28 9 0.27
29 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (26 bp):
ATATATAATATACATAAATTTCAAAA
Found at i:135454 original size:21 final size:20
Alignment explanation
Indices: 135418--135476 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
135408 AAAAATATAT
*
135418 AATATATATA-AATTTTGAA
1 AATATATATATAGTTTTGAA
135437 AATATATAGTATAGTTTTTGAA
1 AATATATA-TATAG-TTTTGAA
*
135459 AACATATTATATAGTTTT
1 AATATA-TATATAGTTTT
135477 TTTTAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
19 8 0.24
20 2 0.06
21 5 0.15
22 17 0.50
23 2 0.06
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (20 bp):
AATATATATATAGTTTTGAA
Found at i:135455 original size:22 final size:22
Alignment explanation
Indices: 135430--135540 Score: 89
Period size: 22 Copynumber: 4.7 Consensus size: 22
135420 TATATATAAA
*
135430 TTTTGAAAATATA-TAGTATAGT
1 TTTTGAAAACATATTA-TATAGT
135452 TTTTGAAAACATATTATATAGTTTT
1 TTTTGAAAACATATTATATAG---T
*
135477 TTTTAAAAAAAACATATAATATATAGT
1 TTTT---GAAAACATAT--TATATAGT
* *
135504 TTTTGAAAATATATAATATAGT
1 TTTTGAAAACATATTATATAGT
*
135526 TTTTAAAAACATATT
1 TTTTGAAAACATATT
135541 GTTACATATA
Statistics
Matches: 72, Mismatches: 8, Indels: 18
0.73 0.08 0.18
Matches are distributed among these distances:
22 36 0.50
23 2 0.03
24 8 0.11
25 5 0.07
27 5 0.07
28 9 0.12
30 7 0.10
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTTGAAAACATATTATATAGT
Found at i:135506 original size:28 final size:27
Alignment explanation
Indices: 135457--135512 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
135447 ATAGTTTTTG
*
135457 AAAACATATTATATAGTTTTTTTTAAAA
1 AAAACATATTATATAG-TTTTTTGAAAA
135485 AAAACATATAATATATAG-TTTTTGAAAA
1 AAAACATAT--TATATAGTTTTTTGAAAA
135513 TATATAATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 18 0.72
30 7 0.28
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (27 bp):
AAAACATATTATATAGTTTTTTGAAAA
Found at i:135576 original size:58 final size:56
Alignment explanation
Indices: 135488--135608 Score: 201
Period size: 58 Copynumber: 2.2 Consensus size: 56
135478 TTTAAAAAAA
135488 ACATATAATATATAGTTTTTGAAAATATATAATATAGTTTTTAAAAACATATTGTT
1 ACATATAATATATAGTTTTTGAAAATATATAATATAGTTTTTAAAAACATATTGTT
*
135544 ACATATAATATATACAGTTTTTGAAAATATATAGTATAGTTTTTAAAAACATATTGTT
1 ACATATAATATAT--AGTTTTTGAAAATATATAATATAGTTTTTAAAAACATATTGTT
135602 -C-TATAAT
1 ACATATAAT
135609 TTTTAAAACG
Statistics
Matches: 62, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
56 19 0.31
57 1 0.02
58 42 0.68
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (56 bp):
ACATATAATATATAGTTTTTGAAAATATATAATATAGTTTTTAAAAACATATTGTT
Found at i:135587 original size:22 final size:21
Alignment explanation
Indices: 135551--135597 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
135541 GTTACATATA
* *
135551 ATATATACAGTTTTTGAAAAT
1 ATATATACAGTTTTTAAAAAC
*
135572 ATATAGTATAGTTTTTAAAAAC
1 ATATA-TACAGTTTTTAAAAAC
135594 ATAT
1 ATAT
135598 TGTTCTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (21 bp):
ATATATACAGTTTTTAAAAAC
Found at i:135656 original size:19 final size:21
Alignment explanation
Indices: 135622--135660 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
135612 TAAAACGTAT
135622 TATATGATTTTGAAAATATAA
1 TATATGATTTTGAAAATATAA
135643 TATAT-ATTTT-AAAATATA
1 TATATGATTTTGAAAATATA
135661 TATTAAGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TATATGATTTTGAAAATATAA
Found at i:135661 original size:21 final size:21
Alignment explanation
Indices: 135622--135662 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
135612 TAAAACGTAT
*
135622 TATATGATTTTGAAAATATAA
1 TATATGATTTTAAAAATATAA
135643 TATAT-ATTTTAAAATATATA
1 TATATGATTTTAAAA-ATATA
135663 TTAAGCTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TATATGATTTTAAAAATATAA
Found at i:136629 original size:21 final size:21
Alignment explanation
Indices: 136583--136629 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
136573 TGGGAAGAGT
**
136583 TGAGAGGTTTTTTAGAGGTGA
1 TGAGAGGTTTTTTAGAAATGA
*
136604 GGAGA-GTTTTTTATGAAATGA
1 TGAGAGGTTTTTTA-GAAATGA
136625 TGAGA
1 TGAGA
136630 TAAATGTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.34, T:0.36
Consensus pattern (21 bp):
TGAGAGGTTTTTTAGAAATGA
Found at i:138026 original size:12 final size:11
Alignment explanation
Indices: 138002--138031 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
137992 TAGGAATTTT
138002 TTATTTTATTA
1 TTATTTTATTA
138013 TTATTTTGATTA
1 TTATTTT-ATTA
138025 TTATTTT
1 TTATTTT
138032 TATCTTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.73
Consensus pattern (11 bp):
TTATTTTATTA
Found at i:140745 original size:24 final size:24
Alignment explanation
Indices: 140718--140775 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
140708 TCATTTGCTA
*
140718 CAAAAGTACAA-TCTTCATCTACTG
1 CAAAAGCACAAGT-TTCATCTACTG
* * *
140742 CAAAGGCACAAGTTTCTTCTGCTG
1 CAAAAGCACAAGTTTCATCTACTG
140766 CAAAAGCACA
1 CAAAAGCACA
140776 GACCTCTGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.36, C:0.26, G:0.14, T:0.24
Consensus pattern (24 bp):
CAAAAGCACAAGTTTCATCTACTG
Found at i:142507 original size:22 final size:23
Alignment explanation
Indices: 142479--142540 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
142469 GAAGTTATGG
142479 AGTTTTTGAAAATATATAG-TAT
1 AGTTTTTGAAAATATATAGTTAT
* * *
142501 AGTTTTTAAAAACATATTGTTAT
1 AGTTTTTGAAAATATATAGTTAT
142524 A-TAATTTTGAAAATATA
1 AGT--TTTTGAAAATATA
142541 ATATATATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 17 0.53
23 4 0.12
24 11 0.34
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (23 bp):
AGTTTTTGAAAATATATAGTTAT
Found at i:144652 original size:209 final size:212
Alignment explanation
Indices: 143989--144800 Score: 1208
Period size: 215 Copynumber: 3.8 Consensus size: 212
143979 ATTTAAGAAT
143989 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A-GAG
* * * *
144054 TGATCAAATCGAAATACTTTTAAATTGTGAGGTTGAAATTAATAAAAAAAATACTAAATTATACT
63 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACT
* * * * * ** * *
144119 CATTTTAAAATTTATGGGCCAATTAAAAAATAGAATTATGTAATATTTATGGATCAATTTCATAT
128 CATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGAT
*
144184 GCAAATAAAATTTGGAGGAA
193 GCAAATAAAATTTGGAGGAC
144204 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACA-T-A-GAG
*
144269 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
63 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-AAAAAGTACTAAATTATAC
* **
144334 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATCGGTATGGGTCAATTTCAGA
127 TCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
144399 TGCAAATAAAATTTGGAGGAC
192 TGCAAATAAAATTTGGAGGAC
* *
144420 TAAATAG-ACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACA-A-A-AGGGA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGGGA
* *
144481 TCAAATCGAAATAATTTTAAGTTTTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACTCAT
66 TCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACTCAT
* *
144546 TTAAAAAGTTGTGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGGTGCA
131 TTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCA
144611 AATAAAATTTGGAGGAC
196 AATAAAATTTGGAGGAC
** * *
144628 TAAATTGAACAAATATGAAATTACAAATAAAAAAGTAAATATATTAAACAACACA-A-A-AAGGA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGGGA
* *
144690 TCAAATCGAAGTAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATACTCA
66 TCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAA-GTACTAAATTATACTCA
*
144755 TTTAAAAAGTTATGGGCCAA-TTAATAAATAGAAAAAAGTAATAAGT
130 TTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
144801 TGAGAAAAAA
Statistics
Matches: 558, Mismatches: 35, Indels: 13
0.92 0.06 0.02
Matches are distributed among these distances:
208 106 0.19
209 144 0.26
210 56 0.10
211 1 0.00
214 1 0.00
215 152 0.27
216 98 0.18
ACGTcount: A:0.50, C:0.08, G:0.13, T:0.30
Consensus pattern (212 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATAGAGGGA
TCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAGTACTAAATTATACTCAT
TTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCA
AATAAAATTTGGAGGAC
Found at i:144864 original size:20 final size:20
Alignment explanation
Indices: 144824--144909 Score: 90
Period size: 20 Copynumber: 4.3 Consensus size: 20
144814 AAAACAACTA
* *
144824 ATATATATA-TATATA-TAT
1 ATATATAAACTATATAGTTT
144842 ATATATAAACTATATAGTTT
1 ATATATAAACTATATAGTTT
*
144862 ATATATAAAGTATAT-GTATTAT
1 ATATATAAACTATATAG--TT-T
144884 ATATATAAACT-TATAGTTT
1 ATATATAAACTATATAGTTT
144903 ATATATA
1 ATATATA
144910 TTATGTATAA
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
18 8 0.14
19 15 0.26
20 18 0.31
21 5 0.09
22 12 0.21
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (20 bp):
ATATATAAACTATATAGTTT
Found at i:144899 original size:41 final size:43
Alignment explanation
Indices: 144829--144909 Score: 139
Period size: 41 Copynumber: 1.9 Consensus size: 43
144819 AACTAATATA
144829 TATATATATATATATATATAAACTATATAGTTTATATATAAAG
1 TATATATATATATATATATAAACTATATAGTTTATATATAAAG
*
144872 TATATGTAT-TATATATATAAACT-TATAGTTTATATATA
1 TATATATATATATATATATAAACTATATAGTTTATATATA
144910 TTATGTATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
41 15 0.41
42 14 0.38
43 8 0.22
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (43 bp):
TATATATATATATATATATAAACTATATAGTTTATATATAAAG
Found at i:144910 original size:2 final size:2
Alignment explanation
Indices: 144824--144890 Score: 64
Period size: 2 Copynumber: 32.5 Consensus size: 2
144814 AAAACAACTA
* *
144824 AT AT AT AT AT AT AT AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT
* *
144868 AA AGT AT AT GT AT -T AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT A
144891 AACTTATAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
1 1 0.02
2 49 0.92
3 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:144997 original size:31 final size:31
Alignment explanation
Indices: 144955--145013 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
144945 AAACTATAAT
* *
144955 ACTATATAGTTTATATATGAACTATATAGAA
1 ACTACATAGTTTATATATAAACTATATAGAA
*
144986 ACTACATAGTTTATATATAAATTATATA
1 ACTACATAGTTTATATATAAACTATATA
145014 TGAATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.41
Consensus pattern (31 bp):
ACTACATAGTTTATATATAAACTATATAGAA
Found at i:145021 original size:22 final size:22
Alignment explanation
Indices: 144966--145033 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
144956 CTATATAGTT
* *
144966 TATATATGAACTATATAGAAAC
1 TATATATGAATTATATATAAAC
* * *
144988 TACATA-G-TTTATATATAAAT
1 TATATATGAATTATATATAAAC
145008 TATATATGAATTATATATAAAC
1 TATATATGAATTATATATAAAC
145030 TATA
1 TATA
145034 CAATTCATAT
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 14 0.39
21 2 0.06
22 20 0.56
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (22 bp):
TATATATGAATTATATATAAAC
Found at i:145100 original size:17 final size:16
Alignment explanation
Indices: 145055--145103 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
145045 TAATATTATG
145055 TATA-ATTATAAATAA
1 TATATATTATAAATAA
*
145070 TATATATTGT--ATAA
1 TATATATTATAAATAA
145084 TACTATATTATAAATAA
1 TA-TATATTATAAATAA
145101 TAT
1 TAT
145104 TAACTTTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 6 0.21
15 11 0.39
16 5 0.18
17 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TATATATTATAAATAA
Found at i:145114 original size:31 final size:29
Alignment explanation
Indices: 145059--145138 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
145049 ATTATGTATA
145059 ATTATAAATAATA-TATATTGTATAATACTAT
1 ATTATAAATAATATTA-ATTGTAT-A-ACTAT
145090 ATTATAAATAATATTAACTT-TATAACTAT
1 ATTATAAATAATATTAA-TTGTATAACTAT
* *
145119 ATTTTATATTAATATTAATT
1 ATTATA-AATAATATTAATT
145139 ACAAATTATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 12 0.27
30 11 0.25
31 17 0.39
32 4 0.09
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (29 bp):
ATTATAAATAATATTAATTGTATAACTAT
Found at i:145133 original size:6 final size:6
Alignment explanation
Indices: 145124--145230 Score: 54
Period size: 6 Copynumber: 18.3 Consensus size: 6
145114 ACTATATTTT
* *
145124 ATATTA ATATT- A-ATTA CAAATTA TACATT- ATATT- ATATTA ATA-TA
1 ATATTA ATATTA ATATTA -ATATTA -ATATTA ATATTA ATATTA ATATTA
*
145169 A-GTTA ATATTA ATATT- A-ATT- ATATTA ATATTA AT-TATA ATATATA
1 ATATTA ATATTA ATATTA ATATTA ATATTA ATATTA ATAT-TA ATAT-TA
145214 ATTATTTTA ATATTA AT
1 A-TA--TTA ATATTA AT
145231 TATAAATAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 26
0.73 0.04 0.23
Matches are distributed among these distances:
4 7 0.08
5 21 0.25
6 34 0.41
7 13 0.16
8 4 0.05
9 3 0.04
10 1 0.01
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:145165 original size:34 final size:32
Alignment explanation
Indices: 145122--145230 Score: 116
Period size: 34 Copynumber: 3.3 Consensus size: 32
145112 TAACTATATT
145122 TTATATTAATATTAATTACAAATTATACATTATA
1 TTATATTAATATTAATTA-AAATTATA-ATTATA
*
145156 TTATATTAATA-TAAGTTAATATTA-ATATTA-A
1 TTATATTAATATTAA-TTAAAATTATA-ATTATA
* *
145187 TTATATTAATATTAATTATAATATATAATTATT
1 TTATATTAATATTAATTAAAAT-TATAATTATA
145220 TTAATATTAAT
1 TT-ATATTAAT
145231 TATAAATAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 12
0.79 0.06 0.15
Matches are distributed among these distances:
31 17 0.27
32 14 0.22
33 11 0.17
34 22 0.34
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (32 bp):
TTATATTAATATTAATTAAAATTATAATTATA
Found at i:145179 original size:21 final size:20
Alignment explanation
Indices: 145122--145204 Score: 66
Period size: 21 Copynumber: 4.0 Consensus size: 20
145112 TAACTATATT
145122 TTATATTAATATTA-ATTACAAA
1 TTATATTAATATTATATT---AA
145144 TTATACATT-ATATTATATTAA
1 TTAT--ATTAATATTATATTAA
145165 -TATAAGTTAATATTAATATTAA
1 TTAT-A-TTAATATT-ATATTAA
145187 TTATATTAATATTA-ATTA
1 TTATATTAATATTATATTA
145205 TAATATATAA
Statistics
Matches: 53, Mismatches: 1, Indels: 17
0.75 0.01 0.24
Matches are distributed among these distances:
19 5 0.09
20 6 0.11
21 15 0.28
22 12 0.23
23 9 0.17
24 6 0.11
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (20 bp):
TTATATTAATATTATATTAA
Found at i:145193 original size:31 final size:31
Alignment explanation
Indices: 145122--145232 Score: 122
Period size: 28 Copynumber: 3.6 Consensus size: 31
145112 TAACTATATT
* *
145122 TTATATTAATATTAATTACAAATTATACATTATA
1 TTATATTAATATTAATTA-ATATTA-ATATTA-A
145156 TTATATTAATA-TAAGTTAATATTAATATTAA
1 TTATATTAATATTAA-TTAATATTAATATTAA
*
145187 TTATATTAATATTAATT-ATAAT-ATA-TAA
1 TTATATTAATATTAATTAATATTAATATTAA
*
145215 TTATTTTAATATTAATTA
1 TTATATTAATATTAATTA
145233 TAAATAATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
28 19 0.27
29 3 0.04
30 4 0.06
31 14 0.20
32 8 0.11
33 8 0.11
34 14 0.20
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (31 bp):
TTATATTAATATTAATTAATATTAATATTAA
Found at i:145224 original size:28 final size:27
Alignment explanation
Indices: 145178--145255 Score: 108
Period size: 28 Copynumber: 3.0 Consensus size: 27
145168 AAGTTAATAT
145178 TAATATTAATTATATTAATATTAATTA
1 TAATATTAATTATATTAATATTAATTA
*
145205 TAATATATAATTATTTTAATATTAATTA
1 TAATAT-TAATTATATTAATATTAATTA
*
145233 TAA-A-TAATT-TATTAATATAAATT
1 TAATATTAATTATATTAATATTAATT
145256 TTATAGGGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
24 12 0.26
25 5 0.11
27 7 0.15
28 23 0.49
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
TAATATTAATTATATTAATATTAATTA
Found at i:147917 original size:24 final size:20
Alignment explanation
Indices: 147872--147909 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
147862 TTGATTCTGC
147872 TTGCTTCTGTTTTATATTGT
1 TTGCTTCTGTTTTATATTGT
*
147892 TTGCTTCTGTTTGATATT
1 TTGCTTCTGTTTTATATT
147910 ACTTGTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.11, C:0.11, G:0.16, T:0.63
Consensus pattern (20 bp):
TTGCTTCTGTTTTATATTGT
Found at i:147919 original size:20 final size:20
Alignment explanation
Indices: 147871--147929 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
147861 CTTGATTCTG
* *
147871 CTTGCTTCTGTTTTATATTG
1 CTTGCTTCTGTTTGATATTA
*
147891 TTTGCTTCTGTTTGATATTA
1 CTTGCTTCTGTTTGATATTA
* **
147911 CTTGTTTCTACTTGATATT
1 CTTGCTTCTGTTTGATATT
147930 TGTACGGGTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (20 bp):
CTTGCTTCTGTTTGATATTA
Found at i:148731 original size:18 final size:17
Alignment explanation
Indices: 148685--148735 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
148675 TATGAATTGG
148685 AATTAATATAAAAATCA
1 AATTAATATAAAAATCA
*
148702 AATTTATAATATAAAAATTA
1 AA--T-TAATATAAAAATCA
148722 TAATTAATATAAAA
1 -AATTAATATAAAA
148736 TTAAATTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 2 0.07
18 10 0.34
19 2 0.07
20 13 0.45
21 2 0.07
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
AATTAATATAAAAATCA
Found at i:148825 original size:17 final size:17
Alignment explanation
Indices: 148803--148842 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
148793 TTAAAGAGTA
148803 ATCATATTAATTTAATT
1 ATCATATTAATTTAATT
148820 ATCATATTAATTTAATT
1 ATCATATTAATTTAATT
148837 ATCATA
1 ATCATA
148843 AGTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (17 bp):
ATCATATTAATTTAATT
Found at i:155944 original size:52 final size:52
Alignment explanation
Indices: 155870--155969 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
155860 GGGCACATAG
*
155870 AAATAGGAAAATAGCCTAGAGTTAGGGGATTACAACTAATTACAAGGAACAT
1 AAATAGGAAAATAGCCTAGAGTTAGGGGATTACAACTAAGTACAAGGAACAT
* *
155922 AAATAGGAGATTAGCCTAGAGTTAGGGGATTACAACTAAGTACAAGGA
1 AAATAGGAAAATAGCCTAGAGTTAGGGGATTACAACTAAGTACAAGGA
155970 TATTATAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.44, C:0.11, G:0.24, T:0.21
Consensus pattern (52 bp):
AAATAGGAAAATAGCCTAGAGTTAGGGGATTACAACTAAGTACAAGGAACAT
Done.