Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006862.1 Hibiscus syriacus cultivar Beakdansim tig00017454_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: 80977
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1417 original size:317 final size:318
Alignment explanation
Indices: 594--1796 Score: 1414
Period size: 317 Copynumber: 3.8 Consensus size: 318
584 TTATTTACTG
* * *
594 AAATCATTTGGCCACCATCATTTGTGGAGAGATATGAAATTGGAG-----TTGTAAGAATAGAGA
1 AAATCATTTGGCCACCATCATTTGTGGAGAGATGTGAAATTGGAGTTTAATTATAATAATAGAGA
*** *
654 ATGAATCA-AAAGTAGGAAGTTGTATATTCATTCAGCCAAACAACTTTCAGATGTCCGGCACAAC
66 ATGAATCAGAAAGTAGGAAGTTG-ATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAAC
* * * * *
718 ACAAATAGACTACTCCAGGAAAACATCGAGGATGAAACCATTCATAATTACCTCCTATACTTCAT
130 ACAAATAGGCTGCACCAGGAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCAT
* * * * * *
783 CACCTTCCGCTCTATTCAAGAAAAAAATCTCTGTACTTATTACTTATAGAAAAGAAAGTTCCAAA
195 CACCTTCCTCTCTATTCAAG-AGAACATCTCTATACTTATTGCTTATAGAAAAGAAAGTTCTAAA
* *
848 TAGGATATTACAAAGAAAAAAT-TTATTTTGGTGCTCGGAACACCTATTCCATATCTGCTGA
259 TA--ATATTACAAAAAAAAAATATTATTTTGGTGCTCGGAACACCTATTCCCTATCTGCTGA
* *
909 AAATTATTTGGCCACCATCATTTGTGGAGAGATGTGAAATTGGAG------T-TAATAATAGATA
1 AAATCATTTGGCCACCATCATTTGTGGAGAGATGTGAAATTGGAGTTTAATTATAATAATAGAGA
* * * * * *
967 ATGAATTAAAAAGTATGAAGTTG-TATTCATTTAGCCAAAC-A-TCCCAGATGTTCGACACAACA
66 ATGAATCAGAAAGTAGGAAGTTGATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAACA
* * **
1029 C-AATAGGCTGCACCAGGAAAATATCAAGTTTGAAACCAGTCATAATTACCTCCTATACTTCATC
131 CAAATAGGCTGCACCAGGAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATC
* *
1093 ACCTTCCTCTCTATTCAAGAGAACATCTCTATGCTTATT-CTTATAGAAAAAAAAAGTT-TAAAT
196 ACCTTCCTCTCTATTCAAGAGAACATCTCTATACTTATTGCTTATAG-AAAAGAAAGTTCTAAAT
* *
1156 AAGATTACAAAAAAAAAATATTATTTTGGTGCTCGGAACACCGATTCCCTATCTGCTGA
260 AATATTACAAAAAAAAAATATTATTTTGGTGCTCGGAACACCTATTCCCTATCTGCTGA
*** *
1215 AAATCATTTGG-CATTGTCATTTGTGAAGAGATGTGAAATTGGAGTTTAAATTATAATAATAGAG
1 AAATCATTTGGCCACCATCATTTGTGGAGAGATGTGAAATTGGAGTTT-AATTATAATAATAGAG
*
1279 AATGAATTAGAAAGTAGGAAGTTGTATATTCATTCAGCCAAACAACCCCCCAGAT-TT-GGCACA
65 AATGAATCAGAAAGTAGGAAGTTG-ATATTCATTCAGCCAAACAA-CCCCCAGATGTTCGGCACA
* * * * *
1342 TCACAAATAGGCTGCACCAGAAAAACATCGAGGCTGAAACCGGTCATAATTACCTCCTGTACTCC
128 ACACAAATAGGCTGCACCAGGAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTC
* *
1407 ATCCCCTTCCTTTCTATTCAAGAGAACATCTCTATACTTATTGCTTATAGAAAAGAAAGTTCTAA
193 ATCACCTTCCTCTCTATTCAAGAGAACATCTCTATACTTATTGCTTATAGAAAAGAAAGTTCTAA
* ** **
1472 ATAGAATATTACAAAGAAAAAATATATTATTTTGGTGCTCGGGACATATATTTTCTATCTGCTGA
258 AT--AATATTACAAA-AAAAAA-ATATTATTTTGGTGCTCGGAACACCTATTCCCTATCTGCTGA
* *
1537 AAATCATTTGGCCACCATCATTTGTGGA-AGATGTGAAATTGGAGTTATAACTTATAAGAATAAA
1 AAATCATTTGGCCACCATCATTTGTGGAGAGATGTGAAATTGGAGTT-TAA-TTATAATAATAGA
* * *
1601 GAATGAATCAGAAAGT----A--TGA-A---GTTCAGCCAAACAACCCTCAGATGTTCGGCACAG
64 GAATGAATCAGAAAGTAGGAAGTTGATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAA
* * *
1656 CAGAAATAGGCTAGCTACACCATGAAAACATCGAGGCTGAAACCAGTCATAATTACCTCATATAC
129 CACAAATAGGCT-G---CACCAGGAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATAC
* *
1721 TTCATCACCTT-ATCTCTATTCAAGAGAACATCTCTATACTTATTGCTTATAGGAAAGAAAGTTC
190 TTCATCACCTTCCTCTCTATTCAAGAGAACATCTCTATACTTATTGCTTATAGAAAAGAAAGTTC
*
1785 CAAATATATATT
255 TAAATA-ATATT
1797 CTCTGTTAAA
Statistics
Matches: 772, Mismatches: 83, Indels: 66
0.84 0.09 0.07
Matches are distributed among these distances:
305 45 0.06
306 47 0.06
307 12 0.02
308 26 0.03
309 73 0.09
310 18 0.02
311 9 0.01
312 32 0.04
313 66 0.09
314 16 0.02
315 65 0.08
316 64 0.08
317 157 0.20
318 19 0.02
319 1 0.00
320 10 0.01
321 6 0.01
322 67 0.09
323 39 0.05
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (318 bp):
AAATCATTTGGCCACCATCATTTGTGGAGAGATGTGAAATTGGAGTTTAATTATAATAATAGAGA
ATGAATCAGAAAGTAGGAAGTTGATATTCATTCAGCCAAACAACCCCCAGATGTTCGGCACAACA
CAAATAGGCTGCACCAGGAAAACATCGAGGCTGAAACCAGTCATAATTACCTCCTATACTTCATC
ACCTTCCTCTCTATTCAAGAGAACATCTCTATACTTATTGCTTATAGAAAAGAAAGTTCTAAATA
ATATTACAAAAAAAAAATATTATTTTGGTGCTCGGAACACCTATTCCCTATCTGCTGA
Found at i:4890 original size:6 final size:6
Alignment explanation
Indices: 4874--4911 Score: 58
Period size: 6 Copynumber: 6.0 Consensus size: 6
4864 CTTGATTGCA
4874 AAAATTT AAAATT AAAATT AAAATT AAAATTT AAAATT
1 AAAA-TT AAAATT AAAATT AAAATT AAAA-TT AAAATT
4912 CCGATTCGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 20 0.67
7 10 0.33
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (6 bp):
AAAATT
Found at i:4896 original size:12 final size:13
Alignment explanation
Indices: 4874--4911 Score: 69
Period size: 12 Copynumber: 3.0 Consensus size: 13
4864 CTTGATTGCA
4874 AAAATTTAAAATT
1 AAAATTTAAAATT
4887 AAAA-TTAAAATT
1 AAAATTTAAAATT
4899 AAAATTTAAAATT
1 AAAATTTAAAATT
4912 CCGATTCGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.50
13 12 0.50
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAATTTAAAATT
Found at i:6412 original size:11 final size:11
Alignment explanation
Indices: 6404--6433 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6394 AAATATAAAT
6404 AATAAATAACA
1 AATAAATAACA
*
6415 AATAAATAATA
1 AATAAATAACA
6426 AATAAATA
1 AATAAATA
6434 GAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAAATAACA
Found at i:6528 original size:38 final size:37
Alignment explanation
Indices: 6483--6802 Score: 140
Period size: 36 Copynumber: 8.9 Consensus size: 37
6473 AAAAAAAATG
6483 TATTCTAAAACCATATGACATA-ATATATTTTCAAAAAA
1 TATTCTAAAACCATAT-A-ATATATATATTTTCAAAAAA
* *
6521 TATTCTAAAACTATATAATATATATGTTTTC---AAA
1 TATTCTAAAACCATATAATATATATATTTTCAAAAAA
* * * *
6555 TAAT-T---A-TATATCATAT-T-TATTTTCAAAACA
1 TATTCTAAAACCATATAATATATATATTTTCAAAAAA
*
6585 T-TT-TAAAAACTATATAATATATAT-TTTT-AAAAAA
1 TATTCT-AAAACCATATAATATATATATTTTCAAAAAA
* * * * * *
6619 TGTTTTAAAATCTATATATTATATTTATTTT--TAAAA
1 TATTCTAAAA-CCATATAATATATATATTTTCAAAAAA
* * *
6655 TATTTTAAAAACTATATAATATATATATTTT-TAAAAA
1 TATTCT-AAAACCATATAATATATATATTTTCAAAAAA
* * * * * *
6692 TGTTTTAAAAACTATATATTATATTTATTTTC--AAAT
1 TATTCT-AAAACCATATAATATATATATTTTCAAAAAA
* * * **
6728 TGTTTTAAAAACTATATAATATATATATATTTTTAAAAA
1 TATTCT-AAAACCATATAATATATATAT-TTTCAAAAAA
* * * *
6767 TATTTTAAAAACTATATATTATATTTATTTTCAAAA
1 TATTCT-AAAACCATATAATATATATATTTTCAAAA
6803 TGTTTAAAAC
Statistics
Matches: 232, Mismatches: 29, Indels: 42
0.77 0.10 0.14
Matches are distributed among these distances:
27 6 0.03
28 1 0.00
29 11 0.05
30 4 0.02
33 2 0.01
34 21 0.09
35 11 0.05
36 74 0.32
37 53 0.23
38 21 0.09
39 28 0.12
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.47
Consensus pattern (37 bp):
TATTCTAAAACCATATAATATATATATTTTCAAAAAA
Found at i:6625 original size:36 final size:36
Alignment explanation
Indices: 6585--6811 Score: 264
Period size: 36 Copynumber: 6.2 Consensus size: 36
6575 TTTCAAAACA
*
6585 TTTTAAAAACTATATAATATATATTTTTAAAAAATG
1 TTTTAAAAACTATATAATATATATTTTTTAAAAATG
* * * *
6621 TTTTAAAATCTATATATTATAT-TTATTTTTAAAATA
1 TTTTAAAAACTATATAATATATATT-TTTTAAAAATG
6657 TTTTAAAAACTATATAATATATATATTTTTAAAAATG
1 TTTTAAAAACTATATAATATATAT-TTTTTAAAAATG
* * *
6694 TTTTAAAAACTATATATTATAT-TTATTTTCAAATTG
1 TTTTAAAAACTATATAATATATATT-TTTTAAAAATG
*
6730 TTTTAAAAACTATATAATATATATATATTTTTAAAAATA
1 TTTTAAAAACTATAT-A-ATATATAT-TTTTTAAAAATG
* *
6769 TTTTAAAAACTATATATTATAT-TTATTTTCAAAATG
1 TTTTAAAAACTATATAATATATATT-TTTTAAAAATG
6805 -TTTAAAA
1 TTTTAAAA
6812 CATAAAAAAA
Statistics
Matches: 163, Mismatches: 19, Indels: 19
0.81 0.09 0.09
Matches are distributed among these distances:
35 11 0.07
36 83 0.51
37 37 0.23
38 7 0.04
39 24 0.15
40 1 0.01
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (36 bp):
TTTTAAAAACTATATAATATATATTTTTTAAAAATG
Found at i:6773 original size:75 final size:73
Alignment explanation
Indices: 6544--6811 Score: 396
Period size: 73 Copynumber: 3.6 Consensus size: 73
6534 TATAATATAT
* * *
6544 ATGTTTTCAAATAATTATATATCATATTTATTTTCAAAACATTTTAAAAACTATATAATATATAT
1 ATGTTTT-AAA-AACTATATATTATATTTATTTTCAAAATATTTTAAAAACTATATAATATATAT
*
6609 -TTTTAAAAA
64 ATTTTTAAAA
* *
6618 ATGTTTTAAAATCTATATATTATATTTATTTTTAAAATATTTTAAAAACTATATAATATATATAT
1 ATGTTTTAAAAACTATATATTATATTTATTTTCAAAATATTTTAAAAACTATATAATATATATAT
6683 TTTTAAAA
66 TTTTAAAA
* *
6691 ATGTTTTAAAAACTATATATTATATTTATTTTCAAATTGTTTTAAAAACTATATAATATATATAT
1 ATGTTTTAAAAACTATATATTATATTTATTTTCAAAATATTTTAAAAACTATAT-A-ATATATAT
6756 ATTTTTAAAA
64 ATTTTTAAAA
* *
6766 ATATTTTAAAAACTATATATTATATTTATTTTCAAAAT-GTTTAAAA
1 ATGTTTTAAAAACTATATATTATATTTATTTTCAAAATATTTTAAAA
6812 CATAAAAAAA
Statistics
Matches: 178, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
72 48 0.27
73 61 0.34
74 15 0.08
75 54 0.30
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (73 bp):
ATGTTTTAAAAACTATATATTATATTTATTTTCAAAATATTTTAAAAACTATATAATATATATAT
TTTTAAAA
Found at i:8646 original size:20 final size:20
Alignment explanation
Indices: 8621--8660 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
8611 TAAAATAAAA
8621 ACTTAAATTTTTAACAATGG
1 ACTTAAATTTTTAACAATGG
8641 ACTTAAATTTTTAACAATGG
1 ACTTAAATTTTTAACAATGG
8661 GGATACTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (20 bp):
ACTTAAATTTTTAACAATGG
Found at i:15134 original size:3 final size:3
Alignment explanation
Indices: 15126--15183 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
15116 TATATGTAAA
* * * * *
15126 TAT TAT TA- TAT TTT TA- AAT TAT TAT TAA TAT TAA TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
15172 TAT TAT TAT TAT
1 TAT TAT TAT TAT
15184 CAAACGAGAA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
2 3 0.07
3 40 0.93
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:19212 original size:29 final size:29
Alignment explanation
Indices: 19180--19275 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
19170 ACATTGGTCT
19180 CTAAACTTTTAAATATTTTAATTTCATCC
1 CTAAACTTTTAAATATTTTAATTTCATCC
* * * *
19209 CTAAACTATGAATATAATTTTAAATT-ATTC
1 CTAAACTTTTAA-AT-ATTTTAATTTCATCC
* * * *
19239 TTCAAACTTTTGAACATTTCAATTTCATCC
1 CT-AAACTTTTAAATATTTTAATTTCATCC
*
19269 CCAAACT
1 CTAAACT
19276 ATACCTTCTT
Statistics
Matches: 49, Mismatches: 14, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 23 0.47
30 10 0.20
31 16 0.33
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.43
Consensus pattern (29 bp):
CTAAACTTTTAAATATTTTAATTTCATCC
Found at i:19892 original size:18 final size:19
Alignment explanation
Indices: 19857--19893 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
19847 CACGGAATGT
19857 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
19877 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
19894 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:20111 original size:32 final size:31
Alignment explanation
Indices: 20035--20111 Score: 73
Period size: 37 Copynumber: 2.3 Consensus size: 31
20025 TTACAAATTG
20035 TAAAAATATTTATATATATTCTTTAAAAAAT
1 TAAAAATATTTATATATATTCTTTAAAAAAT
* * *
20066 TAAATTCATAATATTTATATAATTTTTTTTATAAAAT
1 T-AA---A-AATATTTATAT-ATATTCTTTAAAAAAT
20103 TAAAAATAT
1 TAAAAATAT
20112 AAAAAATGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
31 1 0.03
32 7 0.19
33 1 0.03
35 1 0.03
36 13 0.35
37 14 0.38
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (31 bp):
TAAAAATATTTATATATATTCTTTAAAAAAT
Found at i:24237 original size:26 final size:26
Alignment explanation
Indices: 24194--24257 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
24184 TTTTTGATTC
* * *
24194 TAAAATTTTATAATTTTATTTCTTCT
1 TAAAATTTTAGAAATTTACTTCTTCT
* *
24220 TAAAATTTTGGAAATTTACTTCTTAACA
1 TAAAATTTTAGAAATTTACTTCTT--CT
24248 TAAAATTTTA
1 TAAAATTTTA
24258 TCTTCTGTTG
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 20 0.67
28 10 0.33
ACGTcount: A:0.38, C:0.08, G:0.03, T:0.52
Consensus pattern (26 bp):
TAAAATTTTAGAAATTTACTTCTTCT
Found at i:25063 original size:16 final size:18
Alignment explanation
Indices: 25042--25076 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25032 TTAATATATA
25042 ATTTT-AAT-TTTTTTTT
1 ATTTTAAATATTTTTTTT
25058 ATTTTAAATATTTTTTTT
1 ATTTTAAATATTTTTTTT
25076 A
1 A
25077 AAATTACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 3 0.18
18 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTAAATATTTTTTTT
Found at i:28958 original size:23 final size:23
Alignment explanation
Indices: 28932--28976 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28922 TTTTTTGAGT
28932 TTGAGGATCATATTGAGAAAAAA
1 TTGAGGATCATATTGAGAAAAAA
28955 TTGAGGATCATATTGAGAAAAA
1 TTGAGGATCATATTGAGAAAAA
28977 TAATACAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.47, C:0.04, G:0.22, T:0.27
Consensus pattern (23 bp):
TTGAGGATCATATTGAGAAAAAA
Found at i:32254 original size:24 final size:24
Alignment explanation
Indices: 32233--32279 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
32223 TGTAAATTAT
32233 ATAAAATTTATTTGATATAATTTA
1 ATAAAATTTATTTGATATAATTTA
32257 ATAAAATTTATTTGATATAATTT
1 ATAAAATTTATTTGATATAATTT
32280 TTTTTTAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
ATAAAATTTATTTGATATAATTTA
Found at i:32329 original size:7 final size:7
Alignment explanation
Indices: 32307--32346 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
32297 ATACAATTCA
32307 AAATTTT
1 AAATTTT
*
32314 AACTTTT
1 AAATTTT
*
32321 AAATCTTA
1 AAAT-TTT
32329 AAATTTT
1 AAATTTT
32336 AAATTTT
1 AAATTTT
32343 AAAT
1 AAAT
32347 AAAAACGATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (7 bp):
AAATTTT
Found at i:33621 original size:255 final size:255
Alignment explanation
Indices: 33170--33680 Score: 1022
Period size: 255 Copynumber: 2.0 Consensus size: 255
33160 TATATATATA
33170 TATATATTTCACGAACCAACTTATATTGATGGTTAAATAAATCATTATAGTTTCTAAAGATCACA
1 TATATATTTCACGAACCAACTTATATTGATGGTTAAATAAATCATTATAGTTTCTAAAGATCACA
33235 GATTTAAACGTCAACGGTTATAACATTATGATTTAGTGTTTATTATCAAATGATTTAGAATATTT
66 GATTTAAACGTCAACGGTTATAACATTATGATTTAGTGTTTATTATCAAATGATTTAGAATATTT
33300 AAAGCACATATTATTGTAGATGCTCGTTTCTGTCCGGGGCCAAGTCGGAGCAGACCCGAAGCAAT
131 AAAGCACATATTATTGTAGATGCTCGTTTCTGTCCGGGGCCAAGTCGGAGCAGACCCGAAGCAAT
33365 GAGAGCCTAGATGAGCCCAAACCAGATGAAGGTCCAGCTCAAGACCAATTGACAACAGTT
196 GAGAGCCTAGATGAGCCCAAACCAGATGAAGGTCCAGCTCAAGACCAATTGACAACAGTT
33425 TATATATTTCACGAACCAACTTATATTGATGGTTAAATAAATCATTATAGTTTCTAAAGATCACA
1 TATATATTTCACGAACCAACTTATATTGATGGTTAAATAAATCATTATAGTTTCTAAAGATCACA
33490 GATTTAAACGTCAACGGTTATAACATTATGATTTAGTGTTTATTATCAAATGATTTAGAATATTT
66 GATTTAAACGTCAACGGTTATAACATTATGATTTAGTGTTTATTATCAAATGATTTAGAATATTT
33555 AAAGCACATATTATTGTAGATGCTCGTTTCTGTCCGGGGCCAAGTCGGAGCAGACCCGAAGCAAT
131 AAAGCACATATTATTGTAGATGCTCGTTTCTGTCCGGGGCCAAGTCGGAGCAGACCCGAAGCAAT
33620 GAGAGCCTAGATGAGCCCAAACCAGATGAAGGTCCAGCTCAAGACCAATTGACAACAGTT
196 GAGAGCCTAGATGAGCCCAAACCAGATGAAGGTCCAGCTCAAGACCAATTGACAACAGTT
33680 T
1 T
33681 GATGCAGAAA
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 256 1.00
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (255 bp):
TATATATTTCACGAACCAACTTATATTGATGGTTAAATAAATCATTATAGTTTCTAAAGATCACA
GATTTAAACGTCAACGGTTATAACATTATGATTTAGTGTTTATTATCAAATGATTTAGAATATTT
AAAGCACATATTATTGTAGATGCTCGTTTCTGTCCGGGGCCAAGTCGGAGCAGACCCGAAGCAAT
GAGAGCCTAGATGAGCCCAAACCAGATGAAGGTCCAGCTCAAGACCAATTGACAACAGTT
Found at i:53371 original size:140 final size:135
Alignment explanation
Indices: 53124--53400 Score: 500
Period size: 140 Copynumber: 2.0 Consensus size: 135
53114 AACATAAAAA
53124 TTATTTCACATTATGGACTTACCCCCTCCCCTACTCTCATCGATTTTTATTTTAATATTTCATAT
1 TTATTTCACATTATGGACTTACCCCCTCCCCTACTCTCATCGATTTTTATTTTAATATTTCATAT
53189 TTTATCAATTCACTTAAATTAAACATTATAAAATATACATGAATCAAACGATATTATAATTAGAA
66 TTTATCAATTCACTTAAATTAAACATTATAAAATATACATGAATCAAACGATATTATAATTAGAA
53254 AATTG
131 AATTG
53259 TTATTTCACATTATGGACTTACCCCCCCCGGTCCCCTACTCTCATCGATTTTTATTTTAATATTT
1 TTATTTCACATTATGGACTTA---CCCCC--TCCCCTACTCTCATCGATTTTTATTTTAATATTT
*
53324 CATATTTTATTAATTCACTTAAATTAAACATTATAAAATATACATGAATCAAACGATATTATAAT
61 CATATTTTATCAATTCACTTAAATTAAACATTATAAAATATACATGAATCAAACGATATTATAAT
53389 TAGAAAATTG
126 TAGAAAATTG
53399 TT
1 TT
53401 GTTATTATTT
Statistics
Matches: 136, Mismatches: 1, Indels: 5
0.96 0.01 0.04
Matches are distributed among these distances:
135 21 0.15
138 5 0.04
140 110 0.81
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (135 bp):
TTATTTCACATTATGGACTTACCCCCTCCCCTACTCTCATCGATTTTTATTTTAATATTTCATAT
TTTATCAATTCACTTAAATTAAACATTATAAAATATACATGAATCAAACGATATTATAATTAGAA
AATTG
Found at i:55172 original size:18 final size:19
Alignment explanation
Indices: 55149--55185 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
55139 TAAGAAGGTT
55149 TGGTAATCGGGCT-AAGGA
1 TGGTAATCGGGCTGAAGGA
*
55167 TGGTAATTGGGCTGAAGGA
1 TGGTAATCGGGCTGAAGGA
55186 GTCAACAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.27, C:0.08, G:0.41, T:0.24
Consensus pattern (19 bp):
TGGTAATCGGGCTGAAGGA
Found at i:60225 original size:24 final size:24
Alignment explanation
Indices: 60197--60244 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
60187 GGGAATTGAG
60197 GAAGGAGTTAAGGATTTCGAATTT
1 GAAGGAGTTAAGGATTTCGAATTT
* *
60221 GAAGGAGTTAGGGATTTTGAATTT
1 GAAGGAGTTAAGGATTTCGAATTT
60245 ACCTGATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.35
Consensus pattern (24 bp):
GAAGGAGTTAAGGATTTCGAATTT
Found at i:61422 original size:16 final size:16
Alignment explanation
Indices: 61403--61436 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
61393 CAATATACGA
61403 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
61419 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
61435 AT
1 AT
61437 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:61511 original size:17 final size:19
Alignment explanation
Indices: 61478--61512 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
61468 TATTAATGTA
61478 TGAATCATTTATATTTTTT
1 TGAATCATTTATATTTTTT
61497 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
61513 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (19 bp):
TGAATCATTTATATTTTTT
Found at i:62098 original size:130 final size:130
Alignment explanation
Indices: 61942--62189 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
61932 AATTTTCTTC
* * *
61942 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** * *
62007 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTACTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
62072 TAATTAGGTGGTGACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
62137 CCTAATTAAATGATTAATTTACTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTACTAAATTCTATTTAATTTAGGACCAAATTGAT
62190 TATATAAATA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGTGGTGACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTACTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:62636 original size:35 final size:35
Alignment explanation
Indices: 62586--62661 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
62576 AATTGAATTT
* * *
62586 AATTGAATTATTTTGGAATTTAGGGTTTATAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
62621 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
62656 AATTGA
1 AATTGA
62662 GGACTCTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.22, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:64081 original size:22 final size:22
Alignment explanation
Indices: 64052--64094 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
64042 TTGATTAATA
64052 TTTTA-TTTTAAATAATTTATG
1 TTTTATTTTTAAATAATTTATG
*
64073 TTTTGATTTTTAATTAATTTAT
1 TTTT-ATTTTTAAATAATTTAT
64095 AATTATCCGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 1 0.05
23 14 0.74
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (22 bp):
TTTTATTTTTAAATAATTTATG
Found at i:64132 original size:15 final size:16
Alignment explanation
Indices: 64112--64144 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
64102 CGTTAATTAC
*
64112 TTTATAATTTTA-AAA
1 TTTATAAATTTATAAA
64127 TTTATAAATTTATAAA
1 TTTATAAATTTATAAA
64143 TT
1 TT
64145 AAATTAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATAAATTTATAAA
Found at i:64135 original size:8 final size:8
Alignment explanation
Indices: 64112--64144 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
64102 CGTTAATTAC
*
64112 TTTATAAT
1 TTTATAAA
64120 TTTA-AAA
1 TTTATAAA
64127 TTTATAAA
1 TTTATAAA
64135 TTTATAAA
1 TTTATAAA
64143 TT
1 TT
64145 AAATTAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
TTTATAAA
Found at i:69118 original size:2 final size:2
Alignment explanation
Indices: 69111--69141 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69101 ATTTCGGACT
69111 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
69142 TATTGTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:73617 original size:2 final size:2
Alignment explanation
Indices: 73610--73640 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
73600 ACAAAAAGAC
73610 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73641 GATTAATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:76344 original size:20 final size:20
Alignment explanation
Indices: 76319--76357 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
76309 GTAATCCTAT
*
76319 TCACTGGTAATCTTACATTC
1 TCACTGATAATCTTACATTC
*
76339 TCACTGATAATCTTCCATT
1 TCACTGATAATCTTACATT
76358 TCGTAAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.08, T:0.41
Consensus pattern (20 bp):
TCACTGATAATCTTACATTC
Done.