Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003223.1 Hibiscus syriacus cultivar Beakdansim tig00006787_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: 71684
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:3498 original size:17 final size:17
Alignment explanation
Indices: 3476--3540 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
3466 ACAGATGACA
3476 TCCTTCGGGATGATAGG
1 TCCTTCGGGATGATAGG
* *
3493 TCCTTCGGGACGCAGATGG
1 TCCTTCGGGATG-ATA-GG
*
3512 CATCCTTTGGGATGATAGG
1 --TCCTTCGGGATGATAGG
*
3531 TCTTTCGGGA
1 TCCTTCGGGA
3541 CACAGATTAC
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 19 0.51
18 2 0.05
19 4 0.11
20 2 0.05
21 10 0.27
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (17 bp):
TCCTTCGGGATGATAGG
Found at i:3509 original size:38 final size:38
Alignment explanation
Indices: 3454--3547 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
3444 GGTTACATAT
3454 GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
1 GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
* * *
3492 GTCCTTCGGGACGCAGATGGCATCCTTTGGGATGATAG
1 GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
*
3530 GTCTTTCGGGACACAGAT
1 GTCCTTCGGGACACAGAT
3548 TACCTATGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 51 1.00
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (38 bp):
GTCCTTCGGGACACAGATGACATCCTTCGGGATGATAG
Found at i:3517 original size:21 final size:21
Alignment explanation
Indices: 3455--3523 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
3445 GTTACATATG
* *
3455 TCCTTCGGGACACAGATGACA
1 TCCTTCGGGACGCAGATGGCA
* *
3476 TCCTTCGGGATG-ATA-GG--
1 TCCTTCGGGACGCAGATGGCA
3493 TCCTTCGGGACGCAGATGGCA
1 TCCTTCGGGACGCAGATGGCA
*
3514 TCCTTTGGGA
1 TCCTTCGGGA
3524 TGATAGGTCT
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
17 11 0.30
18 2 0.05
19 3 0.08
20 2 0.05
21 19 0.51
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (21 bp):
TCCTTCGGGACGCAGATGGCA
Found at i:3692 original size:29 final size:30
Alignment explanation
Indices: 3641--3700 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 30
3631 ACCTTAATTC
* *
3641 TTAGTAATGTTAATGGGCTTATAAAA-ATA
1 TTAGTAATGTTAATAGGCCTATAAAAGATA
3670 TTAGTAATG-TATATAGGCCTATAAAAGATA
1 TTAGTAATGTTA-ATAGGCCTATAAAAGATA
3700 T
1 T
3701 CAAAAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 2 0.07
29 21 0.78
30 4 0.15
ACGTcount: A:0.42, C:0.05, G:0.17, T:0.37
Consensus pattern (30 bp):
TTAGTAATGTTAATAGGCCTATAAAAGATA
Found at i:6297 original size:6 final size:6
Alignment explanation
Indices: 6286--6317 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6276 TAAGAGCTAA
6286 AAAAAG AAAAAG AAAAA- AAAAAG AAAAA- AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
6318 TGAGAGATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 9 0.36
6 16 0.64
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:6306 original size:11 final size:11
Alignment explanation
Indices: 6286--6317 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
6276 TAAGAGCTAA
6286 AAAAAGAAAAAG
1 AAAAA-AAAAAG
6298 AAAAAAAAAAG
1 AAAAAAAAAAG
6309 AAAAAAAAA
1 AAAAAAAAA
6318 TGAGAGATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.75
12 5 0.25
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:6306 original size:17 final size:16
Alignment explanation
Indices: 6284--6317 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
6274 CATAAGAGCT
6284 AAAAAAAGAAAAAGAAA
1 AAAAAAAGAAAAA-AAA
6301 AAAAAAAGAAAAAAAA
1 AAAAAAAGAAAAAAAA
6317 A
1 A
6318 TGAGAGATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAA
Found at i:7851 original size:29 final size:31
Alignment explanation
Indices: 7819--7881 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 31
7809 AAATGGATTT
* * *
7819 AGTTTTG-TTACCAAATTATAAA-TTTGTAA
1 AGTTTTGCTGACCAAAGTATAAACTTTGAAA
7848 AG-TTTGCTGACCAAAGTATAAACTTTGAAA
1 AGTTTTGCTGACCAAAGTATAAACTTTGAAA
7878 AGTT
1 AGTT
7882 CAGGTATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
28 4 0.14
29 15 0.54
30 8 0.29
31 1 0.04
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (31 bp):
AGTTTTGCTGACCAAAGTATAAACTTTGAAA
Found at i:8878 original size:30 final size:31
Alignment explanation
Indices: 8831--8901 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
8821 TTCTACAGAC
* **
8831 TTAGAAAA-TTTGGGGACC-ATTTTGTAATT
1 TTAGAAAAGTTGGGGGACCAATTTCATAATT
8860 TT-GTAAAAGTTGGGGGACCAATTTCATAATT
1 TTAG-AAAAGTTGGGGGACCAATTTCATAATT
8891 TTAGAAAAGTT
1 TTAGAAAAGTT
8902 ATGAATGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 1 0.03
29 6 0.17
30 9 0.26
31 18 0.51
32 1 0.03
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (31 bp):
TTAGAAAAGTTGGGGGACCAATTTCATAATT
Found at i:9927 original size:33 final size:33
Alignment explanation
Indices: 9885--9982 Score: 178
Period size: 33 Copynumber: 3.0 Consensus size: 33
9875 TATGAAAAGG
*
9885 GATCTATGAGATCATACAATAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
9918 GATCTATGAGATCATACAAGAATGTTACACAAT
1 GATCTATGAGATCATACAAGAATGTTACACAAT
*
9951 GATCTATGAGATCATACAAGAATGTTATACAA
1 GATCTATGAGATCATACAAGAATGTTACACAA
9983 GTTACATGAT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (33 bp):
GATCTATGAGATCATACAAGAATGTTACACAAT
Found at i:10190 original size:38 final size:38
Alignment explanation
Indices: 10134--10234 Score: 166
Period size: 38 Copynumber: 2.7 Consensus size: 38
10124 TTCGAGACAT
* *
10134 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1 ATGATAGGTCCTTTGGGACACAGATGACATCCTTCAGG
* *
10172 ATGATAAGTCCTTTGGGACACAGATGTCATCCTTCAGG
1 ATGATAGGTCCTTTGGGACACAGATGACATCCTTCAGG
10210 ATGATAGGTCCTTTGGGACACAGAT
1 ATGATAGGTCCTTTGGGACACAGAT
10235 TACCTATGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 58 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (38 bp):
ATGATAGGTCCTTTGGGACACAGATGACATCCTTCAGG
Found at i:10368 original size:30 final size:30
Alignment explanation
Indices: 10332--10394 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
10322 CCTTAAGTTC
*
10332 TCAGTAATATACATGGGCTTATAAAAGATA
1 TCAGTAATATACATGGGCCTATAAAAGATA
* *
10362 TCAGTAATGTATATGGGCCTATAAAAGATA
1 TCAGTAATATACATGGGCCTATAAAAGATA
10392 TCA
1 TCA
10395 AAAGTGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.30
Consensus pattern (30 bp):
TCAGTAATATACATGGGCCTATAAAAGATA
Found at i:11370 original size:3 final size:3
Alignment explanation
Indices: 11362--11399 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
11352 CATATTTTTT
*
11362 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
11400 TATTAAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12525 original size:21 final size:21
Alignment explanation
Indices: 12501--12624 Score: 153
Period size: 21 Copynumber: 5.7 Consensus size: 21
12491 AAATTGCCAT
12501 AGTACACAAAGTACTACTACA
1 AGTACACAAAGTACTACTACA
12522 AGTACACAAAGTACTACTACA
1 AGTACACAAAGTACTACTACA
*
12543 TGTACACAAAGTACT-CTTACCA
1 AGTACACAAAGTACTAC-TA-CA
*
12565 TAGTACACAAAGTACT-CTTGCCA
1 -AGTACACAAAGTACTAC-T-ACA
*
12588 TAGTACACAAAGTACTACTCCA
1 -AGTACACAAAGTACTACTACA
12610 AGTACACAAAGTACT
1 AGTACACAAAGTACT
12625 CTTAAGAAAA
Statistics
Matches: 95, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
20 1 0.01
21 52 0.55
22 5 0.05
23 36 0.38
24 1 0.01
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (21 bp):
AGTACACAAAGTACTACTACA
Found at i:12615 original size:67 final size:65
Alignment explanation
Indices: 12497--12628 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 65
12487 ACACAAATTG
*
12497 CCATAGTACACAAAGTACTACTACAAGTACACAAAGTACTACTACATGTACACAAAGTACTCTTA
1 CCATAGTACACAAAGTACTACTACAAGTACACAAAGTACTACTACAAGTACACAAAGTACTCTTA
* *
12562 CCATAGTACACAAAGTACT-CTTGCCATAGTACACAAAGTACTACTCCAAGTACACAAAGTACTC
1 CCATAGTACACAAAGTACTAC-T-ACA-AGTACACAAAGTACTACTACAAGTACACAAAGTACTC
12626 TTA
63 TTA
12629 AGAAAATGCA
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
64 1 0.02
65 20 0.33
66 2 0.03
67 38 0.62
ACGTcount: A:0.41, C:0.26, G:0.10, T:0.23
Consensus pattern (65 bp):
CCATAGTACACAAAGTACTACTACAAGTACACAAAGTACTACTACAAGTACACAAAGTACTCTTA
Found at i:15115 original size:139 final size:139
Alignment explanation
Indices: 14865--15140 Score: 401
Period size: 139 Copynumber: 2.0 Consensus size: 139
14855 TTGGTTATAT
* * * ** *
14865 GGATGACACTGCTCCTTCACGTTGAGGAGATCTAGTCAGTGGGCGACATTTTTCCTTCGTGTTGA
1 GGATGACACTACTCATTCACGTTGACGAGATCTAGTCAGTGAACGACATTGTTCCTTCGTGTTGA
*
14930 GGATGTCTAGACGTATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCGTTGAGGAAGTCTG
66 GGATGTCTAGACGTATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCATTGAGGAAGTCTG
14995 ATTGTCTGA
131 ATTGTCTGA
* * * *
15004 GGATGACACTACTCATTCGCGTTGACGAGATCTGGTCGGTGAACGACATTGTTCCTTCTTGTTGA
1 GGATGACACTACTCATTCACGTTGACGAGATCTAGTCAGTGAACGACATTGTTCCTTCGTGTTGA
* * *
15069 GGATGTCTAGCCGTAATT-GGAGATAATTTGGAGACAACATTGTTCCTTCGCATTGAGGAATTCT
66 GGATGTCTAGACGT-ATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCATTGAGGAAGTCT
*
15133 TATTGTCT
130 GATTGTCT
15141 AAAGATAGTT
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
139 118 0.98
140 3 0.02
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (139 bp):
GGATGACACTACTCATTCACGTTGACGAGATCTAGTCAGTGAACGACATTGTTCCTTCGTGTTGA
GGATGTCTAGACGTATTGGGAGATAATTTGGAGACAACATGGTTCCTTCGCATTGAGGAAGTCTG
ATTGTCTGA
Found at i:15588 original size:98 final size:101
Alignment explanation
Indices: 15318--15647 Score: 370
Period size: 98 Copynumber: 3.3 Consensus size: 101
15308 GAGTGAAAAT
** * * * *
15318 AAATTTGTTTCCAGAGAAACTATCTCAGGTGAGATAAAATTTTGTTTCGAGGGAAACAATTTCAA
1 AAATTTGTTTTAAGA-AAACAATCTCAAGTGAGAT-AAATTTTGTTTCAAGTGAAACAATTTCAA
* *
15383 AATTTACGT-TTC-AAGGAAAAATTATCTCAAGAGAGACG
64 AATTT--GTGTTCTGAGGGAAAATTATCTCAAGAGAGACG
* *
15421 AAATTTGTTTTAAGAAAACAATCTCAAAG-GAGATCAATTTTTTTTCAAGTGAAACAATTTCAAA
1 AAATTTGTTTTAAGAAAACAATCTC-AAGTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAA
* * *
15485 CTTTGTGTTCTGAGGGAAAATTGTCTCAAGCGAGACG
65 ATTTGTGTTCTGAGGGAAAATTATCTCAAGAGAGACG
* *
15522 AAATTTGTTTT-A-AAAA-AATCTCAAGTGAGATAAATTTTGTTACAAGTGAAACAATTTAAAAA
1 AAATTTGTTTTAAGAAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAA
*
15584 TTTGTGTT-TCGAGGGAAAACTATCTCAAGAGAGAC-
66 TTTGTGTTCT-GAGGGAAAATTATCTCAAGAGAGACG
**
15619 AACATTTGTTTGGAGAGAAACAATCTCAA
1 AA-ATTTGTTTTAAGA-AAACAATCTCAA
15648 AGGTGACCGA
Statistics
Matches: 195, Mismatches: 22, Indels: 21
0.82 0.09 0.09
Matches are distributed among these distances:
97 6 0.03
98 75 0.38
99 7 0.04
100 5 0.03
101 65 0.33
102 22 0.11
103 15 0.08
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (101 bp):
AAATTTGTTTTAAGAAAACAATCTCAAGTGAGATAAATTTTGTTTCAAGTGAAACAATTTCAAAA
TTTGTGTTCTGAGGGAAAATTATCTCAAGAGAGACG
Found at i:16695 original size:40 final size:40
Alignment explanation
Indices: 16640--16720 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
16630 GTGGGTACTT
*
16640 ATGGAGTTGTTGAACATCATTATCAAAACTTCTTATTTTC
1 ATGGAGTTCTTGAACATCATTATCAAAACTTCTTATTTTC
*
16680 ATGGAGTTCTTGAACATCATTGTCAAAACTTCTTATTTTC
1 ATGGAGTTCTTGAACATCATTATCAAAACTTCTTATTTTC
16720 A
1 A
16721 AACTTGCTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (40 bp):
ATGGAGTTCTTGAACATCATTATCAAAACTTCTTATTTTC
Found at i:17893 original size:18 final size:19
Alignment explanation
Indices: 17857--17894 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
17847 CACGGAATGT
17857 AAGATTACCAGTAGGAATAA
1 AAGATTACCAG-AGGAATAA
17877 AAGATTACCAG-GGAATAA
1 AAGATTACCAGAGGAATAA
17895 GATTAATGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
20 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.21, T:0.18
Consensus pattern (19 bp):
AAGATTACCAGAGGAATAA
Found at i:19507 original size:18 final size:19
Alignment explanation
Indices: 19475--19517 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
19465 AATAACAAGC
* *
19475 AAAGAAAAAACCGAACAAT
1 AAAGAAAAAACCGAAAAAG
19494 AAAGAAAAAA-CGAAAAAG
1 AAAGAAAAAACCGAAAAAG
19512 AAAGAA
1 AAAGAA
19518 TGAGAGGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.02
Consensus pattern (19 bp):
AAAGAAAAAACCGAAAAAG
Found at i:20436 original size:14 final size:15
Alignment explanation
Indices: 20412--20450 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
20402 AACTTCTGAC
20412 TTTATATTTATTTAT
1 TTTATATTTATTTAT
20427 TTTA-ATTTATTTAT
1 TTTATATTTATTTAT
*
20441 CTTATTATTT
1 TTTA-TATTT
20451 TTTTCTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 13 0.62
15 4 0.19
16 4 0.19
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATATTTATTTAT
Found at i:20801 original size:31 final size:31
Alignment explanation
Indices: 20766--20834 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 31
20756 ATAATTAGAT
20766 CCTTAAACTTTAGACTTTCT-ACATTTCAGTC
1 CCTTAAACTTTAGA-TTTCTCACATTTCAGTC
* *
20797 CCTT-AACTTTAGATTTCTCATATTTTAGTC
1 CCTTAAACTTTAGATTTCTCACATTTCAGTC
20827 CC-TAAACT
1 CCTTAAACT
20835 ATTAATTAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 6 0.18
30 24 0.71
31 4 0.12
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.43
Consensus pattern (31 bp):
CCTTAAACTTTAGATTTCTCACATTTCAGTC
Found at i:21952 original size:17 final size:17
Alignment explanation
Indices: 21930--21988 Score: 91
Period size: 17 Copynumber: 3.4 Consensus size: 17
21920 TTGACCAGTT
21930 CCGACCCGACCCGTTGA
1 CCGACCCGACCCGTTGA
* *
21947 CCGACCTGACCCGTTGT
1 CCGACCCGACCCGTTGA
21964 CCGACCCGACCCGTTGA
1 CCGACCCGACCCGTTGA
21981 CCAGACCC
1 CC-GACCC
21989 ATTGACCGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
17 32 0.86
18 5 0.14
ACGTcount: A:0.17, C:0.47, G:0.22, T:0.14
Consensus pattern (17 bp):
CCGACCCGACCCGTTGA
Found at i:22156 original size:29 final size:29
Alignment explanation
Indices: 22003--22149 Score: 203
Period size: 29 Copynumber: 5.2 Consensus size: 29
21993 ACCGGGTGAC
* *
22003 ATTTTGGGAA-TTAATTTGAAATGGGTGCT
1 ATTTTGGGAATTTAATTCGAAA-AGGTGCT
*
22032 ATTTTGGGAATTTAATTCGAAAAGGTGCA
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
* *
22061 ATTTTAGGAATTTAATTCGAAAA-GTACT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
*
22089 ATATTGGGAATTTAATTC-AAAA-GTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
22116 ATTTTGGGAATTTAATTCGAAAAGGTGCT
1 ATTTTGGGAATTTAATTCGAAAAGGTGCT
22145 ATTTT
1 ATTTT
22150 AGTAATTATT
Statistics
Matches: 105, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
27 25 0.24
28 23 0.22
29 47 0.45
30 10 0.10
ACGTcount: A:0.33, C:0.06, G:0.21, T:0.39
Consensus pattern (29 bp):
ATTTTGGGAATTTAATTCGAAAAGGTGCT
Found at i:28367 original size:2 final size:2
Alignment explanation
Indices: 28362--28391 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28352 TAAAAAAAAA
28362 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
28392 GAAAATATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30621 original size:2 final size:2
Alignment explanation
Indices: 30614--30650 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
30604 TAATTATTAA
*
30614 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
30651 AAATTTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:31947 original size:18 final size:19
Alignment explanation
Indices: 31903--31952 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 19
31893 GTATTACAAT
*
31903 AATAATTTAAAAAAAATCA
1 AATACTTTAAAAAAAATCA
*
31922 AATACTTTAAAAATAATCA
1 AATACTTTAAAAAAAATCA
*
31941 TAT-CTTTAAAAA
1 AATACTTTAAAAA
31953 CATAATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 9 0.32
19 19 0.68
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (19 bp):
AATACTTTAAAAAAAATCA
Found at i:33967 original size:34 final size:30
Alignment explanation
Indices: 33929--33997 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
33919 TTGATATAAC
33929 AATTTAAGGCAAAATGGTTTTTGGAATTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGAATT-AATTG
*
33963 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGAATTAATTG
33992 AATTTA
1 AATTTA
33998 TTCAAAGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 11 0.33
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGAATTAATTG
Found at i:34008 original size:29 final size:30
Alignment explanation
Indices: 33938--33997 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
33928 CAATTTAAGG
33938 CAAAATGGTTTTTGGAATTGAATTGAATTTA
1 CAAAAT-GTTTTTGGAATTGAATTGAATTTA
*
33969 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGAATTGAATTGAATTTA
33998 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGAATTGAATTGAATTTA
Found at i:34103 original size:21 final size:21
Alignment explanation
Indices: 34077--34132 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
34067 AGGGTGTCAA
*
34077 AGTGCATCCATGCATCCCTAT
1 AGTGCATCCATGCATCCCTAC
*
34098 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTAC
34119 AGTGCATCCATGCA
1 AGTGCATCCATGCA
34133 CCTGCACTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.18, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTAC
Found at i:34166 original size:20 final size:19
Alignment explanation
Indices: 34100--34250 Score: 96
Period size: 20 Copynumber: 7.7 Consensus size: 19
34090 ATCCCTATAG
* *
34100 TGCATCCATGCATCCCTGCAG
1 TGCATCGATGCAT--CTGCAA
* *
34121 TGCATCCATGCACCTGCACTAA
1 TGCATCGATGCATCTG--C-AA
34143 TGCATCGATGCATCATGCAA
1 TGCATCGATGCATC-TGCAA
*
34163 TGCATCCATGCA-CT-CAA
1 TGCATCGATGCATCTGCAA
* *
34180 -GCATCGAATGCA-CT-TAG
1 TGCATCG-ATGCATCTGCAA
*
34197 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCAT-CTGCAA
*
34217 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCAT-CTGCAA
*
34237 TGCATCCATGCATC
1 TGCATCGATGCATC
34251 AAGGCTGCAA
Statistics
Matches: 109, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
16 5 0.05
17 16 0.15
18 7 0.06
19 7 0.06
20 45 0.41
21 14 0.13
22 13 0.12
23 2 0.02
ACGTcount: A:0.25, C:0.33, G:0.18, T:0.25
Consensus pattern (19 bp):
TGCATCGATGCATCTGCAA
Found at i:34221 original size:12 final size:12
Alignment explanation
Indices: 34204--34243 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
34194 TAGTGCATCG
34204 ATGCATCCTGCC
1 ATGCATCCTGCC
34216 ATGCAT-C-G--
1 ATGCATCCTGCC
34224 ATGCATCCTGCC
1 ATGCATCCTGCC
34236 ATGCATCC
1 ATGCATCC
34244 ATGCATCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
8 6 0.25
9 1 0.04
10 2 0.08
11 1 0.04
12 14 0.58
ACGTcount: A:0.20, C:0.38, G:0.17, T:0.25
Consensus pattern (12 bp):
ATGCATCCTGCC
Found at i:36823 original size:65 final size:63
Alignment explanation
Indices: 36706--36913 Score: 224
Period size: 65 Copynumber: 3.2 Consensus size: 63
36696 TTTCAAAGTG
* * **
36706 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGGAATAAATTG-AACATCGAATGCATT
1 ATGCATCGATGCA-CAA-CCATGCATCGATGCACTC--GGGATATTTTGAAACATCGAATGCATT
*
36769 TC
62 TA
*
36771 ATGCATCGATGCACACACCATGCATCGATGCACTGGGGAT-TTTATGAAAACATCGAATGCATTT
1 ATGCATCGATGCACA-ACCATGCATCGATGCACTCGGGATATTT-TG-AAACATCGAATGCATTT
36835 A
63 A
* * * * *
36836 ATGCATCGATGTATCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCA-CAACCATGCATCGATGCACTCGGGATATTTTGAAACATCGAATGCATTTA
36900 ATGCATCGATGCAC
1 ATGCATCGATGCAC
36914 TAAGGGTCCA
Statistics
Matches: 123, Mismatches: 13, Indels: 16
0.81 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 7 0.06
64 46 0.37
65 64 0.52
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACAACCATGCATCGATGCACTCGGGATATTTTGAAACATCGAATGCATTTA
Found at i:37818 original size:16 final size:16
Alignment explanation
Indices: 37793--37826 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
37783 AAGAGGCAAC
* *
37793 AACAAGGAGGAATGGA
1 AACAACGAGGAATAGA
37809 AACAACGAGGAATAGA
1 AACAACGAGGAATAGA
37825 AA
1 AA
37827 ACACGAAAAA
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:0.56, C:0.09, G:0.29, T:0.06
Consensus pattern (16 bp):
AACAACGAGGAATAGA
Found at i:37873 original size:21 final size:20
Alignment explanation
Indices: 37849--37887 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
37839 TGAAAAACCA
*
37849 CAAATAGAGAAAGCAAACATT
1 CAAACAGAGAAA-CAAACATT
*
37870 CAAACAGAGATACAAACA
1 CAAACAGAGAAACAAACA
37888 GTAGCAGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.59, C:0.18, G:0.13, T:0.10
Consensus pattern (20 bp):
CAAACAGAGAAACAAACATT
Found at i:42026 original size:14 final size:14
Alignment explanation
Indices: 42007--42035 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41997 CATTCGTGGG
42007 TCAACTCGGACTAT
1 TCAACTCGGACTAT
42021 TCAACTCGGACTAT
1 TCAACTCGGACTAT
42035 T
1 T
42036 TTACCTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (14 bp):
TCAACTCGGACTAT
Found at i:49613 original size:35 final size:35
Alignment explanation
Indices: 49574--49644 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
49564 ATTAAATAAC
* *
49574 TTAATATAAATGCTA-AATATTTAATATTAATATTA
1 TTAAT-TAAATGATATAATATTTAATATTAAAATTA
* *
49609 TTAATTATATTATATAATATTTAATATTAAAATTA
1 TTAATTAAATGATATAATATTTAATATTAAAATTA
49644 T
1 T
49645 ATAAATTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
TTAATTAAATGATATAATATTTAATATTAAAATTA
Found at i:50985 original size:14 final size:14
Alignment explanation
Indices: 50966--51000 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
50956 ATCATAAATA
50966 ATAATATTTATAAT
1 ATAATATTTATAAT
*
50980 ATAATATTTATTAT
1 ATAATATTTATAAT
50994 ATAATAT
1 ATAATAT
51001 AATGTATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATAATATTTATAAT
Found at i:51008 original size:14 final size:14
Alignment explanation
Indices: 50966--51013 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
50956 ATCATAAATA
* *
50966 ATAATATTTATAAT
1 ATAATATTAATTAT
*
50980 ATAATATTTATTAT
1 ATAATATTAATTAT
50994 ATAATA-TAATGTAT
1 ATAATATTAAT-TAT
51008 ATAATA
1 ATAATA
51014 AACGTCACTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
13 3 0.10
14 28 0.90
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATAATATTAATTAT
Found at i:51108 original size:19 final size:19
Alignment explanation
Indices: 51084--51141 Score: 98
Period size: 19 Copynumber: 3.1 Consensus size: 19
51074 AAGATCATTC
*
51084 AGGAATTAATGCAATGAAT
1 AGGAATTAATGCAACGAAT
*
51103 AGGAATTAATGCAACGATT
1 AGGAATTAATGCAACGAAT
51122 AGGAATTAATGCAACGAAT
1 AGGAATTAATGCAACGAAT
51141 A
1 A
51142 AGGGGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.47, C:0.09, G:0.21, T:0.24
Consensus pattern (19 bp):
AGGAATTAATGCAACGAAT
Found at i:52830 original size:16 final size:17
Alignment explanation
Indices: 52793--52830 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
52783 AGATTCGAAG
52793 AAAAATCTATAAGAATGA
1 AAAAATCTATAAGAAT-A
*
52811 AAAAATCTATAAGGATA
1 AAAAATCTATAAGAATA
52828 AAA
1 AAA
52831 GGAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (17 bp):
AAAAATCTATAAGAATA
Found at i:53055 original size:5 final size:6
Alignment explanation
Indices: 53009--53056 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
52999 TTCAATTTTC
* *
53009 TTTATT TTTATT TTTCTG TTTACTT ATTTATT TTTATTT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTA-TT -TTTATT TTTA-TT TTTATT TTT
53057 TAGGTACCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
6 22 0.63
7 9 0.26
8 4 0.11
ACGTcount: A:0.15, C:0.04, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:56912 original size:34 final size:36
Alignment explanation
Indices: 56841--56920 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 36
56831 GGGGTTGGTC
* * *
56841 ATGTAATTGAAGTATTTTTGGAATTTTAGGTTTAGA
1 ATGTAATTGAAGCATTTTTAGAATTTGAGGTTTAGA
*
56877 ATGTAATTGAAGCA-TTTTAG-ATTTGGGGTTTAGA
1 ATGTAATTGAAGCATTTTTAGAATTTGAGGTTTAGA
56911 ATGTAATTGA
1 ATGTAATTGA
56921 TGATTGTGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 22 0.55
35 5 0.12
36 13 0.32
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.44
Consensus pattern (36 bp):
ATGTAATTGAAGCATTTTTAGAATTTGAGGTTTAGA
Found at i:58414 original size:13 final size:13
Alignment explanation
Indices: 58370--58414 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
58360 GAAACAAATA
58370 TTTGAGATTTATCT
1 TTTG-GATTTATCT
58384 TTT-GA-TTAT-T
1 TTTGGATTTATCT
58394 TTTAGGATTTATCT
1 TTT-GGATTTATCT
58408 TTTGGAT
1 TTTGGAT
58415 ATTTTATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
10 4 0.15
11 4 0.15
12 4 0.15
13 8 0.30
14 7 0.26
ACGTcount: A:0.20, C:0.04, G:0.16, T:0.60
Consensus pattern (13 bp):
TTTGGATTTATCT
Found at i:58601 original size:14 final size:12
Alignment explanation
Indices: 58560--58593 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
58550 TCTTTTTCCA
58560 TCTTTG-TTTTT
1 TCTTTGATTTTT
*
58571 ACTTTGATTTTT
1 TCTTTGATTTTT
58583 TCTTTGATTTT
1 TCTTTGATTTT
58594 CTTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (12 bp):
TCTTTGATTTTT
Found at i:59231 original size:18 final size:20
Alignment explanation
Indices: 59197--59233 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
59187 TTTTTCCTTG
59197 ATTTATTTTCTTTAAATTTT
1 ATTTATTTTCTTTAAATTTT
59217 ATTTA-TTTC-TTAAATTT
1 ATTTATTTTCTTTAAATTT
59234 CACAACCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
ATTTATTTTCTTTAAATTTT
Found at i:68271 original size:28 final size:27
Alignment explanation
Indices: 68233--68370 Score: 179
Period size: 28 Copynumber: 5.0 Consensus size: 27
68223 TATTACCTTT
*
68233 TTTTC-AAATAATGCCCAGAATGTCACC
1 TTTTCAAAATAATTCCCA-AATGTCACC
* **
68260 TTTGCAAAATAATTCCCATAATGTCATTT
1 TTTTCAAAATAATTCCCA-AATGTCA-CC
*
68289 TTTTCAAAATAATTCCCAAATGTCACT
1 TTTTCAAAATAATTCCCAAATGTCACC
68316 TTTTCAAAATAATTCCCAACATGTCACC
1 TTTTCAAAATAATTCCCAA-ATGTCACC
*
68344 TTTTCAAAATAATTCCCAAATATCACC
1 TTTTCAAAATAATTCCCAAATGTCACC
68371 GAGTCGGGTT
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
27 31 0.31
28 51 0.52
29 17 0.17
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (27 bp):
TTTTCAAAATAATTCCCAAATGTCACC
Found at i:68443 original size:19 final size:19
Alignment explanation
Indices: 68419--68455 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
68409 GACTGGTAGA
*
68419 CCGGTTTGGACCGATCAAG
1 CCGGTTTAGACCGATCAAG
*
68438 CCGGTTTAGACCGGTCAA
1 CCGGTTTAGACCGATCAA
68456 CTATTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.22, C:0.27, G:0.30, T:0.22
Consensus pattern (19 bp):
CCGGTTTAGACCGATCAAG
Done.