Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004405.1 Hibiscus syriacus cultivar Beakdansim tig00009653_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: 74861
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4213 original size:100 final size:98
Alignment explanation
Indices: 4027--4226 Score: 309
Period size: 100 Copynumber: 2.0 Consensus size: 98
4017 TTAACAGAAA
4027 TACCTTAAAATAAAAGATTTCAAAACTACCTTTTCATTATGATAAATCCCTAGTTTTATTTTGTC
1 TACCTTAAAATAAAAGATTTCAAAACTACCTTTTCATTATGATAAATCCCTAGTTTTATTTTGTC
4092 CGTTGATTAGAAAAAAAATTCAATTTCTTCTCTGG
66 CGTTGATTAG-AAAAAAATTCAA-TTCTTCTCTGG
4127 TACCTTAAAATAAAAGAAATATTTCAAAACTACC-TTTCATTTATGAT-AATCCCTAG-TTTATT
1 TACCTTAAAATAAAAG----ATTTCAAAACTACCTTTTCA-TTATGATAAATCCCTAGTTTTATT
4189 TTGTCCGTTGATTAG-AAAAAATTCAATTCTTCTCTGG
61 TTGTCCGTTGATTAGAAAAAAATTCAATTCTTCTCTGG
4226 T
1 T
4227 TTTCTCCTTC
Statistics
Matches: 95, Mismatches: 0, Indels: 11
0.90 0.00 0.10
Matches are distributed among these distances:
99 12 0.13
100 27 0.28
102 21 0.22
103 14 0.15
104 21 0.22
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (98 bp):
TACCTTAAAATAAAAGATTTCAAAACTACCTTTTCATTATGATAAATCCCTAGTTTTATTTTGTC
CGTTGATTAGAAAAAAATTCAATTCTTCTCTGG
Found at i:8073 original size:22 final size:20
Alignment explanation
Indices: 8046--8086 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
8036 TAATGTATAC
*
8046 ATTTTATTAAAATATATAAATA
1 ATTTTATCAAAA-AT-TAAATA
8068 ATTTTATCAAAAATTAAAT
1 ATTTTATCAAAAATTAAAT
8087 GTAATAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 2 0.11
22 11 0.61
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
ATTTTATCAAAAATTAAATA
Found at i:11282 original size:34 final size:36
Alignment explanation
Indices: 11244--11328 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
11234 TAAAAGTTAG
* *
11244 TTTCAAAGTTTGG-CAA-CCAACTTTGAAAAATGTT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATATT
****
11278 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATATT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATATT
11314 TTTCAAAGTTTGGTA
1 TTTCAAAGTTTGGTA
11329 GATGTTTGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
34 13 0.30
35 2 0.05
36 28 0.65
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (36 bp):
TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATATT
Found at i:11289 original size:21 final size:21
Alignment explanation
Indices: 11265--11325 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
11255 GGCAACCAAC
11265 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
11286 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
*
11301 TTTGAAAAATATTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
11322 TTTG
1 TTTG
11326 GTAGATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 8 0.28
17 4 0.14
19 4 0.14
21 13 0.45
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:11316 original size:36 final size:36
Alignment explanation
Indices: 11264--11335 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
11254 TGGCAACCAA
*
11264 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
*
11300 CTTTGAAAAATATTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
11336 GTTGGAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.47
Consensus pattern (36 bp):
CTTTGAAAAATATTTTTCAAAGTTTGGTAAATGTTT
Found at i:12549 original size:15 final size:15
Alignment explanation
Indices: 12525--12557 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
12515 TAGCAGATCC
*
12525 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
12540 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
12555 AAA
1 AAA
12558 AAAAGATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.15, G:0.24, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:16143 original size:21 final size:21
Alignment explanation
Indices: 16119--16179 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
16109 GGCAACCAAC
16119 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
16140 TTTGGTAAATG--TTT---A-
1 TTTGAAAAATGTTTTTCAAAG
16155 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
16176 TTTG
1 TTTG
16180 GTAGATGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 9 0.30
16 1 0.03
17 3 0.10
19 3 0.10
20 1 0.03
21 13 0.43
ACGTcount: A:0.33, C:0.03, G:0.16, T:0.48
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:16166 original size:36 final size:35
Alignment explanation
Indices: 16119--16197 Score: 131
Period size: 36 Copynumber: 2.2 Consensus size: 35
16109 GGCAACCAAC
16119 TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
16154 ATTTGAAAAATGTTTTTCAAAGTTTGGTAGATGTTT
1 -TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
16190 GTTGAAAA
1 TTTGAAAA
16198 TAGGAATGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 7 0.17
36 34 0.83
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.46
Consensus pattern (35 bp):
TTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:17998 original size:3 final size:3
Alignment explanation
Indices: 17992--18047 Score: 103
Period size: 3 Copynumber: 18.3 Consensus size: 3
17982 AATGATGATG
17992 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
18041 ATT ATT A
1 ATT ATT A
18048 GGGTAAAGTA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 49 0.94
4 3 0.06
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:18166 original size:31 final size:31
Alignment explanation
Indices: 18126--18193 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
18116 TTGTAATACA
* *
18126 GTCCTCCAACATTTAGTCTATTTGCAATATG
1 GTCCCCCAACATTTAGTCCATTTGCAATATG
18157 GTCCCCCAACATTTAGTCCATTTGCAATATG
1 GTCCCCCAACATTTAGTCCATTTGCAATATG
18188 GTCCCC
1 GTCCCC
18194 ACCGTAACTG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (31 bp):
GTCCCCCAACATTTAGTCCATTTGCAATATG
Found at i:19414 original size:6 final size:6
Alignment explanation
Indices: 19403--19433 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
19393 TTCCAAATTC
19403 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA T
19434 ATATTTCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:22422 original size:10 final size:10
Alignment explanation
Indices: 22407--22442 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
22397 ATAAAAATTA
22407 ATTATTTTTT
1 ATTATTTTTT
22417 ATTA-TTTTT
1 ATTATTTTTT
22426 ATT-TTTTTT
1 ATTATTTTTT
22435 -TTATTTTT
1 ATTATTTTT
22443 GACAATATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.08
9 18 0.75
10 4 0.17
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:22956 original size:39 final size:40
Alignment explanation
Indices: 22866--22961 Score: 149
Period size: 40 Copynumber: 2.4 Consensus size: 40
22856 AAAATGGTGC
* *
22866 TCTAGGCGTCTTTAACACAATTTGCATTCAAACATGGAGG
1 TCTAGGCGTCTTTAACACAACTTACATTCAAACATGGAGG
*
22906 TCTAGGCGTCTTTAACACAACTTACATTCGAACAT-GAGG
1 TCTAGGCGTCTTTAACACAACTTACATTCAAACATGGAGG
*
22945 TCTCGGCGTCTTTAACA
1 TCTAGGCGTCTTTAACA
22962 TAATTCATGG
Statistics
Matches: 52, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 20 0.38
40 32 0.62
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (40 bp):
TCTAGGCGTCTTTAACACAACTTACATTCAAACATGGAGG
Found at i:23119 original size:20 final size:20
Alignment explanation
Indices: 23085--23130 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
23075 GCTGGACGTG
23085 GGAAA-TCACGGGGTGAGCA
1 GGAAATTCACGGGGTGAGCA
*
23104 GGAAATTCATGGGGTGAGCA
1 GGAAATTCACGGGGTGAGCA
23124 GAGAAAT
1 G-GAAAT
23131 ATGCATAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 5 0.21
20 14 0.58
21 5 0.21
ACGTcount: A:0.35, C:0.11, G:0.39, T:0.15
Consensus pattern (20 bp):
GGAAATTCACGGGGTGAGCA
Found at i:23227 original size:31 final size:30
Alignment explanation
Indices: 23186--23297 Score: 120
Period size: 31 Copynumber: 3.6 Consensus size: 30
23176 AGTATAGGAT
*
23186 TTCTCGGCGTCTTCTTCACTTTGGGGTGGA
1 TTCTCAGCGTCTTCTTCACTTTGGGGTGGA
23216 TTGCTCAGCGTCTTCTTCA-TATTGGGGGTGGAA
1 TT-CTCAGCGTCTTCTTCACT-TT-GGGGTGG-A
* * *
23249 TACTCGGCGTCTTCTTCAC-TTGGGAGGGGA
1 TTCTCAGCGTCTTCTTCACTTTGGG-GTGGA
23279 TATCTCAGCGTCTTCTTCA
1 T-TCTCAGCGTCTTCTTCA
23298 GAATAATGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
30 8 0.12
31 37 0.54
32 22 0.32
33 2 0.03
ACGTcount: A:0.12, C:0.23, G:0.28, T:0.37
Consensus pattern (30 bp):
TTCTCAGCGTCTTCTTCACTTTGGGGTGGA
Found at i:26307 original size:14 final size:14
Alignment explanation
Indices: 26066--26314 Score: 195
Period size: 14 Copynumber: 17.8 Consensus size: 14
26056 GTAACTATTA
26066 TTAAATCATTAAAG
1 TTAAATCATTAAAG
26080 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
26094 TT-AATTAATAATTA-
1 TTAAATCATTAA--AG
26108 TTAAATCATTAAAG
1 TTAAATCATTAAAG
26122 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
26136 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
26150 TTGAATCATTAAAG
1 TTAAATCATTAAAG
26164 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
26178 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
* *
26192 TTGAATCATTAAAT
1 TTAAATCATTAAAG
*
26206 TTAGATCATTAAAG
1 TTAAATCATTAAAG
* * *
26220 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
26234 TTGAATCATTAAAG
1 TTAAATCATTAAAG
*
26248 TTAAATCATTGAAG
1 TTAAATCATTAAAG
* * *
26262 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
*
26276 TTAAATCATTAAAT
1 TTAAATCATTAAAG
*
26290 TTAAATCATTAAAA
1 TTAAATCATTAAAG
*
26304 TTAAATAATTA
1 TTAAATCATTA
26315 TTATTAAATA
Statistics
Matches: 182, Mismatches: 41, Indels: 24
0.74 0.17 0.10
Matches are distributed among these distances:
13 12 0.07
14 158 0.87
15 12 0.07
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:26322 original size:42 final size:42
Alignment explanation
Indices: 26019--26323 Score: 468
Period size: 42 Copynumber: 7.3 Consensus size: 42
26009 ATATATTTAG
* * *
26019 TATTATTATATCATTAAA-TATAAATCATTAAAGTCAAGTAAC
1 TATTATTAAATCATTAAAGT-TAAATCATTAAAGTTAAGTAAT
*
26061 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAATTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
*
26103 AATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
*
26145 TATTATTGAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
* * *
26187 TATTATTGAATCATTAAATTTAGATCATTAAAGTTAAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
* *
26229 TATTATTGAATCATTAAAGTTAAATCATTGAAGTTAAGTAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
* * *
26271 TATTATTAAATCATTAAATTTAAATCATTAAAATTAAATAAT
1 TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
26313 TATTATTAAAT
1 TATTATTAAAT
26324 ATGTACTCGA
Statistics
Matches: 244, Mismatches: 18, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
42 243 1.00
43 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (42 bp):
TATTATTAAATCATTAAAGTTAAATCATTAAAGTTAAGTAAT
Found at i:29683 original size:81 final size:82
Alignment explanation
Indices: 29532--29725 Score: 257
Period size: 81 Copynumber: 2.4 Consensus size: 82
29522 TATATTTTTT
* *
29532 TTTTTGCTTTTGCTTTCTTTTATGCTATTTGGTGTGCTGTTTTCGATGGATAATTGCCCATTATC
1 TTTTT-CTTTTGCTTTATTTTATGCTATTTGGTGTGCTGTTTTAGAT-G-TAATTGCCCATTATC
29597 ACATGCATTATTACCCTTTC
63 ACATGCATTATTACCCTTTC
* * * * * *
29617 TTTTTCTTTTGGTTTATTTTATGTTGTTTTGTGTTCTGTTTTAGAT-TAATTGTCCATTATCACA
1 TTTTTCTTTTGCTTTATTTTATGCTATTTGGTGTGCTGTTTTAGATGTAATTGCCCATTATCACA
29681 TGCATTATTACCCTTTC
66 TGCATTATTACCCTTTC
* *
29698 TTTTACTTTT-CTTTATTTTGTGCTATTT
1 TTTTTCTTTTGCTTTATTTTATGCTATTT
29726 TATAGGACCA
Statistics
Matches: 96, Mismatches: 13, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
80 14 0.15
81 43 0.45
84 34 0.35
85 5 0.05
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (82 bp):
TTTTTCTTTTGCTTTATTTTATGCTATTTGGTGTGCTGTTTTAGATGTAATTGCCCATTATCACA
TGCATTATTACCCTTTC
Found at i:29991 original size:30 final size:30
Alignment explanation
Indices: 29950--30006 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
29940 TGCATATAAA
* *
29950 TTCTGCTAAAGACGTTGATAGATCCATGTT
1 TTCTACTAAAGACGTCGATAGATCCATGTT
29980 TTCTACTAAAGACGTCGATAGATCCAT
1 TTCTACTAAAGACGTCGATAGATCCAT
30007 ATTTCCTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (30 bp):
TTCTACTAAAGACGTCGATAGATCCATGTT
Found at i:34836 original size:23 final size:23
Alignment explanation
Indices: 34805--34863 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
34795 TCAAGGGTTT
*
34805 TATGTGGTCCTTCGGGACAAACC
1 TATGTGGTCCTTCGGGACAAAAC
* * *
34828 TATGCGGTCCTTTGGGATAAAAC
1 TATGTGGTCCTTCGGGACAAAAC
34851 TATGTGGTCCTTC
1 TATGTGGTCCTTC
34864 AGAACAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (23 bp):
TATGTGGTCCTTCGGGACAAAAC
Found at i:36982 original size:21 final size:21
Alignment explanation
Indices: 36956--37008 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
36946 TAACAAAGGT
36956 AGTACCGATACTCCCTATAGG
1 AGTACCGATACTCCCTATAGG
36977 AGTACCGATACTCCCTATAGG
1 AGTACCGATACTCCCTATAGG
*
36998 AGTACCAATAC
1 AGTACCGATAC
37009 CTTATGTACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTACCGATACTCCCTATAGG
Found at i:40314 original size:17 final size:17
Alignment explanation
Indices: 40289--40321 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40279 CTAGAATGCA
*
40289 AAAATGGTACCGATACC
1 AAAAGGGTACCGATACC
40306 AAAAGGGTACCGATAC
1 AAAAGGGTACCGATAC
40322 TACTTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.15
Consensus pattern (17 bp):
AAAAGGGTACCGATACC
Found at i:43154 original size:51 final size:50
Alignment explanation
Indices: 43066--43250 Score: 241
Period size: 51 Copynumber: 3.7 Consensus size: 50
43056 AAAAAAAAAA
* *
43066 GTAACACTTAACATATACTTACACT--TGTAAGTGAATAAAATAAACAAGT
1 GTAACACTTAACACATACTTACACTAATGTAAGTAAATAAAATAAA-AAGT
* * *
43115 ATAACACTTAACACATACTTACACTAATGTAACTAAATAAAACAAAAAAGT
1 GTAACACTTAACACATACTTACACTAATGTAAGTAAATAAAA-TAAAAAGT
*
43166 GTAACACTTAACTCATACTTACAAC-AATGTAAGTAAATAAAATAAAAAGT
1 GTAACACTTAACACATACTTAC-ACTAATGTAAGTAAATAAAATAAAAAGT
* **
43216 GTAATACTTAACACATACTTACACCGATGTAAGTA
1 GTAACACTTAACACATACTTACACTAATGTAAGTA
43251 TGCACATCTC
Statistics
Matches: 119, Mismatches: 12, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
49 25 0.21
50 36 0.30
51 53 0.45
52 5 0.04
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.26
Consensus pattern (50 bp):
GTAACACTTAACACATACTTACACTAATGTAAGTAAATAAAATAAAAAGT
Found at i:43246 original size:101 final size:100
Alignment explanation
Indices: 43066--43247 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 100
43056 AAAAAAAAAA
* *
43066 GTAACACTTAACATATACTTACACTTGTAAGTGAATAAAATAAACAAGTATAACACTTAACACAT
1 GTAACACTTAACATATACTTACACATGTAAGTAAATAAAATAAACAAGTATAACACTTAACACAT
*
43131 ACTTACACTAATGTAACTAAATAAAACAAAAAAGT
66 ACTTACACCAATGTAACTAAATAAAACAAAAAAGT
* *
43166 GTAACACTTAAC-TCATACTTACAACAATGTAAGTAAATAAAATAAA-AAGTGTAATACTTAACA
1 GTAACACTTAACAT-ATACTTAC-AC-ATGTAAGTAAATAAAATAAACAAGTATAACACTTAACA
*
43229 CATACTTACACCGATGTAA
63 CATACTTACACCAATGTAA
43248 GTATGCACAT
Statistics
Matches: 73, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
99 1 0.01
100 20 0.27
101 34 0.47
102 18 0.25
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.26
Consensus pattern (100 bp):
GTAACACTTAACATATACTTACACATGTAAGTAAATAAAATAAACAAGTATAACACTTAACACAT
ACTTACACCAATGTAACTAAATAAAACAAAAAAGT
Found at i:58321 original size:125 final size:122
Alignment explanation
Indices: 58128--58374 Score: 341
Period size: 125 Copynumber: 2.0 Consensus size: 122
58118 AGATGAATCT
* * * * *
58128 CAATACACATTTATTTATCCCAAATTTTGTTTGAACATAAAGCATGTGTGGATATTCAACAAATA
1 CAATAAACATTTATTTATCCCAAATTTTGATTGAACATAAAGCATGTGTCGATACTCAACAAAGA
* ** * *
58193 AAGATGCAAAATGATTATTCAGGAAAACTGAAATATGTGTGCAACTGTTTCCAATTC
66 AAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAACTGTTTCCAATTC
**
58250 CAATAAACATTTATTTATCCCGGATTTTGATTGACCAACATAAAGCATGTGTCGATACTCAACAA
1 CAATAAACATTTATTTATCCCAAATTTTGATTG---AACATAAAGCATGTGTCGATACTCAACAA
* *
58315 AGAAAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAATTTTTTCCAATTC
63 AGAAAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAACTGTTTCCAATTC
58375 AACATATTTT
Statistics
Matches: 108, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
122 29 0.27
125 79 0.73
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (122 bp):
CAATAAACATTTATTTATCCCAAATTTTGATTGAACATAAAGCATGTGTCGATACTCAACAAAGA
AAGATACAAAATGATTATTCAGGAAAACCAAAAGATATGTGCAACTGTTTCCAATTC
Found at i:60786 original size:17 final size:17
Alignment explanation
Indices: 60764--60798 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
60754 TATCCATAGA
60764 TTGTATGAAGTTAGAAG
1 TTGTATGAAGTTAGAAG
60781 TTGTATGAAGTTAGAAG
1 TTGTATGAAGTTAGAAG
60798 T
1 T
60799 GTTTGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (17 bp):
TTGTATGAAGTTAGAAG
Found at i:62428 original size:32 final size:32
Alignment explanation
Indices: 62390--62454 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
62380 TAAATCAGAT
62390 TAAATTAGATATCGA-GTCAGATCAATATCAAA
1 TAAATTA-ATATCGAGGTCAGATCAATATCAAA
* ** *
62422 TAAATTAATCTTTAGGTCATATCAATATCAAA
1 TAAATTAATATCGAGGTCAGATCAATATCAAA
62454 T
1 T
62455 TGATTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 4 0.14
32 24 0.86
ACGTcount: A:0.45, C:0.12, G:0.09, T:0.34
Consensus pattern (32 bp):
TAAATTAATATCGAGGTCAGATCAATATCAAA
Found at i:62461 original size:32 final size:32
Alignment explanation
Indices: 62405--62468 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
62395 TAGATATCGA
62405 GTCAGATCAATATCAAATAAATTAATCTTTAG
1 GTCAGATCAATATCAAATAAATTAATCTTTAG
* ** *
62437 GTCATATCAATATCAAATTGATTAATTTTTAG
1 GTCAGATCAATATCAAATAAATTAATCTTTAG
62469 TTTGAAGCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (32 bp):
GTCAGATCAATATCAAATAAATTAATCTTTAG
Found at i:62574 original size:32 final size:31
Alignment explanation
Indices: 62410--62577 Score: 83
Period size: 32 Copynumber: 5.3 Consensus size: 31
62400 ATCGAGTCAG
* * *
62410 ATCAATATCAAATAAATTAATCTTTAGGTCA
1 ATCAATATCAAATCAATTAATTTTTAGATCA
** * *
62441 TATCAATATCAAATTGATTAATTTTTAGTTTGA
1 -ATCAATATCAAATCAATTAATTTTTAG-ATCA
* * *
62474 AGCAATAGT-AGATCAA-T-ATCTTTTCAAATCGA
1 ATCAATA-TCAAATCAATTAAT-TTTT-AGATC-A
* ** * *
62506 GTCAATATTGAATCGATTGACTTTTTA-ATCGA
1 ATCAATATCAAATCAATT-AATTTTTAGATC-A
*
62538 ATCAATATCAAATCAATTAATTTTTAGTTCA
1 ATCAATATCAAATCAATTAATTTTTAGATCA
62569 TATCAATAT
1 -ATCAATAT
62578 TTGGATCTTC
Statistics
Matches: 101, Mismatches: 24, Indels: 22
0.69 0.16 0.15
Matches are distributed among these distances:
30 2 0.02
31 15 0.15
32 74 0.73
33 5 0.05
34 4 0.04
35 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (31 bp):
ATCAATATCAAATCAATTAATTTTTAGATCA
Found at i:63719 original size:17 final size:17
Alignment explanation
Indices: 63685--63717 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
63675 GTTAGGGGTA
63685 AGGGATTTAGGATTTTT
1 AGGGATTTAGGATTTTT
63702 AGGGATTTA-GATTTTT
1 AGGGATTTAGGATTTTT
63718 TATTGTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.48
Consensus pattern (17 bp):
AGGGATTTAGGATTTTT
Found at i:65112 original size:17 final size:18
Alignment explanation
Indices: 65086--65131 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
65076 TCAGATTCAC
*
65086 ATTCCAATTCC-TGACAG
1 ATTCCAATTCCTTCACAG
*
65103 ATTTCAATTCCTTCACAG
1 ATTCCAATTCCTTCACAG
65121 ATTCCAATTCC
1 ATTCCAATTCC
65132 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAG
Found at i:71122 original size:12 final size:13
Alignment explanation
Indices: 71102--71133 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
71092 ACCCGTTTTC
71102 TTATATTTTTATT
1 TTATATTTTTATT
71115 TT-TATTTTTATT
1 TTATATTTTTATT
71127 TTATATT
1 TTATATT
71134 AATTTTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTATATTTTTATT
Done.